@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37702122, year = {2023}, author = {Rasmussen, L and Fontsere, C and Soto-Calderón, ID and Guillen, R and Savage, A and Hansen, AJ and Hvilsom, C and Gilbert, MTP}, title = {Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17130}, pmid = {37702122}, issn = {1365-294X}, support = {//Alfred Benzon Foundation/ ; 143//Danmarks Grundforskningsfond/ ; //Torben &amp; Alice Frimodts Fund/ ; }, abstract = {During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.}, }
@article {pmid37702036, year = {2023}, author = {Peng, L and Hoban, J and Joffe, J and Smith, AH and Carpenter, M and Marcelis, T and Patel, V and Lynn-Bell, N and Oliver, KM and Russell, JA}, title = {Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeb.14216}, pmid = {37702036}, issn = {1420-9101}, support = {1050098//National Science Foundation/ ; 1050128//National Science Foundation/ ; 1754302//National Science Foundation/ ; 1754597//National Science Foundation/ ; }, abstract = {Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.}, }
@article {pmid37694134, year = {2023}, author = {Williams, A and Stephens, TG and Shumaker, A and Bhattacharya, D}, title = {Peeling back the layers of coral holobiont multi-omics data.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107623}, pmid = {37694134}, issn = {2589-0042}, abstract = {The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge and resources, its application to non-model organisms, such as coral holobionts, is less clear-cut. We explore, in the emerging rice coral model Montipora capitata, the intersection of holobiont transcriptomic, proteomic, metabolomic, and microbiome amplicon data and investigate how well they correlate under high temperature treatment. Using a typical thermal stress regime, we show that transcriptomic and proteomic data broadly capture the stress response of the coral, whereas the metabolome and microbiome datasets show patterns that likely reflect stochastic and homeostatic processes associated with each sample. These results provide a framework for interpreting multi-omics data generated from non-model systems, particularly those with complex biotic interactions among microbial partners.}, }
@article {pmid37692426, year = {2023}, author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L}, title = {Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1190304}, doi = {10.3389/fpls.2023.1190304}, pmid = {37692426}, issn = {1664-462X}, abstract = {INTRODUCTION: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.<br><br>METHODS: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.<br><br>RESULTS AND DISCUSSION: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.}, }
@article {pmid37670990, year = {2023}, author = {Pérez-Llano, Y and Yarzábal Rodríguez, LA and Martínez-Romero, E and Dobson, ADW and Gunde-Cimerman, N and Vasconcelos, V and Batista-García, RA}, title = {From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213340}, pmid = {37670990}, issn = {1664-302X}, }
@article {pmid37669892, year = {2023}, author = {Hellal, J and Barthelmebs, L and Bérard, A and Cébron, A and Cheloni, G and Colas, S and Cravo-Laureau, C and De Clerck, C and Gallois, N and Hery, M and Martin-Laurent, F and Martins, J and Morin, S and Palacios, C and Pesce, S and Richaume, A and Vuilleumier, S}, title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad102}, pmid = {37669892}, issn = {1574-6941}, abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment and also play key roles in the fate of pollutants through the degradation, transformation and transfer of organic or inorganic compounds. They are thus crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.}, }
@article {pmid37664515, year = {2023}, author = {Hill, CEL and Abbass, SG and Caporale, G and El-Khaled, YC and Kuhn, L and Schlenzig, T and Wild, C and Tilstra, A}, title = {Physiology of the widespread pulsating soft coral Xenia umbellata is affected by food sources, but not by water flow.}, journal = {Ecology and evolution}, volume = {13}, number = {9}, pages = {e10483}, pmid = {37664515}, issn = {2045-7758}, abstract = {Coral energy and nutrient acquisition strategies are complex and sensitive to environmental conditions such as water flow. While high water flow can enhance feeding in hard corals, knowledge about the effects of water flow on the feeding of soft corals, particularly those pulsating, is still limited. In this study, we thus investigated the effects of feeding and water flow on the physiology of the pulsating soft coral Xenia umbellata. We crossed three feeding treatments: (i) no feeding, (ii) particulate organic matter (POM) in the form of phytoplankton and (iii) dissolved organic carbon (DOC) in the form of glucose, with four water volume exchange rates (200, 350, 500 and 650 L h[-1]) over 15 days. Various ecophysiological parameters were assessed including pulsation rate, growth rate, isotopic and elemental ratios of carbon (C) and nitrogen (N) as well as photo-physiological parameters of the Symbiodiniaceae (cell density, chlorophyll-a and mitotic index). Water flow had no significant effect but feeding had a substantial impact on the physiology of the X. umbellata holobiont. In the absence of food, corals exhibited significantly lower pulsation rates, lower Symbiodiniaceae cell density and lower mitotic indices compared to the fed treatments, yet significantly higher chlorophyll-a per cell and total N content. Differences were also observed between the two feeding treatments, with significantly higher pulsation rates and lower chlorophyll-a per cell in the DOC treatment, but higher C and N content in the POM treatment. Our findings suggest that the X. umbellata holobiont can be viable under different trophic strategies, though favouring mixotrophy. Additionally, the physiology of the X. umbellata may be regulated through its own pulsating behaviour without any positive or negative effects from different water flow. Therefore, this study contributes to our understanding of soft coral ecology, particularly regarding the competitive success and widespread distribution of X. umbellata.}, }
@article {pmid37653089, year = {2023}, author = {Mannochio-Russo, H and Swift, SOI and Nakayama, KK and Wall, CB and Gentry, EC and Panitchpakdi, M and Caraballo-Rodriguez, AM and Aron, AT and Petras, D and Dorrestein, K and Dorrestein, TK and Williams, TM and Nalley, EM and Altman-Kurosaki, NT and Martinelli, M and Kuwabara, JY and Darcy, JL and Bolzani, VS and Wegley Kelly, L and Mora, C and Yew, JY and Amend, AS and McFall-Ngai, M and Hynson, NA and Dorrestein, PC and Nelson, CE}, title = {Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {896}, pmid = {37653089}, issn = {2399-3642}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Coral Reefs ; Symbiosis ; Metabolome ; *Anthozoa ; *Microbiota ; *Seaweed ; }, abstract = {The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.}, }
@article {pmid37652999, year = {2023}, author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ}, title = {Ancient DNA reveals genetic admixture in China during tiger evolution.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {37652999}, issn = {2397-334X}, support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; }, abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.}, }
@article {pmid37650630, year = {2023}, author = {Koziol, A and Odriozola, I and Leonard, A and Eisenhofer, R and San José, C and Aizpurua, O and Alberdi, A}, title = {Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.}, journal = {mBio}, volume = {}, number = {}, pages = {e0160623}, doi = {10.1128/mbio.01606-23}, pmid = {37650630}, issn = {2150-7511}, abstract = {The ability of the gut microbiome has been posited as an additional axis of animals' phenotypic plasticity. However, whether and how such plasticity varies across hosts with different biological features remains unclear. We performed a captivity experiment to compare how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of temperature and dietary disturbances in two mammals: the insectivorous-specialist Crocidura russula and the omnivorous-generalist Apodemus sylvaticus. Combining genome-resolved metagenomics, metabolic pathway distillation and joint species distribution modeling, we observed that, although microbiome alpha diversity of both species remained stable, C. russula exhibited substantially higher variability and directionality of microbial responses than A. sylvaticus. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts. IMPORTANCE In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.}, }
@article {pmid37647612, year = {2023}, author = {Zhou, K and Zhang, T and Chen, XW and Xu, Y and Zhang, R and Qian, PY}, title = {Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts.}, journal = {Annual review of marine science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-marine-021623-093133}, pmid = {37647612}, issn = {1941-0611}, abstract = {Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts. Expected final online publication date for the Annual Review of Marine Science, Volume 16 is January 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37645461, year = {2023}, author = {Zuzolo, D and Ranauda, MA and Maisto, M and Tartaglia, M and Prigioniero, A and Falzarano, A and Marotta, G and Sciarrillo, R and Guarino, C}, title = {The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1205451}, pmid = {37645461}, issn = {1664-462X}, abstract = {The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.}, }
@article {pmid37638757, year = {2023}, author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L}, title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkad685}, pmid = {37638757}, issn = {1362-4962}, support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Sk&#x142;odowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; }, abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.}, }
@article {pmid37626434, year = {2023}, author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG}, title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {192}, pmid = {37626434}, issn = {2049-2618}, support = {This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; This research was supported by a Science Focus Area Grant from the U.S. Department of Energy (DOE), Biological and Environmental Research (BER), Biological System Science Division (BSSD) under the grant number LANLF59T.//U.S. Department of Energy/ ; }, mesh = {*Multiomics ; Data Analysis ; Eukaryota ; *Microbiota/genetics ; Prokaryotic Cells ; }, abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.}, }
@article {pmid37626254, year = {2023}, author = {Hussain, A and Kumar, SHK and Prathiviraj, R and Kumar, AA and Renjith, K and Kiran, GS and Selvin, J}, title = {The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India.}, journal = {Archives of microbiology}, volume = {205}, number = {9}, pages = {319}, pmid = {37626254}, issn = {1432-072X}, support = {BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.}, }
@article {pmid37625782, year = {2023}, author = {Prabhakaran, P and Nazir, MYM and Thananusak, R and Hamid, AA and Vongsangnak, W and Song, Y}, title = {Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {}, number = {}, pages = {159381}, doi = {10.1016/j.bbalip.2023.159381}, pmid = {37625782}, issn = {1879-2618}, abstract = {Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.}, }
@article {pmid37623217, year = {2023}, author = {Petrushin, IS and Vasilev, IA and Markova, YA}, title = {Drought Tolerance of Legumes: Physiology and the Role of the Microbiome.}, journal = {Current issues in molecular biology}, volume = {45}, number = {8}, pages = {6311-6324}, pmid = {37623217}, issn = {1467-3045}, support = {23-26-00204//Russian Science Foundation/ ; }, abstract = {Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering-a promising biotech strategy to improve the yield and stress-resistance of legumes.}, }
@article {pmid37604380, year = {2023}, author = {Yu, X and Yu, K and Liao, Z and Chen, B and Qin, Z and Liang, J and Gao, X}, title = {Adaptation strategies of relatively high-latitude marginal reef corals in response to severe temperature fluctuations.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166439}, doi = {10.1016/j.scitotenv.2023.166439}, pmid = {37604380}, issn = {1879-1026}, abstract = {The large seasonal temperature fluctuations caused by global warming and frequent marine heatwaves pose new challenges to survival of relatively high-latitude marginal reef corals. However, the adaptation strategies of high-latitude marginal corals are not fully understood. We employed integrated approach to investigate the response mechanism of hosts, Symbiodiniaceae, and symbiotic bacteria of marginal reef corals Acropora pruinosa and Pavona decussate in response to large seasonal temperature fluctuations. The coral holobiont maintained a high level of immunity to adapt to seasonal pressure by increasing Symbiodiniaceae energy supply. The symbiotic Symbiodiniaceae of two coral was dominated by C1 subgroup, and was stable across seasons. The α-diversity of symbiotic bacteria P. decussata and A. pruinosa in summer was higher than that in winter. The symbiotic bacterial community of two coral reorganized during different seasons. Scleractinian corals improve adaptability to seasonal stress by increasing energy supply to maintain high levels of immunity, increasing symbiotic bacterial α-diversity, and changing dominant bacteria. This study demonstrates the adaptation strategies of marginal reef corals to seasonal temperature fluctuations and provides novel insights into the study of the adaptation of corals and relatively high-latitude coral refuges in the context of global warming and intensified marine heatwaves.}, }
@article {pmid37601769, year = {2023}, author = {Mochales-Riaño, G and Fontsere, C and de Manuel, M and Talavera, A and Burriel-Carranza, B and Tejero-Cicuéndez, H and AlGethami, RHM and Shobrak, M and Marques-Bonet, T and Carranza, S}, title = {Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).}, journal = {iScience}, volume = {26}, number = {9}, pages = {107481}, pmid = {37601769}, issn = {2589-0042}, abstract = {In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.}, }
@article {pmid37601376, year = {2023}, author = {Caetano-Anollés, G and Claverie, JM and Nasir, A}, title = {A critical analysis of the current state of virus taxonomy.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1240993}, pmid = {37601376}, issn = {1664-302X}, abstract = {Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.}, }
@article {pmid37587369, year = {2023}, author = {Gavriilidou, A and Avcı, B and Galani, A and Schorn, MA and Ingham, CJ and Ettema, TJG and Smidt, H and Sipkema, D}, title = {Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37587369}, issn = {1751-7370}, support = {897121//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 817834//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 679849//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.}, }
@article {pmid37586539, year = {2023}, author = {He, R and Hu, S and Li, Q and Zhao, D and Wu, QL and Zeng, J}, title = {Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {166229}, doi = {10.1016/j.scitotenv.2023.166229}, pmid = {37586539}, issn = {1879-1026}, abstract = {Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) and roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiomes in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.}, }
@article {pmid37580830, year = {2023}, author = {Tignat-Perrier, R and van de Water, JAJM and Allemand, D and Ferrier-Pagès, C}, title = {Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {70}, pmid = {37580830}, issn = {2524-6372}, abstract = {Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.}, }
@article {pmid37570868, year = {2023}, author = {Ujlaki, G and Kovács, T and Vida, A and Kókai, E and Rauch, B and Schwarcz, S and Mikó, E and Janka, E and Sipos, A and Hegedűs, C and Uray, K and Nagy, P and Bai, P}, title = {Identification of Bacterial Metabolites Modulating Breast Cancer Cell Proliferation and Epithelial-Mesenchymal Transition.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {15}, pages = {}, pmid = {37570868}, issn = {1420-3049}, support = {K123975//National Research, Development and Innovation Office/ ; K124141//National Research, Development and Innovation Office/ ; FK128387//National Research, Development and Innovation Office/ ; TKP2021-EGA-19//National Research, Development and Innovation Office/ ; TKP2021-EGA-20//National Research, Development and Innovation Office/ ; POST-COVID2021-33//Hungarian Academy of Sciences/ ; }, mesh = {Humans ; Animals ; Mice ; Female ; *Breast Neoplasms/drug therapy/metabolism ; Epithelial-Mesenchymal Transition ; *Cytostatic Agents/pharmacology ; Butyric Acid/pharmacology ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology/therapeutic use ; Cell Proliferation ; }, abstract = {Breast cancer patients are characterized by the oncobiotic transformation of multiple microbiome communities, including the gut microbiome. Oncobiotic transformation of the gut microbiome impairs the production of antineoplastic bacterial metabolites. The goal of this study was to identify bacterial metabolites with antineoplastic properties. We constructed a 30-member bacterial metabolite library and screened the library compounds for effects on cell proliferation and epithelial-mesenchymal transition. The metabolites were applied to 4T1 murine breast cancer cells in concentrations corresponding to the reference serum concentrations. However, yric acid, glycolic acid, d-mannitol, 2,3-butanediol, and trans-ferulic acid exerted cytostatic effects, and 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, and vanillic acid exerted hyperproliferative effects. Furthermore, 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, 2,3-butanediol, and hydrocinnamic acid inhibited epithelial-to-mesenchymal (EMT) transition. We identified redox sets among the metabolites (d-mannitol-d-mannose, 1-butanol-butyric acid, ethylene glycol-glycolic acid-oxalic acid), wherein only one partner within the set (d-mannitol, butyric acid, glycolic acid) possessed bioactivity in our system, suggesting that changes to the local redox potential may affect the bacterial secretome. Of the nine bioactive metabolites, 2,3-butanediol was the only compound with both cytostatic and anti-EMT properties.}, }
@article {pmid37559898, year = {2023}, author = {Ciucani, MM and Ramos-Madrigal, J and Hernández-Alonso, G and Carmagnini, A and Aninta, SG and Sun, X and Scharff-Olsen, CH and Lanigan, LT and Fracasso, I and Clausen, CG and Aspi, J and Kojola, I and Baltrūnaitė, L and Balčiauskas, L and Moore, J and Åkesson, M and Saarma, U and Hindrikson, M and Hulva, P and Bolfíková, B&#x10c; and Nowak, C and Godinho, R and Smith, S and Paule, L and Nowak, S and Mysłajek, RW and Lo Brutto, S and Ciucci, P and Boitani, L and Vernesi, C and Stenøien, HK and Smith, O and Frantz, L and Rossi, L and Angelici, FM and Cilli, E and Sinding, MS and Gilbert, MTP and Gopalakrishnan, S}, title = {The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs.}, journal = {iScience}, volume = {26}, number = {8}, pages = {107307}, pmid = {37559898}, issn = {2589-0042}, abstract = {The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.}, }
@article {pmid37552896, year = {2023}, author = {González-Pech, RA and Li, VY and Garcia, V and Boville, E and Mammone, M and Kitano, H and Ritchie, KB and Medina, M}, title = {The Evolution, Assembly, and Dynamics of Marine Holobionts.}, journal = {Annual review of marine science}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-marine-022123-104345}, pmid = {37552896}, issn = {1941-0611}, abstract = {The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis. Expected final online publication date for the Annual Review of Marine Science, Volume 16 is January 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid37550887, year = {2023}, author = {Hernández, M and Hereira-Pacheco, S and Alberdi, A and Díaz DE LA Vega-Pérez, AH and Estrada-Torres, A and Ancona, S and Navarro-Noya, YE}, title = {DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus).}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12755}, pmid = {37550887}, issn = {1749-4877}, support = {//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACyT)/ ; 205945//Infraestructura project/ ; 137748//Ciencia de Frontera project/ ; 883//C&#xe1;tedras CONACyT project/ ; //Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM)/ ; }, abstract = {Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.}, }
@article {pmid37549265, year = {2023}, author = {Hung, TH and So, T and Thammavong, B and Chamchumroon, V and Theilade, I and Phourin, C and Bouamanivong, S and Hartvig, I and Gaisberger, H and Jalonen, R and Boshier, DH and MacKay, JJ}, title = {Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {33}, pages = {e2301603120}, doi = {10.1073/pnas.2301603120}, pmid = {37549265}, issn = {1091-6490}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.}, }
@article {pmid37548791, year = {2023}, author = {Rotini, A and Conte, C and Winters, G and Vasquez, MI and Migliore, L}, title = {Undisturbed Posidonia oceanica meadows maintain the epiphytic bacterial community in different environments.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {37548791}, issn = {1614-7499}, support = {COST-STSM- CA15121-39495//COST Action CA 15121 Mar Cons/ ; }, abstract = {Seagrasses harbour different and rich epiphytic bacterial communities. These microbes may establish intimate and symbiotic relationships with the seagrass plants and change according to host species, environmental conditions, and/or ecophysiological status of their seagrass host. Although Posidonia oceanica is one of the most studied seagrasses in the world, and bacteria associated with seagrasses have been studied for over a decade, P. oceanica's microbiome remains hitherto little explored. Here, we applied 16S rRNA amplicon sequencing to explore the microbiome associated with the leaves of P. oceanica growing in two geomorphologically different meadows (e.g. depth, substrate, and turbidity) within the Limassol Bay (Cyprus). The morphometric (leaf area, meadow density) and biochemical (pigments, total phenols) descriptors highlighted the healthy conditions of both meadows. The leaf-associated bacterial communities showed similar structure and composition in the two sites; core microbiota members were dominated by bacteria belonging to the Thalassospiraceae, Microtrichaceae, Enterobacteriaceae, Saprospiraceae, and Hyphomonadaceae families. This analogy, even under different geomorphological conditions, suggest that in the absence of disturbances, P. oceanica maintains characteristic-associated bacterial communities. This study provides a baseline for the knowledge of the P. oceanica microbiome and further supports its use as a putative seagrass descriptor.}, }
@article {pmid37546572, year = {2023}, author = {Hernández-Alonso, G and Ramos-Madrigal, J and Sun, X and Scharff-Olsen, CH and Sinding, MS and Martins, NF and Ciucani, MM and Mak, SST and Lanigan, LT and Clausen, CG and Bhak, J and Jeon, S and Kim, C and Eo, KY and Cho, SH and Boldgiv, B and Gantulga, G and Unudbayasgalan, Z and Kosintsev, PA and Stenøien, HK and Gilbert, MTP and Gopalakrishnan, S}, title = {Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing.}, journal = {Ecology and evolution}, volume = {13}, number = {8}, pages = {e10404}, pmid = {37546572}, issn = {2045-7758}, abstract = {The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.}, }
@article {pmid37540022, year = {2023}, author = {Balasubramaniam, HM and Tze Yan, F and Michelle JiaMin, L and Parimannan, S and Mutusamy, P and Jaya Jothi, S and Rajandas, H}, title = {Genome characterization of Dickeya solani bacteriophage W2B.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0045223}, doi = {10.1128/MRA.00452-23}, pmid = {37540022}, issn = {2576-098X}, abstract = {We have successfully characterized the complete genome sequence of the lytic Dickeya solani bacteriophage W2B, isolated from the Bunus Sewage Treatment Plant. The lytic phage from the Ningirsuvirus family has a 40,385-bp linear double-stranded DNA genome containing 51 coding sequences (CDSs).}, }
@article {pmid37530752, year = {2023}, author = {Jiménez-Guerrero, I and López-Baena, FJ and Borrero-de Acuña, JM and Pérez-Montaño, F}, title = {Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14323}, pmid = {37530752}, issn = {1751-7915}, support = {EMERGIA20_00048//Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n, Ciencia y Empleo, Junta de Andaluc&#xed;a/ ; ProyExcel_00450//Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n, Ciencia y Empleo, Junta de Andaluc&#xed;a/ ; //European Union NextGenerationEU/PRTR/ ; PID2019-107634RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-118279R (MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-122395OA-I00 (MCIN/AEI/ 10.13039/501100011)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; TED2021-130357B-I00 (MCIN/AEI/ 10.13039/5011000110)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.}, }
@article {pmid37525683, year = {2023}, author = {Giraud, &#xc9; and Milon, G}, title = {[Elucidating and characterizing the dynamic biological processes that account for the sustainability of Leishmania populations].}, journal = {Medecine tropicale et sante internationale}, volume = {3}, number = {2}, pages = {}, pmid = {37525683}, issn = {2778-2034}, abstract = {To attempt resolving this issue accurately, it was necessary to anchor our experimental approaches in the observations and pioneering work of our predecessors, notably Alphonse Laveran, Louis Parrot, Edmond and Étienne Sergent. The latter, among other things, had identified as natural hosts of leishmaniasis, rodent populations with which hematophagous telmophagous sand fly populations cohabited closely.When human populations emerged in these natural ecosystems, after the sedentarization of Homo sapiens, more or less important disturbances would have led to a transition of sand fly hematophagy, from zoophilia, to zoo-anthropophilia and anthropophilia.The creation of infrastructures that allow the breeding and integration into experimental groups of both holobiont sand flies and holobiont laboratory rodents (rats, mice, hamsters, etc.) remains crucial. With such infrastructures, it becomes possible to grasp and characterize the multilateral dynamic processes - mostly clinically silent - that account for the biogenesis of tissue and/or cellular niches protecting populations of Leishmania developmental morphotypes, including those ensuring host-to-host transmission, albeit in small numbers.}, }
@article {pmid37520373, year = {2023}, author = {Roy, A and Houot, B and Kushwaha, S and Anderson, P}, title = {Impact of transgenerational host switch on gut bacterial assemblage in generalist pest, Spodoptera littoralis (Lepidoptera: Noctuidae).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172601}, pmid = {37520373}, issn = {1664-302X}, abstract = {Diet composition is vital in shaping gut microbial assemblage in many insects. Minimal knowledge is available about the influence of transgenerational diet transition on gut microbial community structure and function in polyphagous pests. This study investigated transgenerational diet-induced changes in Spodoptera littoralis larval gut bacteriome using 16S ribosomal sequencing. Our data revealed that 88% of bacterial populations in the S. littoralis larval gut comprise Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The first diet transition experiment from an artificial diet (F0) to a plant diet (F1), cabbage and cotton, caused an alteration of bacterial communities in the S. littoralis larval gut. The second transgenerational diet switch, where F1 larvae feed on the same plant in the F2 generation, displayed a significant variation suggesting further restructuring of the microbial communities in the Spodoptera larval gut. F1 larvae were also challenged with the plant diet transition at the F2 generation (cabbage to cotton or cotton to cabbage). After feeding on different plant diets, the microbial assemblage of F2 larvae pointed to considerable differences from other F2 larvae that continued on the same diet. Our results showed that S. littoralis larval gut bacteriome responds rapidly and inexplicably to different diet changes. Further experiments must be conducted to determine the developmental and ecological consequences of such changes. Nevertheless, this study improves our perception of the impact of transgenerational diet switches on the resident gut bacteriome in S. littoralis larvae and could facilitate future research to understand the importance of symbiosis in lepidopteran generalists better.}, }
@article {pmid37516623, year = {2023}, author = {Venegas, L and López, P and Derome, N and Yáñez, JM}, title = {Leveraging microbiome information for animal genetic improvement.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2023.07.004}, pmid = {37516623}, issn = {0168-9525}, abstract = {There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.}, }
@article {pmid37511931, year = {2023}, author = {Costa, DA and Dolbeth, M and Christoffersen, ML and Zúñiga-Upegui, PT and Venâncio, M and de Lucena, RFP}, title = {An Overview of Rhodoliths: Ecological Importance and Conservation Emergency.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/life13071556}, pmid = {37511931}, issn = {2075-1729}, support = {UIDB/04423/2020 and UIDP/04423/2020; CEECINST/00027/2021/CP2789/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Finance Code 001; PDSE/Edital n&#xba; 47/2017//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; Edital n&#xba; 03/2016//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado da Para&#xed;ba/ ; }, abstract = {Red calcareous algae create bio-aggregations ecosystems constituted by carbonate calcium, with two main morphotypes: geniculate and non-geniculate structures (rhodoliths may form bio-encrustations on hard substrata or unattached nodules). This study presents a bibliographic review of the order Corallinales (specifically, rhodoliths), highlighting on morphology, ecology, diversity, related organisms, major anthropogenic influences on climate change and current conservation initiatives. These habitats are often widespread geographically and bathymetrically, occurring in the photic zone from the intertidal area to depths of 270 m. Due to its diverse morphology, this group offers a special biogenic environment that is favourable to epiphyte algae and a number of marine invertebrates. They also include holobiont microbiota made up of tiny eukaryotes, bacteria and viruses. The morphology of red calcareous algae and outside environmental conditions are thought to be the key forces regulating faunistic communities in algae reefs. The impacts of climate change, particularly those related to acidification, might substantially jeopardise the survival of the Corallinales. Despite the significance of these ecosystems, there are a number of anthropogenic stresses on them. Since there have been few attempts to conserve them, programs aimed at their conservation and management need to closely monitor their habitats, research the communities they are linked with and assess the effects they have on the environment.}, }
@article {pmid37508443, year = {2023}, author = {Wuerz, M and Lawson, CA and Oakley, CA and Possell, M and Wilkinson, SP and Grossman, AR and Weis, VM and Suggett, DJ and Davy, SK}, title = {Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/biology12071014}, pmid = {37508443}, issn = {2079-7737}, support = {DP200100091//Australian Research Council discovery project/ ; 19-VUW-086//Marsden Fund/ ; }, abstract = {The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.}, }
@article {pmid37491455, year = {2023}, author = {von der Dunk, SHA and Hogeweg, P and Snel, B}, title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {777}, pmid = {37491455}, issn = {2399-3642}, mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; }, abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.}, }
@article {pmid37486074, year = {2023}, author = {Li, Y and He, X and Lin, Y and Li, YX and Kamenev, GM and Li, J and Qiu, JW and Sun, J}, title = {Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13846}, pmid = {37486074}, issn = {1755-0998}, support = {LSKJ202203104//Science and Technology Innovation Project of Laoshan Laboratory/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 202241002//Fundamental Research Funds for the Central Universities/ ; 12101021//General Research Fund of Hong Kong Special Administrative Region/ ; KF2022NO03//Open Fund of CAS and Shandong Province Key Laboratory of Experimental Marine Biology/ ; tsqn202103036//Young Taishan Scholars Program of Shandong Province/ ; }, abstract = {Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.}, }
@article {pmid37485344, year = {2023}, author = {Sakai, R and Goto-Inoue, N and Yamashita, H and Aimoto, N and Kitai, Y and Maruyama, T}, title = {Smart utilization of betaine lipids in the giant clam Tridacna crocea.}, journal = {iScience}, volume = {26}, number = {7}, pages = {107250}, pmid = {37485344}, issn = {2589-0042}, abstract = {The giant clam Tridacna crocea thrives in poorly nourished coral reef water by forming a holobiont with zooxanthellae and utilizing photosynthetic products of the symbiont. However, detailed metabolic crosstalk between clams and symbionts is elusive. Here, we discovered that the nonphosphorous microalgal betaine lipid DGCC (diacylglycerylcarboxy-hydroxymethylcholine) and its deacylated derivative GCC are present in all tissues and organs, including algae-free sperm and eggs, and are metabolized. Colocalization of DGCC and PC (phosphatidylcholine) evidenced by MS imaging suggested that DGCC functions as a PC substitute. The high content of GCC in digestive diverticula (DD) suggests that the algal DGCC was digested in DD for further utilization. Lipidomics analysis showing the organ-specific distribution pattern of DGCC species suggests active utilization of DGCC as membrane lipids in the clam. Thus, the utilization of zooxanthellal DGCC in animal cells is a unique evolutionary outcome in phosphorous-deficient coral reef waters.}, }
@article {pmid37481685, year = {2023}, author = {Leiva, C and Pérez-Portela, R and Lemer, S}, title = {Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {769}, pmid = {37481685}, issn = {2399-3642}, mesh = {Animals ; *Carbon Dioxide ; *Anthozoa/genetics ; Ocean Acidification ; Hydrogen-Ion Concentration ; Seawater ; Genomics ; }, abstract = {Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.}, }
@article {pmid37475177, year = {2023}, author = {Carvalho, J and Morales, HE and Faria, R and Butlin, RK and Sousa, VC}, title = {Integrating Pool-seq uncertainties into demographic inference.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13834}, pmid = {37475177}, issn = {1755-0998}, support = {2020.00275.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECINST/00032/2018/CP1523/CT0008//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PD/BD/128350/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1614/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.09795.CPCA//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; ERC-2015-AdG-693030-BARRIERS//H2020 European Research Council/ ; RGY0081/2020//Human Frontier Science Program/ ; }, abstract = {Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.}, }
@article {pmid37471099, year = {2023}, author = {Mesny, F and Hacquard, S and Thomma, BP}, title = {Co-evolution within the plant holobiont drives host performance.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {e57455}, doi = {10.15252/embr.202357455}, pmid = {37471099}, issn = {1469-3178}, support = {//Alexander von Humboldt-Stiftung (AvH)/ ; 390686111//Deutsche Forschungsgemeinschaft (DFG)/ ; ME 6064/1-1//Deutsche Forschungsgemeinschaftmeinschaft/ ; 101089198//European Resuscitation Council (ERC)/ ; }, abstract = {Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.}, }
@article {pmid37457347, year = {2023}, author = {Ferrarezi, JA and Defant, H and de Souza, LF and Azevedo, JL and Hungria, M and Quecine, MC}, title = {Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1172839}, pmid = {37457347}, issn = {1664-462X}, abstract = {Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10[-3], 10[-6], 10[-9] and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10[-3] +Ab-V5 and NS 10[-6] Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10[-3] + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.}, }
@article {pmid37437771, year = {2023}, author = {Prosdocimi, F and Cortines, JR and José, MV and de Farias, ST}, title = {Decoding viruses: An alternative perspective on their history, origins and role in nature.}, journal = {Bio Systems}, volume = {}, number = {}, pages = {104960}, doi = {10.1016/j.biosystems.2023.104960}, pmid = {37437771}, issn = {1872-8324}, abstract = {This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.}, }
@article {pmid37423403, year = {2023}, author = {Melo-Bolívar, JF and Ruiz-Pardo, RY and Quintanilla Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM}, title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {108928}, doi = {10.1016/j.fsi.2023.108928}, pmid = {37423403}, issn = {1095-9947}, abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.}, }
@article {pmid37415044, year = {2023}, author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA}, title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37415044}, issn = {1432-184X}, abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.}, }
@article {pmid37404156, year = {2023}, author = {Hu, S and He, R and He, X and Zeng, J and Zhao, D}, title = {Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0071723}, doi = {10.1128/aem.00717-23}, pmid = {37404156}, issn = {1098-5336}, abstract = {Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.}, }
@article {pmid37401172, year = {2023}, author = {Hardoim, CCP and Hardoim, PR and Lôbo-Hajdu, G and Custódio, MR and Thomas, T}, title = {The microbiome of the sponge aplysina caissara in two sites with different levels of anthropogenic impact.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnad064}, pmid = {37401172}, issn = {1574-6968}, abstract = {Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara, however assembly processes are largely determined by the sponge host.}, }
@article {pmid37382454, year = {2023}, author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S}, title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019823}, doi = {10.1128/msystems.00198-23}, pmid = {37382454}, issn = {2379-5077}, abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.}, }
@article {pmid37367660, year = {2023}, author = {Sikorskaya, TV}, title = {Coral Lipidome: Molecular Species of Phospholipids, Glycolipids, Betaine Lipids, and Sphingophosphonolipids.}, journal = {Marine drugs}, volume = {21}, number = {6}, pages = {}, pmid = {37367660}, issn = {1660-3397}, mesh = {Animals ; *Anthozoa/microbiology ; Phospholipids ; Ecosystem ; Lipidomics ; Betaine ; Glycolipids ; Coral Reefs ; Phosphatidylcholines ; *Dinoflagellida ; Phosphatidylglycerols ; Symbiosis ; }, abstract = {Coral reefs are the most biodiversity-rich ecosystems in the world's oceans. Coral establishes complex interactions with various microorganisms that constitute an important part of the coral holobiont. The best-known coral endosymbionts are Symbiodiniaceae dinoflagellates. Each member of the coral microbiome contributes to its total lipidome, which integrates many molecular species. The present study summarizes available information on the molecular species of the plasma membrane lipids of the coral host and its dinoflagellates (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), ceramideaminoethylphosphonate, and diacylglyceryl-3-O-carboxyhydroxymethylcholine), and the thylakoid membrane lipids of dinoflagellates (phosphatidylglycerol (PG) and glycolipids). Alkyl chains of PC and PE molecular species differ between tropical and cold-water coral species, and features of their acyl chains depend on the coral's taxonomic position. PS and PI structural features are associated with the presence of an exoskeleton in the corals. The dinoflagellate thermosensitivity affects the profiles of PG and glycolipid molecular species, which can be modified by the coral host. Coral microbiome members, such as bacteria and fungi, can also be the source of the alkyl and acyl chains of coral membrane lipids. The lipidomics approach, providing broader and more detailed information about coral lipid composition, opens up new opportunities in the study of biochemistry and ecology of corals.}, }
@article {pmid37288516, year = {2023}, author = {Vargas, S and Leiva, L and Eitel, M and Curdt, F and Rohde, S and Arnold, C and Nickel, M and Schupp, P and Orsi, WD and Adamska, M and Wörheide, G}, title = {Body-Plan Reorganization in a Sponge Correlates with Microbiome Change.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, doi = {10.1093/molbev/msad138}, pmid = {37288516}, issn = {1537-1719}, abstract = {Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e., bleaching) upon shading correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-like cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded specimens are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, transforming growth factor β (TGF-β), and TLR-ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge postembryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group.}, }
@article {pmid37360551, year = {2023}, author = {Monti, M and Giorgi, A and Kemp, DW and Olson, JB}, title = {Spatial, temporal and network analyses provide insights into the dynamics of the bacterial communities associated with two species of Caribbean octocorals and indicate possible key taxa.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {1-14}, pmid = {37360551}, issn = {0334-5114}, abstract = {UNLABELLED: Despite the current decline of scleractinian coral populations, octocorals are thriving on reefs in the Caribbean Sea and western North Atlantic Ocean. These cnidarians are holobiont entities, interacting with a diverse array of microorganisms. Few studies have investigated the spatial and temporal stability of the bacterial communities associated with octocoral species and information regarding the co-occurrence and potential interactions between specific members of these bacterial communities remain sparse. To address this knowledge gap, this study investigated the stability of the bacterial assemblages associated with two common Caribbean octocoral species, Eunicea flexuosa and Antillogorgia americana, across time and geographical locations and performed network analyses to investigate potential bacterial interactions. Results demonstrated that general inferences regarding the spatial and temporal stability of octocoral-associated bacterial communities should not be made, as host-specific characteristics may influence these factors. In addition, network analyses revealed differences in the complexity of the interactions between bacteria among the octocoral species analyzed, while highlighting the presence of genera known to produce bioactive secondary metabolites in both octocorals that may play fundamental roles in structuring the octocoral-associated bacteriome.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13199-023-00923-x.}, }
@article {pmid37344276, year = {2023}, author = {Dussex, N and Morales, HE and Grossen, C and Dalén, L and van Oosterhout, C}, title = {Purging and accumulation of genetic load in conservation.}, journal = {Trends in ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2023.05.008}, pmid = {37344276}, issn = {1872-8383}, abstract = {Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.}, }
@article {pmid37336945, year = {2023}, author = {Vinha, B and Rossi, S and Gori, A and Hanz, U and Pennetta, A and De Benedetto, GE and Mienis, F and Huvenne, VAI and Hebbeln, D and Wienberg, C and Titschack, J and Freiwald, A and Piraino, S and Orejas, C}, title = {Trophic ecology of Angolan cold-water coral reefs (SE Atlantic) based on stable isotope analyses.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9933}, pmid = {37336945}, issn = {2045-2322}, mesh = {Animals ; *Coral Reefs ; *Anthozoa ; Ecology ; Water ; Nitrogen Isotopes ; Carbon Isotopes/analysis ; }, abstract = {Cold-water coral (CWC) reefs of the Angolan margin (SE Atlantic) are dominated by Desmophyllum pertusum and support a diverse community of associated fauna, despite hypoxic conditions. In this study, we use carbon and nitrogen stable isotope analyses (δ[13]C and δ[15]N) to decipher the trophic network of this relatively unknown CWC province. Although fresh phytodetritus is available to the reef, δ[15]N signatures indicate that CWCs (12.90 ± 1.00 ‰) sit two trophic levels above Suspended Particulate Organic Matter (SPOM) (4.23 ± 1.64 ‰) suggesting that CWCs are highly reliant on an intermediate food source, which may be zooplankton. Echinoderms and the polychaete Eunice norvegica occupy the same trophic guild, with high δ[13]C signatures (-14.00 ± 1.08 ‰) pointing to a predatory feeding behavior on CWCs and sponges, although detrital feeding on [13]C enriched particles might also be important for this group. Sponges presented the highest δ[15]N values (20.20 ± 1.87 ‰), which could be due to the role of the sponge holobiont and bacterial food in driving intense nitrogen cycling processes in sponges' tissue, helping to cope with the hypoxic conditions of the reef. Our study provides first insights to understand trophic interactions of CWC reefs under low-oxygen conditions.}, }
@article {pmid37332135, year = {2023}, author = {Vadillo Gonzalez, S and Vranken, S and Coleman, MA and Wernberg, T and Steinberg, PD and Marzinelli, EM}, title = {Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17056}, pmid = {37332135}, issn = {1365-294X}, abstract = {A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.}, }
@article {pmid37326290, year = {2023}, author = {Perez-Lamarque, B and Sommeria-Klein, G and Duret, L and Morlon, H}, title = {Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad144}, pmid = {37326290}, issn = {1537-1719}, abstract = {How host-associated microbial communities evolve as their hosts diversify remains equivocal: How conserved is their composition? What was the composition of ancestral microbiota? Do microbial taxa covary in abundance over millions of years? Multivariate phylogenetic models of trait evolution are key to answering similar questions for complex host phenotypes, yet they are not directly applicable to relative abundances, which usually characterize microbiota. Here, we extend these models in this context, thereby providing a powerful approach for estimating phylosymbiosis (the extent to which closely related host species harbor similar microbiota), ancestral microbiota composition, and integration (evolutionary covariations in bacterial abundances). We apply our model to the gut microbiota of mammals and birds. We find significant phylosymbiosis that is not entirely explained by diet and geographic location, indicating that other evolutionary-conserved traits shape microbiota composition. We identify main shifts in microbiota composition during the evolution of the two groups and infer an ancestral mammalian microbiota consistent with an insectivorous diet. We also find remarkably consistent evolutionary covariations among bacterial orders in mammals and birds. Surprisingly, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of host evolutionary history.}, }
@article {pmid37325891, year = {2023}, author = {Urban, L and Perlas, A and Francino, O and Martí-Carreras, J and Muga, BA and Mwangi, JW and Boykin Okalebo, L and Stanton, JL and Black, A and Waipara, N and Fontsere, C and Eccles, D and Urel, H and Reska, T and Morales, HE and Palmada-Flores, M and Marques-Bonet, T and Watsa, M and Libke, Z and Erkenswick, G and van Oosterhout, C}, title = {Real-time genomics for One Health.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {e11686}, doi = {10.15252/msb.202311686}, pmid = {37325891}, issn = {1744-4292}, abstract = {The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.}, }
@article {pmid37317893, year = {2023}, author = {Connelly, MT and Snyder, G and Palacio-Castro, AM and Gillette, PR and Baker, AC and Traylor-Knowles, N}, title = {Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17049}, pmid = {37317893}, issn = {1365-294X}, abstract = {Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.}, }
@article {pmid37317290, year = {2023}, author = {Massé, A and Detang, J and Duval, C and Duperron, S and Woo, AC and Domart-Coulon, I}, title = {Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/microorganisms11051318}, pmid = {37317290}, issn = {2076-2607}, abstract = {Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.}, }
@article {pmid37311801, year = {2023}, author = {Botté, ES and Bennett, H and Engelberts, JP and Thomas, T and Bell, JJ and Webster, NS and Luter, HM}, title = {Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {53}, pmid = {37311801}, issn = {2730-6151}, abstract = {Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.}, }
@article {pmid37310733, year = {2023}, author = {Ma, M and Zhuang, Y and Chang, L and Xiao, L and Lin, Q and Qiu, Q and Chen, D and Egan, S and Wang, G}, title = {Naturally occurring beneficial bacteria Vibrio alginolyticus X-2 protects seaweed from bleaching disease.}, journal = {mBio}, volume = {}, number = {}, pages = {e0006523}, doi = {10.1128/mbio.00065-23}, pmid = {37310733}, issn = {2150-7511}, abstract = {Microbiome manipulation is gaining fresh attention as a way to mitigate diseases in aquaculture. The commercially farmed seaweed Saccharina japonica suffers from a bacterial-induced bleaching disease, which has major implications for the reliable supply of healthy sporelings. Here, we identify a beneficial bacterium, Vibrio alginolyticus X-2 that significantly reduces the risk of bleaching disease. By combining infection assays and multi-omic analyses, we provide evidence to suggest that the underlying protective mechanisms of V. alginolyticus X-2 involve maintaining epibacterial communities, increasing the gene expression of S. japonica related to immune and stress protection pathways, and stimulating betaine concentrations in S. japonica holobionts. Thus, V. alginolyticus X-2 can elicit a suite of microbial and host responses to mitigate the bleaching disease. Our study provides insights into disease control in farmed S. japonica through the application of beneficial bacteria. IMPORTANCE Beneficial bacteria can elicit a suite of microbial and host responses to enhance the resistance to bleaching disease.}, }
@article {pmid37308970, year = {2023}, author = {Mariadassou, M and Nouvel, LX and Constant, F and Morgavi, DP and Rault, L and Barbey, S and Helloin, E and Rué, O and Schbath, S and Launay, F and Sandra, O and Lefebvre, R and Le Loir, Y and Germon, P and Citti, C and Even, S}, title = {Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {32}, pmid = {37308970}, issn = {2524-4671}, abstract = {BACKGROUND: Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing.<br><br>RESULTS: Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7&#xa0;months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (<&#x2009;7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota.<br><br>CONCLUSIONS: This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.}, }
@article {pmid37299176, year = {2023}, author = {Giannelli, G and Potestio, S and Visioli, G}, title = {The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37299176}, issn = {2223-7747}, abstract = {Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.}, }
@article {pmid37287087, year = {2023}, author = {Li, J and Chai, G and Xiao, Y and Li, Z}, title = {The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {49}, pmid = {37287087}, issn = {2524-6372}, abstract = {BACKGROUND: Reef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont's homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification-warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control.<br><br>RESULTS: A, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects.<br><br>CONCLUSIONS: The metatranscriptome-based study indicates that acidification and/or warming might change coral's in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont's ability for acclimatization under future climate change.}, }
@article {pmid37285390, year = {2023}, author = {Rubin, JD and Vogel, NA and Gopalakrishnan, S and Sackett, PW and Renaud, G}, title = {HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph human mtDNA haplogroup inference.}, journal = {PLoS computational biology}, volume = {19}, number = {6}, pages = {e1011148}, doi = {10.1371/journal.pcbi.1011148}, pmid = {37285390}, issn = {1553-7358}, abstract = {Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.}, }
@article {pmid37283898, year = {2023}, author = {McRae, CJ and Keshavmurthy, S and Chen, HK and Ye, ZM and Meng, PJ and Rosset, SL and Huang, WB and Chen, CA and Fan, TY and Côté, IM}, title = {Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15421}, pmid = {37283898}, issn = {2167-8359}, abstract = {Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont.}, }
@article {pmid37277669, year = {2023}, author = {Duval, P and Antonelli, P and Aschan-Leygonie, C and Valiente Moro, C}, title = {Impact of Human Activities on Disease-Spreading Mosquitoes in Urban Areas.}, journal = {Journal of urban health : bulletin of the New York Academy of Medicine}, volume = {}, number = {}, pages = {}, pmid = {37277669}, issn = {1468-2869}, abstract = {Urbanization is one of the leading global trends of the twenty-first century that has a significant impact on health. Among health challenges caused by urbanization, the relationship of urbanization between emergence and the spread of mosquito-borne infectious diseases (MBIDs) is a great public health concern. Urbanization processes encompass social, economic, and environmental changes that directly impact the biology of mosquito species. In particular, urbanized areas experience higher temperatures and pollution levels than outlying areas but also favor the development of infrastructures and objects that are favorable to mosquito development. All these modifications may influence mosquito life history traits and their ability to transmit diseases. This review aimed to summarize the impact of urbanization on mosquito spreading in urban areas and the risk associated with the emergence of MBIDs. Moreover, mosquitoes are considered as holobionts, as evidenced by numerous studies highlighting the role of mosquito-microbiota interactions in mosquito biology. Taking into account this new paradigm, this review also represents an initial synthesis on how human-driven transformations impact microbial communities in larval habitats and further interfere with mosquito behavior and life cycle in urban areas.}, }
@article {pmid37284513, year = {2021}, author = {Mauger, S and Ricono, C and Mony, C and Chable, V and Serpolay, E and Biget, M and Vandenkoornhuyse, P}, title = {Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {2}, number = {5}, pages = {235-248}, pmid = {37284513}, issn = {2575-6265}, abstract = {Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.}, }
@article {pmid37275175, year = {2023}, author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E}, title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141862}, doi = {10.3389/fmicb.2023.1141862}, pmid = {37275175}, issn = {1664-302X}, abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.}, }
@article {pmid37270649, year = {2023}, author = {Khakisahneh, S and Zhang, XY and Han, SY and Song, EJ and Nam, YD and Kim, H}, title = {Yijung-tang improves thermogenesis and reduces inflammation associated with gut microbiota in hypothyroid rats.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {32}, pmid = {37270649}, issn = {2055-5008}, mesh = {Rats ; Humans ; Animals ; *Gastrointestinal Microbiome ; Inflammation/drug therapy ; Thermogenesis ; *Hypothyroidism/drug therapy ; }, abstract = {Currently, considerable attention is focused on exploring the potential relationship between herbal medicine (HM) and the gut microbiome in terms of thermoregulation, which is an important aspect of human health, in modern system biology. However, our knowledge of the mechanisms of HM in thermoregulation is inadequate. Here, we demonstrate that the canonical herbal formula, Yijung-tang (YJT), protects against hypothermia, hyperinflammation, and intestinal microbiota dysbiosis in PTU-induced hypothyroid rats. Notably, these properties were associated with alterations in the gut microbiota and signaling crosstalk between the thermoregulatory and inflammatory mediators in the small intestine and brown adipose tissue (BAT). In contrast to the conventional drug L-thyroxine for curing hypothyroidism, YJT has an efficacy for attenuating systematic inflammatory responses, related with depression in intestinal TLR4 and Nod2/Pglyrp1 signaling pathways. Our findings suggest that YJT could promote BAT thermogenesis and prevent systemic inflammation in PTU-induced hypothyroid rats, which was associated with its prebiotic effect on modulating of the gut microbiota and gene expression with relevance in the enteroendocrine function and innate immune systems. These findings may strengthen the rationale of the microbiota-gut-BAT axis for a paradigm shift to enable holobiont-centric medicine.}, }
@article {pmid37269833, year = {2023}, author = {Kim, SM and Park, S and Hwang, SH and Lee, EY and Kim, JH and Lee, GS and Lee, G and Chang, DH and Lee, JG and Hwang, J and Lee, Y and Kyung, M and Kim, EK and Kim, JH and Kim, TH and Moon, JH and Kim, BC and Ko, G and Kim, SY and Ryu, JH and Lee, JS and Lee, CH and Kim, JY and Kim, S and Lee, WJ and Kim, MH}, title = {Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2023.05.007}, pmid = {37269833}, issn = {1934-6069}, abstract = {Commensal bacteria are critically involved in the establishment of tolerance against inflammatory challenges, the molecular mechanisms of which are just being uncovered. All kingdoms of life produce aminoacyl-tRNA synthetases (ARSs). Thus far, the non-translational roles of ARSs have largely been reported in eukaryotes. Here, we report that the threonyl-tRNA synthetase (AmTARS) of the gut-associated bacterium Akkermansia muciniphila is secreted and functions to monitor and modulate immune homeostasis. Secreted AmTARS triggers M2 macrophage polarization and orchestrates the production of anti-inflammatory IL-10 via its unique, evolutionary-acquired regions, which mediates specific interactions with TLR2. This interaction activates the MAPK and PI3K/AKT signaling pathways, which converge on CREB, leading to an efficient production of IL-10 and suppression of the central inflammatory mediator NF-κB. AmTARS restores IL-10-positive macrophages, increases IL-10 levels in the serum, and attenuates the pathological effects in colitis mice. Thus, commensal tRNA synthetases can act as intrinsic mediators that maintain homeostasis.}, }
@article {pmid37268692, year = {2023}, author = {de Souza, MR and Caruso, C and Ruiz-Jones, L and Drury, C and Gates, RD and Toonen, RJ}, title = {Importance of depth and temperature variability as drivers of coral symbiont composition despite a mass bleaching event.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8957}, pmid = {37268692}, issn = {2045-2322}, abstract = {Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed 'coral bleaching'. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāne'ohe Bay, Hawai'i and compared the algal symbiont composition before and after the 2019 bleaching event. The relative proportion of the heat-tolerant symbiont Durusdinium in corals increased in most parts of the bay following the bleaching event. Despite this widespread increase in abundance of Durusdinium, the overall algal symbiont community composition was largely unchanged, and hydrodynamically defined regions of the bay retained their distinct pre-bleaching compositions. We explain ~ 21% of the total variation, of which depth and temperature variability were the most significant environmental drivers of Symbiodiniaceae community composition by site regardless of bleaching intensity or change in relative proportion of Durusdinium. We hypothesize that the plasticity of symbiont composition in corals may be constrained to adaptively match the long-term environmental conditions surrounding the holobiont, despite an individual coral's stress and bleaching response.}, }
@article {pmid37264047, year = {2023}, author = {Belser, C and Poulain, J and Labadie, K and Gavory, F and Alberti, A and Guy, J and Carradec, Q and Cruaud, C and Da Silva, C and Engelen, S and Mielle, P and Perdereau, A and Samson, G and Gas, S and ,  and Voolstra, CR and Galand, PE and Flores, JM and Hume, BCC and Perna, G and Ziegler, M and Ruscheweyh, HJ and Boissin, E and Romac, S and Bourdin, G and Iwankow, G and Moulin, C and Paz García, DA and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Sunagawa, S and Thomas, OP and Troublé, R and Thurber, RV and Zoccola, D and Scarpelli, C and Jacoby, EK and Oliveira, PH and Aury, JM and Allemand, D and Planes, S and Wincker, P}, title = {Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {326}, pmid = {37264047}, issn = {2052-4463}, abstract = {Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.}, }
@article {pmid37264015, year = {2023}, author = {Hochart, C and Paoli, L and Ruscheweyh, HJ and Salazar, G and Boissin, E and Romac, S and Poulain, J and Bourdin, G and Iwankow, G and Moulin, C and Ziegler, M and Porro, B and Armstrong, EJ and Hume, BCC and Aury, JM and Pogoreutz, C and Paz-García, DA and Nugues, MM and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Thomas, OP and Troublé, R and Wincker, P and Zoccola, D and Allemand, D and Planes, S and Thurber, RV and Voolstra, CR and Sunagawa, S and Galand, PE}, title = {Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3037}, pmid = {37264015}, issn = {2041-1723}, abstract = {Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.}, }
@article {pmid37258653, year = {2023}, author = {Garritano, AN and Majzoub, ME and Ribeiro, B and Damasceno, T and Modolon, F and Messias, C and Vilela, C and Duarte, G and Hill, L and Peixoto, R and Thomas, T}, title = {Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37258653}, issn = {1751-7370}, abstract = {Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.}, }
@article {pmid37255458, year = {2023}, author = {Ramayo-Caldas, Y and Crespo-Piazuelo, D and Morata, J and González-Rodríguez, O and Sebastià, C and Castello, A and Dalmau, A and Ramos-Onsins, S and Alexiou, KG and Folch, JM and Quintanilla, R and Ballester, M}, title = {Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0527122}, doi = {10.1128/spectrum.05271-22}, pmid = {37255458}, issn = {2165-0497}, abstract = {Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness (P = 5.41 × 10[-5], false discovery rate [FDR] = 0.022) and Shannon α-diversity (P = 1.42 × 10[-4], FDR = 0.057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance.}, }
@article {pmid37254353, year = {2023}, author = {Azad, AM and Bernhard, A and Shen, A and Myrmel, LS and Lundebye, AK and Lecaudey, LA and Fjære, E and Tri Ho, Q and Sveier, H and Kristiansen, K and Limborg, MT and Madsen, L}, title = {Metabolic effects of diet containing blue mussel (Mytilus edulis) and blue mussel-fed salmon in a mouse model of obesity.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112927}, doi = {10.1016/j.foodres.2023.112927}, pmid = {37254353}, issn = {1873-7145}, abstract = {Alternative feed ingredients for farmed salmon are warranted due to increasing pressure on wild fish stocks. As locally farmed blue mussels may represent an environmentally sustainable substitute with a lower carbon footprint, we aimed to test the potential and safety of substituting fish meal with blue mussel meal in feed for Atlantic salmon. Salmon were fed diets in which fish meal was partially replaced with blue mussel meal in increments, accounting for up to 13.1 % of the ingredients. Fillets from the salmon were subsequently used to prepare obesity-promoting western diets for a 13-weeks mouse feeding trial. In a second mouse trial, we tested the effects of inclusion of up to 8% blue mussel meal directly in a meat-based western diet. Partial replacement of fish meal with blue mussel meal in fish feed preserved the n-3 polyunsaturated fatty acid (PUFA) content in salmon fillets. The observed blue mussel-induced changes in the fatty acid profiles in salmon fillets did not translate into similar changes in the livers of mice that consumed the salmon, and no clear dose-dependent responses were found. The relative levels of the marine n-3 fatty acids, EPA, and DHA were not reduced, and the n-3/n-6 PUFA ratios in livers from all salmon-fed mice were unchanged. The inclusion of blue mussel meal in a meat-based western diet led to a small, but dose-dependent increase in the n-3/n-6 PUFA ratios in mice livers. Diet-induced obesity, glucose intolerance, and hepatic steatosis were unaffected in both mice trials and no blue mussel-induced adverse effects were observed. In conclusion, our results suggest that replacing fish meal with blue mussel meal in salmon feed will not cause adverse effects in those who consume the salmon fillets.}, }
@article {pmid37249392, year = {2023}, author = {Kliver, S and Houck, ML and Perelman, PL and Totikov, A and Tomarovsky, A and Dudchenko, O and Omer, AD and Colaric, Z and Weisz, D and Aiden, EL and Chan, S and Hastie, A and Komissarov, A and Ryder, OA and Graphodatsky, A and Johnson, WE and Maldonado, JE and Pukazhenthi, BS and Marinari, PE and Wildt, DE and Koepfli, KP}, title = {Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).}, journal = {The Journal of heredity}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhered/esad035}, pmid = {37249392}, issn = {1465-7333}, abstract = {The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex-situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 Kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million years ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.}, }
@article {pmid37237923, year = {2023}, author = {Doering, T and Maire, J and Chan, WY and Perez-Gonzalez, A and Meyers, L and Sakamoto, R and Buthgamuwa, I and Blackall, LL and van Oppen, MJH}, title = {Comparing the Role of ROS and RNS in the Thermal Stress Response of Two Cnidarian Models, Exaiptasia diaphana and Galaxea fascicularis.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37237923}, issn = {2076-3921}, abstract = {Coral reefs are threatened by climate change, because it causes increasingly frequent and severe summer heatwaves, resulting in mass coral bleaching and mortality. Coral bleaching is believed to be driven by an excess production of reactive oxygen (ROS) and nitrogen species (RNS), yet their relative roles during thermal stress remain understudied. Here, we measured ROS and RNS net production, as well as activities of key enzymes involved in ROS scavenging (superoxide dismutase and catalase) and RNS synthesis (nitric oxide synthase) and linked these metrics to physiological measurements of cnidarian holobiont health during thermal stress. We did this for both an established cnidarian model, the sea anemone Exaiptasia diaphana, and an emerging scleractinian model, the coral Galaxea fascicularis, both from the Great Barrier Reef (GBR). Increased ROS production was observed during thermal stress in both species, but it was more apparent in G. fascicularis, which also showed higher levels of physiological stress. RNS did not change in thermally stressed G. fascicularis and decreased in E. diaphana. Our findings in combination with variable ROS levels in previous studies on GBR-sourced E. diaphana suggest G. fascicularis is a more suitable model to study the cellular mechanisms of coral bleaching.}, }
@article {pmid37233466, year = {2023}, author = {De Domenico, S and De Rinaldis, G and Mammone, M and Bosch-Belmar, M and Piraino, S and Leone, A}, title = {The Zooxanthellate Jellyfish Holobiont Cassiopea andromeda, a Source of Soluble Bioactive Compounds.}, journal = {Marine drugs}, volume = {21}, number = {5}, pages = {}, doi = {10.3390/md21050272}, pmid = {37233466}, issn = {1660-3397}, abstract = {Cassiopea andromeda (Forsskål, 1775), commonly found across the Indo-Pacific Ocean, the Red Sea, and now also in the warmest areas of the Mediterranean Sea, is a scyphozoan jellyfish that hosts autotrophic dinoflagellate symbionts (family Symbiodiniaceae). Besides supplying photosynthates to their host, these microalgae are known to produce bioactive compounds as long-chain unsaturated fatty acids, polyphenols, and pigments, including carotenoids, with antioxidant properties and other beneficial biological activities. By the present study, a fractionation method was applied on the hydroalcoholic extract from two main body parts (oral arms and umbrella) of the jellyfish holobiont to obtain an improved biochemical characterization of the obtained fractions from the two body parts. The composition of each fraction (i.e., proteins, phenols, fatty acids, and pigments) as well as the associated antioxidant activity were analyzed. The oral arms proved richer in zooxanthellae and pigments than the umbrella. The applied fractionation method was effective in separating pigments and fatty acids into a lipophilic fraction from proteins and pigment-protein complexes. Therefore, the C. andromeda-dinoflagellate holobiont might be considered as a promising natural source of multiple bioactive compounds produced through mixotrophic metabolism, which are of interest for a wide range of biotechnological applications.}, }
@article {pmid37233257, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, doi = {10.3390/jof9050546}, pmid = {37233257}, issn = {2309-608X}, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, }
@article {pmid37231184, year = {2023}, author = {Zheng, R and Wang, Q and Wu, R and Paradkar, PN and Hoffmann, AA and Wang, GH}, title = {Holobiont perspectives on tripartite interactions among microbiota, mosquitoes, and pathogens.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {37231184}, issn = {1751-7370}, abstract = {Mosquito-borne diseases like dengue and malaria cause a significant global health burden. Unfortunately, current insecticides and environmental control strategies aimed at the vectors of these diseases are only moderately effective in decreasing disease burden. Understanding and manipulating the interaction between the mosquito holobiont (i.e., mosquitoes and their resident microbiota) and the pathogens transmitted by these mosquitoes to humans and animals could help in developing new disease control strategies. Different microorganisms found in the mosquito's microbiota affect traits related to mosquito survival, development, and reproduction. Here, we review the physiological effects of essential microbes on their mosquito hosts; the interactions between the mosquito holobiont and mosquito-borne pathogen (MBP) infections, including microbiota-induced host immune activation and Wolbachia-mediated pathogen blocking (PB); and the effects of environmental factors and host regulation on the composition of the microbiota. Finally, we briefly overview future directions in holobiont studies, and how these may lead to new effective control strategies against mosquitoes and their transmitted diseases.}, }
@article {pmid37145211, year = {2023}, author = {Schwarcz, S and Kovács, P and Kovács, T and Ujlaki, G and Nyerges, P and Uray, K and Bai, P and Mikó, E}, title = {The pro- and antineoplastic effects of deoxycholic acid in pancreatic adenocarcinoma cell models.}, journal = {Molecular biology reports}, volume = {50}, number = {6}, pages = {5273-5282}, pmid = {37145211}, issn = {1573-4978}, mesh = {Humans ; *Pancreatic Neoplasms/drug therapy/genetics/metabolism ; *Adenocarcinoma/drug therapy/genetics ; Epithelial-Mesenchymal Transition ; *Antineoplastic Agents/pharmacology ; Deoxycholic Acid/pharmacology ; Cell Line, Tumor ; }, abstract = {BACKGROUND: Commensal bacteria secrete metabolites that reach distant cancer cells through the circulation and influence cancer behavior. Deoxycholic acid (DCA), a hormone-like metabolite, is a secondary bile acid specifically synthesized by intestinal microbes. DCA may have both pro- and antineoplastic effects in cancers.<br><br>METHODS AND RESULTS: The pancreatic adenocarcinoma cell lines, Capan-2 and BxPC-3, were treated with 0.7&#xa0;&#xb5;M DCA, which corresponds to the reference concentration of DCA in human serum. DCA influenced the expression of epithelial to mesenchymal transition (EMT)-related genes, significantly decreased the expression level of the mesenchymal markers, transcription factor 7- like 2 (TCF7L2), snail family transcriptional repressor 2 (SLUG), CLAUDIN-1, and increased the expression of the epithelial genes, zona occludens 1 (ZO-1) and E-CADHERIN, as shown by real-time PCR and Western blotting. Consequently, DCA reduced the invasion capacity of pancreatic adenocarcinoma cells in Boyden chamber experiments. DCA induced the protein expression of oxidative/nitrosative stress markers. Moreover, DCA reduced aldehyde dehydrogenase 1 (ALDH1) activity in an Aldefluor assay and ALDH1 protein level, suggesting that DCA reduced stemness in pancreatic adenocarcinoma. In Seahorse experiments, DCA induced all fractions of mitochondrial respiration and glycolytic flux. The ratio of mitochondrial oxidation and glycolysis did not change after DCA treatment, suggesting that cells became hypermetabolic.<br><br>CONCLUSION: DCA induced antineoplastic effects in pancreatic adenocarcinoma cells by inhibiting EMT, reducing cancer stemness, and inducing oxidative/nitrosative stress and procarcinogenic effects such as hypermetabolic bioenergetics.}, }
@article {pmid37229712, year = {2023}, author = {Roughgarden, J}, title = {Holobiont Evolution: Population Theory for the Hologenome.}, journal = {The American naturalist}, volume = {201}, number = {6}, pages = {763-778}, doi = {10.1086/723782}, pmid = {37229712}, issn = {1537-5323}, abstract = {AbstractThis article develops mathematical theory for the population dynamics of microbiomes with their hosts and for holobiont evolution caused by holobiont selection. The objective is to account for the formation of microbiome-host integration. Microbial population dynamic parameters must mesh with the host's for coexistence. A horizontally transmitted microbiome is a genetic system with "collective inheritance." The microbial source pool in the environment corresponds to the gamete pool for nuclear genes. Poisson sampling of the microbial source pool corresponds to binomial sampling of the gamete pool. However, holobiont selection on the microbiome does not lead to a counterpart of the Hardy-Weinberg law or to directional selection that always fixes microbial genes conferring the highest holobiont fitness. A microbe might strike an optimal fitness balance between lowering its within-host fitness while increasing holobiont fitness. Such microbes are replaced by otherwise identical microbes that contribute nothing to holobiont fitness. This replacement can be reversed by hosts that initiate immune responses to nonhelpful microbes. This discrimination leads to microbial species sorting. Host-orchestrated species sorting followed by microbial competition, rather than coevolution or multilevel selection, is predicted to be the cause of microbiome-host integration.}, }
@article {pmid37228141, year = {2023}, author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N}, title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286293}, doi = {10.1371/journal.pone.0286293}, pmid = {37228141}, issn = {1932-6203}, abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.}, }
@article {pmid37217641, year = {2023}, author = {Lintner, M and Lintner, B and Schagerl, M and Wanek, W and Heinz, P}, title = {The change in metabolic activity of a large benthic foraminifera as a function of light supply.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8240}, pmid = {37217641}, issn = {2045-2322}, mesh = {*Foraminifera/metabolism ; Photosynthesis ; Isotopes/metabolism ; }, abstract = {We studied metabolic activity of the symbiont-bearing large benthic foraminifer Heterostegina depressa under different light conditions. Besides the overall photosynthetic performance of the photosymbionts estimated by means of variable fluorescence, the isotope uptake ([13]C and [15]N) of the specimens (= holobionts) was measured. Heterostegina depressa was either incubated in darkness over a period of 15 days or exposed to an 16:8 h light:dark cycle mimicking natural light conditions. We found photosynthetic performance to be highly related to light supply. The photosymbionts, however, survived prolonged darkness and could be reactivated after 15 days of darkness. The same pattern was found in the isotope uptake of the holobionts. Based on these results, we propose that [13]C-carbonate and [15]N-nitrate assimilation is mainly controlled by the photosymbionts, whereas [15]N-ammonium and [13]C-glucose utilization is regulated by both, the symbiont and the host cells.}, }
@article {pmid37217368, year = {2023}, author = {Aizpurua, O and Blijleven, K and Trivedi, U and Gilbert, MTP and Alberdi, A}, title = {Unravelling animal-microbiota evolution on a chip.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.04.010}, pmid = {37217368}, issn = {1878-4380}, abstract = {Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.}, }
@article {pmid37214652, year = {2023}, author = {Clokie, M and Sicheritz-Pontén, T}, title = {Lungs, Liposomes, Libraries, and Likely Interactions Between Phages and Eukaryotic Cells.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {4}, number = {1}, pages = {1-2}, doi = {10.1089/phage.2023.29041.editorial}, pmid = {37214652}, issn = {2641-6549}, }
@article {pmid37210404, year = {2023}, author = {Zvi-Kedem, T and Vintila, S and Kleiner, M and Tchernov, D and Rubin-Blum, M}, title = {Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {48}, pmid = {37210404}, issn = {2730-6151}, abstract = {Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.}, }
@article {pmid37209745, year = {2023}, author = {Núñez-Pons, L and Cunning, R and Nelson, C and Amend, A and Sogin, EM and Gates, R and Ritson-Williams, R}, title = {Hawai'ian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164040}, doi = {10.1016/j.scitotenv.2023.164040}, pmid = {37209745}, issn = {1879-1026}, abstract = {Historically, Hawai'i had few massive coral bleaching events, until two consecutive heatwaves in 2014-2015. Consequent mortality and thermal stress were observed in Kane'ohe Bay (O'ahu). The two most dominant local species exhibited a phenotypic dichotomy of either bleaching resistance or susceptibility (Montipora capitata and Porites compressa), while the third predominant species (Pocillopora acuta) was broadly susceptible to bleaching. In order to survey shifts in coral microbiomes during bleaching and recovery, 50 colonies were tagged and periodically monitored. Metabarcoding of three genetic markers (16S rRNA gene ITS1 and ITS2) followed by compositional approaches for community structure analysis, differential abundance and correlations for longitudinal data were used to temporally compare Bacteria/Archaea, Fungi and Symbiodiniaceae dynamics. P. compressa corals recovered faster than P. acuta and Montipora capitata. Prokaryotic and algal communities were majorly shaped by host species, and had no apparent pattern of temporal acclimatization. Symbiodiniaceae signatures were identified at the colony scale, and were often related to bleaching susceptibility. Bacterial compositions were practically constant between bleaching phenotypes, and more diverse in P. acuta and M. capitata. P. compressa's prokaryotic community was dominated by a single bacterium. Compositional approaches (via microbial balances) allowed the identification of fine-scale differences in the abundance of a consortium of microbes, driving changes by bleaching susceptibility and time across all hosts. The three major coral reef founder-species in Kane'ohe Bay revealed different phenotypic and microbiome responses after 2014-2015 heatwaves. It is difficult to forecast, a more successful strategy towards future scenarios of global warming. Differentially abundant microbial taxa across time and/or bleaching susceptibility were broadly shared among all hosts, suggesting that locally, the same microbes may modulate stress responses in sympatric coral species. Our study highlights the potential of investigating microbial balances to identify fine-scale microbiome changes, serving as local diagnostic tools of coral reef fitness.}, }
@article {pmid37209734, year = {2023}, author = {Sun, H and Xie, Z and Yang, X and Yang, B and Liao, B and Yin, J and Xiao, B}, title = {New insights into microbial and metabolite signatures of coral bleaching.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {164258}, doi = {10.1016/j.scitotenv.2023.164258}, pmid = {37209734}, issn = {1879-1026}, abstract = {Coral bleaching and coral reef degradation have been severely increased due to anthropogenic impacts, especially global warming. Studies have indicated the key role of host-microbiome symbiotic relationships for the coral holobiont health and development, although not all of the mechanisms of interaction have been fully explored. Here, we explore bacterial and metabolic shifts within coral holobionts under thermal stress, and its correlation with bleaching. Our results showed obvious signs of coral bleaching after 13 days of heating treatment, and a more-complex co-occurrence network was observed in the coral-associated bacterial community of the heating group. The bacterial community and metabolites changed significantly under thermal stress, and genera Flavobacterium, Shewanella and Psychrobacter increased from <0.1 % to 43.58 %, 6.95 % and 6.35 %, respectively. Bacteria potentially associated with stress tolerance, biofilm formation and mobile elements decreased from 80.93 %, 62.15 % and 49.27 % to 56.28 %, 28.41 % and 18.76 %, respectively. The differentially expressed metabolites of corals after heating treatment, such as Cer(d18:0/17:0), 1-Methyladenosine, Trp-P-1 and Marasmal, were associated with cell cycle regulation and antioxidant properties. Our results can contribute to our current understanding on the correlations between coral-symbiotic bacteria, metabolites and the coral physiological response to thermal stress. These new insights into the metabolomics of heat-stressed coral holobionts may expand our knowledge on the mechanisms underlying bleaching.}, }
@article {pmid37194081, year = {2023}, author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B}, title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {108}, pmid = {37194081}, issn = {2049-2618}, mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; }, abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.<br><br>RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.<br><br>CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.}, }
@article {pmid37191552, year = {2023}, author = {Xu, M and Cheng, K and Xiao, B and Tong, M and Cai, Z and Jong, MC and Chen, G and Zhou, J}, title = {Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0491022}, doi = {10.1128/spectrum.04910-22}, pmid = {37191552}, issn = {2165-0497}, abstract = {Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.}, }
@article {pmid37191521, year = {2023}, author = {Norfolk, WA and Melendez-Declet, C and Lipp, EK}, title = {Coral Disease and Ingestion: Investigating the Role of Heterotrophy in the Transmission of Pathogenic Vibrio spp. using a Sea Anemone (Exaiptasia pallida) Model System.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0018723}, doi = {10.1128/aem.00187-23}, pmid = {37191521}, issn = {1098-5336}, abstract = {Understanding disease transmission in corals can be complicated given the intricacy of the holobiont and difficulties associated with ex situ coral cultivation. As a result, most of the established transmission pathways for coral disease are associated with perturbance (i.e., damage) rather than evasion of immune defenses. Here, we investigate ingestion as a potential pathway for the transmission of coral pathogens that evades the mucus membrane. Using sea anemones (Exaiptasia pallida) and brine shrimp (Artemia sp.) to model coral feeding, we tracked the acquisition of the putative pathogens, Vibrio alginolyticus, V. harveyi, and V. mediterranei using GFP-tagged strains. Vibrio sp. were provided to anemones using 3 experimental exposures (i) direct water exposure alone, (ii) water exposure in the presence of a food source (non-spiked Artemia), and (iii) through a "spiked" food source (Vibrio-colonized Artemia) created by exposing Artemia cultures to GFP-Vibrio via the ambient water overnight. Following a 3 h feeding/exposure duration, the level of acquired GFP-Vibrio was quantified from anemone tissue homogenate. Ingestion of spiked Artemia resulted in a significantly greater burden of GFP-Vibrio equating to an 830-fold, 3,108-fold, and 435-fold increase in CFU mL[-1] when compared to water exposed trials and a 207-fold, 62-fold, and 27-fold increase in CFU mL[-1] compared to water exposed with food trials for V. alginolyticus, V. harveyi, and V. mediterranei, respectively. These data suggest that ingestion can facilitate delivery of an elevated dose of pathogenic bacteria in cnidarians and may describe an important portal of entry for pathogens in the absence of perturbing conditions. IMPORTANCE The front line of pathogen defense in corals is the mucus membrane. This membrane coats the surface body wall creating a semi-impermeable layer that inhibits pathogen entry from the ambient water both physically and biologically through mutualistic antagonism from resident mucus microbes. To date, much of the coral disease transmission research has been focused on mechanisms associated with perturbance of this membrane such as direct contact, vector lesions (predation/biting), and waterborne exposure through preexisting lesions. The present research describes a potential transmission pathway that evades the defenses provided by this membrane allowing unencumbered entry of bacteria as in association with food. This pathway may explain an important portal of entry for emergence of idiopathic infections in otherwise healthy corals and can be used to improve management practices for coral conservation.}, }
@article {pmid37184242, year = {2023}, author = {Quigley, K and Carey, N and Alvarez Roa, C}, title = {Physiological Characterization of the Coral Holobiont Using a New Micro-Respirometry Tool.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {194}, pages = {}, doi = {10.3791/64812}, pmid = {37184242}, issn = {1940-087X}, abstract = {Metabolic activity, defined as the sum of organismal processes that involve energy, is of critical importance in understanding the function and evolution of life on earth. Measuring organismal metabolic rates is, therefore, at the center of explaining the physiological states of organisms, their ecological roles, and the impact of environmental change on species within terrestrial and aquatic ecosystems. On coral reefs, measures of metabolism have been used to quantify symbiosis functioning between corals and their obligate algal symbionts (Symbiodiniaceae), as well as assess how environmental stressors, including climate change, will impact coral health. Despite this significance, there is a lack of methods, and therefore data, relating to metabolic rate measurements in coral offspring, likely due to their small size. To address this gap, this study aimed to develop a custom setup for measuring the respiration of small (millimeter size range) marine animal ecologies. This low cost and easy setup should allow for the improved measurement of metabolic rate. This will be essential for applied ecological research utilizing the sexual production of corals for reef restoration.}, }
@article {pmid37175775, year = {2023}, author = {Kazakova, P and Abasolo, N and de Cripan, SM and Marquès, E and Cereto-Massagué, A and Garcia, L and Canela, N and Tormo, R and Torrell, H}, title = {Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175775}, issn = {1422-0067}, mesh = {Infant, Newborn ; Humans ; Infant ; *Meconium ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Milk, Human ; Bacteria/genetics ; DNA, Viral ; }, abstract = {The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.}, }
@article {pmid37174660, year = {2023}, author = {Cuffaro, B and Boutillier, D and Desramaut, J and Jablaoui, A and Werkmeister, E and Trottein, F and Waligora-Dupriet, AJ and Rhimi, M and Maguin, E and Grangette, C}, title = {Characterization of Two Parabacteroides distasonis Candidate Strains as New Live Biotherapeutics against Obesity.}, journal = {Cells}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/cells12091260}, pmid = {37174660}, issn = {2073-4409}, abstract = {The gut microbiota is now considered as a key player in the development of metabolic dysfunction. Therefore, targeting gut microbiota dysbiosis has emerged as a new therapeutic strategy, notably through the use of live gut microbiota-derived biotherapeutics. We previously highlighted the anti-inflammatory abilities of two Parabacteroides distasonis strains. We herein evaluate their potential anti-obesity abilities and show that the two strains induced the secretion of the incretin glucagon-like peptide 1 in vitro and limited weight gain and adiposity in obese mice. These beneficial effects are associated with reduced inflammation in adipose tissue and the improvement of lipid and bile acid metabolism markers. P. distasonis supplementation also modified the Actinomycetota, Bacillota and Bacteroidota taxa of the mice gut microbiota. These results provide better insight into the capacity of P. distasonis to positively influence host metabolism and to be used as novel source of live biotherapeutics in the treatment and prevention of metabolic-related diseases.}, }
@article {pmid37153718, year = {2023}, author = {W B, M and A S, R and P, M and F, B}, title = {Cellular and Natural Viral Engineering in Cognition-Based Evolution.}, journal = {Communicative &amp; integrative biology}, volume = {16}, number = {1}, pages = {2196145}, pmid = {37153718}, issn = {1942-0889}, abstract = {Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.}, }
@article {pmid37149185, year = {2023}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Nanetti, E and Iuffrida, L and Wathsala, RHGR and Interino, N and Marini, M and Porru, E and Turroni, S and Fiori, J and Franzellitti, S and Candela, M}, title = {Seasonal dynamics of the microbiome-host response to pharmaceuticals and pesticides in Mytilus galloprovincialis farmed in the Northwestern Adriatic Sea.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163948}, doi = {10.1016/j.scitotenv.2023.163948}, pmid = {37149185}, issn = {1879-1026}, abstract = {Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. Even if the response to multiple xenobiotic exposure is well known at the host level, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. Here, we characterized the microbiome-host integrative response of M. galloprovincialis in a real-world setting, involving exposure to a complex pattern of emerging pollutants, as occurs in the Northwestern Adriatic Sea. A total of 387 mussel individuals from 3 commercial farms, spanning about 200 km along the Northwestern Adriatic coast, and in 3 different seasons, were collected. Multiresidue analysis (for quantitative xenobiotic determination), transcriptomics (for host physiological response), and metagenomics (for host-associated microbial taxonomical and functional features) analyses were performed on the digestive glands. According to our findings, M. galloprovincialis responds to the presence of the complex pattern of multiple emerging pollutants - including the antibiotics sulfamethoxazole, erythromycin, and tetracycline, the herbicides atrazine and metolachlor, and the insecticide N,N-diethyl-m-toluamide - integrating host defense mechanisms, e.g., through upregulation of transcripts involved in animal metabolic activity, and microbiome-mediated detoxification functions, including microbial functionalities involved in multidrug or tetracycline resistance. Overall, our data highlight the importance of the mussel-associated microbiome as a strategic player for the orchestration of resistance to the multixenobiotic exposure at the holobiont level, providing strategic functionalities for the detoxification of multiple xenobiotic substances, as occurring in real world exposure settings. Complementing the host with microbiome-dependent xenobiotic degradative and resistance genes, the M. galloprovincialis digestive gland associated microbiome can have an important role in the detoxification of emerging pollutants in a context of high anthropogenic pressure, supporting the relevance of mussel systems as potential animal-based bioremediation tool.}, }
@article {pmid37141369, year = {2023}, author = {Brown, CC and Rudensky, AY}, title = {Spatiotemporal regulation of peripheral T cell tolerance.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6644}, pages = {472-478}, doi = {10.1126/science.adg6425}, pmid = {37141369}, issn = {1095-9203}, abstract = {The incomplete removal of T cells that are reactive against self-proteins during their differentiation in the thymus requires mechanisms of tolerance that prevent their effector function within the periphery. A further challenge is imposed by the need to establish tolerance to the holobiont self, which comprises a highly complex community of commensal microorganisms. Here, we review recent advances in the investigation of peripheral T cell tolerance, focusing on new insights into mechanisms of tolerance to the gut microbiota, including tolerogenic antigen-presenting cell types and immunomodulatory lymphocytes, and their layered ontogeny that underlies developmental windows for establishing intestinal tolerance. While emphasizing the intestine as a model tissue for studying peripheral T cell tolerance, we highlight overlapping and distinct pathways that underlie tolerance to self-antigens versus commensal antigens within a broader framework for immune tolerance.}, }
@article {pmid37138624, year = {2023}, author = {Wolfgang, A and Temme, N and Tilcher, R and Berg, G}, title = {Understanding the sugar beet holobiont for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1151052}, pmid = {37138624}, issn = {1664-302X}, abstract = {The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.}, }
@article {pmid37137926, year = {2023}, author = {Froidevaux, JSP and Toshkova, N and Barbaro, L and Benítez-López, A and Kerbiriou, C and Le Viol, I and Pacifici, M and Santini, L and Stawski, C and Russo, D and Dekker, J and Alberdi, A and Amorim, F and Ancillotto, L and Barré, K and Bas, Y and Cantú-Salazar, L and Dechmann, DKN and Devaux, T and Eldegard, K and Fereidouni, S and Furmankiewicz, J and Hamidovic, D and Hill, DL and Ibáñez, C and Julien, JF and Juste, J and Kaňuch, P and Korine, C and Laforge, A and Legras, G and Leroux, C and Lesiński, G and Mariton, L and Marmet, J and Mata, VA and Mifsud, CM and Nistreanu, V and Novella-Fernandez, R and Rebelo, H and Roche, N and Roemer, C and Ruczyński, I and Sørås, R and Uhrin, M and Vella, A and Voigt, CC and Razgour, O}, title = {A species-level trait dataset of bats in Europe and beyond.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {253}, pmid = {37137926}, issn = {2052-4463}, abstract = {Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.}, }
@article {pmid37137368, year = {2023}, author = {Zhu, W and Liu, X and Zhang, J and Zhao, H and Li, Z and Wang, H and Chen, R and Wang, A and Li, X}, title = {Response of coral bacterial composition and function to water quality variations under anthropogenic influence.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163837}, doi = {10.1016/j.scitotenv.2023.163837}, pmid = {37137368}, issn = {1879-1026}, abstract = {Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.}, }
@article {pmid37133380, year = {2023}, author = {Michelle JiaMin, L and Mutusamy, P and Karthikeyan, P and Kumaresan, R and Millard, A and Parimannan, S and Rajandas, H}, title = {Genome Characterization of Enterococcus faecalis Bacteriophage EFKL.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0016023}, doi = {10.1128/mra.00160-23}, pmid = {37133380}, issn = {2576-098X}, abstract = {We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.}, }
@article {pmid37127575, year = {2023}, author = {Calle-García, J and Ramayo-Caldas, Y and Zingaretti, LM and Quintanilla, R and Ballester, M and Pérez-Enciso, M}, title = {On the holobiont 'predictome' of immunocompetence in pigs.}, journal = {Genetics, selection, evolution : GSE}, volume = {55}, number = {1}, pages = {29}, pmid = {37127575}, issn = {1297-9686}, mesh = {Animals ; Swine ; Bayes Theorem ; Genotype ; Phenotype ; *Genome ; *Genomics/methods ; }, abstract = {BACKGROUND: Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available.<br><br>METHODS: We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70&#xa0;k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only.<br><br>RESULTS: Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy.<br><br>CONCLUSIONS: Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.}, }
@article {pmid37124465, year = {2023}, author = {Cheng, SC and Liu, CB and Yao, XQ and Hu, JY and Yin, TT and Lim, BK and Chen, W and Wang, GD and Zhang, CL and Irwin, DM and Zhang, ZG and Zhang, YP and Yu, L}, title = {Hologenomic insights into mammalian adaptations to myrmecophagy.}, journal = {National science review}, volume = {10}, number = {4}, pages = {nwac174}, pmid = {37124465}, issn = {2053-714X}, abstract = {Highly specialized myrmecophagy (ant- and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes' activities, in the species of three mammalian orders (anteaters, echidnas and pangolins of the orders Xenarthra, Monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants' and termites' chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.}, }
@article {pmid37122591, year = {2023}, author = {Bergman, JL and Ricci, F and Leggat, W and Ainsworth, TD}, title = {Characteristics of The Bleached Microbiome of The Generalist Coral Pocillopora damicornis from Two Distinct Reef Habitats.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {5}, number = {1}, pages = {obad012}, pmid = {37122591}, issn = {2517-4843}, abstract = {Generalist coral species may play an important role in predicting, managing, and responding to the growing coral reef crisis as sea surface temperatures are rising and reef wide bleaching events are becoming more common. Pocilloporids are amongst the most widely distributed and studied of generalist corals, characterized by a broad geographic distribution, phenotypic plasticity, and tolerance of sub-optimal conditions for coral recruitment and survival. Emerging research indicates that microbial communities associated with Pocilloporid corals may be contributing to their persistence on coral reefs impacted by thermal stress; however, we lack detailed information on shifts in the coral-bacterial symbiosis during bleaching events across many of the reef habitats these corals are found. Here, we characterized the bacterial communities of healthy and bleached Pocillopora damicornis corals during the bleaching events that occurred during the austral summer of 2020 on Heron Island, on the southern Great Barrier Reef, and the austral summer of 2019 on Lord Howe Island, the most southerly coral reef in Australia. Regardless of reef location, significant differences in α and β diversities, core bacterial community, and inferred functional profile of the bleached microbiome of P. damicornis were not detected. Consistent with previous reports, patterns in the Pocilloporid coral microbiome, including no increase in pathogenic taxa or evidence of dysbiosis, are conserved during bleaching responses. We hypothesize that the resilience of holobiont interactions may aid the Pocilloporids to survive Symbiodiniaceae loss and contribute to the success of Pocilloporids.}, }
@article {pmid37120592, year = {2023}, author = {Botero, J and Sombolestani, AS and Cnockaert, M and Peeters, C and Borremans, W and De Vuyst, L and Vereecken, NJ and Michez, D and Smagghe, G and Bonilla-Rosso, G and Engel, P and Vandamme, P}, title = {A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {25}, pmid = {37120592}, issn = {2524-4671}, abstract = {BACKGROUND: To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis.<br><br>RESULTS: The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G&#x2009;+&#x2009;C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont.<br><br>CONCLUSION: The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.}, }
@article {pmid37110191, year = {2023}, author = {Clergeaud, F and Giraudo, M and Rodrigues, AMS and Thorel, E and Lebaron, P and Stien, D}, title = {On the Fate of Butyl Methoxydibenzoylmethane (Avobenzone) in Coral Tissue and Its Effect on Coral Metabolome.}, journal = {Metabolites}, volume = {13}, number = {4}, pages = {}, pmid = {37110191}, issn = {2218-1989}, abstract = {The intensive use of sunscreen products has raised concerns regarding their environmental toxicity and the adverse impacts of ultraviolet (UV) filters on ecologically important coral communities. Prior metabolomic analyses on symbiotic coral Pocillopora damicornis exposed to the UV filter butyl methoxydibenzoylmethane (BM, avobenzone) revealed unidentified ions in the holobiont metabolome. In the present study, follow-up differential metabolomic analyses in BM-exposed P. damicornis detected 57 ions with significantly different relative concentrations in exposed corals. The results showed an accumulation of 17 BM derivatives produced through BM reduction and esterification. The major derivative identified C16:0-dihydroBM, which was synthesized and used as a standard to quantify BM derivatives in coral extracts. The results indicated that relative amounts of BM derivatives made up to 95% of the total BM (w/w) absorbed in coral tissue after 7 days of exposure. Among the remaining metabolites annotated, seven compounds significantly affected by BM exposure could be attributed to the coral dinoflagellate symbiont, indicating that BM exposure might impair the photosynthetic capacity of the holobiont. The present results suggest that the potential role of BM in coral bleaching in anthropogenic areas should be investigated and that BM derivatives should be considered in future assessments on the fate and effects of BM in the environment.}, }
@article {pmid37106156, year = {2023}, author = {Germain, RR and Feng, S and Chen, G and Graves, GR and Tobias, JA and Rahbek, C and Lei, F and Fjeldså, J and Hosner, PA and Gilbert, MTP and Zhang, G and Nogués-Bravo, D}, title = {Species-specific traits mediate avian demographic responses under past climate change.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {37106156}, issn = {2397-334X}, abstract = {Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.}, }
@article {pmid37100093, year = {2023}, author = {Hansen, SB and Bozzi, D and Mak, SST and Clausen, CG and Nielsen, TK and Kodama, M and Hansen, LH and Gilbert, MTP and Limborg, MT}, title = {Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition.}, journal = {Genomics}, volume = {}, number = {}, pages = {110629}, doi = {10.1016/j.ygeno.2023.110629}, pmid = {37100093}, issn = {1089-8646}, abstract = {It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value off considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.}, }
@article {pmid37071808, year = {2023}, author = {Roux, F and Frachon, L and Bartoli, C}, title = {The genetic architecture of adaptation to leaf and root bacterial microbiota in Arabidopsis thaliana.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msad093}, pmid = {37071808}, issn = {1537-1719}, abstract = {Understanding the role of the host genome in modulating microbiota variation is a need to shed light on the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolves and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a Genome-Environmental-Association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities in fall and spring, and a large range of non-microbial ecological factors (i.e. climate, soil and plant communities). A much higher fraction of among-population microbiota variance was explained by the host genetics than by non-microbial ecological factors. Importantly, the relative importance of host genetics and non-microbial ecological factors in explaining the presence of particular OTUs differs between bacterial families and genera. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on QTLs of the root microbiota in spring. Finally, plant immunity appears as a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.}, }
@article {pmid37068234, year = {2023}, author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M}, title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2213563120}, doi = {10.1073/pnas.2213563120}, pmid = {37068234}, issn = {1091-6490}, abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.}, }
@article {pmid37067424, year = {2023}, author = {Chakraborty, A and Šobotník, J and Votýpková, K and Hradecký, J and Stiblik, P and Synek, J and Bourguignon, T and Baldrian, P and Engel, MS and Novotný, V and Odriozola, I and Větrovský, T}, title = {Impact of Wood Age on Termite Microbial Assemblages.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0036123}, doi = {10.1128/aem.00361-23}, pmid = {37067424}, issn = {1098-5336}, abstract = {The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have to cope with high concentrations of plant toxins in wood. In this paper, we evaluated the influence of wood age on the gut microbial (bacterial and fungal) communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) (Kollar, 1837) and Microcerotermes biroi (Termitidae) (Desneux, 1905). We confirmed that the secondary metabolite concentration decreased with wood age. We identified a core microbial consortium maintained in the gut of R. flavipes and M. biroi and found that its diversity and composition were not altered by the wood age. Therefore, the concentration of secondary metabolites had no effect on the termite gut microbiome. We also found that both termite feeding activities and wood age affect the wood microbiome. Whether the increasing relative abundance of microbes with termite activities is beneficial to the termites is unknown and remains to be investigated. IMPORTANCE Termites can feed on wood thanks to their association with their gut microbes. However, the current understanding of termites as holobiont is limited. To our knowledge, no studies comprehensively reveal the influence of wood age on the termite-associated microbial assemblage. The wood of many tree species contains high concentrations of plant toxins that can vary with their age and may influence microbes. Here, we studied the impact of Norway spruce wood of varying ages and terpene concentrations on the microbial communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) and Microcerotermes biroi (Termitidae). We performed a bacterial 16S rRNA and fungal ITS2 metabarcoding study to reveal the microbial communities associated with R. flavipes and M. biroi and their impact on shaping the wood microbiome. We noted that a stable core microbiome in the termites was unaltered by the feeding substrate, while termite activities influenced the wood microbiome, suggesting that plant secondary metabolites have negligible effects on the termite gut microbiome. Hence, our study shed new insights into the termite-associated microbial assemblage under the influence of varying amounts of terpene content in wood and provides a groundwork for future investigations for developing symbiont-mediated termite control measures.}, }
@article {pmid37065434, year = {2023}, author = {Reeve, AH and Gower, G and Pujolar, JM and Smith, BT and Petersen, B and Olsson, U and Haryoko, T and Koane, B and Maiah, G and Blom, MPK and Ericson, PGP and Irestedt, M and Racimo, F and Jønsson, KA}, title = {Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.}, journal = {Evolution letters}, volume = {7}, number = {1}, pages = {24-36}, pmid = {37065434}, issn = {2056-3744}, abstract = {Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.}, }
@article {pmid37065131, year = {2023}, author = {Birt, HWG and Pattison, AB and Skarshewski, A and Daniells, J and Raghavendra, A and Dennis, PG}, title = {The core fungal microbiome of banana (Musa spp.).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1127779}, pmid = {37065131}, issn = {1664-302X}, abstract = {Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype - two factors that are likely to differ between farms - on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core 'candidates', which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.}, }
@article {pmid37061589, year = {2023}, author = {Pande, PM and Azarbad, H and Tremblay, J and St-Arnaud, M and Yergeau, E}, title = {Metatranscriptomic response of the wheat holobiont to decreasing soil water content.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {30}, pmid = {37061589}, issn = {2730-6151}, abstract = {Crops associate with microorganisms that help their resistance to biotic stress. However, it is not clear how the different partners of this association react during exposure to stress. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is stronger for the fungal and bacterial partners than for the plant.}, }
@article {pmid37049406, year = {2023}, author = {Cardilli, A and Hamad, I and Dyczko, A and Thijs, S and Vangronsveld, J and Müller, DN and Rosshart, SP and Kleinewietfeld, M}, title = {Impact of High Salt-Intake on a Natural Gut Ecosystem in Wildling Mice.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049406}, issn = {2072-6643}, support = {640116/ERC_/European Research Council/International ; }, mesh = {Mice ; Humans ; Animals ; Bacteria/genetics ; Diet ; *Gastrointestinal Microbiome ; *Microbiota ; Feeding Behavior ; Firmicutes ; Clostridiales/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals ; }, abstract = {The mammalian holobiont harbors a complex and interdependent mutualistic gut bacterial community. Shifts in the composition of this bacterial consortium are known to be a key element in host health, immunity and disease. Among many others, dietary habits are impactful drivers for a potential disruption of the bacteria-host mutualistic interaction. In this context, we previously demonstrated that a high-salt diet (HSD) leads to a dysbiotic condition of murine gut microbiota, characterized by a decrease or depletion of well-known health-promoting gut bacteria. However, due to a controlled and sanitized environment, conventional laboratory mice (CLM) possess a less diverse gut microbiota compared to wild mice, leading to poor translational outcome for gut microbiome studies, since a reduced gut microbiota diversity could fail to depict the complex interdependent networks of the microbiome. Here, we evaluated the HSD effect on gut microbiota in CLM in comparison to wildling mice, which harbor a natural gut ecosystem more closely mimicking the situation in humans. Mice were treated with either control food or HSD and gut microbiota were profiled using amplicon-based methods targeting the 16S ribosomal gene. In line with previous findings, our results revealed that HSD induced significant loss of alpha diversity and extensive modulation of gut microbiota composition in CLM, characterized by the decrease in potentially beneficial bacteria from Firmicutes phylum such as the genera Lactobacillus, Roseburia, Tuzzerella, Anaerovorax and increase in Akkermansia and Parasutterella. However, HSD-treated wildling mice did not show the same changes in terms of alpha diversity and loss of Firmicutes bacteria as CLM, and more generally, wildlings exhibited only minor shifts in the gut microbiota composition upon HSD. In line with this, 16S-based functional analysis suggested only major shifts of gut microbiota ecological functions in CLM compared to wildling mice upon HSD. Our findings indicate that richer and wild-derived gut microbiota is more resistant to dietary interventions such as HSD, compared to gut microbiota of CLM, which may have important implications for future translational microbiome research.}, }
@article {pmid37043058, year = {2023}, author = {Houck, ML and Koepfli, KP and Hains, T and Khan, R and Charter, SJ and Fronczek, JA and Misuraca, AC and Kliver, S and Perelman, PL and Beklemisheva, V and Graphodatsky, A and Luo, SJ and O'Brien, SJ and Lim, NT and Chin, JSC and Guerra, V and Tamazian, G and Omer, A and Weisz, D and Kaemmerer, K and Sturgeon, G and Gaspard, J and Hahn, A and McDonough, M and Garcia-Treviño, I and Gentry, J and Coke, RL and Janecka, JE and Harrigan, RJ and Tinsman, J and Smith, TB and Aiden, EL and Dudchenko, O}, title = {Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {31}, number = {2}, pages = {13}, pmid = {37043058}, issn = {1573-6849}, support = {RM1HG011016/NH/NIH HHS/United States ; }, abstract = {We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.}, }
@article {pmid37032282, year = {2023}, author = {Gonzalez-Recio, O and Scrobota, N and López-Paredes, J and Saborío-Montero, A and Fernández, A and López de Maturana, E and Villanueva, B and Goiri, I and Atxaerandio, R and García-Rodríguez, A}, title = {Review: Diving into the cow hologenome to reduce methane emissions and increase sustainability.}, journal = {Animal : an international journal of animal bioscience}, volume = {}, number = {}, pages = {100780}, doi = {10.1016/j.animal.2023.100780}, pmid = {37032282}, issn = {1751-732X}, abstract = {Interest on methane emissions from livestock has increased in later years as it is an anthropogenic greenhouse gas with an important warming potential. The rumen microbiota has a large influence on the production of enteric methane. Animals harbour a second genome consisting of microbes, collectively referred to as the "microbiome". The rumen microbial community plays an important role in feed digestion, feed efficiency, methane emission and health status. This review recaps the current knowledge on the genetic control that the cow exerts on the rumen microbiota composition. Heritability estimates for the rumen microbiota composition range between 0.05 and 0.40 in the literature, depending on the taxonomical group or microbial gene function. Variables depicting microbial diversity or aggregating microbial information are also heritable within the same range. This study includes a genome-wide association analysis on the microbiota composition, considering the relative abundance of some microbial taxa previously associated to enteric methane in dairy cattle (Archaea, Dialister, Entodinium, Eukaryota, Lentisphaerae, Methanobrevibacter, Neocallimastix, Prevotella and Stentor). Host genomic regions associated with the relative abundance of these microbial taxa were identified after Benjamini-Hoschberg correction (Padj < 0.05). An in-silico functional analysis using FUMA and DAVID online tools revealed that these gene sets were enriched in tissues like brain cortex, brain amigdala, pituitary, salivary glands and other parts of the digestive system, and are related to appetite, satiety and digestion. These results allow us to have greater knowledge about the composition and function of the rumen microbiome in cattle. The state-of-the art strategies to include methane traits in the selection indices in dairy cattle populations is reviewed. Several strategies to include methane traits in the selection indices have been studied worldwide, using bioeconomical models or economic functions under theoretical frameworks. However, their incorporation in the breeding programmes is still scarce. Some potential strategies to include methane traits in the selection indices of dairy cattle population are presented. Future selection indices will need to increase the weight of traits related to methane emissions and sustainability. This review will serve as a compendium of the current state of the art in genetic strategies to reduce methane emissions in dairy cattle.}, }
@article {pmid37030294, year = {2023}, author = {Díez-Del-Molino, D and Dehasque, M and Chacón-Duque, JC and Pečnerová, P and Tikhonov, A and Protopopov, A and Plotnikov, V and Kanellidou, F and Nikolskiy, P and Mortensen, P and Danilov, GK and Vartanyan, S and Gilbert, MTP and Lister, AM and Heintzman, PD and van der Valk, T and Dalén, L}, title = {Genomics of adaptive evolution in the woolly mammoth.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2023.03.084}, pmid = {37030294}, issn = {1879-0445}, abstract = {Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.}, }
@article {pmid37018898, year = {2023}, author = {Rasmussen, JA and Chua, PYS}, title = {Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127372}, doi = {10.1016/j.micres.2023.127372}, pmid = {37018898}, issn = {1618-0623}, abstract = {The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.}, }
@article {pmid37002423, year = {2023}, author = {Pushpakumara, BLDU and Tandon, K and Willis, A and Verbruggen, H}, title = {The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {37002423}, issn = {1432-184X}, abstract = {Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.}, }
@article {pmid36991491, year = {2023}, author = {Hénaff, E and Najjar, D and Perez, M and Flores, R and Woebken, C and Mason, CE and Slavin, K}, title = {Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {23}, pmid = {36991491}, issn = {2524-6372}, support = {1R01MH117406/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Over half of the world's population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city's microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms-bacteria or fungi-with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city.<br><br>RESULTS: Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for "cat scratch fever".<br><br>CONCLUSIONS: We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.}, }
@article {pmid36988668, year = {2023}, author = {Müller, M and Kües, U and Budde, KB and Gailing, O}, title = {Applying molecular and genetic methods to trees and their fungal communities.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36988668}, issn = {1432-0614}, abstract = {Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.}, }
@article {pmid36981014, year = {2023}, author = {Alvarez-Estape, M and Pawar, H and Fontsere, C and Trujillo, AE and Gunson, JL and Bergl, RA and Bermejo, M and Linder, JM and McFarland, K and Oates, JF and Sunderland-Groves, JL and Orkin, J and Higham, JP and Viaud-Martinez, KA and Lizano, E and Marques-Bonet, T}, title = {Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030743}, pmid = {36981014}, issn = {2073-4425}, support = {864203/ERC_/European Research Council/International ; }, abstract = {The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.}, }
@article {pmid36980891, year = {2023}, author = {Yakupova, A and Tomarovsky, A and Totikov, A and Beklemisheva, V and Logacheva, M and Perelman, PL and Komissarov, A and Dobrynin, P and Krasheninnikova, K and Tamazian, G and Serdyukova, NA and Rayko, M and Bulyonkova, T and Cherkasov, N and Pylev, V and Peterfeld, V and Penin, A and Balanovska, E and Lapidus, A and Dna Zoo Consortium,  and OBrien, SJ and Graphodatsky, A and Koepfli, KP and Kliver, S}, title = {Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030619}, pmid = {36980891}, issn = {2073-4425}, abstract = {Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.}, }
@article {pmid36976223, year = {2023}, author = {Tan, LT}, title = {Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals.}, journal = {Marine drugs}, volume = {21}, number = {3}, pages = {}, doi = {10.3390/md21030174}, pmid = {36976223}, issn = {1660-3397}, abstract = {Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms-especially on the production, functionality and perception of allelochemicals-and its implications on drug discovery efforts will be presented.}, }
@article {pmid36973251, year = {2023}, author = {Battlay, P and Wilson, J and Bieker, VC and Lee, C and Prapas, D and Petersen, B and Craig, S and van Boheemen, L and Scalone, R and de Silva, NP and Sharma, A and Konstantinović, B and Nurkowski, KA and Rieseberg, LH and Connallon, T and Martin, MD and Hodgins, KA}, title = {Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1717}, pmid = {36973251}, issn = {2041-1723}, abstract = {Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.}, }
@article {pmid36958561, year = {2023}, author = {Mancuso, FP and Morrissey, KL and De Clerck, O and Airoldi, L}, title = {Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {162919}, doi = {10.1016/j.scitotenv.2023.162919}, pmid = {36958561}, issn = {1879-1026}, abstract = {Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.}, }
@article {pmid36951365, year = {2023}, author = {Ricci, F and Tandon, K and Moßhammer, M and Cho, EH and Blackall, LL and Kühl, M and Verbruggen, H}, title = {Fine-scale mapping of physicochemical and microbial landscapes of the coral skeleton.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16369}, pmid = {36951365}, issn = {1462-2920}, abstract = {The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 and pH gradients, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. In this study, we employed chemical imaging of O2 and pH, hyperspectral reflectance imaging and spatially resolved taxonomic and inferred functional microbiome characterisation to explore links between the skeleton microenvironment and microbiome in the reef-building corals Porites lutea and Paragoniastrea benhami. The physicochemical environment was more stable in the deep skeleton and the diversity and evenness of the bacterial community increased with skeletal depth, suggesting that the microbiome was stratified along the physicochemical gradients. The bulk of the coral skeleton was a low O2 habitat, whereas pH varied from pH 6 to 9 with depth. Physicochemical gradients of O2 and pH of the coral skeleton explained the β-diversity of the bacterial communities, and skeletal layers that showed O2 peaks had a higher relative abundance of endolithic algae, reflecting a link between the abiotic environment and the microbiome composition. Our study links the physicochemical, microbial and functional landscapes of the coral skeleton and provides new insights into the involvement of skeletal microbes in coral holobiont metabolism. This article is protected by copyright. All rights reserved.}, }
@article {pmid36944891, year = {2023}, author = {Penno, C and Tremblay, J and O'Connell Motherway, M and Daburon, V and El Amrani, A}, title = {Analysis of Small Non-coding RNAs as Signaling Intermediates of Environmentally Integrated Responses to Abiotic Stress.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2642}, number = {}, pages = {403-427}, pmid = {36944891}, issn = {1940-6029}, mesh = {*MicroRNAs/genetics ; Gene Library ; Plants/genetics ; Software ; Stress, Physiological/genetics ; Gene Expression Regulation, Plant ; RNA, Plant/genetics ; }, abstract = {Research to date on abiotic stress responses in plants has been largely focused on the plant itself, but current knowledge indicates that microorganisms can interact with and help plants during periods of abiotic stress. In our research, we aim to investigate the interkingdom communication between the plant root and the rhizo-microbiota. Our investigation showed that miRNA plays a pivotal role in this interkingdom communication. Here, we describe a protocol for the analysis of miRNA secreted by the plant root, which includes all of the steps from the isolation of the miRNA to the bioinformatics analysis. Because of their short nucleotide length, Next Generation Sequencing (NGS) library preparation from miRNAs can be challenging due to the presence of dimer adapter contaminants. Therefore, we highlight some strategies we adopt to inhibit the generation of dimer adapters during library preparation. Current screens of miRNA targets mostly focus on the identification of targets present in the same organism expressing the miRNA. Our bioinformatics analysis challenges the barrier of evolutionary divergent organisms to identify candidate sequences of the microbiota targeted by the miRNA of plant roots. This protocol should be of interest to researchers investigating interkingdom RNA-based communication between plants and their associated microorganisms, particularly in the context of holobiont responses to abiotic stresses.}, }
@article {pmid36938541, year = {2023}, author = {Xiang, N and Meyer, A and Pogoreutz, C and Rädecker, N and Voolstra, CR and Wild, C and Gärdes, A}, title = {Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals.}, journal = {Royal Society open science}, volume = {10}, number = {3}, pages = {221268}, pmid = {36938541}, issn = {2054-5703}, abstract = {Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N2 into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of nifH gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral Xenia umbellata and the more autotrophic gorgonian Pinnigorgia flava, under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in X. umbellata and P. flava were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l[-1]) increased the relative abundances of diazotrophs by sixfold in X. umbellata and fourfold in P. flava, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.}, }
@article {pmid36801111, year = {2023}, author = {Theissinger, K and Fernandes, C and Formenti, G and Bista, I and Berg, PR and Bleidorn, C and Bombarely, A and Crottini, A and Gallo, GR and Godoy, JA and Jentoft, S and Malukiewicz, J and Mouton, A and Oomen, RA and Paez, S and Palsbøll, PJ and Pampoulie, C and Ruiz-López, MJ and Secomandi, S and Svardal, H and Theofanopoulou, C and de Vries, J and Waldvogel, AM and Zhang, G and Jarvis, ED and Bálint, M and Ciofi, C and Waterhouse, RM and Mazzoni, CJ and Höglund, J and , }, title = {How genomics can help biodiversity conservation.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2023.01.005}, pmid = {36801111}, issn = {0168-9525}, abstract = {The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.}, }
@article {pmid36924962, year = {2023}, author = {Zhang, J and Huang, Z and Li, Y and Fu, D and Li, Q and Pei, L and Song, Y and Chen, L and Zhao, H and Kao, SJ}, title = {Synergistic/antagonistic effects of nitrate/ammonium enrichment on fatty acid biosynthesis and translocation in coral under heat stress.}, journal = {The Science of the total environment}, volume = {876}, number = {}, pages = {162834}, doi = {10.1016/j.scitotenv.2023.162834}, pmid = {36924962}, issn = {1879-1026}, abstract = {Superimposed on ocean warming, nitrogen enrichment caused by human activity puts corals under even greater pressure. Biosynthesis of fatty acids (FA) is crucial for coral holobiont survival. However, the responses of FA biosynthesis pathways to nitrogen enrichment under heat stress in coral hosts and Symbiodiniaceae remain unknown, as do FA translocation mechanisms in corals. Herein, we used the thermosensitive coral species Acropora hyacinthus to investigate changes in FA biosynthesis pathways and polyunsaturated FA translocation of coral hosts and Symbiodiniaceae with respect to nitrate and ammonium enrichment under heat stress. Heat stress promoted pro-inflammatory FA biosynthesis in coral hosts and inhibited FA biosynthesis in Symbiodiniaceae. Nitrate enrichment inhibited anti-inflammatory FA biosynthesis in Symbiodiniaceae, and promoted pro-inflammatory FA biosynthesis in coral hosts and translocation to Symbiodiniaceae, leading to bleaching after 14 days of culture. Intriguingly, ammonium enrichment promoted anti-inflammatory FA biosynthesis in Symbiodiniaceae and translocation to hosts, allowing corals to better endure heat stress. We constructed schematic diagrams of the shift in FA biosynthesis and translocation in and between A. hyacinthus and its Symbiodiniaceae under heat stress, heat and nitrate co-stress, and heat and ammonium co-stress. The findings provide insight into the mechanisms of coral bleaching under environmental stress from a fatty acid perspective.}, }
@article {pmid36922761, year = {2023}, author = {Marynowska, M and Sillam-Dussès, D and Untereiner, B and Klimek, D and Goux, X and Gawron, P and Roisin, Y and Delfosse, P and Calusinska, M}, title = {A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {115}, pmid = {36922761}, issn = {1471-2164}, abstract = {BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.<br><br>RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.<br><br>CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.}, }
@article {pmid36914757, year = {2023}, author = {Limborg, MT and Chua, PYS and Rasmussen, JA}, title = {Unexpected fishy microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {36914757}, issn = {1740-1534}, }
@article {pmid36906503, year = {2023}, author = {Wu, J and Wang, Q and Wang, D and Wong, ACN and Wang, GH}, title = {Axenic and gnotobiotic insect technologies in research on host-microbiota interactions.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.02.007}, pmid = {36906503}, issn = {1878-4380}, abstract = {Insects are one of the most important animal life forms on earth. Symbiotic microbes are closely related to the growth and development of the host insects and can affect pathogen transmission. For decades, various axenic insect-rearing systems have been developed, allowing further manipulation of symbiotic microbiota composition. Here we review the historical development of axenic rearing systems and the latest progress in using axenic and gnotobiotic approaches to study insect-microbe interactions. We also discuss the challenges of these emerging technologies, possible solutions to address these challenges, and future research directions that can contribute to a more comprehensive understanding of insect-microbe interactions.}, }
@article {pmid36902126, year = {2023}, author = {Minerdi, D and Savoi, S and Sabbatini, P}, title = {Role of Cytochrome P450 Enzyme in Plant Microorganisms' Communication: A Focus on Grapevine.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/ijms24054695}, pmid = {36902126}, issn = {1422-0067}, abstract = {Cytochromes P450 are ancient enzymes diffused in organisms belonging to all kingdoms of life, including viruses, with the largest number of P450 genes found in plants. The functional characterization of cytochromes P450 has been extensively investigated in mammals, where these enzymes are involved in the metabolism of drugs and in the detoxification of pollutants and toxic chemicals. The aim of this work is to present an overview of the often disregarded role of the cytochrome P450 enzymes in mediating the interaction between plants and microorganisms. Quite recently, several research groups have started to investigate the role of P450 enzymes in the interactions between plants and (micro)organisms, focusing on the holobiont Vitis vinifera. Grapevines live in close association with large numbers of microorganisms and interact with each other, regulating several vine physiological functions, from biotic and abiotic stress tolerance to fruit quality at harvest.}, }
@article {pmid36897260, year = {2023}, author = {Reich, HG and Camp, EF and Roger, LM and Putnam, HM}, title = {The trace metal economy of the coral holobiont: supplies, demands and exchanges.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {98}, number = {2}, pages = {623-642}, doi = {10.1111/brv.12922}, pmid = {36897260}, issn = {1469-185X}, abstract = {The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.}, }
@article {pmid36891392, year = {2023}, author = {Fieschi-Méric, L and Van Leeuwen, P and Hopkins, K and Bournonville, M and Denoël, M and Lesbarrères, D}, title = {Strong restructuration of skin microbiota during captivity challenges ex-situ conservation of amphibians.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111018}, pmid = {36891392}, issn = {1664-302X}, abstract = {In response to the current worldwide amphibian extinction crisis, conservation instances have encouraged the establishment of ex-situ collections for endangered species. The resulting assurance populations are managed under strict biosecure protocols, often involving artificial cycles of temperature and humidity to induce active and overwintering phases, which likely affect the bacterial symbionts living on the amphibian skin. However, the skin microbiota is an important first line of defense against pathogens that can cause amphibian declines, such as the chytrid Batrachochytrium dendrobatidis (Bd). Determining whether current husbandry practices for assurance populations might deplete amphibians from their symbionts is therefore essential to conservation success. Here, we characterize the effect of the transitions from the wild to captivity, and between aquatic and overwintering phases, on the skin microbiota of two newt species. While our results confirm differential selectivity of skin microbiota between species, they underscore that captivity and phase-shifts similarly affect their community structure. More specifically, the translocation ex-situ is associated with rapid impoverishment, decrease in alpha diversity and strong species turnover of bacterial communities. Shifts between active and overwintering phases also cause changes in the diversity and composition of the microbiota, and on the prevalence of Bd-inhibitory phylotypes. Altogether, our results suggest that current husbandry practices strongly restructure the amphibian skin microbiota. Although it remains to be determined whether these changes are reversible or have deleterious effects on their hosts, we discuss methods to limit microbial diversity loss ex-situ and emphasize the importance of integrating bacterial communities to applied amphibian conservation.}, }
@article {pmid36882766, year = {2023}, author = {Guo, Y and Meng, L and Wang, M and Zhong, Z and Li, D and Zhang, Y and Li, H and Zhang, H and Seim, I and Li, Y and Jiang, A and Ji, Q and Su, X and Chen, J and Fan, G and Li, C and Liu, S}, title = {Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {51}, pmid = {36882766}, issn = {1741-7007}, mesh = {Animals ; *Bivalvia/genetics ; Biological Transport ; Genome, Bacterial ; Inhibitor of Apoptosis Proteins ; Lipopolysaccharides ; }, abstract = {BACKGROUND: Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution.<br><br>RESULTS: We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta.<br><br>CONCLUSIONS: Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.}, }
@article {pmid36882224, year = {2023}, author = {Mohamed, AR and Ochsenkühn, MA and Kazlak, A and Moustafa, A and Amin, SA}, title = {The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuad005}, pmid = {36882224}, issn = {1574-6976}, abstract = {Corals live in a complex, multi-partite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbor a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially-derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.}, }
@article {pmid36872055, year = {2023}, author = {Fieschi-Méric, L and van Leeuwen, P and Denoël, M and Lesbarrères, D}, title = {Encouraging news for in situ conservation: translocation of salamander larvae has limited impacts on their skin microbiota.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16914}, pmid = {36872055}, issn = {1365-294X}, abstract = {The key role of symbiotic skin bacteria communities in amphibian resistance to emerging pathogens is well recognized, but factors leading to their dysbiosis are not fully understood. In particular, the potential effects of population translocations on the composition and diversity of hosts' skin microbiota have received little attention, although such transfers are widely carried out as a strategy for amphibian conservation. To characterize the potential reorganization of the microbiota over such a sudden environmental change, we conducted a common-garden experiment simulating reciprocal translocations of yellow-spotted salamander larvae across three lakes. We sequenced skin microbiota samples collected before and 15 days after the transfer. Using a database of antifungal isolates, we identified symbionts with known function against the pathogen Batrachochytrium dendrobatidis, a major driver of amphibian declines. Our results indicate an important reorganization of bacterial assemblages throughout ontogeny, with strong changes in composition, diversity and structure of the skin microbiota in both control and translocated individuals over the 15 days of monitoring. Unexpectedly, the diversity and community structure of the microbiota were not significantly affected by the translocation event, thus suggesting a strong resilience of skin bacterial communities to environmental change - at least across the time-window studied here. A few phylotypes were more abundant in the microbiota of translocated larvae, but no differences were found among pathogen-inhibiting symbionts. Taken together, our results support amphibian translocations as a promising strategy for this endangered animal class, with limited impact on their skin microbiota.}, }
@article {pmid36869609, year = {2023}, author = {Buitrago-López, C and Cárdenas, A and Hume, BCC and Gosselin, T and Staubach, F and Aranda, M and Barshis, DJ and Sawall, Y and Voolstra, CR}, title = {Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16871}, pmid = {36869609}, issn = {1365-294X}, abstract = {Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. pistillata exhibited a complex population structure with evidence for within-reef and regional genetic differentiation, in line with differences in their reproductive mode (P. verrucosa is a broadcast spawner and S. pistillata is a brooder). Analysis for genomic loci under positive selection identified 85 sites (18 of which were in coding sequences) that distinguished the southern P. verrucosa population from the remainder of the Red Sea population. By comparison, we found 128 loci (24 of which were residing in coding sequences) in S. pistillata with evidence for local adaptation at various sites. Functional annotation of the underlying proteins revealed putative roles in the response to stress, lipid metabolism, transport, cytoskeletal rearrangement, and ciliary function (among others). Microbial assemblages of both coral species showed pervasive association with microalgal symbionts from the genus Symbiodinium (former clade A) and bacteria from the genus Endozoicomonas that exhibited significant differences according to host genotype and environment. The disparity of population genetic and holobiont assemblage patterns even between closely related species (family Pocilloporidae) highlights the need for multispecies investigations to better understand the role of the environment in shaping evolutionary trajectories. It further emphasizes the importance of networks of reef reserves to achieve conservation of genetic variants critical to the future survival of coral ecosystems.}, }
@article {pmid36859541, year = {2023}, author = {Bergeron, LA and Besenbacher, S and Zheng, J and Li, P and Bertelsen, MF and Quintard, B and Hoffman, JI and Li, Z and St Leger, J and Shao, C and Stiller, J and Gilbert, MTP and Schierup, MH and Zhang, G}, title = {Evolution of the germline mutation rate across vertebrates.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36859541}, issn = {1476-4687}, abstract = {The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself[1]. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies[2]. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis[3]. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.}, }
@article {pmid36853427, year = {2023}, author = {Johnson, NC and Marín, C}, title = {Microbial villages in the geography of arbuscular mycorrhizal symbioses.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18803}, pmid = {36853427}, issn = {1469-8137}, }
@article {pmid36848579, year = {2023}, author = {Chevrier, DM and Juhin, A and Menguy, N and Bolzoni, R and Soto-Rodriguez, PED and Kojadinovic-Sirinelli, M and Paterson, GA and Belkhou, R and Williams, W and Skouri-Panet, F and Kosta, A and Le Guenno, H and Pereiro, E and Faivre, D and Benzerara, K and Monteil, CL and Lefevre, CT}, title = {Collective magnetotaxis of microbial holobionts is optimized by the three-dimensional organization and magnetic properties of ectosymbionts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2216975120}, doi = {10.1073/pnas.2216975120}, pmid = {36848579}, issn = {1091-6490}, abstract = {Over the last few decades, symbiosis and the concept of holobiont-a host entity with a population of symbionts-have gained a central role in our understanding of life functioning and diversification. Regardless of the type of partner interactions, understanding how the biophysical properties of each individual symbiont and their assembly may generate collective behaviors at the holobiont scale remains a fundamental challenge. This is particularly intriguing in the case of the newly discovered magnetotactic holobionts (MHB) whose motility relies on a collective magnetotaxis (i.e., a magnetic field-assisted motility guided by a chemoaerotaxis system). This complex behavior raises many questions regarding how magnetic properties of symbionts determine holobiont magnetism and motility. Here, a suite of light-, electron- and X-ray-based microscopy techniques [including X-ray magnetic circular dichroism (XMCD)] reveals that symbionts optimize the motility, the ultrastructure, and the magnetic properties of MHBs from the microscale to the nanoscale. In the case of these magnetic symbionts, the magnetic moment transferred to the host cell is in excess (10[2] to 10[3] times stronger than free-living magnetotactic bacteria), well above the threshold for the host cell to gain a magnetotactic advantage. The surface organization of symbionts is explicitly presented herein, depicting bacterial membrane structures that ensure longitudinal alignment of cells. Magnetic dipole and nanocrystalline orientations of magnetosomes were also shown to be consistently oriented in the longitudinal direction, maximizing the magnetic moment of each symbiont. With an excessive magnetic moment given to the host cell, the benefit provided by magnetosome biomineralization beyond magnetotaxis can be questioned.}, }
@article {pmid36848561, year = {2023}, author = {Di Lelio, I and Forni, G and Magoga, G and Brunetti, M and Bruno, D and Becchimanzi, A and De Luca, MG and Sinno, M and Barra, E and Bonelli, M and Frusciante, S and Diretto, G and Digilio, MC and Woo, SL and Tettamanti, G and Rao, R and Lorito, M and Casartelli, M and Montagna, M and Pennacchio, F}, title = {A soil fungus confers plant resistance against a phytophagous insect by disrupting the symbiotic role of its gut microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2216922120}, doi = {10.1073/pnas.2216922120}, pmid = {36848561}, issn = {1091-6490}, abstract = {Plants generate energy flows through natural food webs, driven by competition for resources among organisms, which are part of a complex network of multitrophic interactions. Here, we demonstrate that the interaction between tomato plants and a phytophagous insect is driven by a hidden interplay between their respective microbiotas. Tomato plants colonized by the soil fungus Trichoderma afroharzianum, a beneficial microorganism widely used in agriculture as a biocontrol agent, negatively affects the development and survival of the lepidopteran pest Spodoptera littoralis by altering the larval gut microbiota and its nutritional support to the host. Indeed, experiments aimed to restore the functional microbial community in the gut allow a complete rescue. Our results shed light on a novel role played by a soil microorganism in the modulation of plant-insect interaction, setting the stage for a more comprehensive analysis of the impact that biocontrol agents may have on ecological sustainability of agricultural systems.}, }
@article {pmid36840260, year = {2023}, author = {Anguita-Maeso, M and Navas-Cortés, JA and Landa, BB}, title = {Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840260}, issn = {2223-7747}, abstract = {Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.}, }
@article {pmid36838257, year = {2023}, author = {Mashini, AG and Oakley, CA and Beepat, SS and Peng, L and Grossman, AR and Weis, VM and Davy, SK}, title = {The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020292}, pmid = {36838257}, issn = {2076-2607}, abstract = {The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.}, }
@article {pmid36835084, year = {2023}, author = {Mutusamy, P and Banga Singh, KK and Su Yin, L and Petersen, B and Sicheritz-Ponten, T and Clokie, MRJ and Loke, S and Millard, A and Parimannan, S and Rajandas, H}, title = {Phenotypic Characterization and Comparative Genomic Analysis of Novel Salmonella Bacteriophages Isolated from a Tropical Rainforest.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, doi = {10.3390/ijms24043678}, pmid = {36835084}, issn = {1422-0067}, abstract = {Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.}, }
@article {pmid36824281, year = {2023}, author = {Biget, M and Wang, T and Mony, C and Xu, Q and Lecoq, L and Chable, V and Theis, KR and Ling, N and Vandenkoornhuyse, P}, title = {Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants.}, journal = {iScience}, volume = {26}, number = {2}, pages = {106031}, doi = {10.1016/j.isci.2023.106031}, pmid = {36824281}, issn = {2589-0042}, abstract = {The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.}, }
@article {pmid36819038, year = {2023}, author = {Sun, X and Li, Y and Yang, Q and Zhang, H and Xu, N and Tang, Z and Wu, S and Jiang, Y and Mohamed, HF and Ou, D and Zheng, X}, title = {Identification of quorum sensing-regulated Vibrio fortis as potential pathogenic bacteria for coral bleaching and the effects on the microbial shift.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1116737}, pmid = {36819038}, issn = {1664-302X}, abstract = {Coastal pollution, global warming, ocean acidification, and other reasons lead to the imbalance of the coral reef ecosystem, resulting in the increasingly serious problem of coral degradation. Coral bleaching is often accompanied by structural abnormalities of coral symbiotic microbiota, among which Vibrio is highly concerned. In this study, Vibrio fortis S10-1 (MCCC 1H00104), isolated from sea cucumber, was used for the bacterial infection on coral Seriatopora guttatus and Pocillopora damicornis. The infection of S10-1 led to coral bleaching and a significant reduction of photosynthetic function in coral holobiont, and the pathogenicity of V. fortis was regulated by quorum sensing. Meanwhile, Vibrio infection also caused a shift of coral symbiotic microbial community, with significantly increased abundant Proteobacteria and Actinobacteria and significantly reduced abundant Firmicutes; on genus level, the abundance of Bacillus decreased significantly and the abundance of Rhodococcus, Ralstonia, and Burkholderia-Caballeronia-Paraburkholderia increased significantly; S10-1 infection also significantly impacted the water quality in the micro-ecosystem. In contrast, S10-1 infection showed less effect on the microbial community of the live stone, which reflected that the microbes in the epiphytic environment of the live stone might have a stronger ability of self-regulation; the algal symbionts mainly consisted of Cladocopium sp. and showed no significant effect by the Vibrio infection. This study verified that V. fortis is the primary pathogenic bacterium causing coral bleaching, revealed changes in the microbial community caused by its infection, provided strong evidence for the "bacterial bleaching" hypothesis, and provided an experimental experience for the exploration of the interaction mechanism among microbial communities, especially coral-associated Vibrio in the coral ecosystem, and potential probiotic strategy or QS regulation on further coral disease control.}, }
@article {pmid36815841, year = {2023}, author = {Jin, X and Zhu, H and Shi, Y and Chen, Z and Wang, Y and Gui, JF and Zhao, Z}, title = {Host Hybridization Dominates over Cohabitation in Affecting Gut Microbiota of Intrageneric Hybrid Takifugu Pufferfish.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0118122}, doi = {10.1128/msystems.01181-22}, pmid = {36815841}, issn = {2379-5077}, abstract = {Microbial symbionts are of great importance for macroscopic life, including fish, and both collectively comprise an integrated biological entity known as the holobiont. Yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to biotic and/or abiotic influences. Here, through amplicon profiling, the genealogical relationship between artificial F1 hybrid pufferfish with growth heterosis, produced from crossing female Takifugu obscurus with male Takifugu rubripes and its maternal halfsibling purebred, was well recapitulated by their gut microbial community similarities, indicating an evident parallelism between host phylogeny (hybridity) and microbiota relationships therein. Interestingly, modest yet significant fish growth promotion and gut microbiota alteration mediated by hybrid-purebred cohabitation were observed, in comparison with their respective monoculture cohorts that share common genetic makeups, implying a certain degree of environmental influences. Moreover, the underlying assemblage patterns of gut microbial communities were found associated with a trade-off between variable selection and dispersal limitation, which are plausibly driven by the augmented social interactions between hybrid and purebred cohabitants differing in behaviors. Results from this study not only can enrich, from a microbial perspective, the sophisticated understanding of complex and dynamic assemblage of the fish holobiont, but will also provide deeper insights into the ecophysiological factors imposed on the diversity-function relationships thereof. Our findings emphasize the intimate associations of gut microbiota in host genetics-environmental interactions and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve the production of farmed fishes. IMPORTANCE Microbial symbionts are of great importance for macroscopic life, including fish, and yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to the biotic and/or abiotic influences. Through gut microbiota profiling, we show that host intrageneric hybridization and cohabitation can impose a strong disturbance upon pufferfish gut microbiota. Moreover, marked alterations in the composition and function of gut microbiota in both hybrid and purebred pufferfish cohabitants were observed, which are potentially correlated with different metabolic priorities and behaviors between host genealogy. These results can enrich, from a microbial perspective, the sophisticated understanding of the complex and dynamic assemblage of the fish holobiont and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve farmed fish production.}, }
@article {pmid36807754, year = {2023}, author = {Lindner, M and Radke, DI and Elke, G}, title = {[Bacterial gut microbiota-key player in sepsis].}, journal = {Medizinische Klinik, Intensivmedizin und Notfallmedizin}, volume = {}, number = {}, pages = {}, pmid = {36807754}, issn = {2193-6226}, abstract = {The gut microbiota is comprised of over 1200 different bacteria and forms a symbiotic community with the human organism, the holobiont. It plays an important role in the maintenance of homeostasis, e.g., of the immune system and essential metabolic processes. Disturbances in the balance of this reciprocal relationship are called dysbiosis and, in the field of sepsis, are associated with incidence of disease, extent of the systemic inflammatory response, severity of organ dysfunction, and mortality. In addition to providing guiding principles in the fascinating relationship between "human and microbe," this article summarizes recent findings regarding the role of the bacterial gut microbiota in sepsis, which is one a very relevant in intensive care medicine.}, }
@article {pmid36807409, year = {2023}, author = {Rasmussen, JA and Kiilerich, P and Madhun, AS and Waagbø, R and Lock, ER and Madsen, L and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Co-diversification of an intestinal Mycoplasma and its salmonid host.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36807409}, issn = {1751-7370}, abstract = {Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.}, }
@article {pmid36803555, year = {2023}, author = {Poupin, MJ and Ledger, T and Roselló-Móra, R and González, B}, title = {The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {9}, pmid = {36803555}, issn = {2524-6372}, abstract = {As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.}, }
@article {pmid36797336, year = {2023}, author = {Eisenhofer, R and Odriozola, I and Alberdi, A}, title = {Impact of microbial genome completeness on metagenomic functional inference.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {12}, pmid = {36797336}, issn = {2730-6151}, abstract = {Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this overlooked bias in metagenomic functional inference.}, }
@article {pmid36795564, year = {2023}, author = {Zhang, P and Zhu, Y and Guo, Q and Li, J and Zhan, X and Yu, H and Xie, N and Tan, H and Lundholm, N and Garcia-Cuetos, L and Martin, MD and Subirats, MA and Su, YH and Ruiz-Trillo, I and Martindale, MQ and Yu, JK and Gilbert, MTP and Zhang, G and Li, Q}, title = {On the origin and evolution of RNA editing in metazoans.}, journal = {Cell reports}, volume = {42}, number = {2}, pages = {112112}, doi = {10.1016/j.celrep.2023.112112}, pmid = {36795564}, issn = {2211-1247}, abstract = {Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.}, }
@article {pmid36793883, year = {2022}, author = {Clokie, M and Sicheritz-Pontén, T}, title = {Reflections on 2022: A Progressive Year for Phage Therapy.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {4}, pages = {181-182}, doi = {10.1089/phage.2022.29038.editorial}, pmid = {36793883}, issn = {2641-6549}, }
@article {pmid36793689, year = {2023}, author = {Matias, AMA and Popovic, I and Thia, JA and Cooke, IR and Torda, G and Lukoschek, V and Bay, LK and Kim, SW and Riginos, C}, title = {Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef.}, journal = {Evolutionary applications}, volume = {16}, number = {2}, pages = {293-310}, pmid = {36793689}, issn = {1752-4571}, abstract = {Genomic studies are uncovering extensive cryptic diversity within reef-building corals, suggesting that evolutionarily and ecologically relevant diversity is highly underestimated in the very organisms that structure coral reefs. Furthermore, endosymbiotic algae within coral host species can confer adaptive responses to environmental stress and may represent additional axes of coral genetic variation that are not constrained by taxonomic divergence of the cnidarian host. Here, we examine genetic variation in a common and widespread, reef-building coral, Acropora tenuis, and its associated endosymbiotic algae along the entire expanse of the Great Barrier Reef (GBR). We use SNPs derived from genome-wide sequencing to characterize the cnidarian coral host and organelles from zooxanthellate endosymbionts (genus Cladocopium). We discover three distinct and sympatric genetic clusters of coral hosts, whose distributions appear associated with latitude and inshore-offshore reef position. Demographic modelling suggests that the divergence history of the three distinct host taxa ranges from 0.5 to 1.5 million years ago, preceding the GBR's formation, and has been characterized by low-to-moderate ongoing inter-taxon gene flow, consistent with occasional hybridization and introgression typifying coral evolution. Despite this differentiation in the cnidarian host, A. tenuis taxa share a common symbiont pool, dominated by the genus Cladocopium (Clade C). Cladocopium plastid diversity is not strongly associated with host identity but varies with reef location relative to shore: inshore colonies contain lower symbiont diversity on average but have greater differences between colonies as compared with symbiont communities from offshore colonies. Spatial genetic patterns of symbiont communities could reflect local selective pressures maintaining coral holobiont differentiation across an inshore-offshore environmental gradient. The strong influence of environment (but not host identity) on symbiont community composition supports the notion that symbiont community composition responds to habitat and may assist in the adaptation of corals to future environmental change.}, }
@article {pmid36756199, year = {2022}, author = {Choudhary, DK and Vaishnav, A and Jain, S and Mandal, MK and Prasad, R}, title = {Editorial: Climate impact on plant holobiont: Mitigation strategies and sustainability.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1040876}, doi = {10.3389/fmicb.2022.1040876}, pmid = {36756199}, issn = {1664-302X}, }
@article {pmid36750176, year = {2023}, author = {Woltyńska, A and Gawor, J and Olech, MA and Górniak, D and Grzesiak, J}, title = {Bacterial communities of Antarctic lichens explored by gDNA and cDNA 16S rRNA gene amplicon sequencing.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad015}, pmid = {36750176}, issn = {1574-6941}, abstract = {Recently, lichens came once more into the scientific spotlight due to their unique relations with Prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the non-active part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.}, }
@article {pmid36750093, year = {2023}, author = {Kazmi, SA and Hsiao, EY}, title = {Extending genetic risk for Alzheimer's disease from host to holobiont.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2023.01.004}, pmid = {36750093}, issn = {1097-4172}, abstract = {The gut microbiota is implicated in risk for Alzheimer's disease (AD). A study in Science reports that depleting gut bacteria in mice with genetic risk for AD reduces neuropathology in a sex-dependent manner. This is reversed by administering short-chain fatty acids, suggesting that specific bacterial metabolites increase susceptibility to AD.}, }
@article {pmid36748430, year = {2022}, author = {Izraeli, Y and Lepetit, D and Atias, S and Mozes-Daube, N and Wodowski, G and Lachman, O and Luria, N and Steinberg, S and Varaldi, J and Zchori-Fein, E and Chiel, E}, title = {Genomic characterization of viruses associated with the parasitoid Anagyrus vladimiri (Hymenoptera: Encyrtidae).}, journal = {The Journal of general virology}, volume = {103}, number = {12}, pages = {}, doi = {10.1099/jgv.0.001810}, pmid = {36748430}, issn = {1465-2099}, abstract = {Knowledge on symbiotic microorganisms of insects has increased dramatically in recent years, yet relatively little data are available regarding non-pathogenic viruses. Here we studied the virome of the parasitoid wasp Anagyrus vladimiri Triapitsyn (Hymenoptera: Encyrtidae), a biocontrol agent of mealybugs. By high-throughput sequencing of viral nucleic acids, we revealed three novel viruses, belonging to the families Reoviridae [provisionally termed AnvRV (Anagyrus vladimiri reovirus)], Iflaviridae (AnvIFV) and Dicistroviridae (AnvDV). Phylogenetic analysis further classified AnvRV in the genus Idnoreovirus, and AnvDV in the genus Triatovirus. The genome of AnvRV comprises 10 distinct genomic segments ranging in length from 1.5 to 4.2 kb, but only two out of the 10 ORFs have a known function. AnvIFV and AnvDV each have one polypeptide ORF, which is typical of iflaviruses but very un-common among dicistroviruses. Five conserved domains were found along both the ORFs of those two viruses. AnvRV was found to be fixed in an A. vladimiri population that was obtained from a mass rearing facility, whereas its prevalence in field-collected A. vladimiri was ~15 %. Similarly, the prevalence of AnvIFV and AnvDV was much higher in the mass rearing population than in the field population. The presence of AnvDV was positively correlated with the presence of Wolbachia in the same individuals. Transmission electron micrographs of females' ovaries revealed clusters and viroplasms of reovirus-like particles in follicle cells, suggesting that AnvRV is vertically transmitted from mother to offspring. AnvRV was not detected in the mealybugs, supporting the assumption that this virus is truly associated with the wasps. The possible effects of these viruses on A. vladimiri's biology, and on biocontrol agents in general, are discussed. Our findings identify RNA viruses as potentially involved in the multitrophic system of mealybugs, their parasitoids and other members of the holobiont.}, }
@article {pmid36745783, year = {2023}, author = {Germain, RR and Feng, S and Buffan, L and Carmona, CP and Chen, G and Graves, GR and Tobias, JA and Rahbek, C and Lei, F and Fjeldså, J and Hosner, PA and Gilbert, MTP and Zhang, G and Nogués-Bravo, D}, title = {Changes in the functional diversity of modern bird species over the last million years.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {7}, pages = {e2201945119}, doi = {10.1073/pnas.2201945119}, pmid = {36745783}, issn = {1091-6490}, abstract = {Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturbances. We combine morphological, ecological, and life-history trait data for >260 extant bird species with genomic-based estimates of changing effective population size (Ne) to quantify demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. We show that functional diversity was relatively stable over this period, but underwent significant changes in some key areas of trait space due to changing species abundances. Our results suggest that patterns of population decline over the Pleistocene have been concentrated in particular regions of trait space associated with extreme reproductive strategies and low dispersal ability, consistent with an overall erosion of functional diversity. Further, species most sensitive to climate warming occupied a relatively narrow region of functional space, indicating that the largest potential population increases and decreases under climate change will occur among species with relatively similar trait sets. Overall, our results identify fluctuations in functional space of extant species over evolutionary timescales and represent the demographic-based vulnerability of different regions of functional space among these taxa. The integration of paleodemographic dynamics with functional trait data enhances our ability to quantify losses of biosphere integrity before anthropogenic disturbances and attribute contemporary biodiversity loss to different drivers over time.}, }
@article {pmid36736005, year = {2023}, author = {Fujiyoshi, S and Yarimizu, K and Perera, I and Abanto, M and Jorquera, M and Maruyama, F}, title = {Learning from mistakes: challenges in finding holobiont factors from environmental samples and the importance of methodological consistency.}, journal = {Current opinion in biotechnology}, volume = {80}, number = {}, pages = {102897}, doi = {10.1016/j.copbio.2023.102897}, pmid = {36736005}, issn = {1879-0429}, abstract = {The cause of harmful algal blooms has been a mystery, but research to elucidate its mechanism has progressed over the years thanks to genetic technologies. We have monitored toxic algae and its associated bacteria as a community, the so-called 'holobiont' in Chilean coastal waters for years from the perspective of bacteria as an algal bloom driver. This review describes the challenges of holobiont monitoring, specifically with respect to standardizing and compliance with the monitoring protocols to collect reliable and sustainable data. Further, we suggest adopting the high-throughput sequencing (HTS) standard operating procedure (SOP) by the International Human Microbiome to improve the quality and consistency of holobiont monitoring in the harmful algal world.}, }
@article {pmid36731191, year = {2023}, author = {Zhu, W and Wang, H and Li, X and Liu, X and Zhu, M and Wang, A and Li, X}, title = {Consistent responses of coral microbiome to acute and chronic heat stress exposures.}, journal = {Marine environmental research}, volume = {185}, number = {}, pages = {105900}, doi = {10.1016/j.marenvres.2023.105900}, pmid = {36731191}, issn = {1879-0291}, abstract = {Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.}, }
@article {pmid36719456, year = {2023}, author = {Lin, Z and Zheng, X and Chen, J}, title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02183-0}, pmid = {36719456}, issn = {1432-184X}, abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.}, }
@article {pmid36713485, year = {2023}, author = {Bonthond, G and Neu, AK and Bayer, T and Krueger-Hadfield, SA and Künzel, S and Weinberger, F}, title = {Non-native hosts of an invasive seaweed holobiont have more stable microbial communities compared to native hosts in response to thermal stress.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9753}, pmid = {36713485}, issn = {2045-7758}, abstract = {Seaweeds are colonized by a microbial community, which can be directly linked to their performance. This community is shaped by an interplay of stochastic and deterministic processes, including mechanisms which the holobiont host deploys to manipulate its associated microbiota. The Anna Karenina principle predicts that when a holobiont is exposed to suboptimal or stressful conditions, these host mechanisms may be compromised. This leads to a relative increase of stochastic processes that may potentially result in the succession of a microbial community harmful to the host. Based on this principle, we used the variability in microbial communities (i.e., beta diversity) as a proxy for stability within the invasive holobiont Gracilaria vermiculophylla during a simulated invasion in a common garden experiment. Independent of host range, host performance declined at elevated temperature (22°C) and disease incidence and beta diversity increased. Under thermally stressful conditions, beta diversity increased more in epibiota from native populations, suggesting that epibiota from non-native holobionts are thermally more stable. This pattern reflects an increase in deterministic processes acting on epibiota associated with non-native hosts, which in the setting of a common garden can be assumed to originate from the host itself. Therefore, these experimental data suggest that the invasion process may have selected for hosts better able to maintain stable microbiota during stress. Future studies are needed to identify the underlying host mechanisms.}, }
@article {pmid36702670, year = {2023}, author = {Li, JH and Muhammad Aslam, M and Gao, YY and Dai, L and Hao, GF and Wei, Z and Chen, MX and Dini-Andreote, F}, title = {Microbiome-mediated signal transduction within the plant holobiont.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2022.12.005}, pmid = {36702670}, issn = {1878-4380}, abstract = {Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.}, }
@article {pmid36699263, year = {2023}, author = {Bolt Botnen, A and Bjørnsen, MB and Alberdi, A and Gilbert, MTP and Aizpurua, O}, title = {A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12861}, pmid = {36699263}, issn = {2405-8440}, abstract = {As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.}, }
@article {pmid36688656, year = {2023}, author = {Rosado, PM and Cardoso, PM and Rosado, JG and Schultz, J and Nunes da Rocha, U and Keller-Costa, T and Peixoto, RS}, title = {Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0092122}, doi = {10.1128/msystems.00921-22}, pmid = {36688656}, issn = {2379-5077}, abstract = {Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.}, }
@article {pmid36687663, year = {2022}, author = {Burgunter-Delamare, B and Rousvoal, S and Legeay, E and Tanguy, G and Fredriksen, S and Boyen, C and Dittami, SM}, title = {The Saccharina latissima microbiome: Effects of region, season, and physiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1050939}, pmid = {36687663}, issn = {1664-302X}, abstract = {INTRODUCTION: Saccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.<br><br>METHODS: We studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.<br><br>RESULTS AND DISCUSSION: We have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host's condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.}, }
@article {pmid36683362, year = {2022}, author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H}, title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, doi = {10.1093/gigascience/giac127}, pmid = {36683362}, issn = {2047-217X}, abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.}, }
@article {pmid36680370, year = {2023}, author = {Hansen, CCR and Láruson, &#xc1;J and Rasmussen, JA and Ballesteros, JAC and Sinding, MS and Hallgrimsson, GT and von Schmalensee, M and Stefansson, RA and Skarphédinsson, KH and Labansen, AL and Leivits, M and Sonne, C and Dietz, R and Skelmose, K and Boertmann, D and Eulaers, I and Martin, MD and Helgason, AS and Gilbert, MTP and Pálsson, S}, title = {Genomic diversity and differentiation between island and mainland populations of White-tailed Eagles (Haliaeetus albicilla).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16858}, pmid = {36680370}, issn = {1365-294X}, abstract = {Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110-115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.}, }
@article {pmid36679063, year = {2023}, author = {Conte, C and Apostolaki, ET and Vizzini, S and Migliore, L}, title = {A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/plants12020350}, pmid = {36679063}, issn = {2223-7747}, abstract = {Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.}, }
@article {pmid36675911, year = {2023}, author = {Mathew, SA and Helander, M and Saikkonen, K and Vankova, R and Dobrev, PI and Dirihan, S and Fuchs, B}, title = {Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, doi = {10.3390/jof9010090}, pmid = {36675911}, issn = {2309-608X}, abstract = {Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.}, }
@article {pmid36662226, year = {2023}, author = {Deutsch, JM and Green, MO and Akavaram, P and Davis, AC and Diskalkar, SS and Du Plessis, IA and Fallon, HA and Grason, EM and Kauf, EG and Kim, ZM and Miller, JR and Neal, AL and Riera, T and Stroeva, SE and Tran, J and Tran, V and Coronado, AV and Coronado, VV and Wall, BT and Yang, CM and Mohanty, I and Abrahamse, NH and Freeman, CJ and Easson, CG and Fiore, CL and Onstine, AE and Djeddar, N and Biliya, S and Bryksin, AV and Garg, N and Agarwal, V}, title = {Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech.}, journal = {Marine drugs}, volume = {21}, number = {1}, pages = {}, doi = {10.3390/md21010053}, pmid = {36662226}, issn = {1660-3397}, abstract = {Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies.}, }
@article {pmid36653630, year = {2023}, author = {Mayfield, AB}, title = {Multi-macromolecular Extraction from Endosymbiotic Anthozoans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2625}, number = {}, pages = {17-56}, pmid = {36653630}, issn = {1940-6029}, mesh = {Animals ; Ecosystem ; *Anthozoa ; *Sea Anemones ; *Dinoflagellida/physiology ; Symbiosis ; }, abstract = {Obligately symbiotic associations between reef-building corals (anthozoan cnidarians) and photosynthetically active dinoflagellates of the family Symbiodiniaceae comprise the functional basis of all coral reef ecosystems. Given the existential threats of global climate change toward these thermo-sensitive entities, there is an urgent need to better understand the physiological implications of changes in the abiotic milieu of scleractinian corals and their mutualistic algal endosymbionts. Although initially slow to leverage the immense breakthroughs in molecular biotechnology that have benefited humankind, coral biologists are making up for lost time in exploiting an array of ever-advancing molecular tools for answering key questions pertaining to the survival of corals in an ever-changing world. In order to comprehensively characterize the multi-omic landscape of the coral holobiont-the cnidarian host, its intracellular dinoflagellates, and a plethora of other microbial constituents-I introduce a series of protocols herein that yield large quantities of high-quality RNA, DNA, protein, lipids, and polar metabolites from a diverse array of reef corals and endosymbiotic sea anemones. Although numerous published articles in the invertebrate zoology field feature protocols that lead to sufficiently high yield of intact host coral macromolecules, through using the approach outlined herein one may simultaneously acquire a rich, multi-compartmental biochemical pool that truly reflects the complex and dynamic nature of these animal-plant chimeras.}, }
@article {pmid36651852, year = {2023}, author = {Takagi, T and Aoyama, K and Motone, K and Aburaya, S and Yamashiro, H and Miura, N and Inoue, K}, title = {Mutualistic Interactions between Dinoflagellates and Pigmented Bacteria Mitigate Environmental Stress.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0246422}, doi = {10.1128/spectrum.02464-22}, pmid = {36651852}, issn = {2165-0497}, abstract = {Scleractinian corals form symbiotic relationships with a variety of microorganisms, including endosymbiotic dinoflagellates of the family Symbiodiniaceae, and with bacteria, which are collectively termed coral holobionts. Interactions between hosts and their symbionts are critical to the physiological status of corals. Coral-microorganism interactions have been studied extensively, but dinoflagellate-bacterial interactions remain largely unexplored. Here, we developed a microbiome manipulation method employing KAS-antibiotic treatment (kanamycin, ampicillin, and streptomycin) to favor pigmented bacteria residing on cultured Cladocopium and Durusdinium, major endosymbionts of corals, and isolated several carotenoid-producing bacteria from cell surfaces of the microalgae. Following KAS-antibiotic treatment of Cladocopium sp. strain NIES-4077, pigmented bacteria increased 8-fold based on colony-forming assays from the parental strain, and 100% of bacterial sequences retrieved through 16S rRNA amplicon sequencing were affiliated with the genus Maribacter. Microbiome manipulation enabled host microalgae to maintain higher maximum quantum yield of photosystem II (variable fluorescence divided by maximum fluorescence [Fv/Fm]) under light-stress conditions, compared to the parental strain. Furthermore, by combining culture-dependent and -independent techniques, we demonstrated that species of the family Symbiodiniaceae and pigmented bacteria form strong interactions. Dinoflagellates protected bacteria from antibiotics, while pigmented bacteria protected microalgal cells from light stress via carotenoid production. Here, we describe for the first time a symbiotic relationship in which dinoflagellates and bacteria mutually reduce environmental stress. Investigations of microalgal-bacterial interactions further document bacterial contributions to coral holobionts and may facilitate development of novel techniques for microbiome-mediated coral reef conservation. IMPORTANCE Coral reefs cover less than 0.1% of the ocean floor, but about 25% of all marine species depend on coral reefs at some point in their life cycles. However, rising ocean temperatures associated with global climate change are a serious threat to coral reefs, causing dysfunction of the photosynthetic apparatus of endosymbiotic microalgae of corals, and overproducing reactive oxygen species harmful to corals. We manipulated the microbiome using an antibiotic treatment to favor pigmented bacteria, enabling their symbiotic microalgal partners to maintain higher photosynthetic function under insolation stress. Furthermore, we investigated mechanisms underlying microalgal-bacterial interactions, describing for the first time a symbiotic relationship in which the two symbionts mutually reduce environmental stress. Our findings extend current insights about microalgal-bacterial interactions, enabling better understanding of bacterial contributions to coral holobionts under stressful conditions and offering hope of reducing the adverse impacts of global warming on coral reefs.}, }
@article {pmid36647171, year = {2023}, author = {Pirolo, M and Espinosa-Gongora, C and Alberdi, A and Eisenhofer, R and Soverini, M and Eriksen, E&#xd8; and Pedersen, KS and Guardabassi, L}, title = {Bacterial topography of the upper and lower respiratory tract in pigs.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {5}, pmid = {36647171}, issn = {2524-4671}, abstract = {BACKGROUND: Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing.<br><br>RESULTS: The bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT.<br><br>CONCLUSION: We provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.}, }
@article {pmid36637211, year = {2023}, author = {Feldner-Busztin, D and Firbas Nisantzis, P and Jane Edmunds, S and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, G}, title = {Dealing with dimensionality: the application of machine learning to multi-omics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad021}, pmid = {36637211}, issn = {1367-4811}, abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large data sets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.<br><br>RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas data set, which is accessible and contains many diverse experiments.<br><br>AVAILABILITY: All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36629441, year = {2023}, author = {Šigutová, H and Šigut, M and Pyszko, P and Kostovčík, M and Kolařík, M and Drozd, P}, title = {Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0316022}, doi = {10.1128/spectrum.03160-22}, pmid = {36629441}, issn = {2165-0497}, abstract = {Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.}, }
@article {pmid36629118, year = {2023}, author = {Chou, PH and Hu, MY and Guh, YJ and Wu, GC and Yang, SH and Tandon, K and Shao, YT and Lin, LY and Chen, C and Tseng, KY and Wang, MC and Zhang, CM and Han, BC and Lin, CC and Tang, SL and Jeng, MS and Chang, CF and Tseng, YC}, title = {Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1990}, pages = {20221973}, doi = {10.1098/rspb.2022.1973}, pmid = {36629118}, issn = {1471-2954}, abstract = {The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.}, }
@article {pmid36627918, year = {2023}, author = {Singh, T and Sakai, K and Ishida-Castañeda, J and Iguchi, A}, title = {Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14629}, pmid = {36627918}, issn = {2167-8359}, abstract = {Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance.}, }
@article {pmid36621484, year = {2023}, author = {Jiang, M and Li, S and Li, H and Jian, S and Liu, F and Li, X}, title = {Reprogramming of microbial community in barley root endosphere and rhizosphere soil by polystyrene plastics with different particle sizes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161420}, doi = {10.1016/j.scitotenv.2023.161420}, pmid = {36621484}, issn = {1879-1026}, abstract = {Polystyrene plastics is an emerging pollutant affecting plant performance and soil functioning. However, little information is available on the effects of microplastics and nanoplastics on plant root endophytic and rhizospheric soil microbial communities. Here, barley plants were grown in microplastics/nanoplastics -treated soil and the diversity, composition and function of bacteria and fungi in the root and rhizosphere soil were examined. At the seedling stage, greater changes of root endophytes were found compared with rhizosphere microorganisms under the plastic treatments. Nanoplastics decreased the richness and diversity of the fungal community, while microplastics increased the diversity of the root endophytic bacterial community. The network of the bacterial community under nanoplastics showed higher vulnerability while lower complexity than that under the control. However, the bacterial community under microplastics had a relatively higher resistance than the control. For the rhizosphere microbial community, no significant effect of plastics was found on the α-diversity index at the seedling stage. In addition, the nanoplastics resulted in higher sensitivity in the relative abundance and function of rhizosphere soil microbes than root endophytic microbes at the mature stage. Treatments of polystyrene plastics with different particle sizes reprogramed the rhizosphere and root endophytic microbial communities. Different effects of microplastics and nanoplastics were found on the diversity, composition, network structure and function of bacteria and fungi, which might be due to the variation in particle sizes. These results lay a foundation for learning the effects of polystyrene plastics with different particle sizes on the microorganisms in rhizosphere soil and plant roots, which may have important implications for the adaptation of plant-microbial holobiont in polystyrene plastics-polluted soils.}, }
@article {pmid36620745, year = {2023}, author = {Baldo, L and Tavecchia, G and Rotger, A and Igual, JM and Riera, JL}, title = {Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14511}, pmid = {36620745}, issn = {2167-8359}, abstract = {BACKGROUND: Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation.<br><br>METHODS: Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes.<br><br>RESULTS: All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover.<br><br>CONCLUSIONS: These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.}, }
@article {pmid36620197, year = {2022}, author = {Marcos, S and Parejo, M and Estonba, A and Alberdi, A}, title = {Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {3}, number = {3}, pages = {2100065}, pmid = {36620197}, issn = {2641-6573}, abstract = {Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.}, }
@article {pmid36618624, year = {2022}, author = {Lyu, D and Smith, DL}, title = {The root signals in rhizospheric inter-organismal communications.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1064058}, pmid = {36618624}, issn = {1664-462X}, abstract = {Root exudates play a key role in mediating plant-plant and plant-rhizomicrobiome interactions, including regulating biochemical/physiological aspects of plant-associated microorganisms, to enhance host plant growth and resilience. Root exudates can act as signals to reduce the competition from neighboring plants and recruiting/choreographing a wide range of diverse rhizomicrobiome members to make the host plant a good fit with its immediate environment. Root exudate production is a dynamic and key process, but there is a limited understanding of the metabolites or metabolic pathways involved in the inter-organismal communications facilitated by them. Given the well-known symbiotic relationships between plants and associated rhizomicrobiome members, adding root exudates to microbial isolation media may allow some of the large segments of rhizomicrobiome members that are not currently culturable to be grown in vitro. This will provide new insights into how root signals orchestrate associated microbes, will benefit agricultural production in the face of challenges posed by climate change, and will help to sustainably provide food for a growing global human population.}, }
@article {pmid36608656, year = {2023}, author = {Rodríguez-Varela, R and Moore, KHS and Ebenesersdóttir, SS and Kilinc, GM and Kjellström, A and Papmehl-Dufay, L and Alfsdotter, C and Berglund, B and Alrawi, L and Kashuba, N and Sobrado, V and Lagerholm, VK and Gilbert, E and Cavalleri, GL and Hovig, E and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Munters, AR and Bernhardsson, C and Skar, B and Christophersen, A and Turner-Walker, G and Gopalakrishnan, S and Daskalaki, E and Omrak, A and Pérez-Ramallo, P and Skoglund, P and Girdland-Flink, L and Gunnarsson, F and Hedenstierna-Jonson, C and Gilbert, MTP and Lidén, K and Jakobsson, M and Einarsson, L and Victor, H and Krzewińska, M and Zachrisson, T and Storå, J and Stefánsson, K and Helgason, A and Götherström, A}, title = {The genetic history of Scandinavia from the Roman Iron Age to the present.}, journal = {Cell}, volume = {186}, number = {1}, pages = {32-46.e19}, doi = {10.1016/j.cell.2022.11.024}, pmid = {36608656}, issn = {1097-4172}, abstract = {We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.}, }
@article {pmid36619855, year = {2021}, author = {Puetz, LC and Delmont, TO and Aizpurua, O and Guo, C and Zhang, G and Katajamaa, R and Jensen, P and Gilbert, MTP}, title = {Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {4}, pages = {2100018}, pmid = {36619855}, issn = {2641-6573}, abstract = {Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.}, }
@article {pmid36618122, year = {2021}, author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP}, title = {The genomic origin of Zana of Abkhazia.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {2}, pages = {e10051}, pmid = {36618122}, issn = {2641-6573}, abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.}, }
@article {pmid36596505, year = {2023}, author = {Wakimoto, T}, title = {Biosynthesis of Bioactive Natural Products Derived from Theonellidae Family Marine Sponges.}, journal = {Chemical &amp; pharmaceutical bulletin}, volume = {71}, number = {1}, pages = {1-8}, doi = {10.1248/cpb.c22-00715}, pmid = {36596505}, issn = {1347-5223}, mesh = {Animals ; *Biological Products/chemistry ; *Porifera/chemistry ; Bacteria/metabolism ; Peptides/metabolism ; *Polyketides/pharmacology ; *Antineoplastic Agents/pharmacology/metabolism ; }, abstract = {Marine sponges are among the most primitive animals and often contain unique, biologically active compounds. Several of these compounds have played an important roles as pharmaceutical leads for anti-cancer drugs, such as halichondrin B, which led to the development of an anti-breast cancer drug. Some compounds with remarkable biological activities are accumulated in significantly high concentrations in the sponge. How and why the marine sponges produce and accumulate bioactive natural products are long-standing questions with both biochemical and ecological implications, since in sponges, the animal-microbe symbioses are presumed to be responsible for the biosynthetic machinery, consisting of efficient enzymes and regulatory systems for the specific biological activities of medicinally relevant natural products. In this review, I focus on the chemically rich Theonellidae family sponges and discuss the biosynthesis of bioactive peptides and polyketides. In particular, the biosynthetic pathway of calyculin A suggests that crosstalk between the sponge host and bacterial symbiont confers a chemical defense system on the immobile animal-microbe holobiont.}, }
@article {pmid36581277, year = {2022}, author = {Cheng, K and Tong, M and Cai, Z and Jong, MC and Zhou, J and Xiao, B}, title = {Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {161185}, doi = {10.1016/j.scitotenv.2022.161185}, pmid = {36581277}, issn = {1879-1026}, abstract = {Reef-building corals are well known for their obligate association with Symbiodiniaceae, and an array of other microbes, including bacteria, fungi, and symbiotic algae (i.e., total microbiome), which together form the coral holobiont. The total microbiome plays an intricate part in maintaining the homeostasis of the coral holobiont and is closely associated with host health. However, the composition of the coral associated microbiome and interaction between its different members remains elusive because few analyses have bridged taxonomically disparate groups. This research gaps have prevented a holistic understanding of the total microbiome. Thus, to simultaneously characterize the bacterial, fungal and symbiotic algal communities associated with different coral species, and explore the relationship between these symbionts and coral health, healthy and bleached tissues from four coral species, Acropora muricata, Galaxea fascicularis, Platygyra daedalea, and Pavona explanulata, were collected from the Xisha Islands of the South China Sea. Using high throughput sequencing, a high degree of host-specificity was observed among bacterial, fungal, and algal groups across coral species. There were no obvious changes in the microbial community structure of apparently healthy and bleached corals, but host bleaching allowed colonization of the holobionts by diverse opportunistic microbes, resulting in a significant elevation in the α-diversity of microbial communities. In addition, co-occurrence analysis of the coral microbiota also identified more complex microbial interactions in bleached corals than in healthy ones. In summary, this study characterized the structure of coral-associated microbiomes across four coral species, and systematically studied microbiome differences between healthy and bleached corals. The findings improve our understanding of the heterogeneity of symbiotic microorganisms and the impact of coral's physiological status on its associated microbial communities composition.}, }
@article {pmid36561457, year = {2022}, author = {Liu, Y and Morelli, M and Koskimäki, JJ and Qin, S and Zhu, YH and Zhang, XX}, title = {Editorial: Role of endophytic bacteria in improving plant stress resistance.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1106701}, pmid = {36561457}, issn = {1664-462X}, }
@article {pmid36560776, year = {2022}, author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ}, title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/v14122772}, pmid = {36560776}, issn = {1999-4915}, support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.}, }
@article {pmid36558520, year = {2022}, author = {Ramos Meyers, G and Samouda, H and Bohn, T}, title = {Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, doi = {10.3390/nu14245361}, pmid = {36558520}, issn = {2072-6643}, abstract = {It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.}, }
@article {pmid36557214, year = {2022}, author = {Rhimi, S and Kriaa, A and Mariaule, V and Saidi, A and Drut, A and Jablaoui, A and Akermi, N and Maguin, E and Hernandez, J and Rhimi, M}, title = {The Nexus of Diet, Gut Microbiota and Inflammatory Bowel Diseases in Dogs.}, journal = {Metabolites}, volume = {12}, number = {12}, pages = {}, doi = {10.3390/metabo12121176}, pmid = {36557214}, issn = {2218-1989}, abstract = {Canine inflammatory bowel diseases (IBD) are of increasing interest in veterinary medicine. They refer to complex and debilitating conditions of dogs' gastrointestinal tract. Although little evidence for causal inferences is currently available, it is believed that IBD pathophysiology entails intricate interactions between environmental factors, the intestinal immune system, and the microbial communities that colonize the gut. To better understand the mechanisms underlying these disorders, leveraging factors associated with the development of these diseases is imperative. Of these factors, emerging evidence supports the role of dietary patterns as key players influencing the composition and function of gut microbes, with subsequent effects on health and disease. In this review, we particularly focus on addressing IBD in dogs and discuss how specific nutrients may elicit or relieve gut inflammation. Gaining mechanistic insights into such interplay and the underpinning mechanisms is key to inferring dietary recommendations, and setting up new and promising therapeutics.}, }
@article {pmid36547600, year = {2022}, author = {Schulz, M and Schmitt, I and Weber, D and Dal Grande, F}, title = {Fungal Host Affects Photosynthesis in a Lichen Holobiont.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, doi = {10.3390/jof8121267}, pmid = {36547600}, issn = {2309-608X}, abstract = {Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role of the coral host in modulating photosynthesis has been clarified to a large extent in coral holobionts, the role of the fungal host in this regard is far less understood. Here, we address this question by taking advantage of the recent discovery of highly specific fungal-algal pairings corresponding to climatically adapted ecotypes of the lichen-forming genus Umbilicaria. Specifically, we compared chlorophyll a fluorescence kinetics among lichen thalli consisting of different fungal-algal combinations. We show that photosynthetic performance in these lichens is not only driven by algal genotype, but also by fungal host species identity and intra-host genotype. These findings shed new light on the closely intertwined physiological processes of fungal and algal partners in the lichen symbiosis. Indeed, the specific combinations of fungal and algal genotypes within a lichen individual-and the resulting combined functional phenotype-can be regarded as a response to the environment. Our findings suggest that characterizing the genetic composition of both eukaryotic partners is an important complimentary step to understand and predict the lichen holobiont's responses to environmental change.}, }
@article {pmid36546449, year = {2022}, author = {Fontaine, SS and Kohl, KD}, title = {The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.245191}, pmid = {36546449}, issn = {1477-9145}, abstract = {Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that "depleted" tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than "colonized" tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compare gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis, and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.}, }
@article {pmid36539412, year = {2022}, author = {Chen, L and Li, Z and Wu, B and Zhou, B and Heller, R and Zhou, J and Wang, K and Lin, Z and Wu, D and Qiu, Q}, title = {Progressive evolution of secondary aquatic adaptation in hippos and cetaceans.}, journal = {Cell discovery}, volume = {8}, number = {1}, pages = {134}, pmid = {36539412}, issn = {2056-5968}, }
@article {pmid36534288, year = {2023}, author = {Espino-Vázquez, AN and Córdova-López, G and Cabrera-Rangel, JF and Mendoza-Servín, JV and Partida-Martínez, LP}, title = {The Rhizopus Holobiont: A Model to Decipher Fungal-Bacterial-Viral Symbioses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2610}, number = {}, pages = {137-147}, pmid = {36534288}, issn = {1940-6029}, abstract = {Rhizopus microsporus is an early-diverging fungal species that inhabits the soil, is used for the fermentation of diverse Asian and African foods, and can be a pathogen of plants, animals, and humans.Toxin-producing strains of R. microsporus live in symbiosis with Gram-negative betaproteobacteria from the genus Mycetohabitans (Burkholderia sensu lato). These bacterial endosymbionts increase the metabolic plasticity of the fungal holobiont by producing the "mycotoxins," control their asexual reproduction, and influence their sexual success. Recently, we identified two viruses of the genus Narnavirus in some R. microsporus strains that harbor Mycetohabitans. By eliminating bacteria and/or viruses from host R. microsporus strains, we have been able to study the role of these symbionts in fungal biology. Remarkably, the absence of these bacterial and viral symbionts decreases sexual reproduction. In this chapter, the method developed to eliminate and genotype the Narnavirus RmNV-20S and RmNV-23S in R. microsporus is described in detail.}, }
@article {pmid36513413, year = {2022}, author = {Sangiorgio, D and Cellini, A and Donati, I and Ferrari, E and Tanunchai, B and Fareed Mohamed Wahdan, S and Sadubsarn, D and Farneti, B and Checcucci, A and Buscot, F and Spinelli, F and Purahong, W}, title = {Taxonomical and functional composition of strawberry microbiome is genotype-dependent.}, journal = {Journal of advanced research}, volume = {42}, number = {}, pages = {189-204}, doi = {10.1016/j.jare.2022.02.009}, pmid = {36513413}, issn = {2090-1224}, mesh = {*Fragaria/microbiology ; *Microbiota ; Bacteria/genetics ; Genotype ; Symbiosis ; }, abstract = {INTRODUCTION: Specific microbial communities are associated to host plants, influencing their phenotype and fitness.Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked.<br><br>OBJECTIVES: This work provides the first comprehensive descriptionof the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organsof three commercially important strawberry genotypes under cultural conditions.<br><br>METHODS: Strawberry-associatedfungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated.<br><br>RESULTS: Results showed that thestrawberry core microbiome included 24 bacteria and 15 fungal operational taxonomicunits (OTUs).However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highesttolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonasfluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhizaRhizophagus irregularis.<br><br>CONCLUSION: This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.}, }
@article {pmid36510852, year = {2022}, author = {Biggs, E and Taylor, MW and Middleton, DMRL}, title = {Beyond the theory: from holobiont concept to microbiome engineering.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16308}, pmid = {36510852}, issn = {1462-2920}, abstract = {Holobiont research has increasingly moved from descriptive studies to sophisticated field- and laboratory-based manipulations, however the extent to which changes in the holobiont persist remains largely unknown. In this Burning Question, we ask whether the underlying principles of the holobiont concept, whereby an externally applied evolutionary pressure can lead to a beneficial change in host-associated microbial community composition, could be used to facilitate microbiome engineering and thereby addition of a new ecosystem service that persists across generations. The answer to this question has potential implications for diverse fields including symbiosis, conservation and biotechnology.}, }
@article {pmid36504779, year = {2022}, author = {Liberman, R and Benayahu, Y and Huchon, D}, title = {Octocorals in the Gulf of Aqaba exhibit high photosymbiont fidelity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1005471}, pmid = {36504779}, issn = {1664-302X}, abstract = {Symbiotic associations, widespread in terrestrial and marine ecosystems, are of considerable ecological importance. Many tropical coral species are holobionts, formed by the obligate association between a cnidarian host and endosymbiotic dinoflagellates of the family Symbiodiniaceae. The latter are abundant on coral reefs from very shallow water down to the upper mesophotic zone (30-70 m). The research on scleractinians has revealed that the photosymbiont lineages present in the cnidarian host play an important role in the coral's ability to thrive under different environmental conditions, such as light regime and temperature. However, little is known regarding octocoral photosymbionts, and in particular regarding those found deeper than 30 m. Here, we used ribosomal (ITS2) and chloroplast (23S) markers to uncover, for the first time, the dominant Symbiodiniaceae taxa present in 19 mesophotic octocoral species (30-70 m depth) from the Gulf of Aqaba/Eilat (northern Red Sea). In addition, using high-throughput sequencing of the ITS2 region we characterized both the dominant and the rare Symbiodiniaceae lineages found in several species across depth. The phylogenetic analyses of both markers were in agreement and revealed that most of the studied mesophotic octocorals host the genus Cladocopium. Litophyton spp. and Klyxum utinomii were exceptions, as they harbored Symbiodinium and Durusdinium photosymbionts, respectively. While the dominant algal lineage of each coral species did not vary across depth, the endosymbiont community structure significantly differed between host species, as well as between different depths for some host species. The findings from this study contribute to the growing global-catalogue of Cnidaria-Symbiodiniaceae associations. Unravelling the Symbiodiniaceae composition in octocoral holobionts across environmental gradients, depth in particular, may enable a better understanding of how specialized those associations are, and to what extent coral holobionts are able to modify their photosymbionts.}, }
@article {pmid36503639, year = {2022}, author = {Hodžić, A and Dheilly, NM and Cabezas-Cruz, A and Berry, D}, title = {The helminth holobiont: a multidimensional host-parasite-microbiota interaction.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2022.11.012}, pmid = {36503639}, issn = {1471-5007}, abstract = {Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.}, }
@article {pmid36496327, year = {2022}, author = {Zhu, Z and Liu, Y and Hu, H and Wang, GH}, title = {Nasonia-microbiome associations: a model for evolutionary hologenomics research.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2022.11.005}, pmid = {36496327}, issn = {1471-5007}, abstract = {In recent years, with the development of microbial research technologies, microbiota research has received widespread attention. The parasitoid wasp genus Nasonia is a good model organism for studying insect behavior, development, evolutionary genetics, speciation, and symbiosis. This review describes key advances and progress in the field of the Nasonia microbiome interactions. We provide an overview of the advantages of Nasonia as a model organism for microbiome studies, list research methods to study the Nasonia microbiome, and discuss recent discoveries in Nasonia microbiome research. This summary of the complexities of Nasonia-microbiome relationships will help to contribute to a better understanding of the interactions between animals and their microbiomes and establish a clear research direction for Nasonia-microbiome interactions in the future.}, }
@article {pmid36494920, year = {2022}, author = {Gruet, C and Abrouk, D and Börner, A and Muller, D and Moënne-Loccoz, Y}, title = {Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14508}, pmid = {36494920}, issn = {1365-3040}, abstract = {Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by qPCR their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions. This article is protected by copyright. All rights reserved.}, }
@article {pmid36482381, year = {2022}, author = {Zhang, X and Ma, YN and Wang, X and Liao, K and He, S and Zhao, X and Guo, H and Zhao, D and Wei, HL}, title = {Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {216}, pmid = {36482381}, issn = {2049-2618}, abstract = {BACKGROUND: Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored.<br><br>RESULTS: To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae.<br><br>CONCLUSION: Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes.&#xa0; Video Abstract.}, }
@article {pmid36482161, year = {2022}, author = {Nguyen, BT and Dumack, K and Trivedi, P and Islam, Z and Hu, HW}, title = {Plant associated protists - untapped promising candidates for agrifood tools.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16303}, pmid = {36482161}, issn = {1462-2920}, abstract = {The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production. This article is protected by copyright. All rights reserved.}, }
@article {pmid36476670, year = {2022}, author = {Jochum, M and Lee, MD and Curry, K and Zaksas, V and Vitalis, E and Treangen, T and Aagaard, K and Ternus, KL}, title = {Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21125}, pmid = {36476670}, issn = {2045-2322}, support = {Grant Number T32 HD098069 from NIH NICHD/NH/NIH HHS/United States ; }, abstract = {To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We then performed a stratified analysis based on mortality amongst the COVID-19 cohort with known outcomes of deceased (n = 10) versus survived (n = 15). Our overarching hypothesis was that there are detectable and functionally significant relationships between BALF microbial metatranscriptomes and the severity of COVID-19 disease onset and progression. We observed 34 functionally discriminant gene ontology (GO) terms in COVID-19 disease compared to the CAP and uninfected cohorts, and 21 GO terms functionally discriminant to COVID-19 mortality (q < 0.05). GO terms enriched in the COVID-19 disease cohort included hydrolase activity, and significant GO terms under the parental terms of biological regulation, viral process, and interspecies interaction between organisms. Notable GO terms associated with COVID-19 mortality included nucleobase-containing compound biosynthetic process, organonitrogen compound catabolic process, pyrimidine-containing compound biosynthetic process, and DNA recombination, RNA binding, magnesium and zinc ion binding, oxidoreductase activity, and endopeptidase activity. A Dirichlet multinomial mixtures clustering analysis resulted in a best model fit using three distinct clusters that were significantly associated with COVID-19 disease and mortality. We additionally observed discriminant taxonomic differences associated with COVID-19 disease and mortality in the genus Sphingomonas, belonging to the Sphingomonadacae family, Variovorax, belonging to the Comamonadaceae family, and in the class Bacteroidia, belonging to the order Bacteroidales. To our knowledge, this is the first study to evaluate significant differences in taxonomic and functional signatures between BALF metatranscriptomes from COVID-19, CAP, and uninfected cohorts, as well as associating these taxa and microbial gene functions with COVID-19 mortality. Collectively, while this data does not speak to causality nor directionality of the association, it does demonstrate a significant relationship between the human microbiome and COVID-19. The results from this study have rendered testable hypotheses that warrant further investigation to better understand the causality and directionality of host-microbiome-pathogen interactions.}, }
@article {pmid36471953, year = {2022}, author = {Wang, HY and Kang, CZ and Wang, YF and Wang, S and Wang, TL and Zhang, Y and Zhou, L and Liu, DH and Guo, LP}, title = {[Medicinal plant microbiome: advances and prospects].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {47}, number = {20}, pages = {5397-5405}, doi = {10.19540/j.cnki.cjcmm.20220615.102}, pmid = {36471953}, issn = {1001-5302}, mesh = {*Plants, Medicinal ; Plant Breeding ; Medicine, Chinese Traditional ; Agriculture ; *Microbiota ; }, abstract = {Medicinal plants are the main source of clinical medication in traditional Chinese medicine(TCM). China has achieved large-scale cultivation and production of medicinal plants. As an important resource for the sustainable development of agriculture in the future, microorganisms can also promote the green, ecological and high-quality development of Chinese medicine agriculture. However, research on the medicinal plant microbiome is still limited. Therefore, based on the development timeline of microbiome research, the present study reviewed the origin, technology, and hotspots of microbiome research and proposed some suggestions for future research according to the advances in medicinal plant microbiome.(1)Systematic investigation of medicinal plant microbiome on the species, genus, and family levels should be carried out on the medicinal plants of different chemotypes in order to reveal the coevolution of the microorganisms and their host plants.(2)Spatial and temporal research on medicinal plant microbiome should be performed to reveal the effects of microorganisms on the growth, development, and secondary metabolite accumulation of medicinal plants, as well as the underlying mechanisms.(3)Model medicinal plant species should be selected and microorganism-plant interaction research models should be established.(4)Core microbiome of medicinal plants should be explored for the future application of crucial microbes in the sustaina-ble agriculture of Chinese medicine.(5)Breeding of medicinal plant-associated microbes should be carried out to lay the foundation for novel medicinal plant breeding strategies.(6)High-throughput sequencing, traditional incubation, and isolation of microbes should be combined to study medicinal plant microbiome, thereby promoting the exploitation and application of uncultured microbial strains.(7)Platforms for the preservation of medicinal plant-associated microbe strains and data of their metabolites should be established and the exchange of information and cooperation between these platforms should be subsequently enhanced. With these suggestions, the efficient and rapid development of medicinal plant microbiome research is expected to be promoted.}, }
@article {pmid36464145, year = {2022}, author = {Kalra, R and Conlan, XA and Goel, M}, title = {Recent advances in research for potential utilization of unexplored lichen metabolites.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108072}, doi = {10.1016/j.biotechadv.2022.108072}, pmid = {36464145}, issn = {1873-1899}, abstract = {Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.}, }
@article {pmid36445161, year = {2022}, author = {Sylvain, F&#xc9; and Leroux, N and Normandeau, &#xc9; and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0206422}, doi = {10.1128/spectrum.02064-22}, pmid = {36445161}, issn = {2165-0497}, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, }
@article {pmid36435249, year = {2022}, author = {Travesso, M and Missionário, M and Cruz, S and Calado, R and Madeira, D}, title = {Combined effect of marine heatwaves and light intensity on the cellular stress response and photophysiology of the leather coral Sarcophyton cf. glaucum.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {160460}, doi = {10.1016/j.scitotenv.2022.160460}, pmid = {36435249}, issn = {1879-1026}, abstract = {Marine heatwaves (MHW) are threatening tropical coral reef ecosystems, leading to mass bleaching events worldwide. The combination of heat stress with high irradiance is known to shape the health and redox status of corals, but research is biased toward scleractinian corals, while much less is known on tropical symbiotic soft corals. Here, we evaluated the cellular stress response and the photophysiological performance of the soft coral Sarcophyton cf. glaucum, popularly termed as leather coral, under different global change scenarios. Corals were exposed to different light intensities (high light, low light, ∼662 and 253 μmol photons m[-2] s[-1]) for 30 days (time-point 1) and a subsequent MHW simulation was carried out for 10 days (control 26 vs 32 °C) (time-point 2). Subsequently, corals were returned to control temperature and allowed to recover for 30 days (time-point 3). Photophysiological performance (maximum quantum yield of photosystem II (Fv/Fm), a measure of photosynthetic activity; dark-level fluorescence (F0), as a proxy of chlorophyll a content (Chl a); and zooxanthellae density) and stress biomarkers (total protein, antioxidants, lipid peroxidation, ubiquitin, and heat shock protein 70) were assessed in corals at these three time-points. Corals were especially sensitive to the combination of heat and high light stress, experiencing a decrease in their photosynthetic efficiency under these conditions. Heat stress resulted in bleaching via zooxanthellae loss while high light stress led to pigment (Chl a) loss. This species' antioxidant defenses, and protein degradation were particularly enhanced under heat stress. A recovery was clear for molecular parameters after 30 days of recovery, whereby photophysiological performance required more time to return to basal levels. We conclude that soft corals distributed along intertidal areas, where the light intensity is high, could be especially vulnerable to marine heatwave events, highlighting the need to direct conservation efforts toward these organisms.}, }
@article {pmid36430266, year = {2022}, author = {Schaack, B and Hindré, T and Quansah, N and Hannani, D and Mercier, C and Laurin, D}, title = {Microbiota-Derived Extracellular Vesicles Detected in Human Blood from Healthy Donors.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, doi = {10.3390/ijms232213787}, pmid = {36430266}, issn = {1422-0067}, mesh = {Humans ; *Extracellular Vesicles ; *Microbiota ; Health Status ; Erythrocytes ; Monocytes ; Escherichia coli ; }, abstract = {The microbiota constitutes an important part of the holobiont in which extracellular vesicles (EVs) are key players in health, especially regarding inter- and intra-kingdom communications. Analysis of EVs from the red blood cell concentrates of healthy donors revealed variable amounts of OmpA and LPS in 12 of the 14 analyzed samples, providing indirect experimental evidence of the presence of microbiota EVs in human circulating blood in the absence of barrier disruption. To investigate the role of these microbiota EVs, we tracked the fusion of fluorescent Escherichia coli EVs with blood mononuclear cells and showed that, in the circulating blood, these EVs interacted almost exclusively with monocytes. This study demonstrates that bacterial EVs constitute critical elements of the host-microbiota cellular communication. The analysis of bacterial EVs should thus be systematically included in any characterization of human EVs.}, }
@article {pmid36427961, year = {2022}, author = {Sampson, TR}, title = {Introduction: Unraveling the complex contributions of indigenous microbes to neurological health and disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {xi-xvi}, doi = {10.1016/S0074-7742(22)00138-6}, pmid = {36427961}, issn = {2162-5514}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Nervous System Diseases/drug therapy ; *Microbiota ; *Parkinson Disease ; *Alzheimer Disease ; }, abstract = {The complex interactions between the human body and its indigenous microbes have come into focus as key mediators of neurological health. With both established and emerging association studies, alterations to the gut microbiome are observed to co-occur with many neurological diseases. Whether these associations are due to microbiome-mediated contributions to human health or an effect of the neurological disease itself is largely unknown across conditions. Here, we have collected contributions from a broad group of experts that highlight gut microbiome impacts across numerous neurological conditions. Ranging from neurodevelopmental disorders, to Parkinson's disease, Alzheimer's disease, epilepsy, traumatic injury, and amyotrophic lateral sclerosis, among others, we hope to provide a clearer picture of how our indigenous microbes impact neurological health. The study of these indigenous microbes will continue to reveal critical mechanisms that may 1 day be exploited for therapeutic benefits against these recalcitrant diseases.}, }
@article {pmid36427959, year = {2022}, author = {Payami, H}, title = {The many genomes of Parkinson's disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {59-80}, doi = {10.1016/bs.irn.2022.07.007}, pmid = {36427959}, issn = {2162-5514}, mesh = {Humans ; *Parkinson Disease/genetics ; *Microbiota ; }, abstract = {Genetic component of Parkinson's disease, once firmly believed non-existent, involves the human genome, mitochondrial genome, and the microbiome. Understanding the genomics of PD requires identification of PD-relevant genes and learning how they interact within the hologenome and with their environment. This chapter is an evidence-based perspective of a geneticist on how far we have come in this endeavor. The contemporary scientific society started with a naive and simplistic view of PD, evolved to accept that Parkinson's disease is probably the most complex disease there is, the progress we have made in discovering the genes and elucidating their functions, and now assembling the parts to create the whole.}, }
@article {pmid36426357, year = {2022}, author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G}, title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {987655}, pmid = {36426357}, issn = {1664-3224}, mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; }, abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.}, }
@article {pmid36425038, year = {2022}, author = {Zhu, W and Zhu, M and Liu, X and Xia, J and Wang, H and Chen, R and Li, X}, title = {Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1052776}, pmid = {36425038}, issn = {1664-302X}, abstract = {Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.}, }
@article {pmid36422350, year = {2022}, author = {Duval, C and Marie, B and Foucault, P and Duperron, S}, title = {Establishment of the Bacterial Microbiota in a Lab-Reared Model Teleost Fish, the Medaka Oryzias latipes.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422350}, issn = {2076-2607}, abstract = {Oryzias latipes is an important model organism for physiology, genetics, and developmental studies, and has also emerged as a relevant vertebrate model for aquatic ecotoxicology. Knowledge regarding its associated microbiota on the other hand is still scarce and limited to adults, despite the relevance of the associated microbiome to the host's biology. This study provides the first insights into the establishment of bacterial microbiota during early developmental stages of laboratory-reared medaka using a 16S-rRNA-sequencing-based approach. Major shifts in community compositions are observed, from a Proteobacteria-dominated community in larvae and juveniles to a more phylum-diverse community towards adulthood, with no obvious difference between female and male specimens. Major bacterial taxa found in adults, including genera Cetobacterium and ZOR0006, establish progressively and are rare during early stages. Dominance shifts are comparable to those documented in another major model teleost, the zebrafish. Results from this study provide a basis for future work investigating the influence of medaka-associated bacteria during host development.}, }
@article {pmid36416843, year = {2022}, author = {Fujiwara, F and Miyazawa, K and Nihei, N and Ichihashi, Y}, title = {Agroecosystem Engineering Extended from Plant-Microbe Interactions Revealed by Multi-Omics Data.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbac191}, pmid = {36416843}, issn = {1347-6947}, abstract = {In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.}, }
@article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, }
@article {pmid36372339, year = {2023}, author = {Pei, Y and Chen, S and Diao, X and Wang, X and Zhou, H and Li, Y and Li, Z}, title = {Deciphering the disturbance mechanism of BaP on the symbiosis of Montipora digitata via 4D-Proteomics approach.}, journal = {Chemosphere}, volume = {312}, number = {Pt 1}, pages = {137223}, doi = {10.1016/j.chemosphere.2022.137223}, pmid = {36372339}, issn = {1879-1298}, mesh = {Animals ; *Symbiosis ; Ecosystem ; Antioxidants/metabolism ; Proteomics ; RNA, Ribosomal, 16S/metabolism ; *Anthozoa/metabolism ; Coral Reefs ; }, abstract = {The coral holobiont is mainly composed of coral polyps, zooxanthellae, and coral symbiotic microorganisms, which form the basis of coral reef ecosystems. In recent years, the severe degradation of coral reefs caused by climate warming and environmental pollution has aroused widespread concern. Benzo(a)pyrene (BaP) is a widely distributed pollutant in the environment. However, the underlying mechanisms of coral symbiosis destruction due to the stress of BaP are not well understood. In this study, diaPASEF proteomics and 16S rRNA amplicon pyrosequencing technology were used to reveal the effects of 50 μg/L BaP on Montipora digitate. Data analysis was performed from the perspective of the main symbionts of M. digitata (coral polyps, zooxanthellae, and coral symbiotic microorganisms). The results showed that BaP impaired cellular antioxidant capacity by disrupting the GSH/GSSG cycle, and sustained stress causes severe impairment of energy metabolism and protein degradation in coral polyps. In zooxanthellae, BaP downregulated the protein expression of SOD2 and mtHSP70, which then resulted in oxidative free radical accumulation and apoptosis. For coral symbiotic microorganisms, BaP altered the community structure of microorganisms and decreased immunity. Coral symbiotic microorganisms adapted to the stress of BaP by adjusting energy metabolism and enhancing extracellular electron transfer. BaP adversely affected the three main symbionts of M. digitata via different mechanisms. Decreased antioxidant capacity is a common cause of damages to coral polyps and zooxanthellae, whereas coral symbiotic microorganisms are able to appropriately adapt to oxidative stress. This study assessed the effects of BaP on corals from a symbiotic perspective, which is more comprehensive and reliable. At the same time, data from the study supports new directions for coral research and coral reef protection.}, }
@article {pmid36369436, year = {2022}, author = {Paulino, GVB and Félix, CR and da Silva Oliveira, FA and Gomez-Silvan, C and Melo, VMM and Andersen, GL and Landell, MF}, title = {Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36369436}, issn = {1614-7499}, abstract = {Although coral bleaching is increasing worldwide due to warming oceans exacerbated by climate change, there has been a growing recognition that local stressors may play an additional role. Important stressors include the physicochemical and microbiological influences that are related to river runoff. Here, we investigated the microbiota associated to mucus and tissue of endemic coral Siderastrea stellata, collected from Brazilian northeast coral reefs of Barra de Santo Antônio (subject to river runoff) and Maragogi (minimal river runoff) during both the rainy and dry seasons. We sequenced the V4 region of 16S rDNA and used multiple R packages to process raw data and performed statistical analysis to reveal the microbial community structure composition and functional predictions. Major dissimilarities between microbial communities were related to seasonality, while healthy and bleached specimens were mainly associated with the enrichment of several less abundant taxa involved in specific metabolic functions, mainly related to the nitrogen cycle. We were not able to observe the dominance of groups that has been previously associated with bleachings, such as Vibrionaceae or Burkholderiaceae. The influx of freshwater appears to increase the homogeneity between individuals in Barra de Santo Antonio, especially during the rainy season. By contrast, we observed an increased homogeneity between samples in Maragogi during the dry season. Understanding the dynamics of the coral microbiota and how bleaching appears in response to specific environmental variables, in addition to determining the conditions that lead to a more robust coral microbiota, is essential for choosing the most appropriate area and conservation methods, for example.}, }
@article {pmid36365369, year = {2022}, author = {Bunyoo, C and Roongsattham, P and Khumwan, S and Phonmakham, J and Wonnapinij, P and Thamchaipenet, A}, title = {Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365369}, issn = {2223-7747}, abstract = {Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.}, }
@article {pmid36363690, year = {2022}, author = {Wang, R and Zhang, Q and Ju, M and Yan, S and Zhang, Q and Gu, P}, title = {The Endophytic Fungi Diversity, Community Structure, and Ecological Function Prediction of Sophora alopecuroides in Ningxia, China.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363690}, issn = {2076-2607}, abstract = {Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic fungi in the holobiont of S. alopecuroides is relatively lacking. In this article, the fungal community profiling of roots, stems, leaves, and seeds of S. alopecuroides (at the fruit maturity stage) from Huamachi and Baofeng in Ningxia, China were investigated based on the ITS1 region, using high-throughput sequencing technology. As a result, a total of 751 operational taxonomic units (OTUs) were obtained and further classified into 9 phyla, 27 classes, 66 orders, 141 families, 245 genera, and 340 species. The roots had the highest fungal richness and diversity, while the stems had the highest evenness and pedigree diversity. There also was a significant difference in the richness of the endophytic fungal community between root and seed (p < 0.05). The organ was the main factor affecting the community structure of endophytic fungi in S. alopecuroides. The genera of unclassified Ascomycota, Tricholoma, Apiotrichum, Alternaria, and Aspergillus made up the vast majority of relative abundance, which were common in all four organs as well. The dominant and endemic genera and biomarkers of endophytic fungi in four organs of S. alopecuroides were different and exhibited organ specificity or tissue preference. The endophytic fungi of S. alopecuroides were mainly divided into 15 ecological function groups, among which saprotroph was absolutely dominant, followed by mixotrophic and pathotroph, and the symbiotroph was the least. With this study, we revealed the diversity and community structure and predicted the ecological function of the endophytic fungi of S. alopecuroides, which provided a theoretical reference for the further development and utilization of the endophytic fungi resources of S. alopecuroides.}, }
@article {pmid36361844, year = {2022}, author = {Kiruba N, JM and Saeid, A}, title = {An Insight into Microbial Inoculants for Bioconversion of Waste Biomass into Sustainable "Bio-Organic" Fertilizers: A Bibliometric Analysis and Systematic Literature Review.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361844}, issn = {1422-0067}, mesh = {Fertilizers/analysis ; Biomass ; *Agricultural Inoculants ; Food ; *Refuse Disposal ; Sewage/microbiology ; Bibliometrics ; Soil ; }, abstract = {The plant-microbe holobiont has garnered considerable attention in recent years, highlighting its importance as an ecological unit. Similarly, manipulation of the microbial entities involved in the rhizospheric microbiome for sustainable agriculture has also been in the limelight, generating several commercial bioformulations to enhance crop yield and pest resistance. These bioformulations were termed biofertilizers, with the consistent existence and evolution of different types. However, an emerging area of interest has recently focused on the application of these microorganisms for waste valorization and the production of "bio-organic" fertilizers as a result. In this study, we performed a bibliometric analysis and systematic review of the literature retrieved from Scopus and Web of Science to determine the type of microbial inoculants used for the bioconversion of waste into "bio-organic" fertilizers. The Bacillus, Acidothiobacillus species, cyanobacterial biomass species, Aspergillus sp. and Trichoderma sp. were identified to be consistently used for the recovery of nutrients and bioconversion of wastes used for the promotion of plant growth. Cyanobacterial strains were used predominantly for wastewater treatment, while Bacillus, Acidothiobacillus, and Aspergillus were used on a wide variety of wastes such as sawdust, agricultural waste, poultry bone meal, crustacean shell waste, food waste, and wastewater treatment plant (WWTP) sewage sludge ash. Several bioconversion strategies were observed such as submerged fermentation, solid-state fermentation, aerobic composting, granulation with microbiological activation, and biodegradation. Diverse groups of microorganisms (bacteria and fungi) with different enzymatic functionalities such as chitinolysis, lignocellulolytic, and proteolysis, in addition to their plant growth promoting properties being explored as a consortium for application as an inoculum waste bioconversion to fertilizers. Combining the efficiency of such functional and compatible microbial species for efficient bioconversion as well as higher plant growth and crop yield is an enticing opportunity for "bio-organic" fertilizer research.}, }
@article {pmid36361736, year = {2022}, author = {Graindorge, S and Villette, C and Koechler, S and Groh, C and Comtet-Marre, S and Mercier, P and Magerand, R and Peyret, P and Heintz, D and Schaller, H and Arsène-Ploetze, F}, title = {The Arabidopsis thaliana-Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361736}, issn = {1422-0067}, mesh = {*Arabidopsis/metabolism ; *Streptomyces/metabolism ; Plant Diseases/genetics/microbiology ; Pseudomonas syringae/metabolism ; *Arabidopsis Proteins/metabolism ; }, abstract = {How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria-Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.}, }
@article {pmid36357618, year = {2022}, author = {Friedman, Y}, title = {Who is the biological patient? A new gradational and dynamic model for one health medicine.}, journal = {History and philosophy of the life sciences}, volume = {44}, number = {4}, pages = {61}, pmid = {36357618}, issn = {1742-6316}, mesh = {Animals ; Humans ; *One Health ; Interdisciplinary Research ; *Medicine ; }, abstract = {One Health medicine aims to improve health by focusing on the relations between the health of humans, animals, and the environment. However, One Health does not provide a clear idea of these relations, which are still represented as conceptually separated and not as one health, as the name implies. Inspired by holobiont research, I suggest a new model and conceptual framework for One Health that expands the notion of the biological patient by providing a gradational and dynamic understanding of environments, patients, and their relations. This new model conceptualizes humans and non-humans, individual organisms, and collectives, as belonging to one system that allows for more or less inclusive understandings of patients. As such, it resolves the conceptual tensions of different One Health approaches and supports the implementation of One Health as an interdisciplinary research field.}, }
@article {pmid36354996, year = {2022}, author = {Castaldi, A and Teta, R and Esposito, G and Beniddir, MA and De Voogd, NJ and Duperron, S and Costantino, V and Bourguet-Kondracki, ML}, title = {Computational Metabolomics Tools Reveal Subarmigerides, Unprecedented Linear Peptides from the Marine Sponge Holobiont Callyspongia subarmigera.}, journal = {Marine drugs}, volume = {20}, number = {11}, pages = {}, pmid = {36354996}, issn = {1660-3397}, mesh = {Animals ; *Callyspongia/microbiology ; Tandem Mass Spectrometry ; *Porifera/chemistry ; Peptides ; Metabolomics ; Molecular Structure ; }, abstract = {A detailed examination of a unique molecular family, restricted to the Callyspongia genus, in a molecular network obtained from an in-house Haplosclerida marine sponge collection (including Haliclona, Callyspongia, Xestospongia, and Petrosia species) led to the discovery of subarmigerides, a series of rare linear peptides from Callyspongia subarmigera, a genus mainly known for polyacetylenes and lipids. The structure of the sole isolated peptide, subarmigeride A (1) was elucidated through extensive 1D and 2D NMR spectroscopy, HRMS/MS, and Marfey's method to assign its absolute configuration. The putative structures of seven additional linear peptides were proposed by an analysis of their respective MS/MS spectra and a comparison of their fragmentation patterns with the heptapeptide 1. Surprisingly, several structurally related analogues of subarmigeride A (1) occurred in one distinct cluster from the molecular network of the cyanobacteria strains of the Guadeloupe mangroves, suggesting that the true producer of this peptide family might be the microbial sponge-associated community, i.e., the sponge-associated cyanobacteria.}, }
@article {pmid36348188, year = {2022}, author = {Rasmussen, N}, title = {René Dubos, the Autochthonous Flora, and the Discovery of the Microbiome.}, journal = {Journal of the history of biology}, volume = {55}, number = {3}, pages = {537-558}, pmid = {36348188}, issn = {1573-0387}, mesh = {Animals ; Humans ; *Microbiota ; *Anthozoa ; Symbiosis ; }, abstract = {Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, the human "microbiome" (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as "holobionts" like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960s research of biologist René Dubos, a forerunner figure mentioned in some historical accounts of the microbiome, and argue that he arrived at the superorganism concept 40 years before the Human Microbiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it.}, }
@article {pmid36342159, year = {2022}, author = {Cegarra, L and Aguirre, P and Nuñez, MT and Gerdtzen, ZP and Salgado, JC}, title = {Calcium is a non-competitive inhibitor of DMT1 on the intestinal iron absorption process: empirical evidence and mathematical modeling analysis.}, journal = {American journal of physiology. Cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpcell.00411.2022}, pmid = {36342159}, issn = {1522-1563}, abstract = {Iron absorption is a complex and highly controlled process where DMT1 transports nonheme iron through the brush border membrane of enterocytes to the cytoplasm but does not transport alkaline-earth metals such as calcium. However, it has been proposed that high concentrations of calcium from the diet could reduce iron bioavailability. In this work we investigate the effect of intracellular and extracellular calcium on iron uptake by Caco-2 cells, as determined by calcein fluorescence quenching. We found that extracellular calcium inhibits iron uptake by Caco-2 cells in a concentration-dependent manner. Chelation of intracellular calcium with BAPTA did not affect iron uptake, which indicates that the inhibitory effect of calcium is not exerted through intracellular calcium signaling. Kinetic studies performed, provided evidence that calcium acts as a reversible non-competitive inhibitor of the iron transport activity of DMT1. Based on these experimental results, a mathematical model was developed that considers the dynamics of non-competitive inhibition using a four-state mechanism to describe the inhibitory effect of calcium on the DMT1 iron transport process in intestinal cells. The model accurately predicts the calcein fluorescence quenching dynamics observed experimentally after an iron challenge. Therefore, the proposed model structure is capable of representing the inhibitory effect of extracellular calcium on DMT1-mediated iron entry into the cLIP of Caco-2 cells. Considering the range of calcium concentrations that can inhibit iron uptake, the possible inhibition of dietary calcium on intestinal iron uptake is discussed.}, }
@article {pmid36333777, year = {2022}, author = {Aubé, J and Cambon-Bonavita, MA and Velo-Suárez, L and Cueff-Gauchard, V and Lesongeur, F and Guéganton, M and Durand, L and Reveillaud, J}, title = {A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {189}, pmid = {36333777}, issn = {2049-2618}, mesh = {Animals ; Symbiosis ; *Decapoda/genetics ; *Hydrothermal Vents ; Gills ; Immune System ; }, abstract = {BACKGROUND: In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.<br><br>RESULTS: We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.<br><br>CONCLUSION: Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.}, }
@article {pmid36329318, year = {2022}, author = {Shao, Q and Dong, C and Hu, H and Huang, J and Zou, X and Liang, Z and Han, Y}, title = {Effects of Medicinal Plants on Fungal Community Structure and Function in Hospital Grassplot Soil.}, journal = {Current microbiology}, volume = {79}, number = {12}, pages = {377}, pmid = {36329318}, issn = {1432-0991}, mesh = {Animals ; Humans ; *Mycobiome ; Soil ; Soil Microbiology ; *Plants, Medicinal ; *Mirabilis ; Fungi/genetics ; Hospitals ; }, abstract = {Hospital grassplot soil is an important repository of pathogenic fungi exposed to the hospital environment, and the diffusion of these fungi-containing soil particles in the air increases the risk of nosocomial fungal infections. In this study, from the perspective of soil microbes-plant holobiont, four medicinal plants Mirabilis jalapa, Artemisia argyi, Viola philippica, and Plantago depressa were used as materials, based on ITS high-throughput amplicon sequencing and simulated pot experiments to explore the effect of medicinal plants on the fungal community in hospital grassplot soil, in order to provide a new exploration for hospital grassplot soil remediation. The results showed that the fungal community ecological guilds in primary test soil was mainly pathogen, and the abundance of animal pathogen with potential threats to human reached 61.36%. After planting medicinal plants, the composition and function of soil fungal community changed significantly. Although this change varied with plant species and growth stages, all samples collected in the pot experiment showed that the pathogen abundance decreased and the saprotroph abundance increased. In addition, 45 of the 46 core fungal genera defined in all potted samples were present in primary test soil, and many of them were human potential pathogens. These findings imply that the idea of enhancing soil quality in hospital grassplot soil by planting specific plants is feasible. However, the initial fungal community of the hospital grassplot soil has a certain stability, and it is difficult to completely eliminate the threat of pathogenic fungi by planting medicinal plants.}, }
@article {pmid36326449, year = {2022}, author = {KleinJan, H and Frioux, C and Califano, G and Aite, M and Fremy, E and Karimi, E and Corre, E and Wichard, T and Siegel, A and Boyen, C and Dittami, SM}, title = {Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16766}, pmid = {36326449}, issn = {1365-294X}, abstract = {Microbes can modify their hosts' stress tolerance, thus potentially enhancing their ecological range. An example of such interactions is Ectocarpus subulatus, one of the few freshwater-tolerant brown algae. This tolerance is partially due to its (un)cultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. Low salinity acclimation of these algal-bacterial associations was then compared. Salinity significantly impacted bacterial and viral gene expression, albeit in different ways across algal-bacterial communities. In contrast, gene expression of the host and metabolite profiles were affected almost exclusively in the freshwater-intolerant algal-bacterial communities. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, vitamin K synthesis is one possible bacterial service missing specifically in freshwater-intolerant cultures in low salinity. In this condition, we also observed a relative increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a quorum-sensing regulator. This could have resulted in dysbiosis by causing a shift in bacterial behaviour in the intolerant algal-bacterial community. Together, these results provide two promising hypotheses to be examined by future targeted experiments. Although they apply only to the specific study system, they offer an example of how bacteria may impact their host's stress response.}, }
@article {pmid36322483, year = {2022}, author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV}, title = {Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus).}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msac241}, pmid = {36322483}, issn = {1537-1719}, abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (∼200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest palaeogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope's extinction.}, }
@article {pmid36319835, year = {2022}, author = {Moffat, JJ and Coffroth, MA and Wallingford, PD and terHorst, CP}, title = {Symbiont genotype influences holobiont response to increased temperature.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18394}, pmid = {36319835}, issn = {2045-2322}, mesh = {Animals ; Temperature ; Coral Reefs ; *Anthozoa/physiology ; *Dinoflagellida/physiology ; Symbiosis ; Genotype ; }, abstract = {As coral reefs face warming oceans and increased coral bleaching, a whitening of the coral due to loss of microalgal endosymbionts, the possibility of evolutionary rescue offers some hope for reef persistence. In tightly linked mutualisms, evolutionary rescue may occur through evolution of the host and/or endosymbionts. Many obligate mutualisms are composed of relatively small, fast-growing symbionts with greater potential to evolve on ecologically relevant time scales than their relatively large, slower growing hosts. Numerous jellyfish species harbor closely related endosymbiont taxa to other cnidarian species such as coral, and are commonly used as a model system for investigating cnidarian mutualisms. We examined the potential for adaptation of the upside-down jellyfish Cassiopea xamachana to increased temperature via evolution of its microalgal endosymbiont, Symbiodinium microadriaticum. We quantified trait variation among five algal genotypes in response to three temperatures (26 °C, 30 °C, and 32 °C) and fitness of hosts infected with each genotype. All genotypes showed positive growth rates at each temperature, but rates of respiration and photosynthesis decreased with increased temperature. Responses varied among genotypes but were unrelated to genetic similarity. The effect of temperature on asexual reproduction and the timing of development in the host also depended on the genotype of the symbiont. Natural selection could favor different algal genotypes at different temperatures, affecting host fitness. This eco-evolutionary interaction may be a critical component of understanding species resilience in increasingly stressful environments.}, }
@article {pmid36315059, year = {2022}, author = {Shantz, AA and Ladd, MC and Ezzat, L and Schmitt, RJ and Holbrook, SJ and Schmeltzer, E and Vega Thurber, R and Burkepile, DE}, title = {Positive interactions between corals and damselfish increase coral resistance to temperature stress.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16480}, pmid = {36315059}, issn = {1365-2486}, abstract = {By the century's end, many tropical seas will reach temperatures exceeding most coral species' thermal tolerance on an annual basis. The persistence of corals in these regions will, therefore, depend on their abilities to tolerate recurrent thermal stress. Although ecologists have long recognized that positive interspecific interactions can ameliorate environmental stress to expand the realized niche of plants and animals, coral bleaching studies have largely overlooked how interactions with community members outside of the coral holobiont shape the bleaching response. Here, we subjected a common coral, Pocillopora grandis, to 10 days of thermal stress in aquaria with and without the damselfish Dascyllus flavicaudus (yellowtail dascyllus), which commonly shelter within these corals, to examine how interactions with damselfish impacted coral thermal tolerance. Corals often benefit from nutrients excreted by animals they interact with and prior to thermal stress, corals grown with damselfish showed improved photophysiology (Fv /Fm) and developed larger endosymbiont populations. When exposed to thermal stress, corals with fish performed as well as control corals maintained at ambient temperatures without fish. In contrast, corals exposed to thermal stress without fish experienced photophysiological impairment, a more than 50% decline in endosymbiont density, and a 36% decrease in tissue protein content. At the end of the experiment, thermal stress caused average calcification rates to decrease by over 80% when damselfish were absent but increase nearly 25% when damselfish were present. Our study indicates that damselfish-derived nutrients can increase coral thermal tolerance and are consistent with the Stress Gradient Hypothesis, which predicts that positive interactions become increasingly important for structuring communities as environmental stress increases. Because warming of just a few degrees can exceed corals' temperature tolerance to trigger bleaching and mortality, positive interactions could play a critical role in maintaining some coral species in warming regions until climate change is aggressively addressed.}, }
@article {pmid36314753, year = {2022}, author = {Koziol, A and Odriozola, I and Nyholm, L and Leonard, A and San José, C and Pauperio, J and Ferreira, C and Hansen, AJ and Aizpurua, O and Gilbert, MTP and Alberdi, A}, title = {Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1318}, pmid = {36314753}, issn = {2045-8827}, mesh = {Animals ; *Gastrointestinal Microbiome ; Bacteria/genetics ; *Microbiota ; Feces ; Mammals/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild-like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild-caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a "natural" setup enriched with elements freshly collected from nature and a "laboratory" setup with sterile artificial elements. Through sequencing of the V3-V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild-like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.}, }
@article {pmid36300791, year = {2022}, author = {Snelders, NC and Boshoven, JC and Song, Y and Schmitz, N and Fiorin, GL and Rovenich, H and van den Berg, GCM and Torres, DE and Petti, GC and Prockl, Z and Faino, L and Seidl, MF and Thomma, BPHJ}, title = {A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18576}, pmid = {36300791}, issn = {1469-8137}, abstract = {Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.}, }
@article {pmid36298701, year = {2022}, author = {Olesen, AS and Kodama, M and Skovgaard, K and Møbjerg, A and Lohse, L and Limborg, MT and Bøtner, A and Belsham, GJ}, title = {Influence of African Swine Fever Virus on Host Gene Transcription within Peripheral Blood Mononuclear Cells from Infected Pigs.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298701}, issn = {1999-4915}, mesh = {Swine ; Animals ; *African Swine Fever Virus/physiology ; *African Swine Fever ; Leukocytes, Mononuclear/metabolism ; Real-Time Polymerase Chain Reaction ; RNA, Messenger/metabolism ; Transcription, Genetic ; }, abstract = {African swine fever virus (ASFV) has become a global threat to the pig production industry and has caused enormous economic losses in many countries in recent years. Peripheral blood mononuclear cells (PBMCs) from pigs infected with ASFV not only express ASFV genes (almost 200 in number) but have altered patterns of host gene expression as well. Both up- and down-regulation of host cell gene expression can be followed using RNAseq on poly(A)+ mRNAs harvested from the PBMCs of pigs collected at different times post-infection. Consistent with the time course of changes in viral gene expression, only few and limited changes in host gene expression were detected at 3 days post-infection (dpi), but by 6 dpi, marked changes in the expression of over 1300 host genes were apparent. This was co-incident with the major increase in viral gene expression. The majority of the changes in host gene expression were up-regulation, but many down-regulated genes were also identified. The patterns of changes in gene expression within the PBMCs detected by RNAseq were similar in each of the four infected pigs. Furthermore, changes in the expression of about twenty selected host genes, known to be important in host defence and inflammatory responses, were confirmed using high-throughput microfluidic qPCR assays.}, }
@article {pmid36296289, year = {2022}, author = {Carper, DL and Appidi, MR and Mudbhari, S and Shrestha, HK and Hettich, RL and Abraham, PE}, title = {The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296289}, issn = {2076-2607}, abstract = {Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant-microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant-microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.}, }
@article {pmid36293657, year = {2022}, author = {Lim, DW and Wang, JH}, title = {Gut Microbiome: The Interplay of an "Invisible Organ" with Herbal Medicine and Its Derived Compounds in Chronic Metabolic Disorders.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293657}, issn = {1660-4601}, mesh = {Humans ; *Gastrointestinal Microbiome ; Herbal Medicine ; *Plants, Medicinal ; Phytotherapy ; Chronic Disease ; *Metabolic Diseases/drug therapy ; }, abstract = {Resembling a concealed "organ" in a holobiont, trillions of gut microbes play complex roles in the maintenance of homeostasis, including participating in drug metabolism. The conventional opinion is that most of any drug is metabolized by the host and that individual differences are principally due to host genetic factors. However, current evidence indicates that only about 60% of the individual differences in drug metabolism are attributable to host genetics. Although most common chemical drugs regulate the gut microbiota, the gut microbiota is also known to be involved in drug metabolism, like the host. Interestingly, many traditional herbal medicines and derived compounds are biotransformed by gut microbiota, manipulating the compounds' effects. Accordingly, the gut microbiota and its specified metabolic pathways can be deemed a promising target for promoting drug efficacy and safety. However, the evidence regarding causality and the corresponding mechanisms concerning gut microbiota and drug metabolism remains insufficient, especially regarding drugs used to treat metabolic disorders. Therefore, the present review aims to comprehensively summarize the bidirectional roles of gut microbiota in the effects of herbal medicine in metabolic diseases to provide vital clues for guiding the clinical application of precision medicine and personalized drug development.}, }
@article {pmid36287022, year = {2022}, author = {Puntin, G and Sweet, M and Fraune, S and Medina, M and Sharp, K and Weis, VM and Ziegler, M}, title = {Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0005322}, doi = {10.1128/mmbr.00053-22}, pmid = {36287022}, issn = {1098-5557}, abstract = {Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.}, }
@article {pmid36274502, year = {2022}, author = {Foucault, P and Gallet, A and Duval, C and Marie, B and Duperron, S}, title = {Gut microbiota and holobiont metabolome composition of the medaka fish (Oryzias latipes) are affected by a short exposure to the cyanobacterium Microcystis aeruginosa.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {253}, number = {}, pages = {106329}, doi = {10.1016/j.aquatox.2022.106329}, pmid = {36274502}, issn = {1879-1514}, mesh = {Animals ; *Microcystis ; *Oryzias/physiology ; *Gastrointestinal Microbiome ; *Water Pollutants, Chemical/toxicity ; *Cyanobacteria ; Metabolome ; }, abstract = {Blooms of toxic cyanobacteria are a common stress encountered by aquatic fauna. Evidence indicates that long-lasting blooms affect fauna-associated microbiota. Because of their multiple roles, host-associated microbes are nowadays considered relevant to ecotoxicology, yet the respective timing of microbiota versus functional changes in holobionts response needs to be clarified. The response of gut microbiota and holobiont's metabolome to exposure to a dense culture of Microcystis aeruginosa was investigated as a microcosm-simulated bloom in the model fish species Oryzias latipes (medaka). Both gut microbiota and gut metabolome displayed significant composition changes after only 2 days of exposure. A dominant symbiont, member of the Firmicutes, plummeted whereas various genera of Proteobacteria and Actinobacteriota increased in relative abundance. Changes in microbiota composition occurred earlier and faster compared to metabolome composition. Liver and muscle metabolome were much less affected than guts, supporting that the gut and associated microbiota are in the front row upon exposure. This study highlights that even short cyanobacterial blooms, that are increasingly frequent, trigger changes in microbiota composition and holobiont metabolome. It emphasizes the relevance of multi-omics approaches to explore organism's response to an ecotoxicological stress.}, }
@article {pmid36261416, year = {2022}, author = {Siddique, S and Radakovic, ZS and Hiltl, C and Pellegrin, C and Baum, TJ and Beasley, H and Bent, AF and Chitambo, O and Chopra, D and Danchin, EGJ and Grenier, E and Habash, SS and Hasan, MS and Helder, J and Hewezi, T and Holbein, J and Holterman, M and Janakowski, S and Koutsovoulos, GD and Kranse, OP and Lozano-Torres, JL and Maier, TR and Masonbrink, RE and Mendy, B and Riemer, E and Sobczak, M and Sonawala, U and Sterken, MG and Thorpe, P and van Steenbrugge, JJM and Zahid, N and Grundler, F and Eves-van den Akker, S}, title = {The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6190}, pmid = {36261416}, issn = {2041-1723}, mesh = {Animals ; *Parasites ; Pantothenic Acid ; Transcriptome ; *Tylenchida ; *Cysts ; }, abstract = {Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.}, }
@article {pmid36254722, year = {2022}, author = {Jonas, L and Hill, R}, title = {Uptake of inorganic and organic phosphorus compounds by two marine sponges and their associated bacterial communities in aquaria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16250}, pmid = {36254722}, issn = {1462-2920}, abstract = {Marine sponges are abundant filter-feeders in benthic ecosystems and many host copious microorganisms. Sponges and their symbionts have emerged as major players within marine biogeochemical cycles, facilitating uptake and release of carbon, nitrogen, and sulfur. Sponge holobionts' role in transforming dissolved carbon and nitrogen is well established; however, the same depth of understanding has not yet been extended to phosphorus. In this aquaria-based study, [32] P-labelled orthophosphate and ATP were used to determine that two sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both take up ambient dissolved inorganic phosphate (DIP) and dissolved organic phosphorus (DOP). Subsequent genetic analyses and chemical extraction showed that sponge symbionts have the potential to synthesise polyphosphate (poly-P) and that this energy-rich form of stored phosphorus is present in both sponges. L. chondrodes, an oligotrophic sponge with a microbiome dominated by cyanobacteria, stores more phosphorus as poly-P (6%-8% of total phosphorus) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. DIP/DOP uptake, as well as poly-P storage, may be driven by two factors: cyanobacterial abundance and nutrient availability. Considering their prevalence in phosphorus-limited ecosystems and their ability to pump large amounts of seawater, sponge holobionts are likely to be key players within benthic phosphorus cycles.}, }
@article {pmid36250983, year = {2022}, author = {Schmittmann, L and Rahn, T and Busch, K and Fraune, S and Pita, L and Hentschel, U}, title = {Stability of a dominant sponge-symbiont in spite of antibiotic-induced microbiome disturbance.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16249}, pmid = {36250983}, issn = {1462-2920}, abstract = {Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge-model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge-microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom-made, sterile, flow-through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic-resistant bacteria, resulting in more complex, but less specific bacteria-bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic-induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria-bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge-symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host-bacteria and bacteria-bacteria interactions in the sponge holobiont.}, }
@article {pmid36246452, year = {2022}, author = {Iglesias-Carrasco, M and Tobias, JA and Duchêne, DA}, title = {Bird lineages colonizing urban habitats have diversified at high rates across deep time.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {31}, number = {9}, pages = {1784-1793}, pmid = {36246452}, issn = {1466-822X}, abstract = {AIM: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.<br><br>LOCATION: World.<br><br>TIME PERIOD: Current.<br><br>MAJOR TAXA STUDIED: Passerine birds.<br><br>METHODS: We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias.<br><br>RESULTS: We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently.<br><br>MAIN CONCLUSIONS: Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.}, }
@article {pmid36232445, year = {2022}, author = {Han, T and Liao, X and Zhu, Y and Liu, Y and Lu, N and Li, Y and Guo, Z and Chen, JY and He, C and Lu, Z}, title = {Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circadian Genes.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232445}, issn = {1422-0067}, mesh = {ARNTL Transcription Factors/genetics ; Animals ; *Anthozoa/genetics ; *Dinoflagellida/genetics ; Phylogeny ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.}, }
@article {pmid36230966, year = {2022}, author = {Ali, H and Pei, M and Li, H and Fang, W and Mao, H and Khan, HA and Nadeem, T and Lu, G and Olsson, S}, title = {The Wheat Head Blight Pathogen Fusarium graminearum Can Recruit Collaborating Bacteria from Soil.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36230966}, issn = {2073-4409}, mesh = {Bacteria/genetics ; Fusarium ; Gentamicins ; Plant Diseases/microbiology ; *Soil ; *Triticum/microbiology ; }, abstract = {In nature, fungal endophytes often have facultative endohyphal bacteria (FEB). Can a model plant pathogenic fungus have them, and does it affect their phenotype? We constructed a growth system/microcosm to allow an F. graminearum isolate to grow through natural soil and then re-isolated it on a gentamicin-containing medium, allowing endohyphal growth of bacteria while killing other bacteria. F. graminearum PH-1 labelled with a His1mCherry gene staining the fungal nuclei fluorescent red was used to confirm the re-isolation of the fungus. Most new re-isolates contained about 10 16SrRNA genes per fungal mCherry gene determined by qPCR. The F. graminearum + FEB holobiont isolates containing the bacteria were sub-cultured several times, and their bacterial contents were stable. Sequencing the bacterial 16SrRNA gene from several Fg-FEB holobiont isolates revealed endophytic bacteria known to be capable of nitrogen fixation. We tested the pathogenicity of one common Fg-FEB holobiont association, F. graminearum + Stenatrophomonas maltophilia, and found increased pathogenicity. The 16SrRNA gene load per fungal His1mCherry gene inside the wheat stayed the same as previously found in vitro. Finally, strong evidence was found for Fg-S. maltophilia symbiotic nitrogen fixation benefitting the fungus.}, }
@article {pmid36209500, year = {2022}, author = {Armengaud, J}, title = {Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16238}, pmid = {36209500}, issn = {1462-2920}, abstract = {In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. Innovative methods are needed to identify the taxonomic components of individual microbiota, their changes over time, and to determine how microoorganisms interact and function. Metaproteomics is based on the identification and quantification of proteins, and can potentially provide this full picture. Due to the wide molecular panorama and functional insights it provides, metaproteomics is gaining momentum in microbiome and holobiont research. Its full potential should be unleashed in the coming years with progress in speed and cost of analyses. In this exploratory crystal ball exercise, I discuss the technical and conceptual advances in metaproteomics that I expect to drive innovative research over the next few years in microbiology. I also debate the concepts of 'microbial dark matter' and 'Metaproteomics-Assembled Proteomes (MAPs)' and present some long-term prospects for metaproteomics in clinical diagnostics and personalized medicine, environmental monitoring, agriculture, and biotechnology.}, }
@article {pmid36209397, year = {2022}, author = {van Oppen, MJH and Raina, JB}, title = {Coral holobiont research needs spatial analyses at the microbial scale.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16237}, pmid = {36209397}, issn = {1462-2920}, }
@article {pmid36204199, year = {2022}, author = {Marco, S and Loredana, M and Riccardo, V and Raffaella, B and Walter, C and Luca, N}, title = {Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience.}, journal = {Horticulture research}, volume = {9}, number = {}, pages = {uhac160}, pmid = {36204199}, issn = {2662-6810}, abstract = {In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.}, }
@article {pmid36195213, year = {2023}, author = {Connor, KL and Bloise, E and DeSantis, TZ and Lye, SJ}, title = {Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity.}, journal = {The Journal of nutritional biochemistry}, volume = {111}, number = {}, pages = {109172}, doi = {10.1016/j.jnutbio.2022.109172}, pmid = {36195213}, issn = {1873-4847}, mesh = {Animals ; Female ; Mice ; Pregnancy ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Biomarkers ; *Malnutrition/metabolism ; Maternal Nutritional Physiological Phenomena ; *Neoplasm Proteins/metabolism ; RNA, Messenger ; }, abstract = {Malnutrition can influence maternal physiology and programme offspring development. Yet, in pregnancy, little is known about how dietary challenges that influence maternal phenotype affect gut structure and function. Emerging evidence suggests that interactions between the environment, multidrug resistance (MDR) transporters and microbes may influence maternal adaptation to pregnancy and regulate fetoplacental development. We hypothesized that the gut holobiont (host and microbes) during pregnancy adapts differently to suboptimal maternal diets, evidenced by changes in the gut microenvironment, morphology, and expression of key protective MDR transporters during pregnancy. Mice were fed a control diet (CON) during pregnancy, or undernourished (UN) by 30% of control intake from gestational day (GD) 5.5-18.5, or fed 60% high fat diet (HF) for 8 weeks before and during pregnancy. At GD18.5, maternal small intestinal (SI) architecture (H&amp;E), proliferation (Ki67), P-glycoprotein (P-gp - encoded by Abcb1a/b) and breast cancer resistance protein (BCRP/Abcg2) MDR transporter expression and levels of pro-inflammatory biomarkers were assessed. Circulating inflammatory biomarkers and maternal caecal microbiome composition (G3 PhyloChip[TM]) were measured. MDR transporter expression was also assessed in fetal gut. HF diet increased maternal SI crypt depth and proinflammatory load, and decreased SI expression of Abcb1a mRNA, whilst UN increased SI villi proliferation and Abcb1a, but decreased Abcg2, mRNA expression. There were significant associations between Abcb1a and Abcg2 mRNA levels with relative abundance of specific microbial taxa. Using a systems physiology approach we report that common nutritional adversities provoke adaptations in the pregnancy holobiont in mice, and reveal new mechanisms that could influence reproductive outcomes and fetal development.}, }
@article {pmid36183766, year = {2023}, author = {Nalley, EM and Tuttle, LJ and Conklin, EE and Barkman, AL and Wulstein, DM and Schmidbauer, MC and Donahue, MJ}, title = {A systematic review and meta-analysis of the direct effects of nutrients on corals.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159093}, doi = {10.1016/j.scitotenv.2022.159093}, pmid = {36183766}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll A ; Coral Reefs ; Nitrogen/pharmacology ; Nutrients ; }, abstract = {Chronic exposure of coral reefs to elevated nutrient conditions can modify the performance of the coral holobiont and shift the competitive interactions of reef organisms. Many studies have now quantified the links between nutrients and coral performance, but few have translated these studies to directly address coastal water quality standards. To address this management need, we conducted a systematic review of peer-reviewed studies, public reports, and gray literature that examined the impacts of dissolved inorganic nitrogen (DIN: nitrate, nitrite, and ammonium) and dissolved inorganic phosphorus (DIP: phosphate) on scleractinian corals. The systematic review resulted in 47 studies with comparable data on coral holobiont responses to nutrients: symbiont density, chlorophyll a (chl-a) concentration, photosynthesis, photosynthetic efficiency, growth, calcification, adult survival, juvenile survival, and fertilization. Mixed-effects meta-regression meta-analyses were used to determine the magnitude of the positive or negative effects of DIN and DIP on coral responses. Zooxanthellae density (DIN &amp; DIP), chl-a concentration (DIN), photosynthetic rate (DIN), and growth (DIP) all exhibited positive responses to nutrient addition; maximum quantum yield (DIP), growth (DIN), larval survival (DIN), and fertilization (DIN) exhibited negative responses. In lieu of developing specific thresholds for the management of nutrients as a stressor on coral reefs, we highlight important inflection points in the magnitude and direction of the effects of inorganic nutrients and identify trends among coral responses. The responses of corals to nutrients are complex, warranting conservative guidelines for elevated nutrient concentrations on coral reefs.}, }
@article {pmid36175840, year = {2022}, author = {Campana, S and Riesgo, A and Jongepier, E and Fuss, J and Muyzer, G and de Goeij, JM}, title = {Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {674}, pmid = {36175840}, issn = {1471-2164}, mesh = {Amino Acids ; Animals ; *Anthozoa/genetics ; Coral Reefs ; Dissolved Organic Matter ; Lipids ; *Microbiota ; *Porifera/genetics ; Transcriptome ; }, abstract = {BACKGROUND: Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in different abundances and with different bioavailability to sponge holobionts, it is important to understand how the metabolic activity of the host and associated microbiota change in response to the exposure to both DOM sources. Here, we look at the differential gene expression of two sponge holobionts 6 hours after feeding on naturally sourced coral- and macroalgal-DOM using RNA sequencing and meta-transcriptomic analysis.<br><br>RESULTS: We found a slight, but significant differential gene expression in the comparison between the coral- and macroalgal-DOM treatments in both the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Haliclona vansoesti. In the hosts, processes that regulate immune response, signal transduction, and metabolic pathways related to cell proliferation were elicited. In the associated microbiota carbohydrate metabolism was upregulated in both treatments, but coral-DOM induced further lipid and amino acids biosynthesis, while macroalgal-DOM caused a stress response. These differences could be driven by the presence of distinct organic macronutrients in the two DOM sources and of small pathogens or bacterial virulence factors in the macroalgal-DOM.<br><br>CONCLUSIONS: This work provides two new sponge meta-transcriptomes and a database of putative genes and genetic pathways that are involved in the differential processing of coral- versus macroalgal-DOM as food source to sponges with high and low abundances of associated microbes. These pathways include carbohydrate metabolism, signaling pathways, and immune responses. However, the differences in the meta-transcriptomic responses of the sponge holobionts after 6&#x2009;hours of feeding on the two DOM sources were small. Longer-term responses to both DOM sources should be assessed to evaluate how the metabolism and the ecological function of sponges will be affected when reefs shift from coral towards algal dominance.}, }
@article {pmid36172550, year = {2022}, author = {Wu, D and Yang, L and Gu, J and Tarkowska, D and Deng, X and Gan, Q and Zhou, W and Strnad, M and Lu, Y}, title = {A Functional Genomics View of Gibberellin Metabolism in the Cnidarian Symbiont Breviolum minutum.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {927200}, pmid = {36172550}, issn = {1664-462X}, abstract = {Dinoflagellate inhabitants of the reef-building corals exchange nutrients and signals with host cells, which often benefit the growth of both partners. Phytohormones serve as central hubs for signal integration between symbiotic microbes and their hosts, allowing appropriate modulation of plant growth and defense in response to various stresses. However, the presence and function of phytohormones in photosynthetic dinoflagellates and their function in the holobionts remain elusive. We hypothesized that endosymbiotic dinoflagellates may produce and employ phytohormones for stress responses. Using the endosymbiont of reef corals Breviolum minutum as model, this study aims to exam whether the alga employ analogous signaling systems by an integrated multiomics approach. We show that key gibberellin (GA) biosynthetic genes are widely present in the genomes of the selected dinoflagellate algae. The non-13-hydroxylation pathway is the predominant route for GA biosynthesis and the multifunctional GA dioxygenase in B. minutum has distinct substrate preference from high plants. GA biosynthesis is modulated by the investigated bleaching-stimulating stresses at both transcriptional and metabolic levels and the exogenously applied GAs improve the thermal tolerance of the dinoflagellate. Our results demonstrate the innate ability of a selected Symbiodiniaceae to produce the important phytohormone and the active involvement of GAs in the coordination and the integration of the stress response.}, }
@article {pmid36171216, year = {2022}, author = {Sardar, P and Šustr, V and Chroňáková, A and Lorenc, F and Faktorová, L}, title = {De novo metatranscriptomic exploration of gene function in the millipede holobiont.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16173}, pmid = {36171216}, issn = {2045-2322}, mesh = {Amino Acids, Essential ; Animals ; *Arthropods/genetics ; Bacteroidetes ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.}, }
@article {pmid36161195, year = {2022}, author = {Verma, NK and Tan, SJ and Chen, J and Chen, H and Ismail, MH and Rice, SA and Bifani, P and Hariharan, S and Paul, VD and Sriram, B and Dam, LC and Chan, CC and Ho, P and Goh, BC and Chung, SJ and Goh, KCM and Thong, SH and Kwa, AL and Ostrowski, A and Aung, TT and Razali, H and Low, SWY and Bhattacharyya, MS and Gautam, HK and Lakshminarayanan, R and Sicheritz-Pontén, T and Clokie, MRJ and Moreira, W and van Steensel, MAM}, title = {inPhocus: Current State and Challenges of Phage Research in Singapore.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {1}, pages = {6-11}, pmid = {36161195}, issn = {2641-6549}, abstract = {Bacteriophages and phage-derived proteins are a promising class of antibacterial agents that experience a growing worldwide interest. To map ongoing phage research in Singapore and neighboring countries, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore (NTU) and Yong Loo Lin School of Medicine, National University of Singapore (NUS) recently co-organized a virtual symposium on Bacteriophage and Bacteriophage-Derived Technologies, which was attended by more than 80 participants. Topics were discussed relating to phage life cycles, diversity, the roles of phages in biofilms and the human gut microbiome, engineered phage lysins to combat polymicrobial infections in wounds, and the challenges and prospects of clinical phage therapy. This perspective summarizes major points discussed during the symposium and new perceptions that emerged after the panel discussion.}, }
@article {pmid36160957, year = {2022}, author = {Nie, Y and Lau, SYL and Tan, X and Lu, X and Liu, S and Tahvanainen, T and Isoda, R and Ye, Q and Hashidoko, Y}, title = {Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {974251}, pmid = {36160957}, issn = {1664-462X}, abstract = {Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.}, }
@article {pmid36159890, year = {2021}, author = {Shen, A and Millard, A}, title = {Phage Genome Annotation: Where to Begin and End.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {2}, number = {4}, pages = {183-193}, pmid = {36159890}, issn = {2641-6549}, abstract = {With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.}, }
@article {pmid36157287, year = {2022}, author = {Clokie, MRJ and Sicheritz-Pontén, TE}, title = {Phage Therapy: Insights from the Past, the Great Need of the Present, and Glimpses into the Future.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {2}, pages = {65-66}, doi = {10.1089/phage.2022.29031.mcl}, pmid = {36157287}, issn = {2641-6549}, }
@article {pmid36148301, year = {2022}, author = {Tous, N and Marcos, S and Goodarzi Boroojeni, F and Pérez de Rozas, A and Zentek, J and Estonba, A and Sandvang, D and Gilbert, MTP and Esteve-Garcia, E and Finn, R and Alberdi, A and Tarradas, J}, title = {Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {884925}, pmid = {36148301}, issn = {1664-042X}, abstract = {Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.}, }
@article {pmid36147515, year = {2021}, author = {Rangel-Pineros, G and Millard, A and Michniewski, S and Scanlan, D and Sirén, K and Reyes, A and Petersen, B and Clokie, MRJ and Sicheritz-Pontén, T}, title = {From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {2}, number = {4}, pages = {194-203}, pmid = {36147515}, issn = {2641-6549}, abstract = {Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j[®] graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.}, }
@article {pmid36144461, year = {2022}, author = {Miral, A and Kautsky, A and Alves-Carvalho, S and Cottret, L and Guillerm-Erckelboudt, AY and Buguet, M and Rouaud, I and Tranchimand, S and Tomasi, S and Bartoli, C}, title = {Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144461}, issn = {2076-2607}, abstract = {As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.}, }
@article {pmid36138466, year = {2022}, author = {Keller-Costa, T and Kozma, L and Silva, SG and Toscan, R and Gonçalves, J and Lago-Lestón, A and Kyrpides, NC and Nunes da Rocha, U and Costa, R}, title = {Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {151}, pmid = {36138466}, issn = {2049-2618}, mesh = {Animals ; Ankyrins ; *Anthozoa/microbiology ; Chitin ; *Chitinases ; *Gammaproteobacteria ; Metagenomics/methods ; *Microbiota/genetics ; Oxygen ; Phylogeny ; Protein Serine-Threonine Kinases ; *Rhodobacteraceae ; Symbiosis ; }, abstract = {BACKGROUND: The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater.<br><br>RESULTS: Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity.<br><br>CONCLUSION: This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.}, }
@article {pmid36136562, year = {2022}, author = {Favero, C and Giordano, L and Mihaila, SM and Masereeuw, R and Ortiz, A and Sanchez-Niño, MD}, title = {Postbiotics and Kidney Disease.}, journal = {Toxins}, volume = {14}, number = {9}, pages = {}, pmid = {36136562}, issn = {2072-6651}, support = {860329 Marie-Curie ITN "STRATEGY-CKD"/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Humans ; *Kidney Diseases/etiology/therapy ; Prebiotics ; *Probiotics/therapeutic use ; *Synbiotics ; gamma-Aminobutyric Acid ; }, abstract = {Chronic kidney disease (CKD) is projected to become the fifth global cause of death by 2040 as a result of key shortcomings in the current methods available to diagnose and treat kidney diseases. In this regard, the novel holobiont concept, used to describe an individual host and its microbial community, may pave the way towards a better understanding of kidney disease pathogenesis and progression. Microbiota-modulating or -derived interventions include probiotics, prebiotics, synbiotics and postbiotics. As of 2019, the concept of postbiotics was updated by the International Scientific Association of Probiotics and Prebiotics (ISAPP) to refer to preparations of inanimate microorganisms and/or their components that confer a health benefit to the host. By explicitly excluding purified metabolites without a cellular biomass, any literature making use of such term is potentially rendered obsolete. We now review the revised concept of postbiotics concerning their potential clinical applications and research in kidney disease, by discussing in detail several formulations that are undergoing preclinical development such as GABA-salt for diet-induced hypertension and kidney injury, sonicated Lactobacillus paracasei in high fat diet-induced kidney injury, GABA-salt, lacto-GABA-salt and postbiotic-GABA-salt in acute kidney injury, and O. formigenes lysates for hyperoxaluria. Furthermore, we provide a roadmap for postbiotics research in kidney disease to expedite clinical translation.}, }
@article {pmid36135762, year = {2022}, author = {Ghotbi, M and Kelting, O and Blümel, M and Tasdemir, D}, title = {Gut and Gill-Associated Microbiota of the Flatfish European Plaice (Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens.}, journal = {Marine drugs}, volume = {20}, number = {9}, pages = {}, pmid = {36135762}, issn = {1660-3397}, mesh = {Animals ; Aquaculture ; Fishes ; *Flounder ; Gills ; Humans ; Metabolome ; *Methicillin-Resistant Staphylococcus aureus ; *Microbiota ; }, abstract = {Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.}, }
@article {pmid36133177, year = {2022}, author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H}, title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000405}, pmid = {36133177}, issn = {2516-8290}, abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.}, }
@article {pmid36128640, year = {2022}, author = {Perera, IU and Fujiyoshi, S and Nishiuchi, Y and Nakai, T and Maruyama, F}, title = {Zooplankton act as cruise ships promoting the survival and pathogenicity of pathogenic bacteria.}, journal = {Microbiology and immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1348-0421.13029}, pmid = {36128640}, issn = {1348-0421}, abstract = {Bacteria in general interact with zooplankton in aquatic ecosystems. These zooplankton-bacterial interactions help to shape the bacterial community by regulating bacterial abundances. Such interactions are even more significant and crucially in need of investigation in the case of pathogenic bacteria, which cause severe diseases in humans and animals. Among the many associations between a host metazoan and pathogenic bacteria, zooplankton provide nutrition and protection from stressful conditions, promote the horizontal transfer of virulence genes, and act as a mode of pathogen transport. These interactions allow the pathogen to survive and proliferate in aquatic environments and to endure water treatment processes, thereby creating a potential risk to human health. This review highlights current knowledge on the contributions of zooplankton to the survival and pathogenicity of pathogenic bacteria. We also discuss the need to consider these interactions as a risk factor in water treatment processes.}, }
@article {pmid36127636, year = {2022}, author = {Sun, X and Ciucani, MM and Rasmussen, JA and Gilbert, MTP and Sinding, MS}, title = {Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {110}, pmid = {36127636}, issn = {2730-7182}, mesh = {Animals ; Asia, Southeastern ; Borneo ; Cattle ; *Genome, Mitochondrial/genetics ; *Genomics ; }, abstract = {The banteng (Bos javanicus) is an endangered species within the wild Asian Bos complex, that has traditionally been subdivided into three geographically isolated subspecies based on (i) mainland Southeast Asia (B. j. birmanicus), (ii) Java (B. j. javanicus), and (iii) Borneo (B. j. lowi). However, analysis of a single Bornean banteng mitochondrial genome generated through a genome skimming approach was used to suggest that it may actually represent a distinct species (Ishige et al. in Mitochondrial DNA A DNA Mapp Seq Anal 27(4):2453-4. http://doi.org/10.3109/19401736.2015.1033694 , 2016). To explore this hypothesis further, we leveraged on the GenBank (NCBI) raw read sequencing data originally used to construct the mitochondrial genome and reconstructed its nuclear genome at low (0.2×) coverage. When analysed in the context of nuclear genomic data representing a broad reference panel of Asian Bos species, we find the Bornean banteng affiliates strongly with the Javan banteng, in contradiction to the expectation if the separate species hypothesis was correct. Thus, despite the Bornean banteng's unusual mitochondrial lineage, we argue there is no genomic evidence that the Bornean banteng is a distinct species.}, }
@article {pmid36127241, year = {2022}, author = {Arnault, G and Mony, C and Vandenkoornhuyse, P}, title = {Plant microbiota dysbiosis and the Anna Karenina Principle.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2022.08.012}, pmid = {36127241}, issn = {1878-4372}, abstract = {Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.}, }
@article {pmid36125280, year = {2022}, author = {Martinez, S and Grover, R and Baker, DM and Ferrier-Pagès, C}, title = {Symbiodiniaceae Are the First Site of Heterotrophic Nitrogen Assimilation in Reef-Building Corals.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0160122}, pmid = {36125280}, issn = {2150-7511}, mesh = {Animals ; *Anthozoa/metabolism ; Heterotrophic Processes ; Nitrogen/metabolism ; *Dinoflagellida ; Symbiosis ; *Ammonium Compounds/metabolism ; Amino Acids/metabolism ; }, abstract = {Coral reefs depend on the highly optimized mutualistic relationship between corals and Symbiodiniaceae dinoflagellates. Both partners exchange nutrients obtained through heterotrophy of the host and autotrophy of the symbionts. While heterotrophy helps corals withstand the harmful effects of seawater warming, the exchange of heterotrophic nutrients between the two partners is poorly understood. Here, we used compound-specific δ[15]N and δ[13]C of amino acids (δ[15]NAA and δ[13]CAA) and a [15]N pulse-chase experiment with Artemia salina nauplii in two coral-dinoflagellate associations to trace the assimilation and allocation of heterotrophic nutrients within the partners. We observed that changes in the trophic position (TPGlx-Phe), δ[15]NAA, and δ[13]CAA with heterotrophy were holobiont-dependent. Furthermore, while TPGlx-Phe and δ[15]N of all AAs significantly increased with heterotrophy in the symbionts and host of Stylophora pistillata, only the δ[15]NAA of the symbionts changed in Turbinaria reniformis. Together with the pulse-chase experiment, the results suggested a direct transfer of heterotrophically acquired AAs to the symbionts of S. pistillata and a transfer of ammonium to the symbionts of T. reniformis. Overall, we demonstrated that heterotrophy underpinned the nutrition of Symbiodinaceae and possibly influenced their stress tolerance under changing environmental conditions. IMPORTANCE Coral reefs rely upon the highly optimized nutritional symbiosis between corals and Symbiodiniaceae dinoflagellates. Heterotrophic feeding on plankton is key to the resistance of corals to environmental stress. Yet, a detailed understanding of heterotrophic nutrient assimilation and utilization within the symbiosis is lacking. Here, we used the advanced tools of compound-specific isotope analysis of amino acids and [15]N-labeling of plankton to show that heterotrophy underpinned the nutrition of Symbiodinaceae. Symbionts received either heterotrophically acquired amino acids or recycled ammonium due to their association with the coral host. This study brought new insight into the nutrient exchanges in coral-Symbiodiniaceae associations and allowed a better understanding of the mechanisms involved in coral resistance to environmental stress.}, }
@article {pmid36124627, year = {2022}, author = {Drummond, JS and Rosado, BHP}, title = {On the role in the phyllosphere community to leaf wettability and water shedding.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erac350}, pmid = {36124627}, issn = {1460-2431}, }
@article {pmid36115215, year = {2022}, author = {Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Neves, RC and Jørgensen, A and Schiøtt, M and Gilbert, MTP and Møbjerg, N}, title = {Corrigendum to "Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription" [Comparative Biochemistry and Physiology Part A: Molecular &amp; Integrative Physiology 271 (2022), 111245].}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {274}, number = {}, pages = {111317}, doi = {10.1016/j.cbpa.2022.111317}, pmid = {36115215}, issn = {1531-4332}, }
@article {pmid36115214, year = {2022}, author = {Neves, RC and Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Gilbert, MTP and Møbjerg, N}, title = {Corrigendum to "Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome" [Comparative Biochemistry and Physiology Part A: Molecular &amp; Integrative Physiology 267 (2022), 111169].}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {274}, number = {}, pages = {111316}, doi = {10.1016/j.cbpa.2022.111316}, pmid = {36115214}, issn = {1531-4332}, }
@article {pmid36112690, year = {2022}, author = {Rinsky, M and Weizman, E and Ben-Asher, HW and Eyal, G and Zhu, B and Levy, O}, title = {Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis.}, journal = {Science advances}, volume = {8}, number = {37}, pages = {eabo6467}, pmid = {36112690}, issn = {2375-2548}, support = {DP2 GM140924/GM/NIGMS NIH HHS/United States ; }, abstract = {Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.}, }
@article {pmid36110388, year = {2022}, author = {Pinacho-Guendulain, B and Montiel-Castro, AJ and Ramos-Fernández, G and Pacheco-López, G}, title = {Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates.}, journal = {Frontiers in integrative neuroscience}, volume = {16}, number = {}, pages = {876849}, pmid = {36110388}, issn = {1662-5145}, abstract = {The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.}, }
@article {pmid36100860, year = {2022}, author = {Næsborg-Nielsen, C and Eisenhofer, R and Fraser, TA and Wilkinson, V and Burridge, CP and Carver, S}, title = {Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus).}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {323}, pmid = {36100860}, issn = {1756-3305}, mesh = {Animals ; Goats/parasitology ; Humans ; *Marsupialia/parasitology ; *Mycobiome ; RNA, Ribosomal, 16S/genetics ; Sarcoptes scabiei/genetics ; *Scabies/parasitology ; Swine ; }, abstract = {BACKGROUND: Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei, causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species.<br><br>METHODS: Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat (Vombatus ursinus). We compared the alpha and beta diversity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing.<br><br>RESULTS: We detected significant changes in the microbial communities and diversity with mange in BNWs. Severely affected BNWs had lower amplicon sequence variant (ASV) richness compared to that of healthy individuals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri, Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp.<br><br>CONCLUSION: This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange.}, }
@article {pmid36100319, year = {2022}, author = {Bettenfeld, P and Cadena I Canals, J and Jacquens, L and Fernandez, O and Fontaine, F and van Schaik, E and Courty, PE and Trouvelot, S}, title = {The microbiota of the grapevine holobiont: A key component of plant health.}, journal = {Journal of advanced research}, volume = {40}, number = {}, pages = {1-15}, pmid = {36100319}, issn = {2090-1224}, mesh = {Bacteria ; Fungi ; *Microbiota ; Plant Diseases ; Plants ; }, abstract = {BACKGROUND: Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions.<br><br>AIM OF REVIEW: The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed.<br><br>This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.}, }
@article {pmid36099871, year = {2022}, author = {Bove, CB and Ingersoll, MV and Davies, SW}, title = {Help me, symbionts, you're my only hope: Approaches to accelerate our understanding of coral holobiont interactions.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icac141}, pmid = {36099871}, issn = {1557-7023}, abstract = {Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont - the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome - that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.}, }
@article {pmid36059041, year = {2022}, author = {Pei, JY and Yu, WF and Zhang, JJ and Kuo, TH and Chung, HH and Hu, JJ and Hsu, CC and Yu, KF}, title = {Mass spectrometry-based metabolomic signatures of coral bleaching under thermal stress.}, journal = {Analytical and bioanalytical chemistry}, volume = {414}, number = {26}, pages = {7635-7646}, pmid = {36059041}, issn = {1618-2650}, mesh = {Animals ; Coral Bleaching ; Betaine/metabolism ; *Anthozoa ; Mass Spectrometry ; Biomarkers/metabolism ; Amino Acids/metabolism ; *Biological Products ; Tricarboxylic Acids ; Lipids ; }, abstract = {Coral bleaching caused by climate change has resulted in large-scale coral reef decline worldwide. However, the knowledge of physiological response mechanisms of scleractinian corals under high-temperature stress is still challenging. Here, untargeted mass spectrometry-based metabolomics combining with Global Natural Product Social Molecular Networking (GNPS) was utilized to investigate the physiological response of the coral species Pavona decussata under thermal stress. A wide variety of metabolites (including lipids, fatty acids, amino acids, peptides, osmolytes) were identified as the potential biomarkers and subjected to metabolic pathway enrichment analysis. We discovered that, in the thermal-stressed P. decussata coral holobiont, (1) numerous metabolites in classes of lipids and amino acids significantly decreased, indicating an enhanced lipid hydrolysis and aminolysis that contributed to up-regulation in gluconeogenesis to meet energy demand for basic survival; (2) pantothenate and panthenol, two essential intermediates in tricarboxylic acid (TCA) cycle, were up-regulated, implying enhanced efficiency in energy production; (3) small peptides (e.g., Glu-Leu and Glu-Glu-Glu-Glu) and lyso-platelet-activating factor (lysoPAF) possibly implicated a strengthened coral immune response; (4) the down-regulation of betaine and trimethylamine N-oxide (TMAO), known as osmolyte compounds for maintaining holobiont homeostasis, might be the result of disruption of coral holobiont.}, }
@article {pmid36005488, year = {2022}, author = {Sikorskaya, TV and Ermolenko, EV and Efimova, KV and Dang, LTP}, title = {Coral Holobionts Possess Distinct Lipid Profiles That May Be Shaped by Symbiodiniaceae Taxonomy.}, journal = {Marine drugs}, volume = {20}, number = {8}, pages = {}, pmid = {36005488}, issn = {1660-3397}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Complex Mixtures ; Coral Reefs ; *Dinoflagellida ; Symbiosis ; }, abstract = {Symbiotic relationships are very important for corals. Abiotic stressors cause the acclimatization of cell membranes in symbionts, which possess different membrane acclimatization strategies. Membrane stability is determined by a unique lipid composition and, thus, the profile of thylakoid lipids can depend on coral symbiont species. We have analyzed and compared thylakoid lipidomes (mono- and digalactosyldiacylglycerols (MGDG and DGDG), sulfoquinovosyldiacylglycerols (SQDG), and phosphatidylglycerols (PG)) of crude extracts from symbiotic reef-building coral Acropora sp., the hydrocoral Millepora platyphylla, and the octocoral Sinularia flexibilis. S. flexibilis crude extracts were characterized by a very high SQDG/PG ratio, a DGDG/MGDG ratio < 1, a lower degree of galactolipid unsaturation, a higher content of SQDG with polyunsaturated fatty acids, and a thinner thylakoid membrane which may be explained by the presence of thermosensitive dinoflagellates Cladocopium C3. In contrast, crude extracts of M. platyphylla and Acropora sp. exhibited the lipidome features of thermotolerant Symbiodiniaceae. M. platyphylla and Acropora sp. colonies contained Cladocopium C3u and Cladocopium C71/C71a symbionts, respectively, and their lipidome profiles showed features that indicate thermotolerance. We suggest that an association with symbionts that exhibit the thermotolerant thylakoid lipidome features, combined with a high Symbiodiniaceae diversity, may facilitate further acclimatization/adaptation of M. platyphylla and Acropora sp. holobionts in the South China Sea.}, }
@article {pmid36001672, year = {2022}, author = {Bieker, VC and Battlay, P and Petersen, B and Sun, X and Wilson, J and Brealey, JC and Bretagnolle, F and Nurkowski, K and Lee, C and Barreiro, FS and Owens, GL and Lee, JY and Kellner, FL and van Boheeman, L and Gopalakrishnan, S and Gaudeul, M and Mueller-Schaerer, H and Lommen, S and Karrer, G and Chauvel, B and Sun, Y and Kostantinovic, B and Dalén, L and Poczai, P and Rieseberg, LH and Gilbert, MTP and Hodgins, KA and Martin, MD}, title = {Uncovering the genomic basis of an extraordinary plant invasion.}, journal = {Science advances}, volume = {8}, number = {34}, pages = {eabo5115}, pmid = {36001672}, issn = {2375-2548}, mesh = {*Ambrosia/genetics ; Europe ; Genomics ; *Introduced Species ; Sequence Analysis, DNA ; }, abstract = {Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.}, }
@article {pmid35998007, year = {2022}, author = {Indraningrat, AAG and Steinert, G and Becking, LE and Mueller, B and de Goeij, JM and Smidt, H and Sipkema, D}, title = {Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {10}, pages = {1265-1283}, pmid = {35998007}, issn = {1572-9699}, mesh = {*Anti-Bacterial Agents ; *Chloroflexi/genetics ; Complex Mixtures ; Gram-Negative Bacteria ; Gram-Positive Bacteria/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30-60 m (upper mesophotic), and 60-90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.}, }
@article {pmid35997836, year = {2022}, author = {Ide, K and Nakano, Y and Ito, M and Nishikawa, Y and Fujimura, H and Takeyama, H}, title = {The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {24}, number = {5}, pages = {871-881}, pmid = {35997836}, issn = {1436-2236}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biological Factors ; Coculture Techniques ; Coral Reefs ; RNA, Ribosomal, 16S/genetics ; Water ; }, abstract = {Coral symbionts are important members of the coral holobiont, and coral bacterial flora are essential in host health maintenance and coral conservation. Coral symbionts are affected by various environmental factors, such as seawater temperature, pH, and salinity. Although physicochemical and chemical factors have been highlighted as possible causes of these effects, the effects of water flow and the co-culture of different species corals have not been elucidated. In this study, we designed an artificial rearing environment to examine the impact of environmental and biological factors on Acropora tenuis, one of the major coral species in Okinawa, and Montipora digitata, during their co-culture. We intervened with the water flow to reveal that the movement of the rearing environment alters the bacterial flora of A. tenuis. During the rearing under captive environment, the alpha diversity of the coral microbiota increased, suggesting the establishment of rare bacteria from the ocean. No differences in the bacterial composition between the control and water flow groups were observed under the rearing conditions. However, the structure of the bacterial flora was significantly different in the co-culture group. Comparison of bacterial community succession strongly suggested that the differences observed were due to the suppressed transmission of bacteria from the ocean in the co-culture group. These results enhance our understanding of interactions between corals and shed light on the importance of regional differences and bacterial composition of coral flora.}, }
@article {pmid35992720, year = {2022}, author = {Scheuring, I and Rasmussen, JA and Bozzi, D and Limborg, MT}, title = {A strategic model of a host-microbe-microbe system reveals the importance of a joint host-microbe immune response to combat stress-induced gut dysbiosis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912806}, pmid = {35992720}, issn = {1664-302X}, abstract = {Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host-microbe-microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the spread of pathogenic strains, such as Aliivibrio sp. Even after a skin infection, the Mycoplasma does not recover; Aliivibrio sp. often remains the dominant species, or Mycoplasma-Aliivibrio coexistence was occasionally observed. We devised a model involving interactions among the host immune system, Mycoplasma sp. plus a toxin-producing pathogen. Our model embraces a complete microbiota community and is in harmony with experimental results that host-Mycoplasma mutualism prevents the spread of pathogens. Contrary, stress suppresses the host immune system allowing dominance of pathogens, and Mycoplasma does not recover after stress disappears.}, }
@article {pmid35992708, year = {2022}, author = {Stencel, A and Wloch-Salamon, D}, title = {A pluralistic view of holobionts in the context of process ontology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {911577}, pmid = {35992708}, issn = {1664-302X}, abstract = {Developing precise definitions and fine categories is an important part of the scientific endeavour, enabling fidelity of transfers of knowledge and the progress of science. Currently, as a result of research on symbiotic microorganisms, science has been flooded with discoveries which appear to undermine many commonly accepted concepts and to introduce new ones that often require updated conceptualisations. One question currently being debated concerns whether or not a holobiont can be considered an organism. Based on which concept, physiology or evolutionary, of the organism is chosen, the verdict differs. We attempt here to show how a change in perspective, from that of substance ontology into that of process ontology, is capable of reconciling opposing positions within the existing discussion and enabling the implementation of conceptual pluralism.}, }
@article {pmid35976256, year = {2022}, author = {Huang, W and Yang, E and Yu, K and Meng, L and Wang, Y and Liang, J and Huang, X and Wang, G}, title = {Lower cold tolerance of tropical Porites lutea is possibly detrimental to its migration to relatively high latitude refuges in the South China Sea.}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5339-5355}, doi = {10.1111/mec.16662}, pmid = {35976256}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll ; Cold Temperature ; Coral Reefs ; *Dinoflagellida ; }, abstract = {As high temperature stress due to climate change threatens tropical corals, cooler areas at relatively high latitudes may be potential refuges. Tolerance to low temperatures is critical in determining whether corals can successfully migrate to higher latitudes. However, the physiological and molecular adaptations that protect corals from low temperature stress are unclear. In this study, scleractinian Porites lutea samples from the tropical Xisha Islands (XS) and subtropical Daya Bay (DY) in the South China Sea were subjected to a reduction in ambient temperature from 26 to 12°C. Differences in physiological changes and gene expression were analysed. P. lutea from both XS and DY exhibited physiological bleaching under low temperature stress, and the Symbiodiniaceae density, Fv/Fm, and chlorophyll-α content were significantly reduced. Symbiosome antioxidative stress and metabolic enzyme activity first increased and then decreased. RNA-seq analysis showed that the host responded to low temperature stress by activating immune, apoptotic, and autophagic pathways and reducing metabolic levels. Nevertheless, Symbiodiniaceae lacked the physiological regulatory capacity to adapt to low temperatures. The lower cold tolerance of XS tropical P. lutea may attribute to lower oxidative stress resistance, lower photosynthetic capacity, worse energy supply, and higher susceptibility to bacterial and viral infections and diseases in XS corals. The difference in cold tolerance may result from genetic differences between the geographic populations and is possibly detrimental to the migration of tropical coral to relatively high latitude refuges. This study provides a theoretical basis for anthropogenically assisted coral migration as a response to global change.}, }
@article {pmid35965269, year = {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 {pmid35963227, year = {2022}, author = {Ip, JC and Zhang, Y and Xie, JY and Yeung, YH and Qiu, JW}, title = {Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms.}, journal = {Marine pollution bulletin}, volume = {182}, number = {}, pages = {114017}, doi = {10.1016/j.marpolbul.2022.114017}, pmid = {35963227}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll A ; Coral Reefs ; El Nino-Southern Oscillation ; Symbiosis ; Transcriptome ; }, abstract = {Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.}, }
@article {pmid35960256, year = {2022}, author = {Johnston, EC and Cunning, R and Burgess, SC}, title = {Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae).}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5368-5385}, doi = {10.1111/mec.16654}, pmid = {35960256}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {The congruence between phylogenies of tightly associated groups of organisms (cophylogeny) reflects evolutionary links between ecologically important interactions. However, despite being a classic example of an obligate symbiosis, tests of cophylogeny between scleractinian corals and their photosynthetic algal symbionts have been hampered in the past because both corals and algae contain genetically unresolved and morphologically cryptic species. Here, we studied co-occurring, cryptic Pocillopora species from Mo'orea, French Polynesia, that differ in their relative abundance across depth. We constructed new phylogenies of the host Pocillopora (using complete mitochondrial genomes, genomic loci, and thousands of single nucleotide polymorphisms) and their Symbiodiniaceae symbionts (using ITS2 and psbA[ncr] markers) and tested for cophylogeny. The analysis supported the presence of five Pocillopora species on the fore reef at Mo'orea that mostly hosted either Cladocopium latusorum or C. pacificum. Only Pocillopora species hosting C. latusorum also hosted taxa from Symbiodinium and Durusdinium. In general, the Cladocopium phylogeny mirrored the Pocillopora phylogeny. Within Cladocopium species, lineages also differed in their associations with Pocillopora haplotypes, except those showing evidence of nuclear introgression, and with depth in the two most common Pocillopora species. We also found evidence for a new Pocillopora species (haplotype 10), that has so far only been sampled from French Polynesia, that warrants formal identification. The linked phylogenies of these Pocillopora and Cladocopium species and lineages suggest that symbiont speciation is driven by niche diversification in the host, but there is still evidence for symbiont flexibility in some cases.}, }
@article {pmid35958152, year = {2022}, author = {Somera, TS and Mazzola, M}, title = {Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {949404}, pmid = {35958152}, issn = {1664-302X}, abstract = {Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to "reshape" the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.}, }
@article {pmid35943423, year = {2022}, author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV}, title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.}, journal = {Molecular ecology}, volume = {31}, number = {19}, pages = {4979-4990}, doi = {10.1111/mec.16642}, pmid = {35943423}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; DNA, Ancient ; *Dinoflagellida/genetics ; Ecosystem ; Genome ; }, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we utilized aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE to 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence aDNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.}, }
@article {pmid35918644, year = {2022}, author = {Montoya, P and Cadena, CD and Claramunt, S and Duchêne, DA}, title = {Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {95}, pmid = {35918644}, issn = {2730-7182}, mesh = {Animals ; Biological Evolution ; Birds/genetics ; Evolution, Molecular ; *Flight, Animal/physiology ; Phylogeny ; *Wings, Animal/anatomy &amp; histology ; }, abstract = {BACKGROUND: Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation).<br><br>RESULTS: We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity.<br><br>CONCLUSIONS: Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.}, }
@article {pmid35910618, year = {2022}, author = {Vad, J and Duran Suja, L and Summers, S and Henry, TB and Roberts, JM}, title = {Marine Sponges in a Snowstorm - Extreme Sensitivity of a Sponge Holobiont to Marine Oil Snow and Chemically Dispersed Oil Pollution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909853}, pmid = {35910618}, issn = {1664-302X}, abstract = {Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and "marine oil snow" contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.}, }
@article {pmid35902906, year = {2022}, author = {Morrow, KM and Pankey, MS and Lesser, MP}, title = {Community structure of coral microbiomes is dependent on host morphology.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {113}, pmid = {35902906}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; *Microbiota/genetics ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities.<br><br>RESULTS: The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community.<br><br>CONCLUSIONS: The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.}, }
@article {pmid35902758, year = {2022}, author = {Cziesielski, MJ and Liew, YJ and Cui, G and Aranda, M}, title = {Increased incompatibility of heterologous algal symbionts under thermal stress in the cnidarian-dinoflagellate model Aiptasia.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {760}, pmid = {35902758}, issn = {2399-3642}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics/metabolism ; Ecosystem ; *Sea Anemones/genetics/metabolism ; Symbiosis/genetics ; }, abstract = {Rising ocean temperatures are increasing the rate and intensity of coral mass bleaching events, leading to the collapse of coral reef ecosystems. To better understand the dynamics of coral-algae symbioses, it is critical to decipher the role each partner plays in the holobiont's thermotolerance. Here, we investigated the role of the symbiont by comparing transcriptional heat stress responses of anemones from two thermally distinct locations, Florida (CC7) and Hawaii (H2) as well as a heterologous host-symbiont combination composed of CC7 host anemones inoculated with the symbiont Breviolum minutum (SSB01) from H2 anemones (CC7-B01). We find that oxidative stress and apoptosis responses are strongly influenced by symbiont type, as further confirmed by caspase-3 activation assays, but that the overall response to heat stress is dictated by the compatibility of both partners. Expression of genes essential to symbiosis revealed a shift from a nitrogen- to a carbon-limited state only in the heterologous combination CC7-B01, suggesting a bioenergetic disruption of symbiosis during stress. Our results indicate that symbiosis is highly fine-tuned towards particular partner combinations and that heterologous host-symbiont combinations are metabolically less compatible under stress. These results are essential for future strategies aiming at increasing coral resilience using heterologous thermotolerant symbionts.}, }
@article {pmid35895230, year = {2022}, author = {Xiang, X and Poli, D and Degnan, BM and Degnan, SM}, title = {Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {24}, number = {4}, pages = {722-732}, pmid = {35895230}, issn = {1436-2236}, mesh = {Animals ; Bacteria/genetics ; Gene Expression Profiling/methods ; *Porifera/genetics/microbiology ; RNA, Messenger/genetics ; *RNA, Ribosomal ; RNA-Seq ; }, abstract = {Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.}, }
@article {pmid35895126, year = {2022}, author = {Barbato, M and Vacchini, V and Engelen, AH and Patania, G and Mapelli, F and Borin, S and Crotti, E}, title = {What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria.}, journal = {AMB Express}, volume = {12}, number = {1}, pages = {98}, pmid = {35895126}, issn = {2191-0855}, abstract = {Macroalgal surface constitutes a peculiar ecological niche and an advantageous substratum for microorganisms able to degrade the wide diversity of algal glycans. The degrading enzymatic activities of macroalgal epiphytes are of paramount interest for the industrial by-product sector and biomass resource applications. We characterized the polysaccharide hydrolytic profile of bacterial isolates obtained from three macroalgal species: the red macroalgae Asparagopsis taxiformis and Sphaerococcus coronopifolius (Rhodophyceae) and the brown Halopteris scoparia (Phaeophyceae), sampled in South Portugal. Bacterial enrichment cultures supplemented with chlorinated aliphatic compounds, typically released by marine algae, were established using as inoculum the decaying biomass of the three macroalgae, obtaining a collection of 634 bacterial strains. Although collected from the same site and exposed to the same seawater seeding microbiota, macroalgal cultivable bacterial communities in terms of functional and phylogenetic diversity showed host specificity. Isolates were tested for the hydrolysis of starch, pectin, alginate and agar, exhibiting a different hydrolytic potential according to their host: A. taxiformis showed the highest percentage of active isolates (91%), followed by S. coronopifolius (54%) and H. scoparia (46%). Only 30% of the isolates were able to degrade starch, while the other polymers were degraded by 55-58% of the isolates. Interestingly, several isolates showed promiscuous capacities to hydrolyze more than one polysaccharide. The isolate functional fingerprint was statistically correlated to bacterial phylogeny, host species and enrichment medium. In conclusion, this work depicts macroalgae as holobionts with an associated microbiota of interest for blue biotechnologies, suggesting isolation strategies and bacterial targets for polysaccharidases' discovery.}, }
@article {pmid35894614, year = {2022}, author = {Tanabe, N and Takasu, R and Hirose, Y and Kamei, Y and Kondo, M and Nakabachi, A}, title = {Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0175722}, pmid = {35894614}, issn = {2165-0497}, mesh = {Animals ; Bacillus subtilis/metabolism ; Cell Division ; *Citrus/metabolism/microbiology ; Escherichia coli/metabolism ; *Gammaproteobacteria/metabolism ; *Hemiptera/metabolism/microbiology ; *Polyketides/metabolism/pharmacology ; Symbiosis ; }, abstract = {Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri. IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.}, }
@article {pmid35889095, year = {2022}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Junca, H and Sidjabat, HE and Cano-Lozano, JA and Villamil Díaz, LM}, title = {Competitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889095}, issn = {2076-2607}, abstract = {This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.}, }
@article {pmid35884910, year = {2022}, author = {Amedei, A}, title = {Editorial of Special Issue "Pharmacomicrobiomics in Non-Communicable Disease".}, journal = {Biomedicines}, volume = {10}, number = {7}, pages = {}, pmid = {35884910}, issn = {2227-9059}, abstract = {The human superorganism, also known as the human holobiont, is a complex organism made up of host body as well as the bacteria, archaea, viruses, and fungi that live inside it along with their genes [...].}, }
@article {pmid35881247, year = {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 {pmid35868367, year = {2022}, author = {de Menezes, TA and de Freitas, MAM and Lima, MS and Soares, AC and Leal, C and Busch, MS and Tschoeke, DA and de O Vidal, L and Atella, GC and Kruger, RH and Setubal, J and Vasconcelos, AA and de Mahiques, MM and Siegle, E and Asp, NE and Cosenza, C and Hajdu, E and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Fluxes of the Amazon River plume nutrients and microbes into marine sponges.}, journal = {The Science of the total environment}, volume = {847}, number = {}, pages = {157474}, doi = {10.1016/j.scitotenv.2022.157474}, pmid = {35868367}, issn = {1879-1026}, mesh = {Animals ; Nutrients ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S ; *Rivers ; }, abstract = {Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km[2] off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ[13]C and δ[15]N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.}, }
@article {pmid35867396, year = {2022}, author = {Gerna, D and Clara, D and Allwardt, D and Mitter, B and Roach, T}, title = {Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0017222}, pmid = {35867396}, issn = {2165-0497}, mesh = {*Bacteria ; Endophytes ; Germination ; *Microbiota ; Plants ; Seeds/microbiology ; }, abstract = {Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.}, }
@article {pmid35864739, year = {2022}, author = {Martínez-Arias, C and Witzell, J and Solla, A and Martin, JA and Rodríguez-Calcerrada, J}, title = {Beneficial and pathogenic plant-microbe interactions during flooding stress.}, journal = {Plant, cell &amp; environment}, volume = {45}, number = {10}, pages = {2875-2897}, pmid = {35864739}, issn = {1365-3040}, mesh = {*Floods ; *Microbiota/physiology ; Oxygen/metabolism ; Plant Roots/metabolism ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.}, }
@article {pmid35862823, year = {2022}, author = {Loureiro, C and Galani, A and Gavriilidou, A and Chaib de Mares, M and van der Oost, J and Medema, MH and Sipkema, D}, title = {Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0035722}, pmid = {35862823}, issn = {2379-5077}, abstract = {Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.}, }
@article {pmid35862808, year = {2022}, author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA}, title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0012022}, pmid = {35862808}, issn = {2379-5077}, abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.}, }
@article {pmid35862435, year = {2022}, author = {Howe, J and Rink, JC and Wang, B and Griffin, AS}, title = {Multicellularity in animals: The potential for within-organism conflict.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {32}, pages = {e2120457119}, pmid = {35862435}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; *Cell Lineage ; Clone Cells ; Developmental Biology ; *Insecta/growth &amp; development ; Reproduction ; }, abstract = {Metazoans function as individual organisms but also as "colonies" of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicellularity focus on two aspects of development which promote cooperation and limit conflict among cells: a single-cell bottleneck, which creates organisms composed of clones, and a separation of somatic and germ cell lineages, which reduces the selective advantage of cheating. However, many obligately multicellular organisms thrive with neither, creating the potential for within-organism conflict. Here, we argue that the prevalence of such organisms throughout the Metazoa requires us to refine our preconceptions of conflict-free multicellularity. Evolutionary theory must incorporate developmental mechanisms across a broad range of organisms-such as unusual reproductive strategies, totipotency, and cell competition-while developmental biology must incorporate evolutionary principles. To facilitate this cross-disciplinary approach, we provide a conceptual overview from evolutionary biology for developmental biologists, using analogous examples in the well-studied social insects.}, }
@article {pmid35860838, year = {2022}, author = {Miral, A and Jargeat, P and Mambu, L and Rouaud, I and Tranchimand, S and Tomasi, S}, title = {Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods.}, journal = {Environmental microbiology reports}, volume = {14}, number = {6}, pages = {856-872}, doi = {10.1111/1758-2229.13105}, pmid = {35860838}, issn = {1758-2229}, mesh = {*Lichens/microbiology ; Phylogeny ; *Ascomycota ; *Microbiota ; Symbiosis ; }, abstract = {Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture-dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non-studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture-dependent techniques.}, }
@article {pmid35857470, year = {2022}, author = {Wada, N and Hsu, MT and Tandon, K and Hsiao, SS and Chen, HJ and Chen, YH and Chiang, PW and Yu, SP and Lu, CY and Chiou, YJ and Tu, YC and Tian, X and Chen, BC and Lee, DC and Yamashiro, H and Bourne, DG and Tang, SL}, title = {High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata.}, journal = {Science advances}, volume = {8}, number = {27}, pages = {eabo2431}, pmid = {35857470}, issn = {2375-2548}, abstract = {Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.}, }
@article {pmid35847106, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Xu, K and Liu, J and Zhu, W and Zhu, J and He, C and Han, C and Qin, C and Luo, H and Chen, K and Zheng, Y and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916280}, pmid = {35847106}, issn = {1664-302X}, abstract = {The host and its symbiotic bacteria form a biological entity, holobiont, in which they share a dynamic connection characterized by symbiosis, co-metabolism, and coevolution. However, how these collaborative relationships were maintained over evolutionary time remains unclear. In this research, the small non-coding RNA (sncRNA) profiles of cecum and their bacteria contents were measured from lines of chickens that have undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. The results from these lines that originated from a common founder population and maintained under the same husbandry showed an association between host intestinal sncRNA expression profile (miRNA, lncRNA fragment, mRNA fragment, snoRNA, and snRNA) and intestinal microbiota. Correlation analyses suggested that some central miRNAs and mRNA fragments had interactions with the abundance of intestinal microbial species and microbiota functions. miR-6622-3p, a significantly differentially expressed (DE) miRNA was correlated with a body weight gain related bacterium, Alistipes putredinis. Our results showed that host sncRNAs may be mediators of interaction between the host and its intestinal microbiome. This provides additional clue for holobiont concepts.}, }
@article {pmid35832387, year = {2022}, author = {Hernández, M and Mayer, MPA and Santi-Rocca, J}, title = {Editorial: The Human Microbiota in Periodontitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {952205}, pmid = {35832387}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Periodontitis ; }, }
@article {pmid35818766, year = {2022}, author = {Sánchez-Suárez, J and Díaz, L and Junca, H and Garcia-Bonilla, E and Villamil, L}, title = {Microbiome composition of the marine sponge Cliona varians at the neotropical southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae.}, journal = {Journal of applied microbiology}, volume = {133}, number = {3}, pages = {2027-2038}, doi = {10.1111/jam.15714}, pmid = {35818766}, issn = {1365-2672}, mesh = {Animals ; Archaea ; Caribbean Region ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Porifera/microbiology ; Seawater/microbiology ; }, abstract = {AIMS: This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.<br><br>METHODS AND RESULTS: We analysed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. About 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.<br><br>CONCLUSION: Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen sources.<br><br>Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystem units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.}, }
@article {pmid35816968, year = {2022}, author = {Griffin, ME and Hang, HC}, title = {Microbial mechanisms to improve immune checkpoint blockade responsiveness.}, journal = {Neoplasia (New York, N.Y.)}, volume = {31}, number = {}, pages = {100818}, pmid = {35816968}, issn = {1476-5586}, support = {R01 CA245292/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Immunotherapy ; *Microbiota ; *Neoplasms/drug therapy/genetics ; }, abstract = {The human microbiota acts as a diverse source of molecular cues that influence the development and homeostasis of the immune system. Beyond endogenous roles in the human holobiont, host-microbial interactions also alter outcomes for immune-related diseases and treatment regimens. Over the past decade, sequencing analyses of cancer patients have revealed correlations between microbiota composition and the efficacy of cancer immunotherapies such as checkpoint inhibitors. However, very little is known about the exact mechanisms that link specific microbiota with patient responses, limiting our ability to exploit these microbial agents for improved oncology care. Here, we summarize current progress towards a molecular understanding of host-microbial interactions in the context of checkpoint inhibitor immunotherapies. By highlighting the successes of a limited number of studies focused on identifying specific, causal molecules, we underscore how the exploration of specific microbial features such as proteins, enzymes, and metabolites may translate into precise and actionable therapies for personalized patient care in the clinic.}, }
@article {pmid35783967, year = {2022}, author = {Plaszkó, T and Szűcs, Z and Cziáky, Z and Ács-Szabó, L and Csoma, H and Géczi, L and Vasas, G and Gonda, S}, title = {Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish (Armoracia rusticana, Brassicaceae) Roots.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {921008}, pmid = {35783967}, issn = {1664-462X}, abstract = {The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.}, }
@article {pmid35779528, year = {2022}, author = {de Ferran, V and Figueiró, HV and de Jesus Trindade, F and Smith, O and Sinding, MS and Trinca, CS and Lazzari, GZ and Veron, G and Vianna, JA and Barbanera, F and Kliver, S and Serdyukova, N and Bulyonkova, T and Ryder, OA and Gilbert, MTP and Koepfli, KP and Eizirik, E}, title = {Phylogenomics of the world's otters.}, journal = {Current biology : CB}, volume = {32}, number = {16}, pages = {3650-3658.e4}, doi = {10.1016/j.cub.2022.06.036}, pmid = {35779528}, issn = {1879-0445}, mesh = {Animals ; Base Sequence ; *Otters/genetics ; Phylogeny ; }, abstract = {Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,[1-5] a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.}, }
@article {pmid35777916, year = {2022}, author = {Xu, P and Fan, X and Mao, Y and Cheng, H and Xu, A and Lai, W and Lv, T and Hu, Y and Nie, Y and Zheng, X and Meng, Q and Wang, Y and Cernava, T and Wang, M}, title = {Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens.}, journal = {Journal of advanced research}, volume = {39}, number = {}, pages = {49-60}, pmid = {35777916}, issn = {2090-1224}, mesh = {Bacteria ; *Camellia sinensis ; *Microbiota ; Plant Leaves/microbiology ; Plants ; Tea ; }, abstract = {INTRODUCTION: A broad spectrum of rhizosphere bacteria and fungi were shown to play a central role for health, fitness and productivity of their host plants. However, implications of host metabolism on microbiota assembly in the phyllosphere and potential consequences for holobiont functioning were sparsely addressed. Previous observations indicated that tea plants might reduce disease occurrence in various forests located in their proximity; the underlying mechanisms and potential implications of the phyllosphere microbiota remained elusive.<br><br>OBJECTIVES: This study aimed atdeciphering microbiome assembly in the tea plant phyllosphere throughout shoot development as well as elucidating potential implications of host metabolites in this process. The main focus was to explore hidden interconnections between the homeostasis of the phyllosphere microbiome and resistance to fungal pathogens.<br><br>METHODS: Profiling of host metabolites and microbiome analyses based on high-throughput sequencing were integrated to identify drivers of microbiome assembly throughout shoot development in the phyllosphere of tea plants. This was complemented by tracking of beneficial microorganisms in all compartments of the plant. Synthetic assemblages (SynAss), bioassays and field surveys were implemented to verify functioning of the phyllosphere microbiota.<br><br>RESULTS: Theophylline and epigallocatechin gallate, two prevalent metabolites at the early and late shoot development stage respectively, were identified as the main drivers of microbial community assembly. Flavobacterium and Myriangium were distinct microbial responders at the early stage, while Parabacteroides and Mortierella were more enriched at the late stage. Reconstructed, stage-specific SynAss suppressed various tree phytopathogens by 13.0%-69.3% in vitro and reduced disease incidence by 8.24%-41.3% in vivo.<br><br>CONCLUSION: The findings indicate that a functional phyllosphere microbiota was assembled along with development-specific metabolites in tea plants, which continuously suppressed prevalent fungal pathogens. The insights gained into the temporally resolved metabolite response of the tea plant microbiota could provide novel solutions for disease management.}, }
@article {pmid35775576, year = {2022}, author = {Gilbert, SF and Hadfield, MG}, title = {Symbiosis of disciplines: how can developmental biologists join conservationists in sustaining and restoring earth's biodiversity?.}, journal = {Development (Cambridge, England)}, volume = {149}, number = {13}, pages = {}, doi = {10.1242/dev.199960}, pmid = {35775576}, issn = {1477-9129}, mesh = {*Biodiversity ; Ecosystem ; Genomics ; *Symbiosis ; }, abstract = {What can developmental biology contribute toward mitigating the consequences of anthropogenic assaults on the environment and climate change? In this Spotlight article, we advocate a developmental biology that takes seriously Lynn Margulis' claim that 'the environment is part of the body'. We believe this to be a pre-condition for developmental biology playing important roles in conservation and environmental restoration. We need to forge a developmental biology of the holobiont - the multi-genomic physiologically integrated organism that is also a functional biome. To this end, we highlight how developmental biology needs to explore more deeply the interactions between developing organisms, and their chemical, physical and biotic environments.}, }
@article {pmid35773344, year = {2022}, author = {Wang, W and Tang, K and Wang, P and Zeng, Z and Xu, T and Zhan, W and Liu, T and Wang, Y and Wang, X}, title = {The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {8}, pages = {1132-1144}, pmid = {35773344}, issn = {2397-334X}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Vibrio ; Virus Activation ; }, abstract = {The coral reef microbiome is central to reef health and resilience. Competitive interactions between opportunistic coral pathogens and other commensal microbes affect the health of coral. Despite great advances over the years in sequencing-based microbial profiling of healthy and diseased coral, the molecular mechanism underlying colonization competition has been much less explored. In this study, by examining the culturable bacteria inhabiting the gastric cavity of healthy Galaxea fascicularis, a scleractinian coral, we found that temperate phages played a major role in mediating colonization competition in the coral microbiota. Specifically, the non-toxigenic Vibrio sp. inhabiting the healthy coral had a much higher colonization capacity than the coral pathogen Vibrio coralliilyticus, yet this advantage was diminished by the latter killing the former. Pathogen-encoded LodAB, which produces hydrogen peroxide, triggers the lytic cycle of prophage in the non-toxicogenic Vibrio sp. Importantly, V. coralliilyticus could outcompete other coral symbiotic bacteria (for example, Endozoicomonas sp.) through LodAB-dependent prophage induction. Overall, we reveal that LodAB can be used by pathogens as an important weapon to gain a competitive advantage over lysogenic competitors when colonizing corals.}, }
@article {pmid35767862, year = {2022}, author = {Bendová, B and Mikula, O and Vošlajerová Bímová, B and Čížková, D and Daniszová, K and Ďureje, &#x13d; and Hiadlovská, Z and Macholán, M and Martin, JF and Piálek, J and Schmiedová, L and Kreisinger, J}, title = {Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {8}, pages = {}, doi = {10.1093/femsec/fiac078}, pmid = {35767862}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mice ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are, therefore, an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under seminatural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of codivergence with their hosts. Helicobacters represent promising candidates for studying GM-host coadaptations and the fitness effects of their interactions.}, }
@article {pmid35764640, year = {2022}, author = {Cerca, J and Petersen, B and Lazaro-Guevara, JM and Rivera-Colón, A and Birkeland, S and Vizueta, J and Li, S and Li, Q and Loureiro, J and Kosawang, C and Díaz, PJ and Rivas-Torres, G and Fernández-Mazuecos, M and Vargas, P and McCauley, RA and Petersen, G and Santos-Bay, L and Wales, N and Catchen, JM and Machado, D and Nowak, MD and Suh, A and Sinha, NR and Nielsen, LR and Seberg, O and Gilbert, MTP and Leebens-Mack, JH and Rieseberg, LH and Martin, MD}, title = {The genomic basis of the plant island syndrome in Darwin's giant daisies.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3729}, pmid = {35764640}, issn = {2041-1723}, mesh = {Biological Evolution ; *DNA Transposable Elements/genetics ; *Genomics ; Synteny/genetics ; }, abstract = {The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.}, }
@article {pmid35748637, year = {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 = {46}, number = {6}, pages = {}, pmid = {35746877}, issn = {1574-6976}, mesh = {Animals ; Coral Reefs ; Ecosystem ; *Anthozoa/microbiology/physiology ; Symbiosis ; *Microbiota ; Fungi ; }, abstract = {Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.}, }
@article {pmid35729906, year = {2022}, author = {Williams, SD and Klinges, JG and Zinman, S and Clark, AS and Bartels, E and Villoch Diaz Maurino, M and Muller, EM}, title = {Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13574}, pmid = {35729906}, issn = {2167-8359}, abstract = {Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.}, }
@article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, }
@article {pmid35720593, year = {2022}, author = {Toghueo, RMK and Zabalgogeazcoa, I and Pereira, EC and Vazquez de Aldana, BR}, title = {A Diaporthe Fungal Endophyte From a Wild Grass Improves Growth and Salinity Tolerance of Tritordeum and Perennial Ryegrass.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {896755}, pmid = {35720593}, issn = {1664-462X}, abstract = {Some microbiome components can provide functions that extend the capabilities of plants, increasing the environmental adaptability and performance of holobionts. Festuca rubra subsp. pruinosa is a perennial grass adapted to rocky sea cliffs, where soil and nutrients are very limited, and exposure to salinity is continuous. This study aimed to investigate if a Diaporthe fungal endophyte belonging to the core microbiome of Festuca rubra roots could improve the performance of two agricultural grasses. In a greenhouse experiment, plants of tritordeum (Triticum durum x Hordeum chilense) and perennial ryegrass (Lolium perenne) were inoculated with Diaporthe strain EB4 and subjected to two salinity conditions (0 and 200 mM NaCl). Biomass production, mineral elements, proline, hormone profiles, antioxidant capacity, and total phenolic compounds were examined in plants, and fungal functions potentially related to the promotion of plant growth were determined. The inoculation with Diaporthe promoted plant growth of both grasses, increasing leaf biomass (84% in tritordeum and 29% in perennial ryegrass), root biomass, nutrient content (N, Ca, Mg, and Fe), and the production of indole 3-acetic acid, regardless of the salinity treatment. Improved growth and nutrient uptake might occur because Diaporthe produces several extracellular enzymes capable of recycling organic nutrient pools. In addition, the fungus produced indole 3-acetic acid in vitro and modulated the production of this phytohormone in the plant. Under salinity, the activity of Diaporthe ameliorated the stress, increasing proline, nutrient uptake in roots, gibberellins, and indole 3-acetic acid, which in turn results into improved growth. Thus, this fungus can transfer to alternative hosts some advantages useful at its original habitat.}, }
@article {pmid35718641, year = {2022}, author = {Ricci, F and Leggat, W and Page, CE and Ainsworth, TD}, title = {Coral growth anomalies, neoplasms, and tumors in the Anthropocene.}, journal = {Trends in microbiology}, volume = {30}, number = {12}, pages = {1160-1173}, doi = {10.1016/j.tim.2022.05.013}, pmid = {35718641}, issn = {1878-4380}, mesh = {Animals ; *Anthozoa ; Gene Expression Profiling ; *Neoplasms ; Coral Reefs ; }, abstract = {One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.}, }
@article {pmid35715703, year = {2022}, author = {Lan, Y and Sun, J and Chen, C and Wang, H and Xiao, Y and Perez, M and Yang, Y and Kwan, YH and Sun, Y and Zhou, Y and Han, X and Miyazaki, J and Watsuji, TO and Bissessur, D and Qiu, JW and Takai, K and Qian, PY}, title = {Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2132-2143}, pmid = {35715703}, issn = {1751-7370}, mesh = {Animals ; *Hydrothermal Vents/microbiology ; Metagenomics ; Phylogeny ; Snails/physiology ; Symbiosis/genetics ; }, abstract = {The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.}, }
@article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, }
@article {pmid35714829, year = {2022}, author = {Zhu, Y and Liao, X and Han, T and Chen, JY and He, C and Lu, Z}, title = {Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration.}, journal = {Genomics}, volume = {114}, number = {4}, pages = {110404}, doi = {10.1016/j.ygeno.2022.110404}, pmid = {35714829}, issn = {1089-8646}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; *MicroRNAs/genetics ; Symbiosis ; Transcriptome ; }, abstract = {Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.}, }
@article {pmid35698170, year = {2022}, author = {Wang, K and Gao, P and Geng, L and Liu, C and Zhang, J and Shu, C}, title = {Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {90}, pmid = {35698170}, issn = {2049-2618}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Fermentation ; Gastrointestinal Tract ; Larva ; *Lignin/metabolism ; }, abstract = {BACKGROUND: The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.<br><br>RESULTS: Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.<br><br>CONCLUSIONS: This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.}, }
@article {pmid35674443, year = {2022}, author = {Low, A and Soh, M and Miyake, S and Seedorf, H}, title = {Host Age Prediction from Fecal Microbiota Composition in Male C57BL/6J Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0073522}, pmid = {35674443}, issn = {2165-0497}, mesh = {Animals ; Bacteroidetes ; Bayes Theorem ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {The lifelong relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Microbiome composition throughout the life span of a host remains largely understudied. Here, the fecal microbiota of conventionally raised C57BL/6J male mice was characterized throughout almost the entire adult life span, from "maturing" (9 weeks) until "very old" (112 weeks) age. Our results suggest that microbiota changes occur throughout life but are more pronounced in maturing to middle-age mice than in mice later in life. Phylum-level analysis indicates a shift of the Bacteroidota-to-Firmicutes ratio in favor of Firmicutes in old and very old mice. More Firmicutes amplicon sequence variants (ASVs) were transient with varying successional patterns than Bacteroidota ASVs, which varied primarily during maturation. Microbiota configurations from five defined life phases were used as training sets in a Bayesian model, which effectively enabled the prediction of host age. These results suggest that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. The sensitivity of the age prediction to dietary perturbations was tested by applying this approach to two age-matched groups of C57BL/6J mice that were fed either a standard or western diet. The predicted age for the western diet-fed animals was on average 27 ± 11 (mean ± standard deviation) weeks older than that of standard diet-fed animals. This indicates that the fecal microbiota-based predicted age may be influenced not only by the host age and physiology but also potentially by other factors such as diet. IMPORTANCE The gut microbiome of a host changes with age. Cross-sectional studies demonstrate that microbiota of different age groups are distinct but do not demonstrate the temporal change that a longitudinal study is able to show. Here, we performed a longitudinal study of adult mice for over 2 years. We identified life stages where compositional changes were more dynamic and showed temporal changes for the more abundant species. Using a Bayesian model, we could reliably predict the life stages of the mice. Application of the same training set to mice fed different dietary regimens revealed that life-stage age predictions were possible for mice fed the same diet but less so for mice fed different diets. This study sheds light on the temporal changes that occur within the gut microbiota of laboratory mice over their life span and may inform researchers on the appropriate mouse age for their research.}, }
@article {pmid35669951, year = {2022}, author = {Jury, CP and Boeing, BM and Trapido-Rosenthal, H and Gates, RD and Toonen, RJ}, title = {Nitric oxide production rather than oxidative stress and cell death is associated with the onset of coral bleaching in Pocillopora acuta.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13321}, pmid = {35669951}, issn = {2167-8359}, abstract = {Elevated seawater temperatures associated with climate change lead to coral bleaching. While the ultimate causes of bleaching are well understood, the proximate physiological mechanisms underlying the bleaching response are not as well defined. Here we measured nitric oxide synthase activity, oxidative stress, and cell death in algal symbionts (Symbiodinaceae) freshly isolated from the reef-building coral Pocillopora acuta collected in the field under natural non-bleaching conditions and from corals experimentally exposed to elevated temperatures. Nitric oxide synthase activity in the algal symbionts was >3 orders of magnitude higher than that of the host and increased dramatically with increasing temperature and time of exposure (up to 72 h), consistent with the onset of bleaching for these corals. Oxidative stress and cell death among the algal symbionts were highest in coral holobionts exposed to intermediate as opposed to maximal temperatures, suggesting that these mechanisms are not proximal triggers for bleaching in this species. Our results point to nitric oxide production by the algal symbionts, rather than symbiont dysfunction, as a more important driver of coral bleaching under acute thermal stress in this coral.}, }
@article {pmid35654830, year = {2022}, author = {Hudspith, M and de Goeij, JM and Streekstra, M and Kornder, NA and Bougoure, J and Guagliardo, P and Campana, S and van der Wel, NN and Muyzer, G and Rix, L}, title = {Harnessing solar power: photoautotrophy supplements the diet of a low-light dwelling sponge.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2076-2086}, pmid = {35654830}, issn = {1751-7370}, mesh = {Animals ; Carbon ; Diet ; Ecosystem ; *Porifera ; *Solar Energy ; Water ; }, abstract = {The ability of organisms to combine autotrophy and heterotrophy gives rise to one of the most successful nutritional strategies on Earth: mixotrophy. Sponges are integral members of shallow-water ecosystems and many host photosynthetic symbionts, but studies on mixotrophic sponges have focused primarily on species residing in high-light environments. Here, we quantify the contribution of photoautotrophy to the respiratory demand and total carbon diet of the sponge Chondrilla caribensis, which hosts symbiotic cyanobacteria and lives in low-light environments. Although the sponge is net heterotrophic at 20 m water depth, photosynthetically fixed carbon potentially provides up to 52% of the holobiont's respiratory demand. When considering the total mixotrophic diet, photoautotrophy contributed an estimated 7% to total daily carbon uptake. Visualization of inorganic [13]C- and [15]N-incorporation using nanoscale secondary ion mass spectrometry (NanoSIMS) at the single-cell level confirmed that a portion of nutrients assimilated by the prokaryotic community was translocated to host cells. Photoautotrophy can thus provide an important supplemental source of carbon for sponges, even in low-light habitats. This trophic plasticity may represent a widespread strategy for net heterotrophic sponges hosting photosymbionts, enabling the host to buffer against periods of nutritional stress.}, }
@article {pmid35648435, year = {2022}, author = {Høie, MH and Kiehl, EN and Petersen, B and Nielsen, M and Winther, O and Nielsen, H and Hallgren, J and Marcatili, P}, title = {NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W510-5}, pmid = {35648435}, issn = {1362-4962}, abstract = {Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability to accurately predict protein structures and their functions. While such improvements are significantly impacting the fields of biology and biotechnology at large, such methods have the downside of high demands in terms of computing power and runtime, hampering their applicability to large datasets. Here, we present NetSurfP-3.0, a tool for predicting solvent accessibility, secondary structure, structural disorder and backbone dihedral angles for each residue of an amino acid sequence. This NetSurfP update exploits recent advances in pre-trained protein language models to drastically improve the runtime of its predecessor by two orders of magnitude, while displaying similar prediction performance. We assessed the accuracy of NetSurfP-3.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features, with a runtime that is up to to 600 times faster than the most commonly available methods performing the same tasks. The tool is freely available as a web server with a user-friendly interface to navigate the results, as well as a standalone downloadable package.}, }
@article {pmid35640792, year = {2022}, author = {Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Neves, RC and Jørgensen, A and Schiøtt, M and Gilbert, MTP and Møbjerg, N}, title = {Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {271}, number = {}, pages = {111245}, doi = {10.1016/j.cbpa.2022.111245}, pmid = {35640792}, issn = {1531-4332}, mesh = {Animals ; Cold Temperature ; Freezing ; *Ice ; *Tardigrada/genetics ; Temperature ; }, abstract = {Subzero temperatures are among the most significant factors defining the distribution of organisms, yet, certain taxa have evolved to overcome this barrier. The microscopic tardigrades are among the most freeze-tolerant animals, with selected species reported to survive milli-Kelvin temperatures. Here, we estimate survival of fully hydrated eutardigrades of the species Ramazzottius varieornatus following exposures to -20 °C and -80 °C as well as -196 °C with or without initial cooling to -80 °C. The tardigrades easily survive these temperatures, yet with a significant decrease in viability following rapid cooling by direct exposure to -196 °C. Hence, post-freeze recovery of R. varieornatus seems to rely on cooling rate and thus controlled ice formation. Cryophilic organisms are renowned for having cold-active enzymes that secure appropriate reaction rates at low temperatures. Hence, extreme freeze-tolerance in R. varieornatus could potentially involve syntheses of cryoprotectants and de novo transcription. We therefore generated a reference transcriptome for this cryophilic R. varieornatus population and explored for differential gene expression patterns following cooling to -80 °C as compared to active 5 °C controls. Specifically, we tested for fast transcription potentially occurring within 25 min of cooling from room temperature to a supercooling point of ca. -20 °C, at which the tardigrades presumably freeze and enter into the ametabolic state of cryobiosis. Our analyses revealed no evidence for differential gene expression. We, therefore, conclude that extreme freeze-tolerance in R. varieornatus relies on controlled extracellular freezing with any freeze-tolerance related genes being constitutively expressed.}, }
@article {pmid35639297, year = {2022}, author = {Wang, G and Liu, J and Li, Y and Li, J and Luo, J and Chen, B and Liao, Z and Su, H and Liang, J and Yu, K}, title = {Description of Prasinibacter corallicola gen. nov., sp. nov., a zeaxanthin-producing bacterium isolated from stony coral Porites lutea.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {7}, pages = {933-941}, pmid = {35639297}, issn = {1572-9699}, mesh = {Animals ; *Anthozoa/microbiology ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Ninhydrin ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Vitamin K 2/chemistry ; Zeaxanthins ; }, abstract = {Thermal stress is considered one of the main causes of mass scleractinian coral degradation; however, it is still unknown how corals can adapt to future global warming. In this study, 11 strains of coral-associated Flavobacteria were shown to produce zeaxanthin, a carotenoid antioxidant, which may help coral holobionts to alleviate thermal stress. In addition, a novel zeaxanthin-producing Flavobacterium, designated R38[T], was identified using polyphasic taxonomy. Although strain R38[T] shared a maximum 16S rRNA gene sequence similarity of 93% with Mesoflavibacter aestuarii KYW614[T], phylogenetic analyses based on whole genome and 16S rRNA gene sequences revealed that strain R38[T] forms a distinct branch in a robust cluster composed of strain R38[T] and Leptobacterium flavescens KCTC 22160[T] under the family Flavobacteriaceae. Strain R38[T] exhibited average nucleotide identities of 70.2% and 72.5% for M. aestuarii KYW614[T] and L. flavescens KCTC 22160[T], respectively. The only detected respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G + C content was 33.2 mol%. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified ninhydrin phospholipid, three unidentified ninhydrin-positive lipids, and three unidentified lipids. The major cellular fatty acids were iso - C15: 0, iso - C15: 0 ω6c, C16:2 DMA, and C13:1 ω3c. The distinct biochemical, chemotaxonomic, phylogenetic, and phylogenomic differences from validly published taxa suggest that strain R38[T] represents a new species of a new genus, for which Prasinibacter corallicola gen. nov., sp. nov. is proposed. The type strain R38[T] (= MCCC 1K03889[T] = KCTC 72444[T]).}, }
@article {pmid35635927, year = {2022}, author = {Zwart, H}, title = {"Love is a microbe too": Microbiome dialectics.}, journal = {Endeavour}, volume = {46}, number = {1-2}, pages = {100816}, doi = {10.1016/j.endeavour.2022.100816}, pmid = {35635927}, issn = {1873-1929}, mesh = {Human Genome Project ; Humans ; Language ; *Microbiota ; Symbiosis ; }, abstract = {Whereas the Human Genome Project was an anthropocentric research endeavour, microbiome research entails a much more interactive and symbiotic view of human existence, seeing human beings as holobionts, a term coined by Lynn Margulis to emphasise the interconnectedness and multiplicity of organisms. In this paper, building on previous authors, a dialectical perspective on microbiome research will be adopted, striving to supersede the ontological divide between self and other, humans and microbes, and to incorporate the microbiome as a crucial dimension of human existence, not only corporally, but also in terms of mood and cognition. On the practical level, microbiome insights promise to offer opportunities for self-care and self-management, allowing us to consciously interact with our microbiome to foster wellness and health. How to distinguish realistic scenarios from hype? Here again, an interactive (dialectical) approach is adopted, arguing that practices of the self should result from mutual learning between laboratory research and life-world experience.}, }
@article {pmid35630391, year = {2022}, author = {Hernandez, J and Rhimi, S and Kriaa, A and Mariaule, V and Boudaya, H and Drut, A and Jablaoui, A and Mkaouar, H and Saidi, A and Biourge, V and Borgi, MA and Rhimi, M and Maguin, E}, title = {Domestic Environment and Gut Microbiota: Lessons from Pet Dogs.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630391}, issn = {2076-2607}, abstract = {Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota-host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.}, }
@article {pmid35620601, year = {2022}, author = {Lin, S and Yu, K and Zhou, Z}, title = {Editorial: Physiological Regulation and Homeostasis Among Coral Holobiont Partners.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {921401}, pmid = {35620601}, issn = {1664-042X}, }
@article {pmid35619157, year = {2022}, author = {Sahu, KP and Kumar, A and Sakthivel, K and Reddy, B and Kumar, M and Patel, A and Sheoran, N and Gopalakrishnan, S and Prakash, G and Rathour, R and Gautam, RK}, title = {Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {28}, pmid = {35619157}, issn = {2524-6372}, abstract = {BACKGROUND: With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future.<br><br>RESULTS: The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network&#xa0;analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings.<br><br>CONCLUSIONS: PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.}, }
@article {pmid35609205, year = {2022}, author = {Demarchi, B and Stiller, J and Grealy, A and Mackie, M and Deng, Y and Gilbert, T and Clarke, J and Legendre, LJ and Boano, R and Sicheritz-Pontén, T and Magee, J and Zhang, G and Bunce, M and Collins, MJ and Miller, G}, title = {Ancient proteins resolve controversy over the identity of Genyornis eggshell.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {e2109326119}, doi = {10.1073/pnas.2109326119}, pmid = {35609205}, issn = {1091-6490}, abstract = {SignificanceThe controversy over the taxonomic identity of the eggs exploited by Australia's first people around 50,000 y ago is resolved. The birds that laid these eggs are extinct, and distinguishing between two main candidates, a giant flightless "mihirung" Genyornis and a large megapode Progura, had proven impossible using morphological and geochemical methods. Ancient DNA sequencing remains inconclusive because of the age and burial temperature of the eggshell. In contrast, ancient protein sequences recovered from the eggshell enabled estimation of the evolutionary affinity between the egg and a range of extant taxa. The eggs are those of a Galloanseres (a group that includes extinct Dromornithidae, as well as extant landfowl and waterfowl), Genyornis, and not of the megapode (Megapodiidae, crown Galliformes).}, }
@article {pmid35604942, year = {2022}, author = {Ørsted, M and Yashiro, E and Hoffmann, AA and Kristensen, TN}, title = {Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness.}, journal = {PLoS genetics}, volume = {18}, number = {5}, pages = {e1010206}, pmid = {35604942}, issn = {1553-7404}, mesh = {Animals ; Drosophila melanogaster/genetics ; *Genetic Fitness ; Genetic Variation ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is becoming increasingly clear that microbial symbionts influence key aspects of their host's fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.}, }
@article {pmid35604874, year = {2022}, author = {Snelders, NC and Rovenich, H and Thomma, BPHJ}, title = {Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {5}, pages = {}, pmid = {35604874}, issn = {1574-6976}, mesh = {Animals ; Fungi ; Mammals ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.}, }
@article {pmid35602056, year = {2022}, author = {Ren, CG and Kong, CC and Liu, ZY and Zhong, ZH and Yang, JC and Wang, XL and Qin, S}, title = {A Perspective on Developing a Plant 'Holobiont' for Future Saline Agriculture.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {763014}, pmid = {35602056}, issn = {1664-302X}, abstract = {Soil salinity adversely affects plant growth and has become a major limiting factor for agricultural development worldwide. There is a continuing demand for sustainable technology innovation in saline agriculture. Among various bio-techniques being used to reduce the salinity hazard, symbiotic microorganisms such as rhizobia and arbuscular mycorrhizal (AM) fungi have proved to be efficient. These symbiotic associations each deploy an array of well-tuned mechanisms to provide salinity tolerance for the plant. In this review, we first comprehensively cover major research advances in symbiont-induced salinity tolerance in plants. Second, we describe the common signaling process used by legumes to control symbiosis establishment with rhizobia and AM fungi. Multi-omics technologies have enabled us to identify and characterize more genes involved in symbiosis, and eventually, map out the key signaling pathways. These developments have laid the foundation for technological innovations that use symbiotic microorganisms to improve crop salt tolerance on a larger scale. Thus, with the aim of better utilizing symbiotic microorganisms in saline agriculture, we propose the possibility of developing non-legume 'holobionts' by taking advantage of newly developed genome editing technology. This will open a new avenue for capitalizing on symbiotic microorganisms to enhance plant saline tolerance for increased sustainability and yields in saline agriculture.}, }
@article {pmid35590396, year = {2022}, author = {Unzueta-Martínez, A and Scanes, E and Parker, LM and Ross, PM and O'Connor, W and Bowen, JL}, title = {Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {32}, pmid = {35590396}, issn = {2524-4671}, 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}, abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35589814, year = {2022}, author = {Drury, C and Bean, NK and Harris, CI and Hancock, JR and Huckeba, J and H, CM and Roach, TNF and Quinn, RA and Gates, RD}, title = {Intrapopulation adaptive variance supports thermal tolerance in a reef-building coral.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {486}, pmid = {35589814}, issn = {2399-3642}, mesh = {Animals ; *Anthozoa/genetics ; Chromatography, Liquid ; Coral Reefs ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Coral holobionts are multi-species assemblages, which adds significant complexity to genotype-phenotype connections underlying ecologically important traits like coral bleaching. Small scale heterogeneity in bleaching is ubiquitous in the absence of strong environmental gradients, which provides adaptive variance needed for the long-term persistence of coral reefs. We used RAD-seq, qPCR and LC-MS/MS metabolomics to characterize host genomic variation, symbiont community and biochemical correlates in two bleaching phenotypes of the vertically transmitting coral Montipora capitata. Phenotype was driven by symbiosis state and host genetic variance. We documented 5 gene ontologies that were significantly associated with both the binary bleaching phenotype and symbiont composition, representing functions that confer a phenotype via host-symbiont interactions. We bred these corals and show that symbiont communities were broadly conserved in bulk-crosses, resulting in significantly higher survivorship under temperature stress in juveniles, but not larvae, from tolerant parents. Using a select and re-sequence approach, we document numerous gene ontologies selected by heat stress, some of which (cell signaling, antioxidant activity, pH regulation) have unique selection dynamics in larvae from thermally tolerant parents. These data show that vertically transmitting corals may have an adaptive advantage under climate change if host and symbiont variance interact to influence bleaching phenotype.}, }
@article {pmid35588270, year = {2022}, author = {Bashir, F and Kovács, S and Ábrahám, &#xc1; and Nagy, K and Ayaydin, F and Valkony-Kelemen, I and Ferenc, G and Galajda, P and Tóth, SZ and Sass, L and Kós, PB and Vass, I and Szabó, M}, title = {Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform.}, journal = {Lab on a chip}, volume = {22}, number = {16}, pages = {2986-2999}, doi = {10.1039/d2lc00130f}, pmid = {35588270}, issn = {1473-0189}, mesh = {Animals ; *Anthozoa/physiology ; *Dinoflagellida/physiology ; Microfluidics ; Protoplasts ; Reactive Oxygen Species ; Singlet Oxygen ; }, abstract = {Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.}, }
@article {pmid35579919, year = {2022}, author = {Soldan, R and Fusi, M and Preston, GM}, title = {Approaching the domesticated plant holobiont from a community evolution perspective.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {5}, pages = {}, doi = {10.1099/mic.0.001188}, pmid = {35579919}, issn = {1465-2080}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R009236/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Microbiota/genetics ; Phenotype ; *Plants ; }, abstract = {Plants establish a pivotal relationship with their microbiome and are often conceptualized as holobionts. Nonetheless, holobiont theories have attracted much criticism, especially concerning the fact that the holobiont is rarely a unit of selection. In previous work, we discussed how the plant microbiome can be considered to be an 'ecosystem on a leash', which is subject to the influence of natural selection acting on plant traits. We proposed that in domesticated plants the assembly of the plant microbiome can usefully be conceptualized as being subject to a 'double leash', which encompasses both the effect of artificial selection imposed by the domesticator on plant traits and the leash from the plant to the microbiome. Here we approach the domesticated plant holobiont, simply defined as a community of organisms, from a community evolution point of view, and show how community heritability (a measure of community selection) complements the 'double-leash' framework in providing a community-level view of plant domestication and its impact on plant-microbe interactions. We also propose simple experiments that could be performed to investigate whether plant domestication has altered the potential for community selection at the holobiont level.}, }
@article {pmid35578838, year = {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 {pmid35568404, year = {2022}, author = {Chen, Y and Pan, T and Chai, G and Li, Z}, title = {Complete genome of Mycetocola spongiae MSC19[T] isolated from deep-sea sponge Cacospongia mycofijiensis indicates the adaptation to deep-sea environment and sponge-microbe symbioses.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100955}, doi = {10.1016/j.margen.2022.100955}, pmid = {35568404}, issn = {1876-7478}, mesh = {*Actinomycetales ; Animals ; Bacteria ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Porifera/microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Genome of Mycetocola spongiae MSC19[T], a novel marine sponge-associated Actinobacteria isolated from the Mariana Trench sponge Cacospongia mycofijiensis, was sequenced. The genome has one circular chromosome of 3,196,754 bp, with an average GC content of 66.43 mol%, and 2887 coding sequences. Gene annotation shows that M. spongiae MSC19[T] possesses series of genes related to adaptation to deep-sea environmental stresses including cold shock, heat shock, osmotic stress and oxidative stress. Genes encoding for heavy metal resistance, multidrug resistance and multiple natural product biosynthesis which are crucial for survival in the extreme environment are also detected in the genome. The potentials to synthesize kinds of vitamins and eukaryotic-like proteins indicates the possible nutrient exchange and mutual recognization between M. spongiae MSC19[T] and its sponge host. The genome provides insights into the stress resistance and ecological fitness of bacterial symbionts in the deep-sea sponge holobionts.}, }
@article {pmid35546350, year = {2022}, author = {Chua, PYS and Rasmussen, JA}, title = {Taking metagenomics under the wings.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {8}, pages = {447}, pmid = {35546350}, issn = {1740-1534}, mesh = {Animals ; *Metagenomics ; *Wings, Animal ; }, }
@article {pmid35538057, year = {2022}, author = {Patrono, LV and Vrancken, B and Budt, M and Düx, A and Lequime, S and Boral, S and Gilbert, MTP and Gogarten, JF and Hoffmann, L and Horst, D and Merkel, K and Morens, D and Prepoint, B and Schlotterbeck, J and Schuenemann, VJ and Suchard, MA and Taubenberger, JK and Tenkhoff, L and Urban, C and Widulin, N and Winter, E and Worobey, M and Schnalke, T and Wolff, T and Lemey, P and Calvignac-Spencer, S}, title = {Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2314}, pmid = {35538057}, issn = {2041-1723}, support = {R01 HG006139/HG/NHGRI NIH HHS/United States ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genome, Viral/genetics ; Genomics ; Humans ; *Influenza A Virus, H1N1 Subtype/genetics ; *Influenza A virus/genetics ; *Influenza, Human/epidemiology/genetics ; }, abstract = {The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.}, }
@article {pmid35537882, year = {2022}, author = {Oláh, P and Szlávicz, E and Kuchner, M and Nemmer, J and Zeeuwen, P and Lefèvre-Utile, A and Fyhrquist, N and Prast-Nielsen, S and Skoog, T and Serra, A and Rodríguez, E and Raap, U and Meller, S and Gyulai, R and Hupé, P and Kere, J and Levi-Schaffer, F and Tsoka, S and Alexander, H and Nestle, FO and Schröder, JM and Weidinger, S and van den Bogaard, E and Soumelis, V and Greco, D and Barker, J and Lauerma, A and Ranki, A and Andersson, B and Alenius, H and Homey, B}, title = {Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation.}, journal = {Journal of dermatological science}, volume = {106}, number = {3}, pages = {132-140}, doi = {10.1016/j.jdermsci.2022.04.007}, pmid = {35537882}, issn = {1873-569X}, mesh = {*Dermatitis, Atopic/metabolism ; Filaggrin Proteins/*metabolism ; Host Microbial Interactions/genetics ; Humans ; Inflammation/genetics/metabolism ; Intermediate Filament Proteins/genetics/metabolism ; Mutation ; Skin/metabolism ; Staphylococcus aureus ; }, abstract = {BACKGROUND: Loss-of-function mutations in the filaggrin (FLG) gene directly alter skin barrier function and critically influence atopic inflammation. While skin barrier dysfunction, Th2-associated inflammation and bacterial dysbiosis are well-known characteristics of atopic dermatitis (AD), the mechanisms interconnecting genotype, transcriptome and microbiome remain largely elusive.<br><br>OBJECTIVE: In-depth analysis of FLG genotype-associated skin gene expression alterations and host-microbe interactions in AD.<br><br>METHODS: Multi-omics characterization of a cohort of AD patients carrying heterozygous loss-of-function mutations in the FLG gene (AD[Mut]) (n&#xa0;=&#xa0;15), along with matched wild-type (AD[Wt]) patients and healthy controls. Detailed clinical characterization, microarray gene expression and 16&#xa0;S rRNA-based microbial marker gene data were generated and analyzed.<br><br>RESULTS: In the context of filaggrin dysfunction, the transcriptome was characterized by dysregulation of barrier function and water homeostasis, while the lesional skin of AD[Wt] demonstrated the specific upregulation of pro-inflammatory cytokines and T-cell proliferation. S. aureus dominated the microbiome in both patient groups, however, shifting microbial communities could be observed when comparing healthy with non-lesional AD[Wt] or AD[Mut] skin, offering the opportunity to identify microbe-associated transcriptomic signatures. Moreover, an AD core signature with 28 genes, including CCL13, CCL18, BTC, SCIN, RAB31 and PCLO was identified.<br><br>CONCLUSIONS: Our integrative approach provides molecular insights for the concept that FLG loss-of-function mutations are a genetic shortcut to atopic inflammation and unravels the complex interplay between genotype, transcriptome and microbiome in the human holobiont.}, }
@article {pmid35537462, year = {2022}, author = {Cowen, LJ and Putnam, HM}, title = {Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.}, journal = {Annual review of biomedical data science}, volume = {5}, number = {}, pages = {205-231}, doi = {10.1146/annurev-biodatasci-122120-030732}, pmid = {35537462}, issn = {2574-3414}, mesh = {Animals ; *Anthozoa/genetics ; Computational Biology ; Coral Reefs ; *Microbiota/genetics ; Symbiosis/genetics ; }, abstract = {Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience.}, }
@article {pmid35524305, year = {2022}, author = {Carrier, TJ and Maldonado, M and Schmittmann, L and Pita, L and Bosch, TCG and Hentschel, U}, title = {Symbiont transmission in marine sponges: reproduction, development, and metamorphosis.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {100}, pmid = {35524305}, issn = {1741-7007}, mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S ; Reproduction ; Symbiosis ; }, abstract = {Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.}, }
@article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0067922}, pmid = {35502903}, issn = {2150-7511}, mesh = {Animals ; Bacteria/genetics ; *Cestoda/genetics ; Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Parasites ; }, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, }
@article {pmid35482345, year = {2022}, author = {Gennery, AR}, title = {Seek and you shall find: immune lymphoid cells in holobiont health.}, journal = {Blood}, volume = {139}, number = {17}, pages = {2577-2578}, doi = {10.1182/blood.2022015801}, pmid = {35482345}, issn = {1528-0020}, mesh = {*Dysbiosis ; Humans ; Immunity, Mucosal ; Interleukin Receptor Common gamma Subunit ; Janus Kinase 3 ; Lymphocytes ; Severe Combined Immunodeficiency ; *Transplants ; }, }
@article {pmid35481756, year = {2022}, author = {Bell, JK and Mamet, SD and Helgason, B and Siciliano, SD}, title = {Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {10}, pages = {e0027322}, pmid = {35481756}, issn = {1098-5336}, mesh = {*Brassica napus/microbiology ; Plant Breeding ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection. IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.}, }
@article {pmid35480035, year = {2022}, author = {Zhang, XY and Wang, DH}, title = {Gut Microbial Community and Host Thermoregulation in Small Mammals.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {888324}, pmid = {35480035}, issn = {1664-042X}, abstract = {The endotherms, particularly the small mammals living in the polar region and temperate zone, are faced with extreme challenges for maintaining stable core body temperatures in harsh cold winter. The non-hibernating small mammals increase metabolic rate including obligatory thermogenesis (basal/resting metabolic rate, BMR/RMR) and regulatory thermogenesis (mainly nonshivering thermogenesis, NST, in brown adipose tissue and skeletal muscle) to maintain thermal homeostasis in cold conditions. A substantial amount of evidence indicates that the symbiotic gut microbiota are sensitive to air temperature, and play an important function in cold-induced thermoregulation, via bacterial metabolites and byproducts such as short-chain fatty acids and secondary bile acids. Cold signal is sensed by specific thermosensitive transient receptor potential channels (thermo-TRPs), and then norepinephrine (NE) is released from sympathetic nervous system (SNS) and thyroid hormones also increase to induce NST. Meanwhile, these neurotransmitters and hormones can regulate the diversity and compositions of the gut microbiota. Therefore, cold-induced NST is controlled by both Thermo-TRPs-SNS-gut microbiota axis and thyroid-gut microbiota axis. Besides physiological thermoregulation, small mammals also rely on behavioral regulation, such as huddling and coprophagy, to maintain energy and thermal homeostasis, and the gut microbial community is involved in these processes. The present review summarized the recent progress in the gut microbiota and host physiological and behavioral thermoregulation in small mammals for better understanding the evolution and adaption of holobionts (host and symbiotic microorganism). The coevolution of host-microorganism symbionts promotes individual survival, population maintenance, and species coexistence in the ecosystems with complicated, variable environments.}, }
@article {pmid35476981, year = {2022}, author = {Weagley, JS and Zaydman, M and Venkatesh, S and Sasaki, Y and Damaraju, N and Yenkin, A and Buchser, W and Rodionov, DA and Osterman, A and Ahmed, T and Barratt, MJ and DiAntonio, A and Milbrandt, J and Gordon, JI}, title = {Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.}, journal = {Cell reports}, volume = {39}, number = {4}, pages = {110738}, pmid = {35476981}, issn = {2211-1247}, support = {R37 NS065053/NS/NINDS NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 NS087632/NS/NINDS NIH HHS/United States ; RF1 AG013730/AG/NIA NIH HHS/United States ; R01 NS119812/NS/NINDS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; U2C DK119886/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/metabolism ; Child ; Cyclic ADP-Ribose ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; *Malnutrition ; Mice ; NAD/metabolism ; NAD+ Nucleosidase/metabolism ; Receptors, Interleukin-1 ; }, abstract = {Perturbed gut microbiome development has been linked to childhood malnutrition. Here, we characterize bacterial Toll/interleukin-1 receptor (TIR) protein domains that metabolize nicotinamide adenine dinucleotide (NAD), a co-enzyme with far-reaching effects on human physiology. A consortium of 26 human gut bacterial strains, representing the diversity of TIRs observed in the microbiome and the NAD hydrolase (NADase) activities of a subset of 152 bacterial TIRs assayed in vitro, was introduced into germ-free mice. Integrating mass spectrometry and microbial RNA sequencing (RNA-seq) with consortium membership manipulation disclosed that a variant of cyclic-ADPR (v-cADPR-x) is a specific product of TIR NADase activity and a prominent, colonization-discriminatory, taxon-specific metabolite. Guided by bioinformatic analyses of biochemically validated TIRs, we find that acute malnutrition is associated with decreased fecal levels of genes encoding TIRs known or predicted to generate v-cADPR-x, as well as decreased levels of the metabolite itself. These results underscore the need to consider microbiome TIR NADases when evaluating NAD metabolism in the human holobiont.}, }
@article {pmid35459887, year = {2022}, author = {Yang, J and Shin, TS and Kim, JS and Jee, YK and Kim, YK}, title = {A new horizon of precision medicine: combination of the microbiome and extracellular vesicles.}, journal = {Experimental &amp; molecular medicine}, volume = {54}, number = {4}, pages = {466-482}, pmid = {35459887}, issn = {2092-6413}, mesh = {Cell Communication ; *Exosomes/metabolism ; *Extracellular Vesicles/metabolism ; Humans ; *Microbiota ; Precision Medicine ; }, abstract = {Over several decades, the disease pattern of intractable disease has changed from acute infection to chronic disease accompanied by immune and metabolic dysfunction. In addition, scientific evidence has shown that humans are holobionts; of the DNA in humans, 1% is derived from the human genome, and 99% is derived from microbial genomes (the microbiome). Extracellular vesicles (EVs) are lipid bilayer-delimited nanoparticles and key messengers in cell-to-cell communication. Many publications indicate that microbial EVs are both positively and negatively involved in the pathogenesis of various intractable diseases, including inflammatory diseases, metabolic disorders, and cancers. Microbial EVs in feces, blood, and urine show significant differences in their profiles between patients with a particular disease and healthy subjects, demonstrating the potential of microbial EVs as biomarkers for disease diagnosis, especially for assessing disease risk. Furthermore, microbial EV therapy offers a variety of advantages over live biotherapeutics and human cell EV (or exosome) therapy for the treatment of intractable diseases. In summary, microbial EVs are a new tool in medicine, and microbial EV technology might provide us with innovative diagnostic and therapeutic solutions in precision medicine.}, }
@article {pmid35452284, year = {2022}, author = {Field, MA and Yadav, S and Dudchenko, O and Esvaran, M and Rosen, BD and Skvortsova, K and Edwards, RJ and Keilwagen, J and Cochran, BJ and Manandhar, B and Bustamante, S and Rasmussen, JA and Melvin, RG and Chernoff, B and Omer, A and Colaric, Z and Chan, EKF and Minoche, AE and Smith, TPL and Gilbert, MTP and Bogdanovic, O and Zammit, RA and Thomas, T and Aiden, EL and Ballard, JWO}, title = {The Australian dingo is an early offshoot of modern breed dogs.}, journal = {Science advances}, volume = {8}, number = {16}, pages = {eabm5944}, pmid = {35452284}, issn = {2375-2548}, mesh = {Animals ; Australia ; Breeding ; *Canidae/genetics ; Dogs ; Phylogeny ; *Wolves/genetics ; }, abstract = {Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.}, }
@article {pmid35444618, year = {2022}, author = {Happel, L and Rondon, R and Font, A and González-Aravena, M and Cárdenas, CA}, title = {Stability of the Microbiome of the Sponge Mycale (Oxymycale) acerata in the Western Antarctic Peninsula.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {827863}, pmid = {35444618}, issn = {1664-302X}, abstract = {The sponge microbiome, especially in Low Microbial Abundance (LMA) species, is expected to be influenced by the local environment; however, contrasting results exist with evidence showing that host specificity is also important, hence suggesting that the microbiome is influenced by host-specific and environmental factors. Despite sponges being important members of Southern Ocean benthic communities, their relationships with the microbial communities they host remain poorly studied. Here, we studied the spatial and temporal patterns of the microbiota associated with the ecologically important LMA sponge M. acerata at sites along ∼400 km of the Western Antarctic Peninsula (WAP) to assess patterns in the core and variable microbial components of the symbiont communities of this sponge species. The analyses of 31 samples revealed that the microbiome of M. acerata is composed of 35 prokaryotic phyla (3 Archaea, 31 Bacteria, and one unaffiliated), being mainly dominated by Proteobacteria with Gammaproteobacteria as the most dominant class. The core community was composed of six prokaryotic OTUs, with gammaproteobacterial OTU (EC94 Family), showing a mean abundance over 65% of the total abundance. Despite some differences in rare OTUs, the core community did not show clear patterns in diversity and abundance associated with specific sites/environmental conditions, confirming a low variability in community structure of this species along the WAP. The analysis at small scale (Doumer Island, Palmer Archipelago) showed no differences in space and time in the microbiome M. acerata collected at sites around the island, sampled in three consecutive years (2016-2018). Our results highlight the existence of a low spatial and temporal variability in the microbiome of M. acerata, supporting previous suggestions based on limited studies on this and other Antarctic sponges.}, }
@article {pmid35444262, year = {2022}, author = {Pogoreutz, C and Oakley, CA and Rädecker, N and Cárdenas, A and Perna, G and Xiang, N and Peng, L and Davy, SK and Ngugi, DK and Voolstra, CR}, title = {Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1883-1895}, pmid = {35444262}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; Cues ; *Gammaproteobacteria/genetics ; Proteomics ; Symbiosis ; Tissue Extracts ; }, abstract = {Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.}, }
@article {pmid35435631, year = {2022}, author = {Roggatz, CC and Hardege, JD and Saha, M}, title = {Correction to: Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions.}, journal = {Journal of chemical ecology}, volume = {48}, number = {4}, pages = {474}, doi = {10.1007/s10886-022-01357-3}, pmid = {35435631}, issn = {1573-1561}, }
@article {pmid35432258, year = {2022}, author = {Zhu, W and Liu, X and Zhu, M and Li, X and Yin, H and Huang, J and Wang, A and Li, X}, title = {Responses of Symbiodiniaceae Shuffling and Microbial Community Assembly in Thermally Stressed Acropora hyacinthus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {832081}, pmid = {35432258}, issn = {1664-302X}, abstract = {Although the importance of coral holobionts is widely accepted, the relationship between the flexibility of the microbial structure and the coral host is very complicated. Particularly, the community dynamics of holobionts and the stability of host-microbe interactions under different thermal stresses remain largely unknown. In the present study, we holistically explored the physiology and growth of Acropora hyacinthus in response to increased temperatures (from 26 to 33°C). We observed that bleaching corals with loss of algal symbionts reduced lipids and proteins to maintain their survival, leading to decreased tissue biomass and retarded growth. The diversity of Symbiodiniaceae and symbiont shuffling in the community structure was mainly caused by alterations in the relative abundance of the thermally sensitive but dominant clade C symbionts and low abundance of "background types." Bacterial diversity showed a decreasing trend with increasing temperature, whereas no significant shifts were observed in the bacterial community structure. This finding might be attributed to the local adjustment of specific microbial community members that did not affect the overall metabolic state of the coral holobiont, and there was no increase in the proportion of sequences identified as typically pathogenic or opportunistic taxa. The Sloan neutral community model showed that neutral processes could explain 42.37-58.43% of bacterial community variation. The Stegen null model analysis indicates that the stochastic processes explain a significantly higher proportion of community assembly than deterministic processes when the temperature was elevated. The weak effect of temperature on the bacterial community structure and assembly might be related to an increase in stochastic dominance. The interaction of bacterial communities exhibits a fluctuating and simplistic trend with increasing temperature. Moreover, temperature increases were sufficient to establish the high stability of bacterial networks, and a non-linear response was found between the complexity and stability of the networks. Our findings collectively provide new insights into successive changes in the scleractinian coral host and holobionts in response to elevated seawater temperatures, especially the contribution of the community assembly process and species coexistence patterns to the maintenance of the coral-associated bacterial community.}, }
@article {pmid35432234, year = {2022}, author = {Quintanilla, E and Rodrigues, CF and Henriques, I and Hilário, A}, title = {Microbial Associations of Abyssal Gorgonians and Anemones (&gt;4,000 m Depth) at the Clarion-Clipperton Fracture Zone.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828469}, pmid = {35432234}, issn = {1664-302X}, abstract = {Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.}, }
@article {pmid35428831, year = {2022}, author = {Berlinghof, J and Peiffer, F and Marzocchi, U and Munari, M and Quero, GM and Dennis, L and Wild, C and Cardini, U}, title = {The role of epiphytes in seagrass productivity under ocean acidification.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6249}, pmid = {35428831}, issn = {2045-2322}, mesh = {*Alismatales/physiology ; Carbon Dioxide ; Hydrogen-Ion Concentration ; Plant Leaves ; *Seawater/chemistry ; }, abstract = {Ocean Acidification (OA), due to rising atmospheric CO2, can affect the seagrass holobiont by changing the plant's ecophysiology and the composition and functioning of its epiphytic community. However, our knowledge of the role of epiphytes in the productivity of the seagrass holobiont in response to environmental changes is still very limited. CO2 vents off Ischia Island (Italy) naturally reduce seawater pH, allowing to investigate the adaptation of the seagrass Posidonia oceanica L. (Delile) to OA. Here, we analyzed the percent cover of different epiphytic groups and the epiphytic biomass of P. oceanica leaves, collected inside (pH 6.9-7.9) and outside (pH 8.1-8.2) the CO2 vents. We estimated the contribution of epiphytes to net primary production (NPP) and respiration (R) of leaf sections collected from the vent and ambient pH sites in laboratory incubations. Additionally, we quantified net community production (NCP) and community respiration (CR) of seagrass communities in situ at vent and ambient pH sites using benthic chambers. Leaves at ambient pH sites had a 25% higher total epiphytic cover with encrusting red algae (32%) dominating the community, while leaves at vent pH sites were dominated by hydrozoans (21%). Leaf sections with and without epiphytes from the vent pH site produced and respired significantly more oxygen than leaf sections from the ambient pH site, showing an average increase of 47 ± 21% (mean ± SE) in NPP and 50 ± 4% in R, respectively. Epiphytes contributed little to the increase in R; however, their contribution to NPP was important (56 ± 6% of the total flux). The increase in productivity of seagrass leaves adapted to OA was only marginally reflected by the results from the in situ benthic chambers, underlining the complexity of the seagrass community response to naturally occurring OA conditions.}, }
@article {pmid35428367, year = {2022}, author = {Szitenberg, A and Beca-Carretero, P and Azcárate-García, T and Yergaliyev, T and Alexander-Shani, R and Winters, G}, title = {Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {18}, pmid = {35428367}, issn = {2524-6372}, abstract = {BACKGROUND: Halophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf epiphytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host.<br><br>RESULTS: In this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface.<br><br>CONCLUSIONS: Our results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.}, }
@article {pmid35418670, year = {2022}, author = {Titus, BM and Daly, M}, title = {Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?.}, journal = {Heredity}, volume = {128}, number = {5}, pages = {338-351}, pmid = {35418670}, issn = {1365-2540}, mesh = {Animals ; Genome/genetics ; Genomics/methods ; Humans ; *Metagenomics/methods ; Phylogeny ; *Sea Anemones/genetics ; Sequence Analysis, DNA ; }, abstract = {Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.}, }
@article {pmid35398946, year = {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}, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; *Microbiota ; *Nanopore Sequencing ; *Porifera/genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.<br><br>DATA DESCRIPTION: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea-one Illumina MiSeq (2&#x2009;&#xd7;&#x2009;300&#xa0;bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the 'best' assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.}, }
@article {pmid35396623, year = {2022}, author = {Koide, RT}, title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35396623}, issn = {1432-184X}, abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.}, }
@article {pmid35393600, year = {2022}, author = {Sabrina Pankey, M and Plachetzki, DC and Macartney, KJ and Gastaldi, M and Slattery, M and Gochfeld, DJ and Lesser, MP}, title = {Cophylogeny and convergence shape holobiont evolution in sponge-microbe symbioses.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {6}, pages = {750-762}, pmid = {35393600}, issn = {2397-334X}, mesh = {*Bacteria ; Biodiversity ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Symbiotic microbial communities of sponges serve critical functions that have shaped the evolution of reef ecosystems since their origins. Symbiont abundance varies tremendously among sponges, with many species classified as either low microbial abundance (LMA) or high microbial abundance (HMA), but the evolutionary dynamics of these symbiotic states remain unknown. This study examines the LMA/HMA dichotomy across an exhaustive sampling of Caribbean sponge biodiversity and predicts that the LMA symbiotic state is the ancestral state among sponges. Conversely, HMA symbioses, consisting of more specialized microorganisms, have evolved multiple times by recruiting similar assemblages, mostly since the rise of scleractinian-dominated reefs. Additionally, HMA symbioses show stronger signals of phylosymbiosis and cophylogeny, consistent with stronger co-evolutionary interaction in these complex holobionts. These results indicate that HMA holobionts are characterized by increased endemism, metabolic dependence and chemical defences. The selective forces driving these patterns may include the concurrent increase in dissolved organic matter in reef ecosystems or the diversification of spongivorous fishes.}, }
@article {pmid35365219, year = {2022}, author = {Marasco, R and Fusi, M and Mosqueira, M and Booth, JM and Rossi, F and Cardinale, M and Michoud, G and Rolli, E and Mugnai, G and Vergani, L and Borin, S and De Philippis, R and Cherif, A and Daffonchio, D}, title = {Rhizosheath-root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {14}, pmid = {35365219}, issn = {2524-6372}, abstract = {BACKGROUND: In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath-root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert.<br><br>RESULTS: The belowground rhizosheath-root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath-root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath-root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment.<br><br>CONCLUSIONS: Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.}, }
@article {pmid35342582, year = {2022}, author = {Herrán, N and Narayan, GR and Doo, SS and Klicpera, A and Freiwald, A and Westphal, H}, title = {High-resolution imaging sheds new light on a multi-tier symbiotic partnership between a "walking" solitary coral, a sipunculan, and a bivalve from East Africa.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8633}, pmid = {35342582}, issn = {2045-7758}, abstract = {Marine symbioses are integral to the persistence of ecosystem functioning in coral reefs. Solitary corals of the species Heteropsammia cochlea and Heterocyathus aequicostatus have been observed to live in symbiosis with the sipunculan worm Aspidosiphon muelleri muelleri, which inhabits a cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these photosymbiotic corals enables the coral holobiont to move, in fine to coarse unconsolidated substrata, a process termed as "walking." This allows the coral to escape sediment cover in turbid conditions which is crucial for these light-dependent species. An additional commensalistic symbiosis of this coral-worm holobiont is found between the Aspidosiphon worm and the cryptoendolithic bivalve Jousseaumiella sp., which resides within the cavity of the coral skeleton. To understand the morphological alterations caused by these symbioses, interspecific relationships, with respect to the carbonate structures between these three organisms, are documented using high-resolution imaging techniques (scanning electron microscopy and µCT scanning). Documenting multi-layered symbioses can shed light on how morphological plasticity interacts with environmental conditions to contribute to species persistence.}, }
@article {pmid35341677, year = {2023}, author = {Tandon, K and Pasella, MM and Iha, C and Ricci, F and Hu, J and O'Kelly, CJ and Medina, M and Kühl, M and Verbruggen, H}, title = {Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business.}, journal = {Seminars in cell &amp; developmental biology}, volume = {134}, number = {}, pages = {27-36}, doi = {10.1016/j.semcdb.2022.03.010}, pmid = {35341677}, issn = {1096-3634}, mesh = {Animals ; *Chlorophyta ; *Anthozoa ; Coral Reefs ; Ecosystem ; }, abstract = {Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.}, }
@article {pmid35336242, year = {2022}, author = {Ratiner, K and Abdeen, SK and Goldenberg, K and Elinav, E}, title = {Utilization of Host and Microbiome Features in Determination of Biological Aging.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336242}, issn = {2076-2607}, abstract = {The term 'old age' generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person's life. Despite the conventional definition of old age as exceeding the age of 65 years old, quantifying aging as a function of life years does not necessarily reflect how the human body ages. In contrast, characterizing biological (or physiological) aging based on functional parameters may better reflect a person's temporal physiological status and associated disease susceptibility state. As such, differentiating 'chronological aging' from 'biological aging' holds the key to identifying individuals featuring accelerated aging processes despite having a young chronological age and stratifying them to tailored surveillance, diagnosis, prevention, and treatment. Emerging evidence suggests that the gut microbiome changes along with physiological aging and may play a pivotal role in a variety of age-related diseases, in a manner that does not necessarily correlate with chronological age. Harnessing of individualized gut microbiome data and integration of host and microbiome parameters using artificial intelligence and machine learning pipelines may enable us to more accurately define aging clocks. Such holobiont-based estimates of a person's physiological age may facilitate prediction of age-related physiological status and risk of development of age-associated diseases.}, }
@article {pmid35336184, year = {2022}, author = {Ducousso-Détrez, A and Fontaine, J and Lounès-Hadj Sahraoui, A and Hijri, M}, title = {Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336184}, issn = {2076-2607}, abstract = {In many soils, the bioavailability of Phosphorus (P), an essential macronutrient is a limiting factor for crop production. Among the mechanisms developed to facilitate the absorption of phosphorus, the plant, as a holobiont, can rely on its rhizospheric microbial partners. Therefore, microbial P-solubilizing inoculants are proposed to improve soil P fertility in agriculture. However, a better understanding of the interactions of the soil-plant-microorganism continuum with the phosphorus cycle is needed to propose efficient inoculants. Before proposing further methods of research, we carried out a critical review of the literature in two parts. First, we focused on the diversity of P-chemical forms. After a review of P forms in soils, we describe multiple factors that shape these forms in soil and their turnover. Second, we provide an analysis of P as a driver of microbial community diversity in soil. Even if no rule enabling to explain the changes in the composition of microbial communities according to phosphorus has been shown, this element has been perfectly targeted as linked to the presence/absence and/or abundance of particular bacterial taxa. In conclusion, we point out the need to link soil phosphorus chemistry with soil microbiology in order to understand the variations in the composition of microbial communities as a function of P bioavailability. This knowledge will make it possible to propose advanced microbial-based inoculant engineering for the improvement of bioavailable P for plants in sustainable agriculture.}, }
@article {pmid35336179, year = {2022}, author = {Zommiti, M and Chevalier, S and Feuilloley, MGJ and Connil, N}, title = {Special Issue "Enterococci for Probiotic Use: Safety and Risk": Editorial.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336179}, issn = {2076-2607}, abstract = {Microorganisms, their activity, and metabolites are now considered as intrinsic elements of the human body and this awareness gave was leading to the concept of holobiont [...].}, }
@article {pmid35334142, year = {2022}, author = {Derežanin, L and Blažytė, A and Dobrynin, P and Duchêne, DA and Grau, JH and Jeon, S and Kliver, S and Koepfli, KP and Meneghini, D and Preick, M and Tomarovsky, A and Totikov, A and Fickel, J and Förster, DW}, title = {Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.}, journal = {Molecular ecology}, volume = {31}, number = {10}, pages = {2898-2919}, doi = {10.1111/mec.16443}, pmid = {35334142}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Animals ; Genome ; Genomics ; *Mustelidae/genetics ; Phenotype ; }, abstract = {Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.}, }
@article {pmid35322689, year = {2022}, author = {Omae, N and Tsuda, K}, title = {Plant-Microbiota Interactions in Abiotic Stress Environments.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {35}, number = {7}, pages = {511-526}, doi = {10.1094/MPMI-11-21-0281-FI}, pmid = {35322689}, issn = {0894-0282}, mesh = {Agriculture ; Crops, Agricultural ; Humans ; *Microbiota ; Plant Development ; Stress, Physiological ; }, abstract = {Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid35310651, year = {2022}, author = {Chen, P and He, W and Shen, Y and Zhu, L and Yao, X and Sun, R and Dai, C and Sun, B and Chen, Y}, title = {Interspecific Neighbor Stimulates Peanut Growth Through Modulating Root Endophytic Microbial Community Construction.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {830666}, pmid = {35310651}, issn = {1664-462X}, abstract = {Plants have evolved the capability to respond to interspecific neighbors by changing morphological performance and reshaping belowground microbiota. However, whether neighboring plants influence the microbial colonization of the host's root and further affect host performance is less understood. In this study, using 16S rRNA high-throughput sequencing of peanut (Arachis hypogaea L.) roots from over 5 years of mono- and intercropping field systems, we found that neighbor maize can alter the peanut root microbial composition and re-shape microbial community assembly. Interspecific maize coexistence increased the colonization of genera Bradyrhizobium and Streptomyces in intercropped peanut roots. Through endophytic bacterial isolation and isolate back inoculation experiments, we demonstrated that the functional potentials of available nutrient accumulation and phytohormones production from Bradyrhizobium and Streptomyces endowed them with the ability to act as keystones in the microbial network to benefit peanut growth and production with neighbor competition. Our results support the idea that plants establish a plant-endophytic microbial holobiont through root selective filtration to enhance host competitive dominance, and provide a promising direction to develop modern diversified planting for harnessing crop microbiomes for the promotion of crop growth and productivity in sustainable agriculture.}, }
@article {pmid35308397, year = {2022}, author = {Taubenheim, J and Miklós, M and Tökölyi, J and Fraune, S}, title = {Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {799333}, pmid = {35308397}, issn = {1664-302X}, abstract = {Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.}, }
@article {pmid35303955, year = {2022}, author = {Cambon-Bonavita, MA and Aubé, J and Cueff-Gauchard, V and Reveillaud, J}, title = {Correction to: Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {51}, pmid = {35303955}, issn = {2049-2618}, }
@article {pmid35299055, year = {2022}, author = {Burgunter-Delamare, B and Tanguy, G and Legeay, E and Boyen, C and Dittami, SM}, title = {Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100944}, doi = {10.1016/j.margen.2022.100944}, pmid = {35299055}, issn = {1876-7478}, mesh = {DNA, Ribosomal ; *Kelp/genetics ; *Microbiota ; Nitrogen ; RNA ; RNA, Ribosomal, 16S/genetics ; *Seaweed ; Silica Gel ; }, abstract = {Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.}, }
@article {pmid35276225, year = {2022}, author = {Detmer, AR and Cunning, R and Pfab, F and Brown, AL and Stier, AC and Nisbet, RM and Moeller, HV}, title = {Fertilization by coral-dwelling fish promotes coral growth but can exacerbate bleaching response.}, journal = {Journal of theoretical biology}, volume = {541}, number = {}, pages = {111087}, doi = {10.1016/j.jtbi.2022.111087}, pmid = {35276225}, issn = {1095-8541}, mesh = {Animals ; *Anthozoa ; Carbon ; Coral Reefs ; Fertilization ; Fishes ; Nitrogen ; Symbiosis/physiology ; }, abstract = {Many corals form close associations with a diverse assortment of coral-dwelling fishes and other fauna. As coral reefs around the world are increasingly threatened by mass bleaching events, it is important to understand how these biotic interactions influence corals' susceptibility to bleaching. We used dynamic energy budget modeling to explore how nitrogen excreted by coral-dwelling fish affects the physiological performance of host corals. In our model, fish presence influenced the functioning of the coral-Symbiodiniaceae symbiosis by altering nitrogen availability, and the magnitude and sign of these effects depended on environmental conditions. Although our model predicted that fish-derived nitrogen can promote coral growth, the relationship between fish presence and coral tolerance of photo-oxidative stress was non-linear. Fish excretions supported denser symbiont populations that provided protection from incident light through self-shading. However, these symbionts also used more of their photosynthetic products for their own growth, rather than sharing with the coral host, putting the coral holobiont at a higher risk of becoming carbon-limited and bleaching. The balance between the benefits of increased symbiont shading and costs of reduced carbon sharing depended on environmental conditions. Thus, while there were some scenarios under which fish presence increased corals' tolerance of light stress, fish could also exacerbate bleaching and slow or prevent subsequent recovery. We discuss how the contrast between the potentially harmful effects of fish predicted by our model and results of empirical studies may relate to key model assumptions that warrant further investigation. Overall, this study provides a foundation for future work on how coral-associated fauna influence the bioenergetics of their host corals, which in turn has implications for how these corals respond to bleaching-inducing stressors.}, }
@article {pmid35273199, year = {2022}, author = {McLachlan, RH and Price, JT and Muñoz-Garcia, A and Weisleder, NL and Levas, SJ and Jury, CP and Toonen, RJ and Grottoli, AG}, title = {Physiological acclimatization in Hawaiian corals following a 22-month shift in baseline seawater temperature and pH.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {3712}, pmid = {35273199}, issn = {2045-2322}, mesh = {Acclimatization ; Animals ; *Anthozoa/physiology ; Coral Reefs ; Ecosystem ; Hawaii ; Hydrogen-Ion Concentration ; Lipids ; Seawater ; Temperature ; }, abstract = {Climate change poses a major threat to coral reefs. We conducted an outdoor 22-month experiment to investigate if coral could not just survive, but also physiologically cope, with chronic ocean warming and acidification conditions expected later this century under the Paris Climate Agreement. We recorded survivorship and measured eleven phenotypic traits to evaluate the holobiont responses of Hawaiian coral: color, Symbiodiniaceae density, calcification, photosynthesis, respiration, total organic carbon flux, carbon budget, biomass, lipids, protein, and maximum Artemia capture rate. Survivorship was lowest in Montipora capitata and only some survivors were able to meet metabolic demand and physiologically cope with future ocean conditions. Most M. capitata survivors bleached through loss of chlorophyll pigments and simultaneously experienced increased respiration rates and negative carbon budgets due to a 236% increase in total organic carbon losses under combined future ocean conditions. Porites compressa and Porites lobata had the highest survivorship and coped well under future ocean conditions with positive calcification and increased biomass, maintenance of lipids, and the capacity to exceed their metabolic demand through photosynthesis and heterotrophy. Thus, our findings show that significant biological diversity within resilient corals like Porites, and some genotypes of sensitive species, will persist this century provided atmospheric carbon dioxide levels are controlled. Since Porites corals are ubiquitous throughout the world's oceans and often major reef builders, the persistence of this resilient genus provides hope for future reef ecosystem function globally.}, }
@article {pmid35271794, year = {2022}, author = {Lin, J and Duchêne, D and Carøe, C and Smith, O and Ciucani, MM and Niemann, J and Richmond, D and Greenwood, AD and MacPhee, R and Zhang, G and Gopalakrishnan, S and Gilbert, MTP}, title = {Probing the genomic limits of de-extinction in the Christmas Island rat.}, journal = {Current biology : CB}, volume = {32}, number = {7}, pages = {1650-1656.e3}, pmid = {35271794}, issn = {1879-0445}, mesh = {Animals ; Australia ; Biological Evolution ; Extinction, Biological ; *Genome ; *Genomics ; Norway ; Phylogeny ; Rats ; }, abstract = {Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.[1,2] Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.[3-5] We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.}, }
@article {pmid35269523, year = {2022}, author = {Kriaa, A and Mariaule, V and Jablaoui, A and Rhimi, S and Mkaouar, H and Hernandez, J and Korkmaz, B and Lesner, A and Maguin, E and Aghdassi, A and Rhimi, M}, title = {Bile Acids: Key Players in Inflammatory Bowel Diseases?.}, journal = {Cells}, volume = {11}, number = {5}, pages = {}, pmid = {35269523}, issn = {2073-4409}, mesh = {Bile Acids and Salts ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation ; *Inflammatory Bowel Diseases ; }, abstract = {Inflammatory bowel diseases (IBDs) have emerged as a public health problem worldwide with a limited number of efficient therapeutic options despite advances in medical therapy. Although changes in the gut microbiota composition are recognized as key drivers of dysregulated intestinal immunity, alterations in bile acids (BAs) have been shown to influence gut homeostasis and contribute to the pathogenesis of the disease. In this review, we explore the interactions involving BAs and gut microbiota in IBDs, and discuss how the gut microbiota-BA-host axis may influence digestive inflammation.}, }
@article {pmid35261041, year = {2022}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Paus, R and Bosch, TCG}, title = {Hydra and the hair follicle - An unconventional comparative biology approach to exploring the human holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {5}, pages = {e2100233}, doi = {10.1002/bies.202100233}, pmid = {35261041}, issn = {1521-1878}, mesh = {Animals ; Biology ; Hair Follicle ; Humans ; *Hydra/physiology ; Microbial Interactions ; *Microbiota/physiology ; }, abstract = {The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in-depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host-associated microbes, microbial metabolism, microbe-microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host-microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF - microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome-targeting therapeutic interventions in human skin disease.}, }
@article {pmid35260076, year = {2022}, author = {Haas, V and Vollmar, S and Preuß, S and Rodehutscord, M and Camarinha-Silva, A and Bennewitz, J}, title = {Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica).}, journal = {Genetics, selection, evolution : GSE}, volume = {54}, number = {1}, pages = {20}, pmid = {35260076}, issn = {1297-9686}, mesh = {Animals ; *Coturnix/genetics/microbiology ; *Gastrointestinal Microbiome ; Genome ; Genotype ; Ileum/*microbiology ; Phenotype ; Phosphorus/*metabolism ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; }, abstract = {BACKGROUND: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.<br><br>RESULTS: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p&#x2009;&#x2264;&#x2009;0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host's quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host's quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.<br><br>CONCLUSIONS: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host's quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.}, }
@article {pmid35253476, year = {2022}, author = {Ricci, F and Tandon, K and Black, JR and Lê Cao, KA and Blackall, LL and Verbruggen, H}, title = {Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0004422}, pmid = {35253476}, issn = {2379-5077}, abstract = {The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence of host phylogeny, skeletal architecture, and reproductive mode on the microbiome composition, and further investigated the structure of the tissue and skeleton bacterial communities. Our results show that host phylogeny and traits explained 14% of the tissue and 13% of the skeletal microbiome composition, providing evidence that these predictors contributed to shaping the holobiont in terms of presence and relative abundance of bacterial symbionts. Based on our data, we conclude that host phylogeny affects the presence of specific microbial lineages, reproductive mode predictably influences the microbiome composition, and skeletal architecture works like a filter that affects bacterial relative abundance. We show that the β-diversity of coral tissue and skeleton microbiomes differed, but we found that a large overlapping fraction of bacterial sequences were recovered from both anatomical compartments, supporting the hypothesis that the skeleton can function as a microbial reservoir. Additionally, our analysis of the microbiome structure shows that 99.6% of tissue and 99.7% of skeletal amplicon sequence variants (ASVs) were not consistently present in at least 30% of the samples, suggesting that the coral tissue and skeleton are dominated by rare bacteria. Together, these results provide novel insights into the processes driving coral-bacterial symbioses, along with an improved understanding of the scleractinian microbiome.}, }
@article {pmid35242117, year = {2022}, author = {Gómez-Lama Cabanás, C and Wentzien, NM and Zorrilla-Fontanesi, Y and Valverde-Corredor, A and Fernández-González, AJ and Fernández-López, M and Mercado-Blanco, J}, title = {Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {809126}, pmid = {35242117}, issn = {1664-302X}, abstract = {The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.}, }
@article {pmid35237241, year = {2021}, author = {Li, J and Wei, X and Huang, D and Xiao, J}, title = {The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {800190}, pmid = {35237241}, issn = {1664-302X}, abstract = {Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities. Most of the previous studies on phylosymbiosis were conducted across the host families or genera. However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels. In this study, 54 individuals from six species of the fig wasp genus Ceratosolen (Hymenoptera: Agaonidae) collected from nine natural populations and their associated microbiota were investigated. The fig wasp species were morphologically identified and further determined by mitochondrial CO1 gene fragments and nuclear ITS2 sequences, and the V4 region of 16S rRNA gene was sequenced to analyze the bacterial communities. The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus. Moreover, we found that the endosymbiotic Wolbachia carried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities. This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.}, }
@article {pmid35229422, year = {2022}, author = {Taylor, JA and Díez-Vives, C and Nielsen, S and Wemheuer, B and Thomas, T}, title = {Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts.}, journal = {Environmental microbiology}, volume = {24}, number = {5}, pages = {2299-2314}, doi = {10.1111/1462-2920.15962}, pmid = {35229422}, issn = {1462-2920}, mesh = {Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Phylogeny ; *Porifera ; Symbiosis/physiology ; }, abstract = {The diversity and function of sponge-associated symbionts is now increasingly understood; however, we lack an understanding of how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here, we performed a metatransciptomic analysis on three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidizing Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidizing archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our time-series study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change.}, }
@article {pmid35223211, year = {2022}, author = {Nyholm, L and Odriozola, I and Martin Bideguren, G and Aizpurua, O and Alberdi, A}, title = {Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12992}, pmid = {35223211}, issn = {2167-8359}, abstract = {The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.}, }
@article {pmid35222085, year = {2022}, author = {Cotinat, P and Fricano, C and Toullec, G and Röttinger, E and Barnay-Verdier, S and Furla, P}, title = {Intrinsically High Capacity of Animal Cells From a Symbiotic Cnidarian to Deal With Pro-Oxidative Conditions.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {819111}, pmid = {35222085}, issn = {1664-042X}, abstract = {The cnidarian-dinoflagellate symbiosis is a mutualistic intracellular association based on the photosynthetic activity of the endosymbiont. This relationship involves significant constraints and requires co-evolution processes, such as an extensive capacity of the holobiont to counteract pro-oxidative conditions induced by hyperoxia generated during photosynthesis. In this study, we analyzed the capacity of Anemonia viridis cells to deal with pro-oxidative conditions by in vivo and in vitro approaches. Whole specimens and animal primary cell cultures were submitted to 200 and 500 μM of H2O2 during 7 days. Then, we monitored global health parameters (symbiotic state, viability, and cell growth) and stress biomarkers (global antioxidant capacity, oxidative protein damages, and protein ubiquitination). In animal primary cell cultures, the intracellular reactive oxygen species (ROS) levels were also evaluated under H2O2 treatments. At the whole organism scale, both H2O2 concentrations didn't affect the survival and animal tissues exhibited a high resistance to H2O2 treatments. Moreover, no bleaching has been observed, even at high H2O2 concentration and after long exposure (7 days). Although, the community has suggested the role of ROS as the cause of bleaching, our results indicating the absence of bleaching under high H2O2 concentration may exculpate this specific ROS from being involved in the molecular processes inducing bleaching. However, counterintuitively, the symbiont compartment appeared sensitive to an H2O2 burst as it displayed oxidative protein damages, despite an enhancement of antioxidant capacity. The in vitro assays allowed highlighting an intrinsic high capacity of isolated animal cells to deal with pro-oxidative conditions, although we observed differences on tolerance between H2O2 treatments. The 200 μM H2O2 concentration appeared to correspond to the tolerance threshold of animal cells. Indeed, no disequilibrium on redox state was observed and only a cell growth decrease was measured. Contrarily, the 500 μM H2O2 concentration induced a stress state, characterized by a cell viability decrease from 1 day and a drastic cell growth arrest after 7 days leading to an uncomplete recovery after treatment. In conclusion, this study highlights the overall high capacity of cnidarian cells to cope with H2O2 and opens new perspective to investigate the molecular mechanisms involved in this peculiar resistance.}, }
@article {pmid35218086, year = {2022}, author = {Rosenberg, Y and Simon-Blecher, N and Lalzar, M and Yam, R and Shemesh, A and Alon, S and Perna, G and Cárdenas, A and Voolstra, CR and Miller, DJ and Levy, O}, title = {Urbanization comprehensively impairs biological rhythms in coral holobionts.}, journal = {Global change biology}, volume = {28}, number = {10}, pages = {3349-3364}, pmid = {35218086}, issn = {1365-2486}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota ; Periodicity ; Urbanization ; }, abstract = {Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology &amp; Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.}, }
@article {pmid35215934, year = {2022}, author = {Yukgehnaish, K and Rajandas, H and Parimannan, S and Manickam, R and Marimuthu, K and Petersen, B and Clokie, MRJ and Millard, A and Sicheritz-Pontén, T}, title = {PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215934}, issn = {1999-4915}, mesh = {Bacteria/virology ; Bacterial Infections/microbiology/*therapy ; Bacterial Physiological Phenomena ; Bacteriophages/classification/*genetics/physiology ; Genome, Viral ; Humans ; Lysogeny ; *Machine Learning ; *Phage Therapy ; Viral Proteins/genetics/metabolism ; }, abstract = {The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools are available for this purpose. Hence, we have developed a tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates. This tool consists of an ensemble of machine-learning-based predictors for determining the presence of temperate markers (integrase, Cro/CI repressor, immunity repressor, DNA partitioning protein A, and antirepressor) along with the integration of the ABRicate tool to determine the presence of antibiotic resistance genes and virulence genes. Using the biological features of the temperate markers, we were able to predict the presence of the temperate markers with high MCC scores (>0.70), corresponding to the lifestyle of the phages with an accuracy of 96.5%. Additionally, the screening of 183 lytic phage genomes revealed that six phages were found to contain AMR or virulence genes, showing that not all lytic phages are suitable to be used for therapy. The suite of predictors, PhageLeads, along with the integrated ABRicate tool, can be accessed online for in silico selection of suitable therapeutic phage candidates from single genome or metagenomic contigs.}, }
@article {pmid35208935, year = {2022}, author = {Butina, TV and Petrushin, IS and Khanaev, IV and Bukin, YS}, title = {Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208935}, issn = {2076-2607}, abstract = {Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.}, }
@article {pmid35208684, year = {2022}, author = {Dietert, RR and Dietert, JM}, title = {Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan following Adverse Childhood Experiences.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208684}, issn = {2076-2607}, abstract = {Adverse childhood experiences (ACEs), which can include child trafficking, are known to program children for disrupted biological cycles, premature aging, microbiome dysbiosis, immune-inflammatory misregulation, and chronic disease multimorbidity. To date, the microbiome has not been a major focus of deprogramming efforts despite its emerging role in every aspect of ACE-related dysbiosis and dysfunction. This article examines: (1) the utility of incorporating microorganism-based, anti-aging approaches to combat ACE-programmed chronic diseases (also known as noncommunicable diseases and conditions, NCDs) and (2) microbiome regulation of core systems biology cycles that affect NCD comorbid risk. In this review, microbiota influence over three key cyclic rhythms (circadian cycles, the sleep cycle, and the lifespan/longevity cycle) as well as tissue inflammation and oxidative stress are discussed as an opportunity to deprogram ACE-driven chronic disorders. Microbiota, particularly those in the gut, have been shown to affect host-microbe interactions regulating the circadian clock, sleep quality, as well as immune function/senescence, and regulation of tissue inflammation. The microimmunosome is one of several systems biology targets of gut microbiota regulation. Furthermore, correcting misregulated inflammation and increased oxidative stress is key to protecting telomere length and lifespan/longevity and extending what has become known as the healthspan. This review article concludes that to reverse the tragedy of ACE-programmed NCDs and premature aging, managing the human holobiont microbiome should become a routine part of healthcare and preventative medicine across the life course.}, }
@article {pmid35208662, year = {2022}, author = {Qin, Z and Yu, K and Chen, S and Chen, B and Yao, Q and Yu, X and Pan, N and Wei, X}, title = {Significant Changes in Bacterial Communities Associated with Pocillopora Corals Ingestion by Crown-of-Thorns Starfish: An Important Factor Affecting the Coral's Health.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208662}, issn = {2076-2607}, abstract = {Coral ingestion by crown-of-thorns starfish (COTS) is an important cause of coral reef degradation, although the impacts of COTS feeding on coral-associated microbial communities are not well understood. Therefore, in this study, we analyzed the coral tissue-weight, Symbiodiniaceae density (SD), bacterial community composition, and the predicted functions of bacterial genes associated with Pocillopora corals in healthy portions and feeding scars, following COTS feeding. Coral tissue-weight loss rate in the feeding scars was 71.3-94.95%. The SDs were significantly lower in the feeding scars, and the SD-loss rate was 92.05% ± 2.12%. The relative abundances of bacterial communities associated with Pocillopora corals after COTS feeding changed significantly and were almost completely reorganized at the phylum and genus levels. Analysis of the microbial metagenomic-functional capacities showed that numerous physiological functions of the coral-bacterial holobionts in the feeding scars were different, including amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, membrane transport, signal transduction, and cell motility, and all these capacities could be corroborated based on metagenomic, transcriptomic or proteomic technologies. Overall, our research suggests that coral holobionts may be destroyed by COTS, and our findings imply that bacterial communities in feeding scars could affect the health of Pocillopora corals.}, }
@article {pmid35202673, year = {2022}, author = {Tougeron, K}, title = {Homeostasis theory: What can we learn from dormancy and symbiotic associations?.}, journal = {Physiology &amp; behavior}, volume = {249}, number = {}, pages = {113749}, doi = {10.1016/j.physbeh.2022.113749}, pmid = {35202673}, issn = {1873-507X}, mesh = {Animals ; *Diapause/physiology ; Homeostasis ; *Symbiosis ; }, abstract = {In this letter, I discuss the notion of dormancy that De Luca Jr. relies on to criticize the theory of homeostasis. In particular, I try to qualify the issues related to the fact that dormancy is not always a free behavior but is in most situations under the influence of environmental factors. To this end, I discuss diapause in arthropods, which can be obligatory (under the influence of endogenous commands) but which is in most cases facultative (under external command). I emphasize that the notion of stability of a dormant organism must be taken with caution. I briefly mention what the study of sleep in animals can contribute to the notion of homeostasis. Finally, I focus on the role of microbial symbionts and the notion of holobiont. Through this, I question the future of the notions of internal environment and homeostasis and I propose to revisit them in the context of the effects of species interactions on the physiology of organisms.}, }
@article {pmid35191335, year = {2022}, author = {Folkers, A and Opitz, S}, title = {Low-carbon cows: From microbial metabolism to the symbiotic planet.}, journal = {Social studies of science}, volume = {52}, number = {3}, pages = {330-352}, pmid = {35191335}, issn = {1460-3659}, mesh = {Animals ; *Carbon ; Cattle ; Climate Change ; *Planets ; Symbiosis ; }, abstract = {This article focuses on two projects - one at a large chemical company and the other at a small start-up - to intervene in the relations between cows and ruminal microbes to reduce bovine methane emissions. It describes these interventions as 'symbiotic engineering': a biopolitical technique targeting holobionts and becoming effective by working on interlaced sets of living things. Based on the analysis of these cases, the article elucidates a planetary symbiopolitics (Helmreich) that connects 'molecular biopolitics' (Rose) and 'microbiopolitics' (Paxson) to 'bovine biopolitics' (Lorimer, Driessen) and the politics of climate change. We critically investigate the spatial imaginaries of symbiotic engineering practices that single out the microbial realm as an Archimedean point to address planetary problems. This technoscientific vision resonates with the notion of the 'symbiotic planet' advanced by Lynn Margulis that depicts the Earth System, or Gaia, as a vast set of relations among living things down to the tiniest microbes. Margulis' concept, as well as the 'symbiotic view of life' (Gilbert, Scott, Sapp) has been embraced in recent debates in STS as a way to think of multispecies worldings. The article contributes critically to these debates by showing what happens when the topology of the symbiotic Earth becomes the operating space for symbiotic engineering practices.}, }
@article {pmid35187610, year = {2022}, author = {Roggatz, CC and Hardege, JD and Saha, M}, title = {Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions.}, journal = {Journal of chemical ecology}, volume = {48}, number = {4}, pages = {455-473}, pmid = {35187610}, issn = {1573-1561}, support = {ERC-2016-COG GEOSTICK/ERC_/European Research Council/International ; }, mesh = {Bacteria/metabolism ; *Biofouling/prevention &amp; control ; Ecosystem ; Hydrogen-Ion Concentration ; Phylogeny ; Seawater/chemistry ; *Seaweed/microbiology ; }, abstract = {Marine macroalgae are important ecosystem engineers in marine coastal habitats. Macroalgae can be negatively impacted through excessive colonization by harmful bacteria, fungi, microalgae, and macro-colonisers and thus employ a range of chemical compounds to minimize such colonization. Recent research suggests that environmental pH conditions potentially impact the functionality of such chemical compounds. Here we predict if and how naturally fluctuating pH conditions and future conditions caused by ocean acidification will affect macroalgal (antifouling) compounds and thereby potentially alter the chemical defence mediated by these compounds. We defined the relevant ecological pH range, analysed and scored the pH-sensitivity of compounds with antifouling functions based on their modelled chemical properties before assessing their distribution across the phylogenetic macroalgal groups, and the proportion of sensitive compounds for each investigated function. For some key compounds, we also predicted in detail how the associated ecological function may develop across the pH range. The majority of compounds were unaffected by pH, but compounds containing phenolic and amine groups were found to be particularly sensitive to pH. Future pH changes due to predicted average open ocean acidification pH were found to have little effect. Compounds from Rhodophyta were mainly pH-stable. However, key algal species amongst Phaeophyceae and Chlorophyta were found to rely on highly pH-sensitive compounds for their chemical defence against harmful bacteria, microalgae, fungi, and biofouling by macro-organisms. All quorum sensing disruptive compounds were found the be unaffected by pH, but the other ecological functions were all conveyed in part by pH-sensitive compounds. For some ecological keystone species, all of their compounds mediating defence functions were found to be pH-sensitive based on our calculations, which may not only affect the health and fitness of the host alga resulting in host breakdown but also alter the associated ecological interactions of the macroalgal holobiont with micro and macrocolonisers, eventually causing ecosystem restructuring and the functions (e.g. habitat provision) provided by macroalgal hosts. Our study investigates a question of fundamental importance because environments with fluctuating or changing pH are common and apply not only to coastal marine habitats and estuaries but also to freshwater environments or terrestrial systems that are subject to acid rain. Hence, whilst warranting experimental validation, this investigation with macroalgae as model organisms can serve as a basis for future investigations in other aquatic or even terrestrial systems.}, }
@article {pmid35182765, year = {2022}, author = {Neves, RC and Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Gilbert, MTP and Møbjerg, N}, title = {Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {267}, number = {}, pages = {111169}, doi = {10.1016/j.cbpa.2022.111169}, pmid = {35182765}, issn = {1531-4332}, mesh = {Animals ; Heat-Shock Proteins/genetics ; Heat-Shock Response/genetics ; RNA-Seq ; *Tardigrada/genetics ; *Transcriptome ; }, abstract = {Tardigrades are renowned for their extreme stress tolerance, which includes the ability to endure complete desiccation, high levels of radiation and very low sub-zero temperatures. Nevertheless, tardigrades appear to be vulnerable to high temperatures and thus the potential effects of global warming. Here, we provide the first analysis of transcriptome data obtained from heat stressed specimens of the eutardigrade Ramazzottius varieornatus, with the aim of providing new insights into the molecular processes affected by high temperatures. Specifically, we compare RNA-seq datasets obtained from active, heat-exposed (35 °C) tardigrades to that of active controls kept at 5 °C. Our data reveal a surprising shift in transcription, involving 9634 differentially expressed transcripts, corresponding to >35% of the transcriptome. The latter data are in striking contrast to the hitherto observed constitutive expression underlying tardigrade extreme stress tolerance and entrance into the latent state of life, known as cryptobiosis. Thus, when examining the molecular response, heat-stress appears to be more stressful for R. varieornatus than extreme conditions, such as desiccation or freezing. A gene ontology analysis reveals that the heat stress response involves a change in transcription and presumably translation, including an adjustment of metabolism, and, putatively, preparation for encystment and subsequent diapause. Among the differentially expressed transcripts we find heat-shock proteins as well as the eutardigrade specific proteins (CAHS, SAHS, MAHS, RvLEAM, and Dsup). The latter proteins thus seem to contribute to a general stress response, and may not be directly related to cryptobiosis.}, }
@article {pmid35182319, year = {2022}, author = {Ünüvar, &#xd6;C and Zencirci, N and Ünlü, ES}, title = {Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture.}, journal = {Molecular biology reports}, volume = {49}, number = {6}, pages = {5389-5395}, pmid = {35182319}, issn = {1573-4978}, mesh = {Agriculture ; Bacteria/genetics ; DNA, Ribosomal ; Phosphates ; *Plant Breeding ; Plant Roots ; *Triticum/genetics ; }, abstract = {BACKGROUND: Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadağ Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed.<br><br>METHODS AND RESULTS: The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805&#x2009;&#xb1;&#x2009;0.439.<br><br>CONCLUSIONS: All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.}, }
@article {pmid35153869, year = {2021}, author = {Martínez, M and Postolache, TT and García-Bueno, B and Leza, JC and Figuero, E and Lowry, CA and Malan-Müller, S}, title = {The Role of the Oral Microbiota Related to Periodontal Diseases in Anxiety, Mood and Trauma- and Stress-Related Disorders.}, journal = {Frontiers in psychiatry}, volume = {12}, number = {}, pages = {814177}, pmid = {35153869}, issn = {1664-0640}, abstract = {The prevalence of anxiety, mood and trauma- and stress-related disorders are on the rise; however, efforts to develop new and effective treatment strategies have had limited success. To identify novel therapeutic targets, a comprehensive understanding of the disease etiology is needed, especially in the context of the holobiont, i.e., the superorganism consisting of a human and its microbiotas. Much emphasis has been placed on the role of the gut microbiota in the development, exacerbation, and persistence of psychiatric disorders; however, data for the oral microbiota are limited. The oral cavity houses the second most diverse microbial community in the body, with over 700 bacterial species that colonize the soft and hard tissues. Periodontal diseases encompass a group of infectious and inflammatory diseases that affect the periodontium. Among them, periodontitis is defined as a chronic, multi-bacterial infection that elicits low-grade systemic inflammation via the release of pro-inflammatory cytokines, as well as local invasion and long-distance translocation of periodontal pathogens. Periodontitis can also induce or exacerbate other chronic systemic inflammatory diseases such as atherosclerosis and diabetes and can lead to adverse pregnancy outcomes. Recently, periodontal pathogens have been implicated in the etiology and pathophysiology of neuropsychiatric disorders (such as depression and schizophrenia), especially as dysregulation of the immune system also plays an integral role in the etiology and pathophysiology of these disorders. This review will discuss the role of the oral microbiota associated with periodontal diseases in anxiety, mood and trauma- and stress-related disorders. Epidemiological data of periodontal diseases in individuals with these disorders will be presented, followed by a discussion of the microbiological and immunological links between the oral microbiota and the central nervous system. Pre-clinical and clinical findings on the oral microbiota related to periodontal diseases in anxiety, mood and trauma- and stress-related phenotypes will be reviewed, followed by a discussion on the bi-directionality of the oral-brain axis. Lastly, we will focus on the oral microbiota associated with periodontal diseases as a target for future therapeutic interventions to alleviate symptoms of these debilitating psychiatric disorders.}, }
@article {pmid35150917, year = {2022}, author = {Shigenobu, S and Yorimoto, S}, title = {Aphid hologenomics: current status and future challenges.}, journal = {Current opinion in insect science}, volume = {50}, number = {}, pages = {100882}, doi = {10.1016/j.cois.2022.100882}, pmid = {35150917}, issn = {2214-5753}, mesh = {Animals ; *Aphids/genetics ; *Buchnera/genetics ; Genomics ; Symbiosis ; }, abstract = {Aphids are important model organisms in ecological, developmental, and evolutionary studies of, for example, symbiosis, insect-plant interactions, pest management, and developmental polyphenism. Here, we review the recent progress made in the genomics of aphids and their symbionts: hologenomics. The reference genome of Acyrthosiphon pisum has been greatly improved, and chromosome-level assembly is now available. The genomes of over 20 aphid species have been sequenced, and comparative genomic analyses have revealed pervasive gene duplication and dynamic chromosomal rearrangements. Over 120 symbiont genomes (both obligate and facultative) have been sequenced, and modern deep-sequencing technologies have identified novel symbionts. The advances in hologenomics have helped to elucidate the dynamic evolution of facultative and co-obligate symbionts with the ancient obligate symbiont Buchnera.}, }
@article {pmid35147188, year = {2022}, author = {Zouache, K and Martin, E and Rahola, N and Gangue, MF and Minard, G and Dubost, A and Van, VT and Dickson, L and Ayala, D and Lambrechts, L and Moro, CV}, title = {Larval habitat determines the bacterial and fungal microbiota of the mosquito vector Aedes aegypti.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {1}, pages = {}, doi = {10.1093/femsec/fiac016}, pmid = {35147188}, issn = {1574-6941}, mesh = {*Aedes/microbiology ; Animals ; Bacteria/genetics ; Larva/microbiology ; *Microbiota ; Mosquito Vectors/microbiology ; *Mycobiome ; Plant Breeding ; }, abstract = {Mosquito larvae are naturally exposed to microbial communities present in a variety of larval development sites. Several earlier studies have highlighted that the larval habitat influences the composition of the larval bacterial microbiota. However, little information is available on their fungal microbiota, i.e. the mycobiota. In this study, we provide the first simultaneous characterization of the bacterial and fungal microbiota in field-collected Aedes aegypti larvae and their respective aquatic habitats. We evaluated whether the microbial communities associated with the breeding site may affect the composition of both the bacterial and fungal communities in Ae. aegypti larvae. Our results show a higher similarity in microbial community structure for both bacteria and fungi between larvae and the water in which larvae develop than between larvae from different breeding sites. This supports the hypothesis that larval habitat is a major factor driving microbial composition in mosquito larvae. Since the microbiota plays an important role in mosquito biology, unravelling the network of interactions that operate between bacteria and fungi is essential to better understand the functioning of the mosquito holobiont.}, }
@article {pmid35138928, year = {2022}, author = {Riva, V and Mapelli, F and Bagnasco, A and Mengoni, A and Borin, S}, title = {A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0253721}, pmid = {35138928}, issn = {1098-5336}, mesh = {*Bacteria ; Endophytes ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.}, }
@article {pmid35137526, year = {2022}, author = {Ren, CG and Liu, ZY and Wang, XL and Qin, S}, title = {The seaweed holobiont: from microecology to biotechnological applications.}, journal = {Microbial biotechnology}, volume = {15}, number = {3}, pages = {738-754}, pmid = {35137526}, issn = {1751-7915}, mesh = {*Seaweed/chemistry ; }, abstract = {In the ocean, seaweed and microorganisms have coexisted since the earliest stages of evolution and formed an inextricable relationship. Recently, seaweed has attracted extensive attention worldwide for ecological and industrial purposes, but the function of its closely related microbes is often ignored. Microbes play an indispensable role in different stages of seaweed growth, development and maturity. A very diverse group of seaweed-associated microbes have important functions and are dynamically reconstructed as the marine environment fluctuates, forming an inseparable 'holobiont' with their host. To further understand the function and significance of holobionts, this review first reports on recent advances in revealing seaweed-associated microbe spatial and temporal distribution. Then, this review discusses the microbe and seaweed interactions and their ecological significance, and summarizes the current applications of the seaweed-microbe relationship in various environmental and biological technologies. Sustainable industries based on seaweed holobionts could become an integral part of the future bioeconomy because they can provide more resource-efficient food, high-value chemicals and medical materials. Moreover, holobionts may provide a new approach to marine environment restoration.}, }
@article {pmid35136196, year = {2022}, author = {Bertorelle, G and Raffini, F and Bosse, M and Bortoluzzi, C and Iannucci, A and Trucchi, E and Morales, HE and van Oosterhout, C}, title = {Genetic load: genomic estimates and applications in non-model animals.}, journal = {Nature reviews. Genetics}, volume = {23}, number = {8}, pages = {492-503}, pmid = {35136196}, issn = {1471-0064}, support = {WT207492/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Genetic Load ; Genetic Variation ; *Genetics, Population ; Genome ; Genomics ; Inbreeding ; Mutation ; }, abstract = {Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.}, }
@article {pmid35135352, year = {2022}, author = {Frank, HER and Amato, K and Trautwein, M and Maia, P and Liman, ER and Nichols, LM and Schwenk, K and Breslin, PAS and Dunn, RR}, title = {The evolution of sour taste.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1968}, pages = {20211918}, pmid = {35135352}, issn = {1471-2954}, mesh = {Animals ; Humans ; Phylogeny ; *Taste ; }, abstract = {The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.}, }
@article {pmid35134420, year = {2022}, author = {Corinaldesi, C and Varrella, S and Tangherlini, M and Dell'Anno, A and Canensi, S and Cerrano, C and Danovaro, R}, title = {Changes in coral forest microbiomes predict the impact of marine heatwaves on habitat-forming species down to mesophotic depths.}, journal = {The Science of the total environment}, volume = {823}, number = {}, pages = {153701}, doi = {10.1016/j.scitotenv.2022.153701}, pmid = {35134420}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Bacteria ; Coral Reefs ; Ecosystem ; Forests ; *Microbiota ; Seawater/microbiology ; }, abstract = {Global warming is causing the increase in intensity and frequency of heatwaves, which are often associated with mass mortality events of marine organisms from shallow and mesophotic rocky habitats, including gorgonians and other sessile organisms. We investigated the microbiome responses of the gorgonians Paramuricea clavata, Eunicella cavolini, and the red coral Corallium rubrum to the episodic temperature anomalies detected in the North Western Mediterranean, during August 2011. Although the investigated corals showed no signs of visible necrosis, the abundance of associated Bacteria and Archaea increased with increasing seawater temperature, suggesting their temperature-dependent proliferation. Coral microbiomes were highly sensitive to thermal anomaly amplitude and exhibited increased bacterial diversity to greater thermal shifts. This effect was explained by the decline of dominant bacterial members and the increase of new, rare and opportunistic taxa, including pathogens, revealing a direct effect of heatwave-induced alteration of the microbiomes and not a secondary consequence of coral necrosis.}, }
@article {pmid35119475, year = {2022}, author = {Tran, C}, title = {Coral-microbe interactions: their importance to reef function and survival.}, journal = {Emerging topics in life sciences}, volume = {6}, number = {1}, pages = {33-44}, doi = {10.1042/ETLS20210229}, pmid = {35119475}, issn = {2397-8554}, mesh = {*Anemone ; Animals ; *Anthozoa ; Host Microbial Interactions ; Hypochlorous Acid ; *Microbiota ; *Scyphozoa ; Sodium Compounds ; }, abstract = {Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.}, }
@article {pmid35112871, year = {2022}, author = {Deutsch, JM and Mandelare-Ruiz, P and Yang, Y and Foster, G and Routhu, A and Houk, J and De La Flor, YT and Ushijima, B and Meyer, JL and Paul, VJ and Garg, N}, title = {Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria.}, journal = {Journal of natural products}, volume = {85}, number = {3}, pages = {462-478}, doi = {10.1021/acs.jnatprod.1c01110}, pmid = {35112871}, issn = {1520-6025}, mesh = {Animals ; *Anthozoa/microbiology ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/genetics ; *Biological Products/metabolism/pharmacology ; Metabolomics ; Symbiosis ; }, abstract = {Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.}, }
@article {pmid35108095, year = {2022}, author = {Tignat-Perrier, R and van de Water, JAJM and Guillemain, D and Aurelle, D and Allemand, D and Ferrier-Pagès, C}, title = {The Effect of Thermal Stress on the Physiology and Bacterial Communities of Two Key Mediterranean Gorgonians.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0234021}, pmid = {35108095}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Mediterranean Sea ; *Microbiota ; Seawater/microbiology ; }, abstract = {Gorgonians are important habitat-providing species in the Mediterranean Sea, but their populations are declining due to microbial diseases and repeated mass mortality events caused by summer heat waves. Elevated seawater temperatures may impact the stress tolerance and disease resistance of gorgonians and lead to disturbances in their microbiota. However, our knowledge of the biological response of the gorgonian holobiont (i.e., the host and its microbiota) to thermal stress remains limited. Here, we investigated how the holobiont of two gorgonian species (Paramuricea clavata and Eunicella cavolini) are affected throughout a 7-week thermal stress event by following both the corals' physiology and the composition of their bacterial communities. We found that P. clavata was more sensitive to elevated seawater temperatures than E. cavolini, showing a greater loss in energy reserves, reduced feeding ability, and partial mortality. This lower thermotolerance may be linked to the ∼20× lower antioxidant defense capacity in P. clavata compared with E. cavolini. In the first 4 weeks of thermal stress, we also observed minor shifts in the microbiota of both species, suggesting that the microbiota likely plays a limited role in thermal acclimation of the holobiont. However, major stochastic changes occurred later on in some colonies, which were of a transient nature in E. cavolini, but were linked to partial colony mortality in P. clavata. Overall, our results show significant, but differential, effects of thermal stress on the holobionts of both E. cavolini and P. clavata and predict potentially severe impacts on gorgonian populations under future climate scenarios. IMPORTANCE In the Mediterranean Sea, the tree-shaped gorgonian corals form large forests that provide a place to live for many species. Because of this important ecological role, it is crucial to understand how common habitat-forming gorgonians, like Eunicella cavolini and Paramuricea clavata, are affected by high seawater temperatures that are expected in the future due to climate change. We found that both species lost biomass, but P. clavata was more affected, being also unable to feed and showing signs of mortality. The microbiota of both gorgonians also changed substantively under high temperatures. Although this could be linked to partial colony mortality in P. clavata, the changes were temporary in E. cavolini. The overall higher resistance of E. cavolini may be related to its much higher antioxidant defense levels than P. clavata. Climate change may thus have severe impacts on gorgonian populations and the habitats they provide.}, }
@article {pmid35106548, year = {2022}, author = {Nerva, L and Garcia, JF and Favaretto, F and Giudice, G and Moffa, L and Sandrini, M and Cantu, D and Zanzotto, A and Gardiman, M and Velasco, R and Gambino, G and Chitarra, W}, title = {The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes.}, journal = {Journal of experimental botany}, volume = {73}, number = {8}, pages = {2682-2697}, doi = {10.1093/jxb/erac032}, pmid = {35106548}, issn = {1460-2431}, mesh = {Bacteria/genetics ; *Endophytes ; *Microbiota ; Plants ; Wood ; }, abstract = {The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.}, }
@article {pmid35105377, year = {2022}, author = {Zhang, S and Song, W and Nothias, LF and Couvillion, SP and Webster, N and Thomas, T}, title = {Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {22}, pmid = {35105377}, issn = {2049-2618}, mesh = {Chromatography, Liquid ; *Metabolomics ; *Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species.<br><br>RESULTS: Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms.<br><br>CONCLUSIONS: This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.}, }
@article {pmid35104474, year = {2022}, author = {Yoksan, R and Boontanimitr, A and Klompong, N and Phothongsurakun, T}, title = {Poly(lactic acid)/thermoplastic cassava starch blends filled with duckweed biomass.}, journal = {International journal of biological macromolecules}, volume = {203}, number = {}, pages = {369-378}, doi = {10.1016/j.ijbiomac.2022.01.159}, pmid = {35104474}, issn = {1879-0003}, mesh = {*Araceae ; Biomass ; *Manihot/metabolism ; Polyesters ; Starch/metabolism ; }, abstract = {Duckweed (DW) is a highly small, free-floating aquatic plant. It grows and reproduces rapidly, comprises mainly protein and carbohydrate, and has substantial potential as a feedstock to produce bioplastics due to its renewability and having very little impact on the food chain. The aim of this work was to analyze the effect of DW biomass on the characteristics and properties of bio-based and biodegradable plastics based on a poly(lactic acid)/thermoplastic cassava starch (PLA/TPS) blend. Various amounts of DW biomass were compounded with PLA and TPS in a twin-screw extruder and then converted into dumbbell-shaped specimens using an injection molding machine. The obtained PLA/TPS blends filled with DW biomass exhibited a lower melt flow ability, higher moisture content, and increased surface hydrophilicity than the neat PLA/TPS blend. Incorporation of DW with low concentrations of 2.3 and 4.6 wt% increased the tensile strength, Young's modulus, and hardness of the PLA/TPS blend. Moisture and glycerol from DW and TPS played important roles in reducing the Tg, Tcc, Tm, and Td of PLA in the blends. The current work demonstrated that DW could be used as a biofiller for PLA/TPS blends, and the resulting PLA/TPS blends filled with DW biomass have potential in manufacturing injection-molded articles for sustainable, biodegradable, and short-term use.}, }
@article {pmid35104027, year = {2022}, author = {Dungan, AM and Hartman, LM and Blackall, LL and van Oppen, MJH}, title = {Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana.}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {2940-2956}, pmid = {35104027}, issn = {1365-2672}, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; *Microbiota ; *Rhodobacteraceae ; Seawater/microbiology ; }, abstract = {AIMS: Fourteen percent of all living coral, equivalent to more than all the coral on the Great Barrier Reef, has died in the past decade as a result of climate change-driven bleaching. Inspired by the 'oxidative stress theory of coral bleaching', we investigated whether a bacterial consortium designed to scavenge free radicals could integrate into the host microbiome and improve thermal tolerance of the coral model, Exaiptasia diaphana.<br><br>METHODS AND RESULTS: E.&#xa0;diaphana anemones were inoculated with a consortium of high free radical scavenging (FRS) bacteria, a consortium of congeneric low FRS bacteria, or sterile seawater as a control, then exposed to elevated temperature. Increases in the relative abundance of Labrenzia during the first 2&#xa0;weeks following the last inoculation provided evidence for temporary inoculum integration into the E.&#xa0;diaphana microbiome. Initial uptake of other consortium members was inconsistent, and these bacteria did not persist either in E. diaphana's microbiome over time. Given their non-integration into the host microbiome, the ability of the FRS consortium to mitigate thermal stress could not be assessed. Importantly, there were no physiological impacts (negative or positive) of the bacterial inoculations on the holobiont.<br><br>CONCLUSIONS: The introduced bacteria were not maintained in the anemone microbiome over time, thus, their protective effect is unknown. Achieving long-term integration of bacteria into cnidarian microbiomes remains a research priority.<br><br>Microbiome engineering strategies to mitigate coral bleaching may assist coral reefs in their persistence until climate change has been curbed. This study provides insights that will inform microbiome manipulation approaches in coral bleaching mitigation research.}, }
@article {pmid35104026, year = {2022}, author = {Wood, G and Steinberg, PD and Campbell, AH and Vergés, A and Coleman, MA and Marzinelli, EM}, title = {Host genetics, phenotype and geography structure the microbiome of a foundational seaweed.}, journal = {Molecular ecology}, volume = {31}, number = {7}, pages = {2189-2206}, pmid = {35104026}, issn = {1365-294X}, mesh = {Geography ; *Microbiota/genetics ; *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 {pmid35094708, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and Ernst, M and Hansen, M and Forberg, T and Gopalakrishnan, S and Gilbert, MTP and Bojesen, AM and Kristiansen, K and Limborg, MT}, title = {A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss).}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {21}, pmid = {35094708}, issn = {2049-2618}, mesh = {Animals ; Metagenome ; Metagenomics ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Synbiotics ; }, abstract = {BACKGROUND: Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism.<br><br>RESULTS: Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites.<br><br>CONCLUSION: Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.}, }
@article {pmid35090190, year = {2022}, author = {Bonthond, G and Barilo, A and Allen, RJ and Cunliffe, M and Krueger-Hadfield, SA}, title = {Fungal endophytes vary by species, tissue type, and life cycle stage in intertidal macroalgae.}, journal = {Journal of phycology}, volume = {58}, number = {2}, pages = {330-342}, doi = {10.1111/jpy.13237}, pmid = {35090190}, issn = {1529-8817}, mesh = {Animals ; *Chondrus ; Ecosystem ; Endophytes ; Life Cycle Stages ; *Seaweed ; }, abstract = {Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.}, }
@article {pmid35086740, year = {2022}, author = {Jensen, EL and Díez-Del-Molino, D and Gilbert, MTP and Bertola, LD and Borges, F and Cubric-Curik, V and de Navascués, M and Frandsen, P and Heuertz, M and Hvilsom, C and Jiménez-Mena, B and Miettinen, A and Moest, M and Pečnerová, P and Barnes, I and Vernesi, C}, title = {Ancient and historical DNA in conservation policy.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {5}, pages = {420-429}, doi = {10.1016/j.tree.2021.12.010}, pmid = {35086740}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; DNA ; Policy ; }, abstract = {Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (Ne), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.}, }
@article {pmid35086739, year = {2022}, author = {Formenti, G and Theissinger, K and Fernandes, C and Bista, I and Bombarely, A and Bleidorn, C and Ciofi, C and Crottini, A and Godoy, JA and Höglund, J and Malukiewicz, J and Mouton, A and Oomen, RA and Paez, S and Palsbøll, PJ and Pampoulie, C and Ruiz-López, MJ and Svardal, H and Theofanopoulou, C and de Vries, J and Waldvogel, AM and Zhang, G and Mazzoni, CJ and Jarvis, ED and Bálint, M and , }, title = {The era of reference genomes in conservation genomics.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {3}, pages = {197-202}, doi = {10.1016/j.tree.2021.11.008}, pmid = {35086739}, issn = {1872-8383}, mesh = {Biodiversity ; *Genome ; *Genomics ; }, abstract = {Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.}, }
@article {pmid35056519, year = {2021}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations.}, journal = {Microorganisms}, volume = {10}, number = {1}, pages = {}, pmid = {35056519}, issn = {2076-2607}, abstract = {Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.}, }
@article {pmid35054418, year = {2021}, author = {Rusanova, A and Fedorchuk, V and Toshchakov, S and Dubiley, S and Sutormin, D}, title = {An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {35054418}, issn = {2075-1729}, abstract = {Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus-host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.}, }
@article {pmid35050172, year = {2022}, author = {Ortega, MA and Alvarez-Mon, MA and García-Montero, C and Fraile-Martinez, O and Guijarro, LG and Lahera, G and Monserrat, J and Valls, P and Mora, F and Rodríguez-Jiménez, R and Quintero, J and Álvarez-Mon, M}, title = {Gut Microbiota Metabolites in Major Depressive Disorder-Deep Insights into Their Pathophysiological Role and Potential Translational Applications.}, journal = {Metabolites}, volume = {12}, number = {1}, pages = {}, pmid = {35050172}, issn = {2218-1989}, 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}, 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 {pmid35032344, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT}, title = {Integrative analyses of probiotics, pathogenic infections and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {3201-3216}, doi = {10.1111/jam.15433}, pmid = {35032344}, issn = {1365-2672}, mesh = {Animals ; *Fish Diseases/microbiology ; *Gastrointestinal Microbiome ; Immunity ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Yersinia Infections/microbiology/veterinary ; Yersinia ruckeri ; }, abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, great interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, there is a need to better understand of the host-microbiota interactions after disease responses to optimize the use of probiotics to strengthen disease resilience and recovery.<br><br>METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric red mouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host, which were associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.<br><br>CONCLUSIONS: We discuss the relevance of these results emphasizing the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.<br><br>Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota post infection and the resulting host immune response.}, }
@article {pmid35014869, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Dai, R and He, C and Xu, K and Luo, L and Xiao, L and Zheng, Y and Han, C and Akinyemi, FT and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0126121}, pmid = {35014869}, issn = {2379-5077}, 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}, abstract = {The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe-plant interactions. Different aspects of QS systems in bacteria-plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.}, }
@article {pmid34957693, year = {2022}, author = {Cavill, EL and Liu, S and Zhou, X and Gilbert, MTP}, title = {To bee, or not to bee? One leg is the question.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {1868-1874}, doi = {10.1111/1755-0998.13578}, pmid = {34957693}, issn = {1755-0998}, mesh = {Animals ; Bees/genetics ; DNA/genetics ; Genome ; *Genomics/methods ; Insecta/genetics ; *Museums ; Sequence Analysis, DNA/methods ; }, abstract = {Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry-preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a "minimally destructive" method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry-preserved insects for future genomic studies.}, }
@article {pmid34951090, year = {2022}, author = {Rolli, E and de Zélicourt, A and Alzubaidy, H and Karampelias, M and Parween, S and Rayapuram, N and Han, B and Froehlich, K and Abulfaraj, AA and Alhoraibi, H and Mariappan, K and Andrés-Barrao, C and Colcombet, J and Hirt, H}, title = {The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {223-239}, pmid = {34951090}, issn = {1462-2920}, mesh = {*Arabidopsis/genetics/microbiology ; *Arabidopsis Proteins/genetics ; Enterobacter/genetics ; Plant Immunity ; Salt Tolerance ; }, abstract = {Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>10[8] CFUs ml[-1]), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant-microbe interaction.}, }
@article {pmid34950234, year = {2021}, author = {Iannello, M and Mezzelani, M and Dalla Rovere, G and Smits, M and Patarnello, T and Ciofi, C and Carraro, L and Boffo, L and Ferraresso, S and Babbucci, M and Mazzariol, S and Centelleghe, C and Cardazzo, B and Carrer, C and Varagnolo, M and Nardi, A and Pittura, L and Benedetti, M and Fattorini, D and Regoli, F and Ghiselli, F and Gorbi, S and Bargelloni, L and Milan, M}, title = {Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam.}, journal = {Evolutionary applications}, volume = {14}, number = {12}, pages = {2864-2880}, pmid = {34950234}, issn = {1752-4571}, abstract = {Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.}, }
@article {pmid34946024, year = {2021}, author = {Singh, S and Singh, A and Baweja, V and Roy, A and Chakraborty, A and Singh, IK}, title = {Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946024}, issn = {2076-2607}, abstract = {Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host-microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota-brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect-microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect-microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.}, }
@article {pmid34943189, year = {2021}, author = {Liu, Y and Liao, X and Han, T and Su, A and Guo, Z and Lu, N and He, C and Lu, Z}, title = {Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont.}, journal = {Biology}, volume = {10}, number = {12}, pages = {}, pmid = {34943189}, issn = {2079-7737}, abstract = {Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.}, }
@article {pmid34933781, year = {2022}, author = {Bianciotto, V and Selosse, MA and Martos, F and Marmeisse, R}, title = {Herbaria preserve plant microbiota responses to environmental changes.}, journal = {Trends in plant science}, volume = {27}, number = {2}, pages = {120-123}, doi = {10.1016/j.tplants.2021.11.012}, pmid = {34933781}, issn = {1878-4372}, mesh = {*Microbiota ; *Plants ; }, abstract = {Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.}, }
@article {pmid34932575, year = {2021}, author = {Maltseva, AL and Varfolomeeva, MA and Gafarova, ER and Panova, MAZ and Mikhailova, NA and Granovitch, AI}, title = {Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260792}, pmid = {34932575}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Environmental Microbiology ; *Genetic Variation ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/classification/*microbiology ; Species Specificity ; }, abstract = {Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207-603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species-specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome ("scaffolding enterotype") is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.}, }
@article {pmid34931883, year = {2021}, author = {Der Sarkissian, C and Velsko, IM and Fotakis, AK and Vågene, &#xc5;J and Hübner, A and Fellows Yates, JA}, title = {Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0131521}, pmid = {34931883}, issn = {2379-5077}, abstract = {Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions &amp; Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.}, }
@article {pmid34927107, year = {2021}, author = {Cáceres, PFF and Vélez, LP and Junca, H and Moreno-Herrera, CX}, title = {Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100086}, pmid = {34927107}, issn = {2666-5174}, abstract = {Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities' compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.}, }
@article {pmid34926833, year = {2021}, author = {Sinding, MS and Gopalakrishnan, S and Raundrup, K and Dalén, L and Threlfall, J and ,  and ,  and ,  and ,  and ,  and Gilbert, T}, title = {The genome sequence of the grey wolf, Canis lupus Linnaeus 1758.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {310}, pmid = {34926833}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.}, }
@article {pmid34922182, year = {2022}, author = {Formosinho, J and Bencard, A and Whiteley, L}, title = {Environmentality in biomedicine: microbiome research and the perspectival body.}, journal = {Studies in history and philosophy of science}, volume = {91}, number = {}, pages = {148-158}, doi = {10.1016/j.shpsa.2021.11.005}, pmid = {34922182}, issn = {0039-3681}, mesh = {Causality ; Ecology ; Humans ; *Microbiota ; }, abstract = {Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool - environmentality - to think through this problem. Environmentality is the state or quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health.}, }
@article {pmid34917118, year = {2021}, author = {Cesaro, P and Gamalero, E and Zhang, J and Pivato, B}, title = {Editorial: The Plant Holobiont Volume I: Microbiota as Part of the Holobiont; Challenges for Agriculture.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {799168}, pmid = {34917118}, issn = {1664-462X}, }
@article {pmid34912564, year = {2021}, author = {Watson, SA and Neo, ML}, title = {Conserving threatened species during rapid environmental change: using biological responses to inform management strategies of giant clams.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coab082}, pmid = {34912564}, issn = {2051-1434}, abstract = {Giant clams are threatened by overexploitation for human consumption, their valuable shells and the aquarium trade. Consequently, these iconic coral reef megafauna are extinct in some former areas of their range and are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and Convention on International Trade in Endangered Species of Wild Fauna and Flora. Now, giant clams are also threatened by rapid environmental change from both a suite of local and regional scale stressors and global change, including climate change, global warming, marine heatwaves and ocean acidification. The interplay between local- to regional-scale and global-scale drivers is likely to cause an array of lethal and sub-lethal effects on giant clams, potentially limiting their depth distribution on coral reefs and decreasing suitable habitat area within natural ranges of species. Global change stressors, pervasive both in unprotected and protected areas, threaten to diminish conservation efforts to date. International efforts urgently need to reduce carbon dioxide emissions to avoid lethal and sub-lethal effects of global change on giant clams. Meanwhile, knowledge of giant clam physiological and ecological responses to local-regional and global stressors could play a critical role in conservation strategies of these threatened species through rapid environmental change. Further work on how biological responses translate into habitat requirements as global change progresses, selective breeding for resilience, the capacity for rapid adaptive responses of the giant clam holobiont and valuing tourism potential, including recognizing giant clams as a flagship species for coral reefs, may help improve the prospects of these charismatic megafauna over the coming decades.}, }
@article {pmid34911766, year = {2021}, author = {Jaspers, C and Ehrlich, M and Pujolar, JM and Künzel, S and Bayer, T and Limborg, MT and Lombard, F and Browne, WE and Stefanova, K and Reusch, TBH}, title = {Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {51}, pages = {}, pmid = {34911766}, issn = {1091-6490}, mesh = {Animal Distribution ; Animals ; Ctenophora/*genetics/physiology ; *Genetic Variation ; Genome ; *Genomics ; Introduced Species ; }, abstract = {Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.}, }
@article {pmid34905712, year = {2021}, author = {Chapron, L and Galand, PE and Pruski, AM and Peru, E and Vétion, G and Robin, S and Lartaud, F}, title = {Resilience of cold-water coral holobionts to thermal stress.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1965}, pages = {20212117}, pmid = {34905712}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Mediterranean Sea ; *Microbiota ; Seawater ; Water ; }, abstract = {Cold-water corals are threatened by global warming, especially in the Mediterranean Sea where they live close to their upper known thermal limit (i.e. 13°C), yet their response to rising temperatures is not well known. Here, temperature effects on Lophelia pertusa and Madrepora oculata holobionts (i.e. the host and its associated microbiome) were investigated. We found that at warmer seawater temperature (+2°C), L. pertusa showed a modification of its microbiome prior to a change in behaviour, leading to lower energy reserves and skeletal growth, whereas M. oculata was more resilient. At extreme temperature (+4°C), both species quickly lost their specific bacterial signature followed by lower physiological activity prior to death. In addition, our results showing the holobionts' negative response to colder temperatures (-3°C), suggest that Mediterranean corals live close to their thermal optimum. The species-specific response to temperature change highlights that global warming may affect dramatically the main deep-sea reef-builders, which would alter the associated biodiversity and related ecosystem services.}, }
@article {pmid34899619, year = {2021}, author = {Barreto, MM and Ziegler, M and Venn, A and Tambutté, E and Zoccola, D and Tambutté, S and Allemand, D and Antony, CP and Voolstra, CR and Aranda, M}, title = {Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {707674}, pmid = {34899619}, issn = {1664-302X}, abstract = {Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.}, }
@article {pmid34896508, year = {2022}, author = {Lin, Z and Wang, L and Chen, M and Zheng, X and Chen, J}, title = {Proteome and microbiota analyses characterizing dynamic coral-algae-microbe tripartite interactions under simulated rapid ocean acidification.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152266}, doi = {10.1016/j.scitotenv.2021.152266}, pmid = {34896508}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Homeostasis ; Hydrogen-Ion Concentration ; *Microbiota ; Oceans and Seas ; Proteome ; Seawater ; }, abstract = {Ocean acidification (OA) is a pressing issue currently and in the future for coral reefs. The importance of maintenance interactions among partners of the holobiont association in the stress response is well appreciated; however, the candidate molecular and microbial mechanisms that underlie holobiont stress resilience or susceptibility remain unclear. Here, to assess the effects of rapid pH change on coral holobionts at both the protein and microbe levels, combined proteomics and microbiota analyses of the scleractinian coral Galaxea fascicularis exposed to three relevant OA scenarios, including current (pHT = 8.15), preindustrial (pHT = 8.45) and future IPCC-2100 scenarios (pHT = 7.85), were conducted. The results demonstrated that pH changes had no significant effect on the physiological calcification rate of G. fascicularis in a 10-day experiment; however, significant differences were recorded in the proteome and 16S profiling. Proteome variance analysis identified some of the core biological pathways in coral holobionts, including coral host infection and immune defence, and maintaining metabolic compatibility involved in energy homeostasis, nutrient cycling, antibiotic activity and carbon budgets of coral-Symbiodiniaceae interactions were key mechanisms in the early OA stress response. Furthermore, microbiota changes indicate substantial microbial community and functional disturbances in response to OA stress, potentially compromising holobiont health and fitness. Our results may help to elucidate many complex mechanisms to describe scleractinian coral holobiont responses to OA and raise interesting questions for future studies.}, }
@article {pmid34861476, year = {2022}, author = {van de Water, JA and Tignat-Perrier, R and Allemand, D and Ferrier-Pagès, C}, title = {Coral holobionts and biotechnology: from Blue Economy to coral reef conservation.}, journal = {Current opinion in biotechnology}, volume = {74}, number = {}, pages = {110-121}, doi = {10.1016/j.copbio.2021.10.013}, pmid = {34861476}, issn = {1879-0429}, mesh = {Animals ; *Anthozoa ; Bionics ; *Coral Reefs ; Ecosystem ; Photosynthesis ; }, abstract = {Corals are of ecological and economic importance, providing habitat for species and contributing to coastal protection, fisheries, and tourism. Their biotechnological potential is also increasingly recognized. Particularly, the production of pharmaceutically interesting compounds by corals and their microbial associates stimulated natural product-based drug discovery. The efficient light distribution by coral skeletons for optimal photosynthesis by algal symbionts has led to 3D-printed bionic corals that may be used to upscale micro-algal cultivation for bioenergy generation. However, corals are under threat from climate change and pollution, and biotechnological approaches to increase their resilience, like 'probiotics' and 'assisted evolution', are being evaluated. In this review, we summarize the recent biotechnological developments related to corals with an emphasis on coral conservation, drug discovery and bioenergy.}, }
@article {pmid34861071, year = {2022}, author = {Armstrong, EE and Perez-Lamarque, B and Bi, K and Chen, C and Becking, LE and Lim, JY and Linderoth, T and Krehenwinkel, H and Gillespie, RG}, title = {A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates.}, journal = {Molecular ecology}, volume = {31}, number = {4}, pages = {1299-1316}, doi = {10.1111/mec.16301}, pmid = {34861071}, issn = {1365-294X}, mesh = {Animals ; Geography ; Hawaii ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Spiders/genetics ; }, abstract = {The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawai'i, and outgroup taxa on older islands, we tested whether each component of the "holobiont" (spider hosts, intracellular endosymbionts and gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. To investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. The results showed that the host A. waikula is indeed structured by geographical isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawai'i. Conversely, the gut microbiota, which we suspect is generally environmentally derived, was largely conserved across all populations and species. Our results show that different components of the holobiont respond in distinct ways to the dynamic environment of the volcanic archipelago. This highlights the necessity of understanding the interplay between different components of the holobiont, to properly characterize its evolution.}, }
@article {pmid34857934, year = {2022}, author = {Rädecker, N and Pogoreutz, C and Gegner, HM and Cárdenas, A and Perna, G and Geißler, L and Roth, F and Bougoure, J and Guagliardo, P and Struck, U and Wild, C and Pernice, M and Raina, JB and Meibom, A and Voolstra, CR}, title = {Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1110-1118}, pmid = {34857934}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/metabolism ; Coral Reefs ; Heat-Shock Response ; Nitrogen/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Symbiosis ; }, abstract = {Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.}, }
@article {pmid34853170, year = {2021}, author = {Wolinska, KW and Vannier, N and Thiergart, T and Pickel, B and Gremmen, S and Piasecka, A and Piślewska-Bednarek, M and Nakano, RT and Belkhadir, Y and Bednarek, P and Hacquard, S}, title = {Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {49}, pages = {}, pmid = {34853170}, issn = {1091-6490}, mesh = {Arabidopsis/*metabolism/microbiology ; Arabidopsis Proteins/metabolism ; Bacteria/metabolism ; Dysbiosis/metabolism ; Fungi/metabolism ; Microbiota/genetics/physiology ; Mycoses/metabolism ; Oomycetes/metabolism ; Plant Development ; Plant Roots/*growth &amp; development/metabolism/microbiology ; Soil Microbiology ; Symbiosis/physiology ; Tryptophan/*metabolism ; }, abstract = {In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host-microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.}, }
@article {pmid34835139, year = {2021}, author = {Olesen, AS and Kodama, M and Lohse, L and Accensi, F and Rasmussen, TB and Lazov, CM and Limborg, MT and Gilbert, MTP and Bøtner, A and Belsham, GJ}, title = {Identification of African Swine Fever Virus Transcription within Peripheral Blood Mononuclear Cells of Acutely Infected Pigs.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34835139}, issn = {1999-4915}, mesh = {African Swine Fever/*virology ; *African Swine Fever Virus/genetics/isolation &amp; purification ; Animals ; Gene Expression Regulation, Viral ; *Genome, Viral ; Leukocytes, Mononuclear ; Male ; Swine ; }, abstract = {African swine fever virus (ASFV) has become widespread in Europe, Asia and elsewhere, thereby causing extensive economic losses. The viral genome includes nearly 200 genes, but their expression within infected pigs has not been well characterized previously. In this study, four pigs were infected with a genotype II strain (ASFV POL/2015/Podlaskie); blood samples were collected before inoculation and at both 3 and 6 days later. During this period, a range of clinical signs of infection became apparent in the pigs. From the blood, peripheral blood mononuclear cells (PBMCs) were isolated. The transcription of the ASFV genes was determined using RNAseq on poly(A)+ mRNAs isolated from these cells. Only very low levels of virus transcription were detected in the PBMCs at 3 days post-inoculation (dpi) but, at 6 dpi, extensive transcription was apparent. This was co-incident with a large increase in the level of ASFV DNA within these cells. The pattern of the virus gene expression was very reproducible between the individual pigs. Many highly expressed genes have undefined roles. Surprisingly, some genes with key roles in virus replication were expressed at only low levels. As the functions of individual genes are identified, information about their expression becomes important for understanding their contribution to virus biology.}, }
@article {pmid34821475, year = {2021}, author = {Kopprio, GA and Luyen, ND and Cuong, LH and Duc, TM and Fricke, A and Kunzmann, A and Huong, LM and Gärdes, A}, title = {Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1253}, pmid = {34821475}, issn = {2045-8827}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Caulerpa/*microbiology/physiology ; Host Microbial Interactions ; *Microbiota ; Plant Diseases/*microbiology ; }, abstract = {The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.}, }
@article {pmid34820166, year = {2021}, author = {Price, DC and Brennan, JR and Wagner, NE and Egizi, AM}, title = {Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12313}, pmid = {34820166}, issn = {2167-8359}, abstract = {Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome-the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick's own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.}, }
@article {pmid34820163, year = {2021}, author = {Liu, S and Zhang, SM and Buddenborg, SK and Loker, ES and Bonning, BC}, title = {Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12290}, pmid = {34820163}, issn = {2167-8359}, support = {R37 AI101438/AI/NIAID NIH HHS/United States ; }, abstract = {Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.}, }
@article {pmid34811423, year = {2021}, author = {Alberdi, A and Martin Bideguren, G and Aizpurua, O}, title = {Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22660}, pmid = {34811423}, issn = {2045-2322}, mesh = {Animals ; Animals, Wild ; Animals, Zoo/*microbiology ; Bacteria/classification ; Cluster Analysis ; Computational Biology ; Ecology ; *Gastrointestinal Microbiome ; Humans ; Mammals/*microbiology ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Species Specificity ; Vertebrates ; }, abstract = {The gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species. Our analyses yielded no overall pattern of diversity and compositional variation between wild and captive vertebrates, but a heterogeneous landscape of responses, which differed depending on the components of diversity considered. Captive populations showed enrichment patterns of human-associated microorganisms, and the minimal host phylogenetic signal suggests that changes between wild and captive populations are mainly driven by case-specific captivity conditions. Finally, we show that microbiota differences between wild and captive populations can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.}, }
@article {pmid34802818, year = {2022}, author = {Marana, MH and Poulsen, R and Thormar, EA and Clausen, CG and Thit, A and Mathiessen, H and Jaafar, R and Korbut, R and Hansen, AMB and Hansen, M and Limborg, MT and Syberg, K and von Gersdorff Jørgensen, L}, title = {Plastic nanoparticles cause mild inflammation, disrupt metabolic pathways, change the gut microbiota and affect reproduction in zebrafish: A full generation multi-omics study.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt D}, pages = {127705}, doi = {10.1016/j.jhazmat.2021.127705}, pmid = {34802818}, issn = {1873-3336}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; Inflammation/chemically induced ; Male ; Metabolic Networks and Pathways ; *Microplastics ; Reproduction ; Zebrafish ; }, abstract = {Plastic pollution has become a major concern on a global scale. The plastic is broken down into minuscule particles, which have an impact on the biosystems, however long-term impacts through an entire generation is largely unknown. Here, we present the first whole generation study exposing fish to a 500 nm polystyrene plastic particle at environmentally relevant concentrations. Short- and long-term adverse effects were investigated in the zebrafish model organism using a holistic multi-omics approach. The particles accumulated in the yolk sac of young larvae and short-term biological impacts included immune-relevant gene regulation related to inflammation and tolerance as well as disruption of metabolic processes, such as the fatty acid and lipid pathways. The long-term effects comprised gene regulations pointing towards skin and/or gill inflammation, dysbiosis of the gut microbiota, a tendency towards decreased condition factor in adult males as well as a lowered reproductive capability. From this study, it can be concluded that exposures to plastic nanoparticles have an impact on population as well as ecosystem level in fish and likely also in other vertebrates.}, }
@article {pmid34800848, year = {2022}, author = {Cerrano, C and Giovine, M and Steindler, L}, title = {Petrosia ficiformis (Poiret, 1789): an excellent model for holobiont and biotechnological studies.}, journal = {Current opinion in biotechnology}, volume = {74}, number = {}, pages = {61-65}, doi = {10.1016/j.copbio.2021.10.022}, pmid = {34800848}, issn = {1879-0429}, mesh = {Animals ; Biotechnology ; *Petrosia ; Phylogeny ; *Porifera ; Symbiosis ; }, }
@article {pmid34798282, year = {2022}, author = {Decroës, A and Li, JM and Richardson, L and Mutasa-Gottgens, E and Lima-Mendez, G and Mahillon, M and Bragard, C and Finn, RD and Legrève, A}, title = {Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.}, journal = {Genomics}, volume = {114}, number = {1}, pages = {9-22}, doi = {10.1016/j.ygeno.2021.11.018}, pmid = {34798282}, issn = {1089-8646}, mesh = {*Genome, Mitochondrial ; Genomics ; Metagenomics ; *Plasmodiophorida/genetics ; }, abstract = {Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.}, }
@article {pmid34788073, year = {2022}, author = {Xiang, N and Hassenrück, C and Pogoreutz, C and Rädecker, N and Simancas-Giraldo, SM and Voolstra, CR and Wild, C and Gärdes, A}, title = {Contrasting Microbiome Dynamics of Putative Denitrifying Bacteria in Two Octocoral Species Exposed to Dissolved Organic Carbon (DOC) and Warming.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {2}, pages = {e0188621}, pmid = {34788073}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Coral Reefs ; Dissolved Organic Matter ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.}, }
@article {pmid34765156, year = {2021}, author = {Morrissey, KL and Iveša, L and Delva, S and D'Hondt, S and Willems, A and De Clerck, O}, title = {Impacts of environmental stress on resistance and resilience of algal-associated bacterial communities.}, journal = {Ecology and evolution}, volume = {11}, number = {21}, pages = {15004-15019}, pmid = {34765156}, issn = {2045-7758}, abstract = {Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche-specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea. Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo-, epi-, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes.}, }
@article {pmid34749049, year = {2022}, author = {Thatcher, C and Høj, L and Bourne, DG}, title = {Probiotics for coral aquaculture: challenges and considerations.}, journal = {Current opinion in biotechnology}, volume = {73}, number = {}, pages = {380-386}, doi = {10.1016/j.copbio.2021.09.009}, pmid = {34749049}, issn = {1879-0429}, mesh = {Animals ; *Anthozoa/microbiology ; Aquaculture ; Climate Change ; Coral Reefs ; *Probiotics ; }, abstract = {Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.}, }
@article {pmid34737272, year = {2021}, author = {Dubé, CE and Ziegler, M and Mercière, A and Boissin, E and Planes, S and Bourmaud, CA and Voolstra, CR}, title = {Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6402}, pmid = {34737272}, issn = {2041-1723}, mesh = {Coral Reefs ; Ecosystem ; Genotype ; Microbiota/genetics/*physiology ; }, abstract = {Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.}, }
@article {pmid34734290, year = {2021}, author = {Higuita Palacio, MF and Montoya, OI and Saldamando, CI and García-Bonilla, E and Junca, H and Cadavid-Restrepo, GE and Moreno-Herrera, CX}, title = {Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia.}, journal = {Journal of insect science (Online)}, volume = {21}, number = {6}, pages = {}, pmid = {34734290}, issn = {1536-2442}, mesh = {Animals ; Colombia ; *Enterococcus ; *Gastrointestinal Microbiome ; Larva ; *Seasons ; Spodoptera/*microbiology ; Zea mays ; }, abstract = {Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.}, }
@article {pmid34721372, year = {2021}, author = {Wale, M and Daffonchio, D and Fusi, M and Marasco, R and Garuglieri, E and Diele, K}, title = {The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {770245}, pmid = {34721372}, issn = {1664-302X}, }
@article {pmid34718260, year = {2021}, author = {Banić, M and Pleško, S and Urek, M and Babić, &#x17d; and Kardum, D}, title = {Immunosenescence, Inflammaging and Resilience: An Evolutionary Perspective of Adaptation in the Light of COVID-19 Pandemic.}, journal = {Psychiatria Danubina}, volume = {33}, number = {Suppl 4}, pages = {427-431}, pmid = {34718260}, issn = {0353-5053}, mesh = {Aged ; Aging ; *COVID-19 ; Humans ; Immunity, Innate ; *Immunosenescence ; Inflammation ; Lymphocytes ; Pandemics ; SARS-CoV-2 ; }, abstract = {The evolution of immunology enabled the study of role of innate and adaptive immunity in systems biology network of immunosenescence and inflammaging. Due to global reduction in birth rates and reduced mortality, in year 2025 there will be about 1.2 billion of people over age of sixty, worldwide. The notion that the real age is not chronological, but the biological one led to the concept of "bioage", defining the biologic reactivity and resilience, including the immune competence of an individual. A competent immune network, systemic and mucosal is intrinsic to resilience and homeostasis of the human holobiont as the unit of evolution. In elderly, the immunosenescence could be associated with higher levels of proinflammatory mediators (such as IL-6), frialty and mortality. Proi-inflammatory state in elderly is denoted as inflammaging, characterized with low-grade (sterile) inflammation, as a physiologic response to life-long antigenic stimuli. When under control, inflammaging could be regarded as an efficient defense mechanism, oposed and regulated by anti-inflammatory pathways and molecules. Immunosensecence. The emerging concepts of "individual immunobiography" and "trained immunity" speak in favour that the immunological experience during the life would shape the ability of each individual to respond to various stimuli, strongly influencing the elements of innate and adaptive immunity, including macrophages and innate lymphoid cells. Older age is one of the main risk factors for the severe clinical picture and adverse outcome of COVID-19 infection, due to immunosenscence and chronic low-grade inflammation (inflammaging), both characterizing the immune reactioin in elderly. The senescent immune system, along with the advanced process of inflammaging is prone to react with uncontrolled activation of innate immune response that leads to cytokine release syndrome, tissue damage and adverse outcome of infection. Further research is aimed to nutritional and pharmacologic (immunomodulatory) interventions to influence the process of bioaging and immunosenscence, and to modulate the reaction of elderly to infection, including the COVID-19.}, }
@article {pmid34714176, year = {2021}, author = {Czernik, PJ and Golonka, RM and Chakraborty, S and Yeoh, BS and Abokor, AA and Saha, P and Yeo, JY and Mell, B and Cheng, X and Baroi, S and Tian, Y and Patterson, AD and Joe, B and Vijay-Kumar, M and Lecka-Czernik, B}, title = {Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content.}, journal = {Physiological genomics}, volume = {53}, number = {12}, pages = {518-533}, pmid = {34714176}, issn = {1531-2267}, support = {R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Adipocytes/metabolism ; Animals ; Bacteria/*genetics/*metabolism ; Bone Density/physiology ; Bone Development/*physiology ; Bone Marrow Cells/*metabolism ; Cell Proliferation/physiology ; Chondrocytes/metabolism ; Coprophagia ; Dysbiosis ; Fatty Acids, Volatile/analysis/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Germ-Free Life ; Host Microbial Interactions/*genetics ; Male ; Osteogenesis/*physiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Integration of microbiota in a host begins at birth and progresses during adolescence, forming a multidirectional system of physiological interactions. Here, we present an instantaneous effect of natural, bacterial gut colonization on the acceleration of longitudinal and radial bone growth in germ-free born, 7-wk-old male rats. Changes in bone mass and structure were analyzed after 10 days following the onset of colonization through cohousing with conventional rats and revealed unprecedented acceleration of bone accrual in cortical and trabecular compartments, increased bone tissue mineral density, improved proliferation and hypertrophy of growth plate chondrocytes, bone lengthening, and preferential deposition of periosteal bone in the tibia diaphysis. In addition, the number of small in size adipocytes increased, whereas the number of megakaryocytes decreased, in the bone marrow of conventionalized germ-free rats indicating that not only bone mass but also bone marrow environment is under control of gut microbiota signaling. The changes in bone status paralleled with a positive shift in microbiota composition toward short-chain fatty acids (SCFA)-producing microbes and a considerable increase in cecal SCFA concentrations, specifically butyrate. Furthermore, reconstitution of the host holobiont increased hepatic expression of IGF-1 and its circulating levels. Elevated serum levels of 25-hydroxy vitamin D and alkaline phosphatase pointed toward an active process of bone formation. The acute stimulatory effect on bone growth occurred independently of body mass increase. Overall, the presented model of conventionalized germ-free rats could be used to study microbiota-based therapeutics for combatting dysbiosis-related bone disorders.}, }
@article {pmid34713541, year = {2022}, author = {Iltis, C and Tougeron, K and Hance, T and Louâpre, P and Foray, V}, title = {A perspective on insect-microbe holobionts facing thermal fluctuations in a climate-change context.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {18-29}, doi = {10.1111/1462-2920.15826}, pmid = {34713541}, issn = {1462-2920}, mesh = {Animals ; *Climate Change ; Heat-Shock Response ; *Insecta ; Symbiosis ; Temperature ; }, abstract = {Temperature influences the ecology and evolution of insects and their symbionts by impacting each partner independently and their interactions, considering the holobiont as a primary unit of selection. There are sound data about the responses of these partnerships to constant temperatures and sporadic thermal stress (mostly heat shock). However, the current understanding of the thermal ecology of insect-microbe holobionts remains patchy because the complex thermal fluctuations (at different spatial and temporal scales) experienced by these organisms in nature have often been overlooked experimentally. This may drastically constrain our ability to predict the fate of mutualistic interactions under climate change, which will alter both mean temperatures and thermal variability. Here, we tackle down these issues by focusing on the effects of temperature fluctuations on the evolutionary ecology of insect-microbe holobionts. We propose potentially worth-investigating research avenues to (i) evaluate the relevance of theoretical concepts used to predict the biological impacts of temperature fluctuations when applied to holobionts; (ii) acknowledge the plastic (behavioural thermoregulation, physiological acclimation) and genetic responses (evolution) expressed by holobionts in fluctuating thermal environments; and (iii) explore the potential impacts of previously unconsidered patterns of temperature fluctuations on the outcomes and the dynamic of these insect-microbe associations.}, }
@article {pmid34712923, year = {2021}, author = {Sinding, MS and Ciucani, MM and Ramos-Madrigal, J and Carmagnini, A and Rasmussen, JA and Feng, S and Chen, G and Vieira, FG and Mattiangeli, V and Ganjoo, RK and Larson, G and Sicheritz-Pontén, T and Petersen, B and Frantz, L and Gilbert, MTP and Bradley, DG}, title = {Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos.}, journal = {iScience}, volume = {24}, number = {11}, pages = {103226}, pmid = {34712923}, issn = {2589-0042}, abstract = {The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.}, }
@article {pmid34711286, year = {2021}, author = {Aizpurua, O and Nyholm, L and Morris, E and Chaverri, G and Herrera Montalvo, LG and Flores-Martinez, JJ and Lin, A and Razgour, O and Gilbert, MTP and Alberdi, A}, title = {The role of the gut microbiota in the dietary niche expansion of fishing bats.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {76}, pmid = {34711286}, issn = {2524-4671}, abstract = {BACKGROUND: Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.<br><br>RESULTS: We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish.<br><br>CONCLUSIONS: Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory.}, }
@article {pmid34710723, year = {2022}, author = {Varasteh, T and Tschoeke, D and Silva-Lima, AW and Thompson, C and Thompson, F}, title = {Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100912}, doi = {10.1016/j.margen.2021.100912}, pmid = {34710723}, issn = {1876-7478}, mesh = {Animals ; *Anthozoa/genetics ; Biological Transport ; Brazil ; Transcriptome ; }, abstract = {A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.}, }
@article {pmid34709051, year = {2021}, author = {Mead, OL and Hahn, EE and Adamska, MA}, title = {Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn.}, journal = {Microbiology resource announcements}, volume = {10}, number = {43}, pages = {e0085821}, pmid = {34709051}, issn = {2576-098X}, abstract = {Sponges have complex relationships with bacteria, the roles of which include food, important components of the holobiont, pathogens, and accidentally accumulated elements of the environment. Consequently, sponges are reservoirs of microbial genomes and novel compounds. Therefore, we isolated and sequenced the whole genomes of bacterial species from the calcareous sponge Sycon capricorn.}, }
@article {pmid34699617, year = {2022}, author = {Shoguchi, E}, title = {Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae).}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {1-11}, pmid = {34699617}, issn = {1529-8817}, mesh = {*Amino Acids/biosynthesis ; Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; Symbiosis ; }, abstract = {Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.}, }
@article {pmid34697892, year = {2021}, author = {Merges, D and Dal Grande, F and Greve, C and Otte, J and Schmitt, I}, title = {Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6637-6650}, doi = {10.1111/1462-2920.15802}, pmid = {34697892}, issn = {1462-2920}, mesh = {*Ascomycota/genetics ; *Bacteriophages/genetics ; Genome, Viral/genetics ; *Lichens/genetics/microbiology ; Metagenome ; Phylogeny ; Symbiosis ; }, abstract = {Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.}, }
@article {pmid34685796, year = {2021}, author = {Alotaibi, F and Lee, SJ and St-Arnaud, M and Hijri, M}, title = {Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {34685796}, issn = {2223-7747}, 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 {pmid34675394, year = {2022}, author = {Alberdi, A and Andersen, SB and Limborg, MT and Dunn, RR and Gilbert, MTP}, title = {Disentangling host-microbiota complexity through hologenomics.}, journal = {Nature reviews. Genetics}, volume = {23}, number = {5}, pages = {281-297}, pmid = {34675394}, issn = {1471-0064}, mesh = {Animals ; Biological Evolution ; *Microbiota/genetics ; }, abstract = {Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.}, }
@article {pmid34674103, year = {2021}, author = {Bonthond, G and Shalygin, S and Bayer, T and Weinberger, F}, title = {Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont.}, journal = {Antonie van Leeuwenhoek}, volume = {114}, number = {12}, pages = {2189-2203}, pmid = {34674103}, issn = {1572-9699}, 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 &#x3b1;-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.<br><br>CONCLUSION: We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.}, }
@article {pmid34641725, year = {2021}, author = {Muller, EM and Dungan, AM and Million, WC and Eaton, KR and Petrik, C and Bartels, E and Hall, ER and Kenkel, CD}, title = {Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1960}, pages = {20210923}, pmid = {34641725}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/genetics ; *Climate Change ; Coral Reefs ; Ecosystem ; Endangered Species ; }, abstract = {Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.}, }
@article {pmid34638430, year = {2021}, author = {Oldenburg, M and Rüchel, N and Janssen, S and Borkhardt, A and Gössling, KL}, title = {The Microbiome in Childhood Acute Lymphoblastic Leukemia.}, journal = {Cancers}, volume = {13}, number = {19}, pages = {}, pmid = {34638430}, issn = {2072-6694}, abstract = {For almost 30 years, the term "holobiont" has referred to an ecological unit where a host (e.g., human) and all species living in or around it are considered together. The concept highlights the complex interactions between the host and the other species, which, if disturbed may lead to disease and premature aging. Specifically, the impact of microbiome alterations on the etiology of acute lymphoblastic leukemia (ALL) in children is not fully understood, but has been the focus of much research in recent years. In ALL patients, significant reductions in microbiome diversity are already observable at disease onset. It remains unclear whether such alterations at diagnosis are etiologically linked with leukemogenesis or simply due to immunological alteration preceding ALL onset. Regardless, all chemotherapeutic treatment regimens severely affect the microbiome, accompanied by severe side effects, including mucositis, systemic inflammation, and infection. In particular, dominance of Enterococcaceae is predictive of infections during chemotherapy. Long-term dysbiosis, like depletion of Faecalibacterium, has been observed in ALL survivors. Modulation of the microbiome (e.g., by fecal microbiota transplant, probiotics, or prebiotics) is currently being researched for potential protective effects. Herein, we review the latest microbiome studies in pediatric ALL patients.}, }
@article {pmid34637727, year = {2021}, author = {Duchêne, DA}, title = {Phylogenomics.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {R1177-R1181}, doi = {10.1016/j.cub.2021.07.039}, pmid = {34637727}, issn = {1879-0445}, mesh = {Biological Evolution ; *Evolution, Molecular ; Genome ; *Genomics ; Phylogeny ; }, abstract = {The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s. These methods depend on our understanding of how nucleotide or amino acid sequences evolve through time and in different lineages. Armed with this knowledge, researchers can make inferences about the relationships and amount of genomic divergence among species.}, }
@article {pmid34635054, year = {2021}, author = {Fontsere, C and Frandsen, P and Hernandez-Rodriguez, J and Niemann, J and Scharff-Olsen, CH and Vallet, D and Le Gouar, P and Ménard, N and Navarro, A and Siegismund, HR and Hvilsom, C and Gilbert, MTP and Kuhlwilm, M and Hughes, D and Marques-Bonet, T}, title = {The genetic impact of an Ebola outbreak on a wild gorilla population.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {735}, pmid = {34635054}, issn = {1471-2164}, mesh = {Animals ; Disease Outbreaks ; *Gastrointestinal Microbiome ; Gorilla gorilla/genetics ; *Hemorrhagic Fever, Ebola/epidemiology/veterinary ; Humans ; Pan troglodytes ; }, abstract = {BACKGROUND: Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population.<br><br>RESULTS: Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival.<br><br>CONCLUSION: This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.}, }
@article {pmid34612522, year = {2022}, author = {Kaniewska, P and Sampayo, EM}, title = {Macro- and micro-scale adaptations allow distinct Stylophora pistillata-symbiodiniaceae holobionts to optimize performance across a broad light habitat.}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {55-70}, doi = {10.1111/jpy.13215}, pmid = {34612522}, issn = {1529-8817}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida/physiology ; Ecosystem ; Symbiosis/physiology ; }, abstract = {In sessile organisms, phenotypic plasticity represents an important strategy for dealing with environmental variability. Here we test if phenotypic plasticity enables the common coral Stylophora pistillata to occupy a broad niche. We find clear differences in the photo-physiology of four putative species of photosynthetic dinoflagellate symbionts associated with the coral S. pistillata, namely, Cladocopium 'C35a', 'C79', 'C78a' and 'C8a'. Coral phenotypic responses were also tightly linked to symbiont identity. Corals with Cladocopium 'C8a' have more "open" macro-morphology compared to colonies associating with depth-restricted Cladocopium 'C35a' or 'C78a' in the same shallow water habitat. Corals with Cladocopium 'C8a' had 40 to 60% lower symbiont cell densities compared to other holobionts but were more efficient at acclimating over a range of light levels, with clear mechanisms to dissipate excess light energy. This holobiont contains host-based green fluorescent pigments, increased concentrations of symbiont-based mycosporine amino acids, and xanthophyll cycling in high light habitats. Photosynthetic efficiency was also adjusted over the light habitat. In contrast, limited micro-scale responses were observed between three depth-restricted symbionts: Cladocopium 'C79', 'C35a', and 'C78a'. To optimize light levels reaching the photosynthetic unit, these colonies rely on a more closed macro-morphology under high light levels, which reduces incident light levels by up to 43%, and higher symbiont densities . Our results show that distinct macro- and micro-scale adaptations lead to functional differences between four distinct S. pistillata holobionts, allowing them to co-exist by filling specific niches on a small, but environmentally diverse, spatial scale. Key index words: Light, Symbiodiniaceae, coral, pigments, Stylophora pistillata, ITS2, phenotypic plasticity, niche diversification.}, }
@article {pmid34606240, year = {2021}, author = {Webster, TM and McFarland, A and Gebert, MJ and Oliverio, AM and Nichols, LM and Dunn, RR and Hartmann, EM and Fierer, N}, title = {Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {20}, pages = {14105-14114}, doi = {10.1021/acs.est.1c03309}, pmid = {34606240}, issn = {1520-5851}, mesh = {*Drinking Water ; Humans ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; United States ; Water Microbiology ; }, abstract = {Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.}, }
@article {pmid34597574, year = {2022}, author = {Zhang, Y and Ip, JC and Xie, JY and Yeung, YH and Sun, Y and Qiu, JW}, title = {Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150656}, doi = {10.1016/j.scitotenv.2021.150656}, pmid = {34597574}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/genetics ; Chlorophyll A ; Coral Reefs ; Plant Leaves ; Symbiosis ; Transcriptome ; }, abstract = {Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.}, }
@article {pmid34593802, year = {2021}, author = {Avila-Magaña, V and Kamel, B and DeSalvo, M and Gómez-Campo, K and Enríquez, S and Kitano, H and Rohlfs, RV and Iglesias-Prieto, R and Medina, M}, title = {Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5731}, pmid = {34593802}, issn = {2041-1723}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/*microbiology/physiology ; Caribbean Region ; Coral Reefs ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; *Heat-Shock Response ; Metabolic Networks and Pathways/genetics ; Microbiota/*genetics ; Photosynthesis/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.}, }
@article {pmid34591135, year = {2022}, author = {Villegas-Plazas, M and Sanabria, J and Arbeli, Z and Vasquez, Y and Roldan, F and Junca, H}, title = {Metagenomic Analysis of Biochemical Passive Reactors During Acid Mine Drainage Bioremediation Reveals Key Co-selected Metabolic Functions.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {465-472}, pmid = {34591135}, issn = {1432-184X}, mesh = {Acids ; Biodegradation, Environmental ; *Metagenomics ; *Mining ; Sulfates/metabolism ; }, abstract = {Acid mine drainage (AMD) is the major pollutant generated by the mining industry, and it is characterized by low pH and high concentration of metals and sulfate. The use of biochemical passive reactors (BPRs) is a promising strategy for its bioremediation. To date, there are various studies describing the taxonomical composition of BPR microbial communities, generally consisting of an assemblage of sulfate-reducing organisms inside Deltaproteobacteria, and a diverse set of anaerobic (ligno)cellulolytic bacteria; however, insights about its functional metagenomic content are still scarce. In previous studies, a laboratory-scale AMD bioremediation using biochemical passive reactors was designed and performed, tracking operation parameters, chemical composition, and changes, together with taxonomic composition of the microbiomes harbored in these systems. In order to reveal the main functional content of these communities, we used shotgun metagenomics analyses to explore genes of higher relative frequencies and their inferred functions during the AMD bioremediation from three BPRs representing the main microbiome compositions detected in the system. Remarkably, genes encoding for two-component regulatory systems and ABC transporters related to metal and inorganic ions, cellulose degradation enzymes, dicarboxylic acid production, and sulfite reduction complex were all detected at increased frequency. Our results evidenced that higher taxonomic diversity of the microbiome was arising together with a functional redundancy of the specific metabolic roles, indicating its co-selection and suggesting that its enrichment on BPRs may be implicated in the cumulative efficiency of these systems.}, }
@article {pmid34582942, year = {2022}, author = {Ravindran, C and Raveendran, HP and Irudayarajan, L}, title = {Ciliated protozoan occurrence and association in the pathogenesis of coral disease.}, journal = {Microbial pathogenesis}, volume = {162}, number = {}, pages = {105211}, doi = {10.1016/j.micpath.2021.105211}, pmid = {34582942}, issn = {1096-1208}, mesh = {Animals ; *Anthozoa ; *Ciliophora ; }, abstract = {Various microbial infections have significantly contributed to disease progression leading to the mortality of corals. However, the holobiont and the external surfaces of coral, including the secreted mucus, provide a varied microenvironment that attracts ciliates based on their feeding preferences. Besides, some ciliates (e.g., Philasterine scuticociliate) may enter through the injuries or lesions on corals or through their indirect interactions with other types of microbes that influence coral health. Thus, ciliates occurrence and association are described with 12 different diseases worldwide. White syndrome disease lesions have diverse ciliate associations, and higher ciliate diversity was observed with diseased genera Acropora. Also, it was described, about sixteen ciliate species ingest coral Symbiodiniaceae and histophagous ciliates for coral tissue loss as secondary invaders. However, the ciliates nature of association with the coral disease remains unclear for primary or opportunistic secondary pathogenicity. Herein, we explore the urgent need to understand the complex interactions of ciliates in coral health.}, }
@article {pmid34582868, year = {2022}, author = {Kenigsberg, C and Titelboim, D and Ashckenazi-Polivoda, S and Herut, B and Kucera, M and Zukerman, Y and Hyams-Kaphzan, O and Almogi-Labin, A and Abramovich, S}, title = {The combined effects of rising temperature and salinity may halt the future proliferation of symbiont-bearing foraminifera as ecosystem engineers.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150581}, doi = {10.1016/j.scitotenv.2021.150581}, pmid = {34582868}, issn = {1879-1026}, mesh = {Cell Proliferation ; Ecosystem ; *Foraminifera ; Salinity ; Seawater ; Temperature ; }, abstract = {Rising sea surface temperatures and extreme heat waves are affecting symbiont-bearing tropical calcifiers such as corals and Large Benthic Foraminifera (LBF). In many ecosystems, parallel to warming, global change unleashes a host of additional changes to the marine environment, and the combined effect of such multiple stressors may be far greater than those of temperature alone. One such additional stressor, positively correlated to temperature in evaporation-dominated shallow-water settings is rising salinity. Here we used laboratory culture experiments to evaluate the combined thermohaline tolerance of one of the most common LBF species and carbonate producer, Amphistegina lobifera. The experiments were done under ambient (39 psu) and modified (30, 45, 50 psu) salinities and at optimum (25 °C) and warm temperatures (32 °C). Calcification of the A. lobifera holobiont was evaluated by measuring alkalinity loss in the culturing seawater, as an indication of carbonate ion uptake. The vitality of the symbionts was determined by monitoring pigment loss of the holobiont and their photosynthetic performances by measuring dissolved oxygen. We further evaluated the growth of Peneroplis (P. pertusus and P. planatus), a Rhodophyta bearing LBF, which is known to tolerate high temperatures, under elevated salinities. The results show that the A. lobifera holobiont exhibits optimal performance at 39 psu and 25 °C, and its growth is significantly reduced upon exposure to 30, 45, 50 psu and under all 32 °C treatments. Salinity and temperature exhibit a significant interaction, with synergic effects observed in most treatments. Our results confirm that Peneroplis has a higher tolerance to elevated temperature and salinity compared to A. lobifera, implying that a further increase of salinity and temperatures may result in a regime shift from Amphistegina- to Peneroplis-dominated assemblages.}, }
@article {pmid34576867, year = {2021}, author = {Liang, J and Deng, C and Yu, K and Ge, R and Xu, Y and Qin, Z and Chen, B and Wang, Y and Su, H and Huang, X and Huang, W and Wang, G and Gong, S}, title = {Cross-Linked Regulation of Coral-Associated Dinoflagellates and Bacteria in Pocillopora sp. during High-Temperature Stress and Recovery.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576867}, issn = {2076-2607}, 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}, mesh = {Biotechnology ; Crops, Agricultural ; Plant Diseases ; *Plant Viruses ; Vaccination ; }, abstract = {A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.}, }
@article {pmid34561754, year = {2022}, author = {Varasteh, T and Salazar, V and Tschoeke, D and Francini-Filho, RB and Swings, J and Garcia, G and Thompson, CC and Thompson, FL}, title = {Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {325-335}, pmid = {34561754}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/physiology ; Atlantic Ocean ; Coral Reefs ; DNA, Ribosomal/genetics ; *Dinoflagellida/physiology ; Phylogeny ; Symbiosis ; }, abstract = {The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.}, }
@article {pmid34561474, year = {2021}, author = {Ramos, C and Calus, M and Schokker, D}, title = {Persistence of functional microbiota composition across generations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19007}, pmid = {34561474}, issn = {2045-2322}, mesh = {Animals ; Culicidae/microbiology ; Datasets as Topic ; *Host Microbial Interactions ; Host Specificity ; Humans ; Microbiota/*physiology ; Plants/microbiology ; Zooplankton/microbiology ; }, abstract = {Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The "it's the song, not the singer" theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.}, }
@article {pmid34544484, year = {2021}, author = {Zhu, D and Delgado-Baquerizo, M and Ding, J and Gillings, MR and Zhu, YG}, title = {Trophic level drives the host microbiome of soil invertebrates at a continental scale.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {189}, pmid = {34544484}, issn = {2049-2618}, mesh = {Animals ; Biodiversity ; Ecosystem ; Invertebrates ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.<br><br>RESULTS: Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.<br><br>CONCLUSIONS: Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.}, }
@article {pmid34519538, year = {2021}, author = {Waterworth, SC and Parker-Nance, S and Kwan, JC and Dorrington, RA}, title = {Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0157721}, pmid = {34519538}, issn = {2150-7511}, mesh = {Animals ; Bacteria/classification/*genetics ; *Genomics ; *Host Specificity ; Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Symbiosis ; }, abstract = {The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.}, }
@article {pmid34508605, year = {2022}, author = {Duchêne, DA and Mather, N and Van Der Wal, C and Ho, SYW}, title = {Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.}, journal = {Systematic biology}, volume = {71}, number = {3}, pages = {676-689}, pmid = {34508605}, issn = {1076-836X}, mesh = {*Biological Evolution ; *Genome ; Models, Genetic ; Phylogeny ; }, abstract = {The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenom