ISME communications最新文献

{"title":"Variational inference for microbiome survey data with application to global ocean data.","authors":"Aditya Mishra, Jesse McNichol, Jed Fuhrman, David Blei, Christian L Müller","doi":"10.1093/ismeco/ycaf062","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf062","url":null,"abstract":"<p><p>Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (variational inference for microbiome survey data analysis), that enables joint estimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling, which can incorporate spatio-temporal information and taxon-taxon interactions. We leverage mean-field variational inference for posterior VI-MIDAS model parameter estimation and illustrate model building and analysis using Tara Ocean Expedition survey data. Using VI-MIDAS' latent embedding model and tools from network analysis, we show that marine microbial communities can be broadly categorized into five modules, including SAR11-, nitrosopumilus-, and alteromondales-dominated communities, each associated with specific environmental and spatiotemporal signatures. VI-MIDAS also finds evidence for largely positive taxon-taxon associations in SAR11 or Rhodospirillales clades, and negative associations with Alteromonadales and Flavobacteriales classes. Our results indicate that VI-MIDAS provides a powerful integrative statistical analysis framework for discovering broad patterns of associations between microbial taxa and context-specific covariate data from microbiome survey data.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf062"},"PeriodicalIF":5.1,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome analysis reveals diverse novel psychrotolerant <i>Mucilaginibacter</i> species in Arctic tundra soils.","authors":"Anil Kumar, Minna K Männistö, Marika Pätsi, Lee J Kerkhof, Max M Häggblom","doi":"10.1093/ismeco/ycaf071","DOIUrl":"10.1093/ismeco/ycaf071","url":null,"abstract":"<p><p>As Arctic soil ecosystems warm due to climate change, enhanced microbial activity is projected to increase the rate of soil organic matter degradation. Delineating the diversity and activity of Arctic tundra microbial communities active in decomposition is thus of keen interest. Here, we describe novel cold-adapted bacteria in the genus <i>Mucilaginibacter</i> (<i>Bacteroidota</i>) isolated from Artic tundra soils in Finland. These isolates are aerobic chemoorganotrophs and appear well adapted to the low-temperature environment, where they are also exposed to desiccation and a wide regime of annual temperature variation. Initial 16S ribosomal RNA (rRNA)-based phylogenetic analysis suggested that five isolated strains represent new species of the genus <i>Mucilaginibacter</i>, confirmed by whole genome-based phylogenomic and average nucleotide identity. Five novel species are described: <i>Mucilaginibacter geliditolerans</i> sp. nov., <i>Mucilaginibacter tundrae</i> sp. nov., <i>Mucilaginibacter empetricola</i> sp. nov., <i>Mucilaginibacter saanensis</i> sp. nov., and <i>Mucilaginibacter cryoferens</i> sp. nov. Genome and phenotype analysis showed their potential in complex carbon degradation, nitrogen assimilation, polyphenol degradation, and adaptation to their tundra heath habitat. A pangenome analysis of the newly identified species alongside known members of the <i>Mucilaginibacter</i> genus sourced from various environments revealed the distinctive characteristics of the tundra strains. These strains possess unique genes related to energy production, nitrogen uptake, adaptation, and the synthesis of secondary metabolites that aid in their growth, potentially accounting for their prevalence in tundra soil. By uncovering novel species and strains within the <i>Mucilaginibacter</i>, we enhance our understanding of this genus and elucidate how environmental fluctuations shape the microbial functionality and interactions in Arctic tundra ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf071"},"PeriodicalIF":5.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12074574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photosynthetic dependence and filament production in physical bacterial-Symbiodiniaceae interactions.","authors":"Gavin C McLaren, Morgan V Farrell, Nicholas J Shikuma, Cawa Tran","doi":"10.1093/ismeco/ycaf070","DOIUrl":"10.1093/ismeco/ycaf070","url":null,"abstract":"<p><p>The cnidarian microbiome consists of a wide variety of beneficial microbes that play vital roles in maintaining and fortifying host health. Photosynthesis from symbiotic dinoflagellates (in the family Symbiodiniaceae) is crucial for their symbiosis establishment with the cnidarian host. Although more is known regarding interactions between the host and its associated bacteria and dinoflagellates, there has been little investigation into the relationship between the two microbes themselves and whether photosynthesis plays a role. Through two different methods of photosynthetic inhibition of dinoflagellates (incubation in the dark or pre-treatment with a photosystem II inhibitor), we investigated how pathogenic versus beneficial bacteria physically interact with three Symbiodiniaceae strains (symbiotic and free-living). The beneficial bacterium <i>Tritonibacter mobilis</i> appears to interact with photosynthesizing algae only. In the absence of photosynthesis, little to no physical interactions were observed between Symbiodiniaceae and <i>T. mobilis</i>. Bacterial congregation around individual dinoflagellate cells was significantly lower when photosynthesis was impaired, suggesting photosynthesis is a key facilitator of interactions between <i>T. mobilis</i> and all three Symbiodiniaceae strains. We also investigated whether photosynthesis affects interactions between Symbiodiniaceae and the pathogen <i>Vibrio alginolyticus</i>. Although no discernable impacts of photosynthetic inhibition were observed with the pathogen, scanning electron microscopy uncovered various mechanisms of interaction between Symbiodiniaceae and both bacteria, one of which includes the production of filaments not previously described. Overall, our research highlights the importance of photosynthesis in initiating interactions between bacteria and both free-living and symbiotic dinoflagellates, and opens a door to new questions regarding cell-surface interactions among individual microbes.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf070"},"PeriodicalIF":5.1,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12082827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into the biotic factors driving the outcome of coalescence events between soil bacterial communities.","authors":"Sarah Huet, Sana Romdhane, Marie-Christine Breuil, David Bru, Arnaud Mounier, Laurent Philippot, Ayme Spor","doi":"10.1093/ismeco/ycaf048","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf048","url":null,"abstract":"<p><p>Coalescence events, which consist in the mixing of previously separated communities, are frequent in nature or as a result of human activities. Despite recently gaining attention as a tool to test ecological theories and engineer microbial communities, little is known about the factors that influence the outcome of such coalescence events. Here, we evaluated the relative importance of three community properties-namely, diversity, composition, and density-in determining coalescence outcome and biotic interactions among members of the coalescing bacterial communities. We found that manipulation of the density and composition of soil bacterial community resulted in the largest shifts in the structure of the resulting coalesced communities, explaining 24.7% and 6.8% of the variance in the β-diversity of the coalesced communities, respectively. Coalescence events impacted up to 35% of the dominant Operational Taxonomic Unit (OTUs) in the native community, with a predominance of negative effects. Our results also revealed that community density had the greatest explanatory power for the variance in the relative abundance of the OTUs negatively affected by coalescence events. In particular, all significantly affected OTUs that belonged to the Bacillales exhibited a decrease in relative abundance in several of the coalesced communities, which was related to the density of some members of the α-Proteobacteria and γ-Proteobacteria in the manipulated community suspensions. Overall, our data suggest that community density and composition were the main properties determining the outcome of coalescence events and that coalescence experiments can offer insights into multi-species interactions in complex environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf048"},"PeriodicalIF":5.1,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12011082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143999915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phages indirectly maintain tomato plant pathogen defense through regulation of the commensal microbiome.","authors":"Reena Debray, Asa Conover, Britt Koskella","doi":"10.1093/ismeco/ycaf065","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf065","url":null,"abstract":"<p><p>As parasites of bacteria, phages can regulate microbiome diversity and composition and may therefore affect susceptibility to pathogens and disease. Many infectious diseases are associated with altered bacteriophage communities, but observational studies alone do not allow us to determine when altered phage community composition is a contributor to disease risk, a response to infection, or simply an indicator of dysbiosis. To address this question directly, we used size-selective filtration to deplete plant-associated microbial communities of phages, then challenged plants with the bacterial pathogen <i>Pseudomonas syringae</i>. Plants with phage-depleted microbiomes were more susceptible to infection, an effect that could not be explained by direct effects of the phage communities on either <i>P. syringae</i> or the plant host. Moreover, the presence of phages was most impactful when the phage communities were isolated from neighboring field locations rather than from the same host plant as the bacteria, possibly suggesting that moderate rates of lysis maintain a community structure that is most resistant to pathogen invasion. Overall, our results support the idea that phage communities contribute to plant defenses by modulating the microbiome.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf065"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.","authors":"Victoria Celeste Lanclos, Xiaoyuan Feng, Chuankai Cheng, Mingyu Yang, Cole J Hider, Jordan T Coelho, Conner Y Kojima, Shelby J Barnes, Catie S Cleveland, Mei Xie, Yanlin Zhao, Haiwei Luo, James Cameron Thrash","doi":"10.1093/ismeco/ycaf068","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf068","url":null,"abstract":"<p><p>The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name <i>Candidatus</i> Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007^T (= ATCC TSD-433^T = NCMA B160^T).</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf068"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anoxygenic photoautotrophy driven by humus and microplastics in a photosynthetic bacterium.","authors":"Yutong Li, Kongyuang Qu, Jianming Yang, Shuguang Wang, Zhen Yan","doi":"10.1093/ismeco/ycaf067","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf067","url":null,"abstract":"<p><p>Humus and microplastics are recalcitrant organics in soils and aquatic systems, and their role in the geochemical cycling of elements remains elusive. Herein, we have identified a new mechanism by which humus and microplastics participate in anoxic carbon cycling. We demonstrated that the photoexcitation of 5-30 mg/l of humic acid or fulvic acid, two major fractions of humus, can drive CO₂ fixation and enable the photoautotrophic growth of a photosynthetic bacterium, <i>Rhodopseudomonas palustris</i>. This process was enhanced by 10.69%-144.87% upon the addition of 100 mg/l of poly(lactic acid) or poly(ethylene terephthalate). Mechanistic investigations demonstrated that the microplastics act as sacrificial quenchers during humus photoexcitation, leading to their depolymerization. Transcriptomic analyses revealed high expression of genes encoding extracellular electron uptake pathways including extracellular cytochrome <i>c</i> and its oxidases in the photoautotrophic growth of <i>R. palustris</i>. This study expands our understanding of how humus and microplastics are involved in the biogeochemical cycling of carbon and sheds light on how they impact the CO₂ dynamic fluxes in sunlit anoxic environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf067"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variable responses to ocean acidification among mixotrophic protists with different lifestyles.","authors":"Shai Slomka, Jolanda M H Verspagen, Jef Huisman, Susanne Wilken","doi":"10.1093/ismeco/ycaf064","DOIUrl":"10.1093/ismeco/ycaf064","url":null,"abstract":"<p><p>Marine phytoplankton are facing increasing dissolved CO₂ concentrations and ocean acidification caused by anthropogenic CO₂ emissions. Mixotrophic organisms are capable of both photosynthesis and phagotrophy of prey and are found across almost all phytoplankton taxa and diverse environments. Yet, we know very little about how mixotrophs respond to ocean acidification. Therefore, we studied responses to simulated ocean acidification in three strains of the mixotrophic chrysophyte <i>Ochromonas</i> (CCMP1391, CCMP2951, and CCMP1393). After acclimatization of the strains to treatment with high-CO₂ (1000 ppm, pH 7.9) and low-CO₂ concentrations (350 ppm, pH 8.3), strains CCMP1393 and CCMP2951 both exhibited higher growth rates in response to the high-CO₂ treatment. In terms of the balance between phototrophic and heterotrophic metabolism, diverse responses were observed. In response to the high-CO₂ treatment, strain CCMP1393 showed increased photosynthetic carbon fixation rates, while CCMP1391 exhibited higher grazing rates, and CCMP2951 did not show significant alteration of either rate. Hence, all three <i>Ochromonas</i> strains responded to ocean acidification, but in different ways. The variability in their responses highlights the need for better understanding of the functional diversity among mixotrophs in order to enhance predictive understanding of their contributions to global carbon cycling in the future.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf064"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12086424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying evolutionary changes to temperature-CO₂ growth response surfaces in <i>Skeletonema marinoi</i> after adaptation to extreme conditions.","authors":"Charlotte L Briddon, Maria Nicoară, Adriana Hegedűs, Mridul K Thomas, Bogdan Drugă","doi":"10.1093/ismeco/ycaf069","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf069","url":null,"abstract":"<p><p>Global warming and ocean acidification are having an unprecedented impact on marine ecosystems, yet we do not yet know how phytoplankton will respond to simultaneous changes in multiple drivers. To better comprehend the combined impact of oceanic warming and acidification, we experimentally estimated how evolution shifted the temperature-CO₂ growth response surfaces of two strains of <i>Skeletonema marinoi</i> that were each previously adapted to four different temperature × CO₂ combinations. These adapted strains were then grown under a factorial combination of five temperatures and five CO₂ concentrations to capture the temperature-CO₂ response surfaces for their unacclimated growth rates. The development of the first complete temperature-CO₂ response surfaces showed the optimal CO₂ concentration for growth to be substantially higher than expected future CO₂ levels (~6000 ppm). There was minimal variation in the optimal CO₂ concentration across the tested temperatures, suggesting that temperature will have a greater influence on growth rates compared to enhanced CO₂. Optimal temperature did not show a unimodal response to CO₂, either due to the lack of acclimation or the highly efficient CO₂ concentrating mechanisms, which diatoms (e.g. <i>Skeletonema</i>) can up-/downregulate depending on the CO₂ conditions. We also found that both strains showed evidence of evolutionary shifts as a result of adaptation to temperature and CO₂. The evolutionary response differed between strains, underscoring how genetic differences (perhaps related to historical regimes) can impact phytoplankton performance. Understanding how a dominant algal species responds to multiple drivers provides insight into real-world scenarios and helps construct theoretical predictions of environmental change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf069"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Significant role of symbiotic bacteria in the blood digestion and reproduction of <i>Dermanyssus gallinae</i> mites.","authors":"","doi":"10.1093/ismeco/ycae166","DOIUrl":"https://doi.org/10.1093/ismeco/ycae166","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycae127.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae166"},"PeriodicalIF":5.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}