ISME communications最新文献

{"title":"Molecular complexity of the differential growth of freshwater diatoms along pH gradients.","authors":"Xènia Rodríguez-Miret, Marisol Felip, Eric Pelletier, Jordi Catalan","doi":"10.1093/ismeco/ycaf078","DOIUrl":"10.1093/ismeco/ycaf078","url":null,"abstract":"<p><p>Diatoms originated in marine waters, and many clades have invaded fresh waters, radiating throughout the continental aquatic environments. pH gradients have been a primary axis of species differentiation, from which environmental assessments have taken advantage using diatoms as bioindicators. However, a comprehensive view of the molecular variation underlying the diatom sensitivity to pH is missing. This study used 12 freshwater diatom strains across a broad phylogenetic range within raphid pennate clades and 3 distinct environmental pH conditions, pH 4.7, 7.0, and 8.2, for a common garden experiment. The transcriptomic analysis showed that environmental pH variation regulated many molecular processes and biological functions, especially those involved in biosynthesis and transport. Despite sharing many known functions, strains responded to pH changes in a highly idiosyncratic manner. Such specificity in the physiological response to pH aligns with the considerably divergent genetic backgrounds observed among the 12 diatom strains. This variation was likely shaped by different evolutionary trajectories in adaptive molecular landscapes, which were probably already differentiated in the initial marine environment and subjected to varying pH selection pressures in the complex chemical mosaic of inland waters. Overall, our results indicate that continental pH selection pressures do not determine a necessarily unique adaptive physiological response in diatoms, but instead allow for multiple adaptive solutions built on the evolutionary historical background and inland contingencies. Therefore, specific studies on the identified plastic responses to pH are needed to assess their adaptive function across clades.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf078"},"PeriodicalIF":5.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251109","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":"Soil viral communities shifted significantly after wildfire in chaparral and woodland habitats.","authors":"Sara E Geonczy, Anneliek M Ter Horst, Joanne B Emerson","doi":"10.1093/ismeco/ycaf073","DOIUrl":"10.1093/ismeco/ycaf073","url":null,"abstract":"<p><p>Increased wildfire activity warrants more research into fire-driven biotic changes in soil, including soil viral communities, given the roles of soil microbes in organic matter decomposition, nutrient cycling, and post-fire recovery. Leveraging viral size-fraction metagenomes (viromes), here we studied viral community responses to wildfire in woodland and chaparral soils at five timepoints over 1 year following the California LNU Complex wildfire. We also compared post-fire samples to unburned controls at the final three timepoints and leveraged published viromes from the same sites nine months before the fire as pre-burn controls. Viral community composition differed significantly in burned samples compared to controls from both habitats, as did soil chemistry and prokaryotic communities (16S rRNA gene amplicons). Viromic DNA yields (a proxy for viral particle abundances) indicated initial viral biomass reductions due to the fire, but a return to baseline abundances (indistinguishable from controls) within five months. Fire-associated habitat filtering was further indicated by a comparison to the PIGEON viral \"species\" (viral operational taxonomic unit (vOTU)) reference database, with vOTUs from a burned conifer forest representing 19%-31% of PIGEON vOTUs detected in the burned habitats but only 0.6%-6% in controls. Together, these results indicate significant changes in soil viral communities due to wildfire, attributable at least in part to concomitant changes in their prokaryotic host communities and soil physicochemistry.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf073"},"PeriodicalIF":5.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095434","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":"<i>Vibrio</i> are a potential source of novel colistin-resistance genes in European coastal environments.","authors":"Jamal Saad, Viviane Boulo, David Goudenège, Coralie Broquard, Karl B Andree, Manon Auguste, Bruno Petton, Yannick Labreuche, Pablo Tris, Dolors Furones, Augusti Gil, Luigi Vezzulli, Gianluca Corno, Andrea Di Cesare, Hugo Koechlin, Emilie Labadie-Lafforgue, Gaelle Courtay, Océane Romatif, Juliette Pouzadoux, Jean-Michel Escoubas, Dominique Munaron, Guillaume M Charrière, Eve Toulza, Marie-Agnès Travers, Caroline Montagnani, K Mathias Wegner, Delphine Destoumieux-Garzón","doi":"10.1093/ismeco/ycaf055","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf055","url":null,"abstract":"<p><p>Colistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred by <i>mcr</i>-1 in human pathogens has raised concern, but the putative sources and reservoirs of novel <i>mcr</i> genes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly in <i>Vibrio</i> isolated from European coastal waters by using the same cohorts of oysters as bioaccumulators in three sites across Europe. The high sequence diversity found in the <i>mcr/ept</i>A gene family was geographically structured, particularly for three novel <i>eptA</i> gene variants, which were restricted to the Mediterranean (France, Spain) and occurred as a <i>dgk</i>A-<i>ept</i>A operon. The RstA/RstB two component system was shown to control both the <i>dgk</i>A-<i>ept</i>A operon and the Col-R phenotype. The analysis of 29 427 <i>Vibrionaceae</i> genomes revealed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes the human pathogens <i>Vibrio parahaemolyticus</i> and <i>Vibrio alginolyticus</i>. The operon conferred colistin-resistance when transferred to sensitive non-<i>Vibrio</i> strains. In general, <i>ept</i>A gene variants are widespread and evolved with the <i>Vibrio</i> lineage. They occur in clade-specific genomic environments, suggesting that <i>eptA</i> expression responds to distinct environmental signals across the <i>Vibrio</i> phylogeny. However, we also identified mobile <i>ept</i>A paralogues that have been recently transferred between and within <i>Vibrio</i> clades. This highlights <i>Vibrio</i> as a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf055"},"PeriodicalIF":5.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052591","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":"Organic metabolite uptake by diazotrophs in the North Pacific Ocean.","authors":"Alba Filella, Aurélie Cébron, Benoît Paix, Marine Vallet, Pauline Martinot, Léa Guyomarch, Catherine Guigue, Marc Tedetti, Olivier Grosso, Kendra A Turk-Kubo, Lasse Riemann, Mar Benavides","doi":"10.1093/ismeco/ycaf061","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf061","url":null,"abstract":"<p><p>Dinitrogen (N₂) fixation by diazotrophs supports ocean productivity. Diazotrophs include photoautotrophic cyanobacteria, non-cyanobacterial diazotrophs (NCDs), and the recently discovered N₂-fixing haptophyte. While NCDs are ubiquitous in the ocean, their ecology and metabolism remain largely unknown. Unlike cyanobacterial diazotrophs and the haptophyte, NCDs are primarily heterotrophic and depend on dissolved organic matter (DOM) for carbon and energy. However, conventional DOM amendment incubations do not allow discerning how different diazotrophs use DOM molecules, limiting our knowledge on DOM-diazotroph interactions. To identify diazotrophs using DOM, we amended North Pacific microbial communities with ¹³C-labeled DOM from phytoplankton cultures that was molecularly characterized, revealing the dominance of nitrogen-rich compounds. After DOM additions, we observed a community shift from cyanobacterial diazotrophs like <i>Crocosphaera</i> and <i>Trichodesmium</i> to NCDs at stations where the N₂-fixing haptophyte abundance was relatively low. Through DNA stable isotope probing and gene sequencing, we identified diverse diazotrophs capable of taking up DOM. Our findings highlight unexpected DOM uptake by the haptophyte's nitroplast, changes in community structure, and previously unrecognized osmotrophic behavior in NCDs, shaped by local biogeochemical conditions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf061"},"PeriodicalIF":5.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060671","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":"Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities.","authors":"Xiaoyu Zai, Feng Zhu, Meicheng Zhao, Xianmin Diao, Fusuo Zhang, Francisco Dini-Andreote, Chrats Melkonian, Marnix H Medema, Jos M Raaijmakers, Viviane Cordovez, Chunxu Song","doi":"10.1093/ismeco/ycaf066","DOIUrl":"10.1093/ismeco/ycaf066","url":null,"abstract":"<p><p>Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel strategy to enhance resilience to the (a)biotic stresses of domesticated crops. The challenge is determining how to harness the diverse microbiota of wild crop ancestors in their natural habitats in order to design effective synthetic microbial communities (SynComs) that reconstitute specific microbiome-associated plant phenotypes. In this study, we profiled the phyllosphere microbiota of wild green foxtail collected from seven geographically diverse natural ecosystems and showed that variations in soil parameters and climatic conditions as well as plant genetic distance significantly correlated with bacterial and fungal community compositions. Environmental selection and dispersal limitation differently governed the assembly of bacterial and fungal communities with distinct habitat niche breadth. Specific bacterial and yeast genera were identified as core phyllosphere taxa of wild green foxtail millet on the basis of their abundance and prevalence across the seven sampling sites. Moreover, several genera of bacteria (<i>Bacillus</i>, <i>Pantoea</i>, <i>Methylobacterium</i>) and yeast (<i>Vishniacozyma</i>, <i>Filobasidium</i>, <i>Sporobolomyces</i>) displayed significant correlations with the abundances of one or more foliar pathogenic fungi, in particular fungi of the genus <i>Alternaria</i>. Subsequent isolation and characterization of these bacterial and yeast genera allowed the design of cross-kingdom SynComs that protected domesticated foxtail millet from leaf infections by <i>Alternaria alternata</i>. These results provide fundamental insight into the mechanisms governing the phyllosphere microbiota assembly of a wild crop ancestor across large geographic scales and a practical framework to leverage this fundamental knowledge for the design of SynComs that mitigate the biotic stress of the domesticated crop.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf066"},"PeriodicalIF":6.1,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12286919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144710086","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":"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}