ISME communications最新文献

{"title":"The <i>Calcidiscus leptoporus</i> genome reveals vitamin-mediated holobiont interactions.","authors":"Frederic Chaux, Tanja Vojvoda Zeljko, Borna Branimir Vuković, John A Burns, Titouan Le Perrun, Marta Žižek, Briget P Bannerman, Donald Tonye Bara Mason, Clotilde Garrido, Zhou Xu, Richard G Dorrell, Jelena Godrijan","doi":"10.1093/ismeco/ycag222","DOIUrl":"10.1093/ismeco/ycag222","url":null,"abstract":"<p><p>Coccolithophores are major marine phytoplankton that contribute to ocean carbon cycling through both organic carbon fixation and calcium carbonate biomineralization, yet the functional basis of their interactions with phycosphere bacteria remains poorly resolved. Here, we present the nuclear genome of the haploid phase of the coccolithophore <i>Calcidiscus leptoporus</i>, a coccolithophore that calcifies in both life-cycle stages. We combined host genome analysis, genome-resolved characterization of associated bacteria, and a four-month vitamin-manipulation experiment to test how B-vitamin biosynthetic complementarity relates to host performance and phycosphere community assembly. Metabolic reconstructions indicate partitioned B-vitamin biosynthtic potential: the host encodes pathways for B2, B5, B6, and B9, including a rare fused B5 biosynthesis gene, but lacks complete pathways for B1, B3, B7, and B12. These missing functions were distributed among recurrent bacterial taxa, with no single bacterial MAG encoding the full set of host-missing vitamins. Across the experiment, bacterial community composition was structured primarily by the experimental phase, while vitamin treatments secondarily influenced which taxa became enriched at later stages. Consistent with genome-inferred auxotrophy, B-vitamin availability constrained long-term growth under the tested conditions, with B1 alone providing partial rescue and vitamin-replete treatments showing equal or stronger responses. Together, these data establish <i>C. leptoporus</i> as a genomic model for coccolithophore biology and holobiont interactions, while providing a testable framework linking vitamin economies to phycosphere assembly and host performance.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag222"},"PeriodicalIF":6.4,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148834890","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":"Unraveling the diversity, function, and virus-host interactions of archaeal proviruses.","authors":"Yang Zhao, PengFei Liu, LinXing Chen, MeiLing Feng, Rong Wen, ZhiHao Zhang, XueFeng Zhang, HongFei Chi","doi":"10.1093/ismeco/ycag243","DOIUrl":"10.1093/ismeco/ycag243","url":null,"abstract":"<p><p>Archaea, the third domain of life, play critical roles in global biogeochemical cycles. However, archaeal proviruses integrated into host genomes remain largely unexplored. To bridge this gap, we conducted a large-scale mining of genomes spanning all presently known 21 archaeal phyla for their proviruses. We identified 770 archaeal proviruses across 12 archaeal phyla and 84 families, which clustered into 655 viral operational taxonomic units (vOTUs). Among these, 86.1% of the vOTUs were novel at the species level, and 69.3% could not be classified at the family level, substantially expanding the known diversity of archaeal viruses. Additionally, phylogenomic analysis supported the proposal of 16 putative novel viral families, further extending the current taxonomy landscape of archaeal viruses. Notably, 21.8% of the identified proviruses were predicted to adopt a lytic lifestyle, suggesting that these proviruses may retain the capacity to enter the lytic cycle under appropriate conditions. Host prediction indicated only 14 out of the 655 vOTUs might have potential across-lineage infection abilities. We detected 63 anti-defense genes encoded by 61 provirus genomes, such as anti-CRISPR and anti-RM, suggesting an ongoing evolutionary arms race between hosts and proviruses. However, only 10 auxiliary metabolic genes (AMGs) were identified, suggesting a limited impact of proviruses in the modulation of host metabolism through AMGs. This study establishes a systematic global genomic atlas of archaeal proviruses, advancing our understanding of their distribution and diversity while providing a foundation for future research into how proviruses regulate archaeal metabolism and ecosystem functioning.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag243"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972314","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":"Boreal and subarctic freshwaters harbour a diversity of jumbophages.","authors":"Meeri Niemi, Karyna Karneyeva, Lotta-Riina Sundberg, Hanna M Oksanen, Elina Laanto","doi":"10.1093/ismeco/ycag239","DOIUrl":"10.1093/ismeco/ycag239","url":null,"abstract":"<p><p>Bacteriophages (phages) are major drivers of microbial evolution and ecology, yet their diversity and functional roles remain poorly characterized in many natural environments, such as in freshwater systems. In boreal and subarctic freshwater habitats, where bacteria are typically slow-growing and nutrient-limited, phages are predicted to have a critical role in host regulation and horizontal gene exchange. However, only a few isolates have been obtained from such environments, leaving the genetic and functional diversity of these phages largely unexplored. Here, we present a collection of 40 bacteriophages isolated from boreal lakes and rivers using a set of diverse freshwater bacterial hosts. Despite using conventional isolation methods, eight of the isolates possess genomes larger than 200 kilobases and are classified as jumbophages. All jumbophages exhibited myovirus morphology and comparatively slow infection dynamics. These jumbophages include the first known representatives infecting members of <i>Janthinobacterium</i> and <i>Herbaspirillum</i>. Comparative genomic and phylogenetic analyses show that nearly all genomes are distinct from previously described phages, indicating substantial novelty. Diverse auxiliary metabolic and anti-defence systems were identified, including putative NAD⁺ salvage and acyl carrier protein modules, along with predicted Anti-Thoeris and Anti-CBASS elements. The <i>Pseudomonas-</i>infecting jumbophage Ahti encoded homologues of all 21 core genes that define the nucleus-forming family <i>Chimalliviridae.</i> Additionally, Ahti displayed compartmentalization of DNA during infection, establishing it as the first freshwater nucleus-forming phage. These findings expand our understanding of the ecological, genomic, and functional diversity of phages in boreal environments and highlight the role of freshwater ecosystems as significant reservoirs of novel viral lineages.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag239"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972303","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":"Global <i>in silico</i> analysis reveals a core gut microbiota in fall armyworm (<i>Spodoptera frugiperda</i>) shaped by geography and diet.","authors":"Lakshay Anand, Kendall R Corbin","doi":"10.1093/ismeco/ycag233","DOIUrl":"10.1093/ismeco/ycag233","url":null,"abstract":"<p><p>Fall armyworms (<i>Spodoptera frugiperda</i>) are an invasive agricultural pest whose adaptability and resilience are increasingly linked to their gut microbiota. In this study, we performed a global-scale <i>in-silico</i> meta-analysis of publicly available 16S rRNA datasets to identify a conserved core gut microbiota and assess how geography and diet shape microbial community structure and function. Using both prevalence-based and unsupervised clustering approaches, we defined a robust global core microbiota composed of 88 high-confidence ASVs, including genera such as <i>Enterococcus, Pseudomonas</i>, and <i>Acinetobacter</i>, which were consistently present regardless of geographical region or diet. These taxa are important in nutrient metabolism, detoxification, and stress tolerance, contributing to host fitness and ecological success. Geographic origin significantly influenced gut microbiota diversity and composition, with continent- and country-level differences supported by alpha/beta diversity metrics and supervised machine learning classification (AUC = 1.0). Diet also influenced microbial community structure, although its effect was weaker than that of geography, explaining 11.9% of the variation compared to 13.5%. Functional predictions using PICRUSt2 revealed region-specific enrichment of pathways related to xenobiotic degradation, amino acid metabolism, and vitamin biosynthesis, suggesting specific microbial taxa may contribute to host adaptation and resilience through these metabolic functions. This is the first global synthesis of the <i>S. frugiperda</i> gut microbiota that integrates geographic and dietary factors. The identification of a global-level conserved core microbiota provides a foundation for developing synthetic microbial communities and microbiome-informed pest management strategies aimed at enhancing control efficacy.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag233"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13639100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149119426","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":"Gut microbiomics reveals host-microbe crosstalk during sexual differentiation in the shortfin eel <i>Anguilla bicolor</i>.","authors":"Guo-Jie Brandon-Mong, Tzong-Huei Lee, Yi-Lung Chen, Tsun-Hsien Hsiao, Guan-Lun Wu, Yi-Li Lai, Chieh-Yin Weng, Ronnie G Gicana, Yu-Ting Yen, Yi-Fan Xu, Tzi-Yuan Wang, Yin-Ru Chiang","doi":"10.1093/ismeco/ycag241","DOIUrl":"10.1093/ismeco/ycag241","url":null,"abstract":"<p><p>The global decline in anguillid eel populations has intensified interest in understanding their biology for conservation and aquaculture. While host-gut microbiota interactions are well-characterized in homeotherms, these relationships remain poorly understood in poikilotherms during sexual differentiation. We examined gut microbiota dynamics across developmental stages in the shortfin eel <i>Anguilla bicolor</i>, which exhibits early sexual differentiation and a relatively short life cycle. Glass eels were cultivated in controlled freshwater conditions for 3 years, with sampling at key stages: glass eel, elver, sex-undetermined eel, and sex-determined eel. Full-length 16S rRNA gene sequencing revealed significant compositional shifts during development, with higher bacterial richness in adults versus younger eels. Early stages were dominated by Pseudomonadota, while sex-determined adults showed increased Deinococcota abundance. Network analysis identified <i>Deinococcus, Sphingomonas</i>, and <i>Variovorax</i> as key genera in sex-determined eels, with positive correlations between anti-Müllerian hormone gene expression and these taxa. We collected 66 gut bacterial strains capable of metabolizing sex hormones under microaerobic conditions. These isolates, representing 22 genera across four phyla, demonstrated diverse metabolic capabilities from partial oxidation to complete steroid mineralization. Multiple strains achieved complete estradiol degradation as single isolates-a rare metabolic capability of environmental microorganisms. Comparative genomic analysis revealed widespread steroid-metabolizing genes, with <i>Deinococcus</i> species showing previously unreported hormone degradation capabilities. Our microbiomics analysis demonstrates that gut microbiota composition and function are intimately linked to eel sexual development, suggesting bidirectional host-microbe interactions influencing reproductive physiology. These findings advance understanding of host-microbiota interactions in aquatic vertebrates and provide implications for eel aquaculture and conservation.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag241"},"PeriodicalIF":6.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584205/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992773","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":"Detectable effects of bacterial phylogeny on virulence but not phage efficacy in an <i>in vivo Galleria mellonella</i> model.","authors":"Sarah K Walsh, Ryan M Imrie, Angus Buckling, Ben Longdon","doi":"10.1093/ismeco/ycag232","DOIUrl":"10.1093/ismeco/ycag232","url":null,"abstract":"<p><p>Predicting the outcomes of bacteria-phage interactions is a central challenge in microbial ecology, particularly across heterogeneous host environments. Evolutionary relatedness among bacteria can explain variation in phage susceptibility <i>in vitro</i>, but it remains unclear whether this predictive relationship persists in complex host environments and to what extent relatedness also explains variation in other bacterial traits, such as virulence. Here, we used an <i>in vivo</i> infection model to quantify how bacterial phylogeny and host environmental context mediate bacterial virulence and bacteria-phage interactions. We infected 4,608 <i>Galleria mellonella</i> larvae with 64 phylogenetically diverse <i>Staphylococcaceae</i> isolates, both with and without co-inoculation of the bacteriophage ISP, and recorded mortality and melanisation over 24 hours. We found that bacterial virulence varied among <i>Staphylococcaceae</i> strains and that a large proportion of this variation could be explained by the evolutionary relationships between bacteria, indicating that phylogeny may be useful in predicting bacterial virulence. The addition of phage significantly improved the survival of <i>G. mellonella</i> larvae, with an average 15.2% increase in endpoint survival and 10.1% reduction in endpoint melanisation across <i>Staphylococcaceae</i> strains. Unlike previous <i>in vitro</i> studies, the evolutionary relationships between bacterial isolates could not explain variation in <i>in vivo</i> phage efficacy across <i>Staphylococcaceae</i>. Concurrently, we found no evidence of a correlation between <i>in vivo</i> and <i>in vitro</i> measures of phage efficacy across bacterial isolates, highlighting the importance of the host environment in shaping bacteria-phage dynamics.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag232"},"PeriodicalIF":6.4,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066148","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":"Mixed-species interactions constrain diversification and shape biofilm evolution.","authors":"Sanaa Harrass, Joyce To, Parisa Noorian, Gustavo Espinoza-Vergara, Vaughn S Cooper, Scott A Rice, Diane McDougald, M Mozammel Hoque","doi":"10.1093/ismeco/ycag237","DOIUrl":"10.1093/ismeco/ycag237","url":null,"abstract":"<p><p>Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved <i>Klebsiella pneumoniae, Pseudomonas protegens,</i> and <i>P. aeruginosa</i> in single- and mixed-species biofilm communities for 24 weeks and tracked changes in population dynamics, phenotypes, and genomes. In mono-species evolution, all three species exhibited similar dynamics of adaptation, with steadily increasing biofilm-associated populations. In contrast, mixed-species communities displayed striking compositional shifts, with <i>P. protegens</i> emerging as the dominant biofilm former and <i>K. pneumoniae</i> dominating the supernatant. Phenotypic assays revealed that all three species showed enhanced biofilm formation, but this increase was consistently greater in isolates from mono-species than mixed species communities, with <i>P. protegens</i> showing the largest gains. Beyond biofilm production, biofilm-associated isolates exhibited greater phenotypic diversification than planktonic isolates, whereas mixed-species interactions constrained diversification. Whole-genome sequencing identified species-specific putative adaptations such as <i>csrD</i> in <i>K. pneumoniae, yfiBNR</i> in <i>P. protegens</i>, and <i>cheA</i> in <i>P. aeruginosa</i> that arose early, persisted, and were enriched in mixed-species isolates. Functional assays support the contribution of these mutations to enhanced biofilm formation, with <i>yfiBNR</i> mutations in <i>P. protegens</i> increasing cyclic-di-GMP production and producing a competitive advantage that recapitulated its dominance in evolved biofilms. Our findings show that biofilm evolution fosters phenotypic diversification, whereas interspecies interactions shape adaptive trajectories, with specific mutations associated with keystone drivers of ecological dynamics in multi-species communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag237"},"PeriodicalIF":6.4,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13584209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148992806","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":"Chloroplast-mitochondria synergy modulates responses to iron limitation in two <i>Thalassiosira</i> diatom species.","authors":"Jhoanell Angulo, Clarisse Uwizeye, Pascal Albanese, Mathilde Menneteau, Stéphane Ravanel, Benoit Gallet, Pierre-Henri Jouneau, Giovanni Finazzi, Florence Courtois","doi":"10.1093/ismeco/ycag236","DOIUrl":"10.1093/ismeco/ycag236","url":null,"abstract":"<p><p>Iron is naturally present at low levels in modern oceans, where it is essential for life. Ocean-dwelling organisms such as oceanic phytoplankton must therefore adapt to the available levels. Among phytoplankton, diatoms are a highly diverse and successful taxon that includes the <i>Thalassiosira</i> genus. As a group, diatoms contribute around 20% of global primary photosynthetic productivity; they have also developed specific resources allowing them to thrive in low-iron regions. However, the major biological factors underlying their success in these ocean environments remain unknown. Here, we compared two <i>Thalassiosira</i> species: <i>Thalassiosira oceanica</i> from iron-poor open-ocean; and <i>Thalassiosira pseudonana</i>, from iron-rich coastal waters. Since iron is essential for both photosynthesis and respiration, we examined the specificities of the bioenergetic machineries in these organisms using a combination of photo-physiological, proteomics, and focused ion beam scanning electron microscopy methods. We particularly focused on chloroplast-mitochondrial coupling, a mechanism deployed by diatoms to ensure optimal transfer of photosynthetic products to promote cell growth. This study of this mechanism in the context of iron limitation reveals that the two diatoms differentially remodel chloroplast compartments in response to iron limitation. Their tolerance to these conditions is also linked to distinct constitutive mitochondrial architectures.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag236"},"PeriodicalIF":6.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13588709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149009283","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":"Computational mass spectrometry and genome mining guided discovery of metallophores produced by Microbulbifer.","authors":"Mónica Monge-Loría, Colin Brady, Hongwei Wu, Allegra Aron, Neha Garg","doi":"10.1093/ismeco/ycag238","DOIUrl":"10.1093/ismeco/ycag238","url":null,"abstract":"<p><p>Iron is an essential component of cellular biology. Thus, iron's low bioavailability is a key evolutionary pressure guiding microbial dynamics in the marine environment. Among marine bacteria, <i>Microbulbifer</i> is a chemically underexplored and functionally versatile bacterial genus, which is commonly associated with sponges, algae, corals, and sediments. Previously, genome analyses have revealed that <i>Microbulbifer</i> spp. can degrade polymers and synthesize natural products. Despite their recognized potential to produce secondary metabolites, siderophores are yet to be identified in <i>Microbulbifer</i>, and their iron acquisition strategies remain largely unknown. Here, we developed a comprehensive mass spectrometry-based query language code to determine siderophore production by <i>Microbulbifer</i> spp. in mono- and mixed cultures. Using this workflow, we discovered a new metallophore, which we named bulbichelin, as well as a suite of previously unreported petrobactins containing an unprecedented longer chain length acylation on the central spermidine moiety. We applied genome mining methods to describe the biosynthesis of these compounds. Using metal infusion mass spectrometry, we show that bulbichelins bind a variety of metals. Notably, neither of these compounds were produced in a co-culture of <i>Microbulbifer</i> with coral-derived pathogen <i>Vibrio coralliilyticus</i> Cn52-H1. Understanding how siderophores shape interspecies interactions between <i>Microbulbifer</i> spp. and other marine organisms will aid in unraveling the chemical and catalytic versatility of this genus and adaptation in nutrient deplete marine environment.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag238"},"PeriodicalIF":6.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148972309","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":"Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species.","authors":"Emma Derrick, Naíla Barbosa da Costa, Rowan D H Barrett, B Jesse Shapiro","doi":"10.1093/ismeco/ycag201","DOIUrl":"10.1093/ismeco/ycag201","url":null,"abstract":"<p><p>Bacterial populations evolve rapidly in the lab when faced with experimentally applied selective pressures. Yet how bacteria evolve in nature, in more complex multi-species communities, is both challenging to study and essential to our understanding of ecosystem responses to rapid anthropogenic change. To track bacterial evolution in a semi-natural context, we applied Roundup, a glyphosate-based herbicide (GBH) that interferes with aromatic amino acid synthesis, as a selective pressure to 1000 L ponds containing bacterioplankton communities from a pristine lake. We show that both ecological and evolutionary changes can occur on short timescales after a strong selective pressure. Using metagenome-assembled genomes as a proxy for species, we found that GBH treatment substantially affected community diversity but did not purge within-species genetic diversity over the 4 weeks of the experiment. We identified several functional categories of genes consistently targeted by GBH selection across seven different species of bacteria. Genes involved in amino acid transport and metabolism were more likely to experience GBH-driven changes in allele frequency, including the gene <i>aroA</i> targeted by glyphosate, along with other potentially novel targets of selection. Together, these results show how environmental change can rapidly affect bacterial community structure and select for specific genetic targets without purging genetic diversity genome-wide.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"6 1","pages":"ycag201"},"PeriodicalIF":6.4,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615356/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066093","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}