ISME Journal最新文献

{"title":"Density-dependent feedback and higher-order interactions enable coexistence in phage-bacteria community dynamics.","authors":"Raunak Dey, Ashley R Coenen, Natalie E Solonenko, Marie N Burris, Anna I Mackey, Julia Galasso, Christine L Sun, David Demory, Daniel Muratore, Stephen J Beckett, Matthew B Sullivan, Joshua S Weitz","doi":"10.1093/ismejo/wrag041","DOIUrl":"10.1093/ismejo/wrag041","url":null,"abstract":"<p><p>Diverse phage-bacteria communities coexist at high densities in environmental, agricultural, and human-associated microbiomes. Phage-bacteria coexistence is often attributed to coevolutionary processes mediated by complex, pairwise infection networks. Here, using in vitro experiments and mathematical models, we explore how higher-order interactions function as a complementary, ecological feedback mechanism to stabilize phage-bacteria communities. To do so, we examine an environmentally derived, synthetic phage-bacteria community comprised of five marine heterotrophic bacteria (Cellulophaga baltica and Pseudoalteromonas strains) and five associated phage. We used Bayesian inference to reconstruct free phage production in one-step growth experiments and then forecasted pairwise phage-bacteria community dynamics over multiple infection cycles. In contrast to model predictions of rapid bacterial population collapse, each bacterial strain persisted in the community. We hypothesized and then experimentally validated the relevance of infection attenuation at relatively high viral densities. We extended models into a community context, corroborating complex coexistence of all phage and bacteria. Life-history traits inferred in community fits often differed from those inferred in a pairwise context, implicating higher-order interactions as an additional, ecological stabilization mechanism. Follow-up experiments confirm that phage traits (including burst size) can shift when infecting single versus multiple strains. More broadly, these findings suggest that complex community coexistence of phage and bacteria may be more common than anticipated when including feedback mechanisms outside of the growth-dominated regimes of fitted pairwise models that do not reflect the full scope of ecologically relevant contexts.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147500206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments.","authors":"Hideomi Itoh, Kazumori Mise, Miyu Kuniyasu, Sawa Wasai-Hara, Natsumi Ushijima","doi":"10.1093/ismejo/wrag157","DOIUrl":"10.1093/ismejo/wrag157","url":null,"abstract":"<p><p>Acidobacteriota, one of the most abundant and ubiquitous bacterial phyla in soils, are well recognized for their role in carbon cycling. In contrast, their roles in soil nitrogen cycling remain largely unexplored, although recent metagenome-assembled genome (MAG) analyses suggest that Acidobacteriota may harbor genes involved in nitrogen cycling. Here, we provide culture-based evidence of diazotrophy within this phylum and demonstrate the widespread occurrence of nitrogen-fixing Acidobacteriota across diverse soil types. From grassland and agricultural soils, we isolated five Acidobacteriota strains representing novel taxonomic lineages, four of which harbor functional nitrogenase (nif) gene clusters. These strains were capable of fixing atmospheric nitrogen in vitro and/or in soil microcosms, as evidenced by acetylene reduction, N2-dependent growth, transcription of nif genes, incorporation of 15N into biomass and soil, and inhibition of nitrogenase activity by ammonium. Furthermore, global-scale meta-analysis of soil metagenomes revealed that nif-harboring Acidobacteriota are widely distributed and locally dominant across soil types. These results demonstrate the nitrogen-fixing capability of Acidobacteriota at the organismal level, complementing MAG-based inferences, and underscore their adaptive capacity in nitrogen-limited environments and their potential contribution to terrestrial nitrogen fixation. We also propose novel taxa within the class Terriglobia of the phylum Acidobacteriota, including diazotrophic strains, comprising one novel family, three novel genera, and four novel species: Koromonadaceae fam. nov., Koromonas soli gen. nov., sp. nov., Koromonas humicola sp. nov., Oryzophilus luti gen. nov., sp. nov., and Humiphilus diazotrophicus gen. nov., sp. nov.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13362970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148279705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.","authors":"","doi":"10.1093/ismejo/wrag119","DOIUrl":"10.1093/ismejo/wrag119","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13240591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148206833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Widespread marine and freshwater distributions of active sulfoquinovose-degrading bacteria.","authors":"Guohua Liu, Xuanyun Qiu, Rongguang Cao, Changjie Dong, Quanrui Chen, Shujing Liu, Wenhao Li, Xuejing Li, Nianzhi Jiao, Spencer J Williams, Yao Zhang, Kai Tang","doi":"10.1093/ismejo/wrag155","DOIUrl":"10.1093/ismejo/wrag155","url":null,"abstract":"<p><p>Sulfoquinovose (SQ), a sulfonated sugar produced on a gigaton scale each year, contributes to global sulfur cycling, yet the microbes and pathways mediating its turnover in the environment have been inferred largely from genomic potential rather than direct activity. Here, we coupled incubations of environmental samples with 13C-labeled SQ to DNA-stable isotope probing to identify active SQ carbon assimilators across estuary, mangrove, and lake ecosystems. In estuarine communities, Vibrio and Cognatishimia incorporated SQ-derived 13C; Novosphingobium dominated in the mangrove, and Agrobacterium in the lake. Pure-culture experiments, coupled with comparative proteomics and gene knockout validation, demonstrated that Vibrio strains degrade SQ via modified sulfoglycolytic Embden-Meyerhof-Parnas and Entner-Doudoroff pathways to produce the environmentally significant organosulfur 2,3-dihydroxypropanesulfonate. Comparative genomic analyses suggested that closely related genome representatives of Novosphingobium, Cognatishimia, and Agrobacterium encode the sulfolytic SQ monooxygenase pathway. A global survey of aquatic microbial genomes indicated that over 9% harbor SQ degradation clusters, supporting a widespread distribution of bacterial SQ catabolic potential in aquatic environments.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148273661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lactobacillus reuteri targets farnesoid X receptor-dependent bile acid homeostasis to ameliorate alcoholic liver disease.","authors":"Shuo Yuan, Yuhua Liu, Peng Gao, Jiaxu Sun, Yuanshi Wang, Zhiyong Du, Jun Lei, Jiaxin Hong, Xinlan Fang, Pengfei Tu, Yingyuan Lu, Yong Jiang","doi":"10.1093/ismejo/wrag153","DOIUrl":"10.1093/ismejo/wrag153","url":null,"abstract":"<p><p>Alcoholic liver disease (ALD) is characterized by gut dysbiosis, yet the functional contribution of specific commensals remains largely unexplored. Here, we identify a significant reduction of Lactobacillus reuteri in both ALD patients and mouse models compared with their respective healthy controls. Using fecal microbiota transplantation, we first establish a causative role of the dysbiotic gut microbiota in driving ALD pathophysiology. In line with this finding, oral supplementation with L. reuteri ameliorates ALD phenotypes. Mechanistically, L. reuteri activates the farnesoid X receptor (FXR) signaling pathway, thereby restoring bile acid homeostasis, as evidenced by reduced levels of cholic acid (CA) and deoxycholic acid (DCA). The functional importance of FXR is further validated in Fxr-/- mice, where the protective effects of L. reuteri on both ALD and bile acid metabolism are largely abrogated. Moreover, both in vitro and in vivo experiments confirm that CA and DCA directly compromise hepatocyte viability and exacerbate liver injury, reinforcing their roles as pathogenic effectors downstream of FXR dysregulation. Expanding upon these mechanistic insights, we identify the natural compound echinacoside as a gut microbiota-targeting intervention that not only enriches L. reuteri but also potentiates FXR signaling, leading to significant improvement of ALD. Collectively, our findings define a microbiota-host metabolic axis centered on L. reuteri and FXR-dependent bile acid homeostasis, offering a conceptual framework for targeting host-microbe interactions in ALD.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13471275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148267051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Disturbance reshapes functional redundancy and accelerates nitrification in soil nitrifying communities.","authors":"Jun Zhao, Shannon M Brown, Jonathan Rodriguez, Eunkyung Choi, Nina Charissa A Infantado, Christina Hazard, Graeme W Nicol, Sarah L Strauss, Willm Martens-Habbena","doi":"10.1093/ismejo/wrag154","DOIUrl":"10.1093/ismejo/wrag154","url":null,"abstract":"<p><p>Statistical and culture-based models propose that environmental disturbances reshape competitive interactions among functionally redundant microbial taxa. However, the mechanisms driving these changes and their impact on biogeochemical processes remain largely untested in soil, owing to the challenge of linking functions to specific taxa in highly diverse and functionally complex soil microbiomes. Here, we simulated environmental disturbance in microcosms containing organic carbon-rich or sandy soils. Using bacterial and archaeal nitrifiers, a functionally tractable microbial guild, we examined how disturbance restructures competition among diverse microbial taxa within this guild. In both soils, ammonia-oxidizing archaea (AOA) predominated numerically and functionally under steady climax conditions. Following disturbance, ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox) rapidly gained a growth-related competitive advantage, likely due to increased per-cell ammonium availability supporting their intrinsic high growth rates. AOB recolonization was essential for full post-disturbance nitrogen turnover, resulting in elevated nitrification rates and increased nitrous oxide emissions. Nitrification rate did not fully recover when AOB were inhibited. In contrast, AOA and comammox played a dispensable role in recovering post-disturbance nitrification, limited by slower growth and lower per-cell activity, respectively. Competitive regrowth ability of microbial species showed a tradeoff with pre-disturbance abundance, highlighting the enhanced post-disturbance role of rare-abundance AOA, in addition to AOB phylotypes. Our findings demonstrate that bacterial and archaeal nitrifiers constitute a continuous spectrum between r- and K-strategists. Disturbance reshapes competition through differential growth and activity traits among functionally redundant taxa, favoring AOB and thereby transforming community assembly while intensifying nutrient cycling and greenhouse gas fluxes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13372034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148267021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carbon regime structures functional trait trajectories during primary succession in microorganisms.","authors":"Grace A Cagle, Benjamin Baiser, Jessica R Bernardin, Leonora S Bittleston, Erica B Young, Sarah M Gray, Zachary B Freedman","doi":"10.1093/ismejo/wrag134","DOIUrl":"10.1093/ismejo/wrag134","url":null,"abstract":"<p><p>Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148007342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical guide for marine exo-metabolomic sample preparation.","authors":"Catherine C Bannon, Jana K Geuer, Lennart Stock, Bruna Y P Imai, Manuel Liebeke","doi":"10.1093/ismejo/wrag115","DOIUrl":"10.1093/ismejo/wrag115","url":null,"abstract":"<p><p>Metabolomic strategies are being increasingly applied in marine systems, leading to unprecedented insights into the ocean and its inhabitants. In particular, exo-metabolites, small molecules produced by marine organisms and released into the environment, have received recognition as factors that influence marine microbial communities, global nutrient cycles, and ecosystem function. Studying exo-metabolites in the marine system is challenging due to the low metabolite concentrations, high salt content, and substantial chemical diversity, all of which can interfere with metabolite detection and therefore necessitate specialized, often tedious sample preparation. Advantageously, new marine metabolomic methods have recently emerged that improve the coverage and detection of key metabolite classes. Here, we offer a practical guide for selecting suitable extraction methods based on specific research needs alongside a systematic review of five recently published methods designed for marine exo-metabolomics. Specifically, these workflows enable quantification of various primary metabolites using liquid and gas chromatography coupled to mass spectrometry. The selection process is guided by several key questions that consider both experimental design and the specific research questions. Additionally, we highlight both the practical constraints and aspects of sample handling for each method. This guide aims to support researchers in effectively choosing a method that aligns with their study goals and logistical capabilities, while also highlighting the opportunities for innovation in the field moving forward.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13235718/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147934578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation.","authors":"Johannes Cairns, Niina Smolander, Sanna Pausio, Olli Pitkänen, Meri Lindqvist, Manu Tamminen, Rishi Das Roy, Ville-Petri Friman, Lutz Becks, Ville Mustonen, Teppo Hiltunen","doi":"10.1093/ismejo/wrag248","DOIUrl":"10.1093/ismejo/wrag248","url":null,"abstract":"<p><p>Microbial communities frequently encounter recurrent antibiotic disturbance, yet how ecological, evolutionary, and environmental processes jointly shape community responses remains unresolved. Here, we use priming to describe the history-dependent effect whereby prior exposure alters the response to a subsequent disturbance. Using a 23-species bacterial community exposed to sequential ampicillin pulses, we examined two dimensions of priming. The ecological dimension was manipulated by exposing assembled communities to an antibiotic pre-pulse that could alter species composition before a common high-dose pulse. The evolutionary dimension was manipulated by experimentally evolving individual species for increased ampicillin resistance before community assembly. Community-level pre-pulse exposure shifted composition toward resistant taxa before the main disturbance, reducing subsequent compositional change. Prior resistance evolution had the strongest effect on community dynamics, buffering compositional change during the main pulse, relaxing subsequent selection, and altering community-wide gene expression. This buffering arose from both increased resistance within species and accelerated ampicillin detoxification by a dominant degrader, which transiently reduced antibiotic exposure and promoted the persistence of non-degrading taxa. However, greater resistance did not improve recovery. Because resistance was coupled to competitive dominance, diversity after disturbance remained similar to or lower than in ancestral communities, whereas dominant taxa became further enriched. Together, our results show that antibiotic exposure history reshapes microbial disturbance responses through interacting eco-evolutionary and environmental feedbacks. These feedbacks increase resistance to recurrent disturbance but can constrain recovery, revealing a trade-off between resistance and diversity restoration.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.2,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13634194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148978353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice.","authors":"","doi":"10.1093/ismejo/wrag024","DOIUrl":"10.1093/ismejo/wrag024","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":10.0,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12919432/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146229647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}