ISME Journal最新文献

{"title":"Carbon substrate type shapes spatial self-organization in a multi-species biofilm community.","authors":"Deyong Zhu, Anna J Svagan, Nan Yang, Mads Frederik Hansen, Michael Kühl, Mette Burmølle","doi":"10.1093/ismejo/wrag223","DOIUrl":"10.1093/ismejo/wrag223","url":null,"abstract":"<p><p>Spatial organization is a defining feature of multispecies biofilms and critically influences microbial interactions and emergent community properties. However, understanding and manipulating how microbes assemble into spatially structured biofilms remains challenging because most experimental frameworks emphasize species composition and pairwise interactions, while often overlooking the spatial constraints on biofilms imposed by the environment. In this study, we focus on how carbon substrate type, distinguishing between diffusible sugars and polymeric substrates, affects biofilm self-organization in a four-member synthetic bacterial community (SynCom). Across all tested conditions, the SynCom consistently formed more biofilm biomass than any of its subsets, indicating a robust synergistic phenotype. Using chemically defined, 3D-printed hydrogel substrates with consistent physical properties, we varied carbon source composition to identify its impact on biofilm assembly. Microscopic imaging showed that carbon substrate type strongly influenced biofilm self-organization with diffusible simple carbon substrates yielding relatively intermixed communities, whereas polymer-rich carbon substrates promoted a highly structured biofilm organization characterized by the dominance and peripheral localization of polymer-degrading species. Bioinformatic analyses of carbohydrate-active enzyme repertoires and genome-scale metabolic modeling suggested bidirectional metabolite exchange among the SynCom members, which was also supported by analysis of biofilm formation in conditioned community supernatants. Together, our findings suggest carbon substrate type as an important ecological determinant of biofilm self-organization, highlighting the need to integrate environmental factors alongside species composition and metabolic potential to fully understand and manipulate natural and engineered multispecies biofilms.</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/PMC13617570/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148841967","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":"Differential aggregation properties among Baltic Sea picocyanobacterial strains impact their export.","authors":"Martin Ekman, Elina Viinamäki, Anders Verstraaten-Svensson, Ryan W Paerl, Anders F Andersson, Helena Höglander, Jakob Walve, Rachel A Foster","doi":"10.1093/ismejo/wrag214","DOIUrl":"10.1093/ismejo/wrag214","url":null,"abstract":"<p><p>Picocyanobacteria contribute significantly to carbon export but the mechanism by which their biomass is transported to depth is unclear. By analyzing 16S rRNA gene sequences from sediment trap material and size-fractionated water samples from different depths in the Baltic Sea, we show that picocyanobacterial contribution to phytoplankton biomass export was largely proportional (70%-90%) to their surface water abundances. However, we also found that both cell aggregation (enrichment in >10 μm fraction) and sedimentation (trap enrichment) varied among Synechococcus ASVs (amplicon sequence variants). A robust linear relationship was identified between ASV enrichment in traps and ASV enrichment in the >10 μm fraction, suggesting that cell aggregation is a direct determinant of Synechococcus sedimentation. Seasonal abundance patterns were similar among the dominant aggregate-forming ASVs but distinct from those of single-cell ASVs, suggesting aggregate/colony formation being an important trait in determining distribution of Synechococcus strains and their response to environmental conditions. Correlating microscopy- and sequence-based abundances further allowed us to propose genotypes for the dominant Baltic Sea colonial picocyanobacterial morphotypes. Our results provide in situ data linking phenotypic characteristics of picocyanobacteria with sedimentation properties and several lines of evidence for a quantitative dependency between surface water picocyanobacterial aggregate/colony formation and sinking. These findings are important for our understanding of mechanisms involved in export of pico-sized phytoplankton biomass from the photic zone to depth and emphasize the need to investigate occurrence and environmental regulation of cell aggregation in other picophytoplankton-dominated waters (e.g. open ocean gyres).</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/PMC13630569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148841958","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":"Bacterial motility in rhizosphere colonization: mechanisms, constraints, and implications for microbial inoculants.","authors":"Tong Wang, Brajesh K Singh, Pankaj Trivedi, Zahra F Islam, Ji-Zheng He, Hang-Wei Hu","doi":"10.1093/ismejo/wrag236","DOIUrl":"10.1093/ismejo/wrag236","url":null,"abstract":"<p><p>Although the potential of microbial inoculants for sustainable agriculture and environmental restoration has been widely recognized, their field performance remains highly variable and often unpredictable. Current research and development frameworks for microbial inoculants primarily focus on their plant growth-promoting functions and metabolic traits, often overlooking the ecological processes that determine whether introduced strains can successfully disperse, access, and establish within the rhizosphere. Increasing evidence suggests that successful dispersal and establishment cannot be assumed in the highly heterogeneous conditions of soil systems. Here, we summarize the key mechanisms underlying bacterial motility and discuss its role within the broader framework of microbial dispersal, highlighting how motility-mediated processes contribute to rhizosphere colonization. We propose that bacterial motility represents a key mechanistic determinant of biofertilizer efficacy. Its role extends beyond the ability of inoculant strains to physically reach the rhizosphere, encompassing competitive colonization on the root surface, long-term persistence, and the ability to respond to dynamic root-derived chemical gradients associated with newly developing root tissues. We argue that inoculant motility should be elevated from a passive descriptive trait to a core design parameter that can be systematically incorporated and regulated during the development and optimization of microbial inoculants. We outline a multi-tiered strategic framework for next-generation biofertilizer engineering that integrates strain selection, community design, motility regulation, and deployment strategies, thereby unlocking the full potential of synthetic microbial consortia for sustainable agriculture, ecosystem restoration, and climate change mitigation.</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/PMC13634192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148921612","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":"Reply to comment on \"A jumbo cyanophage encodes the most comprehensive ribosomal protein set in the known virosphere\" by LinXing Chen.","authors":"Isaac Meza-Padilla, Sarit Avrani, Kirsten M Müller, Jozef I Nissimov","doi":"10.1093/ismejo/wrag242","DOIUrl":"10.1093/ismejo/wrag242","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/PMC13623530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149082591","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: Horizontal transmission of heat-evolved microalgal symbionts in adult corals.","authors":"","doi":"10.1093/ismejo/wrag027","DOIUrl":"10.1093/ismejo/wrag027","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/PMC12924680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146777133","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":"Global transmission and distribution of phage-encoded cholera toxin genes constrained by toxin-repression genes and anti-phage defense systems.","authors":"Shujian Yuan, Demeng Tan, Dong Zhu, Jose Luis Balcazar, Hui Wang, Ville-Petri Friman, Mingming Sun, Feng Hu","doi":"10.1093/ismejo/wrag139","DOIUrl":"10.1093/ismejo/wrag139","url":null,"abstract":"<p><p>Cholera is a severe diarrheal disease caused by toxigenic Vibrio cholerae, whose virulence depends on lysogenic infection by CTXφ bacteriophages encoding the cholera toxin genes (ctxA and ctxB) and associated accessory genes (ace and zot). However, the global distribution and transmission dynamics of phage-encoded cholera toxin genes across environments remain poorly understood. To address this, we performed a large-scale bioinformatic analysis of publicly available whole genomes. We show that both phages and bacteria carrying toxin genes are globally distributed across human-associated, freshwater, fish, and mammalian habitats, with Vibrio and Aeromonas being the dominant bacterial taxa and Inoviridae is the most prevalent phage family. Phage-mediated horizontal gene transfer (HGT) of toxin genes occurred in both Vibrio and non-Vibrio species, with the highest transfer between Inoviridae and V. cholerae occuring predominantly among bacteria from the same habitat. Temporal analysis revealed an increase in candidate HGT events after 2000, peaking at 377845 events during 2010-2019. HGT events negatively correlated with the presence of CRISPR-Cas system and toxin-repression genes (hns, hapR, and tsrA) in host bacteria. Experimental validation indicated that H-NS and HapR inhibit phage infection by repressing phage release. Together, our results suggest that CRISPR-Cas phage defense system and toxin-repression mechanisms could constrain the spread of toxin-carrying phages, with potential implications for the occurrence and severity of cholera outbreaks worldwide.</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/PMC13310137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148220516","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":"Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.","authors":"Peng Zhang, Meiqi Zhao, Zhikang Cheng, Yuping Ding, Shihai Xia, Jianhua Guo","doi":"10.1093/ismejo/wrag126","DOIUrl":"10.1093/ismejo/wrag126","url":null,"abstract":"<p><p>Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.</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/PMC13271386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147965425","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":"Candidatus Dermatophostum as a novel genus of polyphosphate-accumulating organisms for high-strength wastewater treatment.","authors":"Hui Wang, Ze Zhao, Limin Lin, Ao Dong, Ye Deng, Jizhong Zhou, Feng Ju","doi":"10.1093/ismejo/wrag032","DOIUrl":"10.1093/ismejo/wrag032","url":null,"abstract":"<p><p>Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named here as Candidatus Dermatophostum, which shows specific preference for high-phosphorus environments. Its representative species, Ca. Dermatophostum ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Integrative meta-omics combining genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis, and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across wastewater treatment plants worldwide, underscoring both its diverse metabolic capabilities and potential engineering implications for mitigating nitrous oxide (N2O) emissions for EBPR system. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.</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/PMC12978653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146259984","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":"Rapid adaptive evolution of oxylipin-based chemical defense against algicidal bacteria in a bloom-forming diatom.","authors":"Muhaiminatul Azizah, Janine F M Otto, Nico Ueberschaar, Markus Werner, Oliver Werz, Georg Pohnert","doi":"10.1093/ismejo/wrag111","DOIUrl":"10.1093/ismejo/wrag111","url":null,"abstract":"<p><p>Phytoplankton, the photosynthetic microalgae driving nearly half of Earth's primary production, are the foundation of marine food webs and central to climate regulation. Skeletonema marinoi is a globally distributed and often dominant diatom species in marine phytoplankton communities. It inhabits a dynamic and frequently hostile microbial environment in which interactions with bacteria can negatively affect its survival. Skeletonema marinoi is susceptible to the algicidal bacterium Kordia algicida that can lyse the algal cells and even terminate entire blooms. The extent to which resistance against such a lysis can evolve in diatoms exposed to biotic stress by algicidal bacteria remains unknown. Using adaptive laboratory evolution, we investigated how S. marinoi adapts to toxins produced by K. algicida. Skeletonema marinoi evolved resistance already after 11 growth cycles under sublethal exposure to algicides. This was accompanied by changes in DNA methylation. Untargeted comparative metabolomics of the original and the evolved population revealed the up-regulation of the oxylipins 5-hydroxyeicosapentaenoic acid, prostaglandin E2, and 17-hydroxydocosahexaenoic acid. These oxylipins significantly inhibited the growth of K. algicida, indicating their role in chemical defense. The metabolic plasticity of diatoms and the rapid evolution observed after exposure to bacteria open new perspectives on our understanding of diatom bloom dynamics in nature.</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/PMC13240593/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857602","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":"Expression of Concern: Gut microbiota control host lipid deposition through HDAC9-driven PPARγ acetylation.","authors":"","doi":"10.1093/ismejo/wrag164","DOIUrl":"10.1093/ismejo/wrag164","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/PMC13403907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148594492","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}