The ISME Journal最新文献

{"title":"Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host","authors":"Mark McCauley, Federica Montesanto, Samuel A Bedgood, Cody Miner, Keyla Plichon, Virginia M Weis, Sandra Loesgen","doi":"10.1093/ismejo/wraf189","DOIUrl":"https://doi.org/10.1093/ismejo/wraf189","url":null,"abstract":"Symbiodiniaceae-associated microbiota strongly affect cnidarian symbioses. We systematically reduced the bacterial and fungal communities associated with Symbiodiniaceae to study effects on the cnidarian holobiont Exaiptasia diaphana (Aiptasia). Clonal anemones were inoculated with xenic Breviolum minutum (SSB01) and microbiome manipulated cultures after antibacterial or antifungal treatment. The asexual reproduction of pedal laceration allowed for three generations of clonal aposymbiotic Aiptasia to be included in this study, from the initial adult generation (G0), to the first (G1) and second (G2) generation. We inoculated small and large G1 Aiptasia with algae and monitored onset of symbiosis, rate of algal proliferation, and holobiont characteristics. Sequencing the 16S and 18S rRNA gene regions identified significant differences in the bacterial and fungal communities of the G0 and G1 generations, alongside differences between the size classes of small and large G1 anemones. The microbiome of larger G1 individuals was distinct to the smaller G1 anemones, suggesting a microbiome maturation process. Control B. minutum cultures exhibited a significantly greater proliferation rate in large G1 anemones when compared to antibacterial or antifungal treated cultures, whereas the opposite trend was documented in the small G1 anemones. Although no differences were observed between algal photochemical parameters, or the growth and behavior of G1 juveniles, we observed a significant influence in the production of G2 clones between treatments. Overall, we provide strong ecological implications of manipulating Symbiodiniaceae microbiome, not for the algae themselves, but for the maturation of the host Aiptasia, as well as for the cnidarian holobiont over multiple generations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of microbial life history strategy in shaping the characteristics and evolution of host-microbiota interactions","authors":"Nancy Obeng, Johannes Zimmermann, Anna Czerwinski, Janina Fuß, Hinrich Schulenburg","doi":"10.1093/ismejo/wraf168","DOIUrl":"https://doi.org/10.1093/ismejo/wraf168","url":null,"abstract":"Many host-associated microbes are transmitted between individual hosts via the environment and, therefore, need to succeed both within a host and a connected environmental habitat. These microbes might invest differentially into the two habitats, potentially leading to fitness trade-offs and distinct life history strategies that ultimately shape the host-associated microbial communities. In this study, we investigated how the presence of distinct bacterial life history strategies affects microbiota characteristics along a host-associated life cycle, using the nematode host Caenorhabditis elegans and two naturally associated bacteria, Pseudomonas lurida and Ochrobactrum vermis, as an experimentally tractable model. Based on genomic life history prediction and experimental fitness characterizations, we identified distinct ecological strategies for the bacteria: whereas P. lurida dominated the free-living environment, O. vermis was more abundant in the host. Using mathematical modelling, experimental evolution, and whole genome sequencing, we next assessed whether the two distinct ecological strategies influence further adaptation to the host-associated life cycle. We found that (i) the host-specialist O. vermis did not further adapt to the two habitats, whereas (ii) the initially better environmental competitor P. lurida adapted to the life cycle, leading to its increased abundance in both environment and host. Evolutionary adaptation of P. lurida caused a shift in microbiota composition in the host, which in turn, resulted in a significant increase in host fitness. Overall, our results highlight the role of microbial life history strategies in shaping the characteristics and evolution of host–microbe interactions and suggest a potential selective advantage of better environmental competitors.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning","authors":"Qiushuang Li, Rong Wang, Xiang Zhou, Shuya Li, Shizhe Zhang, Xiumin Zhang, Wenxing Wang, Jinzhen Jiao, Peter H Janssen, Emilio M Ungerfeld, Volker Müller, Ralf Conrad, Chris Greening, Zhiliang Tan, Bo Fu, Min Wang","doi":"10.1093/ismejo/wraf183","DOIUrl":"https://doi.org/10.1093/ismejo/wraf183","url":null,"abstract":"Enteric methane emissions are energy losses from farmed ruminants and contribute to global warming. Diverting electrons and H2 flow toward beneficial fermentation products would mitigate ruminal methane emissions while improving feed efficiency. Acetogens can direct H2 and electrons to acetate production via the Wood–Ljungdahl pathway, but methanogens have more competitive H2 affinities. Thus, it is unclear how acetogenesis subsists in the rumen. An analysis of 2102 globally derived rumen metagenomes from multiple ruminant species revealed that putative acetogens were phylogenetically diverse and capable of using carbohydrates or H2 as electron donors. The metabolic versatility of these acetogens may enable them to outcompete methanogens with lower versatility. Through animal trials, in vitro experiments, and DNA stable isotope probing, we verified the presence of diverse acetogens in beef cattle rumens and revealed that their niche partitioning is driven by contrasting fiber-rich and starch-rich diets. A fiber-rich diet enriched heterotrophic acetogens, which increased acetate formation while decreasing methane production. Overall, this study highlights the overlooked heterotrophy of acetogens in the rumen and their potential for mitigating enteric methane emissions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144924121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses","authors":"Georges Kanaan, Jody W Deming","doi":"10.1093/ismejo/wraf198","DOIUrl":"https://doi.org/10.1093/ismejo/wraf198","url":null,"abstract":"Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and non-adapted bacteria (Pelagibacter); e.g., in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144918992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"End-to-end contact enables long-distance electron transport between filaments in cable bacteria","authors":"Rong Tang, Xiaoxue Zhang, Linyan Huang, Guoping Ren, Yin Ye, Yong Yuan, Shungui Zhou","doi":"10.1093/ismejo/wraf194","DOIUrl":"https://doi.org/10.1093/ismejo/wraf194","url":null,"abstract":"Filamentous cable bacteria are capable of centimeter-scale long-distance electron transport and play crucial roles in the biogeochemistry of aquatic sediments. However, the mechanisms underlying long-distance electron transport remain incompletely understood. This study reports dynamic contacts between separate filaments of cable bacteria, enabling them to relay electrons between sulfidic and oxic zones. Video microscopy of motile filaments in a microchamber slide setup revealed that some filaments did not fully bridge the gap between the sulfidic and oxic zone, but made transient contact with each other. Contacts were always end-to-end and often occurred repeatedly, in which filaments always followed the same trajectory back and forth. The contact frequency gradually increased over the first 20 days, and then declined afterwards. About 5.5% of cable bacterium filaments were observed to engage in contact events during a 2-hour observation window on day 20. Confocal microscopy confirmed the presence of extracellular polymer substance trails between filaments, which appear to guide consecutive end-to-end contacts. In situ Raman spectroscopy showed that connections enabled redox continuity between reduced and oxidized filaments, thus suggesting inter-filament electron transfer during physical contact. This inter-filament electron transport represents a novel type of microbial cooperation, and appears to be a strategy for establishing optimal connections between spatially separated electron donors and acceptors in a dynamic sedimentary environment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144918993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial dispersal into surface soil is limited on a meter scale","authors":"Kendra E Walters, Kristin M Barbour, John M Powers, Jennifer B H Martiny","doi":"10.1093/ismejo/wraf169","DOIUrl":"https://doi.org/10.1093/ismejo/wraf169","url":null,"abstract":"Dispersal shapes microbial communities, yet it is largely unknown how fast or how far free-living microorganisms move in the environment. Here, we deployed microbial traps along transects spanning a grassland and neighboring shrubland to quantify the rate and distance at which microorganisms disperse into the soil surface. We found that bacteria disperse at a similar rate across the two ecosystems, and both bacteria and fungi exhibit a signature of dispersal limitation at a meter scale, indicating highly heterogeneous dispersal of microorganisms into soil.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enrichment of Horizontally Transferred Gene Clusters in Bacterial Extracellular Vesicles via Non-Lytic Mechanisms","authors":"Sotaro Takano, Satoshi Takenawa, Naradasu Divya, Kangmin Yan, XinXin Wen, Tomoko Maehara, Nobuhiko Nomura, Nozomu Obana, Masanori Toyofuku, Michihiko Usui, Wataru Ariyoshi, Akihiro Okamoto","doi":"10.1093/ismejo/wraf193","DOIUrl":"https://doi.org/10.1093/ismejo/wraf193","url":null,"abstract":"Bacterial extracellular vesicles are emerging as key mediators of horizontal gene transfer, enhancing microbial adaptability. A critical factor determining the effectiveness of horizontal gene transfer is the fraction of vesicles containing specific functional genes. However, the proportion of containing specific DNA fragments has not been adequately determined, which hinders the understanding of the conditions and mechanisms that facilitate the incorporation of specific genes into the vesicles and possible evolutionary roles of vesicle-derived DNA. Here, we demonstrate that enrichment of horizontally transferred genes into bacterial extracellular vesicles is driven by cellular processes by profiling the DNA content of hundreds of individual vesicles using a microdroplet-based sequencing technique. This approach revealed unique DNA profiles in vesicles from the oral pathogen Porphyromonas gingivalis, pinpointing genomic regions related to DNA reorganization such as CRISPR-Cas clusters. Comparative genomic and phylogenetic analyses of Porphyromonas genomes revealed traces of horizontal gene transfer in vesicle-enriched genes. Modulating vesicle-biogenesis routes, quantitative real-time PCR revealed that this selective enrichment was driven by blebbing-driven DNA packaging mechanisms rather than stress-induced lysis. Applied to dental plaque-derived bacterial extracellular vesicles, the droplet-based approach reveled O-antigen biosynthetic genes, key for host-bacterial interactions, were prevalent in the vesicles from Alcaligenes faecalis, suggesting the vesicles from this bacterium can modulate pathogenicity in oral biofilms through targeted DNA packaging. These findings suggest the prevalence of functionally relevant gene clusters in bacterial extracellular vesicles in oral microbiota and their evolutionary roles as DNA cargoes for modulating phage-bacterial and host-bacterial interactions via horizontal gene transfer.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plastic leachates promote marine protozoan growth","authors":"Jessy Le Du-Carrée, Cristina Romera-Castillo, Rodrigo Almeda","doi":"10.1093/ismejo/wraf195","DOIUrl":"https://doi.org/10.1093/ismejo/wraf195","url":null,"abstract":"Millions of tons of plastic enter the ocean annually, yet the effects of their leachates on the microbial loop are poorly understood. This study investigates how dissolved organic carbon (DOC) released from field-collected plastics and a bioplastic influences the growth of the protozoan Oxyrrhis marina and its associated bacterial community. Plastics increased dissolved organic carbon (DOC) concentrations in seawater by 5 to 34-fold, stimulating O. marina growth by up to an order of magnitude compared to the control. After exposure to conventional beach plastic leachates and bioplastic leachates, O. marina exhibited growth rates up to 0.3 d$^{-1}$ and 0.4 d$^{-1}$, respectively, even in the absence of microalgal prey. We estimated that each gram of microplastics could lead to daily assimilation of up to 0.7 g of carbon per gram of protozoan, indicating that plastic-derived carbon enhances heterotrophic metabolism in the microbial loop through osmotrophy. Given that autotrophic prokaryotes are negatively impacted by plastic leachates and that plastic pollution is expected to triple in the coming decades, plastic leaching could alter the balance between microbial primary production and heterotrophy in the ocean.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sulfide stress tolerance as a controller of methane production in temperate wetlands","authors":"Emily K Bechtold, Jared B Ellenbogen, Danhui Xin, Maricia Pacheco, Brandy M Toner, Yu-Ping Chin, William A Arnold, Sheel Bansal, Michael J Wilkins","doi":"10.1093/ismejo/wraf196","DOIUrl":"https://doi.org/10.1093/ismejo/wraf196","url":null,"abstract":"Wetlands are a major source of methane emissions and contribute to the observed increase in atmospheric methane over the last 20 years. Methane production in wetlands is the final step of carbon decomposition performed by anaerobic archaea. Although hydrogen/carbon dioxide and acetate are the substrates most often attributed to methanogenesis, other substrates – such as methylated compounds – may additionally play important roles in driving methane production in wetland systems. Here we conducted mesocosm experiments combined with genome-resolved metatranscriptomics to investigate the impact of diverse methanogenic substrate amendment on methanogenesis in two high methane-emitting wetlands with distinct geochemistry, termed P7 and P8. Methanol amendment resulted in high methane production at both sites, whereas acetate and formate amendment only stimulated methanogenesis in P7 mesocosms, where aqueous sulfide concentrations were lower. In P7 sediments, formate amendment fueled acetogenic microbes that produced acetate, which was subsequently utilized by acetoclastic methanogens. In contrast to expression profiles in P7 mesocosms, active methylotrophic methanogen genomes from P8 showed increased expression of genes related to membrane remodeling and DNA damage repair, indicative of stress tolerance mechanisms to counter sulfide toxicity. Methylotrophic methanogenesis generates higher free energy yields than acetoclastic methanogenesis, which likely enables allocation of more energy towards stress responses. These findings contribute to the growing body of literature highlighting methylotrophic methanogenesis as an important methane production pathway in wetlands. By using less competitive substrates like methanol that provide greater energy yields, methylotrophic methanogens may invest in physiological strategies that provide competitive advantages across a range of environmental stresses.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seed-mediated vertical transmission of Pantoea core endophytes","authors":"Irene Sanz-Puente, Santiago Redondo-Salvo, Gloria Torres-Cortés, María de Toro, Susana Fernandes, Andreas Börner, Óscar Lorenzo, Fernando de la Cruz, Marta Robledo","doi":"10.1093/ismejo/wraf192","DOIUrl":"https://doi.org/10.1093/ismejo/wraf192","url":null,"abstract":"Plant-associated microorganisms, particularly endophytes, are essential for plant health and development. Endophytic microbiota is intimately associated with host plants colonizing various tissues, including seeds. Seed endophytes are particularly noteworthy because of their potential for vertical transmission. This pathway may play a role in the long-term establishment and evolution of stable bacteria-host interactions across plant generations. Hundreds of seed-bacteria associations have been recently uncovered; however, most seem to be transient or unspecific. Although it is known that microorganisms can be transmitted from plant tissues to seeds and from seeds to seedlings, the experimental confirmation of bacterial transfer through successive plant generations by inoculation remains unreported. In this study, we identified Pantoea as the unique core endophytic bacteria inhabiting the endosperms of 24 wheat seed samples originally harvested in different worldwide locations. Pantoea is the genus with the highest relative average abundance in wheat seeds (61%) and in germinated roots and shoots grown under gnotobiotic conditions (45–38%). In the field, it was the only genus dwelling roots, shoots, spikes, and seeds of four different wheat varieties tested and its abundance progressively increased across these tissues. This genuine pattern of vertical enrichment, which was not found in other common wheat-associated taxa, suggests a role in the transfer of these endophytic bacteria through the seeds. To confirm intergenerational transmission, parental plants were inoculated with labelled Pantoea isolates, which specifically colonized the next generations of Poaceae plants, experimentally demonstrating bacterial vertical inheritance to the offspring generations and suggesting transmission specificity.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}