ISME Journal最新文献

{"title":"Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.","authors":"Shengjie Li, Xiaoli Dong, Pauline Humez, Joanna Borecki, Jean Birks, Cynthia McClain, Bernhard Mayer, Marc Strous, Muhe Diao","doi":"10.1093/ismejo/wraf024","DOIUrl":"10.1093/ismejo/wraf024","url":null,"abstract":"<p><p>Members of Methylotenera are signature denitrifiers and methylotrophs commonly found together with methanotrophic bacteria in lakes and freshwater sediments. Here, we show that three distinct Methylotenera ecotypes were abundant in methane-rich groundwaters recharged during the Pleistocene. Just like in surface water biomes, groundwater Methylotenera often co-occurred with methane-oxidizing bacteria, even though they were generally unable to denitrify. One abundant Methylotenera ecotype expressed a pathway for aerobic methane production from methylphosphonate. This phosphate-acquisition strategy was recently found to contribute to methane production in the oligotrophic, oxic upper ocean. Gene organization, phylogeny, and 3D protein structure of the key enzyme, carbon-phosphorus lyase subunit PhnJ, were consistent with a role in phosphate uptake. We conclude that phosphate may be a limiting nutrient in productive, methane-rich aquifers, and that methylphosphonate degradation might contribute to groundwater methane production.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11978286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143384060","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":"Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks.","authors":"Hiroki Negishi, Ayumi Ichikawa, Saori Takahashi, Hiroshi Kano, Seiya Makino","doi":"10.1093/ismejo/wraf027","DOIUrl":"10.1093/ismejo/wraf027","url":null,"abstract":"<p><p>The gut microbiome plays a crucial role in human health, and certain bacterial species, such as Faecalibacterium prausnitzii, are particularly beneficial. This study conducted a comprehensive investigation of prebiotic compounds that showed potential for specifically promoting beneficial gut bacteria. Using in vitro fecal cultures and a human intervention study, we identified maltobionic acid and lactobionic acid as compounds that specifically promoted Faecalibacterium growth both in vitro and in vivo without significantly affecting Bifidobacterium, which is typically increased by traditional prebiotics. In a human intervention study (n = 27), a significant increase was observed in Faecalibacterium abundance following maltobionic acid supplementation, with effectiveness correlating with the initial Parabacteroides abundance. Mechanistic investigations revealed a cross-feeding pathway between gut bacteria. In this pathway, Parabacteroides species converted the gluconic acid moiety of maltobionic and lactobionic acids to glucuronic acid, which was then preferentially utilized by Faecalibacterium. These findings suggest that gluconic acid-containing oligosaccharides are promising prebiotics for the targeted enhancement of beneficial Faecalibacterium and underscore the importance of microbial interactions in prebiotic research, offering new avenues for personalized microbiome modulation strategies.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143400615","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":"\"Paraxenoviridae\", a putative family of globally distributed marine bacteriophages with double-stranded RNA genomes.","authors":"Mitsuhiro Yoshida, Sofia Medvedeva, Akihito Fukudome, Yuri I Wolf, Syun-Ichi Urayama, Yosuke Nishimura, Yoshihiro Takaki, Eugene V Koonin, Mart Krupovic, Takuro Nunoura","doi":"10.1093/ismejo/wraf139","DOIUrl":"10.1093/ismejo/wraf139","url":null,"abstract":"<p><p>Metatranscriptome sequencing dramatically expanded the known diversity of the global RNA virome and, in particular, suggested several new candidate phyla in riboviruses. Using a double-stranded RNA (dsRNA) sequencing, here, we report five complete, bisegmented RNA genomes of a putative phylum group, paraxenoviruses, identified from marine environments. Phylogenetic analysis of the RNA-directed RNA polymerases of paraxenoviruses demonstrated their affinity with the ribovirus order Durnavirales within the class Duplopiviricetes of the phylum Pisuviricota. The order Durnavirales includes families Cystoviridae that consists of well-characterized dsRNA bacteriophages and less thoroughly studied Picobirnaviridae that are also suspected to infect bacteria. Consistently, modeling and analysis of the structure of the predicted capsid protein (CP) of several paraxenoviruses revealed similarity to picobirnavirus CP although the paraxenovirus CP is much larger and contains unique structural elaborations. Taken together, these affinities suggest that paraxenoviruses represent a distinct family within Durnavirales, which we provisionally name \"Paraxenoviridae\". Both genomic segments in Picobirnaviridae and \"Paraxenoviridae\" encompass multiple open reading frames, each preceded by a typical bacterial ribosome-binding site, strongly suggesting that these families consist of bacterial viruses. Search for homologs of paraxenovirus genes shows widespread distribution of this virus group in the global ocean, suggesting an important contribution to marine microbial ecosystems. Our findings further expand the diversity and ecological role of the bacterial RNA virome, reveal extensive structural variability of RNA viral CPs, and demonstrate the common ancestry of several distinct families of bacterial viruses with dsRNA genomes.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561818","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":"Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.","authors":"Bénédicte Condamine, Thibaut Morel-Journel, Florian Tesson, Guilhem Royer, Mélanie Magnan, Aude Bernheim, Erick Denamur, François Blanquart, Olivier Clermont","doi":"10.1093/ismejo/wrae245","DOIUrl":"10.1093/ismejo/wrae245","url":null,"abstract":"<p><p>Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynamics in its primary commensal niche, the vertebrate gut. Using Illumina and/or Nanopore technologies, we sequenced whole genomes of 210 E. coli isolates from 22 stools sampled during a 20-year period from a healthy man (ED) living in Paris, France. All phylogroups, except C, were represented, with a predominance of B2 (34.3%), followed by A and F (19% each) phylogroups. Thirty-five clones were identified based on their haplogroup and pairwise genomic single nucleotide polymorphism distance and classified in three phenotypes according to their abundance and residence time: 25 sub-dominant/transient (52 isolates), five dominant/transient (48 isolates) and five dominant/resident (110 isolates). Four over five dominant/resident clones belonged to B2 and closely related F phylogroups, whereas sub-dominant/transient clones belonged mainly to B1, A and D phylogroups. The long residence times of B2 clones seemed to be counterbalanced by lower colonization abilities. Clones with larger within-host frequency persisted for longer. By comparing ED strain genomes to a collection of commensal E. coli genomes from 359 French individuals, we identified ED-specific genomic properties including an enrichment in genes involved in a metabolic pathway (mhp cluster) and the presence of a very rare antiviral defense island. The E. coli colonization within the gut microbiota was shaped by both the intrinsic properties of the strain lineages, in particular longer residence of phylogroup B2, and the environmental constraints such as diet or phages.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11728103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814841","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":"Nitrogen availability shapes evolution of phage resistance in cyanobacteria.","authors":"Maimona Higazi, Dikla Kolan, Esther Cattan-Tsaushu, Zohar Freiman, Shira Ninio, Sarit Avrani","doi":"10.1093/ismejo/wraf180","DOIUrl":"10.1093/ismejo/wraf180","url":null,"abstract":"<p><p>Nitrogen-fixing cyanobacteria play a key role in nitrogen and carbon biogeochemical cycles in aquatic ecosystems. Under nitrogen-limited conditions, their ability to fix nitrogen provides an advantage over other species and enables them to form harmful blooms, which are increasing in frequency and negatively impact aquatic environments. Cyanophages (viruses infecting cyanobacteria) impose strong selective pressures on these populations, and although cyanobacteria can rapidly evolve resistance to these phages, there is a tradeoff between phage resistance and nitrogen fixation. Therefore, it remains unclear whether nitrogen-fixing cyanobacteria can evolve resistance without compromising nitrogen fixation under bloom-inducing nitrogen starvation. Here, we explore the evolution of phage resistance in nitrogen-fixing cyanobacteria (Nostoc sp. strain PCC 7120 and Cylindrospermopsis raciborskii) under nitrogen starvation. We found that phage-resistant strains evolved under nitrogen starvation, although resistance emerged more slowly than in nitrogen-rich environments. Whole-genome sequencing of 34 resistant strains revealed that mutations conferring resistance differed between nitrogen-rich and nitrogen-starved conditions. Nitrogen starvation selected for mutations predominantly in glycosyltransferase genes, which are associated with cell surface modifications. In contrast to resistant strains isolated under nitrogen-replete conditions, which exhibited impaired heterocyst formation, resistant strains selected under nitrogen starvation maintained their ability to form functional heterocysts and persist in nitrogen-limited environments. Our findings suggest that nitrogen availability influences the evolutionary trajectory of phage resistance, favoring mechanisms compatible with nitrogen fixation under nitrogen starvation. These results provide new insights into the ecological resilience of nitrogen-fixing cyanobacteria under phage predation and demonstrate that nitrogen availability affects the cost of resistance, evolutionary trajectories, and resistance mechanisms.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12507012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144876572","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":"Niche creation improves bioaugmentation of an organic micropollutant degrader in oligotrophic waters.","authors":"Jinsong Wang, Bart Raes, Cato Debrabandere, Veerle van Aken, Sebastián Jaramillo-Toro, Steffen Waldherr, Benjamin Horemans, Dirk Springael","doi":"10.1093/ismejo/wraf140","DOIUrl":"10.1093/ismejo/wraf140","url":null,"abstract":"<p><p>Bioaugmentation of sand filters is an alternative process for eliminating organic micropollutants in drinking water treatment. Bioaugmentation resembles an invasion process and niche availability is a prime determinant for successful invasion. This is particularly relevant for bioaugmentation of oligotrophic environments where organic micropollutants (OMPs) hardly provide a selective C-source and exploitative competition for the scarce intrinsic organic carbon exists between inoculated OMP-degraders and resident microbiota. Building on microbial invasion theories, we tested the hypothesis that the success of bioaugmentation and associated OMP degradation can be enhanced through niche creation by supplying a selective carbon source for the introduced degrader. Sand filter microbiota reduced growth of the 2,6-dichlorobenzamide degrading strain Aminobacter niigataensis MSH1 and 2,6-dichlorobenzamide degradation in different natural waters. This was counteracted by adding benzamide as a selective C-source for MSH1 resulting in a 3-fold faster 2,6-dichlorobenzamide biodegradation and a 6-fold increase in MSH1 growth. An additive biokinetic model underpredicted growth of MSH1 in the presence of sand filter microbiota suggesting that the community, despite its overall negative effect, supported MSH1 growth. Moreover, benzamide retarded 2,6-dichlorobenzamide degradation likely due to enzyme competitive inhibition. The results demonstrate the use of deliberately creating dedicated niches selective for the inoculum and the successful translation of ecological invasion theories into microbial community management, for improved bioaugmentation of complex communities.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12445691/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144561828","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: Dryland microbiomes reveal community adaptations to desertification and climate change.","authors":"","doi":"10.1093/ismejo/wraf060","DOIUrl":"https://doi.org/10.1093/ismejo/wraf060","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056530","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":"Identification of stress-alleviating strains from the core drought-responsive microbiome of Arabidopsis ecotypes.","authors":"Zewen Li, Zhenghong Wang, Yujie Zhang, Jianbo Yang, Kaixiang Guan, Yi Song","doi":"10.1093/ismejo/wraf067","DOIUrl":"10.1093/ismejo/wraf067","url":null,"abstract":"<p><p>Plant genetic and metabolic cues are involved in assembling their \"core microbiome\" under normal growth conditions. However, whether there is a core \"stress responsive microbiome\" among natural plant ecotypes remains elusive. Drought is the most significant abiotic stress worldwide. Characterizing conserved core root microbiome changes upon drought stress has the potential to increase plant resistance and resilience in agriculture. We screened the drought tolerance of 130 worldwide Arabidopsis ecotypes and chose the extremely drought tolerant and sensitive ecotypes for comparative microbiome studies. We detected diverse shared differentially abundant ASVs, network driver taxa among ecotypes, suggesting the existence of core drought-responsive microbiome changes. We previously identified 1479 microorganisms through high-throughput culturing, and successfully matched diverse core drought responsive ASVs. Our phenotypic assays validated that only those core drought responsive ASVs with higher fold changes in drought tolerant ecotypes were more likely to protect plants from stress. Transcriptome analysis confirmed that a keystone strain, Massilia sp. 22G3, can broadly reshape osmotic stress responses in roots, such as enhancing the expression of water up-taking, ROS scavenging, and immune genes. Our work reveals the existence of a core drought-responsive microbiome and demonstrates its potential role in enhancing plant stress tolerance. This approach helps characterize keystone \"core drought responsive\" microbes, and we further provided potential mechanisms underlying Massilia sp. 22G3 mediated stress protection. This work also provided a research paradigm for guiding the discovery of core stress-alleviating microbiomes in crops using natural ecotypes (cultivars).</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812833","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: Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.","authors":"","doi":"10.1093/ismejo/wrae254","DOIUrl":"https://doi.org/10.1093/ismejo/wrae254","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996754/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143992914","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":"Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.","authors":"Andreja Kust, Jackie Zorz, Catalina Cruañas Paniker, Keith Bouma-Gregson, Netravathi Krishnappa, Wendy Liu, Jillian F Banfield, Spencer Diamond","doi":"10.1093/ismejo/wraf142","DOIUrl":"10.1093/ismejo/wraf142","url":null,"abstract":"<p><p>Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by coculturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12368963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144585526","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}