ISME Journal最新文献_第7页

Genomic traits associated with copiotrophy decouple from maximum growth rate predictions along temperature gradients. 与Copiotrophy相关的基因组性状与沿温度梯度的最大生长速率预测解耦。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag147

J L Weissman, Alexandra Walling, Hugh Ducklow, Emily J Zakem

{"title":"Genomic traits associated with copiotrophy decouple from maximum growth rate predictions along temperature gradients.","authors":"J L Weissman, Alexandra Walling, Hugh Ducklow, Emily J Zakem","doi":"10.1093/ismejo/wrag147","DOIUrl":"10.1093/ismejo/wrag147","url":null,"abstract":"Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms, in part because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the world's oceans, where deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, leading to the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured along a temperature gradient. Our results suggest that, as a result of temperature's confounding effects, genomic signatures of growth optimization often better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as growth beyond a thermodynamic baseline maximum growth rate, rather than in relation to a static rate cutoff.","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/PMC13359058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148206778","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}

引用次数: 0

Metabolic division of labor drives estuarine-coastal N2O emissions. 代谢分工驱动河口-沿海N2O排放。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag216

Enquan Zhang, Shengjie Li, Ehui Tan, Qiuyun Jiang, Yunxuan Li, Ziqi Wu, Jiaxin Chen, Xianhui Wan, Xianbiao Lin, Nengwang Chen, Yu Cong, Nianzhi Jiao, Xiyang Dong, Qiang Zheng

{"title":"Metabolic division of labor drives estuarine-coastal N2O emissions.","authors":"Enquan Zhang, Shengjie Li, Ehui Tan, Qiuyun Jiang, Yunxuan Li, Ziqi Wu, Jiaxin Chen, Xianhui Wan, Xianbiao Lin, Nengwang Chen, Yu Cong, Nianzhi Jiao, Xiyang Dong, Qiang Zheng","doi":"10.1093/ismejo/wrag216","DOIUrl":"10.1093/ismejo/wrag216","url":null,"abstract":"Estuarine and coastal systems are global hotspots of marine nitrous oxide (N2O) emissions, where microbial nitrification and denitrification are the primary processes regulating N2O dynamics. However, how interactions among different N2O-associated microorganisms influence ecosystem-scale N2O emissions remains poorly understood. This study combined in situ N2O concentrations, 15N-based potential rates, metagenomics, metatranscriptomics, and genome-scale metabolic model analysis to explore N2O production and reduction processes in estuarine and coastal systems. Potential N2O production and reduction rates, together with in situ concentrations, the relative abundance, and the transcriptional activity of associated genes, were significantly higher at low salinity and declined toward coastal regions. Based on the gene content of 974 recovered N2O-associated genomes, microorganisms were classified into three functional groups: net N2O producers, net N2O consumers, and self-sustaining N2O players. The abundance, composition, and activity of these functional groups shifted along estuarine-coastal gradients. A larger NO/N2O exchange gap, reflecting the imbalance between model-inferred NO and N2O handoff potentials, was found at low salinity and was associated with elevated bottom-water N2O concentrations. Together, community-level division of labor and the associated exchange gap provide a conceptual framework for linking N2O-related functional groups to N2O accumulation in estuarine-coastal ecosystems.","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/PMC13592168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148820112","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}

引用次数: 0

Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria. 自然转化驱动人类肠道双歧杆菌的大规模基因组镶嵌。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag208

Yohei Watanabe, Kento Orihara, Naoki Tsukuda, Taeko Hara, Takahiro Matsuki

{"title":"Natural transformation drives large-scale genome mosaicism in human gut bifidobacteria.","authors":"Yohei Watanabe, Kento Orihara, Naoki Tsukuda, Taeko Hara, Takahiro Matsuki","doi":"10.1093/ismejo/wrag208","DOIUrl":"10.1093/ismejo/wrag208","url":null,"abstract":"Although horizontal gene transfer drives bacterial diversification, its contribution to chromosome-scale variation in human gut commensals remains unclear. This study demonstrated that human-associated bifidobacteria undergo extensive chromosomal transfer through natural transformation. Comparative genomics of coexisting Bifidobacterium pseudocatenulatum isolates from a single individual revealed extensive recombination signatures between the lineages. We experimentally reproduced this recombination by co-culturing strains, resulting in the transfer of multiple chromosomal regions and generation of mosaic genomes. Individual recombination tracts reached up to 247 kb per site, with cumulative replacements accounting for up to 28.9% of the recipient chromosome. These transfers occurred with heat-killed donors or purified DNA and were abolished by DNase, thereby identifying natural transformation as the underlying mechanism. Furthermore, we observed that environmental factors strongly influenced transformation frequency, suggesting that gut environmental conditions play a role regulating this process. Using natural transformation, we established a simple markerless genome-editing method that enables efficient gene deletions. Deletions of the Tad pili, ComEA-ComEC, or DprA-ComM-YraN gene clusters abolished transformation, defining the core machinery. The conservation of these genes across the genus Bifidobacterium and experimental demonstration of natural transformation in B. longum and B. breve indicate that natural transformation capacity is widespread within the genus. Our findings establish natural transformation as a key mechanism that promotes genome plasticity and contributes to adaptive evolution in bifidobacteria, thereby expanding our current understanding of horizontal gene transfer in the human gut microbiota.","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/PMC13660472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698166","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}

引用次数: 0

Correction to: Function-based selection of synthetic communities enables mechanistic microbiome studies. 修正：基于功能的合成群落选择使机械微生物组研究成为可能。

IF 1 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag015

引用次数: 0

Correction to: Contrasting viral infection strategies for single cell and colonial Microcystis populations consistent with Black Queen dynamics. 修正：对比单细胞和群体微囊藻群体的病毒感染策略，与黑皇后的动态一致。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag117

引用次数: 0

Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity. 扩大纤毛虫多样性揭示了一种独特的紫绿光共生的进化组合。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag142

Sergio A Muñoz-Gómez, Megan E S Sørensen, Shahed U A Shazib, Mann Kyoon Shin, Thilo Bauer, Martin Kreutz, Sebastian Hess

{"title":"Evolutionary assembly of a unique purple-green photosymbiosis revealed by expanded ciliate diversity.","authors":"Sergio A Muñoz-Gómez, Megan E S Sørensen, Shahed U A Shazib, Mann Kyoon Shin, Thilo Bauer, Martin Kreutz, Sebastian Hess","doi":"10.1093/ismejo/wrag142","DOIUrl":"10.1093/ismejo/wrag142","url":null,"abstract":"Symbioses are widespread in nature and have been the source of much evolutionary innovation. While some types of symbioses evolved multiple times, others are extremely rare. Only two purple photosymbioses between heterotrophic eukaryotes and intracellular purple bacteria have been documented. What factors prevent the more frequent establishment of purple photosymbioses? To shed light on this question, we investigated the evolutionary history of the purple-green ciliate Pseudoblepharisma tenue (Spirostomidae) using a phylogenetic and comparative approach and newly discovered species. We sampled about 30 new isolates of spirostomid ciliates from Germany and South Korea, inferred a comprehensive and robust phylogeny based on >200 proteins, and resolved the sister relationship between Pseudoblepharisma and Spirostomum. Furthermore, we characterized P. tenue's sister species, here renamed Pseudoblepharisma chlorelligerum, and revealed that it constitutes a quadripartite symbiosis between a ciliate, a green alga, and two non-photosynthetic bacteria. This oxygenic photosymbiosis is presumed to be supplemented with amino acids by its bacterial symbionts. In addition, we discovered three colorless, non-photosymbiotic Pseudoblepharisma species, which branch as sister to the photosymbiotic P. tenue and P. chlorelligerum. Our phylogenetic and comparative genomic analyses suggest that the green algal symbionts of P. tenue predated the acquisition of purple bacterial symbionts, and that the ancestor of the extant Pseudoblepharisma species was non-photosymbiotic and facultatively anaerobic. These data allowed us to hypothesize on the evolutionary steps that led to the origin of P. tenue and thus bring us closer to explaining the conditions that led to the evolutionary emergence of a unique purple-green symbiosis.","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/PMC13310139/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148200724","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}

引用次数: 0

Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems. 活动和非活动李斯特菌采用不同的生态和进化策略，在整个土壤生态系统中实现广泛的地理范围。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag158

Ying-Xian Goh, Shannon Hepp, Kevin J Cummings, Martin Wiedmann, Jingqiu Liao

{"title":"Motile and non-motile Listeria species adopt distinct ecological and evolutionary strategies to achieve broad geographic ranges across soil ecosystems.","authors":"Ying-Xian Goh, Shannon Hepp, Kevin J Cummings, Martin Wiedmann, Jingqiu Liao","doi":"10.1093/ismejo/wrag158","DOIUrl":"10.1093/ismejo/wrag158","url":null,"abstract":"Broad geographic ranges often reflect ecological versatility and are associated with lower extinction risk. Motility is a key physiological and ecological trait in bacteria. However, how some motile and non-motile bacteria achieve broad geographic ranges remains poorly understood. Here, we analyzed the genomes of 141 Listeria welshimeri and 90 Listeria booriae isolates systematically obtained from soils, representing widespread motile and non-motile species, respectively. We show that L. welshimeri lacks clear phylogeographic structure, suggesting minimal geographic barriers to dispersal. Its wide distribution is likely associated with enhanced motility and effective host colonization that facilitate wildlife-driven dispersal, particularly by regional-terrestrial birds. This pattern is supported by positive selection on flagellar and chemotaxis genes, strong associations with wildlife movement patterns, and close genomic relatedness between soil and wild bird isolates. In contrast, L. booriae displays clade endemism and a strong distance-decay relationship, suggesting dispersal limitation. Despite lacking a dispersal advantage, L. booriae's wide distribution appears to be linked to genomic flexibility and metabolic versatility that support adaptation to diverse environmental conditions, especially those shaped by iron concentration and precipitation. This is evidenced by its large, open pangenome characterized by abundant and diverse metabolic pathways and broad substrates utilization capacity; pronounced positive selection on genes involved in inorganic ion, amino acid, and coenzyme transport and metabolism; and strong associations between gene richness and abiotic factors as well as bacterial community composition. These findings suggest distinct genomic foundations and ecological and evolutionary mechanisms underlying the success of motile and non-motile cosmopolitan bacteria in soil ecosystems.","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/PMC13374856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148279713","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}

引用次数: 0

Correction to: Keystone protist suppression triggers mesopredator release and biotic homogenization in complex soil microbial communities. 修正：Keystone原生生物抑制触发中捕食者释放和复杂土壤微生物群落的生物均质化。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag161

引用次数: 0

Elucidation of dimethyl sulfide assimilation in soil bacteria expands the enzymatic landscape of terrestrial sulfur cycling. 土壤细菌对二甲基硫同化的阐释扩展了陆地硫循环的酶促景观。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag149

Yasmeen Yousfi, Emilie Pateau, Nadia Perchat, Jean-Louis Petit, Murielle Jérôme, William Buchmann, Ekaterina Darii, Alain Perret

{"title":"Elucidation of dimethyl sulfide assimilation in soil bacteria expands the enzymatic landscape of terrestrial sulfur cycling.","authors":"Yasmeen Yousfi, Emilie Pateau, Nadia Perchat, Jean-Louis Petit, Murielle Jérôme, William Buchmann, Ekaterina Darii, Alain Perret","doi":"10.1093/ismejo/wrag149","DOIUrl":"10.1093/ismejo/wrag149","url":null,"abstract":"Dimethyl sulfide (DMS) is a central volatile sulfur intermediate in the global sulfur cycle, traditionally associated with marine ecosystems. However, despite significant advances, important gaps remain in our understanding of its metabolism in terrestrial environments. Here, we elucidate a complete DMS catabolic pathway for sulfur utilization in the soil bacterium Acinetobacter baylyi ADP1 using an integrative approach combining targeted metabolomics, genetic knockouts, and in vitro enzyme assays. The pathway consists of a series of oxidation reactions catalyzed by two-component monooxygenases, including newly identified enzymes responsible for the sequential conversion of DMS to dimethyl sulfoxide and then dimethyl sulfone. These steps are followed by previously reported downstream enzymes that form methanesulfinate and methanesulfonate, ultimately yielding sulfite for cysteine biosynthesis. Functional redundancy and substrate promiscuity characterize these monooxygenases, all of which are powered by a single flavin reductase. A genomic survey revealed that this pathway is widespread among plant-associated and soil-dwelling Proteobacteria, including Pseudomonas putida and Rhodococcus opacus, which were experimentally confirmed to grow on DMS. Our findings reveal a widespread terrestrial DMS metabolic route that may represent a significant, yet previously unrecognized, component of the global sulfur cycle.","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/PMC13352529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148240488","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}

引用次数: 0

Extracellular wax ester biosynthesis by staphylococcal lipases detoxifies skin fatty acids and shapes interspecies competition. 葡萄球菌脂肪酶的胞外蜡酯生物合成可解毒皮肤脂肪酸并形成种间竞争。

IF 10.2 1区环境科学与生态学

ISME Journal Pub Date : 2026-01-14 DOI: 10.1093/ismejo/wrag148

Justine Camus, Christian D Freeman, Xuanheng Hu, Aaron Komnik, Rebekah L Casey, David T Brewer, Soobin Yang, Kelly M Hines, Arnaud Kengmo Tchoupa

{"title":"Extracellular wax ester biosynthesis by staphylococcal lipases detoxifies skin fatty acids and shapes interspecies competition.","authors":"Justine Camus, Christian D Freeman, Xuanheng Hu, Aaron Komnik, Rebekah L Casey, David T Brewer, Soobin Yang, Kelly M Hines, Arnaud Kengmo Tchoupa","doi":"10.1093/ismejo/wrag148","DOIUrl":"10.1093/ismejo/wrag148","url":null,"abstract":"To maintain its barrier function, human skin requires lipids, including cholesterol, ceramides, free fatty acids, and wax esters. In contrast to other skin lipids, wax esters remain largely unexplored as metabolites of the skin microbiome. Recently, we discovered that Staphylococcus aureus utilises its lipase Lip2 to detoxify antimicrobial fatty acids (AFAs) by esterification with cholesterol. The observed promiscuity of Lip2 and the presence of similar lipases among skin staphylococci prompted the search for novel substrates and products. Here, we identify S. aureus Lip2 and Lip1, Staphylococcus simulans SsL, and Staphylococcus epidermidis GehD and GehC as lipases capable of metabolizing wax esters. These lipases degraded wax esters into AFAs and fatty alcohols, and, except for GehC, shared the ability to esterify AFAs with fatty alcohols, thereby generating wax esters. In monocultures of bacteria heterologously expressing staphylococcal lipases, synthesis of wax esters mirrored protection from AFAs by fatty alcohols in planktonic or biofilm settings. In pairwise cocultures, lipases secreted by lipase-proficient S. aureus, S. simulans, and S. epidermidis functioned as public goods, rescuing lipase-deficient mutants. In the absence of detoxifying substrates/lipases, S. simulans or S. epidermidis outcompeted S. aureus when exposed to AFAs. A skin-mimicking high-salt environment increased the resistance of S. aureus, but not S. simulans, to AFAs, enabling S. aureus to match or outcompete S. simulans in the presence of AFAs or AFAs plus fatty alcohols, respectively. Collectively, our findings suggest that commensal modulation of skin lipids determines whether niche-specific communities are resilient or permissive to pathogenic invasion by S. aureus.","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/PMC13521525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148228798","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}

引用次数: 0