ISME Journal最新文献_第2页

Correction to 29 articles due to inaccurate manuscript submission dates.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf008

引用次数: 0

Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae. 从失落之城热液区分离的Pacmanvirus将转座子的概念扩展到迷你病毒科之外。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf002

Sébastien Santini, Audrey Lartigue, Jean-Marie Alempic, Yohann Couté, Lucid Belmudes, William J Brazelton, Susan Q Lang, Jean-Michel Claverie, Matthieu Legendre, Chantal Abergel

{"title":"Pacmanvirus isolated from the Lost City hydrothermal field extends the concept of transpoviron beyond the family Mimiviridae.","authors":"Sébastien Santini, Audrey Lartigue, Jean-Marie Alempic, Yohann Couté, Lucid Belmudes, William J Brazelton, Susan Q Lang, Jean-Michel Claverie, Matthieu Legendre, Chantal Abergel","doi":"10.1093/ismejo/wraf002","DOIUrl":"10.1093/ismejo/wraf002","url":null,"abstract":"The microbial sampling of submarine hydrothermal vents remains challenging, with even fewer studies focused on viruses. Here we report what is to our knowledge the first isolation of a eukaryotic virus from the Lost City hydrothermal field, by co-culture with the laboratory host Acanthamoeba castellanii. This virus, named pacmanvirus lostcity, is closely related to previously isolated pacmanviruses (strains A23 and S19), clustering in a divergent clade within the long-established family Asfarviridae. The icosahedral particles of this virus are 200 nm in diameter, with an electron-dense core surrounded by an inner membrane. The viral genome of 395 708 bp (33% G + C) has been predicted to encode 473 proteins. However, besides these standard properties, pacmanvirus lostcity was found to be associated with a new type of selfish genetic element, 7 kb in length, whose architecture and gene content are reminiscent of those of transpovirons, hitherto specific to the family Mimiviridae. As in previously described transpovirons, this selfishg genetic element propagates as an episome within its host virus particles and exhibits partial recombination with its genome. In addition, an unrelated episome with a length of 2 kb was also found to be associated with pacmanvirus lostcity. Together, the transpoviron and the 2-kb episome might participate in exchanges between pacmanviruses and other DNA virus families. It remains to be elucidated if the presence of these mobile genetic elements is restricted to pacmanviruses or was simply overlooked in other members of the Asfarviridae.","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/PMC11788076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958163","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

Long-term climate establishes functional legacies by altering microbial traits. 长期气候通过改变微生物特性来建立功能性遗产。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf005

Caitlin M Broderick, Gian Maria Niccolò Benucci, Luciana Ruggiero Bachega, Gabriel D Miller, Sarah E Evans, Christine V Hawkes

{"title":"Long-term climate establishes functional legacies by altering microbial traits.","authors":"Caitlin M Broderick, Gian Maria Niccolò Benucci, Luciana Ruggiero Bachega, Gabriel D Miller, Sarah E Evans, Christine V Hawkes","doi":"10.1093/ismejo/wraf005","DOIUrl":"10.1093/ismejo/wraf005","url":null,"abstract":"Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.","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/PMC11805608/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973118","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

Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf012

Ya Liu, Yu Geng, Yiru Jiang, Peng Li, Yue-Zhong Li, Zheng Zhang

{"title":"Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.","authors":"Ya Liu, Yu Geng, Yiru Jiang, Peng Li, Yue-Zhong Li, Zheng Zhang","doi":"10.1093/ismejo/wraf012","DOIUrl":"10.1093/ismejo/wraf012","url":null,"abstract":"One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.","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/PMC11822679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030278","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

Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut. 生活史策略与生态位分配相辅相成，支持蜜蜂肠道中近缘的吉利拉菌物种共存。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf016

Chengfeng Yang, Benfeng Han, Junbo Tang, Jiawei Hu, Lifei Qiu, Wanzhi Cai, Xin Zhou, Xue Zhang

{"title":"Life history strategies complement niche partitioning to support the coexistence of closely related Gilliamella species in the bee gut.","authors":"Chengfeng Yang, Benfeng Han, Junbo Tang, Jiawei Hu, Lifei Qiu, Wanzhi Cai, Xin Zhou, Xue Zhang","doi":"10.1093/ismejo/wraf016","DOIUrl":"10.1093/ismejo/wraf016","url":null,"abstract":"The maintenance of bacterial diversity at both species and strain levels is crucial for the sustainability of honey bee gut microbiota and host health. Periodic or random fluctuation in diet typically alters the metabolic niches available to gut microbes, thereby continuously reshaping bacterial diversity and interspecific interactions. It remains unclear how closely related bacteria adapt to these fluctuations and maintain coexistence within the bee gut. Here, we demonstrate that the five predominant Gilliamella species associated with Apis cerana, a widely distributed Asiatic honey bee, have diverged in carbohydrate metabolism to adapt to distinct nutrient niches driven by dietary fluctuation. Specifically, the glycan-specialists gain improved growth on a pollen-rich diet, but are overall inferior in competition to non-glycan-specialist on either a simple sugar or sugar-pollen diet, when co-inoculated in the bee host and transmitted across generations. Strikingly, despite of their disadvantage in a high-sugar condition, the glycan-specialists are found prevalent in natural A. cerana guts. We further reveal that these bacteria have adopted a life history strategy characterized by high biomass yield on a low-concentration sugar diet, allowing them to thrive under poor nutritional conditions, such as when the bee hosts undergo periodical starvation. Transcriptome analyses indicate that the divergence in life history strategies is attributed to gene expression programming rather than genetic variation. This study highlights the importance of integrative metabolic strategies in carbohydrate utilization, which facilitate the coexistence of closely related Gilliamella species in a changing bee gut environment.","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/PMC11822680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143076200","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

Spatial sensing as a strategy for public goods regulation by gut microbes. 空间感应是肠道微生物调节公共产品的一种策略。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-11-26 DOI: 10.1093/ismejo/wrae233

I Hashem, A Zhang, J Van Impe

引用次数: 0

High compositional and functional similarity in the microbiome of deep-sea sponges. 深海海绵微生物组在组成和功能上具有高度相似性。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrad030

Cristina Díez-Vives, Ana Riesgo

{"title":"High compositional and functional similarity in the microbiome of deep-sea sponges.","authors":"Cristina Díez-Vives, Ana Riesgo","doi":"10.1093/ismejo/wrad030","DOIUrl":"10.1093/ismejo/wrad030","url":null,"abstract":"Sponges largely depend on their symbiotic microbes for their nutrition, health, and survival. This is especially true in high microbial abundance (HMA) sponges, where filtration is usually deprecated in favor of a larger association with prokaryotic symbionts. Sponge-microbiome association is substantially less understood for deep-sea sponges than for shallow water species. This is most unfortunate, since HMA sponges can form massive sponge grounds in the deep sea, where they dominate the ecosystems, driving their biogeochemical cycles. Here, we assess the microbial transcriptional profile of three different deep-sea HMA sponges in four locations of the Cantabrian Sea and compared them to shallow water HMA and LMA (low microbial abundance) sponge species. Our results reveal that the sponge microbiome has converged in a fundamental metabolic role for deep-sea sponges, independent of taxonomic relationships or geographic location, which is shared in broad terms with shallow HMA species. We also observed a large number of redundant microbial members performing the same functions, likely providing stability to the sponge inner ecosystem. A comparison between the community composition of our deep-sea sponges and another 39 species of HMA sponges from deep-sea and shallow habitats, belonging to the same taxonomic orders, suggested strong homogeneity in microbial composition (i.e. weak species-specificity) in deep sea species, which contrasts with that observed in shallow water counterparts. This convergence in microbiome composition and functionality underscores the adaptation to an extremely restrictive environment with the aim of exploiting the available resources.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"18 1","pages":""},"PeriodicalIF":11.0,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10837836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747726","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

Isolation of a widespread giant virus implicated in cryptophyte bloom collapse. 分离出一种与隐花植物绽放崩溃有关的大范围巨型病毒。

IF 11 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae029

Helena H Vieira, Paul-Adrian Bulzu, Vojtěch Kasalický, Markus Haber, Petr Znachor, Kasia Piwosz, Rohit Ghai

引用次数: 0

Correction to: Anaerobic hydrocarbon biodegradation by alkylotrophic methanogens in deep oil reservoirs. 更正：深层油藏中烷基甲烷菌的厌氧碳氢化合物生物降解。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae196

引用次数: 0

Leveraging genomic information to predict environmental preferences of bacteria. 利用基因组信息预测细菌的环境偏好。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae195

Josep Ramoneda, Michael Hoffert, Elias Stallard-Olivera, Emilio O Casamayor, Noah Fierer

{"title":"Leveraging genomic information to predict environmental preferences of bacteria.","authors":"Josep Ramoneda, Michael Hoffert, Elias Stallard-Olivera, Emilio O Casamayor, Noah Fierer","doi":"10.1093/ismejo/wrae195","DOIUrl":"10.1093/ismejo/wrae195","url":null,"abstract":"Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11488383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373437","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