ISME Journal最新文献_第4页

Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa. 全球微生物群落的生物多样性随着稀有类群抗菌毒素丰度的增加而增加。

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

Strong segregation promotes self-destructive cooperation. 强烈的隔离会促进自我毁灭式的合作。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf043

Lingling Wen, Yang Bai, Yunquan Lan, Yaxin Shen, Xiaoyi She, Peng Dong, Teng Wang, Xiongfei Fu, Shuqiang Huang

{"title":"Strong segregation promotes self-destructive cooperation.","authors":"Lingling Wen, Yang Bai, Yunquan Lan, Yaxin Shen, Xiaoyi She, Peng Dong, Teng Wang, Xiongfei Fu, Shuqiang Huang","doi":"10.1093/ismejo/wraf043","DOIUrl":"10.1093/ismejo/wraf043","url":null,"abstract":"Self-destructive cooperators, which sacrifice themselves for others, challenge traditional group selection theory, as costs often exceed individual benefits. We predict self-destructive cooperators can persist in highly segregated environments where populations are primarily divided into homogenous groups originating from one or two founders. In such contexts, the benefits of self-destructive cooperators remain within homogeneous groups of self-destructive cooperators, preserving the sacrifice value and ensuring its maintenance. To validate our hypothesis, we employ a synthetic self-destructive cooperators-cheaters system and develop automated experiments to monitor and operate the subgroups with diverse growth behaviors due to strong segregation. Ultimately, we demonstrate self-destructive cooperators is maintained under strong segregation. High stress further enhances self-destructive cooperators by reducing the benefits received by cheaters in heterogeneous subgroups. This study advances group selection theory and automation in evolutionary research.","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/PMC11948997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634931","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

Interplay of ecological processes modulates microbial community reassembly following coalescence. 生态过程的相互作用调节了微生物群落合并后的重组。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf041

Luana Bresciani, Gordon F Custer, David Koslicki, Francisco Dini-Andreote

{"title":"Interplay of ecological processes modulates microbial community reassembly following coalescence.","authors":"Luana Bresciani, Gordon F Custer, David Koslicki, Francisco Dini-Andreote","doi":"10.1093/ismejo/wraf041","DOIUrl":"10.1093/ismejo/wraf041","url":null,"abstract":"Microbial community coalescence refers to the mixing of entire microbial communities and their environments. Despite conceptually analogous to a multispecies invasion, the ecological processes driving this phenomenon remain poorly understood. Here, we developed and implemented a beta-diversity-based statistical framework to quantify the contribution of distinct donor communities to community reassembly dynamics over time following coalescence. We conducted a microcosm experiment with soils manipulated at varying levels of community structure (via dilution-to-extinction) and subjected these to pairwise coalescence scenarios. Overall, our results revealed variable patterns of abiotic and biotic donor dominance across distinct treatment sets. First, we show the occasional presence of an upfront stringent abiotic filter to disproportionally favor a donor biotic dominance through a \"home-field advantage\" mechanism, with abiotic factors explaining >90% of the variance in community structure. Functional community metrics (i.e. carbon metabolism and extracellular enzymatic activities) were significantly linked to donor contributions in these cases. Second, in the absence of abiotic dominance, interspecific interactions gained importance, with abiotic variables explaining <40% of the variance. Here, functional redundancy in donor communities (e.g. lower dilution) led to nonsignificant relationships between donor contributions and functional metrics. Collectively, this study advances the integration of coalescence with well-established fundamentals of invasion biology theory, highlighting the interplay of abiotic and biotic factors structuring community reassembly following coalescence. Last, we propose that our beta-diversity-based framework is widely applicable across various microbial systems. We believe this approach will promote research advances by offering a unified method for analyzing and quantifying coalescence.","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/PMC11971568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143774660","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

Pathogen-pathogen interactions during co-infections. 共感染期间病原体-病原体相互作用。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2025-01-02 DOI: 10.1093/ismejo/wraf104

Rosana Barreto Rocha Ferreira, Luis Caetano Martha Antunes, Neta Sal-Man

{"title":"Pathogen-pathogen interactions during co-infections.","authors":"Rosana Barreto Rocha Ferreira, Luis Caetano Martha Antunes, Neta Sal-Man","doi":"10.1093/ismejo/wraf104","DOIUrl":"10.1093/ismejo/wraf104","url":null,"abstract":"For over a century, bacterial infections have been studied through the lens of the one-microbe, one-disease paradigm. However, it is now clear that multi-pathogen infections are common, and many infectious diseases are inherently polymicrobial. These complex infections can involve a variety of pathogens, including viruses, bacteria, fungi, and parasites, with polyviral and viral-bacterial interactions being the most extensively studied. In this review, we focus on polybacterial infections, providing an in-depth analysis of the diverse strategies bacteria employ to thrive in co-infection scenarios. We examine the mechanisms of bacterial competition, competition avoidance through spatial or temporal separation, and cooperation. Given the association of polymicrobial infections with more severe clinical outcomes and heightened antibiotic tolerance, we also explore novel therapeutic targets to treat these increasingly common and complex infections. Although our review summarizes current knowledge, the vast scope of this phenomenon suggests that many more mechanisms remain undiscovered and warrant further investigation.","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/PMC12145878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144129433","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

Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection. 对完整的 crAss-like 噬菌体基因组的招募显示，鸡病毒组中存在这些噬菌体，但人类特异性噬菌体很少，而且缺乏普遍检测。

IF 10.8 1区环境科学与生态学

ISME Journal Pub Date : 2024-01-08 DOI: 10.1093/ismejo/wrae192

María Dolores Ramos-Barbero, Clara Gómez-Gómez, Gloria Vique, Laura Sala-Comorera, Lorena Rodríguez-Rubio, Maite Muniesa

{"title":"Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.","authors":"María Dolores Ramos-Barbero, Clara Gómez-Gómez, Gloria Vique, Laura Sala-Comorera, Lorena Rodríguez-Rubio, Maite Muniesa","doi":"10.1093/ismejo/wrae192","DOIUrl":"10.1093/ismejo/wrae192","url":null,"abstract":"The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.","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/PMC11475920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373438","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