ISME Journal最新文献

{"title":"Laminarin stimulates single cell rates of sulfate reduction whereas oxygen inhibits transcriptomic activity in coastal marine sediment.","authors":"Melody R Lindsay, Timothy D'Angelo, Elizabeth Goodell, Jacob H Munson-McGee, Melissa Herring, Michael Budner, Julia M Brown, Gregory S Gavelis, Corianna Mascena, Laura C Lubelczyk, Nicole J Poulton, Ramunas Stepanauskas, Beth N Orcutt, David Emerson","doi":"10.1093/ismejo/wraf042","DOIUrl":"10.1093/ismejo/wraf042","url":null,"abstract":"<p><p>The chemical cycles carried out by bacteria and archaea living in coastal sediments are vital aspects of benthic ecology. These ecosystems are subject to physical disruption, which may allow for increased respiration and complex carbon consumption-impacting chemical cycling in this environment often thought to be a terminal place of deposition. We use the redox-enzyme sensitive probe RedoxSensor Green to measure rates of electron transfer physiology in individual sulfate reducer cells residing in anoxic sediment, subjected to transient exposure of oxygen and laminarin. We use index fluorescence activated cell sorting and single cell genomics sequencing to link those measurements to genomes of respiring cells. We measure per-cell sulfate reduction rates in marine sediments (0.01-4.7 fmol SO42- cell-1 h-1) and determine that cells within the Chloroflexota phylum are the most active in respiration. Chloroflexota respiration activity is also stimulated with the addition of laminarin, even in marine sediments already rich in organic matter. Evaluating metatranscriptomic data alongside this respiration-based technique, Chloroflexota genomes encode laminarinases indicating a likely ability to degrade laminarin. We also provide evidence that abundant Patescibacteria cells do not use electron transport pathways for energy, and instead likely carry out fermentation of polysaccharides. There is a decoupling of respiration-related activity rates from transcription, as respiration rates increase while transcription decreases with oxygen exposure. Overall, we reveal an active community of respiring Chloroflexota that cycles sulfate at potential rates of 23-40 nmol h-1 per cm3 sediment in incubation settings, and non-respiratory Patescibacteria that can cycle complex polysaccharides.</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/PMC11919646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588029","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":"Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean.","authors":"Changfei He, Michael Gonsior, Jihua Liu, Nianzhi Jiao, Feng Chen","doi":"10.1093/ismejo/wraf049","DOIUrl":"10.1093/ismejo/wraf049","url":null,"abstract":"<p><p>SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (<2 Mbp), low GC content (<40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 is distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.</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/PMC11994032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804519","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":"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":"<p><p>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.</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/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}

{"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":"<p><p>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.</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/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}

{"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":"<p><p>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.</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/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}

{"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":"<p><p>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.</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/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}

{"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":"<p><p>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.</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/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}

{"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":"<p><p>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.</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/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}

{"title":"Spatial sensing as a strategy for public goods regulation by gut microbes.","authors":"I Hashem, A Zhang, J Van Impe","doi":"10.1093/ismejo/wrae233","DOIUrl":"https://doi.org/10.1093/ismejo/wrae233","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142717530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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":"<p><p>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.</p>","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}