ISME Journal最新文献

{"title":"Uncertain fate of pelagic calcifying protists: a cellular perspective on a changing ocean.","authors":"Adva Shemi, Assaf Gal, Assaf Vardi","doi":"10.1093/ismejo/wraf007","DOIUrl":"10.1093/ismejo/wraf007","url":null,"abstract":"<p><p>Pelagic calcifying protists such as coccolithophores and foraminifera represent an important microbial component of the marine carbon cycle. Although their calcitic shells are preserved in oceanic sediments over millennia, their resilience in the future decades is uncertain. We review current literature describing the response of calcifying protists to ocean acidification and temperature warming. We examine these key ecological and biogeochemical processes through the cellular perspective, exploring the physiological, metabolic, and molecular responses of calcifying protists. Ocean acidification is a chemical process that takes place in the seawater outside the cell, whereas protists calcify inside a modified cellular microenvironment. The function of these calcification compartments depends on cellular response to ocean acidification, such as maintaining pH homeostasis. The response of calcifying protists to ocean acidification and temperature warming is species-specific, with no unifying trends but rather a range of sensitivity levels. Coccolithophores and foraminifera display physiological sensitivity that may hamper their ecological success in comparison to noncalcifying species. Yet, certain species may be more adaptable, especially when comparing to highly vulnerable calcifying molluscs as pteropods. As the molecular machinery mediating cellular calcification is not fully resolved, as well as the functional role of the calcitic shell, our ability to predict the fate of calcifying microorganisms in a warmer, more acidic ocean is limited. We propose the urgent need to expand the study of these model systems by advancing cell biology approaches and better understand the impact of climate change on microbial food webs in the ocean.</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/PMC12573260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143469740","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":"Trichodesmium metaproteomes reflect the differential influence of resource availability across ocean regions.","authors":"Hanna S Anderson, Kyle R Frischkorn, Sheean T Haley, Sonya T Dyhrman","doi":"10.1093/ismejo/wraf120","DOIUrl":"10.1093/ismejo/wraf120","url":null,"abstract":"<p><p>The diazotroph Trichodesmium is an important contributor to marine dinitrogen fixation, supplying nitrogen to phytoplankton in typically nitrogen-limited ocean regions. Identifying how iron and phosphorus influence Trichodesmium activity and biogeography is an ongoing area of study, where predicting patterns of resource stress is complicated by the uncertain bioavailability of organically complexed iron and phosphorus. Here, a comparison of 26 metaproteomes from picked Trichodesmium colonies identified significantly different patterns between three ocean regions: the western tropical South Pacific, the western North Atlantic, and the North Pacific Subtropical Gyre. Trichodesmium KEGG submodule signals differed significantly across regions, and vector fitting showed that dissolved iron, dissolved inorganic phosphorus, and temperature significantly correlated with regional metaproteome patterns. Patterns of iron and phosphorus stress marker proteins previously validated in culture studies showed significant enrichment of a phosphorus stress signal in the western North Atlantic and an iron stress signal in the North Pacific. Populations in the western tropical South Pacific appeared to modulate their proteomes in response to both dissolved iron and dissolved inorganic phosphorus bioavailability, with significant enrichment of iron and phosphorus stress marker proteins, concomitant proteome restructuring, and significant decreases in the relative abundance of the dinitrogen fixation protein, NifH. These signals recapitulate established regional patterns of resource stress on phytoplankton communities released from nitrogen stress. Evaluating community stress patterns may therefore predict resource controls on diazotroph biogeography. These data highlight how Trichodesmium modulates its metabolism in the field and provide an opportunity to more accurately constrain controls on Trichodesmium biogeography and dinitrogen fixation.</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/PMC12206446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235786","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":"Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.","authors":"Hokwan Heo, Thanh Nguyen-Dinh, Man-Young Jung, Chris Greening, Sukhwan Yoon","doi":"10.1093/ismejo/wraf092","DOIUrl":"10.1093/ismejo/wraf092","url":null,"abstract":"<p><p>Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterota strains, Aliarcobacter butzleri hDNRA1 and Sulfurospirillum sp. hDNRA2, which grow using H2 as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto (i.e. NO3- reduction that includes stoichiometric NO2--to-NH4+ reduction) was strictly dependent on the presence of H2 and exhibited stoichiometric coupling with H2 oxidation, indicating that electrons required for NO2- reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3--limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552 nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. In addition, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2 can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.</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/PMC12286921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081809","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: Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.","authors":"","doi":"10.1093/ismejo/wraf241","DOIUrl":"10.1093/ismejo/wraf241","url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12596162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477300","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":10.0,"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":"Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes.","authors":"Cecilie R Gotze, Ashley M Dungan, Allison M L van de Meene, Katarina Damjanovic, Gayle K Philip, Justin Maire, Lone Høj, Linda L Blackall, Madeleine J H van Oppen","doi":"10.1093/ismejo/wraf059","DOIUrl":"10.1093/ismejo/wraf059","url":null,"abstract":"<p><p>Bacteria in the genus Endozoicomonas are well-known coral symbionts commonly found as clusters within tissues of several coral species. Mapping the spatial distribution of these microbial communities is critical to gaining a holistic understanding of the potential role they may play within the coral host. This study focuses on characterizing bacterial aggregates associated with the common reef-building coral, Acropora loripes, from the central Great Barrier Reef, Australia. A conventional cultivation-based method was employed to establish a pure culture collection of 11 undescribed Endozoicomonas strains isolated from A. loripes. Subsequent 16S rRNA gene amplicon sequencing revealed their classification into two distinct phylogenetic clades. To resolve their spatial distribution in hospite, clade-specific fluorescence in situ hybridization probes were designed. Aggregates were consistently observed in the gastrodermal tissue layers surrounding the upper and lower gastrovascular cavity and were predominantly formed by cells from the same phylogenetic clade, with a minor proportion of aggregates formed by Endozoicomonas from both targeted clades. Furthermore, a clear distinction in aggregation pattern was observed; one clade exhibited clusters with regular and contained growth patterns, whereas the other formed clusters lacking clear boundaries and having irregular shapes. Scanning electron microscopy revealed the presence of a membrane of unknown origin associated with bacterial aggregates in two instances, suggesting potential structural or functional differences in these aggregates. These morphological differences highlight the importance of further investigations into the mechanisms governing bacterial aggregate formation in corals.</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/PMC12649755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143744253","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":"Wasp intestinal cues drive yeast toward outbreeding strategies.","authors":"Silvia Abbà, Liam D Adair, Francesca Barbero, Luca P Casacci, Ilija Dukovski, Francisca Font-Verdera, Tom Hawtrey, Elizabeth J New, Jukkrit Nootem, Pramsak Patawanich, Lukas Patten, Marco Polin, Daniel Segrè, Nian Kee Tan, Irene Stefanini","doi":"10.1093/ismejo/wraf243","DOIUrl":"10.1093/ismejo/wraf243","url":null,"abstract":"<p><p>Saccharomyces cerevisiae relies on social wasps (e.g. Vespa crabro, Polistes spp.) for dispersal and genetic mixing. Unlike most natural environments, wasp intestines provide conditions that support yeast survival, sporulation, spore germination, and mating. This study explores the mechanisms at the basis of this process by examining the wasp gut environment and yeast responses. Molecular analyses based on yeast deletion collection and transcriptomics showed that yeast sporulates in the crop, spores germinate in the gut, and cells ferment in the gut. The crop and gut differ chemically: the gut has more sugars, a higher pH, and (in workers) greater viscosity. In vitro tests confirmed yeast survival in both environments, with faster germination in gut-like conditions. Computational models based on these physicochemical traits matched the experimental results. The data obtained provide fundamental insights into yeast progression towards mating within wasps' intestines and suggest a possible relation between yeast alcoholic fermentation and wasps' alcohol tolerance, thereby enhancing our understanding of the S. cerevisiae-social wasp association.</p>","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":"19 1","pages":""},"PeriodicalIF":10.0,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12642876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145598176","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":"Distinct microbial communities within and on seep carbonates support long-term anaerobic oxidation of methane and divergent pMMO diversity.","authors":"Magdalena J Mayr, Sergio A Parra, Stephanie A Connon, Aditi K Narayanan, Ranjani Murali, Antoine Crémière, Victoria J Orphan","doi":"10.1093/ismejo/wraf153","DOIUrl":"10.1093/ismejo/wraf153","url":null,"abstract":"<p><p>At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.</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/PMC12422003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145001882","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}