ISME communications最新文献

{"title":"Correction to: Hydrogen-independent CO₂ reduction dominates methanogenesis in five temperate lakes that differ in trophic states.","authors":"","doi":"10.1093/ismeco/ycaf082","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf082","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycae089.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf082"},"PeriodicalIF":5.1,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144164097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils.","authors":"Xingjie Wu, Ye Liu, Zhibin He, Xi Zhou, Werner Liesack, Jingjing Peng","doi":"10.1093/ismeco/ycaf088","DOIUrl":"10.1093/ismeco/ycaf088","url":null,"abstract":"<p><p>Methanogens play a critical role in global methane (CH₄) emissions from rice paddy ecosystems. Through the integration of metagenomic analysis and meta-analysis, we constructed a CRISPR spacer database comprising 14 475 spacers derived from 351 methanogenic genomes. This enabled the identification of viruses targeting key methanogenic families prevalent in rice paddies, including <i>Methanosarcinaceae</i>, <i>Methanotrichaceae</i>, <i>Methanobacteriaceae</i>, <i>Methanocellaceae</i>, and <i>Methanomassiliicoccaceae</i>. We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families <i>Straboviridae</i>, <i>Salasmaviridae</i>, <i>Kyanoviridae</i>, <i>Herelleviridae</i>, and <i>Demerecviridae</i>, along with 126 unclassified viral entities. These findings highlight a virome composition that is markedly distinct from those observed in gut environments. Cross-infection patterns were supported by the presence of specific viruses predicted to infect multiple closely related methanogenic species. Evidence for potential virus-host coevolution was observed in 24 viruses encoding anti-CRISPR proteins, likely facilitating evasion of host CRISPR-mediated immunity. Collectively, this study reveals a complex and dynamic network of virus-host interactions shaping methanogen communities in rice paddy ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf088"},"PeriodicalIF":5.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.","authors":"Yusuke Okazaki, Yohei Nishikawa, Ryota Wagatsuma, Haruko Takeyama, Shin-Ichi Nakano","doi":"10.1093/ismeco/ycaf086","DOIUrl":"10.1093/ismeco/ycaf086","url":null,"abstract":"<p><p>Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf086"},"PeriodicalIF":5.1,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency.","authors":"Emily N Boak, Benjamin P Bowen, Katherine B Louie, Trent R Northen, Marie E Kroeger","doi":"10.1093/ismeco/ycaf084","DOIUrl":"10.1093/ismeco/ycaf084","url":null,"abstract":"<p><p>Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including <i>Nocardiopsis</i> and <i>Kocuria</i> in hydrophilic and <i>Streptomyces</i> and <i>Cutibacterium</i> in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf084"},"PeriodicalIF":5.1,"publicationDate":"2025-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143472/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosensor-aided isolation of anaerobic arsenic-methylating bacteria from soil.","authors":"Hugo Sallet, Luna Kaiser, Matteo Titus, Marion Calvo, Nicolas Jacquemin, Karin Lederballe Meibom, Rizlan Bernier-Latmani","doi":"10.1093/ismeco/ycaf081","DOIUrl":"10.1093/ismeco/ycaf081","url":null,"abstract":"<p><p>Microbial methylation of arsenic impacts both the toxicity and fate of this environmental contaminant and is an important component of its biogeochemical cycle. This transformation occurs in flooded paddy fields where soil microorganisms can produce dimethylated arsenic, which causes the straighthead disease in rice. The responsible anaerobic microorganisms have remained elusive because their isolation is laborious, especially as the active methylators cannot be rapidly screened. Here, we introduce a novel approach to specifically target these microorganisms. This approach is based on a high-throughput isolation technique involving microfluidic encapsulation, fluorescence-activated cell sorting, and biosensor-aided screening of microbial function. Using this method, we isolated two arsenic-methylating anaerobes from a paddy soil. This approach has the potential to rapidly obtain novel isolates. For instance, we show that one isolate actively methylates arsenate (As^V), a previously unknown phenotype in anaerobes.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf081"},"PeriodicalIF":5.1,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12124457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temporal dynamics and biogeography of sympagic and planktonic photosynthetic microbial eukaryotes during the under-ice Arctic bloom.","authors":"Clarence Wei Hung Sim, Catherine Gérikas Ribeiro, Florence Le Gall, Ian Probert, Priscilla Gourvil, Connie Lovejoy, Daniel Vaulot, Adriana Lopes Dos Santos","doi":"10.1093/ismeco/ycaf075","DOIUrl":"10.1093/ismeco/ycaf075","url":null,"abstract":"<p><p>Photosynthetic microbial eukaryotes play a pivotal role as primary producers in the Arctic Ocean, where seasonal blooms within and below the ice are crucial phenomena, contributing significantly to global primary production and biogeochemical cycling. In this study, we investigated the taxonomic composition of sympagic algae and phytoplankton communities during the Arctic under-ice spring bloom using metabarcoding of the 18S rRNA gene. Samples were obtained from three size fractions over a period of nearly three months at an ice camp deployed on landfast ice off the coast of Baffin Island as part of the Green Edge project. We classified the major sympagic and phytoplankton taxa found in this study into biogeographical categories using publicly available metabarcoding data from more than 2800 oceanic and coastal marine samples. This study demonstrated the temporal succession of taxonomic groups during the development of the under-ice bloom, illustrated by an overall transition from polar to polar-temperate taxa, particularly in the smallest size fraction. Overlooked classes such as Pelagophyceae (genera <i>Plocamiomonas</i> and <i>Ankylochrysis</i>), Bolidophyceae (Parmales environmental clade 2), and Cryptophyceae (<i>Baffinella frigidus</i>) might play a greater role than anticipated within the pico-sized communities in and under the ice pack during the pre-bloom period. Finally, we emphasize the importance of microdiversity, taking the example of <i>B. frigidus</i>, for which two ecotypes linked to pelagic and sea ice environments have been identified.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf075"},"PeriodicalIF":5.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144183132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular complexity of the differential growth of freshwater diatoms along pH gradients.","authors":"Xènia Rodríguez-Miret, Marisol Felip, Eric Pelletier, Jordi Catalan","doi":"10.1093/ismeco/ycaf078","DOIUrl":"10.1093/ismeco/ycaf078","url":null,"abstract":"<p><p>Diatoms originated in marine waters, and many clades have invaded fresh waters, radiating throughout the continental aquatic environments. pH gradients have been a primary axis of species differentiation, from which environmental assessments have taken advantage using diatoms as bioindicators. However, a comprehensive view of the molecular variation underlying the diatom sensitivity to pH is missing. This study used 12 freshwater diatom strains across a broad phylogenetic range within raphid pennate clades and 3 distinct environmental pH conditions, pH 4.7, 7.0, and 8.2, for a common garden experiment. The transcriptomic analysis showed that environmental pH variation regulated many molecular processes and biological functions, especially those involved in biosynthesis and transport. Despite sharing many known functions, strains responded to pH changes in a highly idiosyncratic manner. Such specificity in the physiological response to pH aligns with the considerably divergent genetic backgrounds observed among the 12 diatom strains. This variation was likely shaped by different evolutionary trajectories in adaptive molecular landscapes, which were probably already differentiated in the initial marine environment and subjected to varying pH selection pressures in the complex chemical mosaic of inland waters. Overall, our results indicate that continental pH selection pressures do not determine a necessarily unique adaptive physiological response in diatoms, but instead allow for multiple adaptive solutions built on the evolutionary historical background and inland contingencies. Therefore, specific studies on the identified plastic responses to pH are needed to assess their adaptive function across clades.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf078"},"PeriodicalIF":5.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144251109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil viral communities shifted significantly after wildfire in chaparral and woodland habitats.","authors":"Sara E Geonczy, Anneliek M Ter Horst, Joanne B Emerson","doi":"10.1093/ismeco/ycaf073","DOIUrl":"10.1093/ismeco/ycaf073","url":null,"abstract":"<p><p>Increased wildfire activity warrants more research into fire-driven biotic changes in soil, including soil viral communities, given the roles of soil microbes in organic matter decomposition, nutrient cycling, and post-fire recovery. Leveraging viral size-fraction metagenomes (viromes), here we studied viral community responses to wildfire in woodland and chaparral soils at five timepoints over 1 year following the California LNU Complex wildfire. We also compared post-fire samples to unburned controls at the final three timepoints and leveraged published viromes from the same sites nine months before the fire as pre-burn controls. Viral community composition differed significantly in burned samples compared to controls from both habitats, as did soil chemistry and prokaryotic communities (16S rRNA gene amplicons). Viromic DNA yields (a proxy for viral particle abundances) indicated initial viral biomass reductions due to the fire, but a return to baseline abundances (indistinguishable from controls) within five months. Fire-associated habitat filtering was further indicated by a comparison to the PIGEON viral \"species\" (viral operational taxonomic unit (vOTU)) reference database, with vOTUs from a burned conifer forest representing 19%-31% of PIGEON vOTUs detected in the burned habitats but only 0.6%-6% in controls. Together, these results indicate significant changes in soil viral communities due to wildfire, attributable at least in part to concomitant changes in their prokaryotic host communities and soil physicochemistry.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf073"},"PeriodicalIF":5.1,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12085916/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Vibrio</i> are a potential source of novel colistin-resistance genes in European coastal environments.","authors":"Jamal Saad, Viviane Boulo, David Goudenège, Coralie Broquard, Karl B Andree, Manon Auguste, Bruno Petton, Yannick Labreuche, Pablo Tris, Dolors Furones, Augusti Gil, Luigi Vezzulli, Gianluca Corno, Andrea Di Cesare, Hugo Koechlin, Emilie Labadie-Lafforgue, Gaelle Courtay, Océane Romatif, Juliette Pouzadoux, Jean-Michel Escoubas, Dominique Munaron, Guillaume M Charrière, Eve Toulza, Marie-Agnès Travers, Caroline Montagnani, K Mathias Wegner, Delphine Destoumieux-Garzón","doi":"10.1093/ismeco/ycaf055","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf055","url":null,"abstract":"<p><p>Colistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred by <i>mcr</i>-1 in human pathogens has raised concern, but the putative sources and reservoirs of novel <i>mcr</i> genes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly in <i>Vibrio</i> isolated from European coastal waters by using the same cohorts of oysters as bioaccumulators in three sites across Europe. The high sequence diversity found in the <i>mcr/ept</i>A gene family was geographically structured, particularly for three novel <i>eptA</i> gene variants, which were restricted to the Mediterranean (France, Spain) and occurred as a <i>dgk</i>A-<i>ept</i>A operon. The RstA/RstB two component system was shown to control both the <i>dgk</i>A-<i>ept</i>A operon and the Col-R phenotype. The analysis of 29 427 <i>Vibrionaceae</i> genomes revealed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes the human pathogens <i>Vibrio parahaemolyticus</i> and <i>Vibrio alginolyticus</i>. The operon conferred colistin-resistance when transferred to sensitive non-<i>Vibrio</i> strains. In general, <i>ept</i>A gene variants are widespread and evolved with the <i>Vibrio</i> lineage. They occur in clade-specific genomic environments, suggesting that <i>eptA</i> expression responds to distinct environmental signals across the <i>Vibrio</i> phylogeny. However, we also identified mobile <i>ept</i>A paralogues that have been recently transferred between and within <i>Vibrio</i> clades. This highlights <i>Vibrio</i> as a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf055"},"PeriodicalIF":5.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064563/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Organic metabolite uptake by diazotrophs in the North Pacific Ocean.","authors":"Alba Filella, Aurélie Cébron, Benoît Paix, Marine Vallet, Pauline Martinot, Léa Guyomarch, Catherine Guigue, Marc Tedetti, Olivier Grosso, Kendra A Turk-Kubo, Lasse Riemann, Mar Benavides","doi":"10.1093/ismeco/ycaf061","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf061","url":null,"abstract":"<p><p>Dinitrogen (N₂) fixation by diazotrophs supports ocean productivity. Diazotrophs include photoautotrophic cyanobacteria, non-cyanobacterial diazotrophs (NCDs), and the recently discovered N₂-fixing haptophyte. While NCDs are ubiquitous in the ocean, their ecology and metabolism remain largely unknown. Unlike cyanobacterial diazotrophs and the haptophyte, NCDs are primarily heterotrophic and depend on dissolved organic matter (DOM) for carbon and energy. However, conventional DOM amendment incubations do not allow discerning how different diazotrophs use DOM molecules, limiting our knowledge on DOM-diazotroph interactions. To identify diazotrophs using DOM, we amended North Pacific microbial communities with ¹³C-labeled DOM from phytoplankton cultures that was molecularly characterized, revealing the dominance of nitrogen-rich compounds. After DOM additions, we observed a community shift from cyanobacterial diazotrophs like <i>Crocosphaera</i> and <i>Trichodesmium</i> to NCDs at stations where the N₂-fixing haptophyte abundance was relatively low. Through DNA stable isotope probing and gene sequencing, we identified diverse diazotrophs capable of taking up DOM. Our findings highlight unexpected DOM uptake by the haptophyte's nitroplast, changes in community structure, and previously unrecognized osmotrophic behavior in NCDs, shaped by local biogeochemical conditions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf061"},"PeriodicalIF":5.1,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12064561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}