ISME communications最新文献

{"title":"Deciphering community assembly processes of the microbial community in subtropical coastal-estuarine seawater over a 6-year exploration.","authors":"Yu Wang, Qiongqiong Yang, Qi Chen, Shengwei Hou, Nianzhi Jiao, Qiang Zheng","doi":"10.1093/ismeco/ycaf091","DOIUrl":"10.1093/ismeco/ycaf091","url":null,"abstract":"<p><p>Understanding community assembly in ecosystems is crucial for ecology, yet the interplay between selection and dispersal remains unclear. We examined bacterial and microeukaryotic communities in a dynamic estuarine-coastal ecosystem over six years to investigate the roles of dispersal and environmental selection. Our approach combined species-time relationships (STRs) analysis, a temporal approach focusing on colonization and extinction dynamics, and a process model for community dynamics, revealing insights into the interplay between selection and dispersal along environmental gradients. Both communities showed significant STRs, but their responses varied by taxon and environmental conditions. For bacteria, salinity increased STR exponents, indicating faster richness growth over time, whereas microeukaryotic STR exponents decreased, suggesting distinct assembly mechanisms. Higher salinity reduced bacterial community determinism but heightened it for microeukaryotes, affecting community turnover: microeukaryote turnover decreased with rising salinity due to changes in colonization and extinction, while bacterial turnover increased due to slower dynamics. This study highlights the complex interaction between selection and dispersal, shaped by environmental factors and unique microbial traits, emphasizing the need for tailored conservation strategies in fluctuating coastal ecosystems.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf091"},"PeriodicalIF":5.1,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531451","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":"Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis contributes to the spatial colonization of PPFM in the phyllosphere.","authors":"Shiori Katayama, Kosuke Shiraishi, Kanae Kaji, Kazuya Kawabata, Naoki Tamura, Akio Tani, Hiroya Yurimoto, Yasuyoshi Sakai","doi":"10.1093/ismeco/ycaf092","DOIUrl":"10.1093/ismeco/ycaf092","url":null,"abstract":"<p><p>Pink-pigmented facultative methylotrophs (PPFMs) capable of growth on methanol are dominant and versatile phyllosphere bacteria that provide positive effects on plant growth through symbiosis. However, the spatial behavior of PPFMs on plant surfaces and its molecular basis are unknown. Here, we show that <i>Methylobacterium</i> sp. strain OR01 inoculated onto red perilla seeds colonized across the entire plant surface in the phyllosphere concomitant with the plant growth. During its transmission, strain OR01 was found to be present on the entire leaf surface with a preference to sites around the periphery, vein, trichome, and stomata. We found that methanol-sensing chemoreceptor MtpA-dependent chemotaxis (methylotaxis; chemotaxis toward methanol) and flagellin protein FliC-dependent motility facilitated the bacterial entry into the stomatal cavity and their colonization in the phyllosphere.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf092"},"PeriodicalIF":5.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531468","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":"Upcycling human excrement: the gut microbiome to soil microbiome axis.","authors":"Jeff Meilander, Chloe Herman, Andrew Manley, Georgia Augustine, Dawn Birdsell, Evan Bolyen, Kimberly R Celona, Hayden Coffey, Jill Cocking, Teddy Donoghue, Alexis Draves, Daryn Erickson, Marissa Foley, Liz Gehret, Johannah Hagen, Crystal Hepp, Parker Ingram, David John, Katarina Kadar, Paul Keim, Victoria Lloyd, Christina Osterink, Victoria Monsaint-Queeney, Diego Ramirez, Antonio Romero, Megan C Ruby, Jason W Sahl, Sydni Soloway, Nathan E Stone, Shannon Trottier, Kaleb Van Orden, Alexis Painter, Sam Wallace, Larissa Wilcox, Colin V Wood, Jaiden Yancey, J Gregory Caporaso","doi":"10.1093/ismeco/ycaf089","DOIUrl":"10.1093/ismeco/ycaf089","url":null,"abstract":"<p><p>Human excrement composting (HEC) is a sustainable strategy for human excrement (HE) management that recycles nutrients and mitigates health risks while reducing reliance on freshwater, fossil fuels, and fertilizers. A mixture of HE and bulking material was collected from 15 composting toilets and composted as 15 biological replicates in modified 19-liter buckets under mesophilic conditions with weekly sampling for one year. We hypothesized that (i) the microbiome of 1 year old compost would resemble that of a soil and/or food and landscape waste compost microbiome more closely than the original HE; and (ii) the human fecal indicators, <i>Escherichia coli</i> and <i>Clostridium perfringens</i>, would be undetectable after 52 weeks using qPCR and culturing. This investigation identified unique successional trajectories within buckets (i.e. biological replicates) and significant shifts in microbial communities around 25 weeks across buckets, with reductions in fecal-associated taxa and increases in environmental taxa indicating effective composting. We present a comprehensive microbial time series analysis of HEC and show that the initial gut-like microbiome of HEC systems transitions to a microbiome similar to soil and traditional compost but that pathogen risk assessment is important if thermophilic temperatures are not achieved. This study also produced the highest resolution composting microbiome data to date, establishing a baseline for HEC optimization and thermophilic composting studies while serving as a resource for bioprospecting for enzymes and organisms relevant to upcycling waste.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf089"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12393218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981536","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":"Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition.","authors":"Stijn G van den Bergh, Iris Chardon, Marion Meima-Franke, Germán Pérez, Gabriel S Rocha, Kristof Brenzinger, Gerard W Korthals, Jochen Mayer, Mathias Cougnon, Dirk Reheul, Wietse de Boer, Paul L E Bodelier","doi":"10.1093/ismeco/ycaf139","DOIUrl":"10.1093/ismeco/ycaf139","url":null,"abstract":"<p><p>The global atmospheric concentration of the potent greenhouse gas methane (CH₄) is rising rapidly, and agriculture is responsible for 30%-50% of the yearly CH₄ emissions. To limit its global warming effects, strong and sustained reductions are needed. Sustainable agricultural management strategies, as the use of organic amendments like compost, have previously proven to have a potent CH₄ mitigation effect in laboratory experiments. Here we investigated, using an extensive field study, the effect of organic amendments on the CH₄ mitigation potential and CH₄ cycling microbial communities of arable soils. Organic-amended soils had higher potential CH₄ uptake rates and an improved potential to oxidize CH₄ to sub-atmospheric concentrations. Also, we showed for the first time that the methanotrophic and methanogenic microbial communities of arable soils were unequivocally altered after organic amendment application by increasing in size while getting less diverse. Compost-amended soils became dominated by the compost-originating methanotroph <i>Methylocaldum szegediense</i> and methanogen <i>Methanosarcina horonobensis</i>, replacing the indigenous methane cycling community members. However, multivariate analyses didn't point out type Ib methanotrophs like <i>M. szegediense</i> as significant driving factors for the observed improved soil CH₄ uptake potential. Conventional type IIa methanotrophs like <i>Methylocystis</i> sp. also had higher differential abundances in organic-amended soils and are speculated to contribute to the improved CH₄ uptake potential. Altogether, the results showed that compost serves as a vector for the introduction of CH₄ cycling microbes and improves the soil's CH₄ uptake potential, which emphasizes the potential of organic fertilization with compost to contribute to CH₄ mitigation in agricultural soils.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf139"},"PeriodicalIF":6.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12395338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144981507","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":"Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.","authors":"Weiyi Li, Qilian Fan, Yi Yang, Xiang Xiao, Jing Li, Yu Zhang","doi":"10.1093/ismeco/ycaf090","DOIUrl":"10.1093/ismeco/ycaf090","url":null,"abstract":"<p><p>Metatranscriptomic analysis is increasingly performed in environments to provide dynamic gene expression information on ecosystems, responding to their changing conditions. Many computational methods have undergone remarkable development in the past years, but a comprehensive benchmark study is still lacking. There are concerns regarding the accuracies of the qualitative and quantitative profilers obtained from metatranscriptomic analysis, especially for the microbiota in extreme environments, most of them are unculturable and lack well-annotated reference genomes. Here, we presented a benchmark experiment that included 10 single-species and their cell or RNA-admixtures with the predefined species compositions and varying evenness, simulating the low annotation rate and high heterogeneity. In total, 1 metagenome sample and 24 metatranscriptome were sequenced for the comparisons of 36 combination of analysis methods for tasks ranging from sample preparation, quality control, rRNA removal, alignment strategies, taxonomic profiling, and transcript quantification. For each part of the workflow mentioned above, corresponding metrics have been established to serve as standards for assessment and comparison. Evaluation revealed the performances and proposed an optimized pipeline named MT-Enviro (MetaTranscriptomic analysis for ENVIROnmental microbiome). Our data and analysis provide a comprehensive framework for benchmarking computational methods with metatranscriptomic analysis. MT-Enviro is implemented in Nextflow and is freely available from https://github.com/Li-Lab-SJTU/MT-Enviro.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf090"},"PeriodicalIF":5.1,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202999/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531449","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":"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":"Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.","authors":"Miguel A Redondo, Christopher M Jones, Pierre Legendre, Guillaume Guénard, Sara Hallin","doi":"10.1093/ismeco/ycaf087","DOIUrl":"10.1093/ismeco/ycaf087","url":null,"abstract":"<p><p>Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated <i>amoA</i> gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an <i>amoA</i> sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (<i>amt2</i>). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf087"},"PeriodicalIF":5.1,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144627927","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":"Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.","authors":"Anne Ostrzinski, Benoit J Kunath, André Rodrigues Soares, Cédric C Laczny, Rashi Halder, Jens Kallmeyer, Rolando di Primio, Paul Wilmes, Alexander J Probst, Anke Trautwein-Schult, Dörte Becher","doi":"10.1093/ismeco/ycaf074","DOIUrl":"10.1093/ismeco/ycaf074","url":null,"abstract":"<p><p>Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added <i>Escherichia coli</i> cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of <i>E. coli</i> proteins from the supplemented sediment to those from pure <i>E. coli</i> cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf074"},"PeriodicalIF":5.1,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192440/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144499742","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}