ISME communications最新文献_第2页

Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome. 宿主水平的生物多样性塑造了珊瑚礁微生物群的动态和网络。

IF 5.1

ISME communications Pub Date : 2025-06-05 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf097

Fabienne Wiederkehr, Kara Elena Engelhardt, Jana Vetter, Hans-Joachim Ruscheweyh, Guillem Salazar, James O'Brien, Taylor Priest, Maren Ziegler, Shinichi Sunagawa

{"title":"Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.","authors":"Fabienne Wiederkehr, Kara Elena Engelhardt, Jana Vetter, Hans-Joachim Ruscheweyh, Guillem Salazar, James O'Brien, Taylor Priest, Maren Ziegler, Shinichi Sunagawa","doi":"10.1093/ismeco/ycaf097","DOIUrl":"10.1093/ismeco/ycaf097","url":null,"abstract":"Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf097"},"PeriodicalIF":5.1,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12192423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144499741","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}

引用次数: 0

KSGP 3.1: improved taxonomic annotation of Archaea communities using LotuS2, the genome taxonomy database and RNAseq data. KSGP 3.1：使用LotuS2、基因组分类数据库和RNAseq数据对古菌群落进行改进的分类标注。

IF 5.1

ISME communications Pub Date : 2025-06-03 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf094

Alastair Grant, Abdullah Aleidan, Charli S Davies, Solomon C Udochi, Joachim Fritscher, Mohammad Bahram, Falk Hildebrand

{"title":"KSGP 3.1: improved taxonomic annotation of Archaea communities using LotuS2, the genome taxonomy database and RNAseq data.","authors":"Alastair Grant, Abdullah Aleidan, Charli S Davies, Solomon C Udochi, Joachim Fritscher, Mohammad Bahram, Falk Hildebrand","doi":"10.1093/ismeco/ycaf094","DOIUrl":"10.1093/ismeco/ycaf094","url":null,"abstract":"Taxonomic annotation is a substantial challenge for Archaea metabarcoding. A limited number of reference sequences are available; a substantial fraction of phylogenetic diversity is not fully characterized; widely used databases do not reflect current archaeal taxonomy and contain mislabelled sequences. We address these gaps with a systematic and tractable approach based around the Genome Taxonomy Database (GTDB) combined with the eukaryote PR2 and MIDORI mitochondrial databases. After removing incongruent, chimeric and duplicate SSU sequences, this combination (GTDB+) provides a small improvement in annotation of a set of estuarine Archaea Operational Taxonomic Units (OTUs) compared to SILVA. We add to this a collection of near full length rRNA sequences and the prokaryote SSU sequences in SILVA, creating a new reference database, KSGP ( K arst, S ilva, G TDB, and PR2). The additional sequences are (re-)annotated using three different approaches. The most conservative, using lowest common ancestor, gives a further small improvement. Annotation using SINTAX increases Class and Order assignments by 2.7 and 4.2 times over SILVA, although this may include some \"lumping\" of un-named and named clades. Still further improvement can be made using similarity based clustering to group database sequences into putative taxa at all taxonomic levels, assigning 60% and 41% of Archaea OTUs to putative family and genus level taxa respectively. GTDB without cleaning and GreenGenes2 both perform poorly and cannot be recommended for use with Archaea. We make the GTDB+ and KSGP databases available at ksgp.earlham.ac.uk; integrate them into a metabarcoding pipeline, LotuS2 and outline their use to annotate Archaea OTUs and metatranscriptomic data.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf094"},"PeriodicalIF":5.1,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531467","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}

引用次数: 0

Dark ocean archaeal and bacterial chemoautotrophs drive vitamin B1 production in oxygen minimum zones. 暗海洋古细菌和细菌化能自养生物在缺氧区驱动维生素B1的产生。

IF 5.1

ISME communications Pub Date : 2025-05-31 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf077

Kristin Bergauer, Christopher P Suffridge, Fabian Wittmers, Sebastian Sudek, Stephen J Giovannoni, Alexandra Z Worden

{"title":"Dark ocean archaeal and bacterial chemoautotrophs drive vitamin B1 production in oxygen minimum zones.","authors":"Kristin Bergauer, Christopher P Suffridge, Fabian Wittmers, Sebastian Sudek, Stephen J Giovannoni, Alexandra Z Worden","doi":"10.1093/ismeco/ycaf077","DOIUrl":"10.1093/ismeco/ycaf077","url":null,"abstract":"Vitamin B1 (thiamine) is essential for all cells, yet many marine microbes cannot synthesize B1 de novo. Dissolved thiamine and its related chemical congeners (TRCs) concentrations are not well characterized beyond the surface ocean, where they are typically low. Here, we observed unexpected enrichment of TRCs in regions of low dissolved oxygen levels (9.4 < O2 < 12.5 μmol kg-1) across vertical profiles in Monterey Bay and Pacific waters 145 km offshore (Station 67-70). TRC concentrations ranged from fM to pM, with 1.1 to 4.5 fold increases from near-surface waters to the mesopelagic Oxygen Minimum Zone (OMZ). Notably, at 67-70, dissolved B1 increased 3.5-fold within the mesopelagic OMZ. Paired metagenomic analysis suggests that chemoautotrophic ammonia-oxidizing Archaea (AOA) and Thioglobaceae, alongside nitrite-oxidizing Nitrospina, are important B1 producers in OMZs. Metagenome-assembled genomes indicate that Nitrospina may alternate between B1 biosynthesis and energy-preserving salvage pathways in synergy with co-occurring AOA. Re-analysis of metatranscriptomic reads from a previous study established Thioglobaceae can be dominant expressors of key de novo B1 biosynthesis genes in Monterey Bay. These findings suggest that deep ocean chemoautotrophs are B1 prototrophs in OMZs, analogous to photoautotrophs in the epipelagic ocean, and provide the foundation for B1 trafficking.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf077"},"PeriodicalIF":5.1,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12236431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593067","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}

引用次数: 0

Deciphering community assembly processes of the microbial community in subtropical coastal-estuarine seawater over a 6-year exploration. 亚热带沿海-河口海水微生物群落群落组装过程的6年探索。

IF 5.1

ISME communications Pub Date : 2025-05-30 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf091

Yu Wang, Qiongqiong Yang, Qi Chen, Shengwei Hou, Nianzhi Jiao, Qiang Zheng

{"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":"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.","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}

引用次数: 0

Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis contributes to the spatial colonization of PPFM in the phyllosphere. 甲醇化学受体MtpA-和鞭毛蛋白fli依赖的甲基化性有助于PPFM在叶层圈的空间定植。

IF 5.1

ISME communications Pub Date : 2025-05-29 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf092

Shiori Katayama, Kosuke Shiraishi, Kanae Kaji, Kazuya Kawabata, Naoki Tamura, Akio Tani, Hiroya Yurimoto, Yasuyoshi Sakai

引用次数: 0

Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments. 使用混合控制实验对标和优化环境亚转录组学的定性和定量管道。

IF 5.1

ISME communications Pub Date : 2025-05-29 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf090

Weiyi Li, Qilian Fan, Yi Yang, Xiang Xiao, Jing Li, Yu Zhang

{"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":"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.","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}

引用次数: 0

Correction to: Hydrogen-independent CO₂ reduction dominates methanogenesis in five temperate lakes that differ in trophic states. 更正：在营养状态不同的五个温带湖泊中，不依赖氢的二氧化碳减少在甲烷生成中占主导地位。

IF 5.1

ISME communications Pub Date : 2025-05-27 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf082

引用次数: 0

Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils. 水稻土中病毒及其宿主产甲烷菌的协同进化和交叉感染模式。

IF 5.1

ISME communications Pub Date : 2025-05-23 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf088

Xingjie Wu, Ye Liu, Zhibin He, Xi Zhou, Werner Liesack, Jingjing Peng

{"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":"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 Methanosarcinaceae, Methanotrichaceae, Methanobacteriaceae, Methanocellaceae, and Methanomassiliicoccaceae. We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families Straboviridae, Salasmaviridae, Kyanoviridae, Herelleviridae, and Demerecviridae, 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.","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}

引用次数: 0

Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals. 利用系统发育信号预测氨氧化古菌基因分布。

IF 5.1

ISME communications Pub Date : 2025-05-23 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf087

Miguel A Redondo, Christopher M Jones, Pierre Legendre, Guillaume Guénard, Sara Hallin

{"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":"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 amoA 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 amoA 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 (amt2). 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.","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}

引用次数: 0

Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content. 高粘土含量海洋沉积物元蛋白质组学分析中蛋白质提取的系统评价。

IF 5.1

ISME communications Pub Date : 2025-05-22 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf074

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

{"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":"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 Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli 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.","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}

引用次数: 0