ISME communications最新文献

Correction to: Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen. 更正：深海Lucinoma kazani蛤的代谢多功能Ca. thiiodiazotropha共生体具有固定氮的遗传潜力。

IF 5.1

ISME communications Pub Date : 2025-06-23 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae118

引用次数: 0

Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid. 应用hsp60扩增子测序分析与乌贼幼鱼和成鱼相关的微生物群落。

IF 5.1

ISME communications Pub Date : 2025-06-13 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf085

Steph Smith, Clotilde Bongrand, Susannah Lawhorn, Edward G Ruby, Alecia N Septer

{"title":"Application of hsp60 amplicon sequencing to characterize microbial communities associated with juvenile and adult Euprymna scolopes squid.","authors":"Steph Smith, Clotilde Bongrand, Susannah Lawhorn, Edward G Ruby, Alecia N Septer","doi":"10.1093/ismeco/ycaf085","DOIUrl":"10.1093/ismeco/ycaf085","url":null,"abstract":"The symbiotic relationship between Vibrio (Aliivibrio) fischeri and the Hawaiian bobtail squid, Euprymna scolopes, serves as a key model for understanding host-microbe interactions. Traditional culture-based methods have primarily isolated V. fischeri from the light organs of wild-caught squid, yet culture-independent analyses of this symbiotic microbiome remain limited. This study aims to enhance species-level resolution of bacterial communities associated with E. scolopes using hsp60 amplicon sequencing. We validated our hsp60 sequencing approach using pure cultures and mixed bacterial populations, demonstrating its ability to distinguish V. fischeri from other closely related vibrios and the possibility of using this approach for strain-level diversity with further optimization. This approach was applied to whole-animal juvenile squid exposed to either seawater or a clonal V. fischeri inoculum, as well as ventate samples and light organ cores from wild-caught adults. V. fischeri accounted for the majority of the identifiable taxa for whole-animal juvenile samples and comprised 94%-99% of amplicon sequence variants (ASVs) for adult light organ core samples, confirming that V. fischeri is the dominant, if not sole, symbiont typically associated with E. scolopes light organs. In one ventate sample, V. fischeri comprised 82% of reads, indicating the potential for non-invasive community assessments using this approach. Analysis of non-V. fischeri ASVs revealed that Bradyrhizobium spp. and other members of the Rhodobacterales order are conserved across juvenile and adult samples. These findings provide insight into the presence of additional microbial associations with the squid host tissue outside of the light organ that have not been previously detected through traditional culture methods.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf085"},"PeriodicalIF":5.1,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303855","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

Tailocin tail fiber diversity correlates with rfbD variation in the Pseudomonas syringae species complex. 丁香假单胞菌种复合体中尾纤多样性与rfbD变异相关。

IF 5.1

ISME communications Pub Date : 2025-06-12 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf099

Chad Fautt, Kevin Hockett, Simon Delattre, David Baltrus, Estelle Couradeau

{"title":"Tailocin tail fiber diversity correlates with rfbD variation in the Pseudomonas syringae species complex.","authors":"Chad Fautt, Kevin Hockett, Simon Delattre, David Baltrus, Estelle Couradeau","doi":"10.1093/ismeco/ycaf099","DOIUrl":"10.1093/ismeco/ycaf099","url":null,"abstract":"Community assembly dynamics are in part driven by competition between community members. Diverse bacteria can antagonize competitors through the production of toxic compounds, such as bacteriophage-derived tailocins. These toxins are highly specific in their targeting, which is determined by interactions between the tailocin's tail fiber and competitors' lipopolysaccharide O-antigen moieties. Tailocins play a pivotal role in mediating microbial interactions among the economically significant plant pathogens within the Pseudomonas syringae species complex, with the potential to alter community structure and disease progression in host plants. Previous work looking at 45 P.syringae strains has demonstrated that at least two phylogenetic clades of tail fibers are encoded in the conserved tailocin region across the species complex, which roughly corresponds to two clusters of targeting activity. To better understand the full diversity of tail fibers associated with tailocins in the species complex, we screened 2161 publicly available genomes for their tailocin tail fiber content, predicted protein structures that represent the diversity of fibers, and investigated forces possibly driving the distribution of fibers throughout the species complex. Here we present evidence that, while the two previously described tail fiber clades are indeed widespread among virulent P. syringae strains, their distribution displays low congruency with phylogeny. Instead, we found that the presence of one tail fiber or the other is strongly correlated with the allelic diversity of another gene, associated with lipopolysaccharide O-antigen structure, dTDP-4-dehydrorhamnose reductase. Our findings suggest the presence of two reciprocally targeting groups of strains distributed throughout the P. syringae species complex that transcend phylogenetic relationships.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf099"},"PeriodicalIF":5.1,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12208367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531470","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

Potential mode of action of multispecies inoculums on wheat growth under water stress. 水分胁迫下多种接种对小麦生长的潜在作用模式。

IF 5.1

ISME communications Pub Date : 2025-06-09 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf095

Asmaâ Agoussar, Julien Tremblay, Étienne Yergeau

{"title":"Potential mode of action of multispecies inoculums on wheat growth under water stress.","authors":"Asmaâ Agoussar, Julien Tremblay, Étienne Yergeau","doi":"10.1093/ismeco/ycaf095","DOIUrl":"10.1093/ismeco/ycaf095","url":null,"abstract":"Manipulating microbial communities could increase crop resistance to environmental stressors such as drought. It is, however, not clear what would be the best approach to do so and what microbial traits are important. Here, we first compare multispecies inoculums created using different approaches. The only inoculum that increased wheat fresh biomass under drought was the one created from 25 isolates that had showed a capacity to grow under high osmolarity. We then looked at two potential mechanisms of action of this inoculum: (i) direct action, by sequencing and screening the genomes of the inoculated bacteria, (ii) indirect action, by sequencing the 16S ribosomal ribonucleic acid gene and internal transcribed spacer region of rhizosphere, root, and leaves microbial communities. The microbes in the inoculum harbored many traits related to plant growth promotion, competition, and water stress resistance. The inoculation also resulted in significant shifts in the microbial communities associated with wheat, including some microorganisms (e.g. Rhizobium, Shinella, and Klebsiella) previously reported to improve plant drought resistance. We conclude that the inoculum studied here increased wheat growth because it potentially acted on two fronts: directly, through the traits it was selected for, and indirectly, through inducing shifts in the resident plant microbial communities.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf095"},"PeriodicalIF":5.1,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12206444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531469","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

Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments. 水生环境中不可培养的大型病毒样颗粒的意外多样性和生态意义。

IF 5.1

ISME communications Pub Date : 2025-06-05 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf098

Hermine Billard, Maxime Fuster, François Enault, Jean-François Carrias, Léa Fargette, Margot Carrouée, Perrine Desmares, Tom O Delmont, Pauline Nogaret, Estelle Bigeard, Gwenn Tanguy, Anne-Claire Baudoux, Urania Christaki, Télesphore Sime-Ngando, Jonathan Colombet

{"title":"Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments.","authors":"Hermine Billard, Maxime Fuster, François Enault, Jean-François Carrias, Léa Fargette, Margot Carrouée, Perrine Desmares, Tom O Delmont, Pauline Nogaret, Estelle Bigeard, Gwenn Tanguy, Anne-Claire Baudoux, Urania Christaki, Télesphore Sime-Ngando, Jonathan Colombet","doi":"10.1093/ismeco/ycaf098","DOIUrl":"10.1093/ismeco/ycaf098","url":null,"abstract":"The discovery of jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity and significant abundances of large virus-like particles in aquatic environments. We discovered new viral morphotypes, all likely to be associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic virus-like particles and jumbo phage-like particles. This work deepens our understanding of large virus and reveals their key role as regulators of microbial communities.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf098"},"PeriodicalIF":5.1,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12204322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531471","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

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

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