ISME communications最新文献

{"title":"Expanding ISME Communications to taxonomy and nomenclature.","authors":"Maria Chuvochina, Marike Palmer, Stephanus N Venter","doi":"10.1093/ismeco/ycaf106","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf106","url":null,"abstract":"","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf106"},"PeriodicalIF":5.1,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676748","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":"Gradual loss of mobile genetic elements in <i>Staphylococcus aureus</i> USA300 in a closed hospital niche.","authors":"Anne-Gaelle Ranc, Patricia Martins Simões, Benjamin Youenou, Camille Kolenda, Céline Dupieux, Frédéric Laurent, Jean Philippe Rasigade, Anne Tristan, François Vandenesch","doi":"10.1093/ismeco/ycaf105","DOIUrl":"10.1093/ismeco/ycaf105","url":null,"abstract":"<p><p>Our French National Reference Centre for Staphylococci was requested to determine the epidemiological link between 19 methicillin-susceptible/resistant Staphylococcus aureus (MSSA/MRSA) isolates obtained from patients and a healthcare worker in a long-term care hospital, following the death of a nurse from pneumonia presumed to be associated with the drainage of a patient with an active skin infection. Whole genome sequencing was performed on all isolates to characterize their virulome, resistome, and phylogenetic relationships. Phylogenetic analysis revealed that 12 isolates belonged to the North American USA300 lineage, which is the predominant MRSA in North America but is less prevalent in Europe. USA300 strains are typically described as belonging to the clonal complex 8 (CC8) and possessing several mobile genetic elements (MGEs): the pathogenicity island SaPI5, the PVL-encoding bacteriophage ϕSa2USA, the staphylococcal chromosomal cassette <i>mec</i>IVa (SCC<i>mec</i>IVa), and the arginine catabolic mobile element (ACME). All 12 isolates lacked SaPI5, and four possessed the other typical MGEs of the USA300 lineage. However, one isolate did not carry SCC<i>mec</i>IVa, six did not have ACME, and two did not carry ϕSa2USA. The topology of the phylogenetic tree and the phylodynamic analysis suggested the loss of SaPI5 before entry in the long-term hospital, which may have occurred 3-4 years before the current outbreak. As long-term hospital may represent a relatively closed and stable ecosystem, we concluded that this loss of MGEs is a phenomenon of genetic diversification driven by niche specialization, in this case, originally constituted by a healthcare institution.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf105"},"PeriodicalIF":5.1,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651328","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: Metabolically-versatile <i>Ca</i>. Thiodiazotropha symbionts of the deep-sea lucinid clam <i>Lucinoma kazani</i> have the genetic potential to fix nitrogen.","authors":"","doi":"10.1093/ismeco/ycae118","DOIUrl":"https://doi.org/10.1093/ismeco/ycae118","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycae076.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae118"},"PeriodicalIF":5.1,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12206080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144531450","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":"Abiotic environments prevail over plant functional traits in shaping phyllosphere fungal communities of temperate grasslands in China.","authors":"Shanshan Song, Xian Yang, Rong Tang, Zhiyao Tang","doi":"10.1093/ismeco/ycaf096","DOIUrl":"10.1093/ismeco/ycaf096","url":null,"abstract":"<p><p>Phyllosphere fungi play critical roles in plant health and ecosystem functioning. While previous studies have explored the diversity and composition of phyllosphere fungal communities in various ecosystems, they have typically focused on either epiphytic or endophytic fungi at single sites and rarely addressed both groups simultaneously across broad environmental gradients. As a result, the relative importance of abiotic environments, plant traits, and dispersal processes in shaping phyllosphere fungal communities remains unclear, particularly with respect to differences between epiphytic and endophytic fungi. We collected 231 leaf samples from nine sites in temperate grasslands of northern China, and explored the effect of abiotic environments and plant traits on the diversity and structure of phyllosphere fungi at broad spatial scales. Our analysis revealed that aridity, poor soil conditions and leaf pH decreased the relative abundance of endophytic saprophytic fungi, and plants with a \"fast-growing\" strategy promoted the relative abundance of phyllosphere pathogenic fungi. The positive effects of aridity and poor soils on the richness of endophytic fungi were undermined by soil fungal richness, while the richness and Pielou's evenness of epiphytic fungi was inhibited by the availability of soil resource. Soil organic carbon emerged as a key factor influencing the composition of phyllosphere fungal communities, and dispersal limitation was relatively weak and comparable between endophytic and epiphytic fungi. Our findings provide empirical evidence that abiotic environments prevail over plant traits in structuring phyllosphere fungi at broad spatial scales and reveals assembly patterns that differ from those reported in previous single-site or forest-based studies.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf096"},"PeriodicalIF":5.1,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676746","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":"Coupling between bacterial phylogenetic diversity and heterotrophic productivity in a coastal ecosystem affected by estuarine plumes.","authors":"Yao Liu, Shujie Cai, Wenxin Fan, Wupeng Xiao, Xin Liu, Edward A Laws, Bangqin Huang","doi":"10.1093/ismeco/ycaf102","DOIUrl":"10.1093/ismeco/ycaf102","url":null,"abstract":"<p><p>Understanding the diversity-productivity relationship (DPR) is crucial for elucidating the ecological functions of marine bacterioplankton. However, studies have often focused on species diversity, neglecting phylogenetic diversity, which may offer deeper insights into the complex ecological processes shaping DPR in natural systems. This study addressed this gap by exploring the role of phylogenetic diversity in bacterioplankton productivity in the northern South China Sea, a coastal ecosystem influenced by estuarine plumes. We aimed to disentangle the mechanisms driving DPR and investigate how estuarine plumes modulate these processes. Our results show that the substantial enhancement of phytoplankton production by the Pearl River plume increased bacterial production, abundance, and cell-specific production. From a metacommunity perspective, phylogenetic diversity, rather than species diversity, significantly enhanced productivity. The plume reduced positive species interactions and complementarity but amplified the selection effect, where increased phylogenetic diversity raised the likelihood of including highly productive species. In plume-impacted communities, distantly related and highly productive clades dominated the DPR. Phylogenetically diverse assemblages exhibited enhanced niche differentiation that facilitated the stable coexistence of productive clades by mitigating exclusion. We also delineated how the negative selection effect and increased species exclusion contributed to the decoupling of species diversity from productivity in communities unaffected and affected by the plume, respectively. These findings highlighted the pivotal role of estuarine plumes in enhancing productivity via increased phylogenetic diversity and in eliciting complex adaptive responses within bacterioplankton communities. Future comprehensive assessments will be needed to elucidate the implications of these dynamics on marine ecosystem services.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf102"},"PeriodicalIF":5.1,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144676747","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":"Phosphonate-driven oxic CH₄ production by <i>Variovorax xiamenensis</i> sp. nov.: insights from marine and freshwater microbial adaptations to P-limitation.","authors":"Yu Wang, Shaohe Wang, Zifu Xu, Silin Ni, Min Xu, Shuh-Ji Kao","doi":"10.1093/ismeco/ycaf100","DOIUrl":"10.1093/ismeco/ycaf100","url":null,"abstract":"<p><p>Methane (CH₄) emissions in oxygenated aquatic environments challenge traditional views of methanogenesis suggesting the presence of alternative microbial CH₄ production pathways. This study identifies a novel bacterial species, <i>Variovorax xiamenensis</i> W6^T, capable of utilizing methylphosphonate (MPn) as its sole phosphorus (P) source under laboratory conditions, thereby supporting growth and CH₄ production in phosphorus-limited conditions. Transcriptomic analyses, as well as incubation experiments, reveal that CH₄ emission via the phosphonate-degrading <i>phn</i> gene cluster, encoding a C-P lyase, is tightly regulated by inorganic phosphate (Pi) availability, linking nutrient scarcity to methane cycling. A genomic survey of over 16 000 prokaryotic genomes reveals the widespread occurrence of <i>phn</i> gene cluster in 9% of the analyzed genomes, predominantly within the phylum <i>Pseudomonadota</i>. While MPn metabolism has been well-documented in marine environments, its presence and ecological role in freshwater systems remain underexplored. Our findings highlight the potential for phosphonate-driven methane production in freshwater ecosystems and underscore the need for further research to quantify MPn concentrations and its contribution to global methane budgets. This study emphasizes the importance of integrating microbial phosphonate metabolism into models of biogeochemical cycling and climate predictions, particularly under scenarios of increasing phosphorus limitation driven by global warming.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf100"},"PeriodicalIF":5.1,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226003/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562175","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":"Application of <i>hsp60</i> amplicon sequencing to characterize microbial communities associated with juvenile and adult <i>Euprymna scolopes</i> 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":"<p><p>The symbiotic relationship between <i>Vibrio (Aliivibrio) fischeri</i> and the Hawaiian bobtail squid, <i>Euprymna scolopes</i>, serves as a key model for understanding host-microbe interactions. Traditional culture-based methods have primarily isolated <i>V. fischeri</i> 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 <i>E. scolopes</i> using <i>hsp60</i> amplicon sequencing. We validated our <i>hsp60</i> sequencing approach using pure cultures and mixed bacterial populations, demonstrating its ability to distinguish <i>V. fischeri</i> 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 <i>V. fischeri</i> inoculum, as well as ventate samples and light organ cores from wild-caught adults. <i>V. fischeri</i> 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 <i>V. fischeri</i> is the dominant, if not sole, symbiont typically associated with <i>E. scolopes</i> light organs. In one ventate sample, <i>V. fischeri</i> comprised 82% of reads, indicating the potential for non-invasive community assessments using this approach. Analysis of non-<i>V. fischeri</i> ASVs revealed that <i>Bradyrhizobium spp.</i> 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.</p>","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}

{"title":"Tailocin tail fiber diversity correlates with rfbD variation in the <i>Pseudomonas syringae</i> 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":"<p><p>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 <i>Pseudomonas syringae</i> species complex, with the potential to alter community structure and disease progression in host plants. Previous work looking at 45 <i>P.syringae</i> 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 <i>P. syringae</i> 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 <i>P. syringae</i> species complex that transcend phylogenetic relationships.</p>","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}

{"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":"<p><p>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. <i>Rhizobium</i>, <i>Shinella</i>, and <i>Klebsiella</i>) 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.</p>","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}

{"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":"<p><p>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.</p>","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}