ISME communications最新文献

{"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":"Uncoupling growth and division in <i>Chlamydomonas reinhardtii</i> colonies: consistent cell cycle regulation under confinement.","authors":"Sing Teng Chua, Jurij Kotar, Michael Kühl, Alison G Smith, Silvia Vignolini, Pietro Cicuta","doi":"10.1093/ismeco/ycaf104","DOIUrl":"10.1093/ismeco/ycaf104","url":null,"abstract":"<p><p>A planar cell microcolony served as a model system to study the impact of inter-cellular crowding and cell-matrix interactions upon the cell cycle. We studied the development over several days of <i>Chlamydomonas reinhardtii</i> microcolonies, grown from single cells, using a bespoke experimental setup allowing timelapse fluorescence microscopy. Through precise cell segmentation and lineage tracking of a large systematic dataset, characterising individual cell growth and divisions, we uncovered how the external matrix influenced cell cycle and morphology. Experiments also revealed spatial heterogeneity amongst cells within colonies, providing insights into the effects of contact inhibition and micro-gradients of mass transfer. A radial propagation of ring-like pattern, characterised by variations in parent cell size, indicated complex spatio-temporal dynamics in the regulation of the cell cycle within the constrained environment. The mechanisms of commitment and mitotic sizing remained consistent within colonies under this mechanical confinement. These findings contribute to a broader understanding of how matrix immobilisation affects <i>C. reinhardtii</i>, with implications for alternative culture formats such as biofilms and hydrogel encapsulation-approaches increasingly used in biohybrid applications including biophotovoltaics and bioremediation.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf104"},"PeriodicalIF":6.1,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12306439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144746304","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":"Genomic personalities of <i>Dehalococcoides</i> subspecies and <i>Dehalogenimonas</i> illuminate complete trichloroethene dechlorination in high-salt conditions.","authors":"Wei-Yu Chen, Yun-Chi Lan, Jiung-Wen Chen, Jer-Horng Wu","doi":"10.1093/ismeco/ycaf101","DOIUrl":"10.1093/ismeco/ycaf101","url":null,"abstract":"<p><p>Global salinization increasingly threatens ecosystem integrity and the regulation of biogeochemical cycles. Our study reveals novel insights into the microbial contributions to the organohalide decomposition in saline environments, demonstrating the unprecedented ability of organohalide-respiring bacteria <i>Dehalococcoides</i> and <i>Dehalogenimonas</i> to completely dechlorinate trichloroethene to non-toxic ethene under hypersaline conditions (up to 31.3 g/L) in long-term operations. Using gradient salinity reactors and metagenomic analyses, we identified the evolved genomic features associated with high-salt tolerance. The Cornell subgroup of <i>Dehalococcoides</i> and <i>Dehalogenimonas</i> exhibit significantly lower average protein isoelectric points and retain the ribosomal protein L33p gene, unlike the Victoria and Pinellas subgroups. <i>Dehalococcoides</i> shows subspecies-level genomic divergence and unique codon usage biases. Intriguingly, the L33p gene is found in diverse bacterial phyla from saline environments, suggesting it may provide a growth advantage under salt stress. These genomic traits, hypothesized to enhance salt tolerance and dechlorination efficiency under salt stress, correlate with performance at elevated salinity. Our findings advance the understanding of microbial salt adaptation mechanisms and support the development of bioremediation strategies tailored for saline environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf101"},"PeriodicalIF":6.1,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12415852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031212","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":"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}

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

{"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}