Environmental Microbiome最新文献

{"title":"The core taxa connectivity in leaf microbiomes in ash trees stands is modulated by host-related and environmental factors.","authors":"Valentin Burghard, Sonja Wende, Georgia Kahlenberg, Henriette Häuser, Ralf Kätzel, Steffen Kolb, Andreas Ulrich","doi":"10.1186/s40793-026-00967-8","DOIUrl":"10.1186/s40793-026-00967-8","url":null,"abstract":"<p><strong>Background: </strong>Forests cover large areas of the terrestrial land surface and play a key role in climate regulation and biodiversity conservation. Tree-associated microbial communities are integral components of forest ecosystems and contribute to plant functioning, stress tolerance, and interactions with the environment. However, the factors shaping the phyllosphere microbiome of forest trees across large environmental gradients remain less explored. Here, we investigated the bacterial leaf microbiome of Fraxinus excelsior across different climatic regions in Germany to identify its core microbiome and determine the relative importance of environmental and host-related factors shaping the phyllosphere microbiome of forest trees across large environmental gradients assembly. Therefore, 30 ash trees were sampled at each of the 12 sites across Germany, at which we assessed their leaf microbiome, leaf physio-chemical properties and a set of site parameters.</p><p><strong>Results: </strong>In total, 755 genera were detected. Only three genera Hymenobacter, Massilia and Sphingomonas were predominant across all sites. Geographical position, precipitation, tree age and the leaf and soil chemistry parameters were significant factors that explained 22.1% of variance between microbiome structures between the different sites. Seven genera were identified as the core leave microbiome of F. excelsior. The core microbiome assessed for each sampling site was mostly more diverse and differed between sites. Complex co-occurrence networks separated by sites with the identified six hub bacterial taxa proved that they were essential for the local core microbiomes. However, the network complexity differed significantly between the sampling sites.</p><p><strong>Conclusion: </strong>Our findings clearly indicate the existence of an ash core microbiome on leaves that occurred at all sites but was locally differently interconnected to further microbiome members. The network analyses revealed that less frequent genera play important roles as hub taxa. Furthermore, we were also able to prove the modulating role of biotic and abiotic factors on the ash phyllosphere microbiome. An optimized core microbiome may be considered crucial for improving tolerance against plant diseases, such as ash dieback, in future.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13651322/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149138945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative metataxonomic analysis of total, viable, and active rumen microbial communities under methane-mitigated conditions.","authors":"Woohyung Lee, Geonwoo Kim, Wenli Li, Tansol Park","doi":"10.1186/s40793-026-00963-y","DOIUrl":"10.1186/s40793-026-00963-y","url":null,"abstract":"<p><strong>Background: </strong>The rumen microbiota play a central role in digestion and methane production, thereby influencing ruminant productivity. Evaluating methane mitigation strategies requires consideration of both microbial viability and activity. DNA-based methods may include signals from dead or damaged cells, whereas RNA-based approaches may underrepresent viable populations with low transcriptional activity. Propidium monoazide (PMA) reduces DNA signals from membrane-compromised cells, providing an indirect, membrane-integrity-based assessment of microbial viability. This study compared taxonomic and predicted functional profiles obtained by 16S rRNA gene amplicon sequencing of total DNA (tDNA), PMA-treated DNA (vDNA), and RNA-derived cDNA (RNA) from rumen samples subjected to three in vitro methane mitigation treatments: 3-nitrooxypropanol (NOP), monensin (MON), and Asparagopsis sp. (ASP).</p><p><strong>Results: </strong>MON treatment induced the most pronounced changes in fermentation parameters and microbial composition, whereas the NOP and ASP groups exhibited similar fermentation outcomes. RNA-derived profiles exhibited the lowest alpha diversity, with vDNA profiles falling between those of RNA and tDNA. Procrustes analysis revealed metric-dependent similarities among sample types; Bray-Curtis distances showed closer alignment between tDNA and RNA, whereas Jaccard distances showed greater similarity between vDNA and RNA. Parabacteroides exhibited significantly higher relative abundance in vDNA than in tDNA or RNA. Notably, Succiniclasticum showed opposing correlations with the acetate-to-propionate ratio between tDNA and RNA under MON treatment, whereas no significant correlation was detected in vDNA. Differential analysis of PICRUSt2-predicted methanogenesis-related KEGG modules revealed sample type- and treatment-specific patterns.</p><p><strong>Conclusions: </strong>PMA-treated DNA provided a distinct perspective on the rumen microbiota by reducing signals from membrane-compromised cells and revealing populations that were differently represented in tDNA and RNA-derived profiles, including membrane-intact populations with low RNA representation. Thus, vDNA may serve as a practical additional approach when RNA analysis is technically constrained.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149166712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linking microbial community composition of three rootstock genotypes to apple replant disease susceptibility.","authors":"Nils Orth, Nils Siefen, Jannika Staudt, Fatma M Mahmoud, Sarah Benning, Silvia Gschwendtner, Tom P Pielhop, Kristin Hauschild, Michael Schloter, Michaela Schmitz, Traud Winkelmann","doi":"10.1186/s40793-026-00957-w","DOIUrl":"10.1186/s40793-026-00957-w","url":null,"abstract":"<p><strong>Background: </strong>Apple replant disease (ARD) is a worldwide issue of complex biotic origin. The exact aetiology has yet to be fully elucidated and environmentally friendly and economically feasible countermeasures are sparse. The breeding of tolerant apple rootstock genotypes shows some promise as reduced sensitivity on selected ARD-affected soils has been shown for some rootstock genotypes. By adding insights into the root-associated microbiome, we aimed to complement previously published results, examining the response in growth, gene expression and production of phenolic compounds in roots of seven Malus genotypes in ARD soil. We selected the two least susceptible rootstock genotypes of the previous study, EMR.2 and G.935, in addition to the susceptible rootstock genotype M.26. The objective of this study was to gain insights into the bacterial community composition of the rhizosphere and root endosphere of less susceptible rootstock genotypes in comparison to the susceptible one.</p><p><strong>Results: </strong>In an Illumina-based sequencing approach, the composition of rhizosphere as well as endophytic bacterial communities was investigated for apple plants in ARD soil and disinfected ARD soil. ARD impacted the rhizosphere stronger than the endosphere, where rootstock genotype influence was stronger. G.935 generally showed a more distinct and diverse microbiome than the other two rootstock genotypes. In bacterial communities, the relative abundance of Pseudomonadota decreased in ARD samples, while Actinomycetota increased. In the endosphere, this was mostly accounted for by Streptomyces. A qPCR approach confirmed the high abundance of Streptomyces. Interestingly, another qPCR approach did not indicate a high abundance of plant pathogenic Streptomyces in the same samples.</p><p><strong>Conclusions: </strong>ARD strongly influenced the bacterial microbiome in the rhizosphere and, to a lesser extent, the root endophytic microbiome. The distinct and more diverse bacterial microbiome of G.935 might help against biotic stress, such as ARD. However, EMR.2 was previously found to be less susceptible to ARD, too, suggesting additional factors must play a role and additional research is necessary. Pathogenicity of Streptomyces could not be proven but repeatedly high abundance of root endophytic Streptomyces under ARD conditions indicate an important role.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13563949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148931694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual legacy of plant water-deficit-tolerance and watering history shapes rhizosphere microbial transplant outcomes in tomato post-drought recovery.","authors":"Rodrigo Pulgar, Alexis Gaete, Madelaine Mejías, Romina Madrid, Ignacio Chávez, Lucas Pino, Andrea Talamilla-Espinoza, Jeimy Moscote, Claudio Pastenes, Dinka Mandakovic","doi":"10.1186/s40793-026-00953-0","DOIUrl":"https://doi.org/10.1186/s40793-026-00953-0","url":null,"abstract":"<p><strong>Background: </strong>Climate change is intensifying drought events, negatively affecting crop yields and quality. Enhancing plant recovery following drought is therefore critical for agricultural resilience. Within the holobiont framework, the plant microbiome plays a key role in modulating plant responses to environmental stress. Here, we evaluated the contribution of rhizosphere microbial transplants derived from Solanum lycopersicum cultivars differing in water-deficit-tolerance and prior exposure or not to water deficit to post-drought recovery in susceptible tomato plants.</p><p><strong>Results: </strong>Physiological measurements, including net photosynthetic rate, relative water content, and water potential, showed that microbial community transplants from water-deficit-tolerant cultivars previously exposed to water deficit significantly enhanced post-drought recovery in susceptible plants, suggesting a dual legacy effect of host phenotype and irrigation history. High-throughput metabarcoding revealed marked temporal shifts in rhizosphere microbial communities between the initial (Ti) and post-recovery (Tf) stages. Bacterial alpha diversity increased significantly at Tf only for the tolerant inoculant under deficit irrigation, whereas fungal diversity showed more stable response across conditions. Beta-diversity analyses revealed clear separation between Ti and Tf communities for both bacteria and fungi. Community structure changes were highly pronounced in the inoculation treatments that produced the most contrasting post-drought recovery phenotypes (SFI: susceptible cultivar under full irrigation and TDI: tolerant cultivar under deficit irrigation), which formed distinct clusters in hierarchical analyses. Differential abundance analysis identified bacterial taxa enriched at Tf in TDI, while fungal communities displayed stage-specific markers. Functional annotation using FAPROTAX and FUNGuild revealed enrichment of nitrate reduction and anoxygenic photoautotrophy among bacterial functions, and saprotrophic guilds among fungal communities at Tf in TDI, suggesting increased nutrient cycling activity associated with post-drought recovery. Co-occurrence network analysis revealed contrasting interaction patterns, with higher connectivity in SFI and a greater contribution of fungal taxa and positive fungi-fungi interactions in TDI.</p><p><strong>Conclusions: </strong>These results indicate that the legacy of rhizosphere microbiomes shaped by host water-deficit-tolerance and irrigation history is associated with enhanced post-drought recovery, involving the enrichment of specific microbial taxa and functional guilds. The concept of dual legacy provides a useful framework for understanding microbiome-mediated plant resilience.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13633642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149116881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From functional annotation to functional meaning in microbiome research.","authors":"Rajesh Kumar Bajiya, Rania Agabi, Jimena Olabarría García, Vicenzo Paolo Torreno, Jean Armengaud, Lucia Grenga","doi":"10.1186/s40793-026-00956-x","DOIUrl":"10.1186/s40793-026-00956-x","url":null,"abstract":"<p><p>Microbiome research has moved from cataloging community composition to asking what these communities do, but \"function\" is often used to describe fundamentally different levels of evidence. Functional claims may refer to functional capacity (what is encoded), functional realization (what molecular functions are actively engaged under specific conditions), or functional impact (the resulting consequences for hosts, microbial communities, or ecosystems). In this Perspective, we examine how functional annotations in microbiome research generate biological meaning and why current approaches support different kinds of inference. We propose a framework that distinguishes three levels of functional inference: capacity, realization, and impact. Homology-based, domain-centric, pathway-based, machine learning-driven, and multi-omics approaches each contribute differently to these levels, but none alone captures microbiome function in full. We argue that microbiome function should be interpreted as a hierarchy of inferences rather than a single property. Recognizing this distinction should improve how functional findings are interpreted, reported, and compared across microbiome studies. Accordingly, functional studies should explicitly state whether their conclusions concern capacity, realization, or impact, thereby clarifying the evidential basis of functional claims and improving their interpretation and comparison across microbiome studies.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13587530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic insights into mechanisms of coral larval settlement induction and inhibition by marine biofilms.","authors":"Paul A O'Brien, Sara C Bell, Andrew P Negri, Shannon R Kjeldsen, Julian Zaugg, Nicole S Webster, Muhammad Abdul Wahab, Inka Vanwonterghem, Laura Rix","doi":"10.1186/s40793-026-00945-0","DOIUrl":"10.1186/s40793-026-00945-0","url":null,"abstract":"<p><strong>Background: </strong>Biofilms are essential to larval settlement in many marine invertebrates, yet the mechanisms driving settlement induction or inhibition in corals remain poorly resolved. This challenge lies in the vast taxonomic and functional diversity of marine biofilms, making it difficult to identify cues associated with settlement. To address this, we analysed the metagenomes of biofilms used to induce settlement (attachment and metamorphosis) of four broadcast-spawning non-acroporid coral species: Dipsastrea favus, Platygyra sinensis, Echinophyllia aspera and Porites lobata. Biofilms were developed for one or two months, under light or dark treatments, with light biofilms inducing significantly higher settlement than dark biofilms.</p><p><strong>Results: </strong>Gene composition varied strongly among treatments, with light biofilms enriched in genes encoding carotenoid biosynthesis and nitrate reduction, while dark biofilms encoded more genes for denitrification and nitric oxide production. Modelling revealed the abundance of genes encoding GABA biosynthesis and the type III secretion system (SS) were positively associated with settlement, while genes encoding the type II secretion system, flagellar and lipopolysaccharides were negatively associated. Genes predicted to promote settlement were concentrated in metagenome assembled genomes (MAGs) assigned to Flavobacteriaceae, Rhodobacteraceae and Pirellulaceae, consistent with previous research identifying these lineages as potential inducers. While we detected homologues of some biosynthesis genes for the settlement-inducing compounds cycloprodigiosin and tetrabromopyrrole in the MAGs, pathways were incomplete suggesting additional compounds promote settlement on these biofilms.</p><p><strong>Conclusions: </strong>These findings link biofilm metagenomics to coral larval settlement for the first time, suggesting carotenoids may attract larvae to biofilm surfaces, while GABA may promote searching and attachment. Additional compounds, for example cycloprodigiosin, tetrabromopyrrole or effector proteins, may be required to complete metamorphosis, however the specific compounds responsible likely vary across biofilm communities and suggest multiple mechanisms can lead to settlement. Simultaneously, elevated levels of nitric oxide, type II SS exudates or an abundance of flagellar potentially inhibit the settlement process. This study advances our understanding of the complex microbial processes underpinning coral larval settlement.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From the leaf to the gut and back again: using synthetic bacterial communities to trace the fate and influence of phyllosphere bacteria in an Arabidopsis-Pieris brassicae system.","authors":"Moritz Müller, Maryse A P Huve, Michael Kunzler, Mitja N P Remus-Emsermann, Rudolf O Schlechter, Luis R Paniagua Voirol","doi":"10.1186/s40793-026-00947-y","DOIUrl":"10.1186/s40793-026-00947-y","url":null,"abstract":"<p><strong>Background: </strong>The leaf surface, or phyllosphere, hosts abundant and diverse bacterial communities that interact with both the host plant and herbivorous insects, yet their collective influence on plant-insect interactions remains poorly investigated. We established a functionally gnotobiotic insect-plant system combining axenically grown Arabidopsis thaliana, Pieris brassicae larvae, and defined synthetic phyllosphere communities (SynComs) of increasing richness: SynCom5, SynCom10 and SynCom20, containing 5, 10 and 20 bacterial strains, respectively. We investigated how phyllosphere bacteria influence herbivore performance, plant defence responses, and bacterial colonisation of both leaves and the insect gut.</p><p><strong>Results: </strong>While larval weight tended to decrease with increasing bacterial community richness, only the most diverse SynCom (20 members) caused significant weight reductions without affecting survival. Plants harbouring the most diverse community showed enhanced jasmonic acid (JA) levels during feeding, whereas salicylic acid (SA) remained unchanged, suggesting the induction of herbivore-associated defence responses. Compared to plants experiencing no herbivory, feeding strongly reshaped bacterial colonisation on leaves, increasing total bacterial loads about fourfold and driving dominance of Pantoea eucalypti 299R as shown by 16S rRNA gene amplicon sequencing. Larvae acquired a distinct subset of bacteria, primarily recruited from the genera Methylobacterium, Microbacterium, Williamsia, and Curtobacterium.</p><p><strong>Conclusions: </strong>Phyllosphere bacteria can influence plant-insect interactions, with bacterial community richness associated with reduced P. brassicae larval performance and SynCom20 linked to stronger JA accumulation in leaves during feeding. Conversely, herbivory increased leaf bacterial loads, shifted leaf community composition, and filtered leaf-associated bacteria during passage into the larval gut. These findings establish this functionally gnotobiotic insect-plant system as a tractable model for dissecting reciprocal effects between resident phyllosphere bacteria and herbivory.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445934/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148686058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The community, assembly process and potential functions of bacteria with different cell size in a river.","authors":"Pengfei Yang, Xiujin Duan, Qixian Wu, Hua Liu, Shengchao Ren, Kexin Zhang, Yuhao Song, Jie Liu, Guannan Mao, Jing Yang, Wei Hu","doi":"10.1186/s40793-026-00944-1","DOIUrl":"10.1186/s40793-026-00944-1","url":null,"abstract":"<p><strong>Background: </strong>Cell size regulates the evolution and selection of bacterial metabolic strategies through the \"resource acquisition capacity-metabolic cost trade-off\", resulting in significant differences in community and metabolic functions among bacteria with different size. Therefore, phenotypic grouping of bacterial communities based on cell size can directly establish the mechanism connection between the \"phenotypic structure\" of microbial communities and ecological function, which has significant theoretical significance for clarifying the role and status of bacteria of different cell sizes in the biogeochemical cycle process.</p><p><strong>Results: </strong>The results showed that UB and LB were clearly distinguishable in the environment, and their relative proportions varied with environmental conditions. Compared with LB, UB exhibited lower diversity and narrower ecological niche breadth, the community compositions of the two groups showed significant differences, leading to distinct ecological functions. Notably, UB play a crucial role in material cycling, contributing to the maintenance of ecosystem balance and stability, and participating actively in elemental cycles.</p><p><strong>Conclusions: </strong>Our findings highlight the utility of cell size as an indicator of bacterial diversity and reveal a direct link between microbial morphology and ecological characteristics.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13673628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149196770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic insights into the taxonomic and metabolic diversity of the microbiome of Lake Karum in the Danakil Depression, Ethiopia.","authors":"Michael C Macey, Velislava Ilieva, Ben P Stephens, Benjamin Tatton, Ermias Balcha, Susanne P Schwenzer, Terry J McGenity, Hagos Miruts, Felipe Gomez, Barbara Cavalazzi, Karen Olsson-Francis","doi":"10.1186/s40793-026-00938-z","DOIUrl":"10.1186/s40793-026-00938-z","url":null,"abstract":"<p><strong>Background: </strong>Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.</p><p><strong>Results: </strong>The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including Candidatus Bipolaricaulota and Candidatus Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the Candidatus Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.</p><p><strong>Conclusion: </strong>This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13595746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Substrate-driven phage community structure and phage-host dynamics in anaerobic digesters.","authors":"Maliea A Nipko, Zongzhi Wu, Zachary T Aanderud, David M Robinson","doi":"10.1186/s40793-026-00939-y","DOIUrl":"10.1186/s40793-026-00939-y","url":null,"abstract":"<p><strong>Background: </strong>Phages shape microbial communities by regulating metabolic pathways, driving biogeochemical processes, and impacting stability and functionality of ecosystems. Phages contributions to natural ecosystems are undeniable; however, their role in built systems especially in anaerobic digesters remain poorly characterized. To discover the functional role of phage communities in anaerobic digesters, we evaluated phage-bacterial and virus-archaeal relationships in metagenomic sequences from fifteen commercial, full-scale anaerobic digesters of chicken, cattle, and pig manure, the three most commonly utilized organic waste streams globally.</p><p><strong>Results: </strong>Here, we predict the abundance, auxiliary metabolic genes, and microbial-host interactions of phage and archaeal viruses under anaerobic fermentation processes and methanogenesis. We found phages and prokaryote abundances were coupled and both populations were driven by feedstock characteristics (20% phage variance and 25% prokaryotes explained by feedstock), indicating interactions of phage, host, and the environment. Phages encoded auxiliary metabolic genes relevant to and supporting anaerobic digestion including glycoside hydrolase, pyruvate formate lyase, and cobalamin biosynthesis genes.</p><p><strong>Conclusions: </strong>Together, our results reveal that phages are not only integral to bacterial and archaeal community structure and function in anaerobic digesters but are also strongly shaped by feedstock type. These findings provide a basis for understanding and potentially manipulating viral-host interactions to enhance digester performance.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13644194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149116904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}