Environmental Microbiome最新文献

{"title":"Azolla reshapes rhizosphere microbiomes and nutrient cycling in paddy fields.","authors":"Rong Zhao, Ping Huang, Changbing Pu, Feiyu Zhu, Changfeng Wang, Can Cai, Ni Xiang, Mengting Ren, Qinqin Ma, Jinmeng Li","doi":"10.1186/s40793-026-00903-w","DOIUrl":"https://doi.org/10.1186/s40793-026-00903-w","url":null,"abstract":"<p><strong>Background: </strong>Soil quality is a critical determinant of agricultural productivity and sustainability. The symbiotic nitrogen fixation by Azolla plays a key role in enhancing soil quality. However, despite its potential as a green manure for enhancing soil quality, the role of Azolla in paddy systems remains inadequately characterized. This study aims to elucidate the effects of Azolla on soil quality by examining nutrient cycling dynamics and microbial community composition, along with their interactions.</p><p><strong>Results: </strong>We integrated soil physicochemical analyses, enzyme activity assays, bacterial community profiling, co-occurrence network analysis, and correlation assessments to evaluate the effects of Azolla on soil microbial ecology. Rice monoculture (R) and rice-Azolla co-cultivation (RA) systems were established. RA significantly increased activities of carbon- and nitrogen-cycle-related enzymes by 3-44% (P < 0.05), while phosphorus-cycle-related enzyme activities decreased by 12-42%. Under high nitrogen fertilization, Azolla altered bacterial community structure and reduced alpha diversity. Notably, Azolla recruited specific functional taxa-including Haliangium, SC-I-84, Candidatus_Solibacter, Anaerolinea, and Sphingomonas-whose relative abundances were 1.03-1.33 times higher in RA than in R.</p><p><strong>Conclusions: </strong>This study elucidates the interactions between soil properties and microbial communities under Azolla application and uncovers the mechanisms by which Azolla enhances soil quality through nutrient cycling. Our findings demonstrate that Azolla, as a green manure, not only elevates soil nutrient content but also improves soil quality by driving microbe-mediated nutrient recycling. These results underscore the potential of Azolla as a sustainable alternative to conventional fertilization practices, offering novel insights into biofertilizer strategies for agricultural soil enhancement.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ecological drift and host filtering jointly structure foliar endophytes during ecosystem development.","authors":"Caio César Pires de Paula, Petr Macek, Milan Varsadiya, Jakub Borovec, Mehmet A Balkan, Brett S Younginger, Daniel J Ballhorn, Tomáš Picek, Tomáš Hájek, Jan Frouz, Jiří Bárta, Dagmara Sirová","doi":"10.1186/s40793-026-00906-7","DOIUrl":"https://doi.org/10.1186/s40793-026-00906-7","url":null,"abstract":"<p><strong>Background: </strong>Foliar endophytes contribute to plant nutrient acquisition, stress tolerance, and pathogen resistance, yet their responses to ecosystem-level processes remain poorly understood. Using a space-for-time substitution design, we investigated bacterial and fungal community dynamics in the foliar endosphere of four phylogenetically distinct plant hosts across a well-characterized successional chronosequence.</p><p><strong>Results: </strong>Amplicon sequencing revealed that the ecosystem development stage (site age) significantly influenced endophyte community composition, particularly among fungi, but explained only a small proportion of the total variation. Host plant identity and associated leaf stoichiometry were stronger predictors of community structure, with sampling time within the growing season also contributing significantly. Together, these deterministic factors explained 10% and 11% of bacterial and fungal compositional variation, respectively, and 27% of predicted bacterial functional potential. Null model analyses indicated that remaining variation was mostly consistent with stochastic assembly processes, particularly ecological drift. Endophytic communities were characterized by a few persistent dominant taxa and many rare, transient members with overlapping functional potential, including N₂ fixation, methylotrophy, and denitrification.</p><p><strong>Conclusions: </strong>Our findings demonstrate that host identity outweighs ecosystem age in structuring foliar endophyte communities and that stochastic processes play a central role in community assembly. The coexistence of stable dominant taxa and a dynamic rare biosphere may enhance plant responsiveness to environmental changes, while the functional potential of endophytes may remain largely consistent across seasons and successional stages.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147857429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial succession from nursery to vineyard highlights the role of beneficial and pathogenic microbes in young vineyard yield.","authors":"Colin Todd, Philippe E Rolshausen","doi":"10.1186/s40793-026-00905-8","DOIUrl":"https://doi.org/10.1186/s40793-026-00905-8","url":null,"abstract":"<p><strong>Background: </strong>The grapevine microbiome plays a central role in shaping vineyard performance, yet the influence of nursery inherited microbes on vineyard establishment and early productivity remains poorly understood. Our goals were to study the endosphere and rhizosphere microbiome succession as grapevine transition from nursery to vineyard and determine in what capacity the endogenous microbiome from the nursery shapes vineyard outcomes.</p><p><strong>Results: </strong>We profiled, using amplicon-based sequencing, the fungal and bacterial communities across five bio-compartments (scion graft union, rootstock graft union, crown, roots, and rhizosphere) from two sets of grafted vines (Cabernet Sauvignon and Chardonnay grafted on 1103P rootstock) originating from two nurseries and followed their succession over three years after planting in a commercial vineyard. Nurseries produced vines with distinct endospheric microbiomes that converged overtime but that remained significantly different after three years. Microbial turnover occurred at a much faster pace in belowground (root and rhizosphere) compared to trunk compartments post-planting, with 15% of the initial microbes persisting in three-year-old vineyard. The fungal pathobiome partially inherited from nurseries and associated with vascular diseases of the trunk and root was also clearly distinct after three years. Yet, we did not observe typical disease symptoms development or vine death as we would expect, likely because vines were not under stress during the experimental timeframe. Vineyard yield was highly variable among clonal vines, and statistical modeling revealed that a narrow subset of amplicon sequence variants (ASVs) explained a large portion of this variance. Regression models using the top ten high-impact ASVs accounted for 51% and 60% of yield variation in trunk and belowground compartments, respectively. Notably, 16 of the 19 yield-associated ASVs originated from nurseries, underscoring the long-term influence of nursery-derived microbes on vineyard success.</p><p><strong>Conclusion: </strong>These findings highlight the dual role of beneficial and pathogenic nursery microbiota in shaping grapevine performance. It also suggests that the nursery life stage could be leveraged to engineer the grapevine microbiome and improve vineyard resilience.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147844509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.","authors":"Yu Han, Jiaxin Cui, Xiantong Huang, Ping Guo, Shiqi Yang","doi":"10.1186/s40793-026-00898-4","DOIUrl":"https://doi.org/10.1186/s40793-026-00898-4","url":null,"abstract":"<p><strong>Background: </strong>Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.</p><p><strong>Results: </strong>Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.</p><p><strong>Conclusions: </strong>Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147844279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Legacy effects of cover cropping and crop phase on soybean health and associated rhizosphere microbiome in corn-soybean rotation.","authors":"Chuntao Yin, Shannon L Osborne, R Michael Lehman","doi":"10.1186/s40793-026-00899-3","DOIUrl":"https://doi.org/10.1186/s40793-026-00899-3","url":null,"abstract":"<p><strong>Background: </strong>Crop diversification through crop rotation or cover cropping is widely recognized as an important strategy to improve agroecosystem sustainability, enhance soil health, and suppress soilborne diseases. Rotating crops or introducing cover crops can disrupt pathogen life cycles, improve nutrient cycling, and promote beneficial microbes. However, the outcomes of diversification practices are often complex, influenced by soil type, crops, and pathogen pressures. Evaluating how cover crops and crop phase affect crop soilborne diseases and root-associated microbiome is critical for designing resilient cropping systems.</p><p><strong>Results: </strong>This study evaluated the legacy effects of cover crops and crop phase on soybean root diseases and root-associated microbiome. Soybean plants were grown in soils collected from a corn-soybean rotation field experiment with and without cover crops, and then challenged with either Fusarium graminearum inoculum or soybean cyst nematode (SCN) in the growth chamber. Soils with a cover crop history significantly reduced F. graminearum-induced root rot, but had a limited impact on SCN, indicating divergent disease responses. Microbial profiling revealed that F. graminearum inoculum strongly reshaped bacterial communities, reducing Shannon diversity and enriching fast-growing copiotrophic taxa, including Bacteroidota genera (Pedobacter, Chitinophaga, Flavobacterium, and Mucilaginibacter) and Proteobacteria genera (Dyella, Pseudomonas, Rhizobium, and Paraburkholderia) regardless of cover crops. In contrast, SCN infection increased bacterial Shannon diversity in soybean-phase soils regardless of cover crops but decreased fungal Shannon diversity in soybean soils without cover crops, highlighting pathogen-specific microbial shifts. Cover cropping enhanced microbial heterogeneity under both pathogen pressures, enriching microbial taxa potentially involved in nutrient cycling (Chitinophaga and Mucilaginibacter), antagonism (Flavobacterium, Streptomyces, Pseudonocardia, and Nocardioides), and competitive interactions (Paraburkholderia). Correlation analyses further linked specific bacterial and fungal genera with disease suppression.</p><p><strong>Conclusions: </strong>Soilborne pathogens and cropping practices exerted interconnected, pathogen- and crop-specific effects on root microbial communities. Cover cropping offers a promising strategy to enhance microbial-mediated disease resilience in soybean systems, providing ecological insights into microbiome-driven plant health.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147822337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.","authors":"Ana M Cabello, Soluna Salles, Guillermo Domínguez-Huerta, Eric Capo, M Teresa Camarena-Gómez, Candela García-Gómez, Antonio Sánchez, Jean-François Mangot, Isabel Cerezo, Rocío Bautista, Patricia Pérez, Rocío García, Juan M Ruiz, Jesús M Mercado, Isabel Ferrera","doi":"10.1186/s40793-026-00893-9","DOIUrl":"https://doi.org/10.1186/s40793-026-00893-9","url":null,"abstract":"<p><strong>Background: </strong>Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.</p><p><strong>Results: </strong>Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short‑term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine‑scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.</p><p><strong>Conclusions: </strong>The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non‑equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long‑term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial community succession along the entrance to distant zone in karst cave ecosystem: community assembly and distance decay patterns in weathered rock and sediment habitats.","authors":"Jiaming Du, Liyuan Ma, Xinping Huang, Xiaolu Lu, Hongmei Wang","doi":"10.1186/s40793-026-00900-z","DOIUrl":"https://doi.org/10.1186/s40793-026-00900-z","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities in karst caves represent highly specialized and distinct assemblages shaped by the unique physicochemical properties of cave environments. Although recent research has advanced our understanding of community composition, the underlying assembly mechanisms and spatial structuring processes, including distance decay relationships, remain insufficiently resolved. The aim of this research was to elucidate the community assembly mechanisms and distance decay patterns of microbial communities in weathered rock and sediment habitats.</p><p><strong>Results: </strong>We analyzed 16S rRNA gene sequencing data from 333 weathered rock and sediment samples collected across karst caves in the southwestern region of China, India, Italy, and Mexico. Distinct microbial communities were observed between weathered rock and sediment habitats, with sediment communities showing higher alpha diversity and more pronounced compositional shifts with increasing distance from the entrance. Both weathered rock and sediment communities showed distance-decay relationships, suggesting that geographic distance contributes to microbial community differentiation in caves. Moreover, stochastic processes, particularly dispersal limitation, play a dominant role in the assembly of microbial communities in both weathered rock and sediment. However, the influence of ecological drift is more prominent at local scales but declines at larger spatial scales. Sediment habitat and photic zone have higher connectivity, meaning the stable subgroups were formed to enhance ecological adaptability.</p><p><strong>Conclusion: </strong>This study revealed that microbial communities in karst caves are strongly shaped by habitat type, the distance from the cave entrance, and spatial scale. The observed distance-decay patterns indicate that geographic distance contributes to microbial community differentiation in caves, but its influence is weaker than that of local environmental and habitat-specific controls. Stochastic processes dominate community assembly, with dispersal limitation as the key mechanism. The findings provide new insights into the ecological mechanisms underlying microbial distribution in extreme subsurface environments and highlight the importance of integrating large-scale datasets for understanding microbial biogeography in karst systems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiple origins of the apple seed microbiome: disentangling sexual and asexual transmission pathways.","authors":"Maria Faticov, Ayco J M Tack, Doris Köberl, Gabriele Berg, Ahmed Abdelfattah","doi":"10.1186/s40793-026-00901-y","DOIUrl":"10.1186/s40793-026-00901-y","url":null,"abstract":"<p><strong>Background: </strong>The seed microbiome plays a key role in the assembly of the plant microbiome, which has major impacts on plant health. Nonetheless, little is known about the origin of the seed microbiome. We investigated the relative contributions of two potential transmission routes: sexual inheritance (via reproductive organs) and asexual inheritance (via the plant vascular system). To do that, we sampled flower ovaries and pollen sacs, fruiting spurs both before bloom and at seed maturity stages and mature seeds from five field-grown apple trees (Malus domestica BORKH. cv 'Gala Galaxy Selecta').</p><p><strong>Results: </strong>We showed that bacterial alpha diversity differed among tissues: spurs sampled before bloom had significantly higher richness and Shannon diversity than all other compartments, whereas ovary, pollen, spurs at seed maturity, and seeds did not differ in either richness or Shannon diversity. In addition, bacterial community composition differed significantly across all tissue types (ovary, pollen, spurs before bloom, spurs at seed maturity, and seeds). Source tracking revealed that both sexual (30.3%) and asexual (23.8%) pathways contributed to seed microbiome assembly, with spurs at seed maturity being the dominant source. Notably, a large proportion (45.9%) of the seed microbiome originated from unknown sources.</p><p><strong>Conclusions: </strong>Overall, such insights into seed microbiome origin offer new opportunities to enhance seed health and crop productivity through microbiome-assisted breeding.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"21 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13126790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147786007","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":"Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.","authors":"Martial Leroy, Valentine Cyriaque, Thomas Rattei, Isabelle Laurion, Jérôme Comte","doi":"10.1186/s40793-026-00892-w","DOIUrl":"https://doi.org/10.1186/s40793-026-00892-w","url":null,"abstract":"<p><p>Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147718614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.","authors":"Siyu Gu, Chuanqi Jiang, Peng Zhang, Shuai Luo, Yingchun Gong, Weisong Feng, Jie Xiong, Jing Zhang, Kai Chen, Kang Ning, Wei Miao","doi":"10.1186/s40793-026-00897-5","DOIUrl":"https://doi.org/10.1186/s40793-026-00897-5","url":null,"abstract":"<p><strong>Background: </strong>Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.</p><p><strong>Results: </strong>Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.</p><p><strong>Conclusions: </strong>Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147700473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}