Environmental Microbiome最新文献

{"title":"Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.","authors":"Jiahua Zhou, Haojin Cheng, Yulin Zhang, Tianhang Liu, Xing Chen, David J Lea-Smith, Jonathan D Todd, Jiwen Liu, Xinxin He, Ronghua Liu, Xiao-Hua Zhang","doi":"10.1186/s40793-026-00908-5","DOIUrl":"10.1186/s40793-026-00908-5","url":null,"abstract":"<p><strong>Background: </strong>Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.</p><p><strong>Results: </strong>To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH₄⁺ and SiO₃^2-) based on Pearson's correlation analysis.</p><p><strong>Conclusion: </strong>This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13335318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876050","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":"Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.","authors":"Anish Tamang, Anil Kumar, Ankita Thakur, Rakshak Kumar, Dinesh Kumar, Vipin Hallan, Shiv Shanker Pandey","doi":"10.1186/s40793-026-00909-4","DOIUrl":"10.1186/s40793-026-00909-4","url":null,"abstract":"<p><strong>Background: </strong>Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.</p><p><strong>Methods: </strong>Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.</p><p><strong>Results: </strong>Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.</p><p><strong>Conclusions: </strong>These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13330369/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876046","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":"Insights into the role of crustose coralline algae microbiomes on coral larval settlement in the Great Barrier Reef.","authors":"Abigail C Turnlund, Paul A O'Brien, Laura Rix, Sophie Ferguson, Nicole S Webster, Guillermo Diaz-Pulido, Muhammad Abdul Wahab, Miguel Lurgi, Inka Vanwonterghem","doi":"10.1186/s40793-026-00907-6","DOIUrl":"10.1186/s40793-026-00907-6","url":null,"abstract":"<p><strong>Background: </strong>Crustose coralline algae (CCA) enhance coral recruitment, but the response of coral larval settlement to CCA varies between CCA species. Furthermore, it is unclear whether coral larvae respond to settlement cues from the algal host itself or its associated microorganisms. To determine whether CCA-derived settlement cues have a microbial origin, we interrogated the microbiome of 14 coralline algal species and a calcareous non-coralline alga eliciting varying levels of settlement across 14 coral species from a wide diversity of families found in the Great Barrier Reef.</p><p><strong>Results: </strong>Linear regression, differential abundance, indicator species, and random forest analyses were used to identify microbial taxa associated with high or low coral settlement. We found that the relative abundance of specific microbial amplicon sequence variants (ASVs) correlated with settlement and that these responses were largely coral species-specific. A select few microbial taxa associated with high or low settlement were shared across the corals Dipsastrea favus, Echinophyllia aspera, Lobophyllia corymbosa, Mycedium elephantotus, and Platygrya sinensis, suggesting potential shared settlement or inhibition cues. While shared ASVs associated with high coral settlement were found across multiple CCA species, low settlement ASVs were confined to few low settlement CCA species. Candidatus Nitrosopumilus and Filomicrobium microbes were found as potential shared microbial inducers, and members of Pirellulaceae and Flavobacteriaceae were identified as potential settlement inhibitors.</p><p><strong>Conclusions: </strong>These findings contribute to our growing knowledge of potential coral larval settlement cues and provide deeper insights into the link between the CCA microbiomes and coral recruitment.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13162459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864729","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 legacy influences necrosis formation in Diplodia sapinea-infected Scots pine shoots.","authors":"Dániel G Knapp, Alexandra Nagy, Elham Badalzadehe, Anna Molnár, Johan Kroon, Carmen Romeralo, Julio Javier Diez, Johanna Witzell","doi":"10.1186/s40793-026-00904-9","DOIUrl":"10.1186/s40793-026-00904-9","url":null,"abstract":"<p><strong>Background: </strong>Fungal endophytes are important members of the holobiont of all plants, including that of Scots pine (Pinus sylvestris), potentially affecting host performance. One of the most important pathogens of Scots pine in Europe is Diplodia sapinea, which causes necrotic lesions and is becoming increasingly prevalent in northern regions. Although endophytes are known to affect plant performance, it remains unclear whether naturally established fungal communities in Scots pine shoots can modulate D. sapinea-induced necrosis. Using a field experiment, we tested the hypothesis that exclusion of airborne fungal inoculum shapes the endophytic community in shoots of pine seedlings, and that such alterations in this community influence the necrosis-inducing capacity of D. sapinea.</p><p><strong>Results: </strong>In the field site, airborne fungal inoculum was reduced in half of the saplings by covering shoots with mesh bags. Covered (bagged) and free (unbagged) shoots were transported to the laboratory and inoculated with D. sapinea. The morphology and physiological status of the shoots were monitored using a multispectral 3D scanner, and the necrotic lesion development was assessed. The propagule exclusion resulted in endophytic communities with slightly lower richness, while shoots showed no detectable morphological or physiological differences prior to inoculation. Shoots inoculated with D. sapinea developed clear necrotic lesions, which were significantly larger in covered shoots than in the free ones. Long-read Oxford Nanopore metabarcoding revealed that community shifts following inoculation were more pronounced in covered shoots. Community composition clearly separated necrotic and healthy tissues.</p><p><strong>Conclusions: </strong>Our findings suggest that the structure of the resident fungal endophytic community may influence the extent of necrotic lesions caused by D. sapinea in Scots pine shoots. A more established, diverse fungal community was associated with smaller lesion sizes, whereas shoots exposed to lower propagule pressure developed larger lesions following inoculation. These results highlight the functional role of fungal community assembly in shaping disease outcomes and suggest that endophyte-based approaches may provide new opportunities for improving disease resistance in forest tree species. The results also suggest that endophytic status may need to be considered when lesion size is used to evaluate resistance to pathogens in tree breeding programs.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2026-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13162409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147864688","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":"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":"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":6.2,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13330178/pdf/","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":"OA","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":"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":6.2,"publicationDate":"2026-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13321508/pdf/","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":"OA","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":"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":6.2,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13312510/pdf/","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":"OA","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":"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":6.2,"publicationDate":"2026-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13317363/pdf/","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":"OA","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":"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":6.2,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13285196/pdf/","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":"OA","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":"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":6.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13366656/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}