Environmental Microbiome最新文献

{"title":"New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.","authors":"Duncan Sussfeld, Romain Lannes, Eduardo Corel, Guillaume Bernard, Pierre Martin, Eric Bapteste, Eric Pelletier, Philippe Lopez","doi":"10.1186/s40793-025-00697-3","DOIUrl":"10.1186/s40793-025-00697-3","url":null,"abstract":"<p><strong>Background: </strong>Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.</p><p><strong>Results: </strong>Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.</p><p><strong>Conclusions: </strong>These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"65"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12153180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276266","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":"Defining the cultured and uncultured bacterial fractions in Cannabis seeds.","authors":"Carolina Lobato, Ahmed Abdelfattah, Gabriele Berg, Tomislav Cernava","doi":"10.1186/s40793-025-00731-4","DOIUrl":"10.1186/s40793-025-00731-4","url":null,"abstract":"<p><strong>Background: </strong>Seeds provide a unique environment shaped by co-evolutionary processes, hosting diverse microbial communities. While microbiome studies have uncovered an extensive diversity of microorganisms, culture-based approaches remain crucial for understanding microbial potential and functional interactions. However, the factors influencing microbial culturability within seeds are not well understood.</p><p><strong>Results: </strong>In this study, we investigated the culturing patterns of bacteria inside Cannabis seeds, assessing their phylogenetic diversity, abundance, and putative interactions. Bacteria were cultured from 54 different Cannabis accessions using germinated seeds and a range of nutrient media including those supplemented with Cannabis extracts. The cultured fraction consisted of taxa from five prominent classes-Gammaproteobacteria, Bacilli, Actinobacteria, Alphaproteobacteria, and Bacteroidia-encompassing 36 genera. Despite representing only 6.3% of the total microbiota, these cultured bacteria accounted for 89.2% of the microbial population. Almost 60% of the amplicon sequence variants (ASVs) were phylogenetically distant from cultured taxa. Rare bacterial groups such as Acidobacteriae and Verrucomicrobiae, known for their plant growth-promoting traits, were exclusively found in the uncultured fraction. Network analyses revealed that uncultured taxa are centralized and more connected to hubs, suggesting that interspecies interactions strongly influence culturability.</p><p><strong>Conclusion: </strong>Our findings highlight the limitations of culture-based methods in capturing the full microbial diversity of Cannabis seeds and emphasize the importance of microbial interactions in determining culturability. The strong network connectivity of uncultured taxa suggests that interdependencies and competition within the seed microbiome may hinder the isolation of key bacterial groups. These insights provide a framework for refining cultivation strategies to recover ecologically significant microbes with potential agricultural applications.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"68"},"PeriodicalIF":6.2,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276254","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":"Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.","authors":"Monique E Smith, Vanessa N Kavamura, David Hughes, Rodrigo Mendes, George Lund, Ian Clark, Tim H Mauchline","doi":"10.1186/s40793-025-00723-4","DOIUrl":"10.1186/s40793-025-00723-4","url":null,"abstract":"<p><strong>Background: </strong>During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.</p><p><strong>Results: </strong>We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).</p><p><strong>Conclusions: </strong>Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"64"},"PeriodicalIF":6.2,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12145609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250396","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":"Severe drought impacts tree traits and associated soil microbial communities of clonal oaks.","authors":"Camilo Quiroga-González, Luis Daniel Prada-Salcedo, François Buscot, Mika Tarkka, Sylvie Herrmann, Marie-Lara Bouffaud, Kezia Goldmann","doi":"10.1186/s40793-025-00720-7","DOIUrl":"10.1186/s40793-025-00720-7","url":null,"abstract":"<p><strong>Background: </strong>Biotic and abiotic factors, including plant age, soil pH, soil organic matter concentration, and especially water availability, significantly influence soil microbial populations and plant characteristics. While many ecosystems are adapted to occasional droughts, climate change is increasing the frequency and severity of drought events, which negatively impacts plant productivity and survival. Long-lived, drought-sensitive tree species such as Quercus robur are particularly vulnerable to water shortages. Drought also alters soil microbial communities, reducing and reshaping microbial diversity, biomass, and activity, which can in turn disrupt key ecosystem functions. The objective of this study was to investigate the effects of natural drought conditions on soil physicochemical variables, plant traits and microbial communities of the oak clone DF159 in Central Germany. Our research focuses on two study sites, Bad Lauchstädt and Kreinitz, which differ in soil water retention capacity. Data collection spans two periods: before and after a severe drought in 2018. Oak traits and environmental data was collected from 2011 to 2023 covering two oak time series with trees planted annually between 2010 and 2019. Microbial communities were analyzed every second year between 2015 and 2021 around trees representing five different ages.</p><p><strong>Results: </strong>We found that plant traits, including apical growth, branch elongation and number of shoot flushes, were positively correlated with precipitation and relative humidity. Although the study sites differed in oak leaf number per shoot flush and number of shoot flushes, the 2018 drought negatively impacted all measured plant traits, regardless of sites. Soil bacterial richness and diversity declined at both study sites, independent of plant age, while fungal richness specifically increased in Bad Lauchstädt, which has a higher water-holding capacity, following the drought event. Bacterial community composition was more strongly affected by drought than fungal communities, whereas the latter was more responsive to plant age than bacterial communities.</p><p><strong>Conclusions: </strong>Given their strong functional links during drought, interactions among vegetation, microbial communities, and soil functioning may ultimately influence major ecosystem services. Bacterial communities were particularly sensitive to drought, while fungal communities exhibited greater resistance, suggesting their potential role in supporting plant survival under drought stress. These findings highlight the risk that prolonged drought may cause irreversible shifts in microbial communities, with significant implications for soil functions and plant-microbe interactions.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"63"},"PeriodicalIF":6.2,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250376","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":"Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.","authors":"Elizabeth R Denison, Helena L Pound, Eric R Gann, Naomi E Gilbert, David J Weston, Dale A Pelletier, Steven W Wilhelm","doi":"10.1186/s40793-025-00719-0","DOIUrl":"10.1186/s40793-025-00719-0","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"62"},"PeriodicalIF":6.2,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12142844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235586","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":"Mosses as extraordinary reservoir of microbial diversity: a comparative analysing of co-occurring 'plant-moss twins' in natural alpine ecosystem.","authors":"Dinesh Kumar Ramakrishnan, Birgit Wassermann, Christian Berg, Ahmed Abdelfattah, Gabriele Berg","doi":"10.1186/s40793-025-00728-z","DOIUrl":"10.1186/s40793-025-00728-z","url":null,"abstract":"<p><p>The decline in plant biodiversity is evident at global scale, but little is known about the loss of microbial diversity associated with diverse plant phyla and their influencing factors. This study investigates the microbial diversity associated with mosses and co-occurring vascular plants in the Alpine ecosystem, focusing on 52 plant \"twins\" growing on contrasting soil types (carbonate and silicate). Despite co-occurring in the same soil, mosses harbored significantly higher microbial richness and diversity than vascular plants. Across all samples, mosses supporting a total of 3,435 bacterial ASVs and 1,174 fungal ASVs. In contrast, vascular plants hosted a total of 1,760 bacterial ASVs and 911 fungal ASVs. Plant phyla strongly influenced microbial community composition, with vascular plants exhibiting a selective microbial assembly strategy, while mosses showed greater environmental influence. Soil type significantly influenced microbial composition in both plant types, with carbonate soils supporting greater bacterial richness, particularly in mosses. Linear discriminant analysis effect size (LEfSe) analysis highlighted consistent enrichments of Proteobacteria, i.e., Sphingomonadales, Rhizobiales, Burkholderiales and, Pseudomonadales, in vascular plants across soil types, whereas mosses displayed distinct microbial enrichment patterns between carbonate and silicate soils, suggesting a higher environmental connectedness. Our findings demonstrated that plant phyla are a major determinant of the phyllosphere microbiota, and that mosses represent a currently untapped source of microbial biodiversity. This study highlights the importance of considering both host traits and environmental factors for protecting microbial biodiversity and implementing them in global strategies for restoring biodiversity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"61"},"PeriodicalIF":6.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227220","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":"Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.","authors":"Ahmad Nuruddin Khoiri, Nídia Raquel Costa, Carlos Alexandre Costa Crusciol, Cristiano Magalhães Pariz, Ciniro Costa, Juliano Carlos Calonego, André Michel de Castilhos, Daniel Martins de Souza, Paulo Roberto de Lima Meirelles, Igor Vilela Cru, Luiz Gustavo Moretti, João William Bossolani, Eiko Eurya Kuramae","doi":"10.1186/s40793-025-00727-0","DOIUrl":"10.1186/s40793-025-00727-0","url":null,"abstract":"<p><strong>Background: </strong>Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.</p><p><strong>Results: </strong>The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.</p><p><strong>Conclusions: </strong>These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"60"},"PeriodicalIF":6.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12139364/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227221","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":"Metabarcoding insights into microbial drivers of flavor development and quality stability in traditional Chinese red pepper sauce: impacts of varietal selection and solar/shade fermentation.","authors":"Xuefeng Gong, Yi Xu, Sihao Hou, Hong Li, Xin Chen, Zhanfeng Song","doi":"10.1186/s40793-025-00717-2","DOIUrl":"10.1186/s40793-025-00717-2","url":null,"abstract":"<p><strong>Background: </strong>Red pepper sauce is a traditional Chinese condiment, which is rich in nutrients and popular worldwide. However, the changes in the microbial community of red pepper sauce during fermentation and the effects of such changes on quality stability have been under studied. In this study, we systematically analyzed the relationship between the microbial community composition of multiple red pepper sauces and the biochemical indexes. Moreover, we also explored the dynamics of changes in the microbial community composition using metabarcoding sequencing.</p><p><strong>Results: </strong>Our analysis revealed significant differences in amino acids (AA), lactate, pectin, reducing sugar, flavonoids, phenolics, pigments, and alcohol dehydrogenase (ADH) activity among the six red pepper sauces. Moreover, the relative abundance of bacteria and fungi showed significant differences among multiple red pepper sauces. Among these biochemical indexes, water content, pigment, and capsaicin showed a significant negative correlation with the abundance of multiple bacterial genera. ADH activity showed a significant positive correlation with the abundance of multiple bacterial genera. The content of AA, flavonoid, pectin, and gamma-aminobutyric acid (GABA) was significantly correlated with the relative abundance of multiple fungi such as Rhodotorula, Dipodascus, Leucosporidium, Hannaella, and Coniochaeta.</p><p><strong>Conclusions: </strong>These results provide a basis for revealing the biological basis of the quality stability and flavor characteristics of red pepper sauce, which are of great significance for further investigation of the fermentation mechanism and control of the product quality of red pepper sauce.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"59"},"PeriodicalIF":6.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188258","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":"Impact of fluoroquinolone and heavy metal pollution on antibiotic resistance maintenance in aquatic ecosystems.","authors":"Emilie Dehon, Stanislava Vrchovecká, Alban Mathieu, Sabine Favre-Bonté, Stanisław Wacławek, Arnaud Droit, Timothy M Vogel, Concepcion Sanchez-Cid","doi":"10.1186/s40793-025-00722-5","DOIUrl":"10.1186/s40793-025-00722-5","url":null,"abstract":"<p><strong>Background: </strong>Freshwater pollution with compounds used during anthropogenic activities could be a major driver of antibiotic resistance emergence and dissemination in environmental settings. Fluoroquinolones and heavy metals are two widely used aquatic pollutants that show a high stability in the environment and have well-known effects on antibiotic resistance selection. However, the impact of these compounds on antibiotic resistance maintenance in aquatic ecosystems remains unknown. In this study, we used a microcosm approach to determine the persistence of two fluoroquinolones (ciprofloxacin, ofloxacin) and two heavy metals (copper and zinc) in the Rhône river over 27 days. In addition, we established links between antibiotic and metal pollution, alone and in combination, and the composition of freshwater bacterial communities, the selection of specific members and the selection and maintenance of antibiotic and metal resistance genes (ARGs and MRGs) using a metagenomics approach.</p><p><strong>Results: </strong>Whereas ofloxacin was detected at higher levels in freshwater after 27 days, copper had the strongest influence on bacterial communities and antibiotic and metal resistance gene selection. In addition, heavy metal exposure selected for some ARG-harboring bacteria that contained MRGs. Our research shows a heavy metal-driven transient co-selection for fluoroquinolone resistance in an aquatic ecosystem that could be largely explained by the short-term selection of Pseudomonas subpopulations harboring both fluoroquinolone efflux pumps and copper resistance genes.</p><p><strong>Conclusion: </strong>This research highlights the complexity and compound-specificity of dose-response relationships in freshwater ecosystems and provides new insights into the medium-term community structure modifications induced by overall sub-inhibitory levels of antibiotic and heavy metal pollution that may lead to the selection and maintenance of antibiotic resistance in low-impacted ecosystems exposed to multiple pollutants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"58"},"PeriodicalIF":6.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162931","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":"Effect of applying oyster shell powder on soil properties and microbial diversity in the acidified soils of pomelo garden.","authors":"Yuanyuan Li, Qiong Zhang, Lixia Zhu, Jing Yang, Jingjing Wei, Yunhe Li, Xiaohuang Chen","doi":"10.1186/s40793-025-00721-6","DOIUrl":"10.1186/s40793-025-00721-6","url":null,"abstract":"<p><p>The application of oyster shell has recently been used to increase soil pH in Southern China. However, little is known about causal shifts in the rhizosphere microbial community of pomelo trees, especially in orchards that have experienced natural accumulation of heavy metals over many years due to continuous fertilization and soil acidification. This study evaluated the effects of oyster shell powder applied for 1 year (T1), 2 years (T2) and 3 years (T3), alongside a control group with no soil amendments (Control; CK), on soil acidification and microbial diversity. Our findings demonstrated that the application of oyster shell significantly increased soil pH and reduced the concentrations of heavy metals such as thallium (Tl), chromium (Cr), and manganese (Mn). Illumina sequencing-based community analysis revealed that oyster shell application significantly increased the alpha diversity indices of both bacterial and fungal communities and influenced their distribution in the soil. Notably, all oyster shell-treated groups (T1-T3) showed significantly higher relative abundances of beneficial microbes (e.g., Nitrolancea, Vicinamibacterales) and those involved in carbohydrate degradation and nitrogen fixation compared to the control. Conversely, the relative abundances of Acidibacter and Chujaibacter (associated with heavy metal degradation and soil-borne diseases), Trichoderma and Acremonium (plant-beneficial fungi), as well as functionally annotated groups linked to nitrogen assimilation and pathotrophic modes (predicted via FUNGuild analysis), decreased significantly. Our results suggest that the application of oyster shell powder amendments contributes to improved soil properties and microbial environments; however, the effects on soil nitrogen cycling and fungal function are complex, warranting further research.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"57"},"PeriodicalIF":6.2,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144144094","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}