Environmental Microbiome最新文献

{"title":"Seasonal dynamics and factors shaping microbiomes in freshwater finfish earthen aquaculture ponds in Bangladesh.","authors":"Sanjit C Debnath, Dominique L Chaput, Jamie McMurtrie, Ashley G Bell, Ben Temperton, Chadag V Mohan, Md M Alam, Neaz A Hasan, Mohammad M Haque, David Bass, Charles R Tyler","doi":"10.1186/s40793-025-00687-5","DOIUrl":"10.1186/s40793-025-00687-5","url":null,"abstract":"<p><strong>Background: </strong>The pondwater microbiome is believed to play a key role in fish health, including shaping mucosal surface microbiomes that help to protect against disease. How different physiochemical features relating to season, geographical locations, as well as crop species shape the pond water microbiome in the finfish aquaculture system, is not well established. Pangasius (Pangasianodon hypophthalmus) and tilapia (Oreochromis niloticus) are two of the most widely farmed fish species and disease is a major impediment to the expansion of their production. We applied 16S and 18S rRNA metabarcoding to assess how pond physicochemistry and geographical location shape water microbiomes in pangasius and tilapia aquaculture earthen ponds in Bangladesh.</p><p><strong>Results: </strong>Planctomycetota, Pseudomonadota and Actinomycetota were the dominant bacterial phyla while Stramenopiles and Alveolata were the dominant microeukaryotes (divisions) in the pangasius and tilapia ponds water. The relative abundance of Planctomycetota was higher in the pangasius ponds compared with tilapia ponds, and Actinomycetota, and Pseudomonadota were relatively higher in tilapia ponds. Tilapia pond water also exhibited a higher microbial diversity compared to that in pangasius ponds. The pondwater microbial diversity was at its lowest in winter (and/or in monsoon) and highest in the pre-monsoon period. The microbial community structures differed across the different seasons, geographical locations, culture systems, and crop species, with season and geographical locations showing the strongest effects. Of the water physicochemistry features assessed, temperature and pH were found to have a weak but significant effect on the water microbiome content for both pangasius and tilapia ponds. Pangasius and tilapia ponds shared over 46% of ASVs, and around 30% of ASVs were shared across the different study geographical locations.</p><p><strong>Conclusion: </strong>Our findings demonstrate that microbial communities in pangasius and tilapia aquaculture systems in Bangladesh are shaped by season, geographical location, crop species, as well as effects from water physicochemistry. Our results provide insights into the dynamic nature and environmental influences on water microbiomes that may be applied for use in pond management for improving aquaculture productivity and enhancement of overall fish health.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"38"},"PeriodicalIF":6.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755259","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":"Revealing microbial consortia that interfere with grapevine downy mildew through microbiome epidemiology.","authors":"Paola Fournier, Lucile Pellan, Aarti Jaswa, Marine C Cambon, Alexandre Chataigner, Olivier Bonnard, Marc Raynal, Christian Debord, Charlotte Poeydebat, Simon Labarthe, François Delmotte, Patrice This, Corinne Vacher","doi":"10.1186/s40793-025-00691-9","DOIUrl":"10.1186/s40793-025-00691-9","url":null,"abstract":"<p><strong>Background: </strong>Plant and soil microbiomes can interfere with pathogen life cycles, but their influence on disease epidemiology remains understudied. Here, we analyzed the relationships between plant and soil microbiomes and long-term epidemiological records of grapevine downy mildew, a major disease caused by the oomycete Plasmopara viticola.</p><p><strong>Results: </strong>We found that certain microbial taxa were consistently more abundant in plots with lower disease incidence and severity and that the microbial community composition could predict disease incidence and severity. Microbial diversity was not strongly linked to epidemiological records, suggesting that disease incidence and severity is more related to the abundance of specific microbial taxa. These key taxa were identified in the topsoil, where the pathogen's oospores overwinter, and in the phyllosphere, where zoospores infect leaves. By contrast, the leaf endosphere, where the pathogen's mycelium develops, contained few taxa of interest. Surprisingly, the soil microbiota was a better predictor of disease incidence and severity than the leaf microbiota, suggesting that the soil microbiome could be a key indicator of the dynamics of this primarily aerial disease.</p><p><strong>Conclusion: </strong>Our study integrates long-term epidemiological data with microbiome profiles of healthy plants to reveal fungi and bacteria relevant for the biocontrol of grapevine downy mildew. The resulting database provides a valuable resource for designing microbial consortia with potential biocontrol activity. The framework can be applied to other crop systems to guide the development of biocontrol strategies and reduce pesticide use in agriculture.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"37"},"PeriodicalIF":6.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732519","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":"Opposite effects of N on warming-induced changes in bacterial and fungal diversity.","authors":"Jianjun Xu, Hao Liu, Xiaoni Xu, Xiang Liu, Shurong Zhou, Ming Nie","doi":"10.1186/s40793-025-00693-7","DOIUrl":"10.1186/s40793-025-00693-7","url":null,"abstract":"<p><p>The diversity of bacteria and fungi is linked to distinct ecosystem functions, and divergent responses to global changes in these two kingdoms affect the relative contributions of the kingdoms to the soil carbon and nutrient cycles. Climate warming and nitrogen (N) enrichment, which are projected to increase concurrently through modelling efforts, are considered the main drivers of biodiversity loss. However, it is unclear how bacterial and fungal diversity respond differently to the simultaneous occurrence of climate warming and nitrogen enrichment, and the underlying mechanisms involved remain unknown. Using a 9-yr warming and N enrichment experiment in an alpine permafrost area of the Tibetan Plateau, we demonstrated the contrasting response of bacterial and fungal diversity to combined warming and N enrichment, showing a reduction in bacterial richness (8.8%) and an increase in fungal diversity (33.6%). Furthermore, the negative effects of warming on fungal richness were reversed by N enrichment, and the negative effects of nitrogen enrichment on bacteria were amplified by warming. Our results also demonstrated that both biotic interactions, such as bacterial-fungal antagonism, and abiotic factors, primarily the soil C/N ratio and pH, play crucial roles in shaping microbial biodiversity. Our findings suggest that fungal diversity is expected to greatly increase in a warmer and more nitrogen-enriched world, potentially leading to the enhancement of ecosystem functions driven by fungi.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"35"},"PeriodicalIF":6.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The invisible architects: microbial communities and their transformative role in soil health and global climate changes.","authors":"Sajid Iqbal, Farida Begum, Benedictor Alexander Nguchu, Uzabakiriho Pierre Claver, Peter Shaw","doi":"10.1186/s40793-025-00694-6","DOIUrl":"10.1186/s40793-025-00694-6","url":null,"abstract":"<p><p>During the last decades, substantial advancements have been made in identifying soil characteristics that impact the composition of the soil microbiome. However, the impacts of microorganisms on their respective soil habitats have received less attention, with the majority of prior research focusing on the contributions of microbes to the dynamics of soil carbon and nitrogen. Soil microbiome plays a critical role in soil habitats by influencing soil fertility, crop yields, and biotic and abiotic stress tolerance. In addition to their roles in nutrient cycling and organic matter transformations, soil microorganisms affect the soil environment via many biochemical and biophysical mechanisms. For instance, the soil microbiome plays an essential role in soil mechanical stability and pore connectivity and regulates the flow of nutrients, oxygen, and water. Similarly, soil microbiomes perform various critical functions in an ecosystem, which leads to carbon stabilization for a long time and could serve as microbiome engineering targets for global climate change mitigation. In this review, considering soil structure, hydrology, and chemistry, we outline how microorganisms alter the soil ecosystem. Further, this study investigates the mechanisms by which feedback loops can be generated between microorganisms and soil. Moreover, we analyze the potential of microbially mediated modifications of soil properties as a viable strategy to address soil threats and global climate challenges. In addition, the current study propose a deep learning-based approach to develop a synthetic microbial consortium to improve soil health and mitigate climate change.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"36"},"PeriodicalIF":6.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711654","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":"Fungi promote cross-domain interactions even in deep anoxic mangrove sediments.","authors":"Ming Sheng Ng, Nathaniel Soon, Min Yi Chin, Sze Koy Ho, Lynn Drescher, Mohamad Azlin Bin Sani, Kiah Eng Lim, Benjamin J Wainwright, Ying Chang","doi":"10.1186/s40793-025-00686-6","DOIUrl":"10.1186/s40793-025-00686-6","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities in mangrove sediments play vital ecological roles that underpin the functioning of the overall mangrove ecosystem. Fungal communities, in particular, are known to play crucial roles across sediment systems, yet their roles in mangrove sediments, especially in deeper layers, remain poorly understood without a comprehensive inter-domain characterization. To better understand fungal roles in sediment horizons, 10 sediment cores extending down to a depth of 1 m were taken in three mangrove sites to characterise the archaeal, bacterial, and fungal communities at 10 cm depth intervals.</p><p><strong>Results: </strong>We demonstrate that sediment depth has distinct effects on the three microbial communities. While fungal community compositions were similar across sediment depths, bacterial and archaeal community compositions were stratified into three distinct layers, surface (10-30 cm), subsurface (40-60 cm), and deep (70-100 cm). Co-occurrence networks were then constructed to investigate the roles of fungi in these sediment layers, where fungi were consistently identified as keystone taxa in maintaining the microbial network topology, with co-domain interactions constituting more than half of all interactions. Even in the deepest layer, fungal nodes still retained high betweenness centralities, acting as network hubs to potentially augment microbial interactions vital for the functioning of the overall ecosystem.</p><p><strong>Conclusions: </strong>Overall, our results emphasise the important role of fungi in mediating microbial interactions across sediment depths even in deep, anoxic sediment layers, and highlight the importance of cross-domain interactions as integral to a more holistic understanding of the mangrove microbiome.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"34"},"PeriodicalIF":6.2,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11934577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711652","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":"Retraction Note: High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov.","authors":"Cheikh Ibrahima Lo, Senthil Alias Sankar, Bécaye Fall, Bissoume Sambe-Ba, Silman Diawara, Mamadou Wague Gueye, Oleg Mediannikov, Caroline Blanc-Tailleur, Boubacar Wade, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar","doi":"10.1186/s40793-025-00692-8","DOIUrl":"10.1186/s40793-025-00692-8","url":null,"abstract":"","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"33"},"PeriodicalIF":6.2,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677339","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 composition on microplastics mediated by stream impairment.","authors":"Anne L Gilewski, Saurav Shrestha, Sharon N Kahara, Nikolas M Stasulli","doi":"10.1186/s40793-025-00685-7","DOIUrl":"10.1186/s40793-025-00685-7","url":null,"abstract":"<p><strong>Background: </strong>Studies into biofilm interactions with microplastic polymers in marine environments are widespread in the literature. Increasing evidence suggests that lotic microplastics are a significant contributor and may accumulate harmful or pathogenic organisms, thereby contributing to the degradation of marine ecosystems where they meet riverine systems. Suboptimal water quality of these riverine systems may influence these biomes. This project compared the microbial diversity of biofilms that developed on microplastics to natural stone substrates in an impaired and unimpaired section of the Quinnipiac River Watershed. In this project, the influence of impairment was studied based on microbial diversity via 16S rRNA gene sequencing while monitoring total colony and fecal coliform colony counts using standard water sampling methods.</p><p><strong>Results: </strong>Total coliform colony counts were greater in the impaired Quinnipiac River site than in the unimpaired Honeypot Brook tributary and on the microplastic substrate than the stone substrate. Sequenced features to the class level were dominated by Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, comprising 75% of the community biome. Simpson's Diversity indices indicated that within the two substrates, there was little variation between the communities. However, it was noted that microplastic alpha diversity trended slightly lower than the stone. Further analysis of common aquatic enteropathogens showed that the genus Citrobacter was significantly more abundant on the microplastics at both locations.</p><p><strong>Conclusions: </strong>Our results indicate impaired waterbodies with a microplastic burden may retain greater fecal coliform bacterial loads than unimpaired waterbodies. Increased microplastic loads in compromised lotic systems may have an additive impact. Water quality remediation and careful monitoring are recommended to reduce this effect. Comparing this study with environmental community analysis could provide valuable insight into preferential surface attachment of bacteria onto microplastic.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"32"},"PeriodicalIF":6.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916983/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651467","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 transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.","authors":"Victoria Rodríguez, Alexander Bartholomäus, Susanne Liebner, Romulo Oses, Thomas Scholten, Dirk Wagner","doi":"10.1186/s40793-025-00689-3","DOIUrl":"10.1186/s40793-025-00689-3","url":null,"abstract":"<p><strong>Background: </strong>In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches.</p><p><strong>Results: </strong>We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites.</p><p><strong>Conclusions: </strong>Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"31"},"PeriodicalIF":6.2,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11917034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651481","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":"Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.","authors":"Morgane Duret, Adrian Wallner, Ludovic Besaury, Aziz Aziz","doi":"10.1186/s40793-025-00690-w","DOIUrl":"10.1186/s40793-025-00690-w","url":null,"abstract":"<p><strong>Background: </strong>Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.</p><p><strong>Results: </strong>Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.</p><p><strong>Conclusions: </strong>This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"30"},"PeriodicalIF":6.2,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634741","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":"Ironing out the conflicts: iron supplementation reduces negatives bacterial interactions in the rhizosphere of an Atacama-endemic perennial grass.","authors":"Constanza Aguado-Norese, Jonathan E Maldonado, Christian Hodar, Gabriel Galvez, Daniel E Palma, Verónica Cambiazo, Mauricio Gonzalez","doi":"10.1186/s40793-024-00661-7","DOIUrl":"10.1186/s40793-024-00661-7","url":null,"abstract":"<p><strong>Background: </strong>In plants, root exudates selectively influence the growth of bacteria that colonize the rhizosphere. Bacterial communities associated with root systems are involved in macro and micronutrients cycling and organic matter transformation. In particular, iron is an essential micronutrient required for the proper functioning of iron-containing enzymes in processes such as photosynthesis, respiration, biomolecule synthesis, redox homeostasis, and cell growth in plants. However, the impact of changes of iron availability on the structure and set of ecological interactions taking place in the rhizosphere remains poorly understood. In this study, field experiments were conducted to compare the effects of iron supplementation (0.1 and 0.5 mM of FeSO₄) on the assembly of the bacterial community of rhizosphere soil and bulk soil in a perennial grass present in the Andes steppe of Atacama Desert.</p><p><strong>Results: </strong>The results indicated that the difference in beta diversity between bulk soil and rhizosphere soil detected before supplementation did not persist after iron supplementation, in addition, co-occurrence networks showed a significant reduction in negative interactions among soil bacteria, mainly in rare taxa (< 0.1% relative abundance).</p><p><strong>Conclusions: </strong>These observations suggest that iron availability contributes to the differentiation between bulk soil and rhizosphere bacterial communities, a process that is linked to significant changes in the relative abundance of more abundant species (> 0.1% relative abundance) and with a decrease in the negative interactions in both compartments after metal exposure. The differential effect of iron on the competition/cooperation ratio between bulk soils and the rhizosphere microbiome supports the hypothesis that the host limits the degree of cooperation that can be achieved by the bacterial community associated with an organ dedicated to nutrient absorption.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"29"},"PeriodicalIF":6.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606694","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}