Environmental Microbiome最新文献

{"title":"Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.","authors":"Anirban Basu, Danteswari Chalasani, P V S R N Sarma, Sheetal Uikey, Vijaya Ranganatha Chenna, Pushpajeet Lokpal Choudhari, Appa Rao Podile","doi":"10.1186/s40793-025-00707-4","DOIUrl":"https://doi.org/10.1186/s40793-025-00707-4","url":null,"abstract":"<p><strong>Background: </strong>Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.</p><p><strong>Results: </strong>Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.</p><p><strong>Conclusions: </strong>These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"41"},"PeriodicalIF":6.2,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12016423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022891","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 data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.","authors":"Julia M Kelliher, Mashael Aljumaah, Sarah R Bordenstein, J Rodney Brister, Patrick S G Chain, Jose Pablo Dundore-Arias, Joanne B Emerson, Vanessa Moreira C Fernandes, Roberto Flores, Antonio Gonzalez, Zoe A Hansen, Eneida L Hatcher, Scott A Jackson, Christina A Kellogg, Ramana Madupu, Cassandra Maria Luz Miller, Chloe Mirzayi, Ahmed M Moustafa, Christopher Mungall, Aaron Oliver, Nonia Pariente, Jennifer Pett-Ridge, Sydne Record, Linta Reji, Anna-Louise Reysenbach, Virginia I Rich, Lorna Richardson, Lynn M Schriml, Reed S Shabman, Maria A Sierra, Matthew B Sullivan, Punithavathi Sundaramurthy, Katherine M Thibault, Luke R Thompson, Scott Tighe, Ethell Vereen, Emiley A Eloe-Fadrosh","doi":"10.1186/s40793-025-00702-9","DOIUrl":"https://doi.org/10.1186/s40793-025-00702-9","url":null,"abstract":"<p><p>Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"40"},"PeriodicalIF":6.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12009515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143988635","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":"Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of \"Candidatus actinomarinales\".","authors":"Jing Huang, Xiaowei Zheng, Tao Yu, Mohsin Ali, Jutta Wiese, Songnian Hu, Li Huang, Ying Huang","doi":"10.1186/s40793-025-00701-w","DOIUrl":"https://doi.org/10.1186/s40793-025-00701-w","url":null,"abstract":"<p><p>Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with \"Candidatus Actinomarinales\" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"20 1","pages":"39"},"PeriodicalIF":6.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019708","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":"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}