A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats

A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats Ashvini Chauhan, Christian Chukwujindu, Ashish Pathak, Rajneesh Jaswal This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6414247/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 25 Nov, 2025 Read the published version in Scientific Reports → Version 1 posted 12 You are reading this latest preprint version Abstract This study investigated the bacterial and fungal communities, along with their functional gene profiles, in two long-term heavy metal-contaminated sites in the United States: the Savannah River Site (SRS) and the Oak Ridge Reservation (ORR). Soil samples were categorized based on total mercury (THg), methyl mercury (MeHg), and bioavailable mercury (BioaHg) into high, medium, and low contamination levels. Using qPCR, amplicon sequencing, and shotgun metagenomics, we examined the long-term impacts of mercury contamination on microbial taxonomic composition and gene functions. Taxonomic analysis revealed the dominance of bacterial genera Bradyrhizobium , Geobacter , and Burkholderia , previously identified in our studies at the SRS and ORR sites. Among fungi, Fusarium , Pseudogymnoascus , and Aspergillus were the most abundant. Bacterial alpha diversity declined with increasing contamination, whereas fungal alpha diversity remained stable, with the highest diversity observed at the low-contamination site. Canonical correspondence analysis (CCA) linked Burkholderia and Pseudomonas with THg and MeHg, while Pedosphaera and Candidatus Solibacter were associated with BioaHg. Fungal phyla Ascomycota and Basidiomycota correlated with THg and MeHg, whereas Blastocladiomycota was associated with BioaHg. Functional analysis via shotgun metagenomics and PICRUSt2 identified an enrichment of stress response genes, membrane transporters, and metabolic pathways essential for microbial survival in contaminated environments. Genes encoding carbohydrate metabolism, amino acid processing, and protein metabolism were consistently dominant across contamination levels and sampling seasons. These findings highlight the adaptive strategies of soil microbiomes in mercury-contaminated environments, emphasizing their potential role in bioremediation and ecosystem restoration, thus paving the way for improved environmental management and remediation strategies of former nuclear legacy contaminated ecosystems. Biological sciences/Ecology Biological sciences/Ecology/Microbial ecology Earth and environmental sciences/Environmental sciences/Environmental impact Metagenomics Mercury Savannah River Site Oak Ridge Reservation Full Text Additional Declarations No competing interests reported. Table 1 is available in the Supplementary Files section. Supplementary Files Table1.docx Cite Share Download PDF Status: Published Journal Publication published 25 Nov, 2025 Read the published version in Scientific Reports → Version 1 posted Editorial decision: Revision requested 16 Sep, 2025 Reviews received at journal 29 Jul, 2025 Reviewers agreed at journal 10 Jul, 2025 Reviewers agreed at journal 30 Jun, 2025 Reviews received at journal 27 Jun, 2025 Reviewers agreed at journal 26 Jun, 2025 Reviews received at journal 24 Jun, 2025 Reviewers agreed at journal 23 Jun, 2025 Reviewers invited by journal 23 Jun, 2025 Editor assigned by journal 28 Apr, 2025 Submission checks completed at journal 25 Apr, 2025 First submitted to journal 25 Apr, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6414247","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":475606827,"identity":"e43ded13-a116-4f2e-850b-13d63f5a037a","order_by":0,"name":"Ashvini Chauhan","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA/klEQVRIiWNgGAWjYFACHgaGBAYJBhBiBnLl2BvAwszEazHmOUCMFjCAaknsIaSFv//sMYmHOywY+Gc3P5MuqLmT3sN+Ok2CocI6sQGHFokbeWkSiWckGCTuHDOTnnHsWW4PT+42CYYz6Ti1MNzgMTZIbJNgMJBIMJPmYTucu58BqIWx7TBOLfLnz8C0pH+T5vl3OJ2H/y1Qyz/cWgwO5Bg+gGjJMZPmbTucwCMBsqUBtxbDGxAtPBI3coqtefsOG/ZIvN1skXAs3RiXFrnzZwwO/myrk+Ofkb7xNs+3w/I8/Lkbb3yosZbF6X0o4EHlJhBQPgpGwSgYBaMAPwAA1E1ULwgUHyMAAAAASUVORK5CYII=","orcid":"","institution":"Florida A\u0026M University","correspondingAuthor":true,"prefix":"","firstName":"Ashvini","middleName":"","lastName":"Chauhan","suffix":""},{"id":475606828,"identity":"c7c6f6ab-70d2-4864-bc66-4298232cfb5a","order_by":1,"name":"Christian Chukwujindu","email":"","orcid":"","institution":"Florida A\u0026M University","correspondingAuthor":false,"prefix":"","firstName":"Christian","middleName":"","lastName":"Chukwujindu","suffix":""},{"id":475606829,"identity":"add741c9-32db-4070-b4bf-a57851c4aadb","order_by":2,"name":"Ashish Pathak","email":"","orcid":"","institution":"Florida A\u0026M University","correspondingAuthor":false,"prefix":"","firstName":"Ashish","middleName":"","lastName":"Pathak","suffix":""},{"id":475606830,"identity":"45088edf-7f01-4178-a59f-25c487754c89","order_by":3,"name":"Rajneesh Jaswal","email":"","orcid":"","institution":"Florida A\u0026M University","correspondingAuthor":false,"prefix":"","firstName":"Rajneesh","middleName":"","lastName":"Jaswal","suffix":""}],"badges":[],"createdAt":"2025-04-09 18:23:13","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6414247/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6414247/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41598-025-25944-y","type":"published","date":"2025-11-25T15:58:19+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":97179378,"identity":"20fcc454-2898-4832-89c1-8ed3df620868","added_by":"auto","created_at":"2025-12-01 16:15:14","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1570231,"visible":true,"origin":"","legend":"","description":"","filename":"RevisedandeditedHgManuscriptmain.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6414247/v1_covered_7c8c2337-6f2f-47a1-a12f-89d5f34d50d6.pdf"},{"id":85431440,"identity":"2ddf7d07-936c-4c70-8a56-364edb607e7a","added_by":"auto","created_at":"2025-06-25 18:29:32","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":15503,"visible":true,"origin":"","legend":"","description":"","filename":"Table1.docx","url":"https://assets-eu.researchsquare.com/files/rs-6414247/v1/daf23b98be56dea151a765c7.docx"}],"financialInterests":"\u003cp\u003eNo competing interests reported.\u003c/p\u003e\n\u003cp\u003eTable 1 is available in the Supplementary Files section.\u003c/p\u003e","formattedTitle":"A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats ","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Metagenomics, Mercury, Savannah River Site, Oak Ridge Reservation","lastPublishedDoi":"10.21203/rs.3.rs-6414247/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6414247/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThis study investigated the bacterial and fungal communities, along with their functional gene profiles, in two long-term heavy metal-contaminated sites in the United States: the Savannah River Site (SRS) and the Oak Ridge Reservation (ORR). Soil samples were categorized based on total mercury (THg), methyl mercury (MeHg), and bioavailable mercury (BioaHg) into high, medium, and low contamination levels. Using qPCR, amplicon sequencing, and shotgun metagenomics, we examined the long-term impacts of mercury contamination on microbial taxonomic composition and gene functions. Taxonomic analysis revealed the dominance of bacterial genera \u003cem\u003eBradyrhizobium\u003c/em\u003e, \u003cem\u003eGeobacter\u003c/em\u003e, and \u003cem\u003eBurkholderia\u003c/em\u003e, previously identified in our studies at the SRS and ORR sites. Among fungi, \u003cem\u003eFusarium\u003c/em\u003e, \u003cem\u003ePseudogymnoascus\u003c/em\u003e, and \u003cem\u003eAspergillus\u003c/em\u003e were the most abundant. Bacterial alpha diversity declined with increasing contamination, whereas fungal alpha diversity remained stable, with the highest diversity observed at the low-contamination site. Canonical correspondence analysis (CCA) linked \u003cem\u003eBurkholderia\u003c/em\u003e and \u003cem\u003ePseudomonas\u003c/em\u003e with THg and MeHg, while \u003cem\u003ePedosphaera\u003c/em\u003e and Candidatus Solibacter were associated with BioaHg. Fungal phyla Ascomycota and Basidiomycota correlated with THg and MeHg, whereas Blastocladiomycota was associated with BioaHg. Functional analysis via shotgun metagenomics and PICRUSt2 identified an enrichment of stress response genes, membrane transporters, and metabolic pathways essential for microbial survival in contaminated environments. Genes encoding carbohydrate metabolism, amino acid processing, and protein metabolism were consistently dominant across contamination levels and sampling seasons. These findings highlight the adaptive strategies of soil microbiomes in mercury-contaminated environments, emphasizing their potential role in bioremediation and ecosystem restoration, thus paving the way for improved environmental management and remediation strategies of former nuclear legacy contaminated ecosystems.\u003c/p\u003e","manuscriptTitle":"A survey of Bacterial and Fungal Community Structure and Functions in Two Long-term Metalliferous Soil Habitats","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-25 18:29:27","doi":"10.21203/rs.3.rs-6414247/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-09-16T19:36:31+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-07-29T18:17:28+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"115007502304577804704127091318094257389","date":"2025-07-10T10:59:32+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"17788685128017690529502647635929693362","date":"2025-07-01T02:44:25+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-27T06:51:42+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"259388776332150611908651045441501722957","date":"2025-06-26T08:18:22+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-25T01:00:17+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"264852043764510960786770813840592518099","date":"2025-06-24T00:23:27+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-06-23T13:48:09+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-04-28T19:34:10+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-04-25T13:14:06+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-04-25T13:13:01+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"b5d4e513-8271-4c81-9ea7-45e7cf71f7cb","owner":[],"postedDate":"June 25th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":50502122,"name":"Biological sciences/Ecology"},{"id":50502123,"name":"Biological sciences/Ecology/Microbial ecology"},{"id":50502124,"name":"Earth and environmental sciences/Environmental sciences/Environmental impact"}],"tags":[],"updatedAt":"2025-12-01T16:10:54+00:00","versionOfRecord":{"articleIdentity":"rs-6414247","link":"https://doi.org/10.1038/s41598-025-25944-y","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2025-11-25 15:58:19","publishedOnDateReadable":"November 25th, 2025"},"versionCreatedAt":"2025-06-25 18:29:27","video":"","vorDoi":"10.1038/s41598-025-25944-y","vorDoiUrl":"https://doi.org/10.1038/s41598-025-25944-y","workflowStages":[]},"version":"v1","identity":"rs-6414247","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6414247","identity":"rs-6414247","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}