Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles

Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles | 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 Research Article Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles M. Nazmul Hoque, Md. Liton Rana, Md Abu Ahsan Gilman, Pritom Kumar Pramanik, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8462036/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 01 Apr, 2026 Read the published version in Environmental Monitoring and Assessment → Version 1 posted 4 You are reading this latest preprint version Abstract Despite the increasing prevalence of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles ( i.e. , resistome) of microbial communities in rooftop and surface garden soils remain poorly characterized in Bangladesh, limiting our understanding of their role as reservoirs and disseminators of AMR. This study employed shotgun whole-metagenome sequencing (WMS) on 27 soil samples, comprising 7 Dhaka rooftop gardens (DRG), 6 Dhaka surface gardens (DSG), 8 Gazipur rooftop gardens (GRG), and 6 Gazipur surface gardens (GSG), to comprehensively profile resistomes. We identified 88 unique ARGs, with 19 (21.6%) shared across sites, and found significant differences by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG:50, GRG:48) than surface soils (DSG:40, GSG:41), and were dominated by glycopeptide resistance genes ( vanW , vanY , vanT ), collectively representing 62.43–74.07% of ARGs. Rooftop soils were also enriched in efflux pumps ( adeF , 45.21% of rooftop ARGs) and ribosomal protection mechanisms, exemplified by the oxazolidinone resistance gene O23S (62.13% in GRG). Surface soils featured higher abundances of enzymatic inactivation genes, including chloramphenicol acetyltransferase CATA (11.64% in DSG) and fosfomycin resistance gene FOSB , alongside co-selected biocide (e.g., qacG , 3.70% in DSG) and metal resistance genes. Key ARG carriers included Bacillus licheniformis , B. paralicheniformis , Pseudomonas sabulinigri , and Paenibacillus spp. Correlation analyses indicated showed strong positive correlations (r = 1.0) between specific taxa and resistance mechanisms, alongside co-occurrence of ARGs with biocide and metal resistance genes suggested co-selection and potential linkage on mobile genetic elements. These results highlight urban garden soils as critical reservoirs of ARGs, emphasizing the influence of garden type, location, and anthropogenic inputs, and underscore the importance of sustainable management and a One Health framework for monitoring environmental resistomes. Urban agriculture Antibiotic resistance genes Soil microbiome Resistome Shotgun metagenomics One Health Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryFiguresandTables.docx Cite Share Download PDF Status: Published Journal Publication published 01 Apr, 2026 Read the published version in Environmental Monitoring and Assessment → Version 1 posted Editorial decision: Revision requested 22 Jan, 2026 Editor assigned by journal 15 Jan, 2026 Submission checks completed at journal 15 Jan, 2026 First submitted to journal 27 Dec, 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-8462036","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":578970674,"identity":"c93b937c-f474-4ea9-a198-2220e2eeffee","order_by":0,"name":"M. Nazmul Hoque","email":"","orcid":"","institution":"Department of Gynecology, Obstetrics and Reproductive Health, Gazipur Agricultural University","correspondingAuthor":false,"prefix":"","firstName":"M.","middleName":"Nazmul","lastName":"Hoque","suffix":""},{"id":578970675,"identity":"62afb130-db7c-4c7a-9401-5ef2d8f13cd1","order_by":1,"name":"Md. 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Tanvir Rahman","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA5ElEQVRIiWNgGAWjYLCCBDBiYHwM4zIzsOFWzYOkhdmYeC0QXQxs0kRpsWc/e0zi4R67PN32s8eqC2oOM/Cz5xgwF5ThsYUnL00i4VlysdmZvLTbM44dZpDseWPAPOMcPoflGBskHGBO3HYgx+w2D9thBoMbQFt42/Bo4X8D0lKfuO38G7Ninn+HGewJapHIMXyQcOBw4rYbOWZAlUBbJAhpufEGpOU4UMsbY+mZfek8EmeeFRzG5xf2/hyDgz8OVAMdlmP4ueCbtRx/e/LGx/hCDNNaEHGABA2jYBSMglEwCrAAAKO/UTxHBX+UAAAAAElFTkSuQmCC","orcid":"","institution":"Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University","correspondingAuthor":true,"prefix":"","firstName":"Md.","middleName":"Tanvir","lastName":"Rahman","suffix":""}],"badges":[],"createdAt":"2025-12-27 15:38:37","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8462036/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8462036/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s10661-026-15240-1","type":"published","date":"2026-04-01T15:58:11+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":106343989,"identity":"23e00d27-0173-46b5-8379-3ed7be07ee78","added_by":"auto","created_at":"2026-04-07 16:11:35","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1936809,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8462036/v1_covered_4e73878a-bd30-487d-a389-375decf60cb2.pdf"},{"id":103025061,"identity":"13dc41a8-3d90-45de-9e66-36dfaa1b5d45","added_by":"auto","created_at":"2026-02-19 19:52:19","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":61364,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryFiguresandTables.docx","url":"https://assets-eu.researchsquare.com/files/rs-8462036/v1/0e9e5c68a151768561e0a8a2.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles","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":"environmental-monitoring-and-assessment","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"emas","sideBox":"Learn more about [Environmental Monitoring and Assessment](http://link.springer.com/journal/10661)","snPcode":"10661","submissionUrl":"https://submission.nature.com/new-submission/10661/3","title":"Environmental Monitoring and Assessment","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Urban agriculture, Antibiotic resistance genes, Soil microbiome, Resistome, Shotgun metagenomics, One Health","lastPublishedDoi":"10.21203/rs.3.rs-8462036/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8462036/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eDespite the increasing prevalence of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (\u003cem\u003ei.e.\u003c/em\u003e, resistome) of microbial communities in rooftop and surface garden soils remain poorly characterized in Bangladesh, limiting our understanding of their role as reservoirs and disseminators of AMR. This study employed shotgun whole-metagenome sequencing (WMS) on 27 soil samples, comprising 7 Dhaka rooftop gardens (DRG), 6 Dhaka surface gardens (DSG), 8 Gazipur rooftop gardens (GRG), and 6 Gazipur surface gardens (GSG), to comprehensively profile resistomes. We identified 88 unique ARGs, with 19 (21.6%) shared across sites, and found significant differences by garden type (p\u0026thinsp;=\u0026thinsp;0.04). Rooftop soils harbored more ARGs (DRG:50, GRG:48) than surface soils (DSG:40, GSG:41), and were dominated by glycopeptide resistance genes (\u003cem\u003evanW\u003c/em\u003e, \u003cem\u003evanY\u003c/em\u003e, \u003cem\u003evanT\u003c/em\u003e), collectively representing 62.43\u0026ndash;74.07% of ARGs. Rooftop soils were also enriched in efflux pumps (\u003cem\u003eadeF\u003c/em\u003e, 45.21% of rooftop ARGs) and ribosomal protection mechanisms, exemplified by the oxazolidinone resistance gene \u003cem\u003eO23S\u003c/em\u003e (62.13% in GRG). Surface soils featured higher abundances of enzymatic inactivation genes, including chloramphenicol acetyltransferase \u003cem\u003eCATA\u003c/em\u003e (11.64% in DSG) and fosfomycin resistance gene \u003cem\u003eFOSB\u003c/em\u003e, alongside co-selected biocide (e.g., \u003cem\u003eqacG\u003c/em\u003e, 3.70% in DSG) and metal resistance genes. Key ARG carriers included \u003cem\u003eBacillus licheniformis\u003c/em\u003e, \u003cem\u003eB. paralicheniformis\u003c/em\u003e, \u003cem\u003ePseudomonas sabulinigri\u003c/em\u003e, and \u003cem\u003ePaenibacillus\u003c/em\u003e spp. Correlation analyses indicated showed strong positive correlations (r\u0026thinsp;=\u0026thinsp;1.0) between specific taxa and resistance mechanisms, alongside co-occurrence of ARGs with biocide and metal resistance genes suggested co-selection and potential linkage on mobile genetic elements. These results highlight urban garden soils as critical reservoirs of ARGs, emphasizing the influence of garden type, location, and anthropogenic inputs, and underscore the importance of sustainable management and a One Health framework for monitoring environmental resistomes.\u003c/p\u003e","manuscriptTitle":"Rooftop and Surface Garden Soils in Bangladesh Harbor Diverse Resistome Profiles","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-19 19:52:15","doi":"10.21203/rs.3.rs-8462036/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-01-22T20:54:05+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-01-15T12:56:04+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-01-15T12:53:27+00:00","index":"","fulltext":""},{"type":"submitted","content":"Environmental Monitoring and Assessment","date":"2025-12-27T15:24:29+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"environmental-monitoring-and-assessment","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"emas","sideBox":"Learn more about [Environmental Monitoring and Assessment](http://link.springer.com/journal/10661)","snPcode":"10661","submissionUrl":"https://submission.nature.com/new-submission/10661/3","title":"Environmental Monitoring and Assessment","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"da8155b7-e66b-4bbd-b882-8576968dcaf8","owner":[],"postedDate":"February 19th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-04-07T16:07:02+00:00","versionOfRecord":{"articleIdentity":"rs-8462036","link":"https://doi.org/10.1007/s10661-026-15240-1","journal":{"identity":"environmental-monitoring-and-assessment","isVorOnly":false,"title":"Environmental Monitoring and Assessment"},"publishedOn":"2026-04-01 15:58:11","publishedOnDateReadable":"April 1st, 2026"},"versionCreatedAt":"2026-02-19 19:52:15","video":"","vorDoi":"10.1007/s10661-026-15240-1","vorDoiUrl":"https://doi.org/10.1007/s10661-026-15240-1","workflowStages":[]},"version":"v1","identity":"rs-8462036","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8462036","identity":"rs-8462036","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}