Soil type and Wastewater contaminants drive Antibiotic Resistance Genes, Mobile Genetic Elements, and Bacterial Communities in soil, cilantro rhizosphere, and phyllosphere

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Abstract Background : In a previous study evaluating the effects of changing wastewater (WW) irrigation regime on the selection and spread of antibiotic resistance in Mezquital Valley soils—an area with long-term untreated wastewater (UWW) irrigation—we found that wastewater pollutants strongly influenced the distribution and relative abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soils. To further investigate how this transition affects ARG dissemination and bacterial communities in soil-plant systems, we conducted a column experiment using Leptosol and Vertisol monoliths collected from the Mezquital Valley, planted with cilantro ( Coriandrum sativum ) and irrigated for eight weeks with UWW or treated WW (TWW), with or without spiked antibiotics and disinfectants. Total community DNA was extracted from soil (exposed or not to preferential flow path water), rhizosphere, and phyllosphere, and analysed by qPCR and 16S rRNA gene amplicon sequencing. Results : Spiked-WW irrigation significantly affected ARG and MGE profiles in soil, with higher relative abundances in soil exposed to preferential flow path water. In the rhizosphere, soil type was the main driver of ARG and MGE profiles, with Leptosols exhibiting higher relative abundances than Vertisols. Spiked WW irrigation increased the relative abundances of the class 1 integron integrase gene ( intI1 ), sulfonamide ( sul1 , sul2 ), tetracycline ( tetA ) resistance genes in soil and rhizosphere, as well as erythromycin ( ermA ) and fluoroquinolone ( qnrA ) resistance genes in the phyllosphere. Bacterial community composition in preferential flow path soil and rhizosphere was primarily shaped by soil type, followed by spiking level, whereas WW type influenced only the rhizosphere bacterial community composition. Conclusions : Our findings highlight the relevance of WW micropollutants in driving ARG and MGE profiles in soil and shaping bacterial communities in soils —particularly those influenced by preferential flow path water— and rhizosphere of WW-irrigated agroecosystems.
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Soil type and Wastewater Contaminants drive Antibiotic Resistance Genes, Mobile Genetic Elements, and Bacterial Communities in Soil, Cilantro Rhizosphere, and Phyllosphere | 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 Soil type and Wastewater Contaminants drive Antibiotic Resistance Genes, Mobile Genetic Elements, and Bacterial Communities in Soil, Cilantro Rhizosphere, and Phyllosphere Sara Gallego, Leila Soufi, Ioannis Kampouris, Rehana Abdulvakkeil, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8037905/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Antimicrobial resistance (AMR) in wastewater (WW)-irrigated soils is a global concern. Yet, the effects of wastewater irrigation on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in plant-associated microbiomes and different soil compartments are still limited. We conducted a column experiment using Leptosol and Vertisol monoliths, planted with cilantro ( Coriandrum sativum ) and irrigated for eight weeks with untreated (UWW) or treated (TWW) wastewater, with or without spiked antibiotics and disinfectants. Total community-DNA was analysed by qPCR and 16S rRNA gene sequencing. Third-generation-cephalosporin-resistant (3GCR) enterobacteria were isolated. Spiked WW irrigation increased ARG and MGE abundances in preferential flow path soil. In the rhizosphere, Leptosol exhibited higher ARG and MGE abundances than Vertisol. Spiking increased class 1 integrons, sulfonamide, tetracycline resistance genes in soil and rhizosphere, and erythromycin and fluoroquinolone resistance genes in phyllosphere. Soil type primarily shaped bacterial community composition in preferential flow path soil and rhizosphere, followed by spiking. WW type influenced only rhizosphere bacterial community composition, while 3GCR Citrobacter freundii Ci-1a_Bx-C2 was only isolated from TWW-irrigated soil and rhizosphere enrichments. Our findings demonstrate that WW micropollutants drive ARG and MGE profiles and shape bacterial communities—particularly in preferential flow path soil and rhizosphere of WW-irrigated agroecosystems. Mezquital Valley preferential flow path soil 16S rRNA gene amplicon qPCR soil monolith 3GCR enterobacteria Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Full Text Additional Declarations The authors declare no competing interests. Supplementary Files CETablesSGB.docx CESupplFiguresTablesSGB.docx TableS3linearmodelregressionbootstrapsoils.xlsx TableS4linearmodelregressionbootstrap.xlsx TableS5alldiffabundantASVsall.xlsx TableS6Characterizedbacterial3GCRstrains.xlsx TableS7ASVsrepresentingcultivatedgenera.xlsx Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions 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-8037905","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":548494722,"identity":"bf9b21a1-2e0d-47e2-90f9-6589451fafc9","order_by":0,"name":"Sara Gallego","email":"data:image/png;base64,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","orcid":"","institution":"Julius Kühn-Institut","correspondingAuthor":true,"prefix":"","firstName":"Sara","middleName":"","lastName":"Gallego","suffix":""},{"id":548494723,"identity":"22b869a7-b5c8-4926-8ef9-4365c9204518","order_by":1,"name":"Leila Soufi","email":"","orcid":"","institution":"Berlin University of Applied Sciences","correspondingAuthor":false,"prefix":"","firstName":"Leila","middleName":"","lastName":"Soufi","suffix":""},{"id":548494724,"identity":"741ea88f-9433-41cd-ba85-391cdc5bcc63","order_by":2,"name":"Ioannis Kampouris","email":"","orcid":"","institution":"Julius Kühn-Institut","correspondingAuthor":false,"prefix":"","firstName":"Ioannis","middleName":"","lastName":"Kampouris","suffix":""},{"id":634731180,"identity":"71bff84a-a876-4547-8cb2-2802761e820b","order_by":3,"name":"Rehana Abdulvakkeil","email":"","orcid":"","institution":"Justus Liebig University Giessen","correspondingAuthor":false,"prefix":"","firstName":"Rehana","middleName":"","lastName":"Abdulvakkeil","suffix":""},{"id":634731181,"identity":"084339b5-955b-47ca-8d4c-3493d9d434d4","order_by":4,"name":"Dipen Pulami","email":"","orcid":"https://orcid.org/0000-0002-2402-5689","institution":"Justus Liebig University Giessen","correspondingAuthor":false,"prefix":"","firstName":"Dipen","middleName":"","lastName":"Pulami","suffix":""},{"id":548494725,"identity":"f5726757-172d-47ad-ab3c-9f8aa85aea4b","order_by":5,"name":"Kathia Lüneberg","email":"","orcid":"","institution":"National Autonomous University of Mexico","correspondingAuthor":false,"prefix":"","firstName":"Kathia","middleName":"","lastName":"Lüneberg","suffix":""},{"id":548494726,"identity":"6ed6a45f-3e36-4747-8231-ff895ff321e5","order_by":6,"name":"Benjamin J. 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No significant differences observed (\u003cem\u003ep\u003c/em\u003e\u0026gt;0.05; Wilcoxon test).\u003c/p\u003e","description":"","filename":"Picture1.png","url":"https://assets-eu.researchsquare.com/files/rs-8037905/v2/f667b04516ac1c60ed365f93.png"},{"id":109405924,"identity":"69628ef0-963e-45a3-9436-e91d60ca89ac","added_by":"auto","created_at":"2026-05-17 13:22:33","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":186578,"visible":true,"origin":"","legend":"\u003cp\u003eAntibiotic resistance gee (ARG) and mobile genetic element (MGE) relative abundances (log\u003csub\u003e10 \u003c/sub\u003egene copies/16S rRNA gene copies) in samples from unstained soil, preferential water flow path soil (stained soil), cilantro rhizosphere, and phyllosphere samples irrigated with untreated (UWW) or treated (TWW) wastewater, both unspiked and spiked with antibiotics and disinfectants.\u003c/p\u003e","description":"","filename":"Picture2.png","url":"https://assets-eu.researchsquare.com/files/rs-8037905/v2/8a746eaee8ea8db3bbc077c2.png"},{"id":109406219,"identity":"eb15e685-548e-4ca0-9dae-b98534aa2fbf","added_by":"auto","created_at":"2026-05-17 13:27:01","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":3959371,"visible":true,"origin":"","legend":"\u003cp\u003ePrincipal Component Analysis of antibiotic resistance gene (ARG) and mobile genetic element (MGE) distributions in A) Leptosol and Vertisol soils from unstained soil, B) Leptosol and Vertisol soils from preferential water flow path soil (stained soil), C) cilantro rhizosphere, and D) phyllosphere samples irrigated with untreated (UWW) or treated (TWW) wastewater, both unspiked and spiked with antibiotics and disinfectants. Significance of separation was assessed with Global PERMANOVA test (A: spike level: R\u003csup\u003e2\u003c/sup\u003e=0.12, \u003cem\u003ep\u003c/em\u003e=0.0021;\u003cstrong\u003e \u003c/strong\u003esoil type: R\u003csup\u003e2\u003c/sup\u003e=0.03, \u003cem\u003ep\u003c/em\u003e=0.6128; water type: R\u003csup\u003e2\u003c/sup\u003e=0.04, \u003cem\u003ep\u003c/em\u003e=0.2618; B: spike level: R\u003csup\u003e2\u003c/sup\u003e=0.11, \u003cem\u003ep\u003c/em\u003e=0.0015; soil type: R\u003csup\u003e2\u003c/sup\u003e=0.03, \u003cem\u003ep\u003c/em\u003e=0.3901; water type: R\u003csup\u003e2\u003c/sup\u003e=0.02, \u003cem\u003ep\u003c/em\u003e=0.7253; C: spike level: R\u003csup\u003e2\u003c/sup\u003e=0.03, \u003cem\u003ep\u003c/em\u003e=0.1988; soil type: R\u003csup\u003e2\u003c/sup\u003e=0.38, \u003cem\u003ep\u003c/em\u003e=0.0001; water type: R\u003csup\u003e2\u003c/sup\u003e=0.02, \u003cem\u003ep\u003c/em\u003e=0.4767; D: spike level: R\u003csup\u003e2\u003c/sup\u003e=0.05, \u003cem\u003ep\u003c/em\u003e=0.1325; soil type: R\u003csup\u003e2\u003c/sup\u003e=0.018, \u003cem\u003ep\u003c/em\u003e=0.8100; water type: R\u003csup\u003e2\u003c/sup\u003e=0.02, \u003cem\u003ep\u003c/em\u003e=0.8382).\u003c/p\u003e","description":"","filename":"Picture3.png","url":"https://assets-eu.researchsquare.com/files/rs-8037905/v2/1562a51a73d81eb8b6d4f67b.png"},{"id":109406570,"identity":"1d58108b-e67f-4259-8af8-dfc55f177692","added_by":"auto","created_at":"2026-05-17 13:28:46","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":114330,"visible":true,"origin":"","legend":"\u003cp\u003eMultidimensional scaling analysis of bacterial community structure based on Bray-Curtis dissimilarities from 16S rRNA gene amplicon sequencing data in A) soil samples from preferential water flow path soil (stained soil), B) rhizosphere, and C) phyllosphere irrigated with untreated (UWW) or treated (TWW) wastewater, both unspiked and spiked with antibiotics and disinfectants. Significance of separation was assessed with Global PERMANOVA test. (A: soil type: R\u003csup\u003e2\u003c/sup\u003e=0.23, \u003cem\u003ep\u003c/em\u003e=0.0001; spike level: R\u003csup\u003e2\u003c/sup\u003e=0.05, \u003cem\u003ep\u003c/em\u003e=0.0334; water type: R\u003csup\u003e2\u003c/sup\u003e=0.04 \u003cem\u003ep\u003c/em\u003e=0.1118; B: soil type: R\u003csup\u003e2\u003c/sup\u003e=0.16, \u003cem\u003ep\u003c/em\u003e=0.0001; spike level: R\u003csup\u003e2\u003c/sup\u003e=0.06, \u003cem\u003ep\u003c/em\u003e=0.0021; water type: R\u003csup\u003e2\u003c/sup\u003e=0.05, \u003cem\u003ep\u003c/em\u003e=0.0143; C: soil type: R\u003csup\u003e2\u003c/sup\u003e=0.03, \u003cem\u003ep\u003c/em\u003e=0.8690; spike level: R\u003csup\u003e2\u003c/sup\u003e=0.03, \u003cem\u003ep\u003c/em\u003e=0.8135; water type: R\u003csup\u003e2\u003c/sup\u003e=0.04, \u003cem\u003ep\u003c/em\u003e=0.0951).\u003c/p\u003e","description":"","filename":"Picture4.png","url":"https://assets-eu.researchsquare.com/files/rs-8037905/v2/74552f01806286c0c7747222.png"},{"id":109405926,"identity":"cbb26105-c6b9-4234-834a-e10d77c5c1fc","added_by":"auto","created_at":"2026-05-17 13:22:33","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":102093,"visible":true,"origin":"","legend":"\u003cp\u003eDifferentially abundant ASVs in soil from preferential water flow path soil and rhizosphere irrigated with untreated (UWW) or treated (TWW) wastewater, both unspiked and spiked with antibiotics and disinfectants. The x-axis shows the log₁₀-transformed average of their relative abundance (log₁₀ RA), and the y-axis shows the log₂-transformed fold change (log₂ FC) in abundance between two conditions.\u003c/p\u003e","description":"","filename":"Picture5.png","url":"https://assets-eu.researchsquare.com/files/rs-8037905/v2/b8c6fa248eded9bc87c0b156.png"},{"id":109405907,"identity":"a72f850e-8f05-462f-897c-69d57b965303","added_by":"auto","created_at":"2026-05-17 13:22:13","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":97571,"visible":true,"origin":"","legend":"\u003cp\u003e3GCR enterobacteria isolates from stained soil and rhizosphere samples irrigated with UWW and TWW both spiked and unspiked. No growth was obtained from phyllosphere samples. Four replicate soil columns per treatment were analysed. Phylogenetic assignment (phylotype identification based on partial 16S rRNA gene sequencing and phylogenetic analysis, for details see Suppl. Fig. 1) and PCR for \u003cem\u003eE. coli \u003c/em\u003eidentification. 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Phyllosphere\u003c/strong\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":true,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Mezquital Valley, preferential flow path soil, 16S rRNA gene amplicon, qPCR, soil monolith, 3GCR enterobacteria","lastPublishedDoi":"10.21203/rs.3.rs-8037905/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8037905/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eAntimicrobial resistance (AMR) in wastewater (WW)-irrigated soils is a global concern. Yet, the effects of wastewater irrigation on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in plant-associated microbiomes and different soil compartments are still limited. We conducted a column experiment using Leptosol and Vertisol monoliths, planted with cilantro (\u003cem\u003eCoriandrum sativum\u003c/em\u003e) and irrigated for eight weeks with untreated (UWW) or treated (TWW) wastewater, with or without spiked antibiotics and disinfectants. Total community-DNA was analysed by qPCR and 16S rRNA gene sequencing. Third-generation-cephalosporin-resistant (3GCR) enterobacteria were isolated.\u003c/p\u003e\n\u003cp\u003eSpiked WW irrigation increased ARG and MGE abundances in preferential flow path soil. In the rhizosphere, Leptosol exhibited higher ARG and MGE abundances than Vertisol. Spiking increased class 1 integrons, sulfonamide, tetracycline resistance genes in soil and rhizosphere, and erythromycin and fluoroquinolone resistance genes in phyllosphere. Soil type primarily shaped bacterial community composition in preferential flow path soil and rhizosphere, followed by spiking. WW type influenced only rhizosphere bacterial community composition, while 3GCR \u003cem\u003eCitrobacter\u003c/em\u003e \u003cem\u003efreundii\u003c/em\u003e Ci-1a_Bx-C2 was only isolated from TWW-irrigated soil and rhizosphere enrichments.\u003c/p\u003e\n\u003cp\u003eOur findings demonstrate that WW micropollutants drive ARG and MGE profiles and shape bacterial communities—particularly in preferential flow path soil and rhizosphere of WW-irrigated agroecosystems.\u003c/p\u003e","manuscriptTitle":"Soil type and Wastewater Contaminants drive Antibiotic Resistance Genes, Mobile Genetic Elements, and Bacterial Communities in Soil, Cilantro Rhizosphere, and Phyllosphere","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2026-05-15 19:57:25","doi":"10.21203/rs.3.rs-8037905/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-11-21 05:40:10","doi":"10.21203/rs.3.rs-8037905/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"d698add9-00c2-48f6-8ef8-373efbbbd955","owner":[],"postedDate":"May 15th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-12-10T16:04:38+00:00","versionOfRecord":[],"versionCreatedAt":"2026-05-15 19:57:25","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-8037905","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8037905","identity":"rs-8037905","version":["v2"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}

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