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We conducted a column experiment using Leptosol and Vertisol monoliths, planted with cilantro (Coriandrum sativum) and irrigated for eight weeks with untreated or treated (TWW) wastewater, with or without spiked antibiotics and disinfectants. Total community-DNA was analyzed by qPCR and 16S rRNA gene sequencing. Third-generation cephalosporin-resistant (3GCR) enterobacteria were isolated. Spiked WW irrigation increased ARG and MGE relative abundances in preferential flow path soil. In the rhizosphere, Leptosol exhibited higher ARG and MGE relative abundances than Vertisol. Spiking increased relative abundances of 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, whereas WW type influenced only rhizosphere bacterial community composition. 3GCR strains of the Citrobacter freundii complex genotype Ci-1a_Bx-C2 were isolated exclusively from soil and rhizosphere enrichments irrigated with (spiked or unspiked) TWW. We demonstrate the need to combine cultivation-independent and cultivation-based methods to investigate the effects of WW irrigation on soil and plant-associated microbiomes.<\/jats:p>","DOI":"10.1093\/femsec\/fiag087","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T11:47:21Z","timestamp":1786535241000},"source":"Crossref","is-referenced-by-count":0,"title":["Soil-plant microbiomes shaped by soil type and wastewater quality as shown by a combination of cultivation-dependent and independent techniques"],"prefix":"10.1093","volume":"102","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4521-5879","authenticated-orcid":false,"given":"Sara","family":"Gallego","sequence":"first","affiliation":[{"name":"Julius K\u00fchn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics , 38104 Braunschweig 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Bochum, Institute of Geography, Unit Soil Sciences and Soil Resources , 44801 Bochum ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7144-8898","authenticated-orcid":false,"given":"Doreen","family":"Babin","sequence":"additional","affiliation":[{"name":"Julius K\u00fchn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics , 38104 Braunschweig ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina","family":"Siebe","sequence":"additional","affiliation":[{"name":"Instituto de Geolog\u00eda, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Ciudad Universitaria , 04510 M\u00e9xico City ,","place":["M\u00e9xico"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Siemens","sequence":"additional","affiliation":[{"name":"Justus Liebig University Giessen, iFZ Research Center for BioSystems, Land Use and Nutrition, Institute of Soil Science and Soil Conservation , 35392 Giessen ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5258-6195","authenticated-orcid":false,"given":"Stefanie P","family":"Glaeser","sequence":"additional","affiliation":[{"name":"Justus Liebig University Giessen, iFZ Research Center for BioSystems, Land Use and Nutrition, Institute of Soil Science and Soil Conservation , 35392 Giessen ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6980-729X","authenticated-orcid":false,"given":"Kornelia","family":"Smalla","sequence":"additional","affiliation":[{"name":"Julius K\u00fchn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics , 38104 Braunschweig 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