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

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.