Soil-plant microbiomes shaped by soil type and wastewater quality as shown by a combination of cultivation-dependent and independent techniques.

The effects of wastewater irrigation on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in plant-associated microbiomes and soils are still poorly understood. 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.