Over decades, untreated wastewater from Mexico City has been used to irrigate crops in the Mezquital Valley. After the construction of the Atotonilco wastewater treatment plant, the irrigation wastewater has been progressively shifted from untreated to treated. We hypothesized that with the change of irrigation water quality, pollutants accumulated over decades may be released favoring the environmental spread and dissemination of antibiotic resistance genes (ARGs) through mobile genetic elements (MGEs) in a soil type specific manner. Experiments ranging from incubation experiments with homogenized soils under well-defined conditions to experiments with intact soils with plants were performed to investigate the effects of changing irrigation water quality on the resistome, mobilome and microbial community composition in different soil types by means of DNA-based methods (qPCR, 16S amplicon sequencing).

The incubation experiment with homogenized soils showed that wastewater spiked with a mixture of antibiotics and disinfectants affected the soil resistome and mobilome with increases in the relative abundance of specific ARGs and MGEs, but not the soil microbial community composition that was mainly shaped by the soil type. Subsequent experiments with monolithic soil columns with two soil types from the Mezquital Valley planted with cilantro and irrigated with spiked or unspiked untreated or treated wastewater confirmed the results observed in the incubation experiment. Soil collected from preferential flow paths (stained with a non-toxic dye) harbored a higher relative abundance and diversity of ARGs and MGEs compared to unstained soil, which was less exposed to the infiltrating wastewater. In contrast to the bulk soil microbial community, the rhizosphere microbial community was strongly influenced by the quality and level of antibiotics and disinfectants in the irrigation wastewater. Exogenous plasmid capturing experiments will contribute to understand the role of wastewater pollutants and plasmids on the spread of environmental antimicrobial resistance.