Irrigation as a dissemination vector for groundwater antibiotic resistomes into agricultural systems

Groundwater irrigation acts as a pivotal vector for the dissemination of antibiotic resistance genes (ARGs) throughout agricultural ecosystems, yet its role in shaping crop resistomes remains poorly quantified. This study employed multi-compartment sampling (groundwater, soil, maize tissues) coupled with 16S rRNA amplicon sequencing and shotgun metagenomics to track ARG dynamics in a real-world groundwater-irrigated maize system. The results revealed that groundwater constitutes a substantial reservoir of diverse ARGs and mobile genetic elements (MGEs), exhibiting 13-15 times higher MGE abundance than soils. Crucially, irrigation facilitated the transfer of clinically relevant ARGs (e.g., OXA-181 , dfrA21 ) and MGEs (transposases, IS91 ) into soils, triggering pronounced ARG enrichment in rhizosphere and endophytic microhabitats. Metagenomic assembly revealed groundwater-derived Pseudomonadota as key ARG hosts, while soil-specific Acidobacteriota harbored unique resistances (e.g., FOX-4 , vanD ). Network analyses confirmed intensified ARG-MGE co-occurrence from groundwater to rhizosphere soils (from 35.5% to 54.9% positive correlations), indicating enhanced horizontal gene transfer potential. Critically, maize kernels showed selective enrichment of Enterobacteriaceae carrying multidrug resistance, directly linking groundwater-sourced ARGs to edible crop compartments. These findings reveal groundwater irrigation as an underappreciated driver of crop ARG diversity, posing tangible food safety risks through potential human exposure to resistant bacteria and promoting ecological resistance dissemination via MGE-mediated soil recombination hotspots.