Tracking antibiotic resistance genes and microbiome shifts under reclaimed wastewater irrigation: Root-associated selective modulation

The reuse of treated wastewater (TWW) for crop irrigation reduces pressure on freshwater resources but may also disseminate antimicrobial resistance (AMR) through the presence of antibiotics, resistant bacteria and antibiotic resistant genes (ARGs). While many studies have examined the impact of water quality on dissemination of AMR in soils, the role of plants in filtering or accumulating AMR within the soil–plant continuum remains unclear. Here, we investigated the influence of irrigation water quality, plant species, and microbial compartments (soil, rhizosphere, roots) on bacterial communities and selected ARGs under controlled mesocosm conditions. Lettuce and leek were irrigated over two consecutive years with drinking water (DW), TWW, or raw wastewater (RWW). We monitored the abundance of ARGs sul1, ermB , and intI1 and characterized bacterial community composition by 16S rRNA sequencing. Soil microbiomes were influenced by water type and probably irrigation volume, and bacterial enrichment associated with DW, TWW, and RWW were identified. Plant-specific effects on soil microbiome were observed but were minor compared to the effect of water quality. Root microbiomes appeared more resilient than soils, as most taxa enriched in TWW- or RWW-irrigated soils were less or not amplified in roots, suggesting a potential barrier effect or at least selective processes at the root interface. Only Tahibacter and Rhodanobacteraceae increased in roots, while RWW irrigation also promoted the growth of the plant-pathogen Rhizorhapis . ARGs rose significantly in soils under TWW and RWW irrigation, with distinct year-to-year dynamics, but these shifts were not observed in root communities. Overall, our results indicate that root-associated compartments may contribute to modulate the dissemination of sul1, ermB , and intI1 ARGs in the plants irrigated with TWW. • Microbial and ARG dynamics different between 2 successive years of irrigation. • Shifts are driven by irrigation water quantity and quality. • Bacterial indicators specific to water quality and plant type were identified. • Spatial compartments – soil, rhizosphere, roots – influenced indicators. • Root-associated compartments modulate ARG mobility and microbial shifts.