Dominant microbiome iteration and antibiotic resistance genes propagation way dictate the antibiotic resistance genes contamination degree in soil-plant system

The enrichment of antibiotic resistance genes (ARGs) in crops harvested in antibiotics and ARGs contaminated soils has brought concerns for the global public health. Existing studies on ARGs contamination in antibiotic contaminated soil-plant system may be independent and unclarified to elucidate ARGs distribution in such system. This work managed to explain the distributions of ARGs in soil-wheat system where soils were collected from tetracycline polluted farmland and wheat grew for 90 days under four antibiotic conditions by adding no antibiotics, sulfamethoxazole (SMZ), oxytetracycline (OTC) and ciprofloxacin (CIP). Two sulfonamide resistance genes (SRGs) and three tetracycline resistance genes (TRGs) were detected in background soil and assigned to ARGs whose propagations relying on horizontal gene transfer and long-term tetracycline exposure, respectively. Wheat planting dramatically reduced the TRGs abundances by 5–50 times under four conditions because TRGs hosts were outcompeted by the microbiota iteration shock induced by the recruitment of plant probiotics and pathogens. Although SRGs hosts also underwent this shock, emerging SRGs hosts, mainly nitrogen fixation bacteria, were created by intI1 mediated horizontal gene transfer. Then SRGs abundances were not reduced but instead increased as emerging SRGs hosts became the dominant microbes in rhizosphere soil. SMZ stress particularly enriched SRGs by 6–22 times. Both TRGs and SRGs were accumulated in wheat roots and leaves, but owing to intI1 facilitation, SRGs bioaccumulations extremely exceeded TRGs. The invasion of nitrogen fixation bacteria carrying SRGs may also contribute to SRGs bioaccumulation. Consequently, we recapped a theory integrating ARGs propagation way, rhizospheric microbiota iteration and antibiotic stress to comprehend ARGs contamination in soil-plant system conducted in this and published works.