Cropping system exerts stronger influence on antibiotic resistance gene assemblages in greenhouse soils than reclaimed wastewater irrigation

The effects of reclaimed wastewater (RW) irrigation on the spread of antibiotic resistance genes (ARGs) in soil is modulated by a myriad of biotic and abiotic factors and their relative significance remains vague. We compared microbial communities, assemblages of genes associated with microbial resistance to antibiotics, biocides and metals, and insertion sequences (ISs) in soils following 16 years of crop irrigation with groundwater (GW), RW or alternately with GW and RW in two greenhouses with different cropping systems, using shotgun metagenome sequencing. The results showed that cropping system exerted greater influence than irrigation on the profile of ISs and resistance genes. This influence was most strongly associated with concentrations of copper, mercury and perfloxacin in the soils. There was no significant difference in soil ARG profiles between continuous RW irrigation and alternating GW and RW irrigation. Proteobacteria, Actinobacteria and Firmicutes and a limited number of ISs were closely associated with the detected ARGs. Most ARGs were found to co-occur with metal and biocide resistance genes through the mechanism of efflux pumps. These findings highlight the significance of understanding and improving crop management in mitigating the dissemination of ARGs in soils irrigated with RW.