Long-term manure application increased the levels of antibiotics and antibiotic resistance genes in a greenhouse soil

•Application of manure improved the levels of antibiotics, the diversity and abundance of ARGs.•The positive correlations were between antibiotics and the abundances of ARGs and intI1 each other.•The population of ARB was significantly correlated with its half-life.

Land application of animal manure, as an important agronomic practice, represents a potential route to disseminate antibiotic resistance genes (ARGs) into the soil environment. Previous studies have demonstrated that manure-derived ARGs and pathogenic organisms rapidly decline over time following manure application, however, the impacts of long-term and repeated application of animal manure on the diversity and abundance of soil ARGs remain less understood. Here, we investigated the diversity and abundance of ARGs in greenhouse soils with long-term dairy cattle and chicken manure (DM and CM) application, and the half-life of antibiotic resistant bacteria (ARB) isolated from manured soils in Taiyuan, China. Both DM and CM significantly improved the levels of residual antibiotics, the abundances of ARGs, intI1 and soil organic carbon and total nitrogen that there was strong link between them. The half-life of ARB was different, and the correlations of ARGs, intI1 and tnpA genetic elements extracted from ARB with culture times were different. The significantly positive link was between the population of resistance bacteria and the half-life. Our finding suggested that both the levels of antibiotics and the stability of ARGs will determine the diversity and abundance of ARGs in manured soils.