Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China

The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 105-3.57 × 107 copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.