Characterization and risk-quantification of antibiotic resistome in grain-based and non-grain cropping soils

Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018-0.023) and "last-resort" ARGs (from 0.007 to 0.034-0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49-2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.