Co-occurrence of crAssphage and antibiotic resistance genes in agricultural soils of the Yangtze River Delta, China

Agricultural soil is highly susceptible to manure contamination and thus is a potential source for the spread of pathogens and antibiotic resistance genes (ARGs). Routine monitoring fecal contamination in agricultural soil can reduce the manure-derived ARG contaminations. This study investigated the distribution of crAssphage, a highly human-specific indicator of fecal pollution, in agricultural soils in the Yangtze River Delta (YRD) of China, and its potential in serving as an indicator of soil ARGs. CrAssphage was indeed strongly correlated with the abundance of soil ARGs, and particularly tetracycline resistance gene tetW (rho = 0.55, p < 0.01). Meanwhile, with the increasing of crAssphage abundance, the frequency of multiple abundant ARGs is also increased. When the relative abundance of crAssphage in soil samples exceeded 4.94 x 10-4 copies per copy of the 16S rRNA gene, there would be more than three types of co-existing ARGs. Regional differences in crAssphage and ARGs abundances were observed for samples collected from Zhejiang, Shanghai, Jiangsu, and Anhui in the YRD, indicating different levels of fecal pollution therein. High sewage treatment capacity could contribute to the reduce of fecal pollution and the control ARG transmission in agricultural soils.

Automated summary

The study reveals that agricultural soil is highly susceptible to manure contamination and can serve as a potential source for the spread of pathogens and antibiotic resistance genes (ARGs). CrAssphage, a highly human-specific indicator of fecal pollution, is strongly correlated with soil ARGs, with a particularly close relationship with the tetracycline resistance gene tetW. Regional differences in crAssphage and ARG abundances suggest varying levels of fecal pollution in different areas of the Yangtze River Delta. Efforts to reduce fecal pollution and control ARG transmission in agricultural soils could benefit from high sewage treatment capacity.