Long-term rice-eel co-culture system effectively alleviated the accumulation of antibiotic resistance genes in soil.

Abstract

Alleviating the accumulation of antibiotic resistance genes (ARGs) in farmlands is crucial for restricting the transfer of ARGs to crops and controlling the soil-borne microbiological health risk. Rice and eel co-culture (REC) systems have recently been used as an emerging integrated farming model that can stabilize grain yields and improve fertilizer availability. However, the influence of long-term REC system concerning the aggregation and health risk of ARGs in rice fields is still unclear. Here, we deciphered firstly the profile, potential of pathogenicity and mobility, and bacterial hosts for soil ARGs in the long-term REC system compared to the mono-rice (MR) culture system by collecting soil samples from 12 rice fields in Shanghai. The long-term REC system alleviated the accumulation of ARGs in soil, which is manifested in the abundance decrease of total ARGs and 11 ARG types (e.g., multidrug and aminoglycoside). The frequency of ARGs co-occurring with VFGs and MGEs was lower in the long-term REC system than in the MR system, indicating the lower pathogenicity and mobility potential for ARGs. The soil microbial community was identified to primarily drive the ARG discrepancy between the long-term REC and MR systems. In comparison with the MR system, long-term REC weakened the competitive advantage of ARG bacterial hosts, which might contribute to the decreased prevalence of antibiotic resistance. Overall, these findings uncovered the important role of long-term REC system in alleviating the accumulation of soil ARGs, providing theoretical support for antibiotic resistance risk control and sustainable agricultural strategic management.