Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China

• DOI: 10.1016/j.envint.2023.107789
• Publication Date: 2023-01-30T06:50:53Z
• Authors: Shuai Du; Jiao Feng; Li Bi; Hang-Wei Hu; Xiuli Hao; Qiaoyun Huang; Yu-Rong Liu
• Keywords: Salmonella enterica; Horizontal Gene Transfer

Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts this integrated farming model on the dissemination pathogenicity resistance virulence genes remain poorly understood. Here, we characterized antibiotic (ARGs), biocide (BRGs), metal (MRGs) factor (VFGs) using metagenomic methods paired RC rice monoculture (RM) systems across China. did not increase abundance ARGs, BRGs, MRGs, or VFGs comparison to RM model, but selectively enriched 35 subtypes these potential genes. Network analysis revealed that had higher number connections with mobile genetic elements (MGEs) than system, suggesting horizontal transfer Moreover, human opportunistic pathogens such Salmonella enterica, Vibrio cholerae, Shigella dysenteriae which were hosts phoP, fleS, gspE, threat health. We further unraveled stochastic process was main driver assembly system. ARGs primarily associated microbial community compositions, while BRGs MRGs mainly MGEs. Taken together, our results suggest cause genes, important implications for control soil-borne biological risks strategic management agriculture.