摘要
      稻小龙虾联合养殖作为一种可持续的农业体系，在许多国家得到了广泛而迅速的推广。小龙虾残留物的积累可以提高土壤有机质含量；然而，这种综合农业模式对抗性和毒力基因的传播和致病性的影响仍知之甚少。在这里，我们在中国各地的RC和水稻单作（RM）配对系统中使用宏基因组方法对抗生素抗性基因（ARGs）、杀生物剂抗性基因（BRGs），金属抗性基因（MRGs）和毒力因子基因（VFGs）进行了表征。与RM模型相比，RC模型没有增加土壤ARG、BRG、MRG或VFG的丰度，但选择性富集了这些潜在抗性和毒力基因的35个亚型。网络分析显示，与RM系统相比，RC系统中的抗性和毒力基因与移动遗传元件（MGE）的连接数量更高，这表明这些基因具有更高的水平转移潜力。此外，RC模型具有更高丰度的人类机会性病原体，如沙门氏菌、霍乱弧菌和痢疾志贺菌，它们是VFG的潜在宿主，如phoP、fleS和gspE，这表明对人类健康存在潜在威胁。我们进一步揭示了随机过程是RC系统中抗性和毒力基因组装的主要驱动因素。ARGs和VFGs的丰度主要与微生物群落组成有关，而BRGs和MRGs的丰富度主要与MGE的丰度有关。总之，我们的研究结果表明，RC模型有可能引起抗性和毒力基因的传播和致病性，这对控制土传生物风险和可持续农业的战略管理具有重要意义。
Abstract
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 of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.

https://www.sciencedirect.com/science/article/pii/S0160412023000624