Metagenomic Analysis of Virulence Factors and Antibiotic Resistance Genes in Soil Microbial Communities

Widespread use of antibiotics has led to an increase in the virulence factors (VFs) and antibiotic resistance genes (ARGs) within soil microbial communities. However, the impact of agricultural management, plant type and soil compartment on the distribution of VFs and ARGs in both organic systems and conventional systems remains unclear. In this study, we conducted a metagenomic analysis to investigate the distribution. Nonmetric multidimensional scaling analysis revealed that soil samples exhibited clustering primarily based on agricultural management system for both VFs (stressVFDB = 0.071) and ARGs (stressARDB = 0.117, stressCARD = 0.069). We observed significantly higher levels of VFs and ARGs in soils from conventional systems compared with organic systems (p < 0.05). Furthermore, combined analysis of carbohydrate-active enzymes (CAZymes) and KEGG revealed that six classes comprising 445 families of CAZymes were significantly more abundant in conventional system soils than in organic system soils. Notably, the abundance of carbamyl phosphate synthase (ammonia) was relatively higher in organic system samples (53.33%) compared with conventional system samples (48.8%). Our comprehensive analysis suggests that different agricultural management practices lead to alterations in soil microbial communities. Specifically, organic management practices were found to effectively mitigate the pathogenic potential and drug resistance of soil microbial communities. In conclusion, our findings highlight the substantial influence of agricultural management on soil microbial communities, with corresponding clustering patterns observed in VFs and ARGs. Organic farming practices contribute to the promotion of healthier soil microsystems and the sustainable development of agriculture compared with conventional systems.