Characterization of antibiotic resistomes and pathobiomes of soil antibiotic-degrading microbial by stable isotope probing and metagenomics

The presence and spread of antimicrobial resistance genes (ARGs) in soil represent a significant threat to human health. However, the ARGs harbored by antibiotic-degrading microorganisms in soil are inadequately characterized. Employing diverse molecular techniques, we investigate the dynamics of ARGs, mobile genetic elements, and virulence factors in soils contaminated with the antibiotic 13 C-sulfadiazine (SDZ), enabling the identification of active SDZ-degrading bacteria. We find that the addition of biochar-based biofilm to various soil types reduces the abundance of several ARGs and virulence factors associated with active SDZ-degrading bacteria. Furthermore, our results reveal a marked increase in the relative abundance of specific genes within associated microorganisms during SDZ metabolism in the soil. This study elucidates the distribution and composition of antimicrobial resistance in active SDZ-degrading bacteria across diverse soils, suggesting that the utilization of biochar-based biofilm represents an effective strategy for mitigating antimicrobial resistance in soil within the One Health framework.