Antibiotic resistomes and pathobiomes of antibiotic-degrading bacteria in biofilm-enriched soils by DNA-stable isotope probing, high-throughput quantitative PCR, and metagenomics

In this study, we selected red (Ultisol) and black (Mollisol) soils with distinct physical and chemical properties to typify the two types of soils and low and high fertility to reduce soil specificity and increase the generalizability of the conclusions. Our target antibiotic was SDZ, and we utilized biochar as a carrier for the formation of SDZ-degrading bacterial biofilm. We used DNA-SIP in conjunction with high-throughput qPCR and metagenomics sequencing to investigate the following aspects across different soil types: 1) the difference in microbial community structure between SDZ-degrading bacteria and non-SDZ-degrading bacteria; 2) the distribution of ARGs, MGEs, and VFs in SDZ-degrading bacteria of different soil types; and 3) the difference of ARGs in SDZ-degrading bacteria with BB addition in different soils. This study provides a valuable approach to assess the fate of antimicrobial resistance of SDZ-degrading bacteria in soil.