Swine-manure composts induce the enrichment of antibiotic-resistant bacteria but not antibiotic resistance genes in soils

Composting is a common and effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from animal manure. However, it is unclear whether the advantages of composting for the control of ARGs and ARB can be further increased in land application. This study investigated the fate of ARB and ARGs after land application of swine-manure composts (SMCs) to three different soil types (red soil, loess and black soil). The results showed that although the SMCs caused an increase in the abundance of total ARGs in the soil in the short period, they significantly reduced (p < 0.01) the abundance of total ARGs after 82 days compared to the control. The decay rate of ARGs reflected by the half-life times (t1/2) varied by soil type, with red soil being the longest. The SMCs mainly introduced ermF, tetG and tetX into the soils, while these ARGs quickly declined to the control level. Notably, SMCs increased the number of ARB in the soils, especially for cefotaxime-resistant bacteria. Although SMCs only affected the microbiome significantly during the early stage (p < 0.05), it took a much longer time for the microbiome to recover compared to the control. Statistical analysis indicated that changes in the microbial community contributed more to the fate of ARGs during SMCs land application than other factors. Overall, it is proposed that the advantages of ARGs control in the composting process for swine manure can be further increased in land application, but it can still bring some risks in regard to ARB.

Automated summary

Composting is an effective strategy for reducing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in animal manure. This study examined the fate of ARB and ARGs after applying swine-manure composts (SMCs) to different soil types. The results showed that SMCs initially increased total ARG abundance in the soil but significantly reduced it after 82 days. The SMCs introduced specific ARGs into the soils, which declined over time. However, the presence of SMCs increased the number of ARB in the soils, especially cefotaxime-resistant bacteria. The microbiome also took longer to recover compared to the control. Statistical analysis suggested that changes in the microbial community were the main factor influencing the fate of ARGs during SMCs land application.