Effects of composting on the fate of doxycycline, microbial community, and antibiotic resistance genes in swine manure and broiler manure

Aerobic composting is an economical and effective technology that is widely used to treat animal manure. To study the fate of doxycycline (DOX), the microbial community, and antibiotic resistance genes (ARGs) during composting, aer-obic composting of broiler manure and swine manure was carried out under natural environmental conditions. Aero-bic composting effectively removed DOX (with a removal rate > 97%) and most ARGs from animal manure. The microbial diversity and the numbers of ARGs were higher in composted swine manure compared with composted broiler manure. The microbial community structure changed during composting, and the dominant phyla of broiler manure and swine manure changed from Firmicutes to Bacteroidetes and Proteobacteria, respectively. DOX changed the structure and relative abundance of the microbial community during composting, and the relative abundance of multidrug resistance genes and mobile genetic elements (MGEs) increased, which might lead to the risk of transmis-sion of resistance in the environment. The C / N ratio, DOX concentration, Firmicutes, intl1, and intl2 were the key fac-tors driving the change in ARGs during composting. These results help to reveal the effects of DOX on microbial communities, ARGs, and MGEs during composting and clarify the possible ways to reduce the risk of resistance gene transmission in the environment.

Automated summary

Aerobic composting effectively removes doxycycline and antibiotic resistance genes from animal manure, with a removal rate of over 97%. The microbial diversity and abundance of antibiotic resistance genes are higher in composted swine manure compared to composted broiler manure. The composting process leads to changes in microbial community structure and an increase in multidrug resistance genes and mobile genetic elements.