Identification of dominant sulfamethoxazole-degraders in pig farm-impacted soil by DNA and protein stable isotope probing.

Abstract Increasing introduction of antibiotic residues from humans and animal farming into the environment impacts the functioning of natural ecosystems and significantly contributes to the propagation of antibiotic resistance. Microbial degradation is the major sink of antibiotics in soil but the identification of in situ degrading populations is challenging. Here, we investigated sulfamethoxazole-degrading bacteria in soil microcosms by culture-independent DNA and protein stable isotope probing. 0.5% of the carbon from 13C 6 -labeled sulfamethoxazole amended to soil microcosms was transformed to 13CO 2 demonstrating partial mineralization of the antibiotic. DNA stable isotope probing revealed incorporation of 13C from 13C 6 -labeled sulfamethoxazole into Actinobacteria and among them into the families Intrasporangiaceae , Nocardioidaceae , and Gaiellaceae and the order Solirubrobacterales. Protein stable isotope probing demonstrated the incorporation of 13C from 13C 6 -labeled sulfamethoxazole into proteins of bacteria of the families Intrasporangiaceae , Nocardioidaceae and the order Solirubrobacterales , which is consistent with the results of DNA stable isotope probing. The 13C abundance of 60 to 80% in several taxonomically relevant proteins indicated that Intrasporangiaceae directly acquired carbon from 13C 6 -labeled sulfamethoxazole. The results highlight the crucial role of yet-uncultivated indigenous bacteria for antibiotics degradation, and the potential of cultivation-independent stable isotope based molecular approaches to elucidate the structure of antibiotic-degrading populations in complex microbial communities under natural conditions. Highlights • SMX can be mineralized in pig farm soil. • Intrasporangiaceae within the phylum Actinobacteria assimilate SMX in soil. • Stable isotope probing is a crucial method to link microbial identity to function. • DNA-SIP and protein-SIP give complementary results to identify SMX degraders. • Results contribute to rational design of treatment for SMX-containing manure. [ABSTRACT FROM AUTHOR]