Impact of repeated applications of antibiotic containing swine manures on the microbial diversity, nitrification, horizontal transfer and antibiotic resistance markers of agricultural soils

Use of animal manure for soil fertilization may facilitate veterinary antibiotic (VA) release, and antibiotic resistance gene (ARG) and pathogen dispersal, threatening environmental quality and human health. In two agricultural soils, we studied the fate and effects of swine manure mediated application of three VAs, the well-studied sulfamethoxazole (SMX), and the understudied tiamulin (TIA) and tilmicosin (TLM), on the soil microbial community, antibiotic resistance genes and the intl1. Manure introduced significant microbial biomass and diversity, which, in its majority, declined relatively fast (<15 days). Repeated antibiotic applications led to accelerated dissipation of TIA and TLM (but not for SMX), with associated patterns differing significantly according to soil type and application method. The nitrification markers showed strong responses to the antibiotics, but no manure associated effects were observed for nitrifiers and associated activity. Total prokaryotes and ammonia(um) oxidisers showed antibiotic treatment associated community structural shifts whereas fungi and protists followed manure application dependent patterns. SMX triggered an antibiotic specific ARG response, while manure was catalytic for ARG and intl1 abundances, while clostridia seem to play important roles as environmental ARG reservoirs. Our results suggest that VAs warrant more attention and detailed studies like the one presented here.