Application of manure from cattle administered antibiotics has sustained multi-year impacts on soil resistome and microbial community structure

In agroecosystems, application of manure from livestock treated with antibiotics has the potential to spread antibiotic compounds, resistant bacteria, and antibiotic resistance genes (ARGs) to soil. Although environmental transmission of antibiotic resistance is a major human health concern, few studies have looked at long-term effects on soil microbial communities from applying manure from livestock administered antibiotics. We examined the impacts of three years of repeated manure additions from cattle under different antibiotic treatments on microbial community structure and ARG abundances. While manure additions altered both soil bacterial and fungal communities, manure from cattle administered antibiotics further altered soil bacterial communities, but not fungal, compared to manure from antibiotic-free cattle. Furthermore, addition of manure from antibiotic-free cattle resulted in increased abundances of several ARGs compared to soil with no manure inputs, but manure from cattle administered antibiotics did not change overall profiles of ARG abundances compared to manure from antibiotic-free cattle. Finally, although bacterial and fungal community structure and ARG abundances varied among years, manure treatment effects on each were persistent during the full three-year period. Taken together, our results suggest that manure and antibiotic impacts on soil microbial communities can persist for long periods of repeated manure application. Furthermore, soil management strategies for addressing the antibiotic resistance crisis should consider the broader context of manure management. •Manure and antibiotics affected bacterial and fungal communities differently.•Antibiotic-free manure increased antibiotic resistance genes (ARGs) in soil.•Manure from cattle administered antibiotics had little additional effect on ARGs.•Impacts persisted over multiple years with repeated manure application.