Comparison of Stockpiling and Composting on Reducing Antibiotic Resistant Bacteria and Resistance Genes in Beef Cattle Manure

Manure storage methods can affect the concentration and prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles, however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatments during the winter-spring cycle, but a significant reduction of ARGs erm (B) and tet (O) and (Q) over time were observed for both the composting and stockpile during the summer-fall cycle. Results from this study suggest that (1) bulking agent may be an important source of ARB and ARGs for composting; (2) during cold months the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; (3) during warm months both stockpiling and composting can be effective in reducing ARG abundance. IMPORTANCE Proper treatment of manure is essential to reduce the spread of antibiotic resistance and protect human health. Stockpiling and composting are two manure storage methods which can reduce antibiotic resistance bacteria and resistance genes, although few field scale studies have examined the relative efficiency of each method. This study examined the ability of both methods in both a winter-spring and summer-fall cycle, while also accounting for heterogeneity within field scale manure piles. This study determined that bulking agents used in composting could contribute antibiotic resistant bacteria and resistance genes. Additionally, seasonal variation could hinder the efficacy of composting in colder months due to heterogeneity in temperature within the pile; however, in warmer months, either method of manure storage could be effective in reducing the spread of antibiotic resistance.