Simulated Winter Incubation of Soil With Swine Manure Differentially Affects Multiple Antimicrobial Resistance Elements

Gastrointestinal bacteria that harbor antibiotic resistance genes (ARG) become enriched with antibiotic use. Livestock manure application to cropland for soil fertility presents a concern that ARG and bacteria may proliferate and be transported in the environment. In the United States, manure applications typically occur during autumn with slow mineralization until spring planting season. A laboratory soil incubation study was conducted mimicking autumn swine manure application to soils with concentrations of selected ARG monitored during simulated 120-day winter incubation with multiple freeze-thaw events. Additionally, the effects of two soil moistures [10 and 30% water holding capacity (WHC)] and two manure treatments [raw versus hydrated lime alkaline stabilization (HLAS)] were assessed. Fourteen tetracycline resistance genes were evaluated; (D), (G), and (L) were detected in background soil while swine manure contained (A), (B), (C), (G), (M), (O), (Q), and (X). By day 120, the manure-borne (M) and (O) were still detected while (C), (D), (L), and (X) genes were detected less frequently. Other resistance genes were detected rarely, if at all. The sum of unique resistance genes among all treatments decreased during the incubation from an average of 8.9 to 3.8 unique resistance genes. Four resistance elements, I1, , (I), (B), and 16s rRNA genes were measured using quantitative PCR. ARG abundances relative to 16S abundance were initially greater in the raw manure compared to background soil (-1.53 to -3.92 log abundance in manure; -4.02 to