Prairie strips remove swine manure associated antimicrobial resistance genes and bacteria from runoff

Runoff from manured agricultural fields can transport antimicrobial resistance (AMR) contaminants, including genes and bacteria, to downstream ecosystems. Previous work has identified the integration of Conservation Practice 43 (CP 43) prairie strips – a type of vegetative filter strip – within and at the edge of agricultural fields as a potential management solution to reduce the movement of these, and other, manure pollutants, while offering an opportunity for biodiversity conservation. The objectives of this study were to 1) quantify the ability of prairie strips to reduce the presence of antimicrobial resistance genes from manure laden runoff, and 2) characterize the impact of manure on prairie soil microbiomes over time. Simulated rainfall events were used to create artificial runoff on field plots with swine manure amendment and prairie strips as treatment factors. A suite of antibiotic resistance genes and mobile genetic elements were characterized in runoff samples collected during the rainfall simulation, while manure associated bacteria were characterized in soil samples collected over 153 days after the rainfall simulation. Prairie strips placed downslope from manured crop soil significantly reduced the cumulative abundance of resistance genes in both runoff water (p-value < 0.0001) and runoff sediment (p-value < 0.0001). Manure associated bacteria were transported both horizontally, from the manure amended crop soil into the prairie strip soil, and vertically, into the crop and prairie strip soil profiles. The specific manure associated gene tet(M) and the specific manure associated bacterial genus Clostridium sensu stricto 1 were highly enriched in manured runoff and soil, respectively, and could represent future targets of human health concern. Results from this study provide further support for the use of CP 43 prairie strips as a management practice to reduce the transport of manure associated resistance contaminants off agricultural fields.