Increasing levels of antibiotic resistance in clinical settings has led many to believe that animal agriculture antibiotic use is contributing to the global resistance problem; however, that connection is unclear given the limited understanding of antibiotic resistant bacteria (ARB) and resistant genes (ARG) in the soil and water environment. Our previous work has documented differences in ARG concentrations in drainage when compared to measured concentrations of U.S. EPA recommended indicator bacteria. Here, we propose laboratory experiments in a controlled column environment, representative of an agroecosystem, to (1) identify the diversity and quantify the abundance of ARGs and their hosts in manure, soils with varying management histories, and simulated subsurface drainage; and (2) identify the diversity and quantify the abundance of mobile genetic elements and their linkages to ARGs. Results will provide valuable insight into i) the microbial community harboring ARGs and ii) horizontal gene transfer processes occurring in agricultural systems.