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Antimicrobial resistant infections pose a continued threat to human and animal health globally. This work critically evaluated antimicrobial resistance genes (ARGs) present in manure to better quantify and assess the potential human and animal health risks associated with exposure to manure. We first present a systematic review and meta-analysis that identified trends in ARG abundances in cattle manures. We found that the lack of biological replication and insufficient overlap of gene targets between studies prohibited quantitative cross-study comparisons. The meta-analysis identified important methodological gaps and will inform the design of future studies that more effectively and rigorously evaluate ARG abundances in manure. To address the low-throughput limitation of quantitative PCR (qPCR) approaches to quantify gene concentrations, we developed a novel metagenomic gene quantification approach that is achieved via spike-in standards. We found this approach performed comparably to qPCR when applied to specific ARGs yet facilitates the absolute quantification of all ARG concentrations in metagenomes. We then applied this quantitative metagenomic approach to better identify how ARG abundance and microbial community structure vary in different stored manures. With a cross section of manure collected from dairy farms during land application, we found anaerobic digestion treatments correlated with organism and ARG concentrations. This demonstrated that manure management, including anaerobic digestion, shapes manure microbial communities. Finally, to address the complexity of microbial interactions in soil after land application of manures, we introduce a novel mathematical modeling approach. We demonstrate how the approach can extract microbial network dynamics from time-series observations of microbial communities and outline how the approach can be used to quantify the impact of disturbances, like land application, on microbial community dynamics. This dissertation contributes important new tools to better quantify risks of ARG pollution and dissemination in the environment and clarifies the role of manure management in mitigating ARG abundances. Ultimately this work will better inform policy for manure management and land application to reduce the risk of ARG dissemination in the environment and consequently reduce the human and veterinary cost of antimicrobial resistance.