Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils

The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.