The Fate of Antibiotic Resistance Genes and Their Influential Factors During Large-Scale Cattle Manure Composting

Animal manure represents a critical reservoir that facilitates the dissemination of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). However, the current understanding of ARG evolution during extensive composting remains insufficient. This study systematically investigated two common aerobic composting techniques: push-flow trough composting (FC) and membrane-covered composting (FM). Results indicated that both processes demonstrated substantial antibiotic removal capacities, achieving total removal rates of 88.89% (FC) and 79.20% (FM). Nevertheless, their effectiveness in removing ARGs varied considerably. During the 31 days of composting, the total removal rates of ARGs were 59.97% (FC) and 76.11% (FM), while the removal rates for class 1 integron (intI1) were 2.31% (FC) and 69.13% (FM). With the exception of tetX, tetG, and tetW, all other ARGs exhibited a rebound during the later stage of the FC process. In contrast, the FM process effectively reduced the risk of ARG rebound during this phase, which can be attributed to its extended thermophilic period and the physical barrier effect of the semi-permeable membrane. Network analysis indicated that ARGs were primarily associated with Bacillota and Pseudomonadota. The Partial Least Squares Path Model (PLS-PM) revealed that the bacterial community was the main factor influencing ARG dynamics in FC, while in FM, both the bacterial community and intI1 were the primary drivers. This study provides critical insights for optimizing composting strategies to prevent the dissemination of antibiotic resistance.