Effect of Extending High-Temperature Duration on ARG Rebound in a Co-Composting Process for Organic Wastes

High levels of antibiotic resistance genes (ARGs) in compost materials pose a significant threat to the environment and human health. Conventional composting (CC) is widely adopted for waste management. However, mitigating ARG rebound in the late phase remains challenging. This work presents a strategy to extend the high-temperature duration by external heating to achieve rapid composting (RC). An innovative two-stage heating mode (first stage: day 3–6, 55 °C; second stage: day 7–10, 70 °C) was utilized in this study. We aimed to compare the removal and the rebound of ARGs and mobile genetic elements (MGEs) between RC and CC treatments and to identify the key factors driving the fate of ARGs throughout the composting process by integrating with environmental factors, external stress, MGEs, and microbial communities. The results show that on day 40, ARGs increased by 8.2 times in conventional composting. After the high-temperature duration was prolonged from 5 days to 9 days, the highest elimination rates achieved for ARGs and MGEs were 85% and 97%, respectively; concurrently, ARG rebound was suppressed compared to conventional composting. Genes resisting β-lactamase, chloramphenicol, and quinolone showed maximal removal in both treatments. The antibiotics showed a significant reduction in both treatments, with 79.3% in extended high-temperature duration composting and 75.26% in conventional composting. Network analysis revealed that Gammaproteobacteria, Clostridia, Saccharimonadia, Cyanobacteriia, and Campylobacteria were the potential hosts of various ARG subtypes, and their abundance was reduced in extended high-temperature duration composting. Redundancy analysis (RDA) and structural equation model (SEM) confirmed that temperature was the key factor in composting, while the potential hosts of MGEs and ARGs were responsible for the rebounding of ARGs in conventional composting. Prolonging composting temperature is a key strategy for the removal of contaminants from aerobic composting to achieve a safe end-product.