Removal of antibiotic resistance genes and mobile genetic elements in a three-stage pig manure management system: The implications of microbial community structure

In this work, the removal of antibiotic resistance genes (ARGs) in the industrial-scale pig manure management system has been investigated. Additionally, the implications of mobile genetic elements (MGEs) and microbial community structure have been discussed. During the whole period of manure management, 19 ARGs and 7 MGEs were obtained from the system. The results identified that the 9 ARGs and 2 MGEs were removed from the pig manure-based materials after composting, while 5 ARGs and 2 MGEs were still remained, indicating that the ARGs/MGEs could not be removed completely as contaminants by composting. The pig farm without additional antibiotics in-feed was still faced with the risk of ARGs/MGEs from outside. Microbial community analysis illuminated that a greater decrease in the abundance of norank_f__JG30-KF-CM45, Corynebacterium, Terrisporobacter, Truepera, Salinispora and Clostridium, was responsible for the removal of ARGs/MGEs. The genes, including tnpA-01, tnpA-02, tnpA-05, Tp614, tetQ, tetM-01, tetR-02, tetX, cfxA, floR, dfrA1 and ermF exhibited significantly positive correlation with fungal communities. Fungal community analysis verified that a remarkable decrease in the abundance of Aspergillus and Thermomyces after composting was responsible for the ARGs/MGEs removal. The results elucidated the crucial roles of the related bacterial and fungal communities in the removal of ARGs/MGEs. The compound microbial agent assisted the temperature rise of composting, thereby changing the related microbial community structure and resulting in ARGs/MGEs removal.