Fungi serve as a novel biological factor for enriching resistance genes in facultative composting, as exhibited by fungal gradient experiments

Due to the mycelial structure and extracellular secretions of fungi, fungal communities have been found to have a potential role in the spread of antibiotic resistance genes (ARGs) in soil and other environments. However, the effect of fungi on bacterial hosts and resistance genes during facultative composting remains unclear. Therefore, a fungal inhibition experiment was conducted to explore this effect. The results showed that with the addition of fungicides (cycloheximide), the activity of culturable fungi gradually decreased, but there was no significant effect on bacteria. The decrease in the abundance of active fungi that can promote bacterial activity and diffusion led to a synchronous decrease in the cooperation of the fungal community, the bacterial community, and bacterial-fungal cross-species networks. The addition of fungicides enhanced the removal of antibiotic- and metal resistance genes (from 34.32% to 51.50%, and from −173.18% to 20.97%, respectively) and mobile genetic elements (MGEs, from 38.61% to 68.02%), and the removal of hard-to-remove and high-risk ARGs was enhanced simultaneously. The decrease in the abundance of key fungi induced a decrease in the abundance of hosts (such as Lactobacillus and Anaerococcus) carrying resistance genes and MGEs, which indicated that core fungi affected the proliferation and horizontal transfer of ARGs in bacterial hosts during facultative composting, which in turn affected the succession of ARGs. This study provides direct evidence for the driving effect of fungi on resistance genes in facultative composting.