Dynamic changes of resistance genes and carbohydrate enzyme genes in different agricultural waste fermentation beds based on metagenomics analysis

Waste fermentation bed materials from pig farms are often used as organic fertilizers; however, they are a significant source of microorganisms carrying antibiotic-resistance genes (ARGs). Microbes from fermentation bed materials readily introduce ARGs into the soil, causing environmental pollution. We designed four treatments, including RH (rice husk 100 %), RS (rice stalks 50 %, sawdust 40 %, and rice husk 10 %), CS (corn stalks 50 %, sawdust 40 %, and rice husk 10 %), and CTS (cotton stalks 50 %, sawdust 40 %, and rice husk 10 %). The dynamic changes and distribution mechanisms of ARGs in different material fermentation beds are revealed through metagenomic sequencing. The research results indicate that (1) Glycoside hydrolases can increase the abundance of ARGs, while glycosyl transferases can decrease the abundance of ARGs. (2) Lignin promotes the accumulation of glycoside hydrolases, while cellulose and hemicellulose promote the accumulation of glycosyl transferases. (3) At the genus level, Pseudomonas, Parapedobacter, Sphingobacterium, Flavobacterium, Lysobacter, and Myroides mainly rely on their cell membranes to develop ARGs. (4) High lignin content can reduce the accumulation of ARGs, while high cellulose and hemicellulose content can increase the accumulation of ARGs. The results provide a theoretical basis for selecting padding materials that can be widely applied in fermentation bedding systems.