Insights into NH3 and CO2 emission-related mechanisms in different fermentation bedding materials for swine using metagenomic analysis

Bedding materials in piggeries significantly influence NH 3 and CO 2 emissions. To elucidate the mechanisms underlying emission reduction in fermentation bedding systems, four treatments were evaluated: RH (100% rice husk), RS (50% rice stalks + 40% sawdust + 10% rice husk), CS (50% corn stalks + 40% sawdust + 10% rice husk), and CTS (50% cotton stalks + 40% sawdust + 10% rice husk). The microstructure, physicochemical properties, and microbial community functions were characterized using scanning electron microscopy, chemical analysis, and metagenomic sequencing. Results demonstrated that compared to the CTS group, NH 3 emissions were 130%, 202%, and 216% higher in the RH, RS, and CS groups, respectively. Similarly, CO 2 emissions increased by 33%, 6.5%, and 31% in the RH, RS, and CS groups. Pearson correlation analysis indicated that the superior performance of the CTS group was attributed to its dense fiber structure and low water retention capacity. Metagenomic profiling revealed that the relative abundances of Pseudomonas , Psychrobacter , Sphingobacterium , and Acinetobacter were significantly lower in the CTS group, while Moheibacter abundance increased dramatically, transforming the nitrogen metabolism in the fermentation bed from urea hydrolysis and nitrate reduction to ammonia oxidation and nitrate reduction. Furthermore, NH 3 emissions in the CTS group were positively associated with amino acid metabolism pathways. Notably, the CTS group exhibited a higher abundance and diversity of carbohydrate-active enzymes compared to other groups, which contributed to the reduction of NH 3 emissions. In conclusion, the mitigation of NH 3 and CO 2 in cotton stalk-based systems was likely driven by the high lignification degree, the carbon-nitrogen ratio, and pH levels. This system altered the nitrogen utilization patterns by shifting from urea hydrolysis, nitrate reduction to ammonia, nitrate reduction, while downregulating amino acid metabolism and enhancing CAZyme-mediated carbon processing. These findings provide a robust theoretical foundation for utilizing cotton stalks as an effective substrate for emission reduction in swine fermentation bedding systems. • The physical structure of high-lignin materials is stable, which can inhibit the emission of NH 3 and CO 2 . • The TC, TN, hemicellulose content and pH level are the main driving forces for the structural changes of microorganisms. • Active amino acid metabolism promotes NH 3 emission, while active carbohydrate metabolism inhibits NH 3 emission. • Sphingobacterium increases ure and nir abundances, and Moheibacter increases amo and nir abundances.