Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting

This study investigated the effects of adding copper at 3 treatment levels (0 (control: CK), 200 (low: L), and 2000 (high: H) mg.kg(-1) treatments) on the bacterial communities during swine manure composting. The abundances of the bacteria were determined by quantitative PCR and their compositions were evaluated by high-throughput sequencing. The results showed that the abundance of bacteria was inhibited by the H treatment during days 7-35, and principal component analysis clearly separated the H treatment from the CK and L treatments. Actinobacteria, Firmicutes, and Proteobacteria were the dominant bacterial taxa, and a high copper concentration decreased the abundances of bacteria that degrade cellulose and lignin (e.g., class Bacilli and genus Truepera), especially in the mesophilic and thermophilic phases. Moreover, network analysis showed that copper might alter the co-occurrence patterns of bacterial communities by changing the properties of the networks and the keystone taxa, and increase the competition by increasing negative associations between bacteria during composting. Temperature, water-soluble carbohydrates, and copper significantly affected the variations in the bacterial community according to redundancy analysis. The copper content mainly contributed to the bacterial community in the thermophilic and cooling phases, where it had positive relationships with potentially pathogenic bacteria (e.g., Corynebacterium_1 and Acinetobacter).