Molecular mechanisms underlying lignocellulose degradation and antibiotic resistance genes removal revealed via metagenomics analysis during different agricultural wastes composting

In this study, the differences on the physico-chemical parameters, lignocellulose degradation, dynamic succession of microbial community, gene expression of carbohydrate-active enzymes and antibiotics resistance genes were compared during composting systems of bagasse pith/pig manure (BP) and manioc waste/pig manure (MW). The results revealed that biodegradation rates of organic matter, cellulose, hemicellulose and lignin (29.14%, 17.53%,45.36% and 36.48%) in BP were higher than those (15.59%, 16.74%, 41.23% and 29.77%) in MW. In addition, the relative abundance of Bacillus, Luteimonas, Clostridium, Pseudomonas, Streptomyces and expression of genes encoding carbohydrate- active enzymes in BP were higher than those in MW based on metagenomics sequencing. During composting, antibiotics and antibiotic resistance genes were substantially reduced, but the removal efficiency was divergent in the both samples. Taken together, metagenomics analysis was a potential method for evaluating lignocellulose's biodegradation process and determining the elimination of antibiotic and antibiotic resistance genes from different composting sources of biomass.