Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge

► High prevalence of biodegradation genes was reported in activated sludge. ► The p450 gene was determined as the most abundant biodegradation gene. ► The pmo (2-monoxygenase) gene was the most dominant phenol degradation gene. ► Approximately 11.5–40.0% of biodegradation genes were carried on plasmids. ► Mycobacterium was the dominant population for degrading organic pollutants. The abundance, diversity, and distribution of biodegradation genes (BDGs) and phenol degradation genes (PDGs) in activated sludge (AS) from two wastewater treatment plants (WWTPs) at different sampling times were assessed by metagenomic analysis using a total of 15 datasets derived from Illumina high-throughput sequencing and BLAST comparisons to BDGs and PDGs databases. The results showed that the abundance (0.015–0.030%) and diversity of BDGs in AS varied with the WWTP and the sampling times. The p450 and pmo genes were the most abundant genes in the BDGs and PDGs subgroups, respectively. MG-RAST analysis revealed that 87 detected bacterial genera potentially capable of degrading pollutants were mostly affiliated with Proteobacteria (59.8%), Bacteroidetes (17.2%), and Actinobacteria (9.2%). Mycobacterium, belonging to Actinobacteria, was found to be the most abundant genus (23.4%). This method could be used to monitor an AS’s biodegradation ability for organic pollutants and to evaluate its wastewater treatment efficiency.