Pyrene biodegradation and its potential pathway involving Roseobacter clade bacteria

Microbial mineralization plays a significant role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. Bacteria affiliated to the Roseobacter clade are ubiquitous and abundant in various environments, including PAH-polluted areas. However, very little is known about the PAH degradation mechanism utilized by the Roseobacter clade. In this study, eight bacterial strains belonging to the Roseobacter clade were isolated from sediments collected from the estuary of the Pearl River. Degradation of pyrene and two other typical PAHs (phenanthrene and benzo[a]pyrene) was studied in the eight isolated strains of Roseobacter clade bacteria (RCB) and three other type strains. The results revealed that all strains had low PAH-degrading efficiency when PAHs were used as the sole source of carbon. However, upon supplementation with an alternative carbon source, the degradation was greatly stimulated. This implies that RCB degrade PAHs via a co-metabolism pathway. A putative pyrene degradation pathway in RCB was re-constructed based on genomic analysis. pahE, a functional marker gene for PAH degradation, was detected in the genomes of RCB. PAH ring-hydroxylating dioxygenase alpha subunit domain family and beta subunit domain family and PAH degradation-related Rieske [2Fe–2S] domain were also identified in the test strains. These findings provide fundamental evidence that RCB are capable of degrading PAHs through a versatile metabolic pathway.