Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health. The previously isolated phenanthrene-degrading bacterial consortium (PDMC) consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs. To identify the degradation mechanism of PAHs in the consortium PDMC, metagenomic binning was conducted and a Sphingomonadales assembly genome with 100% completeness was obtained. Additionally, Sphingobium sp. SHPJ-2, an efficient degrader of PAHs, was successfully isolated from the consortium PDMC. Strain SHPJ-2 has powerful degrading abilities and various degradation pathways of high-molecular-weight PAHs, including fluoranthene, pyrene, benzo[a]anthracene, and chrysene. Two ring-hydroxylating dioxygenases, five cytochrome P450s, and a pair of electron transfer chains associated with PAH degradation in strain SHPJ-2, which share 83.0%–99.0% similarity with their corresponding homologous proteins, were identified by a combination of Sphingomonadales assembly genome annotation, reverse-transcription quantitative polymerase chain reaction and heterologous expression. Furthermore, when coexpressed in Escherichia coli BL21(DE3) with the appropriate electron transfer chain, PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene, while PhnA2B2 degrade fluoranthene. Altogether, these results provide a comprehensive assessment of strain SHPJ-2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation. Impact statement Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and have attracted widespread attention due to their adverse effects. Several bacteria acquired the capability to degrade PAHs, with Sphingobium strains being the most dominant genus. However, the degradation mechanisms in Sphingobium strains that degrade high-molecular-weight PAHs are poorly understood. Here, Sphingobium sp. strain SHPJ-2, a highly efficient PAH degrader in the phenanthrene-degrading bacterial consortium, was identified and characterized. In addition, several ring-hydroxylating dioxygenases and P450s which can degrade high-molecular-weight PAHs were also identified. Our findings reveal that strain SHPJ-2 has efficient PAHs-degrading genetic resources and could help unveil the degradation mechanisms related to PAH degradation in Sphingomonads.