Genome-guided identification and characterization of bacteria for simultaneous degradation of polycyclic aromatic hydrocarbons and resistance to hexavalent chromium

Bacteria capable of simultaneously degrading organic pollutants and resisting heavy metal contamination are vitally important in bioremediation. However, such bacteria are difficult to obtain and our understanding of their potential use in remediation remains limited. Here, using rhd and chrA as gene markers for PAHs-degradation and Cr (VI)-resistance, genome mining revealed that 11.62% of surveyed species contained both rhd and chrA genes. These bacteria were affiliated to 13 phyla in which Pseudomonas, Acinetobacter, Bacillus, Halomonas, Rhizobium, and Burkholderia were the most prominent genera. Culture-dependent isolation and genome-guided functional validation identified two novel phenanthrene (Phe)-degrading and Cr (VI)-tolerant strains, Pseudarthrobacter phenanthrenivorans J015 and Croceicoccus naphthovorans PQ-2(T). J015 showed an extraordinary potential for Phe-Cr (VI) bioremediation. It could completely degrade 100 mgl(-1) Phe within 17 days under 30 mgl(-1) K2Cr2O7 stress, and could be further improved by optimization of cultivation conditions. Quantitative real time PCR (qRT-PCR) analysis showed that Phe or Cr (VI) affected the expression of chrA or rhd genes in J015, respectively. Overall, Phe-degradation and Cr (VI)-resistance by J015 interacted with each other in a complex pattern. Genome-guided prediction and functional validation is a valuable alternative to culture dependent isolation for exploring PAHs-Cr (VI) bioremediation resources.