Molecular characterization of a polycyclic aromatic hydrocarbons (PAHs) degrader, Burkholderia contaminans strain P14, isolated from aged oil-contaminated soil in Kuwait

Abstract

Soil contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals is a major concern affecting soil quality. Bioremediation is an efficient approach to decontaminate these pollutants while posing the lowest risk to the environment. This technique is based on  identifying microorganisms with the metabolic potential to degrade the pollutants. In this study, the physiochemical properties of oil-contaminated soils in Kuwait were investigated. The soil had alkaline pH (8.36) with a salinity of 0.08% and PAHs compounds were detected at high concentrations (pyrene, 1212 mg/kg), (phenanthrene, 710 mg/kg) and (fluorene 326 mg/kg). Heavy metals such as iron, aluminum, sodium, magnesium, vanadium, copper, etc., were also detected in the soil samples. Then, selective screening for PAH degraders was performed and assessed by colony forming units (CFU) and 16S rDNA gene sequences to determine their growth profiles and taxonomical identification. In total, 21 strains were selected for their resistance to PAHs, which include Pseudomonas (9), Burkholderia (6), Bacillus (2), Bordetella (1), Microbacterium (1), Micrococcus (1), and Kocuria (1). Among all, the growth by Burkholderia sp. P14, in the presence of phenanthrene and fluorene, has maintained a stationary phase from day 5 to 8 with a 6 log CFU/ml bacterial count. The draft genome of the Burkholderia contaminans P14 strain comprised 68 contigs with 8,584,157bp, 66% GC content, 4 rRNA and 75 tRNA. A total of 80 genes were involved in the degradation of the benzoate, naphthalene, and PAH . Genes that encode the PAH degradation were clustered into four distinct groups, including pcaHG, pcaB, pcaIJ, and pcaKFR and were found to be in contigs 5, 11, 8 and 13 of B. contaminans P14, respectively. KEGG analysis suggested that PAHs were degraded in P14 via the protocatechuate and catechol branches of the β-ketoadipate protocatechuate degradation pathway. The genomic island regions in P14 differed from those in the reference genome of B. contaminans M14, indicating the novelty and genomic recombination of the strain. Genomic information on P14 has helped clarify the molecular mechanisms involved in PAH catabolism. Burkholderia contaminans P14 strain will enhance the bioremediation of oil-contaminated soils.