Isolation and substrate screening of polycyclic aromatic hydrocarbon degrading bacteria from soil with long history of contamination

• PAH-degrading bacteria were isolated from bare and planted aged-contaminated soil.
• They belonged to 3 subgroups of Pseudomonas, of which 2 were favored with plants.
• They showed contrasted metabolic capabilities towards 61 organic compounds.
• Genetic/chemical evidence suggests phenanthrene is degraded via protocatechuate.

Microbial degradation is a promising soil remediation strategy for polycyclic aromatic hydrocarbons (PAHs) frequently polluting some post-industrial environments. Thirteen PAH-degrading bacterial strains were isolated from bare or ryegrass-vegetated aged-contaminated soil, based on their potential for phenanthrene biodegradation. 16S rRNA gene phylogeny showed that all isolates were affiliated with three closely related taxonomic subgroups within the Pseudomonas genus. Two of these subgroups were exclusively retrieved from planted soil. Genes encoding PAH-ring hydroxylating dioxygenases were detected in all strains and matched known sequences in other Pseudomonas strains from polluted environments. Genes for protocatechuate-3,4-dioxygenases (pcaH) and catechol-2,3-dioxygenases were also detected in all strains, whereas the catechol-1,2-dioxygenase gene was absent. The presence of pcaH genes, the utilization of protocatechuate, the strong inhibitory effect of salicylate and the detection of phthalate during phenanthrene biodegradation suggest that these isolates preferentially catabolize PAHs via the protocatechuate pathway. Metabolic profiling was further performed for three representative isolates on a large range of 61 organic substrates. Although closely related phylogenetically, they were able to use different sets of labile carbon compounds (e.g. sugars, amino acids), PAHs and their metabolites, and released different degradation products from phenanthrene. These contrasted metabolic capabilities might reflect differential adaptation to their respective environment.