Oil degradation potential and preliminary genomic insights of Pseudomonas veronii strain KHB2.9 isolated from oil-contaminated coastal soil

Abstract

Indigenous bacteria with hydrocarbon-degrading capabilities have consistently been prioritized in strategies for bioremediating oil-contaminated soils. This study reports the isolation, identification, and phenotypic characterization supported by preliminary genomic analysis of Pseudomonas veronii strain KHB2.9 from oil-contaminated sandy soil in Cam Ranh Bay, Khanh Hoa, Vietnam. The strain demonstrated robust growth in Bushnell-Haas medium supplemented with 1% crude oil, diesel, or mixed oil as the sole carbon source, with the highest biomass observed in diesel oil. Redox-based 2,6-dichlorophenol indophenol (DCPIP) assays indicated substantial hydrocarbon oxidation activity, particularly in diesel oil and mixed oil substrates. Further GC-MS analyses revealed that a preferential degradation of medium-chain n-alkanes (C13-C17), whereas only limited removal of branched isoprenoids and long-chain n-alkanes was observed for the strain KHB2.9 under aerobic conditions. The KHB2.9’s genomic analysis revealed a 2.59 Mbp draft genome with 3,010 predicted protein-coding genes, including key alkane, cycloalkane, and aromatic hydrocarbon degradation genes (alkB, pcaH, pcaD, catA, and various dioxygenase and hydrolase genes). Phylogenetic analysis clustered KHB2.9 closely with other P. veronii strains known for their ability to biodegrade hydrocarbons. In addition, strain KHB2.9 exhibited biosurfactant production, as demonstrated by drop-collapse and emulsification assays, which likely contributed to enhanced hydrocarbon bioavailability. Due to the fragmented nature of the draft genome, genomic results are interpreted conservatively and primarily used to support phenotypic observations rather than to exhaustively reconstruct metabolic pathways. These findings highlight P. veronii KHB2.9 as a promising candidate for developing microbial consortia or biopreparations for bioremediation of petroleum-contaminated saline soils in Vietnam and similar coastal environments.