Biodegradation of petroleum hydrocarbon by Gordonia oleivorans sp. nov. isolated from oil-contaminated soil

This study presents a taxonomic description of a novel strain, VNQ95 T , isolated from oil-contaminated soil in Vietnam and capable of degrading crude oil. Preliminary analysis of the 16 S rRNA gene sequence and phylogenetic tree indicated that the strain belongs to the genus Gordonia . Whole-genome analysis revealed significant genetic differences from known species within the Gordonia genus. OrthoANI (≤ 79.28%), dDDH (≤ 22.70%), and AAI (≤ 79.56%) values were markedly below the accepted species delineation thresholds, and these findings were further supported by genomic phylogenetic analyses. The G + C content of strain VNQ95 T was 67.0%. The novel strain was Gram-stain-positive, non-motile, aerobic, rod-shaped. Strain VNQ95 T was catalase-positive and oxidase-negative. Growth occurred at 15–37 °C (optimum, 28–30 °C), at pH 4.0–9.5 (optimum, pH 6.5–8.0), and in the presence of 0–8.5% (w/v) NaCl (optimum ≤ 2.5%). The predominant cellular fatty acids were C 16:0 , C 18:1 ω9c, 10-methyl C 18:0 , summed feature 3 (C 16:1 ω6c and/or C 16:1 ω7c), C 18:0 and C 14:0 . The major respiratory quinone was MK-9(H2), the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, unidentified aminolipid, unidentified phospholipids, and unidentified glycolipid. Genome analysis of strain VNQ95ᵀ revealed the genetic potential to degrade both aliphatic and aromatic hydrocarbons. The reconstructed pathways included terminal oxidation of alkanes and the degradation of benzoate, p-hydroxybenzoate, biphenyl, methoxy aromatic compounds, and 3-hydroxybenzoate, which converge into the catechol, protocatechuate, and gentisate pathways and ultimately feed into central carbon metabolism. Consistent with this genetic potential, VNQ95ᵀ demonstrated efficient biodegradation of crude oil, achieving approximately 70% removal after 5 weeks of incubation and utilizing a broad range of hydrocarbons, including n-alkanes (C 10 –C 35 ), branched alkanes and some aromatic compounds. Phylogenetic, genomic and phenotypic evidence clearly distinguished strain VNQ95 T from its closest relatives, supporting its classification as a novel species of the genus Gordonia , for which the name Gordonia oleivorans sp. nov. is proposed (type strain VNQ95 T = KACC 24002 T = CCTCC AA 2024108 T ).