Genomic Insights into Pseudomonas sp. VD9: A Naphthalene-Degrading and Exopolysaccharide-Producing Strain

This paper presents the results of a comprehensive study of a new, plasmid-free strain of Pseudomonas sp. VD9 isolated from oil-contaminated soil. It addresses the lack of data on the structure and functional properties of exopolysaccharide (EPS) capsules in natural strains that can biodegrade aromatic and aliphatic hydrocarbons, particularly when cultivated on non-carbohydrate substrates. This study aimed to characterise the genome, physiology, biochemistry and morphology of strain VD9, focusing on its hydrocarbon degradation potential and the structure and composition of the capsular exopolysaccharide. Whole-genome sequencing, extended annotation, and bioinformatics were used in this study, in addition to comparative phenotypic and physiological analyses of growth on various substrates, electron microscopy, thin-layer chromatography of the capsule and expression analysis of key EPS synthesis genes. Strain VD9 demonstrated effective degradation of naphthalene (69.7% in 72 h) and limited degradation of decane (25.9% in 77 h), maintaining a developed fibrillar capsule regardless of the carbon source used. The chromosome of the strain bears a complete set of genes for hydrocarbon catabolism and structural polysaccharide synthesis. Notably, the expression of rml and wbbL was observed under different growth conditions, indicating their constitutive transcription. Strain VD9 demonstrated constitutive production of a developed fibrillar capsule, irrespective of the carbon source utilised. This may be indicative of adaptation to oil-contaminated conditions. The novelty of this study lies in demonstrating constitutive capsule production in a plasmid-free, oil-degrading strain capable of efficiently degrading aromatic hydrocarbons.