Pangenome analysis and physiological characterization of Gordonia alkanivorans strains capable of utilizing persistent organic pollutants

Representatives of the bacterial species Gordonia alkanivorans are known as degraders of persistent organic pollutants. We studied 11 G. alkanivorans strains (96, 144, 124, 129, 132, 133, 134, 142, 12, 51, GR1) isolated from various natural sources. All studied strains utilized alkanes from C₁₀ to C₂₂ and benzoate; some strains used dibenzothiophene as a sole source of sulfur. Genomes of all strains were sequenced and assembled. The pangenome of G. alkanivorans strains is represented by 4586 genes where 3606 genes (78.6%) formed the core genome.

The DDH value of the strains with the type strain G. alkanivorans NBRC16433 (BACI00000000) is in the range of 78.10-91.00%, indicating some heterogeneity of the species. Based on the results of genome analysis and individual unique genes, strains can be divided into 2 groups within the species. The representatives of the first group (strains 129, 144, 132, 133) are characterized by unique genes of tyrocidine and gramicidin biosynthesis. The representatives of the second group have a greater catabolic potential: genomes of the strains contained 1) operons for the biosynthesis of steroid compounds, 2) additional copies of genes involved in dibenzothiophene catabolism, and 3) genes of aromatic compound catabolic process: Cytochrome P450-pinF2 and Phenol hydroxylase P5. All studied G. alkanivorans strains lack alkB genes in their genomes; therefore, we assume that ability to utilize alkanes in these strains is controlled by the CYP153 genetic system. The CYP153 hydroxylases have at least 99% identity between strains and contain one amino acid substitution each: one hydroxylase has A/T variants at position 239 and the other hydroxylase has A/S variants at position 7 in the first and second strain groups, respectively.

The presented study reveals that the G. alkanivorans strains are metabolically versatile and could be used in bioremediation of soils contaminated with aliphatic and aromatic pollutants.

This work was financially supported by the Russian Science Foundation, grant number 22-74-10082.