Genomic and transcriptomic characterization revealed key adaptive mechanisms of Marinobacter hydrocarbonoclasticus NI9 for proliferation and degradation of jet fuel

Marinobacter hydrocarbonoclasticus NI9 has the ability to degrade short-chain alkanes (n-C6 to n-C8), which provides a competitive advantage over other microorganisms. Therefore, we sequenced NI9's genome and analyzed its transcriptome using RNAseq when growing in jet fuel. The genome (3.98 Mb) has at least two alkane monooxygenase genes that are differentially expressed with monooxygenase FH712_RS17105 being highly induced compared to monooxygenase FH712_RS06210. FH712_RS17105 is clustered in an operon with a long-chain-fatty-acid--CoA ligase, an aldehyde dehydrogenase family protein, and rubredoxin. The entire gene cluster was induced along with several dioxygenase and cytochrome P450 genes. Genome analyses further revealed aupA and aupB genes encoding proteins involved in the uptake of micelle-solubilized alkanes. M. hydrocarbonoclasticus NI9 cells achieved fuel tolerance through the activation of efflux pumps and blockage of the efflux pumps with an efflux pump inhibitor significantly reduced NI9 growth in fuel. We identified a fuel-inducible RND-efflux pump, which is an orthologue of the P. aeruginosa MexB. M. hydrocarbonoclasticus NI9 also induced ABC iron transport mechanisms suggesting that there is a high demand for iron during fuel degradation. The results collectively suggest that M. hydrocarbonoclasticus NI9 employ similar adaptive mechanisms to those in P. aeruginosa to proliferate in hydrocarbon-containing environments.