Molecular and physiological comparison of two hydrocarbon degrading Rhodococcus strains
1*Krisztián Laczi ; 1Ágnes Kis ; 2Attila Bodor ; 1Gábor Rákhely ; 1Katalin Perei ;
1 University of Szeged, Department of Biotechnology, Hungary; 2 Corax Bioner Zrt., -, Hungary;
Rhodococci are Gram+ rods belonging to the Nocardiaceae family of the order Actinomycetales.
These ubiquitous bacteria can be commonly found in soil and water. Rhodococci have a remarkably large set of enzymes for decomposition of various chemicals. The rhodococcal cell surface is usually hydrophobic due to the mycolic acid moieties which are attached to the arabinogalactane part of cell wall. Consequently, these bacteria can easily attach to hydrophobic compounds/surfaces. A hydrocarbon degrader bacterium strain was isolated in our lab, which was identified as Rhodococcus sp. MK1. The whole genome of the strain was sequenced using SolidTM next generation sequencer. The reads were mapped on the genome of Rhodococcus erythropolis PR4 strain (NCBI database, NC_012490.1), which was previously recognized as the closest relative of the isolated strain. The genome sequence is 6,9Mbp long and covers 79% of the reference genome. In silico analyis of the genomes disclosed that both strains contained genes of at least 34 monooxygenases and many other enzymes which might be involved in hydrocarbon biodegradation. A comparative whole transcriptome analysis of the MK1 strain was performed using cells grown on n-hexadecane and Luria-broth. Two-fold or higher change in relative transcription level was considered as significant. There were 986 genes which had elevated expression level in the culture grown on n-hexadecane. Transcriptional regulators, ABC transporters, enzymes involved in n-alkane oxidation and fatty acid metabolism had the most potent increase in expression. Seven monooxygenases had highly elevated expression under hydrocarbon degrading conditions; two of them were alkane-1-monooxygenases.
Monooxygenase expression data were confirmed by RT-qPCR experiments on both Rhodococcus sp. MK1 and Rhodococcus erythropolis PR4. Hydrocarbon contamination may occur both in soil and water. Therefore, we tested the hydrocarbon degrading efficacy of the two Rhodococcus strains in three different niches: potting soil, saltwater medium and minimal medium. We kept track of respiration and hydrocarbon consumption in the three medium and calculated carbon and oxygen balance. Our results suggest that both strains are equally efficient
hydrocarbon degrader in potting soil, however, the PR4 strain is more potent in water based niches. High salinity condition slightly decreases the hydrocarbon degradation rate of both strains as compared to hydrocarbon consumption on minimal medium. The carbon and oxygen balance estimations suggested that the hexadecane was dominantly converted into biomass.
Acknowledgement: This research was realized in the frames of TÁMOP 4.2.4. A/2-11-1-2012- 0001 „National Excellence Program – Elaborating and operating an inland student and researcher personal support system convergence program” The project was subsidized by the European Union and co-financed by the European Social Fund.” The presentation is supported by the European Union and co-financed by the European Social Fund (grant agreement no. TÁMOP- 4.1.1.C-12/1/KONV-2012-0012).
