Draft Genome Sequence of the Piezotolerant and Crude Oil-Degrading Bacterium Rhodococcus qingshengii Strain TUHH-12

The 2010 Deepwater Horizon oil spill and the recent expansion of deep-sea drilling highlight the importance of understanding biodegradation processes that control the long-term fate of hydrocarbons in deep marine sediments. Although high pressure can inhibit the growth of sedimentary hydrocarbon-degrading bacteria (1), laboratory biodegradation studies are typically performed at ambient pressure, and the extent to which their results are applicable to the deep ocean is uncertain. Comparative studies of piezotolerant hydrocarbon-degrading bacteria grown at surface and deep-sea pressures may help identify the biochemical mechanisms responsible for pressure-related inhibition.

We report here the draft genome sequence of Rhodococcus qingshengii strain TUHH-12, which we have used in high-pressure hydrocarbon degradation studies (2). This strain was isolated from water underlying sea ice in Spitsbergen, Norway, by aerobic enrichment at 4°C in mineral medium supplemented with crude oil and decane. The recent isolation of another R. qingshengii strain (GenBank accession no. KC894023.1) from marine sediment suggests that the results of experiments using R. qingshengii strain TUHH-12 are relevant for deep-sea biodegradation studies.

We sequenced 100 ng of genomic DNA extracted from R. qingshengii TUHH-12 using an Ion PGM system (Life Technologies, Carlsbad, CA), generating 1,319,688 reads, with an N₅₀ of 226 bp, an average length of 205 bp, and a G+C content of 61.7%. The coverage was approximately 35×. The reads were assembled using SPAdes (version 3.0.0 [3]), resulting in 349 contigs, with a total sequence length of 7,430,810 bp and an N₅₀ of 133,054 bp. The longest contig was 418,804 bp. The contigs were annotated using RAST (4).

Rhodococci are agents of contaminant biodegradation in diverse environments. Their large genomes enable catabolic versatility, as alkanes, polycyclic, and halogenated aromatic hydrocarbons, as well as ether bond-containing compounds, such as ethyl tert-butyl ether (ETBE), can all serve as carbon substrates for Rhodococcus species (5).

The R. qingshengii TUHH-12 genome encodes multiple alkane-1 monooxygenases and putative cytochrome P450 hydroxylases, which are components of aerobic alkane degradation pathways. Enzymes in the homogentisate pathway of aromatic compound degradation that are present in the TUHH-12 genome include homogentisate 1,2-dioxygenase, fumarylacetoacetase, 4-hydroxyphenylpyruvate dioxygenase, and IclR family transcriptional regulators. Dehalogenation pathways are represented by haloalkane and type II haloacid dehalogenases. A putative ETBE degradation gene is present. The TUHH-12 genome also encodes probable dibenzothiophene desulfurization pathway enzymes, including multiple copies of dibenzothiophene desulfurization enzyme B.

The capacity for exopolysaccharide (EPS) biosynthesis by TUHH-12 is indicated in the genome by the presence of glycosyl transferase, galactose phosphotransferase, undecaprenyl-phosphate galactose phosphotransferase, GDP-l-fucose synthetase, and other genes associated with capsular EPS production. EPS is thought to enhance hydrocarbon solubilization and floc formation by rhodococci (6) and other hydrocarbon-degrading bacteria, and it likely promoted the formation of oil-rich aggregates in the Gulf of Mexico following the Deepwater Horizon oil spill (7).

Comparative transcriptomic studies of R. qingshengii TUHH-12 grown under ambient laboratory and simulated seafloor pressure conditions will likely provide new insights into hydrocarbon degradation in the deep sea.

We thank Hauke Trinks (Hamburg University of Technology) for the collection of sea ice samples and the Genomics Core Facility at the Huck Institutes of the Life Sciences at Penn State for sequencing.

This research was made possible by a grant from BP/The Gulf of Mexico Research Initiative through the C-IMAGE Consortium.