ABSTRACT
Enterobacter sp. strain ODB01, which was isolated from the Changqing oil field, can degrade crude oil efficiently and use crude oil as its sole source of carbon and energy. We report the complete genome sequence of ODB01. The results promote its application in the remediation of petroleum contaminants.
GENOME ANNOUNCEMENT
Crude oil, also known as petroleum, is unrefined oil exploited from oilfields and contains large amounts of complex hydrocarbons such as paraffins, aromatics, cycloalkanes, and alkenes. Toxic chemicals in the crude oil emphasize the importance of isolating beneficial microorganisms in the bioremediation of oil spills and deep-sea drilling sites (1). Numerous strains, which commonly belong to Pseudomonas sp., Acinetobacter sp., Bacillus sp., and Dietzia sp., were screened and categorized based on their oil degradation abilities (2). Previous studies have demonstrated monooxygenase and/or dioxygenase as rate-limited enzymes that control petroleum degradation (3). Therefore, it is particularly important to mine crude oil-degrading microorganisms with various oxygenase activities when performing the bioremediation of the crude oil contaminants. The Enterobacter sp. strain ODB01, which was isolated from the Changqing oilfield, can degrade crude oil efficiently and use crude oil as its sole source of carbon and energy. Strain ODB01 is a Gram-negative, aerobic, motile, and rod-shaped strain, but little has been known about the molecular mechanism of strain ODB01 in crude oil degradation, so we sequenced the complete genome of Enterobacter sp. strain ODB01.
The genomic DNA of ODB01 was extracted using the TaKaRa MiniBEST bacteria genomic DNA extraction kit. The quantity and quality of genomic DNA were assessed on the Agilent 2100 Bioanalyzer (Agilent, USA). Genomic DNA of strain ODB01 was sequenced using single molecular sequencing technology with the PacBio RS II system (Nextomics Biosciences, Wuhan, China) (4). De novo assembly was accomplished using the PacBio hierarchical genome assembly process (HGAP2.2.3) (5). The gene sequence was predicted using GLIMMER (Gene Locator and Interpolated Markov ModelER) software (version 3.02), which adopts the interpolated Markov models (IMMs) (6). The clustered regularly interspaced short palindromic repeats (CRISPRs) were identified using CRISPRs Finder (7).
This workflow resulted in one contig, a circular chromosome with 4,534,036 bases in the ODB01 strain. This chromosome consists of 54.81% G+C content, 4,117 predicted coding sequences (CDSs), nine rRNA (5S) genes, eight rRNA (16S) genes, eight rRNA (23S) genes, 88 tRNA genes, eight noncoding (ncRNAs), and 61 pseudogenes. In addition, four CRISPRs clusters were identified by CRISPRs Finder, which might provide acquired resistance against foreign genetic material (8).
The analysis of the Enterobacter sp. strain ODB01 annotated genome prompted the discovery of multiple oxygenase genes that may act as key enzymes for hydrocarbon-pollutant degradation pathways, including quercetin 2,3-dioxygenase, anthranilate 1,2- dioxygenase, 3,4-dihydroxyphenylacetate 2,3-dioxygenase, vanillate O-demethylase oxygenase, naphthalene 1,2-dioxygenase, quinol monooxygenase, taurine dioxygenase, acireductone dioxygenase, alkanesulfonate monooxygenase, toluene-4-sulfonate monooxygenase, pyrimidine monooxygenase, monooxygenase MoxC, dioxygenase AlkB, and other monooxygenases. Based on this knowledge, aromatics are believed to be bioconverted to salicylic acid through the actions of a series of oxygenases, hydroxylases, reductases, and decarboxylase, whereas alkanes can be oxidized by monooxygenases such as MoxC in strain ODB01.
The above results provide preliminary insight into the hydrocarbon degradation in Enterobacter sp. strain ODB01. Further research on the genome information of strain ODB01 can clarify the mechanism required for crude oil degradation and highlight strain ODB01 as a promising prospect in the bioremediation of crude-oil contaminants.
Accession number(s).
The complete genome sequence of Enterobacter sp. strain ODB01 was deposited in GenBank under accession no. CP015227.
ACKNOWLEDGMENTS
We thank LetPub (http://www.letpub.com) for its linguistic assistance during the preparation of this manuscript.
This study was supported by the National Natural Science Foundation of China (31571811), the Scientific Research Fund of Hunan Provincial Science & Technology Department (2015GK1017), the Construct Program of the Key discipline in Hunan Province and the Financial Fund of Tibet Autonomous Region.
Footnotes
Citation Lan H, Yang H, Li P, Wang C, Zhou H, Zhou H, Pan H, Yu Y, Lu X, Tian Y. 2017. Complete genome sequence of Enterobacter sp. strain ODB01, a bacterium that degrades crude oil. Genome Announc 5:e01763-16. https://doi.org/10.1128/genomeA.01763-16.
REFERENCES
- 1.Wang W, Zhang R, Zhong R, Shan D, Shao Z. 2014. Indigenous oil-degrading bacteria in crude oil-contaminated seawater of the Yellow Sea, China. Appl Microbiol Biotechnol 98:7253–7269. doi: 10.1007/s00253-014-5817-1. [DOI] [PubMed] [Google Scholar]
- 2.Haritash AK, Kaushik CP. 2009. Biodegradation aspects of polycyclic aromatic hydrocarbons (PAhs): a review. J Hazard Mater 169:1–15. doi: 10.1016/j.jhazmat.2009.03.137. [DOI] [PubMed] [Google Scholar]
- 3.Mallick S, Chakraborty J, Dutta TK. 2011. Role of oxygenases in guiding diverse metabolic pathways in the bacterial degradation of low-molecular-weight polycyclic aromatic hydrocarbons: a review. Crit Rev Microbiol 37:64–90. doi: 10.3109/1040841X.2010.512268. [DOI] [PubMed] [Google Scholar]
- 4.Roberts RJ, Carneiro MO, Schatz MC. 2013. The advantages of SMRT sequencing. Genome Biol 14:405. doi: 10.1186/gb-2013-14-6-405. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
- 6.Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641. doi: 10.1093/nar/27.23.4636. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Grissa I, Vergnaud G, Pourcel C. 2007. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics 8:172. doi: 10.1186/1471-2105-8-172. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Sternberg SH, Richter H, Charpentier E, Qimron U. 2016. Adaptation in CRISPR-Cas systems. Mol Cell 61:797–808. doi: 10.1016/j.molcel.2016.01.030. [DOI] [PubMed] [Google Scholar]