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Abstract: In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 °C and pH 5.5. We sequenced the genome and found a single chromosome of 4 800 175 bp, with a G+C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified: many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains (M86, 229E, and LMG3301^T) showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.

一株分离自地层水的石油降解菌的特性研究：Ochrobactrum intermedium环境分离菌株与临床分离菌株的比较基因组分析

[1]Alikhan, N.F., Petty, N.K., Zakour, N.L.B., et al., 2011. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics, 12(1):402.

[2]Apisarnthanarak, A., Kiratisin, P., Mundy, L.M., 2005. Evaluation of Ochrobactrum intermedium bacteremia in a patient with bladder cancer. Diagn. Micr. Infec. Dis., 53(2):153-155.

[3]Aziz, R.K., Bartels, D., Best, A.A., et al., 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 9(1):75.

[4]Burge, S.W., Daub, J., Eberhardt, R., et al., 2012. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41(D1):D226-D232.

[5]Camacho, C., Coulouris, G., Avagyan, V., et al., 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10(1):421.

[6]Casjens, S., 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol., 49(2):277-300.

[7]Cheng, H., Zhang, S., Huo, Y.Y., et al., 2015. Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus. Int. J. Syst. Evol. Microbiol., 65(Pt 2):562-569.

[8]Creencia, A.R., Mendoza, B.C., Migo, V.P., et al., 2014. Degradation of residual jatropha oil by a promising lipase-producing bacterial consortium. Philipp. J. Sci., 143(1):73-78.

[9]Darling, A.E., Mau, B., Perna, N.T., 2010. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE, 5(6):e11147.

[10]Das, D., Baruah, R., Roy, A.S., et al., 2015. Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation. Genomics, 105(3):182-190.

[11]Dawar, C., Aggarwal, R.K., 2015. Draft genome sequence of hydrocarbon-degrading Pseudomonas putida strain KG-4, isolated from soil samples collected from Krishna-Godavari Basin in India. Genome Announc., 3(3):e00590-e00615.

[12]Dean, A.S., Crump, L., Greter, H., et al., 2012. Global burden of human brucellosis: a systematic review of disease frequency. PLoS Negl. Trop. Dis., 6(10):e1865.

[13]Edelstein, W., Iben, I., Mueller, O., et al., 1994. Radiofrequency ground heating for soil remediation: science and engineering. Environ. Prog., 13(4):247-252.

[14]Genouw, G., de Naeyer, F., van Meenen, P., et al., 1994. Degradation of oil sludge by landfarming—a case-study at the Ghent harbour. Biodegradation, 5(1):37-46.

[15]Griffiths-Jones, S., Bateman, A., Marshall, M., et al., 2003. Rfam: an RNA family database. Nucleic Acids Res., 31(1):439-441.

[16]Hassanshahian, M., Zeynalipour, M.S., Musa, F.H., 2014. Isolation and characterization of crude oil degrading bacteria from the Persian Gulf (Khorramshahr provenance). Mar. Pollut. Bull., 82(1-2):39-44.

[17]Hazen, T.C., Dubinsky, E.A., DeSantis, T.Z., et al., 2010. Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science, 330(6001):204-208.

[18]Holmes, B., Popoff, M., Kiredjian, M., et al., 1988. Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int. J. Syst. Bacteriol., 38(4):406-416.

[19]Holt, J.G., Krieg, N.R., Sneath, P.H., et al., 1994. Bergey’s Manual of Determinative Bacteriology, 9th Ed. Williams and Wilkins, Baltimore.

[20]Jesubunmi, C.O., 2014. Isolation of oil-degrading microorganisms in spent engine oil-contaminated soil. J. Biol. Agric. Healthcare, 4(25):191-195.

[21]Kavita, B., Keharia, H., 2012. Reduction of hexavalent chromium by Ochrobactrum intermedium BCR400 isolated from a chromium-contaminated soil. 3 Biotech, 2(1):79-87.

[22]Kulkarni, G., Dhotre, D., Dharne, M., et al., 2013. Draft genome of Ochrobactrum intermedium strain M86 isolated from non-ulcer dyspeptic individual from India. Gut Pathog., 5:7.

[23]Kulkarni, G., Shetty, S., Dharne, M., et al., 2014. Genome sequencing analysis reveals virulence-related gene content of Ochrobactrum intermedium strain 229E, a urease-positive strain isolated from the human gastric niche. FEMS Microbiol. Lett., 359(1):12-15.

[24]Kumar, V., Singh, S., Manhas, A., et al., 2014. Bioremediation of petroleum hydrocarbon by using Pseudomonas species isolated from petroleum contaminated soil. Analysis, 30(4):1771-1776.

[25]Lagesen, K., Hallin, P., Rødland, E.A., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res., 35(9):3100-3108.

[26]Larkin, M.A., Blackshields, G., Brown, N., et al., 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21):2947-2948.

[27]Lincoln, S.A., Hamilton, T.L., Juárez, A.G.V., et al., 2015. Draft genome sequence of the piezotolerant and crude oil-degrading bacterium Rhodococcus qingshengii strain TUHH-12. Genome Announc., 3(2):e00268-e00315.

[28]Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25(5):955-964.

[29]Marmur, J., Doty, P., 1962. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol., 5(1):109-118.

[30]Mata, J.A., Martínez-Cánovas, J., Quesada, E., et al., 2002. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst. Appl. Microbiol., 25(3):360-375.

[31]Möller, L.V., Arends, J.P., Harmsen, H.J., et al., 1999. Ochrobactrum intermedium infection after liver transplantation. J. Clin. Microbiol., 37(1):241-244.

[32]Mudshingkar, S., Choure, A., Palewar, M., et al., 2013. Ochrobactrum anthropi: an unusual pathogen: are we missing them? Indian J. Med. Microbiol., 31(3):306-308.

[33]Pham, V.H., Kim, J., Jeong, S.W., 2014. Enhanced isolation and culture of highly efficient psychrophilic oil-degrading bacteria from oil-contaminated soils in South Korea. J. Environ. Biol., 35(6):1145-1149.

[34]She, Y.H., Zhang, F., Xia, J.J., et al., 2011. Investigation of biosurfactant-producing indigenous microorganisms that enhance residue oil recovery in an oil reservoir after polymer flooding. Appl. Biochem. Biotech., 163(2):223-234.

[35]She, Y.H., Wu, W.Q., Hang, C.C., et al., 2014. Genome sequence of Brevibacillus agri strain 5-2, isolated from the formation water of petroleum reservoir. Mar. Genomics, 18:123-125.

[36]Silva, D.S.P., de Lima Cavalcanti, D., de Melo, E.J.V., et al., 2015. Bio-removal of diesel oil through a microbial consortium isolated from a polluted environment. Int. Biodeter. Biodegr., 97:85-89.

[37]Swain, M.T., Tsai, I.J., Assefa, S.A., et al., 2012. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat. Protoc., 7(7):1260-1284.

[38]Tamura, K., Stecher, G., Peterson, D., et al., 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol., 30(12):2725-2729.

[39]Tatusov, R.L., Galperin, M.Y., Natale, D.A., et al., 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res., 28(1):33-36.

[40]Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., et al., 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29(1):22-28.

[41]Teyssier, C., Marchandin, H., Jean-Pierre, H., et al., 2005. Molecular and phenotypic features for identification of the opportunistic pathogens Ochrobactrum spp. J. Med. Microbiol., 54(10):945-953.

[42]Velasco, J., Romero, C., López-Goñi, I., et al., 1998. Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int. J. Syst. Bacteriol., 48(3):759-768.

[43]Waranusantigul, P., Lee, H., Kruatrachue, M., et al., 2011. Isolation and characterization of lead-tolerant Ochrobactrum intermedium and its role in enhancing lead accumulation by Eucalyptus camaldulensis. Chemosphere, 85(4):584-590.

[44]Yuan, Y., Lu, Z., Huang, L., et al., 2007. Biodegradation of nicotine from tobacco waste extract by Ochrobactrum intermedium DN2. J. Ind. Microbiol. Biotechnol., 34(8):567-570.

[45]Zerbino, D.R., Birney, E., 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18(5):821-829.

[46]Zhang, F., She, Y., Chai, L., et al., 2012. Microbial diversity in long-term water-flooded oil reservoirs with different in situ temperatures in China. Sci. Rep., 2:760.

[47]Zhang, F., Jiang, X., Chai, L., et al., 2014. Permanent draft genome sequence of Bacillus flexus strain T6186-2, a multidrug-resistant bacterium isolated from a deep-subsurface oil reservoir. Mar. Genomics, 18:135-137.

[48]Zheng, B., Zhang, F., Chai, L., et al., 2014. Permanent draft genome sequence of Geobacillus thermocatenulatus strain GS-1. Mar. Genomics, 18:129-131.

[49]Zhou, Y., Liang, Y., Lynch, K.H., et al., 2011. PHAST: a fast phage search tool. Nucleic Acids Res., 39(Suppl. 2):W347-W352.