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Journal of Zhejiang University SCIENCE B

ISSN 1673-1581(Print), 1862-1783(Online), Monthly

2015 Vol.16 No.10 P.865-874

Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains

Lu-jun Chai, Xia-wei Jiang, Fan Zhang, Bei-wen Zheng, Fu-chang Shu, Zheng-liang Wang, Qing-feng Cui, Han-ping Dong, Zhong-zhi Zhang, Du-jie Hou, Yue-hui She

1Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing 100083, China; 2State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; 3College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China; 4Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China; 5State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 257061, China

zhengbw@zju.edu.cn, sheyuehui@163.com

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 LMG3301T) showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.

Key words: Comparative genome, Ochrobactrum intermedium, Oil degradation, Pathogen

Chinese Summary  <16> 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

目的：对一株地层水分离的石油降解菌Ochrobactrum intermedium 2745-2进行生理生化特性的研究、全基因组测序以及比较基因组研究。
创新点：首次对一株分离自地层水的石油降解菌O. intermedium 2745-2进行了生理生化特性研究以及基因组测序，从基因组角度解释菌株2745-2对石油的降解能力。通过菌株2745-2与同种其他临床分离菌株的比较基因组学分析，表明2745-2仍具有多种与致病性相关的基因。
方法：通过微生物富集培养的方法从油井的地层水中分离石油降解微生物，通过聚合酶链反应（PCR）扩增16S核糖体RNA（rRNA）序列进行比较和分析确定菌株的分类地位属于O. intermedium（图1）。采用Illumina HiSeq2000对菌株2745-2进行高通量测序，采用Velvet 1.2.07和RAST server分别进行数据组装和注释（表1）。PHAST寻找基因组中的噬菌体相关序列（图4和表2）。通过BLAST+和BRIG对环境分离菌株（2745-2）和临床分离菌株（M86、229E和LMG3301T）进行基因组比较（表3、表4和图5）。
结论：首次对一株环境分离的O. intermedium（2745-2）进行全基因组测序，揭示具有多种与石油降解相关的基因。通过环境分离菌株（2745-2）与临床分离菌株（M86, 229E和LMG3301T）的基因组比较分析，表明2745-2仍具有多种致病性相关的基因。

关键词组：Ochrobactrum intermedium；石油降解；比较基因组；病原菌


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DOI:

10.1631/jzus.B1500029

CLC number:

X172

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On-line Access:

2015-10-03

Received:

2015-01-26

Revision Accepted:

2015-07-06

Crosschecked:

2015-09-17

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