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

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（英文）

作　　者：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 

机构地区：[1]Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism,School of Energy Resources, China University of Geosciences [2]State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital,School of Medicine, Zhejiang University [3]College of Chemistry and Environmental Engineering, Yangtze University [4]Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences [5]State Key Laboratory of Heavy Oil Processing, China University of Petroleum

出　　处：《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》2015年第10期865-874,共10页浙江大学学报（英文版）B辑（生物医学与生物技术）

基　　金：supported by the National High-Tech R&D Program(863)of China(No.2013AA064402);the National Natural Science Foundation of China(Nos.81301461 and 51474034);the Zhejiang Provincial Natural Science Foundation of China(No.LQ13H190002);the Scientific Research Foundation of Zhejiang Provincial Health Bureau(No.2012KYB083),China

摘　　要：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 ℃ and pH 5.5. We sequenced the genome and found a single chromosome of 4800175 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.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(r RNA)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 Hi Seq2000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：Comparative genome Ochrobactrum intermedium Oil degradation PATHOGEN 

分 类 号：X172[环境科学与工程—环境科学]