Comparative genome analysis on intraspecific evolution and nitrogen fixation of Leptospirillum ferriphilum isolates  

嗜铁钩端螺旋菌株种内进化和固氮的比较基因组分析

作　　者：Hong-wei LIU Liang-feng XU Xue GUO Hui-dan JIANG Xue-duan LIU Yi-li LIANG Hua-qun YIN Ya-zi LIU 刘宏伟;徐梁枫;郭雪;蒋慧丹;刘学端;梁伊丽;尹华群;刘亚姿(中南大学资源加工与生物工程学院,长沙410083;中南大学生物冶金教育部重点实验室,长沙410083;清华大学环境学院,环境模拟与污染控制国家重点联合实验室,北京100084;湖南省农业科学院农业生物技术研究所,长沙410125)

机构地区：[1]School of Minerals Processing and Bioengineering,Central South University,Changsha 410083,China [2]Key Laboratory of Biometallurgy of Ministry of Education,Central South University,Changsha 410083,China [3]State Key Joint Laboratory of Environment Simulation and Pollution Control,School of Environment,Tsinghua University,Beijing 100084,China [4]Biotechnology Research Institute,Hunan Academy of Agricultural Sciences,Changsha 410125,China

出　　处：《Transactions of Nonferrous Metals Society of China》2020年第6期1635-1646,共12页中国有色金属学报（英文版）

基　　金：Project(2018YFC1801804)supported by the National Key R&D Program of China;Projects(2016JJ3146,2017JJ3160)supported by the Natural Science Foundation of Hunan Province,China。

摘　　要：To reveal the intraspecific evolution of Leptospirillum ferriphilum isolates which thrived in industrial bioleaching ecosystems and acid mine drainages,genome sequences of L.ferriphilum YSK,L.ferriphilum DX and L.ferriphilum ZJ were determined to compare with complete genome of L.ferriphilum ML-04.The genome comparisons reveal that extensive intraspecific variation occurs in their genomes,and that the loss and insertion of novel gene blocks of probable phage origin may mostly contribute to heterogeneity of gene content among L.ferriphilum genomes.Surprisingly,a nif gene cluster is identified in L.ferriphilum YSK and L.ferriphilum ZJ genomes.Intensive analysis and further experiments indicate that the nif gene cluster in L.ferriphilum YSK inherits from ancestor rather than lateral gene transfer.Overall,results suggest that the population of L.ferriphilum undergoes frequent genetic recombination,resulting in many closely related genome types in recent evolution.The combinatorial processes profoundly shape their physiologies and provide the basis for adaptation to different niches.为揭示在生物冶金工业生态系统和酸性矿山排水系统中占主导地位的嗜铁钩端螺旋菌(Leptospirillum ferriphilum)种内进化机制,以嗜铁钩端螺旋菌株L. ferriphilum YSK、L. ferriphilum DX和L. ferriphilum ZJ的全基因组序列为研究对象,通过高通量测序并与已有的L. ferriphilumML-04菌株全基因组序列进行比较基因组学研究。结果表明,嗜铁钩端螺旋菌发生广泛的种内变异,可能来源于噬菌体的新基因片段的缺失与插入是导致嗜铁钩端螺旋菌基因组产生该异质性的主要原因。另外,意外地发现嗜铁钩端螺旋菌株L. ferriphilumYSK和L. ferriphilumZJ的基因组中存在固氮基因簇。深入分析并进一步实验证实菌株L. ferriphilumYSK的固氮基因簇继承自其原始祖先而非源自横向基因转移。综合上述研究结果可知,嗜铁钩端螺旋菌种群正在生物冶金体系中经历频繁的基因重组,在近期的进化中产生许多紧密相关的基因组类型;同时,嗜铁钩端螺旋菌的重组过程深刻塑造其生理特性,并为其适应不同的生态位奠定基础。

关 键 词：Leptospirillum ferriphilum comparative genome nitrogen fixation intraspecific variation recombination 

分 类 号：TF18[冶金工程—冶金物理化学] Q933[生物学—微生物学]