中山大学学报自然科学版 ›› 2017, Vol. 56 ›› Issue (5): 1-11.

• 研究论文 •    下一篇

环境微生物组多样性及功能研究进展

吴波1, 冯凯2,3, 职晓阳4, 何强1,5, 许玫英6, 邓晔2, 肖凡书1, 汪善全1, 于玲1,鲁祺鸿1,连英丽1,罗丽娟7,原珂8,陈保卫8,颜庆云1, 仇荣亮1, 栾天罡7, 贺志理1,9   

  1. 1.中山大学环境科学与工程学院环境微生物组研究中心,广东 广州 510006;
    2.中国科学院生态环境研究中心,北京100085;
    3.中国科学院大学,北京100049;
    4.云南大学生命科学学院微生物研究所, 云南 昆明 650091;
    5.田纳西大学城市与环境工程系及环境生物技术研究中心,田纳西 诺克斯维尔 37996;
    6.广东省微生物研究所,广东 广州 510070;
    7.中山大学生命科学学院,广东 广州 510275;
    8.中山大学海洋科学学院,广东 广州 510275;
    9.俄克拉荷马大学环境基因组学研究所, 俄克拉荷马 诺曼 73019
  • 收稿日期:2017-07-18 出版日期:2017-09-25 发布日期:2017-09-25
  • 通讯作者: 贺志理(1965年生),男; 研究方向:微生物组学;E-mail: hezhili@mail.sysu.edu.cn

Progresses in environmental microbiome diversity and function research

WU Bo 1, FENG Kai 2,3, ZHI Xiaoyang 4, HE Qiang 1,5, XU Meiying 6, DENG Ye 2, XIAO Fanshu 1, WANG Shanquan 1, YU Ling 1, LU Qihong 1, LIAN Yingli 1, LUO Lijuan7, YUAN Ke 8, CHEN Baowei 8, YAN Qingyun 1, QIU Rongliang 1, LUAN Tiangang 7, HE Zhili 1,9   

  1. 1. Environmental Microbiome Research Center and the School of Environmental Science and Engineering, Sun Yat-sen University, Guangz
    hou 510006, China; 
    2. Research Center for EcoEnvironmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; 
    3.University of Chinese Academy of Sciences, Beijing 100049, China; 
    4.Yunnan Institute of Microbiology, School of Life Science, Yunnan University, Kunming 650091, China; 
    5.Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996 ,USA; 
    6.Guangdong Institute of Microbiology, Guangzhou 510070, China;
    7.School of Marine Science, Sun Yat-sen University, Guangzhou 510275, China;
    8.School of Life Science, Sun Yat-sen University, Guangzhou 510275, China;
    9. Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
  • Received:2017-07-18 Online:2017-09-25 Published:2017-09-25

摘要:

快速发展的测序技术和各种高通量手段使我们能够深入探索环境微生物的多样性及其功能。本文中提及的环境微生物组(environmental microbiome)界定为特定环境中所有微生物基因组的集合。环境微生物组研究的主要目的是解读特定环境中微生物的多样性、结构、功能、相互作用和进化,以及它们与环境因子和生态系统功能之间的关系等。本文重点关注土壤、水体及空气中的微生物组研究,回顾了目前的高通量测序技术和主要的环境微生物组学数据分析工具,然后综述了不同的生态环境中微生物组研究的主要的进展,最后,提出了环境微生物组研究中的关键科学问题,并突出了在未来环境微生物组研究中微生物功能和生态机制的重要性。

关键词: 环境微生物组, 微生物功能, 宏基因组, 生物信息学工具

Abstract:

Currently developed sequencing and other high throughput technologies enable us to explore the role of microorganisms in the environment. Here environmental microbiome is defined as the collection of microbial genomes in a particular environment, and the environmental microbiome research (or environmental microbiomics) aims to understand the biodiversity, composition, structure, function, interaction, evolution and dynamics of microbial communities as well as their linkages with environmental drivers and ecosystem functioning. This review is focused on environmental microbiomes from soil, water and air. Firstly, the current advanced sequencing technologies and associated tools for environmental microbiome data analysis are reviewed, then the current research progress in environmental microbiomes were summarized with foci on addressing key scientific questions in microbial ecology and environmental science. This review proposes key scientific questions, and highlights the importance of our understanding of microbial functions and underlying mechanisms in future environmental microbiome studies.

Key words: environmental microbiomes, microbial function, metagenome sequencing, bioinformatics tools

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