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深海微生物基因组学研究组

Deep Sea Microbial Genomics Research Group

文章来源:  |  发布时间:2019-10-23  |  【打印】 【关闭

  

Deep Sea Microbial Genomics Research Group

The “Deep Sea Microbial Genomics Research Group” was established in September 2013. It mainly carried out:1)In situ dynamics and functions of microorganisms in the deep ocean 2) Evolution and ecology of microorganisms in the deep-sea environments 3) Biogeochemistry and origin of life.

   Research  

1. In situ dynamics and functions of microorganisms in the deep ocean
 The microbial community structure of an ecological domain is affected by environmental factors. At the same time, microorganisms also change and use the substances provided by the environment to maintain the number and structure of their own populations. Some deep-sea microbial communities can affect the circulation of essential elements of the Earth such as carbon and nitrogen. The study of the deep-sea hydrothermal zone ecosystem began in the 1970s revealed the metabolic characteristics of the autotrophic microorganisms and the importance of maintaining the deep-sea life circle. There is still a lot of room for research on various typical ecological domains in the deep sea, such as deep sea cold springs, mud volcanoes and salt brine pools. Through the understanding of the community structure, the microbial-mediated biogeological activities carried out in the ecological domain, such as methane oxidation and metal ion deposition, can be roughly inferred. The research team will also study the microbial community structure of the abyss (>6000 m) by participating in the pilot project of the Chinese Academy of Sciences and taking advantage of the deep sea engineering of the Institute. Under the support of the key research and development projects of the Ministry of Science and Technology, in-situ microbial experiments and detections were carried out in depth, and in-situ and group studies were conducted on the community changes and response mechanisms of environmental microbes under continuous time and space and different factors.
2. E
volution and ecology of microorganisms in the deep-sea environments
  
It is extremely difficult to obtain pure microbial cultured strains for genome research due to extreme deep-sea conditions. But with the advancement of high-throughput sequencing technology, we can directly and massively sequence microbes across the entire ecosystem. Subsequent bioinformatics tools allow us to obtain the framework of the environmental microbial genome (metagenome). By comparing metagenomics from different ecological domains, we can derive the differences in microbial function in the genome. For example, in deep sea and abyss environments, what substances are being metabolized by microorganisms and which mechanisms are relied upon to withstand environmental stress. The study of metagenomic functions relies on the skilled use of bioinformatics tools, strong programming and statistical analysis capabilities.
3. Biogeochemistry and origin of life
 
The existing doctrine of the origin of life suggests that the earliest life of the Earth occurred in the deep sea environment. All organisms have evolved from early autotrophic microorganisms. Therefore, the study of microbial molecular evolution is closely related to the origin of life; how the life forms evolved from prokaryotic microbes to humans. The former involves how the generation of life phenomena completes the transition from inorganic to organic world. This requires studying how microbes use minerals and redox gradients under extreme conditions, the autocatalytic and synthetic processes of biomacromolecules in specific environments, and how cells accomplish the construction of relatively closed living environments. Earth eukaryotic multicellular organisms are currently thought to have evolved from archaea, and the environmental pressure that drive them to evolve into eukaryotes is an important scientific issue. Studying the uncultivable chemical chemoautotrophic and new unknown microorganisms in the deep sea environment allows us to explore the evolutionary process from inorganic to organic and from prokaryotic to eukaryotic.

 

            Members 

 

 

  

 

  Wang Yong Researcher, leader in marine ecology, environmental microbiology, genomics and bioinformatics 

    Personal homepage: http://people.ucas.edu.cn/~IDSSEWangy 

   

  Gao Zhaoming (Associate Researcher)  

  Personal homepage: http://people.ucas.edu.cn/~gaozm  

    

Mengying Wang ,experimental scientist of the Deep Sea Microbial Genomics Research Group of the Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences  

Field of work: scientific research project management, financial secretary  

  

Hongyu Bi,research assistant of the Deep Sea Microbial Genomics Research Group of the Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences  

Work for: microgenome database construction,  network maintenance, experimental support,  data maintenance management  

                    Postgraduate:

Jiaomei Huang Ph.D.of Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences. 

2011–2014 South China Sea institute of oceanology, Chinese Academy of Sciences, Marine biology 

2007 – 2011 Ocean university of China biochemistry and molecular biology   

 
 

Zhanfei Wei Ph.D.of Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences 

2013-2016: Master, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences 

2009-2013: Bachelor, Yantai University.  

 

Yingli Zhou Ph.D. of Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences

2015-2018 Graduated from South China Sea Institute of Oceanology of University of Chinese Academy of Sciences with a master degree 

2011-2015 Graduated from College of Animal Science and Technology of Guangxi University  

 

Qingmei Li, Ph.D. of Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences ,2018-2019 Institut Pasteur of Shanghai as research assistant ,2015-2018  China Pharmaceutical University ,2011-2015 Jilin Agricultural University   

  

Rui Lu Master student of the Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences2014-2018 LuDong university  

TaoshuWei Master student of the Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences
                  Graduated: 

Yuzhi Wu graduated from the Institute of Deep Sea Science and Engineering of the Chinese Academy of Sciences in 2018. 2014-2018  MSc in Institute of Deep Sea Science and Engineering Chinese Academy of Sciences (CAS); 2014-2018 B.S. in University Of Hainan 

  

 

Guojie Cui ,graduated from the Institute of Deep Sea Science and Engineering of the Chinese Academy of Sciences in 2018.Ph.D. student with a level of 15 , project assistant at the Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences ,2015-2019 Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences ,2012-2015 Fujian Agriculture and Forestry University/Fujian Academy of Agricultural Sciences ,2008-2012 Henan University of Science and Technology  

 

Wenli Li ,graduated from the Institute of Deep Sea Science and Engineering of the Chinese Academy of Sciences in 2019 ,2016-2019 Ph.D. in Institute of Deep Sea Science and Engineering Chinese Academy of Sciences (CAS),2015-2016 Project Assistant of Institute of Deep Sea Science and Engineering Chinese Academy of Sciences (CAS),2013-2015 MSc in Food Engineering Jilin University, Changchun, Jilin, PR China,2009-2013 B.S.in Food Quality and Safety Jilin University, Changchun, Jilin, PR China    

 

Our selected publications in recent three years  

  1.Li W-L, Huang J-M, Zhang P-W, Cui G-J, Wei Z-F, Wu Y-Z, Gao Z-M, Han Z., Wang Y*. 2019. Periodic and spatial spreading of alkanes and Alcanivorax bacteria in deep waters of the Mariana Trench. Appl. Env. Microbiol. 85: e02089-18  

  2.Wang Y*, Huang J-M, Cui G-J, Nunoura T, Takaki Y. Li W-L, Li J, Gao Z-M, Ken T, Zhang A-Q, Stepanauskas R. 2019. Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean. Environ. Microbiol. 21:716-729.  

  3.Wang Y*, Gao Z-M, Li J, He L-S, Cui G-J, Li W-L, Chen J, Xin Y-Z, Cai D-S, Zhang A-Q. 2019. Hadal water sampling by in situ microbial filtration and fixation (ISMIFF) apparatus. Deep-Sea Res I. 144:132-137  

  4.Gao ZM, Huang JM, Cui GJ, Li WL, Li J, Wei ZF, Chen J, Xin YZ, Cai DS, Zhang AQ, Wang Y* .2019. In situ meta-omic insights into the community compositions and ecological roles of hadal microbes in the Mariana Trench. Environmental Microbiology. doi: 10.1111/1462-2920.14759  

  5.Huang JM, Wang Y*. 2019. Genomic differences within the phylum Marinimicrobia: From waters to sediments in the Mariana Trench. Marine Genomics. 100699  

  6.Huang JM, Baker JB, Li JT, Wang Y*. 2019. New microbial lineages capable of carbon fixation and nutrient cycling in deep-sea sediments of the northern South China Sea. Appl. Env. Microbiol. 85: 00523-19  

  7.Cui G-J. Li J. Gao Z-M, Wang Y*. 2019. Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep. PeerJ 7:e6961  

  8.He L-S, Zhang P-W, Huang J-M, Zhu F-C, Danchin A., Wang Y*. 2018 The enigmatic genome of an obligate ancient Spiroplasma symbiont in a hadal holothurian. Appl Env Microbiol. 84: e01965-17

  9.Wang Y*, Zhu FC, He LS, Danchin A.*. 2018. Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma. Nucleic Acids Res. 46:2197-2203.  

  10.Wu YZ, Qiu JW, Qian PY, Wang Y* 2018. The vertical distribution of prokaryotes in the surface sediment of Jiaolong cold seep at the northern South China Sea. Extremophiles, 22:499-510.

  11.Wang Y*. Huang JM. 2017. LIR: A package for identification of long inverted repeats in genomes. Genomics, Proteomics & Bioinformatics, 15: 141-146.  

  12.Gao Z-M, Zhou G-W, Huang H, Wang Y *. 2017. The Cyanobacteria-dominated spongeDactylospongia elegansin the South China Sea: Prokaryotic community and metagenomic insights. Front Microbiol, 8: 1387.  

  13.Wang Y, Huang JM, Wang SL, Gao ZM, Zhang AQ, Danchin A*, He LS*. 2016. Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp. Environmental Microbiology, 18(8): 13411.  

  14.Wang Y, Gao ZM, Li JT, Bougouffa S, Tian RM, Bajic VB, Qian PY*. 2016. Draft genome of a bacterium in the phylum Aerophobetes (CD12) reveals a facultative lifestyle in deep-sea anaerobic sediments. Science Bulletin, 61: 1176-1186.  

  15.Wang Y*, Li TG, Wang MY, Lai QL, Li JT, Gao ZM, Shao ZZ, Qian PY*. 2016. Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea. Biogeoscience, 13, 6405-6417.  

Our group recruits positions under the special assistant funded project of the Chinese Academy of Sciences (intern researcher, assistant researcher and postdoctoral fellow). Please send your resume to bihy@idsse.ac.cn and rsc@idsse.ac.cn

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