Gene Tyson

Senior Research Fellow
     QEII Fellow

Deputy Director of the
Australian Centre for Ecogenomics

Contact Details

Office 527, Level 5 Molecular Biosciences Building (76)
P  +61 (0)7 3365 3829
F  +61 (0)7 3365 4726

Short Biography    

Associate Professor Gene Tyson is a microbial ecologist whose research applies molecular approaches to understand the structure and function of microbial communities in the environment. During Gene’s dissertation research (University of California, Berkeley with Prof. Jill Banfield) he was the lead author on one of the first studies to use metagenomics. In this work he investigated the metabolic potential and population diversity of microbial communities involved in acid mine drainage (AMD) generation, and demonstrated for the first time that metagenomic data could be used to reconstruct near complete genomes directly from environmental samples. He used these composite genomic assemblies of natural populations to explore microbial evolutionary processes.
Following his PhD, Gene sought more complex microbial communities on which to apply cutting-edge molecular tools with the goal of teasing out general principles in microbial population evolution and ecology. At the Massachusetts Institute of Technology (2006-2009), he conducted postdoctoral research work with Prof. Edward DeLong on the composition, functional potential, regulation, and evolution of complex marine microbial communities at sites around the world’s oceans. A highlight of this research was the use of ‘metatranscriptomics’ to investigate gene expression in microbial assemblage from the Pacific Ocean, demonstrating clear depth-specific signatures in the expression of photosynthesis, carbon fixation and nutrient uptake genes as well as high expression of a number of hypothetical genes. One particularly exciting metatranscriptomic discovery made by Gene and a graduate student in the lab was that marine microorganisms express a surprisingly large number of small RNAs, which previously were not thought to play a major role in bacterial and archaeal gene regulation. This is profoundly changing our understanding of gene regulation in the marine environment and microbial communities in general.
Detailed and up-to-date information for AWMC researchers on publications, research grants obtained and supervised postgraduate thesis for all AWMC researchers can be found here:

Research Interests    

  • Molecular microbial ecology
  • Microbial diversity
  • Microbial evolution
  • The role of microorganism in the biogeochemical cycles that underpin life on Earth
  • Phage – host interactions and co-evolution

Current Projects    

ARC Discovery: The only constant is change: ecology and evolution of phage-host interactions in a model ecosystem
ARC Discovery: Swimming in the sea: microbial behaviour as a driver of ocean biogeochemistry
U.S. Department of Energy: Genes, isotopes, and ecosystem biogeochemistry: dissecting methane flux at the leading edge of global change
ARC Linkage: Coals as methane bioreactors: significance of microbial methane generation in coal seams for coal seam gas (CSG) production and CO2 geosequestration
CSIRO Flagship Cluster: Biotechnological solutions to Australia's transport energy and greenhouse gas challenges
Other projects:

Achievement Highlights    


  • ARC Queen Elizabeth II Fellowship, 2010
  • University of California, Berkeley - Chang-Lin Tien Scholarship, 2005-06.
  • University of California, Berkeley - Prof. Earl Storie Memorial Scholarship, 2002.
Several of Associate Professor Gene Tyson’s papers have been recognized by the Faculty of 1000, and his early metagenomics work was highlighted as one of the Breakthroughs of the Year by Science in 2004, and has been cited more than 840 times since publication in 2004.

Professional Association Memberships   

  • American Society for Microbiology (2004 - present)
  • Australian Society for Microbiology (2009 - present)
  • International Society for Microbial Ecology (2005 - present)

Key Publications    

  • Shi, Y., G.W. Tyson and E. DeLong (2009). Metatranscriptomics reveals unique microbial sRNAs in the ocean’s water column. Nature (in press).
  • Hugenholtz, P., and G.W. Tyson (2008). Microbiology – Metagenomics. Nature, 455:481-483.
  • Frias-Lopez, J., Y. Shi, G.W. Tyson, M. Coleman, P. Chisholm, E. DeLong (2008). Microbial community gene expression in ocean surface waters. Proceeding of the National Academy Sciences, 105:3805-3810.
  • Tyson, G.W., and J.F. Banfield (2007). Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10:200-207.
  • Tyson, G.W.*, J.M. Eppley*, W. Getz, J.F. Banfield (2007). Genetic exchange across an archaeal species boundary. Genetics, 177:407-416.
  • Lo I., V.J. Denef, N.C. Verberkmoes, M.B. Shah, D. Goltsman, G. DiBartolo, G.W. Tyson, E.E Allen, R.J. Ram, J.C. Detter, P. Richardson, M.P. Thelen, R.L. Hettich, J.F. Banfield (2007). Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446:537-541.
  • Allen E.E., G.W. Tyson, C. Detter, R. Whitaker, P. Richardson,J.F. Banfield. (2007) Genome evolution in a natural microbial strain population. Proceeding of the National Academy Sciences, 104:1883-1888.
  • Baker, B.J., G.W. Tyson, R.I. Webb, J. Flanagan, P. Hugenholtz, E.E. Allen, J.F.Banfield. (2006) Novel lineages of acidophilic, ultra-small Archaea revealed by community genome sequencing. Science, 314,1933-1935.
  • Tyson, G.W., and J.F. Banfield (2005). Culturing the unculturable: A community genomics prespective. Trends in Microbiology 13, 411-415.
  • Tyson, G.W., I. Lo, B.J. Baker, E.E. Allen, P. Hugenholtz, J.F. Banfield (2005). Genome directed isolation of the key nitrogen fixer, Leptospirillum ferrodiazotrophum sp. nov., from an acidophilic microbial community. Applied and Environmental Microbiology 71, 6319-6324.
  • Ram, R.J., N.C.VerBerkmoes, M.P. Thelen, G.W. Tyson, B.J. Baker, R.C. Blake II, M. Shah, R.L. Hettich, J.F. Banfield (2005). Community proteomics reveals key roles for “hypothetical” proteins in a natural microbial biofilm. Science 308, 1915-1920.
  • Tyson, G.W., J. Chapman, P. Hugenholtz, E.E. Allen, R.J. Ram, P.M. Richardson, V.V. Solovyev, E.M. Rubin, D.S. Rokhsar, J.F. Banfield (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.
  • Hugenholtz, P., G.W. Tyson, R.I. Webb, A.M. Wagner, L.L. Blackall (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Applied and Environmental Microbiology 67, 411-419.

Current Group

Postdoctoral Researchers: 
Florent Angly
Mike Imelfort
Paul Dennis
Virginia Rich (University of Arizona)
PhD Students:
Mohamed Fauzi Haroon
Co-advised PhD Students:
Hasina Pervin
Hiroshi Izumi
Candice Heath
Roslinda Mohamed
Siew (Stan) Herng Chan
Completed Students:
Barry Cayford
Lauren Bragg
Connor Skennerton
Kai Zhang (Masters)
Keith Chua (Summer vacation student)
Hui Lim (Honours)
Mohammed Fauzi Haroon (Honours)
Kimber Kumbun (Honours)
Jeremy Barr (PhD)


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