Research Interests

1. Extremophiles. 16S rRNA-based microbial ecology techniques have revealed that the vast majority of bacterial species in nature have never been cultivated in a laboratory. Determining the ecological lifestyles of these bacteria is a major task facing microbial ecologists. We combine modern cultivation techniques with DNA-based molecular methods to explore the metabolic potential of this uncultured diversity. The work focuses particularly on geothermal environments such as Hell’s Gate in New Zealand (photo), as these environments are known to be “hotspots” for exotic microbial diversity. For example, we have isolated the first member of Candidate Division OP10, a phylum-level group previously known only from cultivation-independent surveys of 16S rRNA genes.

2. Environmental microbiology and genomics of the methane cycle. Some bacteria are able to consume the major greenhouse gas methane, and are therefore potential targets for strategies to combat climate change. By searching for DNA and phospholipid signature molecules of these bacteria in soil, and applying molecular methods such as stable-isotope-probing, quantitative PCR, and fluorescence in situ hybridization, it is possible to study them without the need for cultivation. Collectively, these methods can give a convincing picture of “who is doing what, and how?” in the environment.

Methanotrophic bacteria have been studied since the early 1900’s. All species discovered until recently belonged to a single bacterial group (the phylum Proteobacteria). However, we have recently isolated the first non-proteobacterium capable of oxidizing methane. Methanotrophy in the Bacteria is therefore more taxonomically and genetically diverse than previously thought. In collaboration with The Joint Genome Institute (JGI) http://www.jgi.doe.gov/sequencing/cspseqplans2007.html and with colleagues at the University of Hawaii Centre for Genomics Proteomics and Bioinformatics Research Initiative, we are comparing the complete genomes of different methanotrophic bacteria in order to determine how they have evolved and diversified.

Courses Taught

Funding and Support

Alberta Ingenuity: Bioenergy and the uncultured microbial majority
NSERC: Ecology of methanotrophic bacteria
Genome Canada: Hydrocarbon metagenomics http://www.hydrocarbonmetagenomics.com/
Foundation for Research Science and Technology, New Zealand: Bioethanol from thermophilic bacteria
Joint Genome Institute Community Sequencing Program: Genomics of methanotrophs http://www.jgi.doe.gov/sequencing/why/50021.html
Laboratory infrastructure supported by the Canadian Foundation for Innovation and Alberta Advanced Education & Technology

Graduate Students

Selected publications

• Dunfield, P.F., and Dedysh, S.N. (2010) Acidic environments. in K.N. Timmis (ed). Handbook of Hydrocarbon and Lipid Microbiology, Springer-Verlag: Berlin, pp 2181-2192.
• Dedysh, S.N., and Dunfield, P.F. (2010) Facultative methanotrophs. in K.N. Timmis (ed). Handbook of Hydrocarbon and Lipid Microbiology, Springer-Verlag: Berlin, pp 1967-1976.
• Op den en Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM, Birkeland NK, Pol A and Dunfield PF (2009) Minireview: Environmental, genomic, and taxonomic perspectives on methanotrophic Verrucomicrobia. Environmental Microbiology Reports, in press
• Bodelier PLE, Gillisen MJB, Hordijk K, Sinninghe-Damsté J, Rijpstra IWC, Geenevasen JAJ and Dunfield PF (2009) A reanalysis of phospholipid fatty acids as ecological biomarkers for methanotrophic bacteria. ISME Journal 3: 606-617.
• Saw JH, Mountain BW, Feng L, Omelchenko MV, Hou S, Saito JA, Stott MB, Li D, Zhao G, Wu J, Galperin MY, Koonin EV, Makarova KS, Wolf YI, Rigden DJ, Dunfield PF, Wang L and Alam M. (2008) Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus. Genome Biology 9: R161
  
• Koch, I.H., Gich, F., Dunfield, P.F., and Overmann, J. (2008) Edaphobacter modestum gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., two novel acidobacteria isolated from alpine and forest soils. Int. J. Syst. Evol. Microbiol. 58:1114–1122.
• Stott, M.B., Crowe, M.A., Mountain, B.W., Smirnova, A.V., Alam, M., and Dunfield, P.F. (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ. Microbiol. 10:2030-2041.
• Hou, S., Makarova, K.S., Saw J.H.W., Senin, P., Ly, B.V., Zhou, Z., Ren, Y., Wang, J., Galperin, M.Y.,Omelchenko, M.V., Wolf, Y.I., Yutin, N., Koonin, E.V., Stott, M.B., Mountain, B.W., Crowe, M., Smirnova, A.V., Dunfield, P.F., Feng, L., Wang, L., and Alam, M. (2008) Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biology Direct. 3:25
• Stott, M.B., Saito, J.A., Crowe, M.A., Dunfield, P.F., Hou, S., Nakasone, E., Daughney, C.J., Smirnova, A.V., Mountain, B.W., Takai, K., and Alam, M. (2008) Culture-independent characterization of a novel microbial community at a hydrothermal vent at Brothers volcano, Kermadec arc, New Zealand. J. Geophys. Res. Solid Earth, 113, B08S06.
  
• Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Saw JH, Zhou Z, Ren Y, Wang J, Mountain BW, Crowe MA, Weatherby TM, Bodelier PLE, Liesack W, Feng L, Wang L, and Alam M (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450: 879-882.
  
• Dunfield PF (2007) The soil methane sink. In D Reay, CN Hewitt, K Smith, and J Grace, eds. Greenhouse Gas Sinks. pp 152-170.Wallingford, UK. CABI Publishing.
  
• Dedysh SN, Belova SE, Bodelier PLE, Smirnova KV, Khmelenina VN, Chidthaisong A, Trotsenko YA, Liesack W, Dunfield PF (2007) Methylocystis heyerii sp. nov., a novel type II methanotrophic bacterium possessing the “signature” fatty acid of type I methanotrophs. International Journal of Systematic and Evolutionary Microbiology. 57: 472-479.
  
• Knief C, Kolb S, Bodelier PLE, Lipski A, Dunfield PF (2006) The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environmental Microbiology 8: 321-333.
  
• Theisen AR, Hanif Ali M, Radajewski S, Dumont MG, Dunfield PF, McDonald IR, Dedysh SN, Miguez CB, Murrell JC (2005) Regulation of methane oxidation in the facultative methanotroph Methylocella silvestris BL2. Molecular Microbiology 58: 682-692.
  
• Knief C, Dunfield PF (2005) Response and adaptation of methanotrophic bacteria to low methane concentrations. Environmental Microbiology 7: 1307-1317.
  
• Heyer J, Berger U, Hardt M, Dunfield PF (2005) Methylohalobius crimeensis gen. nov. sp. nov., a moderately halophilic methanotrophic bacterium isolated from hypersaline lakes of Crimea. International Journal of Systematic and Evolutionary Microbiology 55: 1817-1826.
  
• Kolb S, Knief C, Dunfield PF, Conrad R (2005) Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environmental Microbiology 7: 1150-1161.
  
• Knief C, Vanitchung S, Harvey NW, Conrad R., Dunfield PF, Chidthaisong A (2005) Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Applied and Environmental Microbiology 71: 3826-2831.
  
• Dedysh SN, Knief C, Dunfield PF (2005) Methylocella species are facultatively methanotrophic. Journal of Bacteriology 187: 4665-4670. The results of this paper were highlighted by in ASM News 71:371 (Journal Highlights) and J. Bacteriol. 187 4303–4305 (Guest Commentary).
  
• Jaatinen K, Knief C, Dunfield PF, Yrjälä K, Fritze H (2004) Methanotrophic bacteria in boreal forest soil: Long-term effects of prescribed burning and wood ash fertilization. FEMS Microbiology Ecology 50: 195-202.
  
• Dedysh SN, Dunfield PF, Trotsenko YA (2004) Methane utilization by Methylobacterium species: new evidence but still no proof for an old controversy. International Journal of Systematic and Evolutionary Microbiology 54: 1919-1920.
  
• Liesack W, Dunfield PF (2004) T-RFLP analysis: A rapid fingerprinting method for studying diversity, structure, and dynamics of microbial communities. in J.F.T. Spencer and A.L. Ragout de Spencer, eds. Methods in Biotechnology: Environmental Microbiology: Methods and Protocols. pp 23-37, Totowa, NJ, Humana Press.
  
• Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Applied and Environmental Microbiology, 69: 6703-6714.
  
• Dunfield PF, Khmelenina VN, Suzina NE, Trotsenko YA, Dedysh SN (2003) Methylocella silvestris sp. nov., a novel methanotrophic bacterium isolated from an acidic forest Cambisol. International Journal of Systematic and Evolutionary Microbiology 53: 1231-1239.
  
• Tchawa Yimga M, Dunfield PF, Ricke P, Heyer J, Liesack W (2003) Wide distribution of a novel pmoA-like gene copy among type II methanotrophs, and its expression in Methylocystis strain SC2. Applied and Environmental Microbiology 69: 5593-5602.
  
• Dedysh SN, Dunfield PF, Derakshani M, Stubner S, Heyer J, Liesack W (2003) Differential detection of type II methanotrophic bacteria in acidic peatlands using newly developed 16S rRNA-targeted fluorescent oligonucleotide probes. FEMS Microbiology Ecology 43: 299-308.
  
• Liesack W, Dunfield PF (2002) Use of molecular methods to study soil microbial diversity. in G. Bitton, ed. Encyclopedia of Environmental Microbiology. pp 528-554. New York, John Wiley & Sons.