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  Dr. Peter Dunfield  
     
 

Position:

Associate Professor, Alberta Ingenuity New Faculty

 

Qualifications:

1988 BSc (Biology) Dalhousie University, Halifax, Canada
1991 MSc (Geography) McGill University, Montreal, Canada
1997 PhD (Microbiology) McGill University, Montreal, Canada
2001-2004 Research Group Leader, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
2004-2007 Senior Scientist, Institute of Geological and Nuclear Sciences, Taupo, New Zealand


Room:

BI 319D

Phone:

403-220-2469

Email:

pfdunfie (at) ucalgary.ca

 
     
 

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

CMMB 343 Microbiology
CMMB 563 Microbial Diversity
CMMB 637 Advanced Topics in Molecular and Microbial Biology

 

 
     
 

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
 Canada School of Energy and Environment
-Climate Change and Emissions Management Corporation (CCEMC)

 

 
     
 

Graduate Students

Name

Degree

Topic
Haupt, Evan MSc  
Jones, Gareth Ph.D.  
Khadka, Roshan MSc  
Rochman, Fauziah Ph.D.  
Ruhl, Ilona Ph.D.  
       
Smirnova, Angela RA  
Jong Jae Kim PDF  

 

 
     
 

Selected publications

   

  • Stott, M.B., Lee, K.C-Y., Morgan, X.C., Dunfield, P.F., Tamas, I., and McDonald, I.R. (2014) The first genomic analysis of a phylum Armatimonadetes isolate reveals its ecological role as a carbohydrate scavenger. ISME J. in press.
  • Morgan, X.C., Anders, H., Houghton, K.M., Vyssotski, M., Ryan, J.M., Lagutin, K., Dunfield, P.F., and Stott, M.B. (2014) Thermogemmatispora tikiterensis sp. nov., a thermophilic isolate of class Ktedonobacteria, and emended description of the clade Thermogemmatispora gen. nov. (Yabe et al., 2011). Int. J. Syst. Evol. Microbiol. in press.
  • Sharp, C.E., Brady, A.L., Sharp, G.H., Grasby, S.E., Stott, M.B., and Dunfield, P.F. (2014) Humboldt's spa: Microbial diversity is controlled by temperature in geothermal environments. ISME J. doi: ismej.2013.237
  • Tamas, I., Smirnova, A.V., He, Z., Dunfield P.F. (2014) The (d)evolution of methanotrophy in the Beijerinckiaceae, a comparative genomics analysis. ISME J. 8:369-382.
  • Crowe, M.A., Power, J.F., Morgan, X.C., Dunfield, P.F., Lagutin, K., Rijpstra, W.I.C., Vyssotski, M., Sinninghe Damste, J.S., Houghton, K.M., Ryan, J.L.J., and Stott, M.B. (2014) Pyrinomonas alimethylogenes gen. nov. sp. nov., a novel group 4 thermophilic Acidobacteria from geothermal soils. Int. J. Syst. Evol. Microbiol: 64:220-227.
  • Basiliko, N., Henry, K., Gupta, V., Moore, T.R., Driscoll, B.T., and Dunfield, P.F. (2013) Controls on bacterial and archaeal community structure and links to greenhouse gas production in natural, mined, and restored Canadian peatlands. Frontiers Microbiol. 4: Article 215.
  • Lee, K.C.Y., Herbold, C., Dunfield, P.F., Morgan, X.C., McDonald, I.R., and Stott, M.B. (2013) Phylogenetic delineation of the novel phylum Armatimonadetes (the former candidate division OP10) and its constituent groups. Appl. Environ. Microbiol. 74:2484-2487.
  • Kim, J.J., Al-Kawally, M., Brady, A.L., Rijpstra, I.C., Damsté, J.S., and Dunfield, P.F. (2013) Chryseolinea serpens gen. nov. sp. nov., a novel member of the Bacteroidetes. Int. J. Syst. Evol. Microbiol. 63: 654–660.
  • Grasby, S.E., Sharp, C.E., Brady, A.L., Jones, G.M., and Dunfield, P.F. (2013) The Paint Pots acid spring – A Mars analogue. Can. J. Earth Sci. 50:94-108.
  • Dunfield P.F., Tamas, I, Lee K.Y., Morgan, X., McDonald, I.R., and Stott, M.B. (2012) Electing a candidate: A speculative history of the bacterial phylum OP10. Environ. Microbiol. 14:3069-3080.
  • Saidi-Mehrabad, A., He, Z., Tamas, I., Sharp, C.E., Brady, A.L., Rochman, F.F., Bodrossy, L., Abell, G.C.J., Penner, T., Dong, X., Sensen, C.W., Dunfield, P.F. (2013) Methanotrophic bacteria in oilsands tailings ponds of northern Alberta. ISME J. doi:10.1038/ismej.2012.163
  • Sharp, C.E., Stott, M.B., Dunfield, P.F. (2012) Stable isotope probing analysis of methanotrophic Verrucomicrobia in geothermal environments. Frontiers Microbiol. (Evol Genomic Microbiol): 3: Article 303.
  • Stein, L.Y., Roy R., and Dunfield, P.F. (2012) Aerobic methanotrophy and nitrification: Processes and connections. in J. Battista et al (eds) Encyclopedia of Life Sciences. John Wiley and Sons, Chichester. www.els.net.
  • Teh, A.H., Saito, J., Baharuddin, A., Tuckerman, J., Newhouse, J., Kanbe, M., Newhouse, E., Rahim, R., Didierjean, C., Sousa, E., Stott, M.B., Dunfield, P.F., Gonzalez, G., Gilles-Gonzalez, M.A., Najimudin, N., and Alam M. (2011) Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin. FEBS Letters 585:3250-3258
  • Dedysh, S.N., and Dunfield, P.F. (2011) Facultative and obligate methanotrophs: how to identify and differentiate them? Meth. Enzymol. 495:31-44. (2)
  • Lee, K.C-Y. Dunfield, P.F., Morgan, X.C., Crowe, M.A., Houghton, K.M., Vyssotski, M. Ryan, J.L., Lagutin, K., McDonald, I.R., and Stott, M.B. (2011) Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic microorganism of a novel bacterial class, Chthonomonadetes classis. nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int. J. Syst. Evol. Microbiol. 61:2482-2490.
  • Vorob'ev, A.V., Baani, M., Doronina, N.V., Brady, A.L., Liesack, W., Dunfield, P.F., and Dedysh, S.N. (2011) Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int. J. Syst. Evol. Microbiol. 61: 2456-2463.
  • Tamas, I., Dedysh, S.N., Liesack, W., Stott, M.B., Alam, M., Murrell J.C., and Dunfield, P.F. (2010) Complete Genome Sequence of Beijerinckia indica subsp. indica. J. Bacteriol. 192:4532-4533.
  • Chen, Y., Crombie, A, Tanvir Rahman, Md., Dedysh, S.N., Liesack, W., Stott, M.B., Alam, M., Theisen, A.R., Murrell, J.C. and Dunfield, P.F. (2010) Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2. J. Bacteriol. 192:3840-3841.
  • Dunfield, P.F., Belova, S.E., Vorob'ev, A.V., Cornish, S.L., and Dedysh, S.L. (2010) Methylocapsa aurea sp. nov., a facultatively methanotrophic bacterium possessing a particulate methane monooxygenase. Int. J. Syst. Evol. Microbiol. 60, 2659–2664
  • 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).

 

 

 

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