Peter Dunfield

1. Extremophiles:16S rRNA gene-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 goal of microbial ecology. 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 Dewar Creek in BC (photo), as these environments are known to be hotspots for exotic microbial diversity. For example, we recently isolated the first member of Candidate Division OP10, a phylum-level group previously known only from cultivation-independent surveys of 16S rRNA genes. We are presently studying the genomes of some of these uncultured bacteria using single-cell genomic methods.

2. Methane is both an extremely potent greenhouse gas and an inexpensive fuel. Our group studies methane-eating or methanotrophic bacteria in diverse natural and man-made environments. We have discovered a number of new methanotrophic species. Methanotrophs are useful for diverse biotechnologies, including: i) biofiltration to reduce atmospheric methane emissions from industrial point sources such as abandoned oil wells or oilsands tailings ponds; ii) co-oxidation of a diverse array of pollutants for bioremediation of oilsands tailings waste in situ; and iii) production of value-added products from natural gas with natural and engineered methanotroph strains.

- NSERC Discovery: Ecology and genomics of extremophilic bacteria

- NSERC Collaborative Research and Development:Microbial communities and methane oxidation processes in Base Mine Lake, a model end-pit lake in the Alberta oilsands (with Syncrude, Inc.)

- Climate Change and Emissions Management Corporation (CCEMC) and Mitacs:Control of point source low volume methane emissions using methanobiofiltration (MBF) technology

- Laboratory infrastructure supported by the Canadian Foundation for Innovation and Alberta Advanced Education & Technology

- Recent support also received from:Genome Canada/Genome Alberta; Canada School of Energy and Environment;US Department of Energy Joint Genomic Institute (JGI);Alberta Innovates Technology Futures

Staff and Students

 Albakistani, Emad                   MSc

Haupt, Evan                           MSc

Jones, Gareth                        PhD

Khadka, Roshan                    PhD

Rochman, Fauziah                 PhD

Sheremet, Andrey                  PhD

Ruhl, Ilona                              PhD

Zeb, Gul                                 MSc

Smirnova, Angela                   RA

Kim, JoongJae                       RA

Google Scholar Link
 

2016

Lee KC, Stott MB, Dunfield PF, Huttenhower C, McDonald IR, Morgan XC (2016) The Chthonomonas calidirosea genome is highly conserved across geography and distinct chemical and microbial environments in the Taupō Volcanic Zone, New Zealand. Appl Environ Microbiol. in press

Aguilar M, Richardson E, Tan B, Walker G, Dunfield PF, Bass D, Nesbø C, Foght J, Dacks JB (2016) Next-generation sequencing assessment of eukaryotic diversity in oil sands tailings ponds sediments and surface water. J Eukaryotic Microbiol. in press

Grasby SE, Fergusson G, Brady AL, Sharp CE, Dunfield PF, McMechan M (2016) Deep groundwater circulation and associated methane leakage in the Northern Canadian Rocky Mountains. Appl Geochem 68:10-18

Dedysh SN, Dunfield, PF (2016) Genus Methylocella in Whitman, WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria 3rd Edition, vol 1, Springer-Verlag, New York, NY

Dunfield, PF (2016) Genus Methylohalobius in Whitman, WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria 3rd Edition, vol 1, Springer-Verlag, New York, NY

Dedysh SN, Dunfield, PF (2016) Genus Methyloferula in Whitman, WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria 3rd Edition, vol 1, Springer-Verlag, New York, NY

Flynn J, Hirayama H, Sakai Y, Dunfield PF, et al. (2016) Draft genomes of gammaproteobacterial methanotrophs isolated from marine ecosystems Genome Announce in press

Eloe-Fadrosh EA, Paez-Espino D, Jarett J, Dunfield PF, Hedlund BP, Grasby SE, Brady AL, Dong H, Briggs BR, Li WJ, Goudeau D, Malmtrom R, Pati A, Rubin EM, Woyke T, Kyrpides NC, Ivanova NN (2016) Kryptonia, a novel bacterial phylum discovered through a global metagenomic survey. Nature Commun 7: Article 1047.

       Featured in: Hiding in Plain Sight, The Scientist,  http://wwwthe-scientistcom/?articlesview/articleNo/42569/title/Hiding-in-Plain-Sight/

2015

Lee KCY, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB (2015) Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22^T. Stand Genom Sci, 10: Article 101

Brady AL, Sharp CE, Grasby SE, Dunfield PF (2015) Anaerobic carboxydotrophic bacteria in Canadian geothermal springs identified using stable isotope probing. Front Microbiol 6: Article 897

Sharp CE, Smirnova AV, Kalyuzhnaya M, Bringel F, et al. (2015) Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki. Genome Announce 3:Paper e00644-15

Wang X, Sharp CE, Jones GM, Brady AL, Grasby SE, Dunfield PF (2015) Stable-isotope-probing detects uncultured Planctomycetes as primary degraders of a complex heteropolysaccharide in soil. Appl Environ Microbiol 81: 4607-4615

Hamilton R, Kits K, Ramonovskay V, Rozova O, et al. (2015) Draft genomes of gammaproteobacterial methanotrophs Isolated from terrestrial ecosystems. Genome Announce 3: Paper e00515-15

Dedysh SN, Naumoff D, Vorobev A, Kyrpides N, et al. (2015) Draft genome sequence of Methyloferula stellata AR4, an obligate methanotroph possessing only a soluble methane monooxygenase. Genome Announce 3:e01555-14

Kollah B, Dubey G, Dunfield PF, Mohanty SR (2015) Bioenergy crop Jatropha curcas amendment influences soil biogeochemistry in a tropical vertisol. Mitig Adapt Strat Glob Change 20:1459-1470

2014

Dedysh SN, Dunfield PF (2014) Cultivation of methanotrophs in McGenity, T, Timmis, K, and Nogales, N Springer Protocols Handbooks Springer-Verlag Berlin Heidelberg (wwwspringerprotocolscom) Online resource doi: 101007/8623_2014_14

Sharp CE, Martinez A, Grasby SE, Dunfield, PF (2014) Methanotrophic bacteria in warm geothermal springs identified using stable isotope probing. FEMS Microbiol Ecol 90:92-102

Sinninghe Damsté JS, Rijpstra WIC, Hopmans EC, Foesel BU, Wüst PK, Overmann J, Tank M, Bryant DA, Dunfield PF, Stott MB (2014) Ether- and ester-bound iso-diabolic acid and other lipids in members of Acidobacteria subdivision 4. Appl Environ Microbiol 80:5207-5218

Dunfield PF, Dedysh SN (2014) Methylocella: A gourmand among methanotrophs (Invited spotlight article). Trends Microbiol 22:368-369

Sharp CE, Smirnova AV, Graham JM, Stott MB, Khadka R, Moore TR, Grasby SE, Strack M, Dunfield PF (2014) Distribution and diversity of verrucomicrobial methanotrophs in geothermal and acidic environments. Environ Microbiol 16:1867-1878

Lee KCY, Morgan XC, Dunfield PF, Tamas I, McDonald IR, Stott MB (2014) Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes.ISME J 8:1522-1533

Sharp CE, Brady AL, Sharp GH, Grasby SE, Stott MB, Dunfield, PF (2014) Humboldt’s spa: Microbial diversity is controlled by temperature in geothermal environments. ISME J 8:1166-1174

Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hansen E, Moreau J, Stott MB (2014) Thermoflavifilum aggregans gen nov sp nov, a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteriodetes. Int J Syst Evol Microbiol 64:1264-1270

Lee KCY Stott MB, Dunfield, PF (2014) The phylum Armatimonadetes in E Rosenberg et al (eds) The Prokaryotes, 4^th Edition: Other Major Lineages of Bacteria and The Archaea Springer-Verlag: Berlin pp 447-458

Tamas I, Smirnova AV, He Z, Dunfield PF (2014) The (d)evolution of methanotrophy in the Beijerinckiaceae, a comparative genomics analysis.ISME J8:369-382

Crowe MA, Power JF, Morgan XC, Dunfield PF, Lagutin K, Rijpstra WIC, Vyssotski M, Sinninghe Damste JS, Houghton KM, Ryan JLJ, Stott MB (2014) Pyrinomonas alimethylogenes gen nov sp nov, a novel group 4 thermophilic Acidobacteria from geothermal soils. Int J Syst Evol Microbiol: 64:220-227

2013

An D, Caffrey S, Soh J, Agrawal A, et al. (2013) Metagenomics of hydrocarbon resource environments indicates aerobic taxa and genes to be unexpectedly common. Environ Sci Technol 47:10708-10717

Sharp CE, Op den Camp HJM, Tamas I, Dunfield PF (2013) Unusual members of the PVC superphylum: the methanotrophic Verrucomicrobia genus “Methylacidiphilum” in JA Fuerst (ed) Planctomycetes: Cell Structure, Origins and Biology Springer-Verlag: Berlin, pp 211-228

Basiliko N, Henry K, Gupta V, Moore TR, Driscoll BT, Dunfield PF (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

Khmelenina V, Beck D, Munk C, Davenport K, et al. (2013) Draft genome sequence of Methylomicrobium buryatense 5G, a haloalkaline-tolerant methanotrophic bacterium. Genome Announc 1: 4 e00053-13

Lee KCY, Herbold C, Dunfield PF, Morgan XC, McDonald IR, Stott MB (2013) Phylogenetic delineation of the novel phylum Armatimonadetes (the former candidate division OP10) and its constituent groups. Appl Environ Microbiol 74:2484-2487.

Kim JJ, Al-Kawally M, Brady AL, Rijpstra IC, Damsté JS, Dunfield PF (2013) Chryseolinea serpens gen nov sp nov, a novel member of the Bacteroidetes isolated from soilInt J Syst Evol Microbiol 63: 654–660.

Saidi-Mehrabad A, He Z, Tamas I, Sharp CE, Brady AL, Rochman F, Bodrossy L, Abell GCJ, Penner T, Dong X, Sensen CW, Dunfield PF (2013) Methanotrophic bacteria in oilsands tailings ponds of northern Alberta.ISME J 7:908-921.

Grasby SE, Richards BC, Sharp CE, Brady AL, Jones GM, Dunfield, PF (2013) The Paint Pots, Kootenay National Park, Canada — a natural acid spring analogue for Mars.Can J Earth Sci 50:94-108

selected others

Sharp CE, Stott MB, Dunfield PF (2012) Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing Frontiers Microbiol 3: Article 303

        Recommended by the Faculty of 1000 http://f1000com/717953974

 Op den en Camp HJM, Islam T, Stott MB, Harhangi HR, Hynes A, Schouten S, Jetten MSM,  Birkeland NK, Pol A, Dunfield PF (2009) Minireview: Environmental, genomic, and taxonomic perspectives on methanotrophic Verrucomicrobia. Environ Microbiol Reports 1:293-306. (207 citations)

Stott MB, Crowe MA, Mountain BW, Smirnova AV, Alam M, Dunfield PF (2008) Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol 10:2030-2041 (131 citations)

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, Alam M (2007) Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879-882 (319 citations)

        Featured in Nature Reviews Microbiology6:4-5. “How low can you grow?”,

 Dedysh SN, Knief C, Dunfield PF (2005) Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665-4670 (193 citations)

        Featured by ASM in: American Society for Microbiology (2005) Journal Highlights: New methanotroph metabolizing C-C may benefit greenhouse mitigation. ASM News 71:371. and Theisen, A.R., and J. C. Murrell (2005) Guest Commentary: Facultative methanotrophs revisited. J Bacteriol 187:4303–4305.

 Knief C, Lipski A, Dunfield PF (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl Environ Microbiol 69: 6703-6714 (226 citations)

Dunfield P, Knowles R, Dumont R, Moore TR (1993) Methane production and consumption in temperate and subarctic peat soils: Response to temperature and pH. Soil Biol Biochem 25:321-326 (519 citations)

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