Home
Runar Stokke's picture
  • E-mailRunar.Stokke@uib.no
  • Phone+47 55 58 38 61+47 908 36 074
  • Visitor Address
    Thormøhlensgt. 53 A/B
  • Postal Address
    Postboks 7803
    5020 Bergen


- Metagenomics

- Genomics

- Enzyme discovery

- Microbiology (hyper)thermophilic microorganisms

- Thermal stability of enzymes

Journal articles
  • Coscolin, Cristina; Martínez-Martínez, Mónica; Chow, Jennifer; Bargiela, Rafael; Garcia-Moyano, Antonio; Bjerga, Gro Elin Kjæreng; Bollinger, Alexander; Stokke, Runar; Steen, Ida Helene; Golyshina, Olga V.; Yakimov, Michail M.; Jaeger, Karl-Erich; Yakunin, Alexander F.; Streit, Wolfgang R.; Golyshin, Peter N.; Ferrer, Manuel. 2018. Relationships between substrate promiscuity and chiral selectivity of esterases from phylogenetically and environmentally diverse microorganisms. Catalysts. 8: 1-8. doi: 10.3390/catal8010010
  • Martínez-Martínez, Monica; Cascolín, Cristina; Santiago, Gerard; Chow, Jennifer; Stogios, Peter J.; Bargiela, Rafael; Gertler, Christoph; Navarro-Fernandez, Jose; Bollinger, Alexander; Thies, Stephan; Méndez-García, Celia; Popovic, Ana; Brown, Greg; Chernikova, Tatyana N.; Garcia-Moyano, Antonio; Bjerga, Gro Elin Kjæreng; Pérez-García, Pablo; Hai, Tran; Del Pozo, Merceded V.; Stokke, Runar; Steen, Ida Helene; Cui, Hong; Xiaohui, Xui; Nocek, Boguslaw P.; Alcaide, María; Distaso, Marco; Mesa, Victoria; Peláez, Ana I.; Sánchez, Jesùs; Buchholz, Patrick C. F.; Pleiss, Jürgen; Fernándes-Guerra, Antonio; Glöckner, Frank O.; Golyshina, Olga V.; Yakimov, Michail M.; Savchenko, Alexei; Jaeger, Karl-Erich; Yakunin, Alexander F.; Streit, Wolfgang R.; Golyshin, Peter N.; Guallar, Víctor; Ferrer, Manuel. 2017. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. Journal of the American Chemical Society. 13: 225-234. Published 2017-11-28. doi: 10.1021/acschembio.7b00996
  • Wissuwa, Juliane; Le Moine Bauer, Sven; Steen, Ida Helene; Stokke, Runar. 2017. Complete genome sequence of Lutibacter profoundi LP1T isolatet from an Arctic deep-sea hydrothermal vent system. Standards in Genomic Sciences. 12:5: 1-11. doi: 10.1186/s40793-016-0219-x
  • Schouw, Anders; Eide, Tove Leiknes; Stokke, Runar; Pedersen, Rolf B.; Steen, Ida Helene; Bødtker, Gunhild. 2016. Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica. International Journal of Systematic and Evolutionary Microbiology. 66: 1724-1734. doi: 10.1099/ijsem.0.000934
  • Steen, Ida Helene; Dahle, Håkon; Stokke, Runar; Roalkvam, Irene; Daae, Frida Lise; Rapp, Hans Tore; Pedersen, Rolf B.; Thorseth, Ingunn Hindenes. 2016. Novel barite chimneys at the Loki´s Castle vent field shed light on key factors shaping microbial communities and functions in hydrothermal systems. Frontiers in Microbiology. 6:1510. doi: 10.3389/fmicb.2015.01510
  • Wissuwa, Juliane; Stokke, Runar; Fedøy, Anita-Elin; Lian, Kjersti; Smalås, Arne O.; Steen, Ida Helene. 2016. Isolation and complete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from an Arctic deep-sea hydrothermal vent site. Standards in Genomic Sciences. 11:16: 1-12. doi: 10.1186/s40793-016-0137-y
  • Hocking, William Peter; Roalkvam, Irene; Magnussen, Carina; Stokke, Runar; Steen, Ida Helene. 2015. Assessment of the carbon monoxide metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus VC-16 by comparative transcriptome analyses. Archaea. 2015:235384. 12 pages. doi: 10.1155/2015/235384
  • Roalkvam, Irene; Drønen, Karine; Stokke, Runar; Daae, Frida Lise; Dahle, Håkon; Steen, Ida Helene. 2015. Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria. Frontiers in Microbiology. 6. doi: 10.3389/fmicb.2015.00987
  • Stokke, Runar; Dahle, Håkon; Roalkvam, Irene; Wissuwa, Juliane; Daae, Frida Lise; Tooming-Klunderud, Ave; Thorseth, Ingunn Hindenes; Pedersen, Rolf B.; Steen, Ida Helene. 2015. Functional interactions among filamentous Epsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm. Environmental Microbiology. 17: 4063-4077. doi: 10.1111/1462-2920.12970
  • Hocking, William Peter; Stokke, Runar; Roalkvam, Irene; Steen, Ida Helene. 2014. Identification of key components in the energy metabolism of Archaeoglobus fulgidus by transcriptome analyses. Frontiers in Microbiology. 5:95. doi: 10.3389/fmicb.2014.00095
  • Urich, Tim; Lanzén, Anders; Stokke, Runar; Pedersen, Rolf B.; Bayer, Christoph; Thorseth, Ingunn Hindenes; Schleper, Christa Maria; Steen, Ida Helene; Øvreås, Lise. 2014. Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics. Environmental Microbiology. 16: 2699-2710. doi: 10.1111/1462-2920.12283
  • Stokke, Runar; Hocking, William Peter; Steinsbu, Bjørn Olav; Steen, Ida Helene. 2013. Complete genome sequence of the thermophilic and facultatively chemolithoautotrophic sulfate reducer Archaeoglobus sulfaticallidus PM70-1T. Genome Announcements.
  • Stokke, Runar; Roalkvam, Irene; Lanzén, Anders; Haflidason, Haflidi; Steen, Ida Helene. 2012. Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environmental Microbiology. 14: 1333-1346. doi: 10.1111/j.1462-2920.2012.02716.x
  • Roalkvam, Irene; Jørgensen, Steffen Leth; Chen, Yifeng; Stokke, Runar; Dahle, Håkon; Hocking, William Peter; Lanzén, Anders; Haflidason, Haflidi; Steen, Ida Helene. 2011. New insight into stratification of anaerobic methanotrophs in cold seep sediments. FEMS Microbiology Ecology. 78: 233-243. doi: 10.1111/j.1574-6941.2011.01153.x
  • Stokke, R; Leiros, Ingar; Karlström, Mikael; Karlstrom, M; Yang, Nannan; Ladenstein, R; Birkeland, NK; Steen, IH. 2007. Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers. Extremophiles. 11. doi: 10.1007/s00792-006-0060-z
  • Stokke, Runar; Birkeland, Nils-Kåre; Steen, Ida Helene. 2007. Thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles. 11: 397-402. doi: 10.1007/s00792-006-0045-y
  • Stokke, Runar; Madern, Dominique; Fedøy, Anita-Elin; Fedøy, Anita-Elin; Karlsen, Solveig; Birkeland, Nils-Kåre; Steen, Ida Helene. 2007. Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD(+)-dependent homotetrameric enzyme. Archives of Microbiology. 187. doi: 10.1007/s00203-006-0200-y
  • Karlström, Mikael; Stokke, Runar; Steen, Ida Helene; Birkeland, Nils-Kåre; Ladenstein, Rudolf. 2005. Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. Journal of Molecular Biology. 345: 559-577.
Reports and theses
  • Stokke, Runar. 2006. Isocitrate dehydrogenase from extremophiles; Molecular adaptations to high temperatures. University of Bergen, Bergen, Norway. 100 pages.

More information in national current research information system (CRIStin)

Coscolín, C., Martínez-Martínez, M., Chow, J., Bargiela, R., García-Moyano, A., Bjerga, G., Bollinger, A., Stokke, R., Steen, I., Golyshina, O., Yakimov, M., Jaeger, K.-E., Yakunin, A., Streit, W., Golyshin, P. & Ferrer, M. Relationships between Substrate Promiscuity and Chiral Selectivity of Esterases from Phylogenetically and Environmentally Diverse Microorganisms. Catalysts 8, 10 (2018)

Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R,Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A,Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, DelPozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V,Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO,Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, GolyshinPN, Guallar V, Ferrer M, The Inmare Consortium. Determinants and Prediction ofEsterase Substrate Promiscuity Patterns. ACS Chem Biol. 2018 Jan19;13(1):225-234. doi: 10.1021/acschembio.7b00996. Epub 2017 Dec 20. PubMed PMID:29182315.

Wissuwa J, Bauer SL, Steen IH, Stokke R. Complete genome sequence ofLutibacter profundi LP1(T) isolated from an Arctic deep-sea hydrothermal ventsystem. Stand Genomic Sci. 2017 Jan 7;12:5. doi: 10.1186/s40793-016-0219-x.eCollection 2017. PubMed PMID: 28078050; PubMed Central PMCID: PMC5219744.

Wissuwa J, Stokke R, Fedøy AE, Lian K, Smalås AO, Steen IH. Isolation andcomplete genome sequence of the thermophilic Geobacillus sp. 12AMOR1 from anArctic deep-sea hydrothermal vent site. Stand Genomic Sci. 2016 Feb 24;11:16.doi: 10.1186/s40793-016-0137-y. eCollection 2016. PubMed PMID: 26913091; PubMedCentral PMCID: PMC4765119.

Schouw A, Leiknes Eide T, Stokke R, Birger Pedersen R, Helene Steen I, BødtkerG. Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobicbacterium from a deep-sea hydrothermal vent system, and emended descriptions ofNatranaerovirga pectinivora and Natranaerovirga hydrolytica. Int J Syst EvolMicrobiol. 2016 Apr;66(4):1724-34. doi: 10.1099/ijsem.0.000934. Epub 2016 Jan 28.PubMed PMID: 26822139.

Steen IH, Dahle H, Stokke R, Roalkvam I, Daae FL, Rapp HT, Pedersen RB,Thorseth IH. Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light onKey Factors Shaping Microbial Communities and Functions in Hydrothermal Systems.Front Microbiol. 2016 Jan 7;6:1510. doi: 10.3389/fmicb.2015.01510. eCollection2015. PubMed PMID: 26779165; PubMed Central PMCID: PMC4703759.

Roalkvam I, Drønen K, Stokke R, Daae FL, Dahle H, Steen IH. Physiological andgenomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolicfeatures in Epsilonproteobacteria. Front Microbiol. 2015 Sep 16;6:987. doi:10.3389/fmicb.2015.00987. eCollection 2015. PubMed PMID: 26441916; PubMed CentralPMCID: PMC4584990.

Hocking WP, Roalkvam I, Magnussen C, Stokke R, Steen IH. Assessment of theCarbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing ArchaeonArchaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses. Archaea. 2015Aug 6;2015:235384. doi: 10.1155/2015/235384. eCollection 2015. PubMed PMID:26345487; PubMed Central PMCID: PMC4543118.

Stokke R, Dahle H, Roalkvam I, Wissuwa J, Daae FL, Tooming-Klunderud A,Thorseth IH, Pedersen RB, Steen IH. Functional interactions among filamentousEpsilonproteobacteria and Bacteroidetes in a deep-sea hydrothermal vent biofilm.Environ Microbiol. 2015 Oct;17(10):4063-77. doi: 10.1111/1462-2920.12970. Epub2015 Aug 17. PubMed PMID: 26147346.

 

Key qualifications:
• Cultivations of extremophilic microorganisms
• DNA-isolation
• PCR-techniques
• Protein expression and purification
• Protein chemistry and structural biology
• Protein stability; enzyme kinetics and differential scanning calorimetry
• Advanced Bioinformatics
• Cell fractionation of environmental samples
• Proteomics and Mass spectrometry
• Metagenomics, metaproteomics and metatranscriptomics
• Genome assembly and annotation


Work Experience:
July 2013 – present; Department of Biology, UoB, Researcher:
Researcher on National Biotek2021 project NorzymeD where the overall goal is to develop competitive enzyme technology for processing of Norwegian biomass to increase value creation in the Norwegian Bio-based industry. Main responsibilities: Screen metagenomes and bacterial genomes from extreme habitats at the Arctic Mid-Ocean Ridge system.

June 2011 – June 2013; Department of Biology, UoB, Researcher:
Researcher at Centre for Geobiology on the Project Biogoldmine, search for possible Industrial applicable bio-compounds using –omics technology.

May 2008 – June 2011; Centre for Geobiology, UoB, Post. Doc:                             Post.Doc position at Centre for Geobiolgy within the research program “Roots of Life”. Establish a metagenomic and metaproteomic pipeline at Centre for Geobiology, University of Bergen.

September 2007 – April 2008; Centre for Geobiology, UoB, Research fellow:
Sulfate metabolism in Archaeoglobus fulgidus. In this period I was also involved in two other projects:

1) The diversity of microorganisms associated with lowtemperature iron mounds at a hydrothermal vent field along the Artic Ridges.

2) Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation” led by Professor Christa Schleper. I was involved in the start of the project by testing the genome stability of different strains of S. solfataricus.

January 2007 – August 2008; Centre for Geobiology, UoB, Engineer:
Temporary employed as overengineer (50%) to develop proteomic tools for physiological studies of
microorganisms involved in central biogeochemical cycles in extreme environments.

Education:

2003 – 2006 Form. Department of Microbiology/University of Bergen, Philosophiae doctor (PhD).

Dissertation: Biological adaptations to extreme temperatures.

2001 – 2003 Form. Department of Microbiology/University of Bergen, Master of Science

Dissertation: Cloning, expresion and characterization of recombinant isocitrate dehydrogenase from Methylococcus capsulatus and Thermoplasma acidophilum.

1999 – 2001 University of Bergen, Norway
Bachelor in microbiology/molecular biology.