Dr. Dagmar Wöbken, Group Leader
University of Vienna
Department of Microbiology and Ecosystem Science
Division of Microbial Ecology
Althanstr. 14
A-1090 Wien
phone: +43 1 4277 76613

 Curriculum Vitae as PDF
Main areas of research
My research interests can be defined in the fields of microbial ecology, nutrient/element cycling, the global nitrogen (N)-cycle and particularly the process N2 fixation therein, terrestrial ecosystems and structured ecosystems such as microbial mats and biological soil crusts. My long-term goal is to identify the active participants in key processes within the carbon (C)- and N-cycle, the factors that regulate and govern their activities, the trophic interactions among microorganisms, but also between plants and microorganisms within an ecosystem, and the interdependence of C- and N-cycle in terrestrial ecosystems. To reach this goal I use a combined approach of activity measurements on the process-level, analysis of the genetic potential on the community-level and confirmation of the targeted activity on the single-cell level.
The research in my group at the University of Vienna focuses on the active microbial participants involved in the N- and C-cycle across terrestrial ecosystems, with particular emphasis on the linkages of these two cycles. We are currently investigating the active participants as well as edaphic drivers and limitations of complex C degradation. In another project we are studying the active N2-fixing community (diazotrophs) in soils along with the factors that govern their activity such as different energy sources for this highly energy-costly process. In this project we are also including biological soil crusts, where autotrophically fixed CO2 will be the major source of C for N fixation. I am currently extending the on-going diazotrophy studies to the investigation of diazotrophs associated with plant roots. Plants excrete C compounds into the rhizosphere, which can be utilized by the microorganism inhabiting this niche as a source of energy. Therefore, this represents a niche particularly suited for bacteria that fix N2 and have a high need of energy for this energy-costly process. Both systems, biological soil crusts and the rhizosphere, are prime examples of the linkage of the N- and C-cycle in terrestrial systems that I am particularly interested in.
This summer we will start a project that will focus on the activity of microorganisms under microoxic conditions in terrestrial ecosystems. Evidence exists that most of microbial activity in natural habitats is actually not performed under atmospheric but under reduced O2 levels. The diversity of microorganisms with the capacity to make a living under reduced O2 concentrations is not well understood and will be particularly investigated in terrestrial ecosystems in this project.
On-going research projects
- Diversity and activity of free-living diazotrophs in terrestrial ecosystems
   (funded by the Austrian Science Fund, project No. P 25700-B20)
- Plant-associated diazotrophs
   (funded by Marie Curie FP7, project No. 628361)
- Microbial mediated cellulose degradation
   (funded by Marie Curie FP7, project No. 300807)
- Activity of microorganisms under microoxic conditions in terrestrial ecosystems
   (funded by the Austrian Science Fund, project No. P 26392-B20)
- Application of single-cell methods in terrestrial ecosystems
   (funded by Marie Curie FP7, project No. 321742)
 Sampling sites
Lab members

 Roye Angel
 Stephanie A. Eichorst
 Raphael Gabriel
 Florian Höggerl
 Mariko Kuno
 Christopher Panhölzl
 Florian Strasser
Publications in peer reviewed journals
  1. Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, Palatinszky M, Schintlmeister A, Schmid MC, Hanson BT, Shterzer , Mizrahi I, Rauch I, Decker T, Bocklitz T, Popp J, Gibson CM, Fowler PW, Huang WE, Wagner M. 2015. Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc. Natl. Acad. Sci. USA , in press.
     Full text    PUBMED
  2. Woebken D, Burow L, Behnam F, Mayali X, Schintlmeister A, Fleming E, Prufert-Bebout L, Singer S, López Cortés A, Hoehler T, Pett-Ridge J, Spormann A, Wagner M, Weber P, Bebout B. 2015. Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 9: 485-496.
     Full text    PUBMED
  3. Lee JZ, Burow LC, Woebken D, Everroad RC, Kubo MD, Spormann AM, Weber PK, Pett-Ridge J, Bebout BM, Hoehler TM.. 2014. Fermentation couples Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats. Front. Microbiol. 5: 61.
     Full text   
  4. Burow LC, Woebken D, Bebout BM, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler TM.. 2014. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiol. 12: 221-230.
  5. Everroad RC, Woebken D, Singer SW, Burow LC, Kyrpides N, Woyke T, Goodwin L, Detweiler A, Prufert-Bebout L, Pett-Ridge J. 2013. Draft genome sequence of an oscillatorian cyanobacterium, strain ESFC-1 Genome Announc. 1: e00527-13.
     Full text    PUBMED
  6. van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs K-J, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM. 2013. The metagenome of the marine anammox bacterium ‘Candidatus Scalindua profunda’ illustrates the versatility of this globally important nitrogen cycle bacterium. Environ. Microbiol. 15: 1275-89.
     Full text    PUBMED
  7. Burow LC§, Woebken D§, Marshall IPG, Lindquist EA, Bebout BM, Prufert-Bebout L, Hoehler TM, Tringe SG, Pett-Ridge J, Weber PK, Spormann AM, Singer SW.. 2013. Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS. ISME J. 7: 817-829.
     Full text    PUBMED
  8. Burow LB, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler T. 2012. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J. 6: 863-874.
     Full text    PUBMED
  9. Woebken D, Burow LB, Prufert-Bebout L, Bebout BM, Hoehler T, Pett-Ridge J, Singer SW, Spormann AM, Weber PK. 2012. Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis. ISME J. 6: 1427-1439.
     Full text    PUBMED
  10. Musat F, Wilkes H, Behrends A, Woebken D, Widdel F. 2010. Microbial nitrate-dependent cyclohexane degradation coupled with anaerobic ammonium oxidation. ISME J. 4: 1290-1301.
  11. Galan A, Molina V, Thamdrup B, Woebken D, Lavik G, Kuypers MMM, Ulloa O. 2009. Anammox bacteria and the anaerobic oxidation of ammonium in the oxygen minimum zone off northern Chile. Deep-Sea Res. II 56: 1021-1031.
  12. Hoffmann F, Radax R, Woebken D, Holtappels M, Lavik G, Rapp HT, Schläppy M-L, Schleper C, Kuypers MMM. 2009. Complex nitrogen cycling in the sponge Geodia barretti. Environ. Microbiol. 11: 2228-2243.
  13. Hamersley MR, Woebken D, Boehrer D, Schulze M, Lavik G, Kuypers MMM. 2009. Water column anammox and denitrification in a temperate permanently-stratified lake (Lake Rassnitzer, Germany). Syst. Appl. Microbiol. 32: 571-582.
  14. Lam P, Lavik G, Jensen MM, van de Vossenberg J, Schmid MC, Woebken D, Gutiérrez D, Amann R, Jetten MS, Kuypers MM. 2009. Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. USA 106: 4752-4757.
  15. Woebken D, Lam P, Fuchs BM, Kuypers MMM, Naqvi SWA, Kartal B, Strous M, Jetten MSM, Amann R. 2008. Microdiversity study of marine anammox bacteria reveals a novel Candidatus Scalindua phylotype in marine oxygen minimum zones. Environ. Microbiol. 10: 3106-3119.
  16. Schmid MC, Hooper AB, Klotz MG, Woebken D, Lam P, Kuypers MM, Pommerening-Roeser A, Op den Camp HJ, Jetten MS.. 2008. Environmental detection of octahaem cytochrome c hydroxylamine/hydrazine oxidoreductase genes of aerobic and anaerobic ammonium-oxidizing bacteria Environ Microbiol. 10: 3140-3149.
  17. Wakeham SG, Amann R, Freeman KH, Hopmans EC, Jørgensen BB, Putnam IF, Schouten S, Sinninghe Damsté JS, Talbot HM, Woebken D. 2007. Microbial ecology of the stratified water column of the Black Sea as revealed by a comprehensive biomarker study. Org. Geochem. 38: 2070-2097.
  18. Hannig M, Lavik G, Kuypers MMM, Woebken D, Martens-Habbena W, Jürgens K. 2007. Shift from denitrification to anammox after inflow events in the central Baltic Sea. Limnol. Oceanogr. 52: 1336-1345.
  19. Hamersley MR, Lavik G, Woebken D, Rattray JE, Lam P, Hopmans EC, Sinninghe Damsté JS, Krüger S, Graco M, Gutiérrez D, Kuypers MMM. 2007. Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone. Limnol. Oceanogr. 52: 923-933.
  20. Woebken D, Fuchs BM, Kuypers MMM, Amann R. 2007. Potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the Namibian upwelling system. Appl. Environ. Microbiol. 73: 4648-4657.
  21. Woebken D, Teeling H, Dumitriu A, Kostadinov I, Amann R, Glöckner FO. 2007. Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J. 1: 419-435.
  22. Bauer M, Kube M, Teeling H, Richter M, Lombardot T, Allers E, Wurdemann CA, Quast C, Kuhl H, Knaust F, Woebken D, Bischof K, Mussmann M, Choudhuri JV, Meyer F, Reinhardt R, Amann R, Glöckner FO. 2006. Whole genome analysis of the marine Bacteroidetes 'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8: 2201-2213.
  23. Fuchs BM, Woebken D, Zubkov MV, Burkhill P, Amann R. 2005. Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea. Aquat. Microb. Ecol. 39: 145-157.
  24. Kuypers MM, Lavik G, Woebken D, Schmid MC, Fuchs BM, Amann R, Jørgensen BB, Jetten MS. 2005. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation Proc. Natl. Acad. Sci. USA 102: 6478-6483.

Book chapters and other publications
  1. Eichorst SA, Woebken D. 2014. Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In Molecular Methods and Applications in Microbiology, pp. 203-211. (Skovhus TL, Caffrey S, Hubert CRJ, ed.). Caister Academic Press, Norfolk, UK.
  2. Eichorst SA, Woebken D.. 2014. Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In Molecular Methods and Applications in Microbiology, in press. (Skovhus, T.L., Caffrey, S., and Hubert, C.R.J., ed.). Caister Academic Press, Norfolk, UK.
Public outreach
 Im Reich der wichtigen Kleinen [German]