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

Dr. Dagmar Woebken is the leader of the new NanoSIMS Group at the Department of Microbial Ecology, starting in January 2012. Dr. Woebken did her postdoctoral work investigating diazotrophy in coastal microbial mats using next generation sequencing combined with FISH and NanoSIMS at Stanford University/NASA Ames/Lawrence Livermore National Laboratory. Her group will be investigating active participants in the N and C cycle across terrestrial and aquatic ecosystems using single cell techniques.
Publications in peer reviewed journals
  1. 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.
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  2. 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. , in press.
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  3. 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: 1427-39.
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  4. Burow LB, Woebken D, Bebout BM, McMurdie PJ, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Weber PK, Hoehler T. 2011. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J. 6: 863-74.
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  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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, in press. (Skovhus, T.L., Caffrey, S., and Hubert, C.R.J., ed.). Caister Academic Press, Norfolk, UK.