Assoz.-Prof. Dr. Dagmar Woebken

Associate Professor
University of Vienna
Department of Microbiology and Ecosystem Science
Division of Microbial Ecology
Djerassiplatz 1
A-1030 Vienna
Phone: +43 1 4277 91213

Main areas of research                           

The overarching goal of my research group is to better understand the active microbial participants in key processes within the terrestrial carbon (C)- and nitrogen (N) -cycle, the factors that govern these activities, the trophic interactions among microorganisms, but also between plants and microorganisms within an ecosystem, and the physiologies that allow for the success of soil microorganisms. Furthermore, my research group strives to integrate the concepts of ecological theory into the realm of microbial ecology to address fundamental questions about niche differentiation, dormancy and microbial seed bank for processes in the soil C- and N- cycles. In many projects, we are including single-cell methods such as fluorescence in situ hybridization (FISH), high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy to answer our research questions. 

Diazotrophy. One of my major research interests explores the diversity of free-living diazotrophs in temperate grasslands and deserts, as free-living diazotrophs may provide more fixed N in these ecosystems than symbiotic diazotrophs. We are using the multidisciplinary approach that was used previously to identify the active diazotroph microbial community members in photosynthetic microbial mats (Woebken et al., 2012 and Woebken et al., 2015). More specifically, we are investigating the diversity of free-living diazotrophs in grassland soil and the dependence of their activity on external factors such as available C sources (e.g. simple sugars in form of root exudates), since N2 fixation is a highly energy demanding process. As a second focus, we are investigating diazotrophy in biological soil crusts, which contribute to ~30% of the total biological N2 fixation in terrestrial ecosystems.

Plant microbiome. Plants and soil microorganisms are major drivers in the terrestrial C- and N- cycles and live in tight associations. The plant-associated microbial community is oftentimes referred to as the ‘plant microbiome’, which is defined as the microorganisms in close proximity or associated with (1) the aerial part of the plant, such as the leaves and stem; and (2) below-ground parts of the plant such as root, the root surface (rhizoplane) and the soil surrounding the roots (rhizosphere).

Soils are believed to be the microbial seed bank or reservoir for this microbiome, from which the plant recruits its associated microbiome by exuding up to 40% of its fixed C into the surrounding soil. With these exudates, a tremendous amount of chemical communication occurs between the plant and microorganisms in this dynamic system and is believed to promote beneficial interactions. As plants can influence microbial N-cycle processes and supply microorganisms with C sources via root exudates, we have extended our diazotrophy investigations into the ‘plant microbiome’ that inhabit the rhizosphere, the rhizoplane or the endosphere compartment of plants. Our model systems include meadow grass plants in Austrian grasslands and rice plants, one of the most important agricultural plant worldwide.

Microbial cellulose degradation. In addition to the N-cycle, we are currently investigating the active participants as well as edaphic drivers and limitations of microbial cellulose degradation. Soils contain the largest pool of C on Earth with cellulose being the most abundant polymer, as it is a key component of plant structural C. Members of the Bacteria and Fungi are responsible for degrading cellulose, but their contributions remain unresolved. For a better understanding of the terrestrial C-cycle it is vital to elucidate the active participants in cellulose degradation and identify different niches of cellulose-responsive guilds. We are combing stable isotope probing with next generation sequencing to characterize cellulose-responsive guilds across various amendments, along with single-cell based approaches to appreciate this process at a more relevant spatial scale.

Acidobacteria. Pick up any handful of soil worldwide, and members of the phylum Acidobacteria will probably be one of the most dominant groups. They comprise a monophyletic phylum of astonishing diversity similar to the proteobacteria, with 26 currently recognized subdivisions. Their prevalence suggests that they play ecologically significant roles in the soil environment, yet we still know very little about (i) the genes/functions, which allow them to be prevalent and (ii) the physiological traits that are important to terrestrial biogeochemical cycles.

Our overarching goal is to better link the genetic potential of acidobacteria with their in situ functions in soil in order to elucidate the ecophysiology and therefore the success and ubiquity of members of the phylum Acidobacteria in terrestrial ecosystems. For this, we combine genomic, growth-based, molecular and single-cell functional analyses. In addition, we are also attempting to cultivate additional strains in this diverse phylum, which is highly unrepresented in culture collections and databases. 

Microbial dormancy. Soils are considered the last scientific frontiers that harbor one of the most diverse microbial communities on Earth. It is hypothesized that this diversity allows for redundancy in microbial key processes, thereby ensuring ecosystem stability. Much of this functional redundancy is embodied in non-active, dormant microorganisms that represent the ‘microbial seed bank’. It is hypothesized that dormant microorganisms can be recruited to participate in a given function upon resuscitation with environmental cue(s). We are addressing fundamental questions about functional redundancy, dormancy and the ‘microbial seed bank’ that could explain the extensive diversity of soil microbial communities. The goals of this project are to reveal environmental cues that resuscitate dormant microorganisms involved in major soil functions and to identify the activated microorganisms using an arid ecosystem as a model system and by combining stable isotope probing (SIP) and sequencing with process-level and single-cell activity analysis.

Method development. Across many of these aforementioned projects, we are constantly developing, testing and optimizing single-cell methods to facilitate their application to microorganisms in terrestrial habitats. Single-cell based approaches such as high-resolution secondary ion mass spectrometry (NanoSIMS) and Raman microspectroscopy are increasingly applied in microbial ecology studies. Raman microspectroscopy and NanoSIMS are techniques that permit the analysis of microbiological samples down to the single-cell level. These powerful techniques have recently helped define the field of single-cell ecophysiology especially when combined with stable isotope tracers (such as 13C, 15N and D) and/or identification of the targeted cell using fluorescence in situ hybridization (FISH).

Some of these developments have been highlighted by the Joint Genome Institute, Science Highlights: A Single-Cell Pipeline for Soil Samples.

Current Research projects


Google scholar, complete publication list for Dagmar Woebken


  • Schagerl M, Angel R, Donabaum U, Gschwandner AM, Woebken D. 2022. Limnospira fusiformis harbors dinitrogenase reductase (nifH)-like genes, but does not show N2 fixation activity. Algal Research. 66:102771.
  • Falkenberg R, Fochler M, Sigl L, Bürstmayr H, Eichorst SA, Michel A, Oburger E, Staudinger A, Steiner B, Woebken D. 2022. The breakthrough paradox - How focusing on one form of innovation jeopardizes the advancement of science. EMBO Reports. 23:e54772.
  • Nepel M*, Pfeifer J, Oberhauser FB, Richter A, Woebken D*, Mayer VE. 2022. Nitrogen fixation by diverse diazotrophic communities can support population growth in arboreal ants. BMC Biology. 20:135. *denotes co-corresponding authors.
  • Nepel M, Angel R, Borer ET, Frey B, MacDougall AS, McCulley RL, Risch AC, Schütz M, Seabloom EW, Woebken D. 2022. Global grassland diazotrophic communities are structured by combined abiotic, biotic, and spatial distance factors but resilient to fertilization. Front. Microbiol. 13: 1-12.


  • Trojan D, Garcia-Robledo E, Meier DV, Hausmann B, Revsbech NP, Eichorst SA, Woebken D. 2021. Microaerobic lifestyle at nanomolar O2 concdentrations mediated by low-affinity terminal oxidases in abudnant soil bacteria. mSystems. 6(4): e00250-21.
  • Mayerhofer W, Schintlmeister A, Dietrich M, Gorka S, Wiesenbauer J, Martin V, Gabriel R, Reipert S, Weidinger M, Clode P, Wagner M, Woebken D, Richter A, Kasier C. 2021. Recently photoassimilated carbon and fungal-delivered nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica. New Phytol. 232(6):2457-2474.
  • Meier DV, Greve AJ, Chennu A, van Erk MR, Muthukrishnan T, Abed RMM, Woebken D, de Beer D. 2021. Limitation of microbial processes at saturation-level salinities in a microbial mat covering a coastal salt flat. Appl Environ Microbiol. 87(17): e0069821
  • Meier DV, Imminger S, Gillnor O, Woebken D. 2021. Distribution of mixotrophy and desiccation survival mechanisms across microbial genomes in an arid biological soil crust community. mySystems. 6(1):e00786-20.
  • Giguere AT*, Eichorst SA*, Meier D, Herbold CW, Richter A, Greening C, Woebken D. 2021. Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils. The ISME J. 15(2): 363-376. *denotes co-first authors.


  • Man Leung P, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C. 2020. Energetic basis of microbial growth and persistence in desert ecosystems. mSystems. 5(2): e00495-19. Associated video. 
  • Eichorst SA, Trojan D, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Goodwin LA, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Woebken D. 2020. One complete and seven draft genome sequences of subdivision 1 and 3 Acidobacteria isolated from soil. Microbiol Resour Announc. 9(5): e01087-19.
  • Sedlacek CJ, Giguere AT, Dobie MD, Mellbye BL, Ferrell RV, Woebken D, Sayavedra-Soto LA, Bottomley PJ, Daims H, Wagner M, Pjevac P. 2020. Transcriptomic reponse of Nitrosomonas europaea transitioned from ammonia- to oxygen-limited steady-state growth. mSystems. 5(1): e00562-19.


  • Zheng Q, Hu Y, Zhang S, Noll L, Böckle T, Dietrich M, Herbold CW, Eichorst SA, Woebken D, Richter A, Wanek W. 2019. Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity. Soil Bio Biochem. 136: 107521.
  • Gorka S, Dietrich M, Mayerhofer W, Gabriel R, Wiesenbauer J, Martin V, Zheng Q, Imai B, Prommer J, Weidinger M, Schweiger P, Eichorst SA, Wagner M, Richter A, Schintlmeister A, Woebken D, Kaiser C. 2019. Rapid transfer of plant photosynthates to soil bacteria via ectomycorrhizal hyphae and its interaction with nitrogen availability. Front. Microbiol. 10(168): 1-20.
  • Schneider S, Schintlmeister A, Becana M, Wagner M, Woebken D, Wienkoop S. 2019. Sulfate is transported at significant rates through the symbiosome membrane and is crucial for nitrogenase biosynthesis. Plant Cell Enviorn 42(4): 1180-1189.


  • Walker TWN, Kaiser C, Strasser F, Herbold CW, Leblans NIW, Woebken D, Janssens IA, Sigurdsson BD, Richter A. 2018. Microbial temperature sensitivity and biomass change explain soil carbon loss with warming. Nature Climate Change 8: 885-889.
  • Zumstein MT, Schintlmeister A, Nelson TF, Baumgartner R, Woebken D, Wagner M, Kohler HE, McNeill K, Sander M. 2018. Biodegradation of synthetic polymers in soils: Tracking carbon into CO2 and microbial biomass. Sci Adv. 4(7): eaas9024.
  • Schmidt H, Nunan N, Höck A, Eickhorst T, Kaiser C, Woebken D, Raynaud X. 2018. Recognizing patterns: spatial analysis of observed microbial colonization on root surfaces. Front Env Sci 6(61): 1-12.
  • Angel R, Nepel M, Panhölzl C, Schmidt H, Herbold C, Eichorst SA, Woebken D. 2018. Evaluation of primers targeting the diazotroph functional gene and development of NifMAP - a bioinformatics pipeline for analyzing nifH amplicon data. Front. Microbiol. 9(703):1-15. 
  • Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. 2018. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 20(3): 1041-1063. 
  • Hausmann B, Pelikan C, Herbold CW, Köstlbacher S, Albertsen M, Eichorst SA, Glavina Del Rio T, Huemer M, Nielsen PH, Rattei T, Stingl U, Tringe SG, Trojan D, Wentrup C, Woebken D, Pester M, Loy A. 2018. Peatland Acidobacteria with a dissimilatory sulfur metabolism. ISME J. 12:1729-1742.
  • Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA, Woebken D. 2018. Application of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 20: 44-61


  • Eichorst SA, Trojan D, Woebken D. 2017. Terriglobus. In Bergey's Manual of Systematics of Archaea and Bacteria. (eds W.B. Whitman, F. Rainey, P. Kämpfer, M. Trujillo, J. Chun, P. DeVos, B. Hedlund and S. Dedysh). doi:10.1002/9781118960608.gbm00003.pub2


  • Spohn M, Pötsch EM, Eichorst SA, Woebken D, Wanek W, Richter A. 2016. Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a termperate grassland. Soil Biol Biochem 97:168-175.
  • Everroad RC, Stuart RK, Bebout BM, Detweiler AM, Lee JZ, Woebken D, Prufert-Bebout L, Pett-Ridge J. 2016. Permanent draft genome of strain ESFC-1: ecological genomics of a newly discovered lineage of filamentous diazotrophic cyanobacteria. Standards in Genomice Sciences 11:53.


  • Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, Woebken D. 2015. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol. Ecol. DOI: fiv106.
  • Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, López Cortés A, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. 2015. Revisiting N2 fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. ISME J. 9:485-496.
  • Berry D, Mader E, Lee TK, Woebken D, Wang Y, Zhu D, Palatinszky M, Schintlmeister A, Schmid MC, Hanson BT, Shterzer N, 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. PNAS 112: E194-203.


  • Eichorst, SA and Woebken, D. 2014. Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In: Skovhus TL, Caffrey S, editors. Molecular Methods and Applications in MIcrobiology. Norfolk, UK: Caister Academic Press; p 203-211.
  • Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, Spormann AM, Van Treuren W, Ursell LK, Pirrung M, Robbins-Pianka A, Cantarel BL, Lombard V, Henrissat B, Knight R, Gordon JI. 2014. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159: 253-266.
  • 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. Geobiology 12: 221–230.
  • Lee JZ, Burow LC, Woebken D, Everroad RC, Kubo MD, Spormann AM, Weber PK, Pett-Ridge J, Bebout BM, Hoehler TM. 2014. Fermentation couple Chloroflexi and sulfate-reducing bacteria to Cyanobacteria in hypersaline microbial mats. Front Microbiol 5(61):1-17.

Before 2013

  • 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. (*co-first authors)
  • Woebken D, Burow LC, Prufert-Bebout L, Bebout BM, Hoehler TM, 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
  • Burow LC, Woebken D, Bebout BM , McMurdie PJ , Singer SW , Pett-Ridge J , Prufert-Bebout L, Spormann AM , Weber PK, Hoehler TM. 2012. Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay. ISME J. 6:863–874

The Woebken GROUP

Joining the team

Information on open research positions can be found here or can be obtained by contacting Dagmar. If you are interested in joining our team with your own fellowship, please check out our PhD & postdoc program.

Courses taught by Dr. Woebken at the University of Vienna. 
FISH Workshop at the University of Costa Rica, CIEMIC (2018) 
PhD students in the Woebken group (Florian Strasser and Maximillian Nepel) provided hands-on training in various fluorescence in situ hybridization (FISH) techniques, while Stephanie A. Eichorst and Dagmar Woebken gave webinars on the theory and principle of FISH.
This workshop was highlighted in the University of Costa Rica news


Falter Article: Leben auf trockenem Boden (2020)

Semesterfrage der Uni Wien: Mikroorganismen: Artenvielfalt im Boden (2020)

Junge-Akademie-Blog/Der Standard. Bodenmikroorganismen als Überlebenskünstler: Wie schaffen die das? (2019)

Junge-Akademie-Blog/DerStandard. Bodenmikroorganismen sind wahre Überlebenskünstler (2018)

Semesterfrage der Uni Wien: Klima Ist biologische Landwirtschaft global einsetzbar? (2018)

Semesterfrage der Uni Wien: Klima Wie hängt unsere Ernährung mit dem Klima zusammen? (2018)

Uni Wien forscht: Mikrobiologin Dagmar Wöbken auf Spurensuche (2014)

Im Reich der wichtigen Kleinen (2014)

University of Vienna, KinderUni (since 2014 - current)
Summer Workshop entitled "What would the world look like without microbes?". Course description: Microbes are all around us and are very important. Imagine what the world would look like without them? Come spend some time at our Microbe Exhibition and learn more. We will explore what microbes do in nature, for instance in dirt and in lakes, how they help us make food, and how they help plants to grow.
3-day workshop for school children entitled "An Underground Adventure. Dirt - The Scoop on Soil". This 3-day workshop was a synthesis of presentations, discussions and hand-on activities designed to develop an awareness and appreciation for soil and soil microorganisms. The themes covered topics such as "What is Soil?", "What lives in soil?", and what we can do to save/preserve the soil, jobs with soil and a question-and-answer session with the students.