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
Austria
Phone: +43 1 4277 91213

Main areas of research

Terrestrial ecosystems represent habitats with unpredictable conditions for soil microorganisms due to environmental stressors, often confronting them with suboptimal conditions for growth. Yet, this environment harbors an enormous microbial diversity. Soil encompasses different habitats such as the rhizosphere, rhizoplane and bulk soil in conjunction with various scales (macro- vs. micro-scale, such as in the realm of soil aggregates). Often, these habitats represent challenging conditions for the residing microbes, but nevertheless they endure and might even flourish in specific situations. This vast soil microbial diversity along with its maintenance has fascinated me for many years now.

Until now, many questions regarding the adaptation of soil microorganisms to stressful conditions in their habitats and the factors that govern their activity remain unanswered. My group investigates the genomic and physiological features that allow for the survival and thus success of soil microorganisms. We focus on desert microorganisms that endure long periods of drought, in addition to microorganisms in temperate soils that are limited in readily available carbon sources. We also investigate more favorable soil habitats, such as the rhizosphere, where soil microorganisms are provided with energy-rich root exudates. We are particularly interested how plants influence the microbial community structure and activity in their vicinity and in the effect of this association.

We aim to gain a holistic view on the function of the “soil microbiome”. To do so, we combine molecular techniques (such as amplicon sequencing, metagenomics and metatranscriptomics), stable isotope probing and single-cell approaches (such as NanoSIMS analysis and Raman microspectroscopy) with enzyme kinetics and ecosystem-level biogeochemical methods. 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.

 

Current research projects:
 
Dormancy and reactivation of desert soil microorganisms

Soil microorganisms are faced with unpredictable conditions due to environmental stressors (such as water, energy or nutrient limitation), and therefore the majority is assumed to be in a state of ‘dormancy’ – a state with low metabolic activity enabling long-term persistence. In this project, we focus on microbial communities that inhabit surface soils of arid deserts – so-called biological soil crusts. This environment experiences persistent (high) UV irradiation, heat and osmotic stress in addition to limited water availability, with favorable conditions (i.e. due to rain) surmounting to only a couple months per year.

A metagenome investigation of crusts in the Negev Desert, Israel, revealed diverse physiological potential and diverse survival strategies within the microbial community. While the potential for sporulation was only found in a small proportion of the community, oxidation of atmospheric hydrogen gas (H2) seemed to be a more common survival mechanism. However, dormancy cannot be sustained indefinitely, and therefore phases of resuscitation must also play an important role for long-term survival of desert soil microorganisms. We are currently focusing on this aspect, which we propose plays a major role in maintaining microbial diversity in one of the harshest environments on the planet.

Selected publications:
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. mSystems. 6(1):e00786-20.
 
Man Leung P, Bay SK, Meier DV, Chiri E, Cowan DA, Gillor O, Woebken D, Greening C. 2021. Energetic basis of microbial growth and persistence in desert ecosystems. mSystems 5(2): e00495-19. 
 
Giguere AT*, Eichorst SA*, Meier DV, Herbold CW, Ricther A, Greening C, Woebken D. 2021. Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils. The ISME Journal 15:363–376.  (*co-first authors)
 
 
A particular successful clade in temperate soils – the Acidobacteriota

The Acidobacteriota are characterized by large phylogenetic diversity and great abundance in soils worldwide. Being particularly successful in these often carbon-limited soils, we focus on this group with the goal to elucidate the physiological features that enable them to survive or even thrive in the often-challenging soil habitats. In a comparative genomic investigation, we identified different physiological capacities that could provide them with an advantage in soil. These features were investigated in detail in a multidisciplinary approach, revealing the unexpected use of low-affinity terminal oxidases to respire nano-molar concentrations of oxygen and the oxidation of H2 during starvation. Our studies uncovered great physiological flexibility of this abundant group of soil bacteria, which, together with H2 scavenging as a survival strategy, might explain the success and thus ubiquity of these bacteria.      

Selected publications:
Giguere AT*, Eichorst SA*, Meier DV, Herbold CW, Ricther A, Greening C, Woebken D. 2021. Acidobacteria are active and abundant members of diverse atmospheric H2-oxidizing communities detected in temperate soils. The ISME Journal 15:363–376.  (*co-first authors)
 
Trojan D, García-Robledo E, Meier DV, Hausmann B, Revsbech NP, Eichorst EA, Woebken D. 2021. Microaerobic lifestyle at nanomolar O2 concentrations mediated by low-affinity terminal oxidases in abundant soil bacteria. mSystems. 6:e00250-21.
 
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. Environmental Microbiology 20:1041–1063.
 
 
Plant-microbe associations

Plant-associated habitats in soil, such as the rhizosphere, represent more favorable situations for microorganisms, as plant roots excrete carbon compounds that can be readily utilized. In several projects, we investigate how plants influence the microbial community structure and as well as activity in their vicinity and the effect of this association. One focus are bacteria that fix atmospheric N2 in association with plants, as the carbon-rich rhizosphere could be a suitable niche for them considering the high energy demand for this process. We are currently investigating diazotrophs associated with grasses and herbs in an Austrian Alpine grassland, with the goal to decipher the processes influencing the diazotroph community assembly and activity, such as fertilization and vegetation. For our investigations of diazotrophs in soils, we developed a toolbox of stable-isotope labeling techniques along with a bioinformatic pipeline, NifMAP, to analyze nifH amplicons.

Another focus is the plant-ectomycorrhiza-bacteria symbiosis, where we explored the assembly of bacteria and were able to follow the transfer of recent plant photosynthates to ectomycorrhizal hyphae-associated bacteria via nanoSIMS. The Woebken group is also involved in a project led by Veronika Mayer investigating microbial communities in tropical ant-plant associations. In an exciting new project, we are studying the associated microbiome of halophytic plants together with Stefanie Wienkoop with the goal to decipher the beneficial effects of this association.

Selected publications:
Nepel M, Mayer VE, Barrajon-Santos V, Woebken D. 2023. Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stages. Communications Biology. 6:1217.
 
Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. 2023. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. New Phytologist. 240:439-451.
 
Dietrich M, Montesinos-Navarro A, Gabriel R, Strasser F, Meier DV, Mayerhofer W, Gorka S, Wiesenbauer J, Martin V, Weidinger M, Richter A, Kaiser A, Woebken D. 2022. Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities. Communications Biology 5:1261.
 
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. (*co-corresponding authors).
 
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, Kaiser C. 2021. Recently photoassimilated carbon and fungal-delivered nitrogen are spatially correlated at the cellular scale in the ectomycorrhizal tissue of Fagus sylvatica. New Phytologist 232:2457–2474.
 
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. Frontiers in Microbiology 10:168. (*co-corresponding authors)
 
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.

 
SELECTED PUBLICATIONS
 

2023

  • Nepel M, Mayer VE, Barrajon-Santos V, Woebken D. 2023. Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stages. Communications Biology. 6:1217.
  • Schmidt H, Gorka S, Seki D, Schintlmeister A, Woebken D. 2023. Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria. New Phytologist. 240:439-451.

2022

  • 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.

2021

  • 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.

2020

  • 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): e00495-19Associated 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.

2019

  • 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.
TEACHING
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
 
 
PUBLIC OUTREACH

Junge-Akademie-Blog: 15 Jahre Junge Akademie (2023)

Junge-Akademie-Blog: Was ist Leben? (2023)

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)