Assoc.-Prof. Dr. Dagmar Woebken

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. We are particulalrly interested in microbial communities that inhabit surface soils of arid deserts – so-called biological soil crusts or biocrusts. This environment experiences persistent (high) UV irradiation, heat and osmotic stress in addition to limited water availability, with favorable conditions caused by rain surmounting to only few days during 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.
By mimicking rain events and combining metagenome-centered metatranscriptomics with heavy-water incubations and NanoSIMS, we revealed that biocrust microbial communities are perfectly adapted to unpredictable and short-lived rain events. This is mediated via rapid and simultaneous resuscitation of the majority of cells and taxonomical and physiological diverse groups. Additionally, these microorganisms are prepared for sudden osmotic changes and thus protected from significant cell loss. Together, these mechanisms enable long-term survival of biocrusts bacteria and explain the observed limited productivity.

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.