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Microbial ecology and Environmental Microbiology of natural and engineered ecosystems

1.    Community to gene scale regulation of nitrogen dissimilating microbes: Relevance for nitrate removal and greenhouse gas production in wetlands, temperate and permafrost affected soils.

2.    Symbiotic nitrogen fixation associated with wetland plants: Diazotrophs as key microbes (Fig. 1).

3.    Earthworm-microbe interactions in soils and their relevance to soil processes: Greenhous gas metabolism and pollutant degradation.

4.    Regulation of the anaerobic feed chain in natural and engineered ecosystems: From biopolymers to methane

5.    Microbial (Micro-)pollutant transformations in soils and sediments: Potential for bioremediation.

My research addresses the regulation of microbial community structure and model organisms with molecular, microbiological, biochemical and analytical methods. Next generation sequencing, transcriptomics, gene expression studies as well as RNA-based stable isotope probing techniques to trace process associated organisms and intermediates are applied. The isolation, description and validation of new corner stone species complements molecular methods to enable utilization of new metabolic potentials for biotechnical purposes.

Soils and sediments host app. 1 billion (109) microbes per gram. Up to 1 million different microbial species per gram illustrate an extreme diversity, suggesting that soils and sediments belong to the habitats on earth with the greatest richness in microbial species. Numerous microbes catalyse elemental cycles (e.g., carbon, nitrogen, and sulfur cycles) that are essential for life on earth. Pollutant degradation, (waste)water treatment, production and consumption of atmospheric greenhouse gases, nitrogen fixation, as well as the promotion of plant growth are a few examples for the importance of microbes in the environment. Such activities are mediated by complex microbial communites whose activities impact global change, renewable energy production, land usage and world nutrition. The quest for new metabolic potentials of hitherto uncultured microbes and their regulation is therefore a promising task.

However, there is still a great imbalance between the importance of microbial communities and in-depth knowledge on their identity and regulation in many natural and technical ecosystems. Thus, central questions guiding my research are:

  • Which new organisms, structural genes and regulators on cellular level are associated with a certain process?
  • Which environmental parameters regulate the community structure and thus the genetic and metabolic potential?
  • What regulates the expression of the available genetic potential in the environment?
  • How do higher organisms interact with microbial communities?
  • Do common reaction- and activity patterns of microbial communities exist, when environmental conditions change?
  • Can new ecological theories be delineated from microbial community dynamics?
  • What are measures for microbiological process management?

Fig. 1. Ombrotrophic Patagonian bogs (Chile) rely on diazotrophic, i.e. dinitrogen fixing bacteria. Such members of the Beijerinckiaceae are associated with the nodule like structures of wetland plants, representing a good example for plant-microbe interactions driving a N-limited ecosystem.