Research Focus

Microbial Physiology

Redox processes in lake sediments
In littoral sediment of Lake Constance, iron oxides are an important constituent of the insoluble mineral phase and contribute substantially to redox processes in the sediment. We are interested in the biochemical mechanism of ferric oxide reduction, of anaerobic reoxidation of ferrous iron under the influence of light and nitrate, and in the dynamics of these processes and their interference with the sulfur cycle. We are also looking for microaerobic methane oxidation as a key process of oxygen consumption in the anoxic-oxic transition phase.

Energetics of anaerobic degradation processes
Microbial life in the absence of oxygen has to operate with substantially smaller energy budgets than aerobic life. At the very end, the conversion of biomass to methane and CO₂ yields only 15% of the energy available to aerobic oxidation, and this small amount has to be shared by 3-4 trophic groups (guilds) of functionally different bacteria. In the last steps of methanogenic fermentation processes, every single organism has less than 1 ATP equivalent available to its energy metabolism. We try to understand microbial energy metabolism with such small energy increments as model systems to define the energetic limits of life in general. These studies are of key importance to understand the mechanisms of survival of huge amounts of prokaryotes in deep sediments. Our studies also help to improve the production of methane (“biogas”) from waste materials.

Biochemistry of anaerobic degradation of comparably stable compounds
The degradation of natural and synthetic substrates in anoxic environments such as sediments cannot employ oxygen in the activation of comparably stable compounds such as aromatic compounds, hydrocarbons or polyethers (e.g. lignin). Degradation of such compounds in the absence of oxygen has to employ basically different biochemical strategies than in the presence of oxygen. Primary substrate activation reactions include reductive destabilizations, oxygen-independent hydroxylations via molybdenum enzymes, carboxylations, and radical-catalyzed rearrangements of carbon skeletons. In some cases, e.g., with the bifunctional phenol resorcinol, even two different strategies of anaerobic degradation were observed, depending on whether nitrate is available as an alternative electron acceptor or not. We try to understand the biochemical strategies of substrate degradation in the absence of oxygen in order to analyze the limits of anaerobic biodegradation capacities in general. The results help to define the limitations of biomass utilization in the production of microbial energy feedstocks (ethanol, biogas) for mankind, or in the development of biodegradable polymers, e.g., in the packaging industry. 

Microbial Ecology

The hidden sulfur cycle in freshwater wetlands
Freshwater wetlands are a major source of the greenhouse gas methane but also can act as carbon sink, storing currently more than one third of the terrestrial organic carbon. Understanding their microbiology is important to predict their influence to climate change. We aim to elucidate the identity and ecophysiology of sulfate reducing microorganisms (SRM) driving a highly active but hidden sulfur cycle in wetlands. This sulfur cycling is not apparent from the low standing pools of sulfate and thus has been severely understudied. Since sulfate reduction effectively competes with methanogenic degradation of organic matter, SRM have an important control function on methane production in wetlands. Little is known about wetland SRM. This stands in contrast to the high diversity of evolutionary deep-branching dsrAB genes, which are functional markers for SRM, indicating a large number of yet undiscovered SRM in wetlands. We aim to identify microorganisms driving the hidden sulfur cycle and to understand their ecology and physiology. To achieve these goals, we apply state-of-the-art molecular methods like stable isotope probing, metaproteogenomics, and high-throughput amplicon sequencing but also tradiotional approaches like cultivation.

Nitrification in a changing lake environment
Aerobic nitrification is an essential step in the nitrogen (N) cycle that catalyzes the conversion of ammonia to nitrate via the intermediate nitrite. Nitrification is well studied in marine and soil environments but knowledge on this process in lakes and streams is scarce. Lake Constance represents an excellent study site to investigate freshwater nitrification. Most of the dissolved inorganic nitrogen in this lake is present as nitrate as the end product of nitrification, indicating active nitrifying microorganisms. This is important since the total ammonium concentration in water should not exceed 0.5 mg/L to be suitable for drinking water (Deutsche Trinkwasserverordnung 2001). Due to climate change, the average annual temperature of Lake Constance is steadily increasing bei 0.03°C per year accompanied by an increasing frequency of a weak annual mixture of the water column during winter, which leads to a decreasing oxygen supply of the deepest water layers. We aim to study how this influences the composition of the nitrifying community and its performance in this important drinking water reservoir.

Methane oxidation in lake sediments
Methane is an important greenhouse gas with its global warming potential being 25 times higher that that of carbon dioxide. Its concentration in the atmosphere has risen from 400-700 ppb in pre-industrial times to 1770 ppb in 2005. As in most oxygenated lakes, methane is formed in anoxic sediment layers in Lake Constance. Close to the sediment surface, where methane and oxygen countergradients meet, methane oxidizing bacteria (MOB) act as biological filter and utilize the upwards diffusing methane. In our work, we investigate the distribution of methane and oxygen in the sediment at high resolution using microsensors. In addition, we use molecular biology tools to get insights into the MOB community in situ. Besides arobic methane oxidation, we also started to explore anaerobic methane oxidation in this prealpine lake. Recently, methane seeps have been observed in the lake floor of Lake Constance that can be one meter deep and several meters wide, providing another interesting habitat for MOB that we investigate. A recently often neglected part of microbial ecology is to isolate pure cultures of novel strains to study their physiology in detail and to verify findings from in situ studies. We are continuously isolating novel methane oxidizers by using new or adapting well-known isolation techniques.