​Research at the department centers around microbes and their impact on biological systems across broad scales, from single cells to ecosystems.

Division of Computational Systems Biology

The mission of CUBE is to advance our understanding of biological systems, ranging from single species to multi-species systems and ecosystems, based on data from large-scale bioanalytical methods. We develop, improve and apply computational methods for the interpretation of molecular information in biology, and establishes and analyses quantitative mathematical models. CUBE is highly engaged in basic research, in the translation of basic knowledge to medical and biological applications, and in the training of students on all educational levels. We support an innovative and open-minded, creative and collaborative atmosphere inside and outside our team, facilitate the exchange with the society and contribute to a vital and responsible research community in computational biology.
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Division of Microbial Ecology

Microbes are the hidden powers on planet earth. They are by far the most abundant life form, drive biogeochemical cycles and are essential partners in biological interactions with other organisms. Yet our knowledge of microbial diversity and function is only limited. The division’s research spans frome cophysiology, genomics, and evolution of key microorganisms in selected ecosystems to interactions of microbes among each other and with eukaryotes. This is achieved by cultivation-independent state-of-the-art molecular tools including for example single cell isotope probing and sorting as well meta-omics techniques.
We seek to analyze the biodiversity, to reveal the evolutionary history, and to understand the ecological function of microbes catalyzing the global carbon, sulfur, and nitrogen cycles. These organisms are not only indispensable in nature, they are also of great importance for biotechnological applications.
We study the evolution of intracellular symbiotic associations and their mechanisms of interaction by focussing on amoebae and their bacterial endosymbionts. As model system we investigate the chlamydiae, which are among the most successful bacterial pathogens of humans and thrive as symbionts in diverse hosts such as protozoa, insects, and crustaceans.
We investigate the complex symbiotic microbiota of humans and animals. We want to understand how host diet shapes physiological interactions among the many intestinal microorganisms and how individual microorganisms impact health of their host.
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Division of Terrestrial Ecosystem Research

Soil microorganisms and plants are key players in the production and breakdown of organic matter, and together control global biogeochemical cycles of carbon, nitrogen and phosphorus. TER, the Division of Terrestrial Ecosystem Research, aims to advance our fundamental understanding of how plants and soil microorganisms respond to, and in turn shape, their abiotic and biotic environment, and to determine the consequences for the functioning of Earth’s ecosystems.
Primarily dedicated to basic research, TER addresses pressing environmental issues, such as the impact of climate and land-use change on ecosystem functioning and the role of soils in the global carbon cycle and in food security. In doing so, we work on scales from µm (i.e. the scale at which microbes operate) to the biosphere (i.e. where plant and microbial processes become evident), and in ecosystems spanning the Arctic tundra to tropical rainforests. We integrate this scale of thinking with state-of-the-art methods, including stable isotope tracing and biomarker fingerprinting, and are developing novel approaches to estimate gross environmental processes with isotope pool dilution techniques.
We are strongly committed to conduct world-leading research in a motivating and intellectually stimulating environment, and to train our students to become independent and internationally competitive scientists who enjoy research and contribute to society as conscientious citizens.
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Research foci

Members of the department are affiliated with several reserach foci at the Faculty of Life Sciences
• Research Focus Climate Change Biology
• Research Focus Computational Life Sciences
• Research Focus Ecology and Biodiversity of Tropical Forests
• Research Focus Microbial Ecology and Ecosystems

Specific research topics

  • Comparative genomics

    Life on earth has evolved for some billion years. Living organisms are found in virtually every environment, surviving and thriving in extremes of heat, cold, radiation, pressure, salt, acidity, and darkness. Often in these environments, only “simple” microorganisms are found [...]

  • Studying microbiomes by high-definition metagenomics

    Although microbial communities (“microbiomes”) are central to life on earth, they largely remained terra incognita until recently. By developing a quickly growing collection of tools in microbial systems biology we have just started learning about the compositions, interactions and functions [...]

  • Microbial symbionts and pathogens

    Annoying for most of us, but dangerous or even life threatening for particular persons: infections by pathogenic bacteria are never welcome. However, pathogenic lifestyle in nature is no bad habit – it has developed in evolution. Just the balance of [...]

  • Structuring the Protein Sequence Space

    Many biological and evolutionary questions are related to the structure of the protein sequence space and its partitioning into substructures represented by the all-against-all similarity relations. We are developing database resources providing pre-calculated sequence similarities and features for all known [...]