The IMPRS research groups in biochemistry study the molecular basis of fundamental biological processes to understand the chemistry of life. How do microbes move and attach? The groups of Gert Bange and Lars Oliver Essen are interested in the structure and formation of flagella and adhesion proteins. How do microbes "see"? The photochemistry of light sensitive proteins is another focus of Lars Oliver Essen's research. Microbial metabolism controls the global cycling of elements. But how do microbes catalyse chemically challenging reactions? The groups of Tobias Erb, Johann Heider and Seigo Shima aim at understanding and engineering enzymes and pathways that affect the climate, the environment, and our every day's life. This includes enzymes involved in CO2 fixation and antibiotic biosynthesis (Tobias Erb), the degradation of aromatic compounds and pollutants (Johann Heider), and the transformation of methane and hydrogen (Seigo Shima).
The IMPRS research groups in microbial ecology study the interaction of microorganisms with one other and with their environment. The group of Werner Liesack aims to understand how global warming and environmental stress affect the composition and activity of soil microbial communities. Special attention is given to methane-oxidising bacteria. The group of Andreas Brune studies the gut microbiota of termites. Central questions are the evolutionary history of the intestinal symbiosis and the functional role of individual populations in the digestion of lignocellulose and humus. Given the heterogeneity of soil and intestinal microhabitats and the small fraction of the community that can be cultivated with routine methods, both groups employ cultivation-independent metagenomic and metatranscriptomics approaches, novel cultivation techniques, and a highly resolved localisation of microorganisms and their metabolic processes.
Microorganisms grow and divide faithfully and they have a phenomenal ability to adapt to changes in their environment. The IMPRS-Mic research groups in molecular & cellular microbiology focus on understanding how microorganisms (bacteria, archaea and single-celled eukaryotes) execute these basic tasks. During growth, microorganisms coordinate cell growth with chromosome replication and segregation as well as with cell division. Several research groups specifically focus on understanding this coordination. To respond to environmental changes, microbes need to sense a particular stimulus, process this information, and then generate an appropriate output response. These responses include changes in gene expression, changes in motility behavior, changes in metabolism, changes in the cell cycle and sometimes even in cell morphology leading to cell differentiation. Several research groups study the signal transduction pathways and networks that regulate these processes. Method-wise we use molecular genetics, live cell fluorescence microscopy, in vitro analysis of purified proteins and electron microscopy.
The IMPRS-Mic research groups in microbial genomics are capitalising on novel high-throughput sequencing technologies to sequence microbial genomes and characterise transcriptomes of individual microbes as well as of microbial communities. Using bioinformatics and comparative genomics these research groups aim to gain insights into the extant enormous microbial diversity and possible evolutionary trajectories culminating in microbial speciation events. Phylogenomics is also used to describe in details the evolution of various protein families. Transcriptomics using RNAseq is also an important tool for the research groups in this area to understand the genetic programs underlying adaptation and differentiation in response to environmental change.
The IMPRS-Mic research groups in plant-microbe interactions focus on microorganisms (fungi or bacteria) that are either plant parasites or plant endophytes benefitting plant growth and plant health. For plant-fungi interactions, our interest is to elucidate how such fungi manage to grow inside a plant host and establish a biotrophic interaction in which plant cells are maintained alive. This requires intricate signaling between both partners and involves a large repertoire of secreted fungal protein effectors, which downregulate plant immunity and metabolically reprogram the host to accommodate the fungi. These fungal effectors are mostly novel and target specific plant processes in the apoplast or within the pant cell. The aim is to elucidate how such effectors function molecularly, how they are taken up by plant cells and how their regulation is fine tuned with plant infection.
The IMPRS-Mic research groups in systems and synthetic microbiology focus on quantitative analysis of cellular networks and their dynamics in microorganisms. We are particularly interested in elucidating mechanisms that enable cellular networks to detect and integrate multiple extra- and intracellular cues, to robustly function in noisy and perturbing environments, and to plastically adjust their function dependent on the environment. We further study self-organization of cellular networks into higher-order protein structures within the cells, as well as multicellular self-organization involved in formation of biofilms. Ultimately, we would like to use the established design principles of cellular networks for rational construction of novel synthetic networks, such as biosensory systems or artificial microbial communities. We use a range of advanced fluorescence microscopy techniques, including super-resolution microscopy, FRET, FCS and FLIM, microfluidics, mass-spectrometry, and flow cytometry, as well as computational modeling.