"Chlamydiae are a unique group of obligate intracellular bacteria that comprises symbionts of protozoa as well as important pathogens of humans and a wide range of animals. The intracellular life style and the obligate association with a eukaryotic host was established early in chlamydial evolution and possibly also contributed to the origin of the primary phototrophic eukaryote. While much has been learned during the past decade with respect to chlamydial diversity, their evolutionary history, pathogenesis and mechanisms for host cell interaction, very little is known about genome dynamics, genome evolution, and adaptation in this important group of microorganisms. This project aims to fill this gap by three complementary work packages using experimental evolution approaches and state-of-the-art genome sequencing techniques.Chlamydiae that naturally infect free-living amoebae, namely Protochlamydia amoebophila and Simkania negevensis, will be established as model systems for studying genome evolution of obligate intracellular bacteria (living in protozoa). Due to their larger, less reduced genomes compared to chlamydial pathogens, amoeba-associated Chlamydiae are ideally suited for these investigations. Experimental evolution approaches – among the prokaryotes so far almost exclusively used for studying free-living bacteria – will be applied to understand the genomic and molecular basis of the intracellular life style of Chlamydiae with respect to host adaptation, host interaction, and the character of the symbioses (mutualism versus parasitism). In addition, the role of amoebae for horizontal gene transfer among intracellular bacteria will be investigated experimentally. Taken together, this project will break new ground with respect to evolution experiments with intracellular bacteria, and it will provide unprecedented insights into the evolution and adaptive processes of intracellular bacteria in general, and the Chlamydiae in particular."