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Abstract

Many eukaryotes harbor intracellular bacterial symbionts that are believed to confer beneficial traits to their hosts. Several bacterial lineages in the class of Endomicrobia are frequently encountered as intracellular symbionts of termite gut flagellates. They represent a deep-branching lineage in the phylum of Elusimicrobia that comprise both endosymbiotic and putatively free-living lineages. Since the acquisition of the endosymbionts probably occurred around 40–70 million years ago, the genomes of the endosymbionts are still in an early stage of genome reduction. Therefore, genomic information on free-living members of this class would provide a perfect model to investigate the mechanisms of genome evolution that have contributed to the evolution of such a young endosymbiosis. In my dissertation, I first describe the endosymbiotic population of Endomicrobia in single flagellate hosts with highly resolved analyses. These endosymbionts are strictly vertically transmitted by their respective hosts indicating a frequent population bottleneck during transmission for Endomicrobia. Moreover, I report the isolatation of Endomicrobium proavitum, the first cultured representative of the class Endomicrobia and a close relative of “Candidatus Endomicrobium trichonymphae”, the intracellular symbionts that colonize the flagellates of the same termite species. This free-living, obligately anaerobic ultramicrobacterium has an unusual cell cycle and fixes nitrogen employing a set of nif genes (Group IV) that so far had been considered not to encode a functional nitrogenase. Its circular genome (1.59 Mbp) is substantially larger than that of “Ca. E. trichonymphae” strain Rs-D17, and many of the pathways that are disrupted by pseudogenes in the endosymbiont are intact in E. proavitum. However, during the process of symbiosis, the endosymbionts also appear to have acquired novel pathways to alter their fermentation strategy, which have apparently helped the establishment of the associations. The comparative analyses not only revealed that the genome of strain Rs-D17 shows a typical purifying selection throughout the genome independent on the gene functions but also provided evidence for massive genome rearrangements in the endosymbionts. Surprisingly, the rearrangement sites are typically flanked by restriction-modification genes that are abnormally dense in the genome of strain Rs-D17 but entirely absent from its free-living relative. This is the first case where RM systems acting as mobile genetic elements are responsible for shaping a bacterial genome in the early stages of endosymbiosis.