Expanding the Chlamydiae tree : Insights into genome diversity and evolution

Abstract: Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles.Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions. Anaerobic metabolism is found across modern eukaryotes, and syntrophic hydrogen exchange is central in many hypotheses for eukaryotic evolution, but its origin is unknown. Chlamydial and eukaryotic homologs were the closest relatives in several of these gene phylogenies, providing evidence for a chlamydial contribution of these genes during eukaryotic evolution.Gene-tree aware ancestral-state-reconstruction revealed a fermentative, mobile, facultatively anaerobic Chlamydiae ancestor, which was capable of endosymbiosis. Examination of Chlamydiae gene content evolution indicated complex dynamics, with a central role of horizontal gene transfer in major evolutionary transitions, related to energy metabolism and aerobiosis. Furthermore, chlamydiae have evolved through genome expansion in addition to gene loss, counter to many other obligate endosymbionts.Sponge microbiome-associated chlamydiae were found in high relative abundance in some sponge species. Genome-resolved metagenomics identified diverse, yet co-associating chlamydial lineages, with distinctive genetic repertoires, including unexpected degradative and biosynthetic potential. Biosynthetic gene clusters were found across Chlamydiae, suggestive of secondary metabolite production and host-defence roles. Surveying environmental prevalence indicated wider associations between chlamydiae and marine invertebrates.Finally, a wide-scale assessment of chlamydiae genetic contributions to eukaryotic evolution was performed. Over 100 distinct Chlamydiae-eukaryotic clades were identified in phylogenies across shared protein families. Although patterns are complex and direction of transfers often unclear, our results indicate larger avenues of chlamydial gene exchange with both plastid-bearing eukaryotes, and the last eukaryotic common ancestor.  In summary, in this thesis, cultivation-independent methods and evolutionary-driven investigations were used to expand the Chlamydiae tree, and to provide new insights into genomic diversity and evolution of the phylum.