Chlamydial contribution to anaerobic metabolism during eukaryotic evolution

The origin of eukaryotes is a major open question in evolutionary biology. Multiple hypotheses posit that eukaryotes likely evolved from a syntrophic relationship between an archaeon and an alphaproteobacterium based on H-2 exchange. However, there are no strong indications that modern eukaryotic H-2 metabolism originated from archaea or alphaproteobacteria. Here, we present evidence for the origin of H-2 metabolism genes in eukaryotes from an ancestor of the Anoxychlamydiales-a group of anaerobic chlamydiae, newly described here, from marine sediments. Among Chlamydiae, these bacteria uniquely encode genes for H-2 metabolism and other anaerobiosis-associated pathways. Phylogenetic analyses of several components of H-2 metabolism reveal that Anoxychlamydiales homologs are the closest relatives to eukaryotic sequences. We propose that an ancestor of the Anoxychlamydiales contributed these key genes during the evolution of eukaryotes, supporting a mosaic evolutionary origin of eukaryotic metabolism

Expanding the Chlamydiae tree : Insights into genome diversity and evolution

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

Expanding the Chlamydiae tree : Insights into genome diversity and evolution

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

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies. Dharamshi et al. find abundant, diverse, and active Chlamydiae in deep anoxic marine sediments. Using metagenomics, chlamydial genomes are obtained that form several new clades. Analyses of these genomes provide new insights into the evolution and host association of the Chlamydiae phylum, indicating that some are not symbionts of eukaryotic hosts.</p