Lost and Found at Sea: a Phylomentagenomic Exploration of Mitochondrial Affiliations with Oceanic Bacteria.
(English)Manuscript (Other academic)
According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from a free-living bacterium related to present-day alpha-proteobacteria. Recent studies have identified two lineages as the closest mitochondrial relatives among bacteria with sequenced genomes; the Rickettsiales, a lineage comprising obligate intracellular pathogens, and Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the upper surface waters of the global oceans.
Here, we present a phylogenetic study incorporating metagenomic data of mitochondrial genes for aerobic respiration that includes sequence data from the Global Ocean Sampling (GOS) Expedition, thereby increasing the sampling of alpha-proteobacterial sequences available for analysis greatly. Phylogenetic analysis of these expanded datasets including oceanic sequences that had been pruned down in numbers but still maintained the full genetic diversity present failed to show an increased support for a specific mitochondrial affiliation to any alpha-proteobacterial group, although concatenated datasets of different genes gave good support for conflicting mitochondrial placement. We utilized a jack-knifing method to randomly sample sequences from the GOS dataset and examined how the inclusion of such sequences influenced the support for mitochondrial affiliation in trees inferred from proteins in aerobic respiration. No evidence of an increased support for a specific mitochondrial placement in the alpha-proteobacterial tree in the jack-knifing analysis was obtained. A systematic search for sequences affiliated with mitochondria in the GOS dataset suggests the existence of previously unidentified clades of deeply diverging alpha-proteobacteria, with an unclear affiliation.
Our findings have several important implications. First, they support an early divergence of the mitochondrial ancestor from the alpha-proteobacterial lineage, possibly pre-dating the radiation of alpha-proteobacterial species with sequenced genomes. Second, they reject the hypothesis that the system for aerobic respiration in mitochondria is affiliated with the SAR11 clade. Third, they indicate horizontal transfer of genes for respiratory chain proteins in bacteria adapted to the upper surface waters of the oceans. Fourth, they show the presence of oceanic sequences for respiratory chain proteins that diverge as deeply as mitochondria in the alpha-proteobacterial phylogeny, possibly indicating a previously unidentified alpha-proteobacterial group at a basal position of the alpha-proteobacterial tree, underscoring the importance of expanding studies on mitochondrial origins beyond those of cultivated and intracellular bacteria. Finally, our study outlines a new methodology, phylometagenomics, which provides guidance on how to incorporate metagenome data into a phylogenetic framework for inferences of early evolutionary events.
Biochemistry and Molecular Biology
Research subject Molecular Biology
IdentifiersURN: urn:nbn:se:uu:diva-100841OAI: oai:DiVA.org:uu-100841DiVA: diva2:211101