Genome evolutionary analysis of the Candidate Phyla Radiation
: an enigmatic clade of tiny vampires?

  • Amy E Russell

Student thesis: Master's ThesisMaster of Science by Research (MScR)

Abstract

Until recently the discovery of a new microorganism was reliant on its culturability. The advent of genomic sequencing revolutionised the characterisation of microscopic organisms and, at last, created an accurate taxonomic system to define the phylogeny of early-life forms. Metagenomic studies have illuminated the diversity of microbial communities and identified numerous uncultivated clades, such as the bacterial Candidate Phyla Radiation (CPR). CPR lineages show unusual characteristics: reduced genomes (typically <1Mb), ultrasmall cell sizes, and reduced metabolic capacities for the synthesis of key biomolecules. Much of what is understood about the clade is derived from the metagenomic data, where most analyses suggest an obligate symbiosis with a host. The clade is difficult to culture, however recent landmark studies established the first host-CPR co-cultures. The characterisation of host-CPR (from clades Saccharimonadia and Gracilibacteria) interactions has identified an obligate epibiotic association that varies from parasitic to (vampiric-like) predatory. The diversity, size, and unusual genomic traits of the clade has created uncertainty regarding its placement and scale within the bacterial domain. Building on initial, high-throughput phylogenetic trees generated as part of an unpublished study (Davin et al., in prep) we conducted phylogenetic, comparative genomic, and trait mapping analyses of all bacteria, with a focus on the CPR clade. We suggest that CPR is a monophyletic clade, related through extensive gene loss that occurred in the ancestor of CPR. Across the clade, we found the loss and enrichment of specific protein functions to be suggestive of an epibiotic association defined by adherence to a host via pili. We further propose that the loss of key OM proteins in the root of the monoderm CPR, Chloroflexota and Dormibacterota clade, confers the ‘diderm-first’ hypothesis and is in support of the placement of CPR as a sister group to Chloroflexota and Dormibacterota.
Date of Award9 May 2023
Original languageEnglish
Awarding Institution
  • University of Bristol
SupervisorTom Williams (Supervisor) & Jordi Paps Montserrat (Supervisor)

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