Abstract
Since enough genomic data has been available for Armatimonadetes bacteria, phylogenetic trees have indicated non-monophyletic distribution of extremophilic bacteria. However, these trees were made with 16S rRNA data rather than isolate genomes or Metagenome-Assembled Genomes (MAGs) due to this data being limited. An updated Armatimonadetes phylogenetic tree has been constructed using seven isolate genomes and 150 MAGs from different temperature niches (psychrophilic, mesophilic and thermophilic) and confirmed the lack of monophyletic extremophile distribution. To investigate how genomes may be distributed in a non-monophyletic distribution, thermophilic traits were investigated in Armatimonadetes genomes: high GC content, small genome size, amino acid bias and presence of thermophily-promoting genes. Thermophilic Armatimonadetes genomes and MAGs did not have higher GC content than mesophiles, a codon usage bias, nor an amino acid bias, yet had smaller genomes. The proportion of sigma factors in a genome significantly increased in thermophilic Armatimonadetes genomes as did chaperone genes.
Thermophilic traits were then investigated in a phylogenetically balanced dataset of ~2,000 bacterial and archaeal genomes and MAGs as the lack of GC content difference and amino acid bias in Armatimonadetes was unexpected. Only archaeal thermophiles had an amino acid bias as described by previous literature, making the amino acid biases studied in this thesis archaeal-specific. Thermophilic bacterial genomes had a significantly higher GC content than mesophilic genomes, however, the median difference was small (41% GC content in mesophiles and 46% GC content in thermophiles).
This study concludes that Armatimonadetes genomes continue to have a non-monophyletic distribution of extreme temperature niche genomes. Thermophilic Armatimonadetes genomic traits are not consistent with previously studied thermophiles nor were thermophilic traits from a larger bacterial collection. Other thermophilic traits may have come from studies of small sample size, much like the traits investigated in this thesis, and other thermophilic genomic tendencies should also be reinvestigated with the increase genome data available.