The Geobacillus Pan-Genome: Implications for the Evolution of the Genus

Abstract

The genus Geobacillus is comprised of a diverse group of spore-forming Gram-positive thermophilic bacterial species and is well known for both its ecological diversity and as a source of novel thermostable enzymes. Although the mechanisms underlying the thermophilicity of the organism and the thermostability of its macromolecules are reasonably well understood, relatively little is known of the evolutionary mechanisms, which underlie the structural and functional properties of members of this genus. In this study, we have compared 29 Geobacillus genomes, with a specific focus on the elements, which comprise the conserved core and flexible genomes. Based on comparisons of conserved core and flexible genomes, we present evidence of habitat delineation with specific Geobacillus genomes linked to specific niches. Our analysis revealed that Geobacillus and Anoxybacillus share a high proportion of genes. Moreover, the results strongly suggest that horizontal gene transfer is a major factor deriving the evolution of Geobacillus from Bacillus, with genetic contributions from other phylogenetically distant taxa.

Keywords: Geobacillus; conserved core; flexible genomes; horizontal gene transfer; pan-genome; soft core.

FIGURE 1

Heatmap representing the degree of similarity of the genomes based on the average amino acid identities of their protein coding genes. The heatmap was derived from an average amino acid identity matrix determined from the high similarity (dark orange) and low similarity (light yellow) of CDSs in the 4 pan-genomic clusters derived from the 29 Geobacillus genomes.

FIGURE 2

Bar plots representing the frequency of the top five genera with regards to sequence similarity of proteins of the core, softcore, shell, and cloud against proteins contained in Pre_GI. Only the highest scoring hit subject for a protein was included to avoid over-representation of certain genera.

FIGURE 3

Heatmap representing the degree of similarity among Geobacillus and Anoxybacillus based on the average nucleotide identities of their coding sequences (CDSs). The heatmap was derived from an average nucleotide identity matrix determined from the high similarity (dark orange) and low similarity (light yellow) of CDSs derived from the Geobacillus and Anoxybacillus genomes.

FIGURE 4

Graphical representation of general information regarding the genera of highest scoring hits against Pre_GI with only the highest subject included. The top five word frequencies reflecting island host lifestyle, habitat and isolation are presented in the bar plot for the core, softcore, shell, and cloud.