A Genomic Perspective on Ecological Diversification in Bacillus in Death Valley National Park

<p>Bacterial species have traditionally been broadly defined to contain large amounts of ecological and genetic diversity, making it difficult to characterize the process by which one lineage splits into two (or speciation). The ability to determine the most newly divergent phylogenetic groups is necessary for discovering the ecological dimensions on which bacteria diverge and become able to coexist indefinitely. The dynamics of lineage splitting, and the ecological parameters that drive the divergence of bacterial lineages into irreversible groups, are not well characterized. Closely related bacterial genomes have been shown to differ in gene content, suggesting that almost every strain in nature may be ecologically unique. I test this hypothesis by performing whole-genome sequencing of extremely close relatives within recognized taxa, and analyzing the gene content of strains for ecological distinctness. I first reconstructed the phylogenetic relationships between 14 Death Valley isolates collected along an elevation gradient, previously classified within <em>Bacillus atrophaeus</em>, <em>B. subtilis </em>subsp. <em>inaquosorum</em>, and <em>B. subtilis </em>subsp. <em>spizizenii</em>, and hypothesized through <em>gyrA </em>phylogenetic analysis to be members of eight different ecotypes (an ecologically distinct population whose members are ecologically homogenous). I then compared the genomes of seven isolates, previously classified within <em>B. atrophaeus</em>, and hypothesized to be members of three closely related ecotypes, PE 45, PE 47, and PE 48. The members of the <em>B. atrophaeus </em>clade were found to contain unique functional genes involved in carbohydrate utilization, as well as unique genes involving resistance to heavy metals, specifically cadmium. Surprisingly, no unique gene conferred a metabolic system or subsystem function that was not already present in all <em>B. atrophaeus </em>strains sampled. Resistance and growth assays uncovered the ecological significance of gene content differences, illustrating evidence of quantitative divergence in resource utilization and resistance levels among all strains. Post-hoc analyses indicated nearly all differences to be between ecotypes, except among members of PE 48. Thus, while all ecotypes were shown to be ecologically distinct from one another, only the members of PE 45 and PE 47 were found to be ecologically homogeneous in resource utilization and resistance. Future analyses including more strains within ecotypes, as well as positive selection analyses, will continue to uncover the ecological interchangeability of these ecotypes.</p>