Clone Wars in Niche Space: Exploring the evolutionary and genetic basis for bacterial species

Abstract

Bacterial phylogenies often contain distinct clusters or “clades”, associated with different ecological niches despite frequent horizontal gene transfer (HGT) between clades. An excellent example is the Bacillus cereus (Bc) group, whose members share common adaptations but are often found in different clades, raising questions over each clade’s specific ecology and pathogenic potential. Identifying consistent genetic and phenotypic differences between clades within the Bc group will determine whether clades truly possess specific ecologies and reduce confusion regarding the pathogenic potential of the different clades. The ecology of each Bc clade was explored through identification and comparison of genes under selection within the core and accessory genomes within the three largest clades within the Bc group. Each clade had its own distinctive signature of selection, with Clade 3 showing signatures of adaptation to low temperatures, supporting the hypotheses of previous studies.Experimental evolution explored the effect of different thermal niches on the ability of a Clade 2 B. thuringiensis and Clade 3 B. mycoides strain to adapt to novel environmental conditions. After 700 generations of adaptation to a novel growth medium, fitness gains in each strain were found to be highly dependent on temperature. Single nucleotide polymorphism (SNP) variant analysis of evolved strains indicated each strain responded differently to each temperature, suggesting adaptation in these strains was constrained by thermal niche. Inactivation of a putative thermal niche defining gene, cspA, in B. thuringiensis caused the fitness of the strain to increase at low temperatures contrary to predictions, with different levels of temperature dependence in variants of the gene from mesophilic and psychrotolerant strains. However, neither inactivation of the cspA gene or complementation with the psychrotolerant variant affected the B. thuringiensis strain’s ability to adapt during a second experimental evolution experiment. The phenotypic inertia of thermal niche within members of the Bc clades suggests that thermal niche may form a basis for the maintenance of distinct clades within the Bc group. The reason for thermal niche constraint is unclear, but further study can provide insight into how clades with distinct ecologies are maintained over time.