Clone wars in niche space: exploring the evolutionary and genetic basis for bacterial species.

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Bacteria reproduce clonally and lack the homogenizing influence of eukaryotic sex. Nevertheless bacterial genetic variation is not haphazardly distributed. Bacteria commonly form coherent clades with overlapping ecological niches in the same manner as sexual species (Figure 1). Therefore, although key adaptive traits (secondary metabolites, virulence factors etc) are often associated with the accessory genome, genetic variation in essential metabolic genes produces ecologically coherent clades. This leads to questions including: what drives the formation of these distinct genetic clusters? Why does genetic variation in core or essential genes (which are not obviously related to niche) predict ecological association? In this project we will evaluate competing hypotheses (a) that genetic divergence follows neutral accumulation of alleles after selective sweeps and or (b) core genomic variation is shaped by adaptation, either because different allelic variants are favoured in different habitats or because epistatic interactions within the core and accessory genome favour particular allele or gene combinations. In other words, key adaptations to exploit new niches may determine which mutations are favoured in the core genome.Research will focus on the Bacillus cereus group, which contains bacteria with significant importance for human and animal health (B. cereus, B. anthracis) and bacteria with significant economic importance in pest management (Bacillus thuringiensis). Clades in this group are well characterized, ecologically distinct and can have characteristic thermal biology. Importantly, distinct clades have similar synteny and very similar core genomes. This project will involve bioinformatics, field ecology, phenotype characterization, the application of experimental evolution and genomics approaches, as well as CRIPSR Cas9 genome editing to investigate how distinct niches shape core and accessory genetic variation. We will directly compare the relative importance of the neutral and adaptive models. In addition to furthering the ecological and population genomic characterization of this group we will use experimental evolution to test adaptive hypotheses directly. We will take replicate isolate pairs from two of the best ecologically characterized clades: clade 2 the mesotolerant insect pathogenic clade and clade 3 the cold-adapted rhizosphere clade and evolve these isolates in conditions simulating their own niche and an atypical niche (plant root derived media or insect hosts) at cold (12 deg C) or warm (32 deg C) temperatures. Under our adaptive hypothesis, strains in novel habitats are predicted to acquire mutations in essential genes that may provide advantages in their new habitats, and that may be correspond to clade-specific alleles in the core genome of the isolates associated with the new niche.