Genome evolution in bacteria isolated from million-year-old subseafloor sediments

Deep below the seafloor, microbial life subsists in isolation from the surface world under perpetual energy limitation. The extent to which subsurface microbes evolve and adapt to their subseafloor habitat is unclear, given their ultra-slow metabolic rates.

Here we show that genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve by point mutation, with a relatively low rate of homologous recombination and a high frequency of pseudogenes. Ratios of synonymous to non-synonymous mutation rates correlate with the accumulation of pseudogenes, consistent with a dominant role for genetic drift in the subseafloor genomes, but not in type strains of Thalassospira isolated from surface world habitats.

The genome evolution of these anciently buried bacteria has apparently proceeded in a genetic drift-like manner, whereby under long-term isolation with reduced access to novel genetic material from neighbors, new mutations became fixed into the populations leading to the emergence of new genotypes.