RT Journal Article
SR Electronic
T1 Genome evolution in bacteria isolated from million-year-old subseafloor sediments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.19.423498
DO 10.1101/2020.12.19.423498
A1 William D. Orsi
A1 Tobias Magritsch
A1 Sergio Vargas
A1 Ömer K. Coskun
A1 Aurele Vuillemin
A1 Sebastian Höhna
A1 Gert Wörheide
A1 Steven D’Hondt
A1 B. Jesse Shapiro
A1 Paul Carini
YR 2020
UL http://biorxiv.org/content/early/2020/12/20/2020.12.19.423498.abstract
AB 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.Significance statement In microbial populations that subsist in isolation from the surface world in deep subseafloor sediment over millions of years, ultra-slow metabolic rates caused by long term energy limitation are hypothesized to restrict the spread of newly evolved traits. It remains unknown whether genomic evolution occurs under these extreme conditions. Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and widespread evidence of relaxed purifying selection. Our findings show that the genome evolution of these anciently buried bacteria has proceeded in a manner dominated by genetic drift, whereby in small population sizes, and in the absence of homologous recombination, mutations became fixed into the population which has led to the emergence of new genotypes.Competing Interest StatementThe authors have declared no competing interest.