Lawrence Berkeley National Laboratory

Environmental genomics is permitting a more complete understanding of life on and in the Earth, even when the isolation of organisms from a given ecosystem has proven intractable. The study of deep subsurface organisms is of particular interest as such investigations illuminate a mode of life that exists without input from the photosphere, giving us a better understanding of the physiology of anaerobic microorganisms that may be used in bioremediation applications. DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This uncultured Gram-positive bacterium, Candidatus Desulforudis audaxviator, is prevalent at depths > 1.5 km and its near-clonal population comprises > 99.9percent of the microorganisms inhabiting the fluid phase of the MP104 fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that is capable of fixing its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator appears capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth's crust, and offers the first example of a natural ecosystem that has its biological component entirely encoded within a single genome.