D. audaxviator

[kmar]

Journey Toward The Center Of The Earth: One-of-a-kind Microorganism Lives All Alone

ScienceDaily (Oct. 10, 200 — The first ecosystem ever found having only a single biological species has been discovered 2.8 kilometers (1.74 miles) beneath the surface of the earth in the Mponeng gold mine near Johannesburg, South Africa. There the rod-shaped bacterium Desulforudis audaxviator exists in complete isolation, total darkness, a lack of oxygen, and 60-degree-Celsius heat (140 degrees Fahrenheit).




The rod-shaped D. audaxviator was recovered from thousands of liters of water collected deep in the Mponeng Mine in South Africa. (Credit: Micrograph by Greg Wanger, J. Craig Venter Institute, and Gordon Southam, University of Western Ontario, used with permission)

"The great thing about environmental genomics is that it has made it possible to form a much more complete picture of microscopic life everywhere on Earth, instead of being limited to the very small proportion of bugs" – microorganisms, that is – "that can be cultured in the lab," says Dylan Chivian of Berkeley Lab's Physical Biosciences Division (PBD), lead author of the Science paper. "Almost all organisms live in communities with subdivided roles within their ecosystems. By extracting DNA from environmental samples, the various players in these microbial communities and the abilities of their dominant members can be identified, even if complete genomes of most of them are impossible to sort out."

"Part of the strength of comparative genomics comes from the fact that we now have the genomes of over a thousand bacteria and archaea and we know what many of these genes can do," says Chivian. "At a simple level, it allows us to look at a new genome and put Humpty Dumpty's metabolism back together again, based on the similarity to genes in the genomes of these more well-studied microorganisms. This is particularly powerful for understanding novel bugs from the environment that are otherwise not well characterized."



Previous work had identified sulfates as the most readily available energy source in D. audaxviator 's environment. D. audaxviator not only has the equipment to reduce sulfates, this capacity is backed up by additional genes that appear to have been borrowed from archaea by horizontal gene transfer, the incorporation of genetic material from an unrelated species. Archaea, a domain distinct from bacteria, first attracted attention as extremophiles, although many other kinds of archaea have been found since. Some 280 types of bacteria and 44 types of archaea have been found in microbial communities in the South African mines.
Other genes shared with archaea confer such traits as defense against viruses, but one system of self-protection is unique to D. audaxviator 's bacterial phylum, Firmicutes: the ability to form endospores, tough structures that shield DNA and RNA from drying out, and from heat, starvation, and chemical attack. Like many bacteria, D. audaxviator is equipped with a flagellum, a whiplike structure that allows it to swim toward sources of nourishment such as might be found in pores in the rock and other mineral surfaces.