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Science 10 October 2008:
Vol. 322. no. 5899, pp. 275 - 278
DOI: 10.1126/science.1155495
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Reports

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

Dylan Chivian,1,2* Eoin L. Brodie,2,3 Eric J. Alm,2,4 David E. Culley,5 Paramvir S. Dehal,1,2 Todd Z. DeSantis,2,3 Thomas M. Gihring,6 Alla Lapidus,7 Li-Hung Lin,8 Stephen R. Lowry,7 Duane P. Moser,9 Paul M. Richardson,7 Gordon Southam,10 Greg Wanger,10 Lisa M. Pratt,11,12 Gary L. Andersen,2,3 Terry C. Hazen,2,3,12 Fred J. Brockman,13 Adam P. Arkin,1,2,14 Tullis C. Onstott12,15

DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth's crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

1 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
2 Virtual Institute for Microbial Stress and Survival, Berkeley, CA 94720, USA.
3 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4 Departments of Biological and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
5 Energy and Efficiency Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
6 Department of Oceanography, Florida State University, Tallahassee, FL 32306, USA.
7 Genomic Technology Program, U.S. Department of Energy (DOE) Joint Genomics Institute, Berkeley, CA 94598, USA.
8 Department of Geosciences, National Taiwan University, Taipei 106, Taiwan.
9 Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV 89119, USA.
10 Department of Earth Sciences, University of Western Ontario, London, ON N6A 5B7, Canada
11 Department of Geological Sciences, Indiana University, Bloomington, IN 47405, USA.
12 Indiana Princeton Tennessee Astrobiology Initiative (IPTAI), NASA Astrobiology Institute, Bloomington, IN 47405, USA.
13 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
14 Department of Bioengineering, University of California, Berkeley, CA 94720, USA.
15 Department of Geosciences, Princeton University, Princeton, NJ 08544, USA.

* To whom correspondence should be addressed. E-mail: DCChivian{at}lbl.gov

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Science. ISSN 0036-8075 (print), 1095-9203 (online)