NASA Astrobiology Institute (NAI)

1. Environmental genomics reveals a single species ecosystem deep within the Earth.

   Project Investigators: Dylan Chivian, Thomas Gihring, Terry Hazen, Tullis Onstott, Susan Pfiffner, Lisa Pratt, Gordon Southam

   Summary

   The first metagenome sequence from a deep subsurface environment of South Africa has not only described the genetic composition of a new genera/species of sulfate reducing bacteria, Desulforudis Audaxviator, but has also revealed that it is by far the most dominant and most likely the sole resident of its environment. A single species ecosystem has never been reported before and runs counter to the prevalent concept that microorganisms live and evolve as communities of mixed species. Whether this bacterial species occurs in other deep subsurface environments around the world or whether other deep subsurface environments are also occupied by single species remains to be determined.

   Astrobiology Roadmap Objectives:

   • Objective 2.1: Mars exploration
   • Objective 5.1: Environment-dependent, molecular evolution in microorganisms
   • Objective 5.2: Co-evolution of microbial communities
   • Objective 5.3: Biochemical adaptation to extreme environments
   • Objective 6.2: Adaptation and evolution of life beyond Earth

   Project Progress

   Environmental genomics reveals a single species ecosystem deep within the Earth.

   A manuscript describing the metagenome of Desulforudis Audaxviator was sent to Science where it was accepted for review. In response to a request by one reviewer, CARD-FISH and SEM analyses were performed on some stored water samples from the same suite of samples that was the source of the metagenomic DNA in order to verify that the cells were actually cells and not spores and that the cells were Desulforudis Audaxviator. New data was incorporated into the manuscript. After a second review, the manuscript was returned with additional reviewer questions regarding the FISH technique and interpretation of the trace species with respect to the “rare biosphere” hypothesis. These second-round questions have been addressed and the manuscript has been sent back to the editor for what we hope is the final step toward acceptance for publication.

   Several additional manuscripts on deep-subsurface microorganisms from gold mines in South Africa are accepted for publication or are in review. These papers describe microbially-mediated sulfur and methane cycling in a dolomite aquifer, an anaerobic biofilm from a deep borehole, and microorganisms associated with a deep mafic sill. All of these papers derive from field campaigns in previous years.

   Mission Involvement

   MSR

   Onstott and Pratt are active participants in NASA science committees and open meetings currently addressing the goals and strategies for a future Mars Sample Return Mission. Their experience working in the deep-subsurface provides critical perspective on the challenges of sampling the deep-subsurface on Mars.

Publications

Chivan, D.  (2008).  Environmental genomics reveals a single species ecosystem deep within the Earth.  Science (in review).

Chivian, D.  (2008).  Environmental genomics reveals a single species ecosystem deep within the Earth.  AbSciCon.  Santa Clara CA.

DeFlaun, M.F.  (2007).  Isolation and characterization of a Geobacillus thermoleovorans species from an ultra-deep South African gold mine.  Systematic and Applied Microbiology, 30:152-162.

Gihring, T.M.  (2008).  Genetic and Geochemical Evidence for Microbially-Mediated Sulfur and Methane Cycling in a Dolomite Aquifer 0.9 km Below the Surface.  Environmental Microbiology (in review).

Mac Lean, L.C.W.  (2008).  High-resolution structural and chemical studies of framboidal pyrite formed within a bacterial biofilm.  Geobiology (in press).

MacLean, L.C.W.  (2007).  Mineralogical, Chemical and Biological Characterization of an Anaerobic Biofilm Collected from a Borehole in a Deep Gold Mine in South Africa.  Geomicrobiology Journal, 24:491-504.

Mislowack, B.J.  (2008).  In situ cultivation of subsurface microorganisms in a deep mafic sill: implications for SLiMEs.  Environmental Microbiology (in review).

Wanger, G.  (2008).  Stars of the terrestrial deep subsurface: A novel ‘star-shaped’ bacterial morphotype from a South African platinum mine.  Geobiology, 6:325-330.