NASA Astrobiology Institute (NAI)

1. Synergism, evolution, and functional ecogenomics of deep-subsurface microbial communities based on molecular analyses

   Project Investigators: Terry Hazen

   Other Project Members

   Eric Alm (Collaborator)

   Adam P. Arkin (Collaborator)

   Fred Brockman (Collaborator)

   Eoin Brodie (Collaborator)

   Dylan Chivian (Collaborator)

   David Culley (Collaborator)

   Thomas Gihring (Collaborator)

   Alla Lapidus (Collaborator)

   Li-Huang Lin (Collaborator)

   Duane Moser (Collaborator)

   Tullis Onstott (Co-Investigator)

   Paul Richardson (Collaborator)

   Astrobiology Roadmap Objectives:

   • 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 6.1: Environmental changes and the cycling of elements by the biota, communities, and ecosystems

   Project Progress

   NAI Teams Annual Project Report
   

   Planktonic microbes in anaerobic fracture water and biofilm microbial communities on aerobic rock surfaces were compared from the deep subsurface of the Witwatersrand Basin, South Africa. A deep-branching clade of nearly identical Firmicutes 16S rDNA sequences (>99% homology) has been identified as the dominant microorganism in fracture water from multiple gold mines of the Witwatersrand Basin, South Africa. This Firmicutes bacterium is only the dominant form in the planktonic phase of the deepest (2 -- 3 km depth), most saline fracture water.

   DNA from fissure water and rock biofilm samples collected from 3m, 6m and 9m into a vertical borehole with fracture water was amplified, fragmented and hybridized to our high density 16S microarrays containing 300,000 probes capable of detecting 8,735 prokaryotic operational taxonomic units (OTUs). Clone libraries of 16S rDNA were also generated in order to validate array results. 16S rRNA microarray analysis indicated that the fracture water where the Firmicutes type bacterium dominated the clone library was more complex than clone libraries had indicated (19 OTUs). No archaea were detected in the fracture water, however, which is consistent with the high concentrations of abiotic methane in fissure water. Biofilm samples showed far greater diversity with 195, 224 and 97 OTU's detected, respectively. Significantly, the Firmicutes type bacterium was present, but the relative proportion of this bacterium was substantially lower in all biofilm samples. However, both Crenarchaeota and methanogenic Euryarchaeota were detected in biofilms, consistent with the methanogenic isotopic signature of the methane. Other functional groups of significance to this sulfate, hydrogen, methane dominated system detected in biofilms but not in the planktonic phase, included, methanotrophs, sulfur oxidizers, and syntrophs. This is also consistent with the trace levels of oxygen in the open borehole.

   Biofilm microbial communities in open boreholes are considerably more diverse than planktonic communities present in fracture water and appear to contain many of the functional groups expected given the geochemistry of an ecosystem where highly reduced, metal, sulfide, H2 and CH4 rich water encounter oxygenated mine air. Although clone library analyses indicated that this biome was dominated by a single bacterial species forming a deep-branching clade within the Firmicutes, high density array analyses also demonstrated the presence of other relatively abundant Firmicutes (Bacillus) and less abundant Alpha-, Beta-, Gamma and Delta-proteobacteria, Cyanobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, Actinobacteria, Spirochaetes, Verrucomicrobia and Planctomycetes.

   
   Figure 1. Phylogenetic tree of closest isolated relatives and other characteristic species. Tree built from MUSCLE multiple sequence alignment with PHYLIP neighbor joining tree using F84 substitution model. Identity with respect to Desulforudis audaxviator 16S over 1305 aligned positions shown in parentheses.

   Mission Involvement

   Long-lead future mission

Publications

Brodie, E.  (2006).  Integration of the Omics, Bioinformatics, and Biogeochemistry: The New Frontier for Environmental Biotechnology.  The Fifth International Conference on Remediation of Chlorinated and Recalcitrant Compounds.  Monterey, CA.

Brodie, E.L.  (2005).  A High Density Microarray for Rapid Profiling of 16S rDNA and 16S rRNA of Prokaryotic Communities.  International Symposium Subsurface Microbiology.  Jackson Hole, WY.

Chivian, D.  (2006).  Environmental Genomic Characterization of a Deep Subsurface Microorganism.  American Society for Microbiology Annual Meeting.  Orlando, FL.

Chivian, D.  (2006).  Environmental Genomic Characterization of a Deep Subsurface Microorganism.  JGI Users Meeting.  Walnut Creek, CA.

Hazen, T.C.  (2005).  Comparison of planktonic and biofilm microbial communities in million year old fissure water from a deep subsurface gold mine..  International Symposium Subsurface Microbiology.  Jackson Hole, WY.

Hazen, T.C.  (2005).  Omics and Biogeochemistry: The New Frontier for Environmental Biotechnology (Lab to the Field and back).  Invited lecture, Department of Plant and Microbial Biology, University of California at Berkeley.  Berkeley, CA.

Hazen, T.C.  (2006).  Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology, Ecology and Evolution.  Invited lecture, Wake Forest University.  Winston-Salem, NC.

Hazen, T.C.  (2006).  Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology, Ecology and Evolution.  Orton K. Stark General Lecture, Miami University.  Miami, OH.

Hazen, T.C.  (2006).  Microbial Ecology in the deep subsurface.  NSF Deep Underground Science and Engineering Lab Workshop.  Lead, SD.

Onstott, T.C.  (2006).  Metagenomic characterization of a deep subsurface microorganism..  AbSciCon2006.  Washington, DC..