Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Science (Impact Factor: 33.61). 10/2008; 322(5899):275-8. DOI: 10.1126/science.1155495
Source: PubMed

ABSTRACT 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 Follower
65 Reads
  • Source
    • "Catalogue_of_Planetary_Analogues.pdf). These include the Antarctic Dry Valleys (Ascaso and Wierzchos 2003; Friedmann 1982; Omelon 2008; Wierzchos et al. 2005), hot springs (Glamoclija et al. 2004; Parenteau and Cady 2010; Preston et al. 2008; Preston and Genge 2010), sulfur-rich surface habitats (Engel 2007), hypersaline environments (Barbieri et al. 2006; Benison et al. 2008; Blackhurst et al. 2005; Douglas 2004; Foster et al. 2010; Mancinelli et al. 2004; Sadooni et al. 2010), Fe-rich environments (Fern andez- Remolar et al. 2008; Gillan and De Ridder 2001; Izawa et al. 2010; Preston et al. 2011a; Villar et al. 2006), impact deposits (e.g., impact-induced hydrothermal systems, Hode et al. 2008; Osinski et al. 2013), and the focus of this study subsurface environments (Boston et al. 2001; Chivian et al. 2008; Fern andez-Remolar et al. 2008; Izawa et al. 2010; McKay and Stoker 1989; Preston et al. 2011b). A particular type of subsurface environment and habitat is the focus of this study: caves. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Subsurface environments are known to support and preserve diverse microbial communities. Giant pool fingers from Hidden Cave, New Mexico consist of mm-scale dark micritic calcite layers alternating with clear dogtooth spar crystals and contain morphological and geochemical evidence of past microbial communities. We used Fourier Transform infrared spectroscopy to identify fatty acids, proteins, PO2-carrying compounds, and polysaccharides spatially related to morphological fossil filaments throughout the surface micritic laminations and central pool finger regions. These biomolecular signatures are important components that contribute to the biosignature suite under development that identify microbial involvement in carbonate precipitation on Earth and remotely.
    Geomicrobiology 11/2014; 31(10). DOI:10.1080/01490451.2014.913096 · 1.44 Impact Factor
  • Source
    • "Microbes closely related to known chemolithotrophs (based on 16S rRNA gene sequences) are found in abundance; however, the scope of this analysis is incomplete, because many sequences are from uncharacterized strains. To identify likely physiologies, sequencing data were analyzed at the family level for each site, and the families were classified as physiotypes based on the predominant metabolism of cultured representatives as identified in Bergey's Manual of Systematic Bacteriology and in recent publications of newly defined or cultured groups by Iino et al. (2010), Yamada (2006), Bollmann et al. (2014), Chivian et al. (2008). Where metabolisms were unknown (such as for the unclassified groups, Candidate Phyla, or OTUs with only coarse phylogenetic affiliation), the family was placed into the physiotype marked " ? "
    [Show abstract] [Hide abstract]
    ABSTRACT: The deep subsurface is an enormous repository of microbial life. However, the metabolic capabilities of these microorganisms and the degree to which they are dependent on surface processes are largely unknown. Due to the logistical difficulty of sampling and inherent heterogeneity, the microbial populations of the terrestrial subsurface are poorly characterized. In an effort to better understand the biogeochemistry of deep terrestrial habitats, we evaluate the energetic yield of chemolithotrophic metabolisms and microbial diversity in the Sanford Underground Research Facility (SURF) in the former Homestake Gold Mine, SD, USA. Geochemical data, energetic modeling, and DNA sequencing were combined with principle component analysis to describe this deep (down to 8100 ft below surface), terrestrial environment. SURF provides access into an iron-rich Paleoproterozoic metasedimentary deposit that contains deeply circulating groundwater. Geochemical analyses of subsurface fluids reveal enormous geochemical diversity ranging widely in salinity, oxidation state (ORP 330 to -328 mV), and concentrations of redox sensitive species (e.g., Fe2+ from near 0 to 6.2 mg/L and ΣS2- from 7 to 2778 μg/L). As a direct result of this compositional buffet, Gibbs energy calculations reveal an abundance of energy for microorganisms from the oxidation of sulfur, iron, nitrogen, methane, and manganese. Pyrotag DNA sequencing reveals diverse communities of chemolithoautotrophs, thermophiles, aerobic and anaerobic heterotrophs, and numerous uncultivated clades. Extrapolated across the mine footprint, these data suggest a complex spatial mosaic of subsurface primary productivity that is in good agreement with predicted energy yields. Notably, we report Gibbs energy normalized both per mole of reaction and per kg fluid (energy density) and find the later to be more consistent with observed physiologies and environmental conditions. Further application of this approach will significantly expand our
    Frontiers in Microbiology 11/2014; 5(610):1. DOI:10.3389/fmicb.2014.00610 · 3.99 Impact Factor
  • Source
    • "A number of techniques can be leveraged to determine microbial community structure, function, biomass concentration, and activity in the deep biosphere. DNA-based analyses are tractable in these environments, and can range from single gene biomarker studies to shotgun community genomic investigations that inform microbial community structure and functional potential (Zhang et al., 2005; Chivian et al., 2008; Wrighton et al., 2012, 2013; Dong et al., 2014). Catalyzed reported deposition fluorescent in situ hybridization (CARD-FISH) has been used in some environments to identify active cells, while demonstrating that DNA is sufficiently intact to hybridize with primers and probes (Hoehler and Jorgensen, 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.
    Frontiers in Microbiology 09/2014; 5:481. DOI:10.3389/fmicb.2014.00481 · 3.99 Impact Factor
Show more