Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

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.

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

“…In addition, besides Desulfohalobium and Desulfotomaculum, sequences affiliated to a Candidatus Desulforudis audaxviator were frequently detected in fluids produced from the cold well. Sequences of Candidatus Desulforudis audaxviator were also found in 60°C tempered fracture water collected from a South African gold mine at a depth of 2.8 km (Chivian et al 2008). Recently, a study by Alawi et al (2011) identified sequences similar to Candidatus Desulforudis audaxviator in 61°C tempered fluid samples taken after heat extraction in the topside facility of a geothermal plant in the Molasse Basin (Germany).…”

“…were detected in fluids cooled at the heat exchanger from 75°C to 46°C. Physiological characteristics of detected SRB and Halanaerobiaceae correspond to the subsurface environment with respect to optimum temperature, salt concentration, and pH, and are commonly found in similar anaerobic saline environments such as sediments from salt lakes (Cayol et al 1994;Jakobsen et al 2006), geothermal groundwater (Daumas et al 1988), fracture water (Chivian et al 2008), as well as in oil fields and petroleum hydrocarbon contaminated sites (Magot et al 2000;Cayol et al 2002;Denger et al 2002;Bonch-Osmolovskaya et al 2003). Halophilic Desulfohalobium utahense are known moderate halophilic and mesophilic sulfate and thiosulfate reducers that use a broad range of electron donors including various short-chain fatty acids and primary (C 1-5 ) alcohols, amino acids, H 2 /acetate and H 2 /yeast extract (Jakobsen et al 2006).…”

“…Recently, a study by Alawi et al (2011) identified sequences similar to Candidatus Desulforudis audaxviator in 61°C tempered fluid samples taken after heat extraction in the topside facility of a geothermal plant in the Molasse Basin (Germany). Candidatus Desulforudis audaxviator is a rarely detected microorganism so far, whereas it has the ability to subsist as a single species ecosystem that is based on hydrogen originating from radiochemical reactions in deep crustal rocks and sulfate reduction as the dominant electronaccepting process (Lin et al 2006;Chivian et al 2008). The repeated detection of sequences affiliated to this species in a saline aquifer of the NGB (TDS 130 g l -1 ) as well as in a low mineralized Malm aquifer of the Molasse Basin (TDS < 1 g l -1 ) indicates that this organism is much more distributed in the deep subsurface than previously assumed and co-existing with other SRB.…”

[FeFe]-hydrogenase in Yellowstone National Park: evidence for dispersal limitation and phylogenetic niche conservatism

“…Recently, PCR primers for the specific amplification of the large subunit of the [FeFe]hydrogenase gene (hydA) were developed to examine the diversity of hydA as a proxy for fermentative bacteria in a H 2 -generating saline microbial-mat system (Boyd et al, 2009b) and in a H 2 -generating anaerobic bioreactor (Xing et al, 2008). The results of these studies, as well as those from a number of metagenomic investigations that include the deep subsurface (Chivian et al, 2008) and termite hindgut environments (Warnecke et al, 2007), collectively indicate a widespread distribution and diversity of [FeFe]-hydrogenase in nature. However, our understanding of the environmental constraints that control the distribution and diversity of [FeFe]hydrogenase-mediated H 2 production in natural systems is confounded by the tight coupling between H 2 production and consumption and by the abiological reactions that contribute to H 2 production and consumption in natural systems.…”

Disposal systems evaluations and tool development : Engineered Barrier System (EBS) evaluation.

“…Lovley and Chapelle (1995) give a general summary of deep subsurface microbial processes. Chivian et al (2008) provide a schematic illustration of microbial processes in a deep single-species ecosystem, including mineralogic reactions and the radioactive and radiolytic processes that contribute energy and nutrients. Pedersen (1996) provided a review of investigations of bacteria in deep crystalline bedrock and their potential importance for nuclear-waste disposal in underground repositories.…”