Deep Rock Sediment

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Description of Niche (Why unique?)

Deep rock sediment has recently been discovered as a home to microbial life. Microbiologists have found organisms as deep as 5 km below the earth’s surface, and are continuing to probe deeper into the Earth’s crust (2). Microbial life at this depth depends on factors very different from those found on the surface of the Earth. This extreme environment contains a variety of microbes that must utilize unconventional means of sustaining life. Light does not reach theses depths eliminating photosynthesis thereby forcing the microbes to find alternative energy sources (6). Furthermore, microbes at this depth must be able to live in an environment of increased pH, pressure, and temperature.

Where located?

Scientists have investigated deep sediments that have some sort of underground water supply, because water is essential to life on Earth. Research has been conducted in various mines across Africa, Canada, and the United States, as well as rock formations that contain aquifers embedded within the faults. Research sites include the Witwatersrand Basin, Canadian Artic, Area 2 (of the Field Research Center) and various granite formations.

Enviroment and microbial life?

The deep sediment of the gold mines in South Africa, is home to various microbes. Studies have documented various microbes living in these mines that have found different ways of utilizing their environment, such as the Firmicutes family.

Niche: South African gold mines (Desulfoto maculum, Methanobacterium)

Two groups of microbes have recently been discovered in a 4-5 km fault running beneath these gold mines (2). The environment at these depths is extremely different than surface environments. The temperature ranges from 54C to 60C, the average pH is 9.1, the pressure is augmented, and there is no O2 present (anaerobic/thermophilic/psycrophilic conditions) (2). Water is present, flowing from its meteoric origin through various quartzite fractures to depths of up to 5 km. The increased pH, H2, and CH4, as well as limited inorganic carbon and SO42- flux found in this setting suggests the existence of two specific types of microbes that work in a symbiotic relationship.

Desulfoto maculum and Methanobacterium were the two main microbial groups found in the deep sediment of South Africa (2). D8A-1, a gram+ bacteria from the family Peptococcaceae, was discovered and classified within the Desulfotomaculum species because of overwhelming similiarities. D. maculum contains a sulfite reductase gene, dsrAB, for the reduction of SO42- as an energy source (2). D. maculum works with other surrounding Methanobacterium (samples including D8A-3, D8A-4, D8A-5) to attain energy (2). The Methanobacterium were classified into the Methanobacteriaceae, Comamonadaceae, and Firmicutes family respectively, and are all characterized by their ability to complete methanogenis. Methanogenis, the production of methane through metabolism, is a function of the methyl-coenzyme reductase gene, mcrA, and gives them the ability to aid D. maculum (2). These microbes attain energy by coupling their reactions during H2 and or formate transfer, thereby utilizing the high concentration of H2 gas for methanogenis and SO42- reduction.

(Methanobacterium subterraneum)

Niche: South African gold mines (Firmicutes)

Another study of these mines at depths up to 2.8 km found a group of organisms that utilize the products of the decomposition of water and sulfur from radioactive Uranium (1). Microbes from the division of Firmicutes, have developed the ability to use the H2 gas and SO42- produced as an energy supply (1). The reaction of these two molecules is extremely thermodynamically favorable and therefore supplies the Firmicutes bacteria with a sufficient source of energy. Furthermore, the reaction is so energetically efficient that the waste produced by these microbes still contains enough energy for other microbes to use it as an energy supply (1). Phylogenetic studies of the Firmicutes bacterial genome show that they last shared a common ancestor with their surface relatives as many as 27 million years ago(1). How they colonized these depths is not understood.

Niche: Granite rock

Microbial life has also been discovered in granitinic rock containing aquifers (4). This enviroment is similar to those already discussed, thermophilic and pyscrophilic. Bacteria found in these environments include members of the genera Bacillus, Desulfovibrio, Desulfomicrobium, Eubacterium, Methanomicrobium, Pseudomonas, Serratia and Shewalla (4). In addition, certain chemolithotrophic bacteria can be seen given a suitable environment: groundwater high in ferrous iron, and an open area where oxygen can react with reduced sulfur molecules. The bacteria within the sediment perform a variety of metabolic pathways such as the conversion of solid-state ferric iron oxy-hydroxides to ferrous iron (a liquid-state) with organic carbon donating the electrons (4). Deep granite studies have also documented sulfate-reducing bacteria converting sulfate to sulfide given moderate levels of salinity (5).

(Aquifer formation)

Niche:Subterranean ancient groundwater

Deep ancient groundwater far below the Earth’s crust is home to another subterranean microbial community. These reserves contain water as old as 120 million years and flow through a saline fracture from a meteoric source (3). Studies of the isotopic composition of hydrogen suggest that the water source may be as deep as 5 km. Sulfur fractionation studies of Desulfotomaculum nigrificans indicate that sulfur is being reduced as well as being used in the terminal electron accepting process (3). Surprisingly, the limits on microbial life are not from a lack of energy-laden compounds, (methane, ethane, propane, butane etc.) but rather from insufficient inorganic nutrients such as phosphate or iron (3).

Current Research

Dr. Pratt, of Indiana University, is currently studying microbial life on a subterranean level. She currently conducts her research at the mines of Witwatersrand in South Africa, as well as the Canadian Artic. The general goal of her research is to explore the microbial world beneath the earth’s crust. To do so she examines the metabolic pathways the employ in order to sustain life. In addition, her work provides implications to the possibility of life on Mars, another severely water limited environment.

Dr. Onstott of Princeton University is conducting a similar experiment. Dr Onstott is more concerned with the mechanisms behind the evolution of subterranean microbes, and how these microbes adapted to their given environment. Furthermore, he is studying the different limitaitions on deep sediment microbial density and diversity. He is also studying in the Canadian Artic and the gold mines of South Africa.

Dr. Hazen also studies sediment-based microbes, but focuses on the role of Uranium and the effects it has on the microbial environment. Uranium can oxidized by Fe or Mn, two inorganic nutrients that certain microbes require. Because these three elements and microbial life are often found in the same environment there is a functional relationship among them. Dr. Hazen is exploring how microbes react to changing levels of oxidation in Uranium. He conducts his research at areas that have previously been contaminated with Uranium, such as Area 2 of the Field Research Center.

The process of studying subterranean microbes is extremely difficult and presents a major challenge for current researchers. The initial problem arises from the extraction of core samples. In order to achieve conclusive results the researchers must go to extreme lengths to ensure the sample is uncontaminated. A pure sample must be free from outside water, air, and other factors. Furthermore, the samples are obtained from depths up to 5 km deep, a procedure that requires extremely expensive machinery and immense time. Finally, once a sample is isolated, the proper conditions (pH, temperature, pressure etc.) must be met or the organism will not survive.

 (Drilling Tunnel)


The mere evidence that life can exist in such extreme environments is astonishing. In view of the harsh conditions (pH, temperature, pressure etc.) and limited nutrient supply the documentation of the existence of subterranean microbial survival is astounding. Shockingly, results from deep sediment studies imply that the microbes are endemic to their environment (no cell division was observed along the faults into the sediment) (6). These seemingly unlivable conditions, some of which are similar to the conditions on Mars, point to the possibility that there could also be endemic microbial life on Mars (1).


1) Indiana University. "Bacteria Use Radioactive Uranium To Convert Water Molecules To Useable Energy." ScienceDaily 19 October 2006. 29 August 2008 <>

2) Moser, D.P., Gihring, T.M., Brockman, F.J., Frederickson. J.K., Balkwell, D.L., Dolhopf., M.E., Sherwood Lollar, B., Pratt, L.M., Boice, E., Southam, G., Wanger, G., Baker, B.J., Pfiffner, S.M., Lin, L., and Onstott, T.C., 2005, Desiulfotomaculum and Methanobacterium spp. Dominate a 4- to 5-kilometer deep fault, Applied and Environmental Microbiology, v.71, p. 8773-8783.

3) Kieft, Thomas L., McCuddy, Sean M., Onstott, T. C., Davidson, Mark, Lin, Li-Hung, Mislowack, Bianca, Pratt, Lisa, Boice, Erik, Lollar, Barbara Sherwood, Lippmann-Pipke, Johanna, Pfiffner, Susan M., Phelps, Tommy J., Gihring, Thomas, Moser, Duane and van Heerden, Arnand(2005)'Geochemically Generated, Energy-Rich Substrates and Indigenous Microorganisms in Deep, Ancient Groundwater',Geomicrobiology Journal,22:6,325 — 335

4) Pedersena, Karsten. "Microbial life in deep granitic rock." FEMS Microbiology Reviews 3-4(1997): 399-414.

5) Pedersena, Karsten. "Exploration of deep intraterrestrial microbial life: current perspectives." FEMS Microbiology Letters 185(200): 9-16.

6) Lihung, L.-H., Wang, P-L, Rumble, D., Lippmann-Pipke, J., Boice, E., Pratt, L. M., Sherwood Lollar, B., Brodie, Eoin, Hazen, T., Andersen, G., DeSantis, T., Moser, D. P., Kershaw, D. and Onstott, T. C. (2006) Long term biosustainability in a high energy, low diversity crustal biotome. Science 314:479-482.

Edited by Joseph Raleigh, student of Rachel Larsen