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Geomicrobiology refers to the activities of microorganisms (usually bacteria) that live beneath the surface of the Earth. The field of study is also referred to as biogeochemistry and subsurface microbiology. Habitats of the organisms include the ocean and deep within the rock that makes up Earth's crust. The study of the identities and activities of such organisms is important from a basic science standpoint and for commercial reasons.

Microorganisms are a vital part of the cycling of carbon, nitrogen, and sulfur between the surface of Earth and the surrounding atmosphere. These cycles in turn support the diversity of life that exists on the planet. As well, microorganisms break down other compounds that are present in water, soil, and the bedrock.

Many of the bacteria involved in geomicrobiological activities live in environments that are extremely harsh to other life forms. For example, bacteria such as Thermus aquaticus thrives in boiling hot springs, where the temperature approaches the boiling point of water. Such bacteria have been dubbed "extremophiles" because of their extraordinary resilience and adaptation to environmental pressures of temperature, pressure, acidity, salt concentration, or radiation. Other extremophiles live deep in the ocean under enormous atmospheric pressure. The bacteria that live around hot vents at the ocean floor, for example, use the minerals expelled by the vent in a way that supports the development of all the other life that can exist in the vicinity of the vent. Another type of bacteria lives within rock located miles under the surface of the Earth. Indeed, bacteria have been recovered from almost two miles beneath the Earth's surface, an environment that is hostile to all other forms of life. It is presumed that the ancestors of these bacteria entered the rock through nearby oil deposits or by percolating into the rock through microscopic cracks.

These and other bacteria have adapted to live in the absence of oxygen and light. They use materials from the surrounding surface as their fuel for survival and growth. These bacteria are very different from those traditional bacteria, such as Escherichia coli, that use carbon as a basis for growth.

The origin of geomicrobiology dates back to the 1920s. Then, Edson Bastin, a geologist at the University of Chicago, studied the source of hydrogen sulfide in water from oil fields that were located far underground. Bastin found that a type of bacteria subsequently named sulfate-reducing bacteria were responsible for the production of hydrogen sulfide. Critics were skeptical, arguing that the nature of the drilling for oil had introduced the microbes into the subsurface environment. Ultimately, however, the reality of Bastin's observations were confirmed.

Geomicrobiology took on additional significance in the 1970s and 1980s, as the fragility of groundwater to contamination was realized. The activity of microbes within the surface on the Earth, particularly the use of toxic substances as food by the microbes, is important for the health of groundwater. In the United States, for example, about 40% of the nation's drinking water comes from underground. The increasing use of land for human activity is degrading this resource and has spurred research geared towards understanding the microbiology of the soil and the underlying rock.

The study of geomicrobiological processes has required the development of techniques that are not in the repertoire of conventional laboratory microbiologists. Thus, geomicrobiology has brought together microbiologists, geologists, hydrologists, geochemists, and environmental engineers to study subsurface microbiology in a multi-disciplinary fashion.

Aside from fostering a collaborative approach to science, geomicrobiology has had, and continues to have practical value both commercially and socially. For example, Thermus aquaticus contains an enzyme that forms the basis of the polymerase chain reaction (PCR). The use of PCR to increase the amount of genetic material so as to permit analysis or manipulation revolutionized the field of biotechnology. Other heat-tolerant bacterial enzymes are being exploited for use in detergents, to provide cleaning power in hot water. A third example is the use of bacteria resident in the environment to clean up spills such as oil and polychlorinated biphenols in water, soil, and other environmental niches.

Since the 1970s, the participation of bacteria in the degradation of radioactive substances has been discovered. One such microbe, a bacterium of the Thermus sp., can utilize uranium, iron, chromium, and cobalt. These elements can be found in contaminated soils. Research is underway to try to harness the bacteria to detoxify soil and radioactive waste.

The field of geomicrobiology can yield information on the development of life on Earth. This is because many of the extremophilic bacteria that live in the Earth's surface or in the oceans are ancient forms of life. Such microbes have lived at and within the Earth's surface for about 85 percent of the planet's age. Organisms such as cyanobacteria were vital in shaping the planet's atmosphere. By understanding the structure and functioning of these microbes, more light is shed on the characteristics of the ancient Earth that spawned the organisms, and on the development of other life.

Geomicrobiology will continue to increase in importance as the number and diversity of microbes on the planet becomes known more clearly. As of 2002, microbes that live in environments that include the oceans and the subsurface are estimated to make up over half of all living matter on Earth. Yet, less than one percent of all the predicted microbes have been identified. Most of what is known about bacteria comes from studies that require microbial growth. Yet, it is estimated that more than 99% of all microbes cannot be grown in the lab. So, the current number of known microbes represents the limit to what is attainable using culturing techniques.

Discovering and learning about such microbes is difficult, since, even if a bacterium is capable of being grown, the growth conditions are not always easy to reproduce in the laboratory. For example, many laboratory detection methods rely on the rapid growth (i.e., hours to a few days) of the bacteria. Bacterial growth in the Earth's oceans and subsurface, however, can occur extremely slowly, as the metals required for growth (such as iron, manganese, zinc, nickel, and copper) are slowly leached from the surrounding rock by the bacteria. In the subsurface world, growth is measured in years, not days.

A promising avenue of discovery is the detection and deciphering of genetic sequences, since the growth of the microbes is not required. Indeed, in 2001, species of archaebacteria that are thought to play a major role in the cycling of nutrients in the ocean were discovered based on their genetic sequences. Such studies are very daunting, since the deciphering of the bacterial sequence information from all the other genetic information in the environment requires massive computer power. Improved methods of bioinformatics will make genetic studies more feasible.

Geomicrobiology is not only important for life on Earth, but may be important in identifying life on other planets. For example, the presence of calcium carbonate crystals in meteorites is mimicked by certain bacteria that live in the hot springs of Yellowstone National Park in the United States. Study of the bacteria could provide clues as to how microbial life might arise in hostile environments elsewhere in the solar system.



Fredrickson, J.K., and M. Fletcher. Subsurface Microbiology and Biogeochemistry. New York: Wiley, 2001.


Bekins, B.A., E.M. Godsy, and E. Warren. "Distribution of Microbial Physiologic Types in an Aquifer Contaminated by Crude Oil." Microbial Ecology 37 (1999): 263–275.

Brian Hoyle

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