Among the oldest life forms known, the Archaea make up one of three phylogenetic or evolutionary domains into which all life is classified. The other two are the Eukarya and the Bacteria. Archaea found thriving in extreme environments of heat and cold, acidity, pressure, and salinity are known as extremophiles ("extreme-loving" organisms). Understanding the biological mechanisms underlying their hardiness may help researchers develop new industrial, biomedical, and environmental applications.

Microbes may, for example, contain enzymes that are effective in driving chemical reactions in extreme environments. Some may provide enzymes useful in research; one such "extremozyme" derived from a bacterium living in hot springs in Yellowstone National Park has become critical to current protocols for sequencing any genome, including that of humans. Other microbes have metabolic processes with potential for breaking down toxic waste or even producing methane, an energy source.

Comparisons of the genomes of organisms from all three domains are helping scientists better understand the evolution of all living things. Descriptions of MGP-supported research on some other microbes follow.

• Methanococcus jannaschii was among the first archaea chosen for sequencing. In 1996 its completed sequencing and analysis confirmed that the "tree of life" has three domains, a hypothesis first advanced nearly 20 years ago by Carl Woese (University of Illinois) but not given much credence at the time. The single-celled M. jannaschii was isolated from a sample collected beneath more than 8000 feet of water at the base of a deep-sea thermal vent on the floor of the Pacific Ocean. The microbe lives without the sunlight, oxygen, and organic carbon important to most other forms of life and uses carbon dioxide, nitrogen, and hydrogen expelled from the thermal vent for its life functions. When the entire DNA sequence of M. jannaschii was determined, scientists found that about 65% of its potential gene sequences were not related to any gene previously discovered, representing an exciting area for future investigation.
• The archaeon Archaeoglobus fulgidus and the bacterium Thermotoga maritima have potential for practical applications in industry and government-funded environmental remediation. Because they thrive in water temperatures above the boiling point, these organisms may provide DOE, the Department of Defense, and private companies with heat-stable enzymes for use in industrial processes. These processes could include conversion of wastes to useful chemicals. A. fulgidus has the added capability of surviving at the high pressures associated with deep oil wells, and T. maritima metabolizes simple and complex carbohydrates, including glucose, sucrose, starch, xylan, and cellulose. Cellulose and xylan are the most abundant biopolymers on Earth and, through their conversion to fuels such as ethanol, have major potential as sources of renewable energy. Comparisons of the genomic sequences of these two microbes will contribute to a greater understanding of evolutionary relationships as well as high-temperature protein function.
• The archaeon Pyrobaculum aerophilum, first isolated from a boiling marine vent, thrives at temperatures close to the maximum tolerated by living systems (113^oC). Unlike most hyperthermophiles, P. aerophilum is able to withstand exposure to oxygen and can thus be manipulated more easily in the laboratory. Also, the proteins encoded by hyperthermophilic genomes are more stable than those of organisms living in more temperate environments.
• The bacterium Shewanella putrefaciens, which can grow with or without oxygen, is an excellent model system for manipulating organisms for remediation. Whole-genome sequencing will elucidate metabolic pathways including those involved in corrosion, consumption of toxic organic pollutants, and removal of toxic metals and radiation waste by conversion to insoluble forms.

Other organisms that could be of great genetic and biochemical interest are present in extreme surface environments but are almost impossible to grow in the laboratory. The MGP funds a project to identify and determine the abundance and activity of novel hard-to-cultivate organisms in two extreme surface environments in the arid southwestern United States. Preliminary samples indicate that most of these bacterial species contain few similarities to the previously described cultivated bacteria. These collections offer a rich resource for identifying and isolating novel species with potentially unique sets of genes as well as proteins with environmental, energy, biotechnological, and other applications.