Imagine! A future in which we can

  • use “super bugs” to detect chemical contamination in soil, air, and water and clean up oil spills and chemicals in landfills;
  • cook and heat with natural gas collected from a backyard septic tank or bottled at a local waste-treatment facility;
  • obtain affordable alcohol-based fuels and solvents from cornstalks, wood chips, and other plant by-products; and
  • produce new classes of antibiotics and process food and chemicals more efficiently.

These scenarios represent only a few of the possible ways that microbes—the invisible bacteria, archaea, protozoa, and fungi that inhabit our environment, our bodies, our food and water, and even the air we breathe—can be harnessed to serve humankind. Technological advances developed over the last decade, particularly in genetic research conducted as part of the international Human Genome Project, are enabling researchers to learn about microbes at their most fundamental level and to begin to ask questions about how the basic parts work together to form a functioning organism.

The answers may challenge accepted scientific thought and offer beneficial applications in areas important to DOE’s Biological and Environmental Research (BER) program, among them bioremediation, global climate change, biotechnology, and energy production.

Why Microbes?

By some estimates, microbes make up about 60% of the earth’s biomass, yet less than 1% of microbial species have been identified. Microbes play a critical role in natural biogeochemical cycles. Because most do not cause disease in humans, animals, or plants and are difficult to culture, they have received little attention.

Microbes have been found surviving and thriving in an amazing diversity of habitats, in extremes of heat, cold, radiation, pressure, salinity, and acidity, often where no other life forms could exist. Identifying and harnessing their unique capabilities, which have evolved over 3.8 billion years, will offer us new solutions to longstanding challenges in environmental and waste cleanup, energy production and use, medicine, industrial processes, agriculture, and other areas.

Scientists also are starting to appreciate the role played by microbes in global climate processes, and we can expect insights about both the biological underpinnings of climate change and the contributions of microbes to the earth’s biosphere. Their capabilities soon will be added to the list of traditional commercial uses for microbes in brewing, baking, dairy, and other industries.

In 1995, the MGP’s first full year, DOE-funded four microbial genome sequencing projects focused on the bacterium Mycoplasma genitalium and three other microbes. Now fully characterized, the tiny M. genitalium genome—thought to have the smallest genome of any known free-living bacterium—provides a model for a minimal set of genes necessary for life. Its genome contains only 580,000 base pairs of DNA and yet encodes 470 genes. Future studies on this and other minimal genomes will help increase our understanding of more complex genomes.

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 the 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. For a complete list see the brochure.

  • 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 before 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 (113oC). 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 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.

The Microbial Genome Program brochure lists current and completed DOE projects (Acrobat pdf file, 400kb, designed for 11″ x 17″ paper, landscape. To print on standard sizes, choose “fit to page, landscape” on the print menu). Visit Adobe for free Acrobat Reader software.

Text from Human Genome Program, U.S. Department of Energy, Microbial Genome Program Report, 2000.

See also: Microbial Genomes: An Information Base for 21st Century Microbiology by Daniel W. Drell, Anna Palmisano, and Marvin E. Frazier. iMP Magazine (November 22, 1999)