Diatoms are photosynthetic micro-organisms.
The New Microbe Hunters
February / March 06
Volume 4 Number 1
Microbes may be the Rodney Dangerfields of the living world—€”getting lots of attention but no respect.
Avian influenza makes headlines every day and has us worried about the possibility of an influenza pandemic.
Experts on the Oprah Winfrey Show make us cringe as they show us that our houses, our pillows, our telephones, our kitchen counters are teeming with microbial life.
We hear about the threats from antibiotic resistant microbes, resistant to our most powerful antibiotics, and the growing concern that we could get life threatening infections even in hospitals.
What we don't hear is that microbes rule the Earth. How most microbes don't cause disease. How microbes are responsible for creating our oxygen-containing atmosphere, for the fertility of our soil, for our global environment.
Scientists estimate that there are a billion times more microbes on Earth than there are stars in the universe —€” an estimated nonillion (one followed by thirty zeroes) microbes. A spoonful of soil can contain 2,000 to 3,000 different species (not different microbes but different species!) of microbes yet we have only described about 5,700 species. Amazingly, the total mass of all of these invisible creatures exceeds the mass of all plant or animal life on Earth, yet they are largely invisible to us.
Microbes and their communities make up the foundation of the biosphere and sustain all life on earth. These single-celled organisms are masters at living in almost every environment and harvesting energy in almost any form, from solar radiation to photosynthesis-generated organic chemicals to minerals in the deep subsurface. They have amassed unique biochemistries over more than 3.5 billion years in every niche on the planet. In the complex "simplicity" of microbes, we find a deep and virtually limitless resource of capabilities needed by DOE and the nation for clean and secure energy, cleanup of environmental contamination, and sequestration of atmospheric carbon dioxide that contributes to global warming.
Genomics: GTL
Understanding these diverse capabilities in exquisite detail, enough detail so that we can use the biochemical sophistication of microbes for a broad range of innovative applications, is the goal of the Department of Energy's Genomics: GTL program. The fundamental research conducted in the GTL program brings us closer to biology-based solutions for these important national energy and environmental needs.
GTL's goal is simple in concept but complicated in practice—€”to reveal how the static information in genome sequences drives the intricate and dynamic processes of life. Through predictive models of these life processes and supporting research infrastructure, we seek to harness the capabilities of microbes and complex microbial communities, which are the foundation of the biosphere and sustain all life on earth. Gaining reliable use of microbial processes requires understanding the whole living system, not just genomic DNA sequences or collections of proteins or cell by-products. GTL will study critical microbial properties and processes on three systems levels—€”molecular, cellular and community—€”each requiring advances in fundamental capabilities and concepts.
This new understanding of microbes will provide the basis for a revolution in industrial biotechnology. By understanding how microbes function at these different systems levels and in their many natural environments we can reveal their contributions to earth ecosystems, their relationships to climate change, develop biology-based strategies for environmental remediation and create new sources of renewable, less polluting energy sources.
Biotechnology Solutions
for the Environment
As discussed in a recent issue of TechComm (October/November 2005), global energy demand is projected to rise rapidly in this century due to population growth and increasing worldwide gross domestic products, standards of living and the energy intensity of developing economies. The central tenet of our national energy strategy is that technology development will enable deployment of necessary energy resources and greenhouse gas (GHG) abatement as world economies build out the energy infrastructure to meet increased demand.
By 2100, biotechnology-based energy use could equal all global fossil energy use today. Biologically derived fuels are renewable and expandable to meet the growing demand. They are domestically and globally available for energy security, with most being carbon neutral—€”or potentially carbon negative (if coupled with sequestration)—€”and supportable within the current agricultural infrastructure.
Two example biofuels are cellulose-derived ethanol and biophotolytic hydrogen. Cellulosic ethanol (ethanol produced from cellulose, the main structural component of plant cell walls) is a carbon-neutral fuel that is usable with the existing energy infrastructure. Hydrogen is the ultimate carbon-free energy carrier that can be converted efficiently to energy in fuel cells with water as the only chemical by-product.
Biofuels such as cellulosic ethanol can provide alternatives to oil, displacing it as a transportation fuel with security, economic and environmental benefits. Cellulosic ethanol can be cost competitive with oil-based gasoline and can reduce net CO2 emissions from the transportation sector (roughly one-third of U.S. emissions) by more than 80 percent. The cellulosic ethanol option would allow us to invest our energy dollars domestically, providing a profitable crop for farmers and jobs for America's heartland. In addition to reducing GHGs, these crops improve air and soil quality, reduce soil erosion, and expand wildlife habitat. GTL research can contribute to making cellulosic ethanol more economical and practical by decreasing the complexity and cost of processing cellulose to ethanol.
Today, the commercial conversion of cellulose into ethanol is a multistep process that combines thermochemical and biological methods in large centralized processing plants. The vision of GTL is that through fundamental research we can develop a microbe-based one step process that combines all key hydrolytic and fermentative steps in one process using either a single microbe or stable mixed culture, an advance that would enable smaller-scale and more cost-effective and energy-efficient distributed processing plants.
Microbes also hold the key to biological production of hydrogen. As the planet's dominant photosynthetic organisms, microbes are capable of using solar energy to drive the direct conversion of water to hydrogen and oxygen (biophotolysis). One technology option for deploying biophotolytic hydrogen-production systems would involve the use of living organisms. Extensive farms of sealed enclosures (photobioreactors) containing photosynthetic microbes would split water to produce hydrogen for collection; oxygen would be released as the only by-product.
GTL research will, for example, identify novel enzymes with desirable properties and new metabolic pathways that generate hydrogen; uncover the mysteries of biophotolysis possible in oxygenic photosynthetic microbes (e.g., algae and cyanobacteria that split water to generate oxygen); and discover, characterize and even modify enzymes such as hydrogenases to make them more efficient and less sensitive to oxygen.
One recent experiment in the Sargasso Sea has uncovered more than a million new genes, doubling the total amassed set of sequenced genes in the world. This same experiment identified hundreds of light receptor genes, bacteriorhodopsins, that could prove critical in developing the ultimate biophotolysis system. Mining the global gene presents a unique opportunity to discover new genes, processes, and species that could point the way for biotechnology applications for DOE missions.
Microbes also offer great promise for the development of novel and cost-effective alternatives for the remediation of some of the large volumes of soil, sediments and groundwater contaminated with metals, radionuclides and a variety of organics at diverse defense facilities and sites across the nation. GTL science is contributing to the detailed, large-scale discovery and investigation of microbes with important contaminant-transformation capabilities. DOE bioremediation strategies and biogeochemistry research focus on using natural microbial communities to directly or indirectly remove contaminants from groundwater, immobilize mixed waste or transform toxic contaminants into benign chemical products.
DOE's Genomics: GTL program is giving the microbial world the respect it deserves. GTL is a research program of remarkable challenge, complexity, excitement and promise. It is uniquely relevant for DOE with its long-range focus on grand challenges in energy security, environment and climate. It brings together DOE's unique resources and capabilities in the biological, physical and computing sciences. Through the new knowledge it will generate on microbes and microbial communities GTL research will transform microbes from the unsung heroes of our planet to the superstars of tomorrow.
David Thomassen is Chief Scientist for the Office of Biological and Environmental Research in the Department of Energy's Office of Science.
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