March 4, 2011
The high speed networking that ESnet provides supports an incredibly varied range of scientific projects. The express purpose of DOE national labs is to conduct research in the national interest. Much is basic research, exploring fundamental issue in physics, energy, cosmology, and climate science. However the study of microbial evolution is one intriguing area that is already changing our lives with everything from new medicines to potential fuels.
Microbes are single-cell organisms that live in colonies and can be found in nearly every corner of our planet, in places ranging from insects’ intestines to some of the most toxic chemical environments. The site for the most detailed information on the genetic makeup of these organisms only lives in one place – at the DOE’s Joint Genome Institute – and is accessed via ESnet. The Integrated Microbial Genomes (IMG) Data Management System provides the genetic makeup of thousands of microbes and tools for analyzing the functional capability of microbial communities based on their metagenome DNA sequence. Understanding these tiny organisms can provide new insights into a wide range of important problems, but in order to study the microbes, scientists need reliable access to the genomic data.
Microbes such as bacteria are responsible for a number of diseases, such as plague, tuberculosis and anthrax, while microbes known as protozoa cause diseases such as malaria, sleeping sickness and toxoplasmosis. On the plus side, microbes also live helpfully in human digestive systems, helping to digest carbohydrates and synthesize certain vitamins.
Famously, taq polymerase, an enzyme isolated from the bacterium Thermus aquaticus found in a hot spring at Yellowstone National Park in 1965, became the basis for PCR, the technique for amplifying short strands of DNA that has revolutionized biologic and genetic research. While some scientists examine exotic microbes like Deinococcus radiodurans, the most radiation-resistant organism known (and the darling of exobiologists, found as a contaminant of irradiated canned meat in 1956) for clues to how life began on earth and could evolve on other planets, your laundry detergent probably contains enzymes developed from bacteria that evolved in hot, alkaline conditions.
In the private sector, microbes are genetically modified to develop innovative drugs as well as industrial products. In an example close to home, a few years back, LBNL’s Joint BioEnergy Institute director Jay Keasling used microbial evolution techniques to synthesize artemisinic acid, a precursor to artemisinin, an anti-malarial compound. Artemisinin is derived from Artemisia annua or wormwood, a plant known to Chinese medicine for centuries. Keasling made a steady supply that could be manufactured extremely cheaply and at large volumes, so accessible to people in developing countries.
Keasling’s next project is to use microbes as potential energy sources by turning them into factories to produce sugars. Certain microbes living in termite guts are essential for digesting the wood fibers eaten by the insect. While this can be bad news for homeowners, the chemical capabilities of the “bugs” in these bugs are being studied as for their potential in converting wood and other plant matter into new energy sources. Successfully producing fuel using plant waste instead of food crops like corn, could improve our country’s future energy options. To be sure, there still are prosaic bars to overcome, such as chemical separation and processing in volumes high enough to meet our insatiable demand for transport fuels. Other scientists at DOE national labs such as NREL and a host of private companies, some right across San Francisco Bay from our headquarters at ESnet, are investigating how to make gasoline and jet fuel from microorganisms. Genetic analysis is the essential first step in growing hardworking bacteria with the desired qualities.
Another promising microbial application is environmental cleanup. One form of bacteria found almost 2 miles underground in a South African gold mine lives in total darkness, 140 degrees Fahrenheit – and no oxygen. The organism gets its energy not from the sun but from hydrogen and sulfate produced by the radioactive decay of uranium. By understanding how life can thrive in such an apparently toxic setting, scientists may get new insight into using microbes to clean up environmental contamination.
Currently, the IMG database contains complete genomes for 4,879 microbes, with another 1,569 in draft form. Of the total, 1,107 are bacteria and 2,536 are viruses. The information, containing data for more than 20 million genes, is provided freely to interested researchers.