The DOE Joint Genome Institute (JGI) has issued a progress report on the projects it undertook between 2002 and 2005 to support energy and environmental science.
The JGI, supported by the DOE Office of Science, unites the expertise of five national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest, along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy generation and environmental characterization and clean-up.
The Institute’s more specific overarching mission is to develop and exploit new sequencing and other high-throughput, genome-scale, and computational technologies as a means for discovering and characterizing the basic principles and relationships underlying the organization, function, and evolution of living systems—especially as applied to challenges in energy and the environment.
Just as one example, JGI will be sequencing the community of microbes that inhabit the hindgut of the termite—one of the planet’s most efficient hydrogen bioreactors.
A termite can produce two liters of hydrogen from fermenting just one sheet of paper. Sequencing the microbes will provide a better understanding of the biochemical pathways used in the termite hindgut, which may lead to more efficient strategies for converting biomass to fuels and chemicals.
Similarly, an ability to harness the pathways directly involved in hydrogen production in the termite gut may one day make its biological production a more viable option.
During the three-year period, JGI contributed to the sequencing of more than 300 organisms, amounting to more than 100 billion letters of DNA logged into the public databases. This enabled more than 250 peer-reviewed publications. Some of the projects include:
The poplar tree Populus trichocarpa (black cottonwood), the first tree to be sequenced, provides a resource to fully exploit the possibilities of trees—to grow faster, to convert biomass to fuel more effectively, to sequester more carbon from the atmosphere, and to clean up waste sites.
The diatom—a single-celled ocean organism— is a key player in global carbon management, absorbing CO2 in amounts comparable to all the world’s tropical rain forests combined.
In 2004, JGI produced the first sequence of the diatom Thalassiosira pseudonana, providing insights into how the creature uses nitrogen, fats, and silica. The information enables a better understanding of the vital role that diatoms and other phytoplankton play in mediating global warming.
All together, diatoms generate as much as 40% of the 50 billion to 55 billion tons of organic carbon produced each year in the sea, while also using carbon dioxide and producing oxygen. They are also an important food source for many other marine organisms.
Scientists need to better understand how these organisms react to changes in sea temperatures, the amount of light penetrating the oceans, and nutrients.
The JGI project revealed that diatoms have a urea cycle. A urea cycle is a nitrogen waste pathway found in animals and has never before been seen in a photosynthetic eukaryote like a diatom. Nitrogen is crucial for diatom growth and is often in short supply in seawater, depending on ocean conditions. The genome work revealed that the diatom Thalassiosira pseudonana has the genes to produce urea-cycle enzymes that may help to reduce its dependence on nitrogen from the surrounding waters. (Published in Science, 1 October, 2004.)
White rot fungi are capable of efficiently degrading the tough plant polymer lignin, one of the most abundant natural materials on earth. Called white rot fungi because they degrade the brown lignin and leave behind white cellulose, the organisms are of the group basidiomycetes, which also includes edible mushrooms and plant pathogens such as smuts and rust.
JGI contributed to the sequencing of Phanerochaete chrysosporium. The first white rot fungus to be sequenced, it secretes an array of peroxidases and oxidases that act nonspecifically via the generation of lignin-free radicals.
The nonspecific nature and exceptional oxidation potential of the enzymes has attracted considerable interest for application in bioprocesses such as organopollutant degradation and fiber bleaching.
Furthermore, it leaves the cellulose of wood virtually untouched. It also has a very high optimum temperature (about 40° C), which means it can grow on wood chips in compost piles that attain a very high temperature. (Published in Nature Biotechnology, June 2004.)
Sequencing sulfate-reducing bacteria—a DOE Genomics:GTL program undertaking—has helped chart the previously unseen metabolic processes of Desulfovibrio desulfuricans G20, a microbe that has a robust appetite for such toxic metals as uranium and chromium.
DOE JGI scientists are pushing ahead in the emerging field of metagenomics—isolating, sequencing, and characterizing DNA extracted directly from environmental samples—to obtain a profile of the microbial community residing in a particular environment. DOE JGI and collaborators used a metagenomic strategy to characterize the microbial community responsible for the production of sulfuric acid deep inside an abandoned mine. (Published in Nature, 1 February 2004.)
A full list of projects and publications is contained in the report.