WALNUT CREEK, CA–Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year. Drawing submissions from DOE JGI’s more than 400-strong user community, the genomes of these organisms will be sequenced and characterized as part of the DOE JGI Community Sequencing Program (CSP). Over 15 billion letters of genetic code–or the equivalent of the human genome five times over–will be processed through the DNA sequencers at the DOE JGI Production Genomics Facility for this year’s program and ultimately, the information will be made freely available to the greater scientific community.
“By coupling DNA sequencing technology with fundamental research, we seek to make cellulosic ethanol a major part of the nation’s energy future,” said DOE JGI Director Eddy Rubin. His remarks and the CSP selections echo recommendations outlined in the “Breaking the Biological Barriers to Cellulosic Ethanol” report issued by DOE on July 7. “The newest direction in biosciences research–systems biology–is built on a strong foundation of DOE’s investment in genomics, with DNA sequence as the starting material of that endeavor and DOE JGI as the generator of that information through the CSP. Downstream characterization of the pathways inferred by the genetic code of the target CSP organisms is then supported through the DOE Genomics:GTL program.”
In his 2006 State of the Union Address, President George W. Bush specifically cited the promise of switchgrass as a bioenergy crop. A tall perennial grass, a dominant species of the North American prairie, switchgrass (Panicum virgatum) is particularly compelling because of its relatively low production costs, minimal nutrient and pesticide requirements, perennial growth habit, as well as its ability to adapt to a broad range of growing conditions. The net energy gain for ethanol production from switchgrass is exceptionally favorable, coupled with low greenhouse gas emissions. The switchgrass project, which entails sequencing the gene transcripts, or Expressed Sequence Tags (ESTs) of the plant, is led by Christian Tobias and researchers at the U.S. Department of Agriculture Western Regional Research Center in Albany, Calif. and Gautam Sarath at the University of Nebraska, Lincoln.
“Switchgrass has enormous potential as an energy crop and environmental benefits that are associated with its cultivation,” said Chris Somerville, professor of biological sciences at Stanford University and director of the Carnegie Institution’s department of plant biology. “I envision that switchgrass will be an important feedstock for the emerging lignocellulose to ethanol industry. An enhanced understanding of gene structure and diversity at the molecular level may lead to new approaches to enhance both biomass productivity and feedstock quality for bioenergy production.”
In complement to switchgrass, DOE JGI will be sequencing Brachypodium distachyon, a temperate grass model system with a simple genome more amenable to sequencing. This choice responds to the urgent need for developing grasses into superior energy crops and improving grain crops and forage grasses for food production. Brachypodium will be undertaken via a two-pronged strategy: the first, a whole-genome shotgun sequencing approach, a collaboration between John Vogel and David Garvin, both of the USDA, and Michael Bevan at the John Innes Centre in England; and the second, an expressed gene sequencing effort, led by Todd Mockler and Jeff Chang at Oregon State University, with Todd Michael of The Salk Institute for Biological Studies, and Samuel Hazen from The Scripps Research Institute.
Another major CSP project is the selection of cassava (Manihot esculenta), an excellent energy source and food for approximately one billion people around the planet. Its roots contain 20 to 40 percent starch, from which ethanol can be derived, making it an attractive and strategic source of renewable energy. Cassava grows in diverse environments, from extremely dry to humid climates, acidic to alkaline soils, from sea level to high altitudes, and in nutrient-poor soil.
“Sequencing the cassava genome will help bring this important crop to the forefront of modern science and generate new possibilities for agronomic and nutritional improvement,” said Norman Borlaug, Nobel laureate, father of the “Green Revolution,” and Distinguished Professor of International Agriculture, Texas A&M University. “It is a most welcome development.”
The cassava project will extend broad benefits to its vast research community, including a better understanding of starch and protein biosynthesis, root storage, and stress controls, and enable crop improvements, while shedding light on such mechanisms shared by other important related plants, including the rubber tree and castor bean.
The cassava project, led by Claude M. Fauquet, Director of the International Laboratory for Tropical Agricultural Biotechnology and colleagues at the Danforth Plant Science Center in St. Louis, and includes contributions from the USDA laboratory in Fargo, ND; Washington University St Louis; University of Chicago; The Institute for Genomic Research (TIGR); Missouri Botanical Garden; the Broad Institute; Ohio State University; the International Center for Tropical Agriculture (CIAT) in Cali, Colombia; and the Smithsonian Institution.
Adding to the list of crops to be sequenced by DOE JGI is the oyster mushroom, Pleurotus ostreatus, for its prospective role in bioenergy and bioremediation. This white-rot fungus is an active lignin degrader in the forests. Lignin, a poly-aromatic hydrocarbon, is the second most abundant biopolymer on earth and its breakdown is a necessary step for making cellulose–the most abundant carbon biopolymer–available for conversion to biofuels. This organism will serve as a valuable comparison to the reference genome of white-rot fungus Phanerochaete chrysosporium, previously sequenced by DOE JGI, which belongs to a different phylogenetic branch and carries a different set of ligninolytic enzymes. Understanding the whole-genome regulation of the P. ostreatus will add further value in that its lignocellulolytic enzymes could facilitate bioremediation and other biotechnological processes. The poly-aromatic hydrocarbon oxidizing enzymes present in P. ostreatus can participate in the biodegradation of dyes, of contaminating wastes produced in agroindustries, and of forest, pulp and paper industrial by-products. This project is led by Antonio Pisabarro of the Public University of Navarre, Spain and includes more than a dozen other institutions including University of Wisconsin, Michigan State, Texas A&M, Duke, and Southeast Missouri State.
The CSP has tapped important projects from the most extreme locales, including the pristine cold environment described by a system of lakes in the Vestfold Hills region of Antarctica. This project, led by Rick Cavicchioli of the University of New South Wales in Sydney, Australia, seeks to define a microbial model for the biogeochemical process that take place in extreme cold conditions. This project entails the strategy of metagenomics, pioneered by DOE JGI, for isolating, sequencing, and characterizing DNA extracted directly from environmental samples. These data are then used to define a profile of the microbial community residing in a particular environment.
“Microbes are too small to be seen with the naked eye,” said Carl Woese, professor of microbiology at the University of Illinois at Urbana-Champaign, whose pioneering contribution of phylogenetic taxonomy of 16S ribosomal RNA led to the definition of the domain of life known as Archaea. “That is why the average person and most scientists pay little or no attention to them–except, of course, when they cause us problems or make us money. Nature does not look at the living world this way,” Woese said. His remarks on the significance of the Antarctic project ring true for other CSP microbial investigations.
“Microbes constitute as much or more of the living mass on this planet than do the ‘higher forms,'” Woese said. “Microbes are absolutely basal to the great flows of organic matter and energy that underlie the biosphere; without them macroscopic life on this planet is impossible. In other words, the existence of macroscopic life is totally conditioned upon the prior and continued existence of microbial life. You can see why the proposed work delights an old evolutionist like myself. Here you see the microbial world in its full glory–its true significance to the biosphere, and so to mankind. Here is the microbiology of the 21st century.”
The genomic and functional data gleaned from the Antarctic environmental samples, linked to meteorological, geological, chemical and physical data, will provide a better understanding about how these microorganisms have evolved, transformed, and presently interact with their frigid environment. These studies, while basic to understanding how microbes cope with environmental challenges, also seek to unlock the potential of cold-adapted microbes as sources of fuel, for example, transforming carbon dioxide effluent into methane. The work has even more astronomical ramifications–modeling extraterrestrial environments and processes.
Plant pests are the target of another international collaboration, linking researchers in Sweden, France, Norway, Germany, Canada and at the University of California, Berkeley. Heterobasidion annosum is the most economically devastating forest pathogen in the northern hemisphere, causing root rot in conifers, a major renewable biological energy resource. These forests support biodiversity and serve as an important CO2 sink buffering global climate change. Improved knowledge of this tree pathogen will help build strategies to protect these wooden resources and enable a better understanding of important enzymatic systems involved in oxidation and degradation of polyphenolic substances–pollutants that are targets for bioremediation.
Actinobacteria, which can be found in soil, can be harnessed for environmental clean-up as well. Strains, the subject of another CSP project, proposed by researchers at the Swedish University of Agricultural Sciences and Hebrew University, have promise for the development of environmentally sound, cost effective biological strategies to reduce environmental pollution.
The DOE Joint Genome Institute, 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. DOE JGI’s Walnut Creek, Calif. Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.