The U.S. Department of Energy (DOE), which is tasked – among other things -- with promoting energy independence, is turning the search for answer to a time immemorial source of inspiration:  nature.  The DOE is launching a major project to sequence the genomes of many species with promising biologic processes.  The hope is that the results will yield enzymes which can be synthetically manufactured and used in the next generation of biofuels.

The DOE Joint Genome Institute (DOE JGI) received 150 proposals from the Community Sequencing Program (CSP), and selected the best 44 for sequencing.  The work will begin next year.

Eddy Rubin, DOE JGI Director stated:

The scientific and technological advances enabled by the information that we generate from these selections promise to take us faster and further down the path toward clean, renewable transportation fuels while affording us a more comprehensive understanding of the global carbon cycle.  The range of projects spans important terrestrial contributors to biomass production in the Loblolly pine—the cornerstone of the U.S. forest products industry—to phytoplankton, barely visible to the naked eye, but no less important to the massive generation of fixed carbon in our marine ecosystems.

The work is possible thanks to new sequencing strategies coming online this year.  The Loblolly pine (Pinus taeda); with a massive genome of over 21 billion bases, is finally within sequencing reach thanks to these developments.  This type of pine accounts for 75 percent of the seedlings planted each year in the U.S.

The research aims to find genes that can be manipulated to increase growth, carbon sequestration, and the quality of raw materials for lumber and pulp fiber.  Another common plant being tested is Greater Duckweed, Spirodela polyrhiza.  Duckweed is a waste water remediator, biotech protein factory (yielding high protein animal feed), toxicity testing organism, and a key player in the carbon cycle.  By understanding the genes for these valuable characteristics, they can be improved or transferred to other plants.

"These plants produce biomass faster than any other flowering plant, and their carbohydrate content is readily converted to fermentable sugars by using commercially available enzymes developed for corn-based ethanol production.  Moreover, duckweed relates to all three of DOE JGI's mission areas: bioenergy, bioremediation, and global carbon cycling," added Rubin.

Duckweed reduces algal growth (by shading), coliform bacteria counts, suspended solids, evaporation, biological oxygen demand, and mosquito larvae.  It also balances the pH and sequesters or breaks down heavy metal residues, halogenated organic, and phenolic organic compounds.

The study also focuses on so called "meta-genomes" genese from several species living together symbiotically; for example, and invertebrate and organism in its gut.  The perfect example is the Bankia setacea, the giant Pacific shipworm.  It is a superior wood eater to termites in that it can completely digest lignocellulose with the help of only a handful of microbial partners.  The end product is ethanol; so scientists hope to discover the cellulases and other hydrolases that it employs, which could be used in commercial cellulosic ethanol production.

Yet another promising organism is Botryococcus braunii, which is a colony-forming green microalga.  The algae sequesters carbons and makes them into long chains which provide the organism with buoyancy.  The chemical chains are called botryococcenes and make up part of current petroleum deposits.  If they could be synthetically produced, they could be made into synthetic gasoline.

Other organisms to be sequenced include the Opisthocomus hoazin -- a leaf-eating Amazonian pheasant-like stinkbird, or hoatzin. It features ruminative digestion via fermentation, similar to a cow and Nanoflagellates, a group of marine microbes which prey on phytoplankton and play a critical role in the ocean ecosystem and the carbon cycle. 

Another target is white rot fungi, which depolymerize lignin, the toughest component of plant cell walls.  Desulfurococcus fermentans, an archaebacteria which produces hydrogen from cellulose (the only known archaebacteria to digest cellulose) will also be sequenced.  Rhodopseudomonas palustris strain DX-1, which generates electricity directly from biomass generation, will likewise be analyzed.

A complete list of the projects can be found here -- in short they encompass how nature makes a variety of fuels, and how such enzymes might be reproduced or harvested cost effectively.

The research will be carried out at five national labs -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center.  It is funded by the DOE Office of Science, which receives funding in the Congressional budget.