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Virginia Tech, U.S. Department of Energy, Russians, collaborators study rare microorganism that produces hydrogen


BLACKSBURG, Va., July 3, 2008 – An ancient organism from the pit of a collapsed volcano may hold the key to tomorrow's hydrogen economy. Scientists from across the world have formed a team to unlock the process refined by a billions-year old archaea. The U.S. Department of Energy Joint Genome Institute will expedite the research by sequencing the hydrogen-producing organism for comparative genomics.

When members of the Russian Academy of Sciences isolated a rare archaeal microorganism that breaks down cellulose and produces hydrogen, Biswarup Mukhopadhyay, an assistant professor with the Virginia Bioinformatics Institute at Virginia Tech, saw an opportunity to open a door for development of a cellulose-based high-temperature hydrogen production process. “Hydrogen can be easily converted to electrical and mechanical energy without any production of carbon dioxide,” said Mukhopadhyay, whose lab specializes in very high temperature or hyperthermophilic archaea and in energy production.

Elizaveta Bonch-Osmolovskaya and her colleagues at the Winogradsky Institute of Microbiology of the Russian Academy of Sciences discovered the rare archaeon that can chew up cellulose and exhale hydrogen. They found Desulfurococcus fermentans in the Uzon Caldera on the Kamchatka Peninsula, an isolated spit of land in eastern Siberia that is full of volcanoes and their remnants. D. fermentans degrades cellulose from the higher plants that fall in the caldera. Meanwhile, this renegade archaeon’s four closest relatives do not degrade cellulose or make hydrogen, Bonch-Osmolovskaya wrote in the February 2005 edition of the International Journal of Systematic and Evolutionary Microbiology. Like most such organisms, these relatives reduce sulfur to hydrogen sulfide (think rotten eggs).

“Since hydrogen blocks the growth for most fermenting archaea, they rarely produce hydrogen,” said Mukhopadhyay. “But D. fermentans is not bothered by hydrogen. We want to discover why. One way will be to compare the genomes of D. fermentans and its relatives that do not have the special abilities.”

This novel hyperthermophilic archaea grows best at 80 to 82 degrees Celsius (176-180 Farenheit), close to the boiling point of water. “The ability to operate at high temperatures has advantages – it is faster and the hydrogen producing bioreactor will not be contaminated by common microbes,” said Mukhopadhyay.

At the Thermophiles 2007 conference in Bergen, Norway, Mukhopadhyay discussed collaboration with Bonch-Osmolovskaya, Haruyuki Atomi of Kyoto University, and Todd Lowe of the University of California, Santa Cruz. He had similar conversations with Venkat Gopalan of the Ohio State University and Nikos Kyrpides and Iain Anderson of the U.S. Department of Energy Joint Genome Institute (JGI).

Mukhopadhyay’s laboratory began conducting physiological studies with D. fermentans, which provided some information on the growth and hydrogen production kinetics with cellulose and starch as substrates. With these preparations and with support from the team, Mukhopadhyay submitted a proposal to sequence the genomes of D. fermentans and two of it cousins to the Joint Genome Institute’s Community Sequencing Program, which sequences the genomes of organisms relevant to department of energy missions at no charge. Organisms to be sequenced are selected from proposals based on scientific merit and the degree of interest by the scientific community. The researchers then have six months to use the information before it is submitted to a gene bank for use by the world’s scientific community. In mid-June, the Joint Genome Institute approved the proposal titled “A Comparative Genomics Investigation on Hydrogen Production from Cellulosic Materials and Starch by a Hyperthermophilic Archaeon.” (See the department of energy announcement.)

The Joint Genome Institute had already targeted another sulfur-reducing cousin of D. fermentans to fill in a gap in the Genomic Encyclopedia of Bacteria and Archaea (GEBA). “Therefore, we will have genome information of D. fermentans that degrade cellulose and make hydrogen and similar information for three cousins that do not have these properties. We will perform genomic subtraction exercises to figure out which genes and regulatory circuits make D. fermentans so capable. These data will guide more intensive and focused investigations on the cellulose degradation and hydrogen production,” Mukhopadhyay said. “This is just the beginning of an exploration of hitherto unknown processes with potential to advance energy production and having a team will make it more innovative, productive and fun.”