Microbes dwelling in oil fields and coal beds could inspire new methods of extracting fossil fuels from the depths of the earth. That's the hope of Ari Patrinos, a genomics pioneer who helped run the Human Genome Project and is now the president of Synthetic Genomics, a Maryland-based biotech startup founded by J. Craig Venter. Synthetic Genomics's goal is to use genomics to develop new energy technologies.As part of a new partnership with oil giant BP, Synthetic Genomics will study microbes that naturally feed off hydrocarbons for clues into biological means of extracting and processing oil and coal.

After several decades at the Department of Energy (DOE), Patrinos is a strong advocate of using biotech solutions to the world's energy problems. He helped found the DOE's Joint Genome Institute and created the agency's Genomes to Life program, which, among other things, develops energy-related applications for microbes. Patrinos was lured away from the DOE by Venter last year. He talks with Technology Review about Synthetic Genomics's plans and the future of biofuels.

Technology Review: Why look to microbes as sources of alternative energy?

Ari Patrinos: Microbes are the virtuosos of the living world. They have been around about four billion years, a third of the time the planet has been in existence, and they have developed tremendous variability and diversity. We have a lot to learn from them as we face global warming and try to learn to use our resources more efficiently.

TR: How is genomics helping us take advantage of microbes' diverse functional repertoire?

AP: As a result of genomics, we have discovered there are microbes everywhere, living at every temperature and pressure. They can survive at 100 times the atmospheric pressure and at temperatures almost 100 degrees Celsius. People have identified microbes that can withstand huge amounts of radiation. Microbes play a crucial role in the carbon cycle, taking up carbon dioxide in the ocean. More than 50 percent of living biomass on this planet is microbial in nature. That's why we should be looking to microbes to solve some of our problems. They have become extremely effective in life's processes. We need to understand them and then mimic them for some of these applications.

TR: Synthetic Genomics recently formed a partnership with BP. What is the emphasis of that deal?

AP: We have huge reserves of heavy oils in this continent, but their extraction is difficult. It requires energy and water, and produces a lot of carbon dioxide. There may be ways to use microbial communities to improve the quality of the oil while still in the subsurface. So we'll look at microbes that live in coal beds or oil fields and oil sands.

TR: How will that help fuel production?

AP: The idea of oil fields as a reservoir you can tap is naive. Oil exists as a matrix in different layers. When you produce oils from wells, you leave as much as 50 percent behind. As many as 30 to 40 years ago, people were contemplating microbially enhanced oil recovery--ways they could manipulate microbes to enhance oil recovery from wells. But their ability to discover and study these microbes was impaired because of primitive microbiology tools. This never made it into commercial practice, as far as I know.

We have significantly more accurate and powerful tools than our colleagues back then, and we suspect the number and diversity of microbes we discover will be much higher than was contemplated back then.