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Building a Bug to Harvest Oil

A genomics pioneer turns his attention to synthetic biology’s potential.
June 27, 2007

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.

Microbial advocate: Ari Patrinos, president of Synthetic Genomics, is a pioneer in applying microbial genomics to energy problems. He says that microbes that feed on hydrocarbons could offer 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.

TR: What will you do with the microbes once they are discovered?

AP: Perhaps we could use them to change the density of the hydrocarbons, breaking them up so they are smaller and making the oil easier to move. Or microbes could change the surface-adherence properties of the oil by modifying the hydrocarbon molecules.

For coal beds, rather than extract the coal and burn it, which produces a lot of carbon dioxide, maybe there is a way to convert it into methane. [Burning] methane produces carbon dioxide but also hydrogen, which is a very clean and more climate-friendly fuel. Eventually, perhaps we can combine production of methane with carbon sequestration, so the net release into the atmosphere would be zero.

There has been a long history of improving the quality of oil using chemistry. But most of what chemistry can do may be even better accomplished with biological means that are much cheaper and more ecologically friendly. That doesn’t mean that chemistry will be abandoned. But I think this revolution in biology has revealed that biochemical pathways will ultimately be the most productive and can perform the task in a more environmentally-friendly way. Biochemical reactions can be performed at lower temperatures and pressures, and ultimately may have fewer toxic byproducts.

TR: So is Synthetic Genomics also looking for microbes that can sequester carbon dioxide?

AP: We do plan to do that, though I can’t speak to our exact hand.

TR: Prior to joining Synthetic Genomics, you worked at the DOE for more than 30 years. Has the department’s view of the biotech approach to energy issues changed over the years?

AP: In the DOE, interest in biofuels was limited and perceived to be a niche application. There was more emphasis on physical sciences with respect to energy. But I pushed very hard for the importance of biofuels. At the beginning, I wasn’t successful because oil is very cheap.But I finally hit the jackpot a few years ago. In a couple of State of the Union addresses, President Bush, an oil and gas man, started talking about our addiction to oil and the importance of biofuels. When I heard that, I knew I was finally successful.

TR: Alternative energy is a hot topic right now, garnering lots of interest–and cash–from government and investors. But will this funding fade once gas prices drop, as has happened before?

AP: It can always happen, but I think it seems less likely to happen now than in the nineties and seventies. Even if the price of oil was much lower, I think there is a general recognition in the public and in the policy world that it behooves us to be more independent with respect to liquid fuel: we still have to import 60 percent of the oil we consume. It has become a national-security issue, as opposed to something economic. A lot of countries producing oil are countries that do not like us very much. Feelings may change in all kinds of directions, so reducing dependence on imported fuel is very important.

I also think more and more of the world is recognizing that global climate change is a serious threat. The tipping points in the climate system are not hypothetical anymore. We should start tallying up an insurance policy against climate change, but that won’t be possible until we rely more on cleaner fuels.

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