A spiral staircase is at the center of the LEED Gold–certified Energy Biosciences Institute building, adjacent to the Berkeley campus.
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Brewing Biofuels

A peek inside the world’s largest energy bioscience research center

In February 2007, excitement ran high on the Berkeley campus with the announcement that the University would enter into a partnership with Lawrence Berkeley National Laboratory, the University of Illinois at Urbana-Champaign, and energy giant BP to form the Energy Biosciences Institute (EBI), with the goal of helping to wean humanity from its dependence on fossil fuels for transportation. Backed by $500 million in funding over a 10-year period, the EBI was poised to launch a broad, interdisciplinary research effort into one of the planet’s most pressing and complex issues.

Chris Somerville

BP had asked a handful of universities around the world to submit proposals for an institute that would explore the applications of modern biology to the energy sector. “That’s our only real instruction from the company, and that’s a very attractive kind of mandate,” says Chris Somerville, the EBI’s director and a professor in the Department of Plant and Microbial Biology (PMB).

Although some in the campus community worried that this public-private partnership might compromise the University’s mission, the institute’s many supporters were excited by the opportunity to focus Berkeley’s research capabilities on the energy crisis and climate change — with the help of a partner that was well-positioned to translate new research discoveries into commercial applications.

Five years after that initial burst of enthusiasm and controversy, the EBI is the world’s largest research institution devoted to energy bioscience. Its primary mission is to develop sustainable, environmentally friendly, and commercially viable biofuels from lignocellulosic biomass, the inedible portions of plants. It funds approximately 70 programs and projects to the tune of $35 million per year.

The EBI has amassed a significant body of work that includes identifying promising sources of new biofuel feedstocks, advancing the understanding of plant cell wall structures and how to more efficiently convert them into ethanol, and providing insights into the ecological, economic, and political complexities of producing a new generation of transportation fuels.

Plant cell wall structures have evolved to resist being broken down; they provide protection for the plant…. They have to be very good at it because, as Associate Professor Markus Pauly puts it, “Plants can’t run.”

Somerville says their understanding has improved tremendously and across a broad front, and he is optimistic that BP will extend the Institute’s funding beyond the five years remaining on the current grant. But he cautions against the notion that a single breakthrough, or even a series of breakthroughs, will revolutionize this complex field in which advances tend to be incremental.

“From our perspective, a twofold reduction in the cost of a gallon of biofuel would be a home run. I realize that doesn’t sound like a breakthrough, but it requires a lot of innovation to get there. We’re competing with something that’s a very efficiently produced commodity right now; it’s hard to beat pumping petroleum out of the ground.”

Beyond corn

Markus Pauly (left) and Sascha Gille.

Corn can be converted into ethanol relatively easily and is already competitive with fossil fuels. But growing corn and processing it into ethanol requires a lot of energy and water, has significant environmental downsides, competes with food crops for highly productive agricultural land, and can drive up food prices.

“We’re interested in plants that can be grown with low inputs on land that doesn’t compete for food production,” Somerville says — plants like switchgrass and Agave. Species such as Agave use about one-tenth the water that wheat or rice requires per ton of biomass produced, he says, and “that’s very attractive, because there are about 3 billion acres worldwide that are too arid for agriculture, but quite a bit of it could support these very drought-tolerant species.”

But producing fuel from such plants is currently much more costly than using corn, and while government subsidies can help initially, as they did for corn ethanol, so-called second-generation or advanced biofuels will have to quickly become competitive on their own. The challenge, Somerville says, is enormous.

“From our perspective, a twofold reduction in the cost of a gallon of biofuel would be a home run. I realize that doesn’t sound like a breakthrough, but it requires a lot of innovation to get there.”
Chris Somerville

“I think one thing people fail to understand is the scale. This could be a trillion-dollar-a-year industry; anything that operates at that scale has got to be very, very efficient, and the capital investments required to build that industry are vast. The organizations that could make that investment won’t do so until the technology gets to a certain level of maturity.”

Blue-sky research, real-world applications

Although there are many reasons why lignocellulosic biomass isn’t yet competitive as a biofuel source, one of the biggest technical hurdles is breaking down the sugars in the plant cell walls, a process known as depolymerization, currently the most expensive step in turning biomass into fuel. Once that breakdown has been accomplished, using enzymes, heat, or other pre-treatments, the sugars can be fermented to produce ethanol or other fuels that resemble gasoline, jet-fuel, and diesel. But plant cell wall structures have evolved to resist being broken down; they provide protection for the plant, allow it to stand upright, and ward off pathogens. They have to be very good at it because, as Markus Pauly, a PMB associate professor puts it, “Plants can’t run.”

N. Louise Glass (right) and student.

An early EBI success story involves a fungus called Neurospora crassa, which grows on plants that have recently been killed or damaged by fire, devouring the plant’s dead cell wall material. N. Louise Glass, a PMB professor, in collaboration with chemistry faculty Jamie Cate and Michael Marletta, used EBI funding to genetically profile N. crassa growing on Miscanthus, a perennial grass related to sugarcane that shows promise as a biofuel feedstock. That initial project led to several lines of research. One project, a collaboration between Glass and Cate, led to the discovery of a protein that transports sugars in and out of N. crassa cells. This was used by Glass, Cate, and colleagues at the University of Illinois to modify industrial yeast strains, allowing them to utilize more of the sugars that comprise plant biomass and thus convert plant biomass to ethanol more efficiently and cheaply.

Glass’s and Cate’s discovery has great potential for industrial use in the future, but Somerville likes to point out that it arose from a “very blue-sky piece of basic work, in which we were hoping we would find new insights but weren’t directed toward any specific thing. It’s quite typical of the level of research we’re trying to do here; we’re trying to find genuinely new things we can bring to the industrial process.”


Other EBI researchers are looking for ways to breed advantageous characteristics into potential feedstocks, creating new varieties that are easier to break down or that produce more sugar. This is Markus Pauly’s area of specialization, and one of his biggest advances to date was inspired by EBI colleagues he refers to as “the microbial guys” — who, he says, “complained that there was too much acid in the stuff we gave them.”

They were talking about acetic acid, which is produced when plant biomass is treated thermo-chemically during processing. In much the same way that vinegar acts to prevent foods from spoiling, acetate “pickles” biomass, preventing the microbes from fermenting the plant’s sugars into fuel. Working with a plant in the mustard family called Arabidopsis, Pauly was able to identify a gene that’s responsible for adding acetate to the polymers of plant cell walls.

“So now we can block the gene,” he says, “and we can also use it as a molecular marker for breeding,” allowing crops with the low-acetate trait to be bred using traditional techniques.

Economics for a new commodity

David Zilberman

While biologists and geneticists are teasing apart the complex microscopic structures and networks involved in plant biology, David Zilberman, an agricultural and resource economics professor, is trying to answer some of the large-scale economic and social questions, such as how biofuels affect food and energy prices, and what elements will be most important in convincing farmers and manufacturers to shift to second-generation biofuels.

Zilberman’s EBI-funded research has led to a number of unexpected findings. Early on he determined that, while conventional biofuels can and do contribute to increases in food prices, increased demand for food, spurred by population and income growth, is a bigger factor. He also discovered that some of the indirect effects caused by increasing conventional biofuels production — for example, reducing the amount of petroleum byproducts produced, along with their associated greenhouse gas (GHG) emissions — would offset some of the GHG emissions associated with biofuels.

His research into the effects of renewable fuel standards — like the U.S. requirement that a certain volume of biofuels be blended into gasoline — indicates that they are less effective than other policies in reducing GHG emissions. “Renewable fuel standards are really good from the perspective of energy security and balance of trade, but for greenhouse gases they’re not a big help,” he says.

Bioenergy 101

Perhaps the EBI’s biggest achievement is its holistic approach of funding research in a broad spectrum of relevant disciplines: agronomy, chemical engineering, mechanical engineering, chemistry, biochemistry, microbiology, economics, environmental science, ecology, law, and policy. From the beginning, the Institute envisioned researchers from the various disciplines working together and sharing knowledge — in the same space, whenever possible.

To foster this collaboration, the EBI hosts regular seminars, presents a series of half-day workshops for non-specialists called “Bioenergy 101,” and creates briefing papers to help researchers understand topics outside their field. Collaboration is built right into the architecture of the EBI’s new downtown Berkeley building, which has social rooms on every floor, complete with walls that double as whiteboards, to capture ideas.

Cumulatively, these interactions “force people to look beyond their own plate,” Pauly says, and not only lead to new insights but help researchers avoid wasting time on ideas that may, for example, be too expensive to be feasible. “This whole next-generation plants-to-biofuels is really sort of like a pipeline,” he says, “and there are lots of knobs you can turn — to change the plants, to change processes, to change the microbes you use. And every time you turn a knob on the plant side, you also need to turn a knob on the microbe side; they’re all integrated. Neither plant nor microbe scientists can do this type of research by themselves to be effective.”

“Universities are tremendous resources of knowledge,” says Somerville, “but the knowledge is fragmented in the conventional academic structure. Institutes such as EBI provide a way for society to access all those individual pieces of knowledge in a coherent way, to bring them all together toward a common focus. I see the EBI as a model for how universities can become a more effective engine for solving societal problems.”

Of course, advances in biofuels and other forms of bioenergy alone can’t solve such an enormous and multifaceted problem as global warming. But Somerville believes it can be one of many partial solutions that include conservation, improved efficiency, solar and wind power, and other alternative technologies. “We need everything we can possibly get,” he says.