Ebi Annual Report 2008

TABLE OF CONTENTS

Exploring the Applications of Modern Biology to the Energy Sector 01

Message from the Director EBI Director Chris Somerville offers a personal perspective on the development of the Institute: “We can look back at having successfully navigated a myriad of typical startup challenges as well as a few that were unusual, if not unique.”

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The EBI at 1 Year Old—a BP Perspective EBI Associate Director Paul Willems reflects upon the energy company’s goals and how the Institute has fared in year one: “We are positioned for successful collaboration and delivery of great innovation in years ahead.”

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About the Energy Biosciences Institute Responding to increasing evidence that continued dependence on fossil fuels is causing climate change, with consequences both uncertain and unwelcome, BP steps up to create a visionary collaboration of academia and industry.

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An Introduction to Biofuels Understanding the complex issues surrounding biofuels is key for the EBI in order to ensure a successful research agenda. Challenges span the entire life cycle of the fuel, from the first seed in the ground to its use in transportation.

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Feedstock: Agronomy, Engineering, and the Environment EBI scientists are at the literal ground level of the search for the most productive biofuel crops, seeking feedstock that grow in difficult environments, using sustainable fertilizers, and maximizing cultivation and harvest techniques.

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Bioconversion: Attacking Cellulosic Degradation on Several Fronts

» 2-5 » 6-7 » 8-19 » 20-27 » 28-35 » 36-41

Research at the EBI is addressing several of the major bottlenecks impeding the breakdown of lignocellulosic feedstock into fermentable sugars.

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Biofuels Production: Transforming Feedstock to Fuel with Microbes

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The routes to biological production of fuel molecules are numerous—but one of the most effective is through microbial fermentation and synthesis.

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Societal and Economic Impacts of Biofuels

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Education and Outreach

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EBI Research Programs, Projects, and Research Personnel

EBI scientists are developing modeling frameworks to project the potential impacts of a biofuels industry on factors such as land use, food production, carbon emissions, the global economy, and environmental stability.

The EBI recognizes its role in educating and training young researchers so that they are prepared for the coming bio-revolution, as well as sponsoring a broad range of activities that facilitate information sharing and staff enrichment.

A listing of the first 50 funded projects in the Institute, including the teams of principal investigators, research associates, postdocs, graduate, and undergraduate students.

» 46-53 » 54-57 » 58-63

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c h a p t e r

Message from the Director

Translating the Vision into Reality The creation of a new organization is inevitably tumultuous and unfailingly exciting. Plans are tested against reality, conflicts are resolved, people are recruited to new roles, processes are put in place, space and facilities are adapted and occupied, and the activities of the organization begin to be realized. As the first year of the Energy Biosciences Institute’s formal existence as an organization draws to a close, we can look back at having successfully navigated a myriad of typical startup challenges as well as a few that were unusual, if not unique. The most important accomplishment of the startup phase was the implementation of a broad research portfolio within the three academic partner institutions—the University of California at Berkeley, Lawrence Berkeley National Laboratory, and the University of Illinois at Urbana-Champaign. The EBI is currently supporting 50 research groups composed of approximately 130 faculty members and 160 graduate students, postdocs, and undergraduates. At this juncture, the research topics encompassed by this group are largely focused on understanding the issues associated with the proposed development of a cellulosic biofuels industry. Our goal is to probe all aspects of the topic with the highest quality academic research and to integrate knowledge from this broad investigation into a coherent understanding of the overall topic. In pursuit of this goal, EBI investigators are engaging in research in a wide range of academic disciplines

Our goal is to probe all aspects of the topic with the highest quality academic research and to integrate knowledge from this broad investigation into a coherent understanding of the overall topic.

that include agronomy, agricultural engineering, biochemistry, chemistry, chemical engineering, ecology and environmental science, economics, geography, law, microbiology, plant breeding, public policy, and systems biology. It is our hope that by supporting a broad investigation within a single framework, including common space, we can facilitate interdisciplinary research that leads to holistic understanding, innovation, and insight while simultaneously minimizing the risks of pursuing ideas that lead to dead ends. The general thrust of the EBI research portfolio was developed by a group of interested faculty in response to a solicitation by BP in the summer of 2006. Following the selection by BP of the EBI proposal in early 2007, and the appointment of a leadership group charged with development of the EBI as an operating unit within the academic partnership, a competitive proposal process was implemented to identify specific research topics. Most of the current research programs and projects were selected from approximately 250 pre-proposals. Additionally, several projects have been implemented outside the first general proposal process to support recruitment of new faculty members who proposed research topics of central importance to the EBI mission, or to initiate research on timely concepts that emerged after the proposal process. A second call for proposals was issued recently in the general area of microbially enhanced hydrocarbon recovery. This solicitation was based on ideas that emerged from an EBI-sponsored workshop held at UC Berkeley in late 2007. Proposals were received from 37 faculty who self-organized into several consortia. These proposals are currently undergoing external peer review, and we envision making funding decisions shortly. Additional solicitations are envisioned in 2009 and in subsequent years. In 2010, funding for the first round of projects expires, and we anticipate new proposals will be submitted to compete with current projects and programs. An important component of EBI activities this year has been sponsorship or co-sponsorship of a number

of workshops and seminars on topics related to the EBI mission (listed on pages 54–57). Many of these meetings were focused on illuminating issues associated with environmental, economic, and social consequences of potential land use changes that may result from expanded production of biofuels. We were pleased to be able to assist with meetings sponsored by organizations that have included the American Society for Plant Biologists, Ecological Society of America, Environmental Defense Fund, the Farm Foundation, Berkeley Energy Resources Collaborative, and the UK Renewable Fuels Association, in addition to supporting a series of workshops developed by EBI investigators. Many of these meetings were filled to the capacity of the venues, and all engendered stimulating and productive exchanges that helped to define the research frontiers, compare the outcomes of various models, and facilitate networking and data sharing among experts. My own conclusion from having participated in many of the meetings was that the issues are complex, but there are points of consensus. For example, an important component of strategies to reduce greenhouse gas emissions from human activities is to prevent expansion of agriculture onto land, such as native tropical forests, that currently supports carbon-rich natural ecosystems. Cellulosic biofuels will have the greatest environmental benefits if produced on land that has been farmed in the past but is no longer used for food production. Recent studies have suggested that at least a billion acres of land worldwide meet these criteria. EBI investigators are using sophisticated crop models in conjunction with detailed geographical information to evaluate the productive potential of such lands. A founding principle of the EBI was to develop comprehensive research capabilities in the area of energy biosciences with the three academic partners. The partnership with the University of Illinois was created with the specific goal of broadening the base of expertise within the EBI beyond the range of UC Berkeley and Lawrence Berkeley National Lab. The collaboration with Illinois has been remarkably

Chris Somerville 2

ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT

MESSAGE FROM THE DIRECTOR

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smooth and enjoyable for everyone involved and represents an unrivaled success. Not unexpectedly, several topics of central importance to the field of energy biosciences are underrepresented in the EBI because no faculty member at the partner institutions proposed a research program in these areas. I expect that some of the topics will be developed by newly recruited faculty. An important aspect of the research program is the co-location of a team of engineers and scientists from BP within the EBI. At present, BP leases a small amount of office space on the UC Berkeley campus where a number of BP scientists and engineers are engaged in studying energy biosciences from an industrial perspective. Unlike the academic members of the EBI, who are focused on fundamental academic questions, the BP fellows are engaged in envisioning how knowledge might be used in practice. The dialectic between those engaged in basic research and those charged with applied research is fertile ground for the development of new questions and a highly efficient way to translate basic research. Equally importantly, the arrangement provides a wonderful opportunity for education across both sides of the basic/applied boundary. Standing-room-only seminars at EBI venues this year by BP chief economist Christof Ruehl and BP chief scientist Steve Koonin provided exceptional opportunities for the Berkeley and Illinois communities to understand perspectives on important aspects of the world energy situation from people who participate directly in providing energy. One-day tourde-force workshops at Berkeley and Illinois on the chemistry of fuels by BP engineer Frank Gerry were also sellout events.

conservative influences and financial limitations that impair much federally funded research. Many brilliant and engaged people who had not previously worked on topics related to energy biosciences are now testing their ideas, and I expect an outpouring of innovation and creativity. A goal of the EBI management team is to develop institutional capabilities and processes that will support and facilitate bold and creative research by providing access to resources that might normally be beyond the reach of an individual research group. Towards this end, EBI investigators at Illinois are developing a 320-acre energy farm where relatively large-scale trials of prospective energy crops can be tested in a wide variety of ways that include productivity studies, identification of pests and pathogens, carbon sequestration measurements, greenhouse gas balances, and development of methods for harvesting and storage. We expect that the experience gained with this first test site will inform the development of additional sites at locations around the world. We have also taken the first steps toward development of an analytical laboratory at Berkeley that will provide specialized services and characterized biomaterials to EBI researchers, and several of the analytical instruments that will facilitate the work have been installed in Calvin Laboratory. The analytical team will facilitate investigations of the composition and properties of biomass proposed by many EBI investigators.

The EBI’s initial year has been filled with a hopeful energy, tireless dedication of researchers and support staff, and productive first steps on our journey as Looking forward, I expect many exciting discoveries to reflected in these pages. Deputy Director Steve Long, Associate Director Paul Willems and I are privileged emerge from EBI research. The exceptional resources to lead the EBI forward. provided by BP have afforded a unique opportunity to explore many new areas without some of the

The EBI at a Glance Comprehensive biofuels research agenda

160 postdoctoral researchers, graduate, and undergraduate students

4 research partners

$500 million grant from BP

50 research groups and 130 faculty

Lab space at Illinois and UC Berkeley

144,000-sq-foot Helios Building, complete in 2013

320-acre Energy Farm

" It is our hope that by supporting a broad investigation within a single framework, we can facilitate interdisciplinary research that leads to holistic understanding, innovation, and insight..." ~ CHRIS SOMERVILLE

www.energybiosciencesinstitute.org CHRIS SOMERVILLE

December 2008

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MESSAGE FROM THE DIRECTOR

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02 c h a p t e r

The EBI at 1 Year Old— a BP Perspective By PAUL WILLEMS Associate Director, EBI Technology Vice President, Energy Biosciences, BP

When BP decided to create the Energy Biosciences Institute in partnership with the University of California at Berkeley, the University of Illinois in Urbana-Champaign, and the Lawrence Berkeley National Laboratory, we had several objectives. As we reach our first anniversary, it is a good time to reflect on how we have done so far. Our goals can be categorized in three groups: science, collaboration, and people. Let’s start with science. The creation of the EBI was rooted in a belief that modern biology as a science is ready to start making significant contributions to energy problems. Lignocellulose-based biofuels have come a long way, and the first commercially viable processes (at least in the current environment of high energy prices) are starting to emerge. However, tremendous scope exists for further technical innovation, and the processes we will employ in 10 years’ time likely will bear little resemblance to these first installations. We have chosen to engage in a broad research portfolio, spanning the entire field addressing dedicated energy crops, their management practices, the technology used to convert them to fuels, a variety of target fuel molecules, chemical and biological conversion pathways, etc. In doing so, we have assembled a great team of researchers, led by distinguished faculty members at our partner institutions. While these partners had some a priori idea of faculty members interested in the field, we have been pleasantly surprised at the level of engagement in the community. Many faculty members are involved with the EBI today who were not on the radar screen initially. Our investment in socio-economic research is one of the features that makes the EBI unique: biofuels done the right way is of crucial importance to us. A clear focus on moving the debate in this arena from opinionbased to fact-based is the mantra of the EBI. In our first

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year, we have already seen the fruits of this philosophy as we have been approached by various agencies involved in policy-setting to provide assistance in “getting to the bottom” of the various debates taking place. Next, collaboration. The EBI is a public/private collaboration of unprecedented scale and scope. The EBI is a mission-oriented, multidisciplinary, teamscience-based institute. These are new expectations for most of our collaborators, as well as for the partnering institutions. While change brings a certain amount of uneasiness, it also brings excitement: new possibilities, new relationships, new perspectives, new innovations. Even as we are just getting under way in our first year of operation, we have already seen the kinds of examples we were hoping for: science taking an unexpected turn, and new dialogue between individuals who had never worked together leading to new avenues of investigation. And last but not least, people. Great people are the foundation of great work. On the backs of our partner institutions, we have been able to create a great reputation for the EBI. Not a week goes by without an important visitor to the EBI from somewhere around the globe. Our reputation has allowed us to tap into the great talent pool on our campuses. It is also our calling card for attracting future students and researchers. Part of the vision for the EBI was to create a talent pool for a future energy biosciences-based industry. This is obviously important to BP as we try to grow our own internal technical capability in this area. It is equally important to the wider world. We anticipate that in due course this will result in a formal energy biosciences curriculum, at both the undergraduate and graduate level, at our partner institutions. In summary, I would say we can be very proud of our first year. We have a great portfolio of research projects in place. We are continuing to create the collaborative and multidisciplinary environment envisioned for the EBI. We are positioned for successful collaboration and delivery of great innovation in years ahead. We couldn’t have asked for much more than this.

THE EBI AT 1 YEAR OLD—A BP PERSPECTIVE

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03 c h a p t e r

ENTER BP

About 87 percent of human energy use is presently obtained by combustion of fossil fuels. This dependence on fossil fuel has increased the amount of carbon dioxide in the atmosphere by about one-third since the preindustrial era. It is now apparent that continued dependence on fossil fuels is causing climate change, and that the consequences are both uncertain and unwelcome. If global climate models are correct, temperatures will increase and rainfall patterns will change with devastating effects on food production in many areas of the world along with the potential for attendant societal disruptions. Also, many of the world’s ecologically sensitive areas may be unable to support the species that currently define the ecological character of the region and may be lost along with potentially devastating effects of biodiversity. These are the changes forecast by the most recent Scientific Assessment of the Intergovernmental Panel on Climate Change (IPCC). The realization that the polar ice caps are currently melting at a faster rate than forecast by this assessment underlines the urgency of addressing net carbon emissions.

THE ENERGY BIOSCIENCES INSTITUTE Empowering outstanding academic researchers to envision and enable new approaches to the production of energy

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The multinational company BP was the first major energy corporation to publicly recognize that continued burning of fossil fuels was problematic. In 1998 in a speech at Stanford, BP Chief Executive Officer John Browne committed the company to comply internally with the Kyoto Protocol. “It would be unwise and potentially dangerous to ignore the mounting concern” about climate change, said Browne. As a result, BP created a renewable energy division that has grown to become one of the largest photovoltaic and wind energy producers in the world. More recently, Browne’s successor, Tony Hayward, has called for the implementation of a cap-and-trade system in which emissions of greenhouse gases are monetized so that the environmental costs and benefits of various energy options can be factored into the cost of energy. In 2006, as part of its overall strategy for developing renewable energy sources, BP issued an international call for proposals to engage in a 10-year, $500 million research partnership to explore the application of scientific advances in basic biological sciences to the energy sector. This bold concept was based on the recognition that our understanding of biology is undergoing a revolution in which major discoveries are being made on a daily basis. This is supported by a series of technical and conceptual advances in subjects such as genomics, computational biology, synthetic biology and analytical chemistry that have become the major tools of discovery in many areas, especially in the medical sciences. By contrast, the area of “energy biosciences” is relatively unexplored and underinvested compared with the vast investment that has been made in healthrelated aspects of the biosciences. In 2007, following an international competition involving about 20 major research universities, BP selected a consortium consisting of the University of California at Berkeley, Lawrence Berkeley National

Laboratory and the University of Illinois at Urbana-Champaign to host the new Energy Biosciences Institute (EBI), and a new era of groundbreaking public-private partnerships was launched. Following a period of contractual negotiations, the EBI began operations in November 2007.

AN INSTITUTE OF COLLABORATIONS An overriding goal of the EBI is to develop an integrated holistic understanding of the research topics related to energy biosciences. The motivation for this arises from the recognition that topics of interest such as cellulosic biofuels are unusually complex and involve research questions in subjects that include agronomy, microbiology, mechanical and chemical engineering, biochemistry, chemistry, geography, economics, law and policy analysis. Because advances in one area may have important impacts in other areas, the EBI’s goal is to create dynamic intellectual bridges between the various disciplines so that information and insights flow efficiently, and new research initiatives can be adopted based on a “big picture” view of the overall topic. To this end, the EBI is working toward placing the full-time researchers that it supports into a common space on each campus. This is facilitating horizontal integration of disciplines, which range from genomics and agronomy to environmental sciences and economics. This multidisciplinary approach will facilitate discovery and will ultimately enable optimal decision-making by the sectors in society that are responsible for implementing trade and regulatory policies and business activities. In this respect, the close association within the EBI of academics from the partner institutions and industrial managers, engineers and scientists from BP offers a rare opportunity to accelerate the feed-forward and feedback processes that are associated with conversion of academic discovery into real-world applications.

ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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The Areas of Study The primary initial thrust of EBI research is an exploration of the feasibility of commercially viable, sustainable and environmentally benign transportation fuels from biomass. The most promising opportunities are currently thought to be cellulosic biofuels, but the EBI is also supporting a study on the feasibility of algal biofuels. The development of cellulosic fuels involves identifying the most suitable species of plants for use as energy crops; improving methods of breeding, propagation, planting, harvesting, storage and processing; and ensuring that this is done in a sustainable way without negative impacts on food production or the environment. Production of biofuels also involves the development of biomass-to-liquid fuels technologies that yield major benefits in regard to both net energy output and net greenhouse gas balance based on consideration of all inputs. To accomplish this, research is divided into several areas of inquiry:

Societal and Economic Impacts of Biofuels A major goal of the EBI is to understand the potential environmental, economic, and societal impacts of meeting a growing portion of the world’s energy needs through cellulosic or algal biofuels. Many in the world are concerned that the demand for energy is so large that unrestrained conversion of land to biofuel production could have negative environmental effects and could further disadvantage many poor people by increasing prices for food, feed, and fiber. Therefore, the EBI is working to understand how land is used around the world and to model the impacts of growing bioenergy crops on land that is not used for food production or is providing key ecosystem services, such as carbon storage or biodiversity. EBI investigators are also testing the environmental impacts of various bioenergy crops and developing economic models that may help to understand the feasibility of bioenergy crop production around the world. An important aspect of understanding the environmental effects of cellulosic biofuels will include development of complete life cycle models that incorporate both direct and indirect effects of the biofuels.

Feedstock: Agronomy, Engineering, and the Environment Work in this area seeks to identify and characterize plant species that can maximize cellulosic biomass production in various regions around the world, and to learn how to grow and harvest them sustainably. A primary goal is to discover plants that maximize the production of cellulosic biomass, using minimal land, water, and energy. Because of the importance of soil carbon in the global greenhouse gas balance, the EBI is particularly interested in identifying species that can be grown on the large amounts of minimally productive land around the world. These considerations favor the use of perennial grasses and certain woody species. However, the possible utility of algal species is also being explored.

Bioconversion: Attacking Cellulosic Degradation on Several Fronts

environments where biomass degradation takes place. In parallel, it is also exploring the development of new synthetic catalysts that can accelerate the degradation of polysaccharides and lignin.

An overriding goal of the EBI is to develop an integrated holistic understanding of the research topics related to energy biosciences.

Biofuels Production: Transforming Feedstock to Fuel with Microbes In order to convert sugars to liquid fuels, the proportion of oxygen must be reduced. This can be accomplished by bioconversion, such as fermentation, or by chemical transformations. With no clear front-runner at the present time, the EBI is exploring several methods in parallel. Methods used for production of biofuels today are similar to the fermentation practices used to make beer and wine, but these traditional methods are not optimized for the large-scale, energy-efficient production of cellulosic biofuels. EBI researchers are exploring ways of improving bioconversion of sugars to next-generation fuels by using the methods of systems biology to characterize new types of microbes and by testing genetic modifications of promising organisms. They are particularly interested in exploring ways of producing biofuels that will not require major changes in the transportation infrastructure. This involves researching chemical and fermentation routes to products more hydrophobic than ethanol and butanol. The EBI is also interested in exploring alternatives to bioconversion technologies, such as the use of non-biological catalysts to transform biologically derived chemicals into fuels.

Microbiology of Fossil Fuel Reserves During the past several decades, it has become apparent that significant populations of microorganisms are found in both coal and petroleum reservoirs deep underground. These microbial populations can contribute to the properties of the reservoirs in deleterious ways, such as through catalyzing the souring of petroleum, but they may also contribute positively by activities such as altering the porosity of the reservoirs. This could allow more efficient recovery of oil. In order to understand the effects of these microbial populations, the EBI intends to support studies into characterization of the organisms found in various reservoirs using the tools of modern biology, such as high-throughput DNA sequencing and analysis. By understanding the genomics of the reservoir microbes, it may be possible to infer how their activities can be better controlled toward useful purposes. The collaboration with BP provides a rare opportunity for academic scientists to access deep-earth samples from reservoirs that have been geologically characterized.

The main constituents of the body of higher plants are polysaccharides and lignin. Fashioning fuel from plants requires conversion of the polysaccharides to sugars by severing the chemical bond that holds them together, among the most critical and difficult steps in the process. Today’s practices are costly and inefficient. EBI scientists are investigating nature’s methods of releasing these sugars to achieve an effective and less costly method of breaking down these substances. This will be key to ensuring that biofuels can be reasonably priced. The EBI is examining the processes that take place in cow rumen, termites, compost heaps, and other

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ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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PROGRAMS AND PROJECTS The EBI is a mission-oriented research organization. One approach to realizing the EBI mission is to develop a consortium of comprehensive expertise and research activities concerning energy biosciences within the partner organizations. To achieve adequate breadth of scope, research funds are allocated to various topics based on predefined targets. Workshops are scheduled throughout the year to share data and to help define key questions to be answered. Topical proposals that address problems defined by the EBI are solicited from faculty and scientists in the partner institutions. Thus, the EBI mandate defines the problem, but the EBI investigators propose the research approaches to solutions. A peer-review process narrows proposals drawn from solicitations to a focused set of projects and programs for funding. During the startup phase of the EBI in the summer of 2007, a very broad solicitation was announced. From an initial list of more than 250 pre-proposals from researchers at the three partner institutions, EBI management and advisors requested 85 full research proposals and, following external peer review, narrowed the field to 50 high-priority research efforts that received the first round of funding. A second solicitation in the summer of 2008 was more narrowly focused. Awards are divided into two categories: programs and projects. Programs are typically large integrated multi-investigator efforts with broad goals, funded at anywhere from about $400,000 per year up to about $1 million per year, and may continue for the 10-year life of the institute. Projects are smaller activities of 2-3 years in duration that are usually narrower in scope. These average about $150,000 per year. Program research is conducted mostly within EBI space so that postdoctoral, support, and graduate student researchers from different disciplines will work side-by-side, and so that space constraints will not limit the ability of EBI investigators to participate in the EBI mission. This will facilitate synergy across fields and will provide a training environment and a broad appreciation of the scientific, technological, environmental, economic, and policy issues that must all be addressed to achieve the Institute’s goal of environmentally sustainable bioenergy.

THE RESEARCH ENTERPRISE— PUBLIC AND PRIVATE Openness of the research enterprise—and the academic freedom of its faculty, graduate students, and university researchers—is paramount for the three public institutions in the EBI. Inventions made during the course of research within the EBI are owned by the academic institutions according to U.S. patent law, and BP receives an automatic non-exclusive license in return for funding the research. All four partners have representation in the EBI’s two management panels, with none having a majority or veto power on the governing board, ensuring consensus in all decisions. The Executive Committee, which provides scientific direction and operational oversight, is mostly composed of professors from the academic partners. The Licensing Executives Society, a professional organization for intellectual property specialists, chose the EBI for its 2008 “Deal of Distinction” award for being “an innovative model for collaboration between academia, government labs, and industry.” Collaborative research between universities and industry yields new ideas and more effective pathways for moving discoveries from the laboratory into com-

The close association within the EBI of university academics and industrial managers from BP offers a rare opportunity to accelerate the processes that are associated with conversion of academic discovery into real-world applications. mercial use. These collaborations also help prepare students for non-academic careers and address the need for real-world evaluation and implementation of solutions science. In the EBI, intellectual resources of leading research institutions are being brought to bear on the quest for sustainable, affordable, renewable energy. The expertise of an international corporation is being employed to ensure that commercialization and application can happen as rapidly as the discoveries allow.

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ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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The Partners It is an enticing formula—take the technical and intellectual strengths of three internationally known public research institutions, add the successful commercial legacy of one of the world’s leading energy companies, and blend together in a unique partnership in which collaborations are forged and innovation is maximized. The sum is greater than all of these impressive parts.

BP

The University of California, Berkeley

BP, one of the world’s largest energy companies, is the leading producer of oil and natural gas in the United States, and the largest investor in U.S. energy development. BP provides its customers with fuel for transportation and energy for heat and light, employing more than 100,000 people worldwide and more than 35,000 in the U.S. BP was the first major energy company to acknowledge the need for precautionary action to reduce greenhouse gas emissions, and today it continues to lead the effort to meet the world’s growing demand for sustainable, environmentally responsible energy.

Founded in 1868, the University of California, Berkeley, is the nation’s top-ranked public university and the flagship of the 10-campus University of California system. It enrolls over 24,000 undergraduates, distributed among 80 degree programs, and more than 10,000 graduate students each year. The campus not only produces more PhDs than any other university in the country, but a greater number of its graduates go on to earn a PhD at Berkeley or elsewhere than do graduates of any other institution. The university is distinguished by its research programs, which were funded in fiscal year 2006 by $469 million in contract and grant awards from outside sponsors. Berkeley faculty and researchers have won 20 Nobel Prizes, 6 Pulitzer Prizes, 30 National Medals of Science and 29 MacArthur “genius” Awards. Of its academic staff, more than 130 are current members of the National Academy of Sciences, and 85 belong to the National Academy of Engineering.

The University of Illinois at Urbana-Champaign The University of Illinois at Urbana-Champaign is a world-class public university whose faculty, student, and alumni honors have brought international distinction. Home of the largest public university library collection in the world, Illinois is also a leader in supercomputing design and application and boasts multi-disciplinary research excellence in dozens of fields. The University has a pioneering history of sustainability research as the originator of no-till agriculture, and is home to the longest running investigation of the impacts of varied crop management methods on soil quality (1876, Morrow plots) outside of Europe. Founded in 1867, Illinois enrolls over 29,000 undergraduates in more than 150 fields of study, and over 11,000 graduate and professional students in over 100 programs. It is among the top five universities in the United States in the number of annual doctorates awarded. Among its array of faculty honors, the U of I is one of only 11 campuses worldwide to have been awarded two separate Nobel Prizes in one year (2003).

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UC Berkeley

Lawrence Berkeley National Laboratory Lawrence Berkeley National Laboratory (Berkeley Lab) has been a leader in science and engineering research for more than 75 years. Located on a 200-acre site in the hills above UC Berkeley’s campus, the Lab is the oldest of the U.S. Department of Energy’s national laboratories. Managed by the University of California, it operates with an annual budget of more than $550 million and a staff of about 3,800 employees, including more than 500 students and 250 principal investigators with joint appointments at UC Berkeley. It employs a “team” concept to its research, as developed by founder Ernest Orlando Lawrence, and boasts a legacy that has yielded rich dividends in basic knowledge and applied technology, and a profusion of awards. Berkeley Lab conducts unclassified research across a wide range of scientific disciplines, with key efforts in fundamental studies of the universe, quantitative biology, nanoscience, new energy systems and environmental solutions, and the use of integrated computing as a tool for discovery. Its unique user facilities include the Advanced Light Source, the Molecular Foundry, the National Center for Electron Microscopy, and the Joint Genome Institute.

Berkeley Lab

University of Illinois ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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The Facilities From the hills of Berkeley to the farm fields of Illinois, EBI research spans the nation— and the world.

Research in the Energy Biosciences Institute is being conducted at two primary locations—in California, at the historic Calvin Laboratory and the nearby Hildebrand Hall chemistry building at UC Berkeley; and at the new Institute for Genomic Biology building in the heart of the University of Illinois campus. A 320-acre Energy Farm, the largest of its type (just south of the Illinois campus), includes land for demonstrations, large-scale production, plant breeding and storage. In 2008, 120 acres of this farm were planted, and another 160 are slated for development in the near future. The Berkeley center includes dedicated biotechnology laboratories and specialized facilities for high-throughput chemical synthesis and assays of many types. The Illinois program is housed in a building specifically designed for integrated research and development efforts, with a complete suite of microscopy, imaging, plant growth, microfabrication, and bioanalysis facilities and tools. In addition, individual researchers have access to the offices, technical laboratories and user facilities of their home campuses. In 2013, the EBI is planning to move its permanent headquarters into a 144,000square-foot facility dedicated to renewable energy research to be built on UC Berkeley land adjacent to Berkeley Lab. The “Helios” building, as it will be called, will have office and laboratory space for 150 co-located institute staff, including the EBI investigators, BP scientists, and laboratory personnel. The building will have space and amenities that will promote a collegial and collaborative research environment, including meeting and seminar rooms, lounges, and a café.

Architect's design of proposed Helios Energy Research Facility in Berkeley, future home of the EBI

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EBI Leadership Governance and leadership are critical components of the EBI agreement. Completed in 2007, the EBI contract combines the resources of the partner institutions into an agreement that provides BP a non-exclusive, royalty-free license to an invention. The EBI operates as one of several research centers within the partner institutions. The faculty and students that design and carry out the research activities of the EBI have appointments and academic responsibilities within the various academic departments of the partners. The EBI administers the financial and material resources and facilities supported by funding from BP. The EBI is managed on a day-to-day basis by a Director and a small team of colleagues and advisors from the four partners (the Executive Committee). This administrative team implements processes for deciding what research opportunities to fund, for providing or facilitating research and administrative support to EBI investigators, and for facilitating communications within the EBI and between EBI investigators and various stakeholders and interested parties around the world. The Governance Board has the responsibility to define, oversee and review the implementation of EBI programs in the open component of research. It also appoints the EBI Director and Deputy Director. The Board has eight voting members, four from the research partners—at least one each from the Berkeley and Illinois campuses and one from Berkeley Lab—and four appointed by BP. The EBI Director, Associate Director, and Deputy Director are ex-officio members.

The EBI Director, Chris Somerville, manages the conduct of research projects and EBI’s public communications, education, and outreach activities. He works with the Executive Committee to develop an annual program plan with goals and milestones, and he prepares the annual budget request. The EBI’s Deputy Director, Steve Long, manages research conducted at the Illinois EBI site and its integration into the Institute as a whole. The Associate Director, Paul Willems, is the BP representative on the EBI management team. He also leads the team of BP employees who are located at the EBI. The Executive Committee is the EBI’s program management body, with Director Somerville as chair. He, the deputy and associate directors, and five other professors from the partner institutions (currently Adam Arkin, Dan Kammen, David Zilberman, Evan DeLucia, Michael Marletta) comprise the committee membership. This panel proposes the annual strategic work plan, including priority research projects for institute funding, for approval by the Governance Board.

ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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The Directors EBI Administrators and Managers

Chris Somerville, Director

Assistant Director Susan Jenkins manages the administrative team for the EBI at Berkeley and oversees all aspects of implementing the activities sponsored by the institute. Before joining the EBI, she was the assistant chair of the Department of Plant and Microbial Biology at UC Berkeley. Deputy Assistant Director Jenny Kokini manages the implementation of all EBI activities at the University of Illinois. She moved to the EBI from Princeton University, where she was the departmental business administrator for Mechanical and Aerospace Engineering. Professor Brad Moore, an emeritus professor of chemistry, is the manager for Strategic Planning. He has extensive experience in academic administration, including most recently serving as the vice president for research at Northwestern University. Mitch Altschuler manages processes related to Intellectual Property. He was formerly a professor of biology at Northern Illinois University and has also worked in the technology transfer offices of the University of Minnesota and Cargill, Inc. Computing systems and networking specialist Adam Cohen moved from the UC Berkeley web applications team to become Information Technologies manager. Ron Kolb is the communications manager. Before joining the EBI, he was communications director for Lawrence Berkeley National Laboratory. Melissa Edwards is his counterpart at the University of Illinois. Deputy Operations Director Tim Mies manages the

Somerville is a professor in the Department of Plant and Microbial Biology at UC Berkeley and a faculty scientist at the Lawrence Berkeley National Laboratory. His research focuses on the characterization of proteins implicated in plant cell wall synthesis and modification. He has published more than 200 scientific papers in plant and microbial genetics, genomics, biochemistry and biotechnology. Somerville has served on the scientific advisory boards of many corporations, academic institutions and private foundations in Europe and North America. He is a member of the U.S. National Academy of Sciences, the Royal Society of London and the Royal Society of Canada.

Stephen Long, Deputy Director Long is the Robert Emerson Professor of Plant Biology and Crop Sciences at the University of Illinois. He is a researcher with the U of I’s Institute for Genomic Biology and a resident scientist with the National Center for Supercomputing Applications. Much of Long’s research focuses on the effects of atmospheric change on vegetation and ecosystems and on how certain perennial crops might be used as biomass energy sources. He was a contributing author and referee to the Intergovernmental Panel on Climate Change, and he has served on committees worldwide that research global climate change. He has been named one of the 250 most cited authors in animal and plant biology and one of the 25 most cited authors on global climate change. Long is a Fellow of the American Association for the Advancement of Science.

Paul Willems, Associate Director As Technology Vice President for Energy Biosciences in BP, Willems is responsible for integrating biotechnology into BP’s business activity. His duties include leading the development and execution of an integrated technology strategy which incorporates all of BP’s biorelated activity and which is fully integrated with BP’s company-wide business strategies. He has held a variety of technical, manufacturing and commercial leadership roles throughout his 20-year career, including business technology manager for BP’s global PTA (purified terephthalic acid, a polyester raw material) business, and technology vice president for acetyls and aromatics. Willems earned his PhD in Chemical Engineering from the University of Ghent in Belgium.

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From left, Willems, Somerville, and Long

construction, engineering, and operation of the Energy Farm at Illinois. He previously constructed and managed SoyFACE, the largest open-air facility for investigating the effects of global atmospheric change on crops, and before that he ran the University of Maryland’s controlled environment plant growth facility. Safety and building manager Zack Phillips was a radiation safety officer at UC Berkeley before joining the EBI’s Berkeley staff. He is paralleled at Illinois by Safety Officer John Pingel, who coordinates safety training and implementation for the farm and laboratory. He previously coordinated safety at the U of I’s chemistry labs, is a primary author of the “Science Safety Handbook for Illinois Schools,” and is principal lecturer in the Illinois “Fundamentals of Laboratory Safety” class. Stefan Bauer manages the Analytical Services group at the EBI. Before joining the Institute, he was the head of analytical chemistry at Fresenius. Mara Bryant and Rachel Knepp are laboratory managers for the EBI at Berkeley and Illinois, respectively. Bryant recently completed postdoctoral studies in biology at Michigan State University, and Knepp completed an MS in global change impacts on forests and was a USDA laboratory manager before joining the EBI. Anne Krysiak and Trisha Togonon at Berkeley and Becky Heid and Connie Wilder at Illinois provide a wide range of EBI administrative services and assist investigators in interactions with other service providers within the host institutions.

ABOUT THE ENERGY BIOSCIENCES INSTITUTE

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04 c h a p t e r

Understanding the complex issues surrounding biofuels—truly grounding the EBI in the challenges that surround the industry—is the key to ensuring a successful research agenda. To do so, the Institute must address the debate over food vs. fuel, concerns over land use and the environment, the challenges of producing high-quality liquid fuels from plant materials, and the multiple other issues that surround cellulosic biofuels.

An Introduction to Biofuels

Seeking an Understanding, from Field to Fuel Tank

First, the EBI is investigating how much land can be used sustainably for cellulosic fuel production around the world without negatively impacting food production or the environment. Because many aspects of human economic activity are internationalized, it is important to understand the issues on a global scale to avoid displacement effects. Second, investigations are probing which types of plants can be used for energy, how they can be grown sustainably with minimal inputs, and how they can be harvested, stored, and transported to the point of utilization. This type of research involves aligning models of the properties of different types of plants with information from global geographic information systems. Third, the EBI is exploring new ways of converting cellulosic biomass to liquid fuels. This involves a broad investigation of how various types of organisms, ranging from those found in compost heaps to the complex systems in termite guts and cow rumen, degrade biomass. Work is also proceeding on new chemical catalysts that can convert the components of biomass to novel fuels. The rationale for this portfolio of research topics is summarized in the following review, which is based upon an article by EBI Director Chris Somerville published in the journal Current Biology (17[4]R2).

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AN INTRODUCTION TO BIOFUELS

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CORN AND CANE ETHANOL At present, most biofuel is produced from cornstarch and from sugar extracted from sugarcane using relatively mature technology and established production practices. Research within the EBI is generally not concerned with these sources of fuels but is directed toward next-generation opportunities based on using the lignocellulose that comprises the body of plants. But an understanding of the processes involved in current biofuel production is important if improvement is to be achieved in the second generation.

...it would be possible to produce about half of all transportation fuels by growing a plant like Miscanthus on about 1 percent of the terrestrial surface area. WHY BIOFUELS? The global energy market provides humans with about 370 exajoules of energy per year, which is equivalent to the energy content of about 170 million barrels of oil per day. Approximately 87 percent of energy purchased globally comes from fossil fuels. Although humans may eventually deplete reserves of fossil fuels, that moment is quite far off. In addition to substantial remaining reserves of oil and gas, abundant coal deposits are projected to be adequate to meet human energy needs for several hundred years. Coal can be converted into a wide variety of liquid fuels that can substitute for petroleum. Thus, if concerns about greenhouse gas-induced climate change and energy are ignored, there is not a pressing need to develop biofuels.

Sugarcane (Saccharum sp.) is a highly productive tropical grass that accumulates sucrose in the stem tissues. The stalks are crushed to produce a sucrose solution that can be fermented to produce a dilute ethanol solution. The crushed stalks or “bagasse” that comprise the body of the plants are currently burned to produce heat that is used to distill the ethanol from the fermentation broth and to produce excess electricity. It is possible that, with the development of efficient technologies for conversion of lignocellulose to fuels, a large proportion of the sugarcane bagasse will also be used to produce liquid fuels in the future.

The linkage between climate change and biofuels arises from the fact that some types of biofuels can be substantially less carbon-intensive sources of energy than fossil fuels. Energy from sunlight is collected by the photosynthetic system of plants and used to reduce and condense atmospheric CO2 into the chemicals that comprise the body of plants. When plants are burned, the energy is released as heat that can be used for work, such as generating electricity, and the CO2 is recycled. With highly productive plants such as Miscanthus giganteus growing on good soils with adequate rainfall and favorable mean temperature, such as is found in central Illinois, more than 1 percent of annual incident solar insolation (exposure to sunlight) is retained as chemical energy in biomass. If one uses a value for total solar insolation of 120,000 TW (terawatts), 1 percent solar conversion efficiency, and an energy recovery value of 50 percent, it would be possible to produce about half of all transportation fuels by growing a plant like Miscanthus on about 1 percent of the terrestrial surface area.

In Brazil, where land suitable for growing sugarcane is abundant, about 4.2 billion gallons of cane ethanol was produced in 2005 on less than four million hectares (a hectare is 2.47 acres) of land. Ethanol now comprises about 40 percent of all liquid transportation fuel used in Brazil. The automobile fleet is largely composed of “flex-fuel” vehicles that can utilize widely varying ratios of ethanol and gasoline. By contrast, only about 2 percent of the fleet in the United States is flex-fuel vehicles; the remainder cannot use alcohol/ gasoline mixtures containing more than 10 percent ethanol without mechanical modifications.

...an understanding of the processes involved in current biofuel production is important if improvement is to be achieved in the second generation.

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Corn (Zea mays) is the largest U.S. crop with about 81 million acres planted in 2005, yielding about 11.1 billion bushels of corn seed. Approximately 60 percent of the mass of corn seed is starch. The starch is released by grinding the seed in either a dry or wet process, cooked to gelatinize the starch, hydrolyzed with enzymes to glucose, and fermented. Following fermentation and separation of ethanol by distillation, the residual slurry of insoluble fiber, protein, and lipid, called “distiller dry grains with solubles” (DDGS), is used as animal food. The U.S. is expected to produce about eight billion gallons of ethanol from about 21 percent of the corn crop in 2008.

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The technology required for cane sugar or cornstarch ethanol production is mature, and most of the technical issues concern improvements in engineering related to the efficient use of heat and water. However, unlike cane ethanol, which has an energy output-input ratio of about 8-to-1, calculations of the life cycle costs of making corn ethanol have stirred substantial scientific debate. These calculations typically include things such as the energy costs of producing and distributing fertilizer, of planting and harvesting, of making the farm machinery and the factories that process the grain, in addition to the costs of converting grain to ethanol. The results have been controversial because of the uncertain assumptions about variables, such as heat reuse.

BIODIESEL A wide variety of chemicals or mixtures of chemicals, including biologically produced fatty acids or lipids, undergo combustion in conventional diesel engines. The methyl or ethyl esters of biologically derived fatty acids are capable of being mixed with petroleum-based diesel fuel. These esters can be produced from biological lipids or fatty acids by very simple reactions. Thus, establishing a commercial biodiesel

than 1,500 gallons of cellulosic ethanol. Additionally, vegetable oils are a quantitatively important component of human diets and, therefore, relatively small disruptions in supply result in large increases in price because of inelasticity of food demand. The U.S. Congressional Research Service conducted a study that concluded if every ounce of plant and animal lipid produced in the United States was used for biodiesel production, the total

significant energy inputs for production. In addition, mature plantations reportedly produce up to ten metric tons per hectare per year of cellulosic biomass (e.g., senescent fronds) that can also be used for fuel production. Thus oil palm acreage has continued to expand due to increasing demand for edible oil and for projected use in biodiesel. However, the expansion of palm production is generally considered undesirable from an environmental

"Cellulosic biofuels will have the greatest environmental benefits if produced on land that has been farmed in the past but is A recent analysis of all such calculations concluded no longer used for food production." that corn ethanol provides about 25 percent more energy than is consumed in producing it if the process heat is provided by natural gas or coal (versus burning the cobs and stalks). Because of the low net energy ratio, corn ethanol is generally not considered an attractive long-term solution to meeting energy needs in an environmentally sustainable way.

One development that may change this is carbon sequestration. In fermenting sugars to fuels, about 33 percent of the carbon is released as pure CO2. Like a number of other locations around the world, a large area of the Midwest is underlain by deep saline aquifers into which very large volumes of CO2 may be dissolved. The aquifer is below shale and oil deposits that provide additional seals against any release of “buried” CO2, which is why Illinois was chosen for the “Futurgen” clean coal plant. The U of I, together with Archer Daniels Midland and the Department of Energy, is now operating a pilot burial of the CO2 produced from fermentation in making corn ethanol. Life cycle analyses suggest manufacture of cellulosic ethanol from low perennial grasses could achieve input:output energy and carbon ratios of 1:5. Coupled with CO2 burial, this raises the exciting possibility of being able to achieve a carbon-negative biofuel. There are also concerns that use of cropland for biofuels, whether corn or perennial grasses, will indirectly cause encroachment of agricultural production onto ecologically sensitive land. A major effort of the Institute seeks to identify opportunities to grow a range of perennial feedstock on abandoned agricultural and non-crop lands to avoid such effects.

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~ CHRIS SOMERVILLE

production facility is inexpensive and technically simple. The U.S. currently has a number of small biodiesel production facilities, many of which include used cooking oils from restaurants as feedstock. This is an environmentally and economically attractive use of a material that would otherwise be a waste disposal problem. However, domestic biodiesel will not become more than a niche component of the liquid fuel supply, because the amount of lipid produced per acre of crop is small relative to the total amount of biomass. Thus, for instance, the average soybean crop yields only about 63 gallons of biodiesel per acre. Contrast this with the much higher yields of cellulosic biomass that could be grown on the same acres—estimated at more

amount would be about four billion gallons. When compared with the roughly 200 billion gallons of liquid fuels used in the U.S. each year, domestic biodiesel derived from seeds and fruit is not likely to be a significant contributor to transportation fuels in the developed world, nor an effective use of land. In contrast to annual oilseeds, several tropical plants are used to produce relatively large amounts of lipids in tropical countries. Oil palm (Elaeis sp.), which grows in high rainfall zones within 15 degrees of the equator, produces clusters of oil-rich fruits that are similar to small avocados. Yields of up to seven metric tons of oil per hectare per year have been recorded, although the average is lower. The plants have very long life cycles and do not require

perspective, because the expansion is associated with clearing of tropical forests that are some of the richest reservoirs of biodiversity. Additionally, clearing of tropical forests causes large emissions of greenhouse gases from both soil emissions and from the burning of the biomass, resulting in negative greenhouse gas balances for biofuel production. Recent interest has been shown in a drought-tolerant bush, Jatropha curcus, which reportedly yields up to several metric tons of oil per hectare per year with little or no input. This plant may allow production of oil on land that is too drought-prone for food crop production, and acreage has been expanding rapidly in Africa, India, and Southeast Asia.

CELLULOSIC ETHANOL All higher plant cells are enclosed in cell walls composed primarily of polysaccharides (polymers of sugar) and lignin (polymer of phenolics) that, in many plant species, comprise more than 90 percent of the dry body mass. The principal cell wall polysaccharide is cellulose, a fibrous material composed of hydrogenbonded chains of the sugar glucose. Cellulose is coated with another class of polysaccharides called hemicellulose, the most abundant of which is xylan, a polymer of xylose that may, depending on the plant species, have branches containing other sugars such as arabinose or glucuronic acid. The principal sugars in most tissues that are useful for biofuels are glucose and xylose, but many other sugars are also present in significant amounts. Cell walls from vascular tissues usually also contain lignin, a complex polymer. These structural polysaccharides are less readily hydrolyzed to sugars than storage polysaccharides such as starch. Acids are being used to obtain sugars from celluloses, but this is inefficient. Efficient hydrolysis occurs in nature, for example by bacteria and fungi in the digestive systems of animals, such as ruminants and termites, who derive their energy from the sugars released from cellulose and hemicellulose. Replicating this in industrial processing facilities would then provide sugars that can be converted to ethanol or other fuels by fermentation in much the same way as cornstarch. However, because the whole plant can be used, the yield of sugar per unit of land per year is much higher than can be obtained using only corn grain. No large-scale cellulosic ethanol facilities are yet in commercial production, although several companies have small-scale test production facilities. A typical pilot-scale process involves treatment of pulverized biomass with hot acid, which partially hydrolyzes hemicellulose and other polysaccharides and disrupts the association of lignin with the polysaccharides. The hydrolysate is neutralized, separated from the insolubles, and fermented to produce ethanol. The insoluble fraction is then treated with cellulase and glycosidases to release glucose, which is also fermented to produce ethanol. The residual insoluble material, mostly lignin, could then be burned to generate energy for the overall process. The fermentation process produces a nutrient-rich microbial cell mass that can be deactivated and used as fertilizer to recycle the mineral nutrients to the land.

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Many components of the cellulosic ethanol bioconversion process are not yet optimized for commercial production. For instance, the strains of yeast that are used for industrial fermentations do not normally utilize sugars other than glucose. Strains of yeast (Saccharomyces cerevisiae) and Eschericia coli have been engineered to ferment xylose to ethanol, but additional work needs to be done to adapt such lines to industrial conditions, to optimize metabolic control of the pathways, and to enable fermentation of other sugars. Another problem is that large amounts of cellulase are required to hydrolyze cellulose. Process improvements during the past decade have reduced the cost of cellulase per gallon of ethanol from about $5 to about 50 cents but that is still considered too expensive compared to other enzyme-based processes. There is widespread interest in finding enzymes with higher activity than current cellulases by surveying the properties of enzymes from poorly explored sources such as termite guts, rumen, compost heaps, and tropical forests. Alternatively, it may be possible to improve the activity of industrial cellulases by protein engineering. It is also important to understand the structure and function of cellulosomes, extracellular enzyme complexes that catalyze hydrolysis of cellulose and other polysaccharides. Industrial ethanol production has used yeasts that ferment glucose. To make use of the sugars derived from hemicelluloses, yeasts and other organisms are being engineered to use these sugars as well as glucose. The holy grail of cellulosic ethanol production is to incorporate improvements in both cellulases and fermentation into a single organism that would secrete all of the necessary enzymes and utilize all of the available sugars in a process referred to as “integrated bioprocessing.”

organisms, by altering the chemical composition of the biomass, or by process improvements. The development of a biofuel industry is only feasible in regions where land and water resources are available to support the growth of plant biomass that is excess to other needs. The Departments of Energy and Agriculture conducted a study of biomass availability and concluded that approximately 1.3 billion dry metric tons of excess cellulosic biomass is available each year in the U.S. This includes half the corn stover (the leaves and stalks of the corn plant) and wheat straw, and about 40 million acres of set-aside land to grow perennial grasses such as switchgrass and Miscanthus. At a conversion value of about 100 gallons of ethanol per ton of lignocellulosic biomass, this would be equivalent to about 130 billion gallons of ethanol, or about 40 percent of U.S. liquid fuel consumption on an energy-equivalent basis. Based upon the proportion of transportation fuel already produced by Brazil, it seems likely that South America could meet all its needs for transportation fuels with biofuels. A recent analysis of the 15 countries in the European Union concluded that Europe could produce approximately 11.7 exajoules (units of energy) per year of biofuels, an amount similar to the U.S. goal of 30 percent of transportation fuels (11.6 exajoules).

A recent study by ecologists at Stanford concluded that about a billion acres of land around the world that was farmed in the past has been abandoned. It seems likely that much of this land could be used for production of energy crops without impacts on food production and without incurring production of greenhouse gases from land conversion. Although cellulosic fuels will Many other problems may have multiple solutions, but not completely meet global needs for transportation fuels anytime soon, they are expected to become a relatively little progress has been made. For instance, significant component worldwide. The widespread many plant polysaccharides, during biomass hydrolyimplementation of trading in carbon credits could sis, release acetic acid that inhibits the growth of the fermentative organisms. Similarly, furfural, an organic accelerate progress toward that goal and could encourage best practices in terms of land management and liquid compound produced by a side reaction during fuel production. acid-catalyzed polysaccharide hydrolysis, inhibits microbial growth. In principle, these and related problems may be overcome by developing resistant

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OTHER BIOFUELS

No miracles are required to develop cost-effective cellulosic biofuels; however, implementing rational improvements in the overall process is challenging.

Ethanol is not an ideal fuel in several respects and may not be the major biofuel in 20 years. The main problem is its ability to mix with water, which imposes an energy cost for distillation, creates problems in transporting the fuel via pipelines, and leads to poisoning of the microorganisms that produce it. Thus there is interest in developing biofuels that are more hydrophobic and spontaneously partition out of the aqueous phase. For instance, butanol dehydrates spontaneously at about 9 percent solution, has very low vapor pressure, and has a latent heat similar to octane so that fuel-air mixing at low temperature is not a problem. When added to ethanol-gasoline mixtures, small amounts of butanol depress the vapor pressure, reducing the hazards of explosions during fuel handling. Unfortunately, butanol is toxic to organisms that produce it at concentrations very much lower than 9 percent solution. Several companies have recently announced plans to produce butanol by fermentation of sugars from biomass. Some microorganisms have been reported to secrete alkanes, which do not mix with water. Plants and other organisms have a wide array of lipid synthetic pathways, raising the opportunity for engineering these pathways into bacteria or yeasts. It seems likely that additional types of biofuels with physical properties similar to those in current use will be developed. Although much of the current research on cellulosic fuels is focused on bioconversion technologies, other approaches are being explored within the EBI. In particular, it is possible to convert biomass to liquid fuels by direct chemical conversions using either gasification followed by re-forming of the gaseous products to fuels, or by chemically catalyzed conversion of biomass to fuels. Because the mandate of the EBI is to explore biological technologies, it is not pursuing research based on gasification technologies. However, a number of EBI research groups are exploring the development of new catalysts for hydrolysis of biomass to soluble molecules and conversion of such molecules to liquid fuels.

COORDINATION, INTEGRATION The major opportunity to expand the use of biofuels will be found in improving the various components of cellulosic biofuels production. No miracles are required to develop cost-effective cellulosic biofuels; a series of two-fold improvements in the efficiency of various steps could make biofuels less expensive than liquid fossil fuels. However, implementing rational improvements in the overall process is challenging. Managing the various components will have to be coordinated, integrating knowledge from many scientific and engineering disciplines. Integration is encouraged through the placement of researchers from different disciplines in shared space. This is what the EBI was established to do.

AN INTRODUCTION TO BIOFUELS

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05 c h a p t e r

Can microbes be superheroes? Can crops grown for biofuels actually help the environment? Can a giant Asian grass really power a biofuels revolution? Perhaps. EBI scientists are quite literally on the ground level of the search for the most productive biofuels plants, conducting field trials, studying essential farm machinery, searching for sustainable fertilizers, and exploring the issues surrounding agro-ecosystem diversity that may make second-generation biofuels a boon for the environment. Most fuel ethanol today is produced from cornstarch. The Energy Biosciences Institute is looking beyond the major food crops as the feedstock for biofuels, with a focus on sustainable crops that could be grown on land unsuited for food production.

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to achieve sufficient feedstock while ensuring environmental and economic sustainability.

If the use of lignocellulose opens up all plants as potential feedstock, how has the EBI narrowed this down to a manageable task? Examination of yields in terms of conversion of incident solar energy Dried stems, roots and leaves of most plants are made up largely of into biomass has shown a group three types of polymers: cellulose, of grasses, the Androponodae, to appear particularly efficient. This hemicelluloses and lignin. This group includes sugarcane, sorghum mixture of the three polymers, and Miscanthus. The EBI Feedstock termed lignocellulose, comprises Program, and those looking at most of the structural mass of all utilization, have chosen these plants plants. as their first targets for detailed Tree trunks, crop residues, and investigations. These species are fall-harvested shoots of perennials also of primary interest to the such as switchgrass and Miscanthus Feedstock Genomics group led by are predominantly lignocellulose. the University of Illinois’ Stephen If the sugars of the cellulose and Moose, since sorghum has now hemicellulose can be efficiently been sequenced and many molecureleased, then these can be lar markers have been developed for fermented or chemically converted sugarcane. This allows the program to ethanol and other fuels. This a jump-start with Miscanthus, makes any plant material a potential since the DNA sequences in the feedstock for the manufacture of protein-coding regions appear “cellulosic biofuels.” highly homologous with its close relatives, sorghum and sugarcane. The ideal cellulosic biofuel Genetic similarity among grasses feedstock will vary with location, may also facilitate mechanistic but as a general rule they will all studies by Berkeley scientist Sheila provide high productivity with a McCormick of self-incompatibility minimum of inputs. Such crops will mechanisms that impede breeding minimize the footprint required in Miscanthus and other grasses

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such as switchgrass. The development of transformation technology for grasses by Jack Widholm, Don Duvick and colleagues in Illinois is expected to facilitate direct tests of hypotheses about the mechanists basis of important traits such as self-incompatibility

costs? The Agricultural Engineering Program, led by KC Ting at Illinois, is developing and testing machinery that can improve efficiency in production and transport. For example, harvesting can today require three operations. The EBI program has tested a machine that may integrate the three into one. It The Agronomy Program led by is also looking at the cost/benefit Tom Voigt at Illinois is in the of on-farm compaction to facilitate process of establishing comparative transport. trials of Miscanthus and switchgrass around North America. All these options are evaluated in a This includes comparisons with systems analysis context to identify sorghum and sugarcane at more the key bottlenecks—engineering, southern locations and with prairie environmental and economic— plants at other locations. About from planting to delivery to half of the spectacular gain in biofuel synthesis. While Miscanyields of the major food crops has thus, switchgrass, sorghum and been achieved through improved sugarcane are the current program agronomy, and it is expected that focus, it will certainly expand into agronomy will be similarly importrees, such as poplar and willow, tant for optimizing production of for locations where trees will be energy crops. The agronomy group more appropriate feedstocks—e.g. is examining how plant spacing, on terrain that is too irregular for weed control and fertilizers can be conventional machine harvesting. optimized to increase yields and A wide range of other perennials is minimize inputs. A project lead by also being tested on the EBI Energy German Bollero at Illinois is devel- Farm at Illinois. oping a computer model that will be able to predict how energy crops The Engineering, Agronomy, respond to factors such as climate, and Genomics groups are also soils and nutrients. The plants used collaborating on the development of remote sensing methods of trackin the sustainability trials are also ing plant growth and production, being used by the Biotic Stress Program, under Illinois’ Mike Gray, which will allow rapid assessment of thousands of different genetic to identify the diseases and pests lines non-destructively. Methods that may emerge with these new crops, and strategies for protecting are currently being tested that promise far more rapid identificathem. The group is monitoring insects, nematodes, fungi, bacteria tion of the most promising materials. In parallel, Michael Dietze and viruses. in Illinois is building a database New crops present on-farm engiof the broad basket of potential neering challenges. In particular, cellulosic feedstocks coupled with how can these crops be planted, the development of mechanistic harvested, stored and transported models of growth, production and efficiently, and without large energy ecosystems services.

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STEVE LONG:

Passionate About Plants and Their Potential It all begins with the feedstock, the source plant material. Commercial biofuel production will require lots of it, preferably grown where food crops can’t, and in quantities that yield huge amounts of biomass.

The answer might be found in crops not currently known. He will be looking at over 20 different grasses at the farm, and many more variants within those species.

Meet Steve Long. He was looking through old family photographs the other day, and he came upon one in which he was teaching a college course in 1978. The subject of his lecture? Biofuels. “I was surprised it was that long ago,” he says. Since that prescient moment, Long has become one of the world’s foremost experts on the so-called “C4” perennial grasses like Miscanthus, which has emerged as a major bioenergy crop in the United Kingdom, where he conducted some of the first analyses of this crop. His work in the U.S. has now shown it to be a promising candidate as a dedicated biofuel feedstock. He is deputy director of the EBI and the Robert Emerson Professor of Crop Sciences and Plant Biology at the University of Illinois UrbanaChampaign. And he is passionate about plants, in particular about the impacts of global atmospheric change on photosynthesis. “I’ve always been fascinated about how plants work,” says the soft-

spoken, British-born Long. “And I’ve been curious about how we can maximize the efficiency with which they convert solar energy into biomass, to achieve more yield per acre.” When the opportunity arose to apply his expertise to a potential solution to the world energy crisis, he seized it.

enable the production of plantbased transportation fuels. The two colleagues had never met, but when the Berkeley leadership team introduced the prospect of competing for the BP-funded EBI, together they jumped at the chance.

Long, the feedstock expert, has already reported research results After a productive 23-year career as that indicate Miscanthus is a supescientist and professor at England’s rior crop in terms of biomass yield and sustainability in poor soils. But University of Essex, he decided to the search is far from over. pull up roots in 1999 and headed overseas, to Illinois, where “there “What the EBI allows us to do is was a much larger concentration to explore options, to look at many of plant biologists, as befitted the more plants than we have before,” land-grant schools in the United he says. “We are open to the posStates. There were broad intellectual resources, and access to the sibility that there might be other possible feedstocks. There will not farm.” be one solution. For example, in drier areas, switchgrass might be “The farm” is UIUC’s vast acreage the better option, and in the driest of experimental croplands, in Agaves.” which he could test cultivation and nutrition techniques on the Or, he says, the answer might carbon-fixing grasses he had been be found in crops not currently studying in Europe—Miscanthus known. With others he will be x giganteus, found naturally in the highland areas of Japan and China, looking at over 20 different grasses and switchgrass, a variety on which at the EBI Energy Farm in Illinois American agronomists were focus- and many more variants within those species. He is also interested ing for fuel conversion. in pursuing salt-tolerant plants When Lawrence Berkeley National that could thrive on saline lands— salinated through geology, past Laboratory Director Steve Chu invited him in 2006 to join a panel irrigation practices or hydrated of experts to brainstorm alternative with sea water. fuels, he traveled to Berkeley and listened to Chris Somerville talk about the potential of biology to

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ANGELA KENT: Looking to Microscopic ‘Superpowers’ to Sustain Plant Growth Forgive Angela Kent if she’s biased, but she believes that microbes are the most important organisms in the world. She is especially high on bacteria, the most abundant group of organisms on the planet. And she thinks they could be key to the efficient productivity of future biofuel feedstocks. “Microbes have the greatest reservoir of genetic diversity on earth,” says the young microbial ecologist at the University of Illinois, Urbana-Champaign. “They can do incredible things. It’s almost like they have superpowers. They can find a way to make a living with any kind of compound.” The EBI believes in Kent and her bacterial troops, supporting a project that seeks to exploit the nitrogen-fixing capabilities of microbes to enhance the sustainability of bioenergy crops. “Production of nitrogen fertilizer requires a lot of energy input from fossil fuel,” Kent says. “It takes chemicals to make and farm machinery to apply. But microbes can do that essentially for free. If we can find conditions that favor bacterial nitrogen fixation in the plants, we can influence their long-term sustainability.” The first step is to understand how the association of certain bacteria with targeted biofuel grasses will work, and then how that association is affected by environmental factors—water, climate, soil texture and fertility, etc. Then there is the task of analyzing the characteristics of individual microbes through genetic phenotyping, searching for the genes that are involved in the nitrogen production. Considering that there can be millions of microbes in a gram of soil (such as the samples seen at right), Kent’s task is daunting.

but Kent thinks the prospects are high. With the assistance of two postdocs and two undergraduate students in her laboratory, she hopes to build a library of relevant bacteria and then apply them to Miscanthus and other plants in the EBI Energy Farm. She says she suspects that both growth and sustainability will be improved. Kent’s early studies at the University of Wisconsin focused on a medical career, her fascination about microbes leading her

" They can do incredible things. It’s almost like they have superpowers. They can find a way to make a living with any kind of compound." into the study of pathogens and their role in causing disease. But applications to human health were long-term, and she admits to looking for something more immediate. Environmental microbiology “felt much more applied to me, looking at microbes involved in plant health. I knew I could make a difference,” she recalls. Now that difference might be the application of microbiology, and her “super” microbes, to the development and nurturing of a new class of plant-based transportation fuels.

“In three years, we should have a pretty good idea of the inventory of microbes that work on Miscanthus, and we will be able to demonstrate whether nitrogen fixation plays an important role.”

“In three years,” Kent says, “we should have a pretty good idea of the inventory of microbes that work on Miscanthus, and we will be able to demonstrate whether nitrogen fixation plays an important role, as well as what traits contribute to the colonization of the plant.”

There’s no guarantee that inoculations of naturally occurring nitrogen-fixing bacteria will improve the growth of crops like Miscanthus,

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Environmental and Life Cycle Analysis

EVAN DELUCIA: Reviving Depleted Agricultural Land— A Biofuel Bonus?

The Environment Program is using the trials established by the Agronomy Program to provide the first actual measurements, as opposed to projections, of greenhouse gas balances and impacts on water availability and quality.

Biofuels are often touted as a solution to rising oil prices and global climate change—but they could also help solve agricultural problems caused by centuries of land abuse. That possibility is being put to the test in the EBI research program being conducted by University of Illinois Professor Evan DeLucia, who is heading an investigation of the impact and sustainability of feedstock production. “I am hopeful,” says DeLucia, “that not only will biofuel crops provide sustainable energy, but that they will diversify and improve the health of our agricultural ecosystem.”

In 2008, large-scale (up to 10 acres each) replicated trials of Miscanthus x giganteus, switchgrass, mixed species restored prairie, and continuous corn were established on the energy farm above instrumented field drains that monitor the volumes of water, nutrients and carbon draining out of each crop. Simultaneously, using a technique known as eddy-covariance, the net fluxes of gases containing carbon and nitrogen emitted and absorbed by these plots are being monitored continuously. This will be a unique data set, critical to constraining Life Cycle Assessment models and greenhouse gas balance models of the ecosystems services provided by different biofuel cropping systems. It will also test the predictions that the group has already made using the state-of-the-art models of soil carbon balance in conjunction with consultant Bill Parton. These studies will also be vital to gaining informed Life Cycle Assessments (LCAs), an activity that is the focus of research by Arpad Horvath and Thomas McKone at Berkeley. A key motivation for developing second-generation biofuels is to provide truly renewable liquid transportation fuel—fuel that may be made without degrading the ability of the land to produce the feedstock, and with a minimum of greenhouse gas emissions in their production, utilization and indirect impacts compared to fossil fuels. Any new activity that is likely to impact the environment, for better or worse, is typically subject to an LCA. An LCA examines, in the case of a second-generation biofuel, the environmental costs and benefits at each step from the conversion of land and planting of the crop through the combustion of the fuel. What are the inputs and outputs of carbon, energy and other resources at each stage? Projections around farm operations are currently hypothetical, because there have been no thorough measurements of greenhouse gas balances over these new cropping systems and conversion operations. This is further complicated by the fact that, as with any new technology in its infancy, there is uncertainty as to the appearance of the mature technology. The experience gained on the energy farm will be critical to adding more substance and reality to LCAs Two major tasks of the Feedstock Programs on Agronomy, Engineering, and Environment are 1) to actually measure greenhouse gas and energy balances; and 2) to define the most sustainable farm operations and opportunities for land conversion that would maximize opportunities for sequestering carbon from the atmosphere, as opposed to releasing carbon. 34

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Such an improvement is long overdue. Years of cornsoybean rotation in the Midwest have eroded soil, polluted water, and disrupted carbon and nitrogen cycles. Continuing that cycle could spell disaster for farmland, while introducing new, low-maintenance crops like Miscanthus or switchgrass could replenish the nutrients that have been leached from the soil.

A complementary project led by Ryan Stewart at Illinois is focused on studying the effects on soil quality of stands of Miscanthus in Japan that are more than 1,000 years old. One of the key environmental issues surrounding production of biofuels concerns effects on water quality and availability. Plants transpire enormous amounts of water during growth, and such water emissions can affect soil moisture and the amount of water runoff that may support streams and lakes. The potential effects of cellulosic crops on water are being modeled using climate and soil data in a collaboration between Carl Bernacchi at Illinois and Tracy Twine at the University of Minnesota. In addition, a detailed analysis of the potential effects on the well-characterized Lake Bloomington watershed is being carried out by Ximing Cai, John Braden, Wayland Eheart and George Czapar at Illinois. Concerns about water and land use have stimulated interest in the possibility of using algae to produce biofuels. Preliminary analyses of the costs of fuels produced from algae indicate that there are challenges associated with bringing the costs of production in line with alternatives. To understand the opportunity, the EBI is supporting a feasibility study by a large group of algal biologists led by Berkeley Lab scientist Nigel Quinn.

DeLucia’s team is trying to turn these hypotheticals into hard facts. They have planted plots of four biomass crops at Illinois’ new EBI Energy Farm—corn, Miscanthus, switchgrass, and mixed restored prairie grass. “This is the first time that side-by-side comparisons of the ecology of different biofuel feedstocks will be conducted under realistic field conditions,” says DeLucia. As the crops continue to grow over their three-year establishment period, high-tech instrumentation will carefully monitor the plants’ effects on the environment. And that effect is complex, to say the least. To provide a full sense of the crops’ impact, tests range from soil carbon measurements to energy exchange readings to analysis of arthropod activity. The variety of data requires researchers with all kinds of specialties: the EBI team includes ecologists, entomologists, physiologists, and many others. Their program reflects the unique interdisciplinary nature of EBI research. DeLucia, a plant biologist, calls working with scientists from such diverse fields “invigorating and exciting” and says this breadth of experience can “provide deep insight into the sustainability of biofuel crops.” This isn’t the first foray into environmental research for DeLucia, who has spent his career studying global carbon cycles, climate change, forest preservation, and pollution. His previous research has shown him the pressing need for sustainable biofuels, and now he hopes that biofuels could solve more than one environmental problem.

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Bioconversion research at the EBI is addressing several of the major bottlenecks impeding the practical production of biofuels, such as ethanol and butanol, from lignocellulosic feedstocks. These programs have several interrelated components—the discovery and characterization of fungi and thermophiles that produce new enzymes for lignin and cellulose deconstruction; protein engineering and kinetic modeling of improved cellulases; new organism discovery and cellular engineering for enhanced biofuel production and improved tolerance of the biofuel product; and bioprocess engineering to optimize fermentation.

VISUALIZING LIGNOCELLULOSE Lignocellulose is a composite material made up of a variety of polymers that are tightly bound to one another. Because the polymers are too small to be seen by most types of microscopy, the exact molecular structure of the cell walls that comprise plant biomass is not known. Berkeley Lab scientist Manfred Auer and colleagues are using new methods of electron microscopy to visualize biomass at nanometer resolution. His colleagues Paul Adams and Jim Schuck are building a novel Raman microscope that they expect will provide spatially resolved chemical information about cell walls that will be complementary to other types of imaging. Used together, these types of imaging provide insights into how various treatments affect the structure of biomass and facilitate improvements in the overall conversion process.

BIOPROSPECTING AND DISCOVERY OF NOVEL ORGANISMS AND ENZYMES FOR BIOMASS DEPOLYMERIZATION AND CONVERSION TO BIOFUELS

BIOCONVERSION:

Attacking Cellulosic Degradation on Several Fronts

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The ability to carry out biomass processing or fermentation at relatively high temperatures has several advantages. In addition to lower risk of microbial contamination, a higher temperature accelerates enzyme-catalyzed reactions and would reduce cooling costs and facilitate ethanol (or butanol) removal and recovery. To enable translation of these advantages to practice, EBI investigators are seeking to isolate and characterize enzymes from several extremely thermophilic bacterial strains specifically adapted for cellulose and hemicellulose degradation. For example, Doug Clark, Harvey Blanch, and co-workers at UC Berkeley, in collaboration with the Frank Robb laboratory at the University of Maryland, are cultivating communities of organisms from hot springs with cellulosic substrates with the aim of enriching for, and isolating, novel thermophiles that produce biofuels and/or thermostable cellulolytic BIOCONVERSION: ATTACKING CELLULOSIC DEGRADATION ON SEVERAL FRONTS

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enzymes. Bioprospecting for cellulose/hemicellulose degradation systems is assisted by whole genome sequencing of novel isolates. Efforts to exploit the advantages of thermophilic microorganisms for biofuels production are also underway at the University of Illinois in a program led by Isaac Cann (photo, page 36), Rob Mackie, and co-workers. Research in their laboratory has resulted in isolation and characterization of three novel thermophilic bacteria with maximum growth temperatures of about 70°C.

segments, and fecal pellets of grass-feeding termites. Thus, today’s wood-chomping pests may prove to be important players in tomorrow’s biofuel-producing technology.

In addition to cellulose, a particularly problematic component of plant biomass is lignin. Lignin is a complex, decay-resistant, highly cross-linked aromatic polymer. Almost all research on lignin and lignocellulose biological degradation has so far focused on fungi that decay wood. However, grass cell walls are very different from the walls of conifers, and in nature, none of the wood-decaying fungi are known They are also turning to ruminant animals as a promis- to decompose grasses. To find the fungal enzymes ing source of cellulolytic microorganisms that function best adapted to deconstruction of grass cell walls, efficiently at more moderate temperatures. Ruminant the Berkeley team headed by John Taylor, N. Louise animals are specialized in the utilization of grasses as Glass, and Tom Bruns aims to discover and bring into a source of feed. Both switchgrass and Miscanthus, in cultivation the fungi that decompose the litter that mesh bags, have been placed in the rumen of fistulated has been accumulated at Illinois under the feedstock cattle at the University of Illinois. These have then of choice—Miscanthus giganteus, a C4 grass closely been recovered and the attached microbes investigated related to sugarcane. by Eddy Rubin (photo, page 39) and co-workers at Berkeley Lab’s DOE Joint Genome Institute to identify Using modern high-throughput culture methods possible sources of robust cellulolytic enzymes for developed by the pharmaceutical industry, among efficient conversion of cellulosic biomass into ferment- other techniques, fungi capable of deconstructing Misable sugars. These two complementary programs canthus cell walls will be identified and considered for aim to identify enzymes produced by the abundant relevant enzyme production. The Taylor team is also microbes responsible for degradation of plant cell using transcriptional profiling and lignocellulolytic wall polymers in the rumen of forage-feeding animals enzyme characterization of the filamentous fungus, that can potentially be co-opted for cellulosic biomass Neurospora crassa, growing on Miscanthus cell walls to

PROTEIN ENGINEERING OF IMPROVED CELLULASES

wall. The goal of research carried out by Jamie Cate, Michael Marletta, and co-workers at UC Berkeley is to develop new experimental systems to study cellulosome degradation of cellulosic biomass. The Cate and Marletta team aims to develop model systems that will enable them to study the enzymatic properties of cellulosomes at a fundamental level. Understanding the molecular mechanisms may provide the key insights needed to reconstitute “designer cellulosomes” optimized for depolymerization of plant biomass.

Protein engineering has proven to be a powerful tool in creating enzymes with new and improved properties. However, designing and employing methods to screen or select cellulase mutants using solid cellulosic substrates remains a largely unmet challenge. Research by Clark, Blanch, and co-workers aims to overcome this challenge as well as that of developing more costeffective cellulases, by developing high-throughput solid substrate assays and applying them in the directed evolution of thermophilic cellulases and of cellulases MODELING FOR OPTIMAL CELLULASE with high activity in ionic liquids. The methodology DESIGN AND CELLULOSE HYDROLYSIS developed will be applicable to the generation and study of improved cellulases that can be used in various Accurate kinetic models of cellulose hydrolysis by process configurations for the production of biofuels cellulases are of critical importance for evaluating from cellulosic biomass. cellulase-component compositions and for designing and optimizing processes for cellulose conversion to Enzyme and metabolic pathway engineering are also biofuels. Such models will also aid in the development among the tools being used by the Illinois group and characterization of improved cellulolytic systems

Understanding the molecular mechanisms (of degradation of cellulosic biomass) may provide the key insights needed to reconstitute "designer cellulosomes..."

conversion. A related goal is to develop tailor-made learn how a fungus regulates genes responsible for cell enzyme “cocktails” optimized for saccharification of wall deconstructing enzymes. specific bioenergy crops with their subsequent converBerkeley chemist Michelle Chang is taking a different sion to alcohol fuels. approach—in order to explore mechanistic aspects of Another natural bioconverter that efficiently breaks how certain organisms degrade lignin, she is exploring down and transforms plant biomass is the termite how to modify yeast and bacteria that are normally hindgut. In a program aimed at discovering novel unable to degrade lignin so that they are able to carry enzymes capable of degrading wood lignocellulose, out the chemical transformations associated with Phil Hugenholtz and co-workers at the DOE Joint lignin breakdown. In this way she will test whether Genome Institute are performing metagenomic and our understanding of the pathway is correct and bioinformatic analyses of several species of woodalso whether there may be opportunities to alter the feeding and grass-feeding termites. These studies pathway for increased activity in industrial conditions. will be complemented by functional screening of selected enzymes and characterization of the plant cell wall polymers present in the food sources, hindgut 38

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led by principal investigators John Gerlt and John Cronan in a program directed toward overcoming biomass recalcitrance as a key obstacle in biofuel production. The objectives of their program are to identify and characterize degradation pathways for lignin, characterize the enzymes that are involved in those pathways, engineer these enzymes so that they will have enhanced catalytic properties, and design new metabolic pathways in organisms so that biofuel production can be enhanced.

generated by protein engineering and synthetic biology.

In addition to soluble cellulases, some organisms degrade cellulose using cellulosomes, which are comprised of cellulases organized in a complex assembly of enzymes and scaffolding on the bacterial cell

As an important first step toward modeling cellulose hydrolysis and engineering improved cellulases, Clark, Blanch, and co-workers have isolated the individual components of the cellulase mixture secreted by the

Projects under way at UC Berkeley headed by Clark, Blanch, and Clayton Radke aim to develop a comprehensive model of cellulose hydrolysis that can be used to predict cellulase performance, guide cellulase design, and optimize the hydrolysis of various cellulosic substrates, including those obtained from EBI investigators.

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JAMIE CATE: fungus Trichoderma reesei. Determining the kinetics of these enzymes toward various recalcitrant substrates, with and without pretreatment, including cellulosic substrates dissolved in ionic liquids, will provide a useful baseline against which the activities of newly discovered and developed cellulases can be compared.

CHEMICAL TRANSFORMATIONS— ALTERNATIVES TO BIOCONVERSION

An alternative approach to bioconversion of biomass to fuels is to use synthetic chemical catalysts to either hydrolyze biomass or convert hydrolysis products to fuels, or both. This relatively undeveloped area is being explored on several fronts. Berkeley chemical engineers Alexis Bell, Berend Smit, John Prausnitz and Harvey Blanch are analyzing the utility of ionic liquids ALLEVIATING PRODUCT TOXICITY to solubilize biomass as a prelude to subsequent IN BIOFUEL PRODUCTION chemical or enzyme-catalyzed hydrolysis. They are also looking into the possibility of using synthetic The development of new microbes with greater catalysts to directly reform sugars released from tolerance toward the final fuel product, such as butanol, could lead to substantial improvements in the biomass hydrolysis to fuels. Berkeley chemist Dean cost-effectiveness of producing biofuels from cellulosic Toste is exploring the development of novel synthetic homogeneous catalysts for polysaccharide hydrolysis, biomass. To this end, the Clark/Blanch program and Berkeley chemical engineer Alex Katz is studying is working to engineer enhanced tolerance toward butanol into bacteria, yeast and Clostridia. The group the use of heterogeneous catalysts. Lignin cleavage by is also exploring the design of extractive fermentation synthetic catalysts is also being researched by Berkeley chemists Jonathan Ellman and Robert Bergman and systems that may be used to minimize inhibition of Illinois chemist Tom Rauchfuss. The promise of this cultures by the products of fermentation. The use of additives that reduce toxicity of fuels during fermenta- new line of research is that entirely novel ways of transforming biomass to fuels may be discovered. This work tion is being explored by Illinois engineer Hao Feng. also opens up the possibility of finding routes to types of He is also researching novel biomass pretreatment fuels that cannot be produced by bioconversions. methods that reduce production of toxic byproducts. Another component of the proposed effort is the development of a simultaneous saccharification and fermentation process that can operate near the boiling point of ethanol. Ethanol production during saccharification of cellulose/hemicellulose at 75º will increase process efficiency, minimize contamination, and facilitate removal of the fuel product. One of the disadvantages of low-mass alcohols like ethanol and butanol is that they are miscible with water. This feature contributes to the toxicity of such fuels to the producing organisms and also imposes energy costs in dehydrating the fuels by distillation. Berkeley engineer Nitash Balsara is exploring the development of advanced membranes that can selectively separate fuels from the aqueous phase. The successful development of membrane separation technologies could facilitate the implementation of much more efficient processes than are currently possible.

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Quest for Reliable, Responsible Biofuel Runs Through Biochemist's Lab What’s an RNA biochemist like Jamie Cate doing in a place like this? Up until a few years ago, the UC Berkeley associate professor was totally preoccupied with the mechanisms of protein synthesis, how antibiotics stop the bacterial ribosome and how viruses take over protein synthesis in human cells. Then, as he recalls, “I started thinking about climate change and the fossil fuel issue.” He says he installed solar panels on his house and bought a Prius, but it wasn’t enough. “What can I do with my science?” he asked himself. And the answer was found in an Energy Biosciences Institute program that three graduate students—Veronica Zepeda, Padma Gunda, and Will Beeson—helped him to develop. Cate and his team—the students, plus four subject matter expert colleagues from the campus and Lawrence Berkeley National Laboratory—are studying how organisms like bacterial microbes make the enzymes that break down plant biomass into fermentable sugars. His experience with the tools of structural biology research are being put to use as probes into the workings of cellulosomes; that is, clusters of protein enzymes, or catalysts, whose interactions enable the decomposition of complex plant infrastructure. “We ultimately want to get to a designer cellulosome,” Cate says, “whose enzymes can work as well or better than nature to degrade plant material.” He explains it as a “combinatorial” challenge, in which a central protein called scaffoldin has six sites on which enzymes can bind, and 70 different enzymes to choose from. So, which enzymes go to which sites, and why? The team’s model organism is a Clostridium species, an anaerobic bacterium that degrades cellulose. And their strategy of study involves multiple approaches: analysis of the genomic sequence; surface enzymology using mass spectrometry, in which electrically charge samples are accelerated through a magnetic field and “fingerprinted” on a screen; and atomic force microscopy, which can sense the surfaces of biomass as it’s broken down. “Eventually, we will begin to focus our attention on breaking down increasingly complex potential feedstock for biofuel production, like corn stover, switchgrass, and Miscanthus giganteus,” Cate says. “So for the first three years, our goal is to set up an integrated experimental system to predict and test properties of our ‘designer cellulosomes’ and, eventually, to optimize the deploymerization of feedstock for biofuel production.” The work is a graphic example of how the techniques of modern biology can be applied to solving one of society’s most challenging problems—finding a sustainable, environment-friendly alternative to fossil fuels for transportation energy.

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BIOFUELS PRODUCTION:

Transforming Feedstock to Fuel with Microbes

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The current method of converting plant sugars to fuels is similar to centuries-old fermentation practices that we have relied on to make beer and wine. While those methods are successful for spirits, they've proven inadequate in the production of biofuels, especially on the large scale. Biofuels production researchers at the EBI are searching for ways to boost the concentration of fuel produced by the biofuel fermentation process by improving yeast, bacteria, and other microbes for industrial use.

A number of molecules of biological origin can serve as fuels. Ethanol is perhaps the most industrially successful biologically produced fuel. Other molecules—ranging from more complex branched-chain alcohols to fatty acids and hydrocarbons—have a variety of properties that make them more or less attractive as targets for production. And they can be made in plants and microbes. Some burn cleaner than others; some have higher energy density, possess different octane ratings, or can be physically transported or produced more cost-effectively and reliably with less energy input. Those closer in form to what is found in gasoline, diesel and jet fuel may prove superior. The routes to biological production of fuel molecules are numerous and include sources such as plant oils or algae. However, one of the most effective routes is through microbial fermentation and synthesis. Deconstruction of feedstocks leads to hydrolysates rich in 5- and 6-carbon sugars such as glucose, xylose, and arabinose along with other compounds that can be toxic. Natural or engineered yeast and bacteria can metabolize the sugars into different variants of the possible fuel molecules but are inhibited to various extents by toxins and the fuel products themselves. Nonetheless, the relative success of this approach derives from a number of factors. Microbes express an amazing array of natural abilities to consume simple feed molecules and create complex organic chemicals. The revolutions in molecular biology and genomics have enabled scientists to discover the genes responsible for these capabilities and to transplant their function into industrially robust host microbes. Advances in quantitative and genome-scale measurement of cellular physiology down to the single-cell level give unprecedented insight into the factors that restrict optimal production by limiting metabolic flux and microbial growth. These tools have only just begun to be applied systematically to improve microbial fuel production and, despite some early successes, there remains much room for improvement. The Energy Biosciences Institute has initiated a cutting-edge microbial engineering program combining both synthetic biology and metabolic engineering approaches to create new routes to fuels in bacteria and fungi as well as systems biology and genomics approaches to measure and diagnose function. 42

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ENGINEERING YEAST FOR SUGAR UTILIZATION

PRODUCING DIESEL SUBSTITUTES IN BACTERIA

Two research groups at the University of Illinois seek to improve the utilization of the different sugars present in hydrolysates. Most microbes used for fuel production cannot effectively use both the 5 (like xylose and arabinose) and 6-carbon sugars (such as mannose and glucose) that are the most abundant products from the feedstock deconstruction. Complete fermentation of all these sugars to biofuels is necessary to maximize yield and minimize waste in the production process. Investigators led by chemical engineer Huimin Zhao and microbial geneticist YongSu Jin will identify genes that transport the sugars into the cell and metabolize them into common precursors for fuel synthesis in a number of different fungi. These will be transplanted into industrially important host cells starting with the ethanol-producing yeast Saccharomyces cerevisiae. Advanced approaches for metabolic analysis and engineering will be employed to optimize yield and rate of production.

While ethanol production is an initial target for the EBI, other fuel molecules may prove to have superior properties. Biodiesel is an alternative fuel, widely used in the alternative energy economy. It is usually composed mostly of fatty acid alkyl esters (FAAE). These molecules are often produced by catalyzed reaction of methanol with fatty acids from plants, tallow and used cooking oils. Current estimates predict that production costs for this fuel will remain substantially higher than petroleum-based products. Berkeley Lab scientists led by Nikos Krypides and Athanasios Lykidis are therefore applying biochemical and metabolic engineering approaches, similar to those above, augmented with experimental evolution to generate bacteria with enhanced production of free fatty acids, triacylglycerols, or FAAE.

ALEX BELL: Finding Chemical Keys to Open the Cellulose Lock Cellulose, that tough organic component of all plant cell walls, is itself constructed of complex chains of sugars that hold the key to biofuel development. Unless cellulose and the related polysaccharide, hemicellulose, are effectively liberated from their lignin seal, then broken down and dissolved, sugars for fuel fermentation will not be released. Enter chemical engineer Alex Bell, whose EBI program challenge is to pretreat the biomass in a way that can efficiently dissolve cellulose and process the residue through depolymerization into sugars. He thinks the answer might lie in inorganic solvents called ionic liquids—salts in liquid form. They have the benefits of functioning at room temperature, rather than requiring heat, and they are inert, meaning they won’t interfere chemically with the reaction.

Together these programs and projects are creating an integrated engineering framework for designing microbes for transformation of feedstock into fuels. In the next few years, the EBI will add synergetic programs to the Biofuels Production effort that will push the frontiers even farther.

These programs and projects are creating THE MICROBIAL CHARACTERIZATION PROGRAM Researchers at UC Berkeley and Lawrence Berkeley National Laboratory have established a highthroughput genetics and genomics capability and are developing an experimental and computational program to determine the genetic mediators of optimal fuel production in microbes. Using the ethanol-producing bacterium Zymomonas mobilis as a model system, program scientists headed by Berkeley bioengineer Adam Arkin will screen large-scale genetic knockout libraries and generate high-resolution wholegenome gene expression compendia of the bacterium exposed to different feedstock hydrolysates, their purified inhibitors and sugars, and the various possible fuel products. This data will allow dissection of the mechanisms that impact the ability of Zymomonas to grow and metabolize sugars into fuel and suggest routes for engineering more efficient production. The computational framework and experimental facility created as part of this program will ultimately scale to aid the engineering of resistance and fuel molecule synthesis in this organism and the others being pursued at the EBI. 44

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ELUCIDATING THE IMPACT OF REGULATION AND HETEROGENEITY ON SUGAR METABOLISM IN BACTERIA Engineered pathways are usually dependent upon the normal metabolism of the host. The endogenous regulatory machinery often hampers fuel yields. Metabolic regulation is evolved to sense environmental conditions and deploy the right pathways to allow organisms to survive in an uncertain and competitive world. However, they may be triggered by the particular conditions found in industrial bioreactors and lead to poor sugar utilization and production. These effects are further complicated in large-scale fermentations where cells experience fluctuating nutrient conditions due to imperfect mixing. The populations will be physiologically heterogeneous, and thus not all individuals will be producing optimally. EBI scientists in Illinois under biochemical engineers Christopher Rao and Ido Golding seek to overcome this problem in Escherichia coli by creating a quantitative model of the system that will facilitate the design of strains capable of homogeneously, simultaneously and efficiently metabolizing the arabinose, xylose, and glucose.

an integrated engineering framework for designing microbes for transfromation of feedstock into fuels.

“The challenge is in understanding what properties ionic fluids require to dissolve crystalline cellulose,” says Bell, an expert on the form and function of catalysts. He’s certain his team will solve the dissolution and depolymerization puzzles; he’s less sure about controlling the chemical transformation of the sugars into transportation fuels. The search is both practical and theoretical. While a half-dozen lab researchers, mostly postdocs and graduate students, employ high-throughput screening of candidate solvents (almost 100 reactions at a time on automated assay machines), Bell’s faculty colleagues will be looking at the theoretical aspects of cellulose and carbohydrate dissolution in ionic liquids. They have a three-year commitment to find the answers, in order to determine whether or not this process will successfully lead to commercialization and industrial application. That’s where the BP partnership comes in handy. “Having BP’s experts in residence, to interact with us, will be invaluable in determining which of the approaches will be fruitful,” says Bell.

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How much land globally is available for the production of biofuels? What might be the consequences of devoting vast amounts of land for raising crops used to produce biofuels? Will food production be affected? What impact would a dynamic biofuels market have on the environment? As we transition to a sustainable energy system, EBI scientists are scrutinizing the potential impacts of these issues on our society. The socio-economic program in the Energy Biosciences Institute is developing modeling frameworks and applying them using extensive economic and biophysical data to investigate the socio-economic, environmental and intellectual property issues associated with the introduction of the next generation of biofuels. Researchers are using both a micro-economic (bottom-up) approach to assess impacts on land use, food production and carbon emissions at the local and regional level and then aggregate them to a national level; and a macroeconomic (top-down) approach that examines national and global impacts of biofuels on food and fuel markets, welfare of consumers and producers and the environment. In particular, teams are conducting research in the following areas:

ASSESSMENT OF LAND USE CHANGES

SOCIETAL AND ECONOMIC IMPACTS OF BIOFUELS: Implications for Land Use, Markets, and the Environment

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Madhu Khanna’s program at Illinois is developing an integrated, interdisciplinary framework to investigate the effects of large-scale production of cellulosic biofuels in the U.S. on land use, crop production, farm income and carbon mitigation over a 15-year horizon. A key component of this framework is the application of a mechanistic crop productivity model (MISCANMOD) by Fernando Miguez and German Bollero to simulate the yields of switchgrass and Miscanthus in the U.S. The model projects daily crop growth with detailed spatial data at a 0.1-by-0.1-degree level on temperature, precipitation, and solar radiation and soil moisture limitations. Its mechanistic base allows seamless integration with improvements identified by the Feedstock Programs.

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Simulated growth and crop yields are within 10 percent of observed values for Illinois and the Midwest, and for a range of sites in Europe. Ecosystem services, including soil moisture and carbon balances, are determined by integrating this model and the CENTURY model used by the Environment Program in the Integrated Science Assessment Model (ISAM) developed by Atul Jain as one of the three key models for projecting global carbon balances for the Intergovernmental Panel on Climate Change. Madhu Khanna and Hayri Onal have developed an economic model that integrates these findings to examine the economically viable land use allocation among various food and fuel crops and the costs of meeting biofuel production targets. But it is also capable of assessing the impacts of systems of crediting carbon storage. Initial application of this model to Illinois shows that there is considerable spatial heterogeneity in the competitiveness of various feedstock for biofuel production and that per-acre yields of biofuel crops as well as the cost of the land are key determinants of that competitiveness. They find that a mix of cellulosic feedstock is likely to be more economically viable than a single feedstock, and this mix is expected to evolve from greater reliance on crop residues initially, then to reliance on energy crops, like Miscanthus, over time. They are currently working on applying this model to the Midwestern states and then to other states where energy crop production is likely to be viable. A related approach to a global assessment of land use is being developed by UC Berkeley and Berkeley Lab scientists Norm Miller, David Sunding, Maggi Kelly, and David Zilberman. They are integrating production models for a variety of potential energy crops with spatially and temporally defined global geographic and economic data in order to develop an assessment of global potential for cellulosic fuels. A key feature of such studies is an assessment of how land use is expected to change in response to changing climate and population density.

Researchers are examining national and global impacts of biofuels on food and fuel markets, welfare of consumers and producers, and the environment.

LOGISTICS, POLICY, AND INFRASTRUCTURE The group led by Jürgen Scheffran is developing a framework to determine the optimal capacity and location of biorefineries as a function of the regional distribution of bioenergy feedstocks in the Midwest, the costs of transportation of feedstocks and biofuels, and the demand centers for biofuels. Mathematical programming tools are used to identify location of biorefineries that minimize the costs, including transportation to and processing of bioenergy crops at refineries, transportation of fuel from refineries to the demand destinations, capital investment of refineries, with a net of by-product credits. A multi-year transshipment and facility location model determines the optimal time to build each plant in the system, water needs and availability, the amount of raw material processed by individual plants, and the distribution patterns of inputs from crop-producing regions to the refineries and shipment of ethanol to the demand destinations. Illinois legal scholars Jay Kesan and Brian Endres are examining how the regulatory framework in various regions may impact the establishment of a cellulosic fuels industry in the U.S. The group is also investigating the implications of the new Renewable Fuels Standard that the Environmental Protection Agency is expected to release early in 2009. Further afield, UC Berkeley’s Dick Norgaard and Alastair Iles are studying the structure of the existing biofuel industry in Brazil in order to develop a basis for evaluating how future development of the industry may occur. Berkeley political scientist Steve Weber is developing an analysis of how previous transitions in the energy sector have occurred with a view to understanding the impacts of current and future energy policies on emergence of a biofuels industry.

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FOOD AND FUEL MARKET IMPACTS

ROLE OF INNOVATION, INTELLECTUAL PROPERTY RIGHTS, AND TECHNOLOGY ADOPTION AND LAW

David Zilberman’s Berkeley team is developing quantitative models and measures to assess the impact of different kinds of biofuels on food and energy prices, farmers, consumers, and overall economic welfare. Analyzing the impact of corn ethanol in 200607, they find that biofuels reduced the average price of fuel between 1 and 3 percent and increased corn price by between 5 and 20 percent in the U.S. This saved up to $45 billion in fuel costs, increased the food bill by up to $20 billion, and raised farm income by up to $18 billion. The Berkeley group is also developing a model to explain global oil prices, which suggests that OPEC does not behave like an “economic cartel” that maximizes profit but rather as a political cartel that maximizes the overall welfare of oil-exporting nations. This will be used to make quantitative assessments of resource allocation and pricing in fuel, food, and biofuel markets.

Zilberman and colleagues are analyzing the potential role of productivity-enhancing agricultural biotechnology in the growth of the biofuel sector. Early results suggest that the capacity of biofuel to meet energy demand largely depends on the increased productivity of traditional crops that may partially compete with biofuel for land, water, and other resources. UC Berkeley economist Brian Wright is assessing the intellectual property (IP) issues relevant to biofuels research beyond current ethanol production. An initial assessment of the landscape indicates that IP ownership is fragmented and that over 50 assignees are active in this technology arena, with Genencor holding the largest portfolio. His analysis shows that the public sector is highly active in biofuels research, and it points to the need to understand public/private relationships in this area. He plans to measure and assess the evolving effects of intellectual property protection of inputs and outputs of research and of some relevant regulatory constraints, from the viewpoints of the EBI scientists involved in activities relevant to the initiative. Work is also proceeding on a study of the relationship between the terms of research sponsorship and subsequent patenting and licensing at the UC Office of Technology Transfer. This has generated interest and an offer of modest support at the National Academies.

Zilberman’s work analyzing the profitability of corn ethanol incorporates stochastic influences on economic decisions arising from randomness in natural phenomena and economic processes. Early results indicate that there may be significant losses in the biofuel industry during periods of low supply inventories of corn and large profits during periods of abundant corn supply and high oil prices. His work is currently analyzing the implications of this “boombust” nature of corn biofuel for the design of contracts and will be extended to analyze the effect of random forces on the economics of cellulosic biofuels. Khanna is also analyzing the effects of liberalizing trade in biofuels with Brazil on food and fuel prices, consumer and producer well-being, and greenhouse gas emissions. She finds that the current biofuel policy of an import tariff and a subsidy on ethanol imposes an economic cost of over $3 billion annually and results in significantly higher corn and ethanol prices in the U.S. with negligible current reductions in carbon emissions as compared to those with no policy intervention.

Work will seek to understand how adoption of biofuel technologies can incorporate the interdependencies between farmer,

Zilberman is also developing a conceptual framework to explain adoption of biofuel technologies while incorporating the interdependencies between the farmer, processor and oil marketers and to analyze the types of production contracts needed to induce adoption. The Illinois team of Anne Heinze Silvis, Michael Gray, German Bollero and Maria Villamil is engaged in surveys of farmers and investors in ethanol plants to examine the factors that will influence their decisions to produce and use cellulosic feedstock.

processor, and oil marketers

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The EBI is developing collaborations with other organizations around the world to increase the critical mass of researchers with expertise and access to data that is relevant to understanding core issues. ENVIRONMENTAL AND SOCIETAL IMPACTS OF BIOFUELS

Seeking a Biofuels Policy Where Everybody Wins Creating a national biofuels policy is tricky because it has to work for diverse interests. Ideally, such a policy would cut oil imports, curtail greenhouse gas emissions, and be profitable for agriculture. And, the biofuels policy can’t act as a drag on the economy or limit food production.

Several research teams within the socio-economic program are assessing various aspects of the environmental and societal impacts of biofuels from an economic perspective. Atul Jain is using biophysical models to assess the soil carbon sequestration potential and nitrogen requirements of biofuel crops. Khanna’s team is analyzing data on life cycle emissions in conjunction with detailed spatial data on production methods and land use to determine the potential for biofuel-driven land use changes and displacement of gasoline to mitigate carbon and the costs of achieving mitigation. They find that biofuel production in Illinois, to meet 20 percent of the ethanol mandate by 2022, has the potential to reduce cumulative greenhouse gas emissions by 45 percent relative to baseline levels over the next 15 years by displacing energy equivalent gasoline, but that the enhanced production of corn ethanol to meet a part of the mandate increases nitrogen use by 27 percent over this period.

“We should be able to assess the benefits and unintended consequences of biofuels policies as they stand today, particularly for the environment,” said Madhu Khanna, an environmental economist at the University of Illinois at Urbana-Champaign and lead investigator for the EBI team. “And we should be able to determine how those policies might be better designed to achieve social goals.”

Using a macro-economic computable general equilibrium model of the U.S., John Braden’s Illinois group is analyzing the efficient mix of biofuel pathways based on their economic and environmental impacts which considers the trade-offs between reduced carbon emissions due to biofuels and water quality degradation due to greater fertilizer use for some feedstock, such as corn. Zilberman’s team is developing ways to integrate economics into the methods currently used to assess life cycle carbon emissions of biofuels. The group is developing measures that modify the standard life cycle analysis to reflect the effects of changing market conditions and policies on choice of production methods and carbon emissions.

To come up with a broadly acceptable biofuels policy, she and her colleagues must collect huge amounts of research data, much of it dealing with the logistics of creating a massive new industry. “We need to know how much switchgrass, Miscanthus, and crop residues can be grown or collected in different parts of the country,” said Khanna. “We don’t know because we’ve never done it. We want to know how much carbon each of those biofuel crops is going to sequester in the soil. And we want to know how much carbon will be produced (by) each crop.”

One of the complexities of understanding the life cycle aspects of various types of biofuels is the recent recognition of potential indirect land use effects. The concept is that, because demand for food is inelastic, if land is converted from food production to fuel production, previously unused land will be converted to food production with attendant releases of greenhouse gases. However, the situation is complex because demand for food can also be satisfied by increasing production on fewer acres in response to price signals. Michael O’Hare and his Berkeley colleagues are working to develop economic models that can be used to understand this issue quantitatively. Their findings may have important implications for future policies that place economic value on greenhouse gas emissions.

One complicating factor is a federal mandate that requires production of 36 billion gallons of biofuel annually by 2022. Of that, 21 billion gallons must come from advanced biofuels—fuels which produce no more than half as much greenhouse gas as gasoline. “We want to find the lowest-cost way we could meet that mandate,” Khanna said. “The first step is to figure out where to grow corn, where to grow Miscanthus, and where to grow switchgrass in order to meet the 36-billion-gallon mark.”

Another matter of potential concern regarding biofuels is the possibility that diversion of land to production of biofuels could negatively impact food availability for disadvantaged people around the world. This is a complex issue that appears to be more related to the structure and operation of markets rather than about the availability of land. Berkeley economist Brian Wright and colleagues are studying this issue, as are Ximing Cai at Illinois and collaborators Siwa Msangi and Tingju Zhu at the International Food Policy Institute. Much of the other economics research in the EBI also impinges on this important question from various perspectives. This topic is so important that the EBI is developing collaborations with other organizations around the world to increase the critical mass of researchers with expertise and access to data that is relevant to understanding the core issues.

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That’s a tall order. Nonetheless, an EBI research team has waded into the debate by undertaking a massive study of the economic issues related to biofuel development.

Ultimately, the team expects to give policymakers the information they need to help craft a national biofuels policy that works for the environment, the economy, and farmers. “Farmers won’t do this unless they see the right price signals,” Khanna added. “The price signals provided by the market may not reflect the various environmental effects of biofuels produced from different feedstocks. So the government may have to provide appropriate incentives so that farmers produce a sustainable mix of biofuel crops.”

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09

Education and Outreach

Conferences, Symposia, Workshops, Seminars

From a symposium on using microbes to recover earth-bound oil supplies, held in October of 2007, to an economic modeling conference on biofuels in November 2008, the EBI has sponsored or co-sponsored a wide range of workshops and meetings during its first year of operations. The knowledge shared by participants broadened and enriched the global quality of scientific inquiry within and about bioenergy. Of special note was the EBI-sponsored Pan American Plants and Bioenergy Symposium at Merida, Mexico, co-organized by Deputy Director Steve Long. This brought together groups working on feedstock improvement from the EBI and many institutes throughout the Americas, and in particular teams from São Paulo advancing the use of sugarcane. Within EBI, investigators benefitted from three seminar series launched in Berkeley and two in Illinois to provide forums for the exchange of project information and the prospective collaborations between research units.

In chronological order, the meetings included: Research Priorities in Microbially Enhanced Hydrocarbon Recovery (MEHR) October 24, 2007 Microbially Enhanced Hydrocarbon Recovery involves using microbes in the subsurface to recover additional oil or hydrocarbon gas from conventional oil and gas reservoirs, or to liberate methane from other hydrocarbon-rich environments (e.g., coal beds, tar sands, oil shales). This workshop defined the research parameters for a project solicitation that will lead to EBI funding of research in this area. Biologically Enhanced Carbon Sequestration: Research Needs and Opportunities October 29, 2007 Fossil fuel combustion, deforestation and biomass burning are the dominant contributors to increasing atmospheric carbon dioxide concentrations and global warming. This workshop explored the promising current approaches and research roadmaps to mitigating CO2 emissions in both terrestrial and geologic carbon sequestration. Advances in ecology and microbial biology offer new possibilities for enhanced sequestration.

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5th Annual Bioenergy Feedstocks Symposium January 9-10, 2008 This symposium at the University of Illinois was part of a series established with the State Program on Bioenergy Feedstocks. The symposium has grown from 20 participants in 2004 to 300 from four continents in 2008. It brought together agronomists, environmentalists, industry and pioneering farmers experimenting with potential cellulosic feedstocks. Beside reports on five years of trials with Miscanthus and switchgrass in Illinois, a highlight was the agronomic approaches and business model being adopted in Ireland to achieve self-sufficiency in fuels, via feedstocks that include Miscanthus, and a parallel program in SW Ontario. This has led to valuable interactions between the EBI Agronomy and Engineering Programs and these activities in Ireland and Canada. Berkeley Energy and Resources Collaborative (BERC) Symposium March 7, 2008 The symposium featured leaders in research and technology, industry and academia, and economic and political organizations, who discussed the need for concerted global action to address climate change and sustainable solutions to energy needs. EBI supported this student-run program and participated through talks and panel discussions.

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Greenhouse Gas Emissions from Biofuels June 8-9, 2008 In this workshop, participants discussed the current state of knowledge of greenhouse gas emissions associated with biofuel crops and new research needed to understand mechanisms of greenhouse gas release, sensitivity of that release to land use management and farming practices, and strategies for extrapolation of greenhouse gas emissions to the global scale. Pan American Congress on Plants and Bioenergy June 22-25, 2008 This international conference in Merida, Mexico featured plant biologists meeting with government policy makers, agronomists, microbiologists, economists and ecologists to forge a path toward Western Hemisphere bioenergy security that is sustainable and environmentally and economically sound. EBI Deputy Director Steve Long was co-organizer of the conference and gave the opening lecture. Transition to a Bioeconomy: Risk, Infrastructure and Industry Evolution June 24-25, 2008 Co-sponsored by EBI, this Farm Foundation conference in Berkeley focused on risk and infrastructure for the biofuel industry of the future. Participants examined such issues as finances, business models, and transportation infrastructure.

Measuring and Modeling the Life Cycle GHG Impacts of Transportation Fuels July 1-2, 2008 This Berkeley workshop explored the differences among the fuel life cycle Greenhouse Gas (GHG) estimates from leading models, including system boundaries and other judgments about land-use change. Experts from the academic and fuels analysis communities addressed both current and emerging biofuels and other options for reducing the carbon footprint of motor fuels. The Environmental Defense Fund was primary sponsor. Biofuels and Sustainability October 21-22, 2008 EBI joined with the Illinois Sustainable Technology Center to convene this conference in Champaign, dedicated to issues and innovations that can improve the sustainability of biofuels. Discussions focused on the economic, social, and environmental feasibility and ethics of biofuels options for meeting energy needs. Linking Biophysical and Economic Models of Biofuel Production and Environmental Impacts November 13-14, 2008 This workshop in Chicago focused on the need to develop simulation models to understand how much cellulose biofuel crops would yield under alternative growing conditions and what would be their implications for water quality, climate change and biodiversity. Participants reviewed recent developments in biophysical models of bioenergy feedstocks and their integration with economic models to study the economic and environmental impacts of bioenergy crops. The meeting was co-sponsored by the B-Basic program at Delft University of The Netherlands and the Great Lakes Bioenergy Center sponsored by the U.S. Department of Energy.

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In addition to the aforementioned programs, EBI investigators attended national and international symposia on relevant topics and gave talks and poster sessions on the work being conducted in the Institute. They also accepted invitations as lecturers in university classrooms and at industry conferences.

EBI in Education In the decades ahead, the students of today will help to establish and maintain this new industry as well as manage its impacts on global society. The EBI recognizes its role in educating and training these young researchers so that they are prepared for the coming bio-revolution. Nearly 200 graduate and undergraduate students and postdoctoral scientists were engaged in EBI programs during its first year in laboratories and offices at both Berkeley and Illinois campuses. Partnership with India Five top undergraduates from the Indian Institute of Technology (IIT) at Kharagpur spent eight weeks during the summer of 2008 conducting research with EBI faculty as part of a new Berkeley-IIT Kharagpur collaboration in biofuels sponsored by the EBI. The scientific partnership was brokered by UC Berkeley Deans Mark Richards, of the College of Letters and Science, and of Physical and Mathematical Sciences; and Geoff Owen, of Biological Sciences. The EBI and its Director, Chris Somerville, are supporting sponsors. The collaboration involves two phases. The first seeks to build relationships among faculty and students of both institutions while increasing the pool of researchers focused on addressing the energy challenge. The second phase will focus on joint targeted research projects. As part of the first phase, five IIT Kharagpur students were mentored by, and assisted, UC Berkeley and Lawrence Berkeley National Laboratory principal investigators in the EBI research program—Poulami Mondal, with Paul Adams; Shailabh Kumar, with Manfred Auer; Akhilesh Jain, with Alex Bell; Aniket, with Doug Clark; and Raj Shekhar Singh, with Norm Miller.

Elementary and Middle Schools At the other end of the spectrum, EBI graduate student Becky Arundale and office manager Becky Heid in Illinois have developed resources in collaboration with a local teacher to explain the EBI to elementary school students. EBI graduate student Ashley Spence developed and presented a program of EBI mission-based activities for girls from area middle schools at Illinois for GAMES (Girls Adventures in Math, Engineering, and Science). Cal Day “Voyage” Berkeley students, as well as campus visitors during the annual spring Cal Day open house program, learned about Robert Swan’s “Voyage for Clean Energy” in two talks sponsored by the EBI. Explorer Swan, one of the few to have successfully walked to both the north and south poles, was kicking off his next venture, a five-year sail around the world to raise awareness about climate change and saving the environment. Two Berkeley graduate students actually took Swan up on his offer to work on his BP-sponsored biofuel-powered sailboat during its West Coast journey—Vasanth Mohan, a graduating MBA student in the Haas School of Business, and Bret Strogen, a second-year doctoral student in environmental engineering. Strogen is currently working on an EBI program headed by Arpad Horvath and Tom McKone entitled “Life Cycle Environmental and Economic Decision-Making for Alternative Biofuels.”

Bioenergy Crop Modeling and Land Use October 9-10, 2008 To understand bioenergy crop production potential in marginal and abandoned lands, a well-planned modeling and data analysis strategy is required. This workshop was conducted to design a crop modeling validation exercise and to define methods for quantifying targeted land distributions. Biofuels Research Seminar Series Recognizing the need for interdisciplinary information exchange as well as collegial partnerships with parallel groups, EBI management launched two internal seminar series in 2008 addressing the challenges, progress, and promise of biofuels research. Biweekly presentations from researchers in EBIsupported programs and projects have been held in Berkeley’s Calvin Laboratory since debuting with EBI Intellectual Property Manager Mitch Altschuler on Aug. 26. A second series of monthly talks jointly sponsored by EBI and the U.S. Department of Energy’s Joint BioEnergy Institute ( JBEI), located in Emeryville, CA, debuted on Sept. 10 with a seminar by University of Illinois microbiologist Roderick I. Mackie. This series will resume in the first quarter of 2009.

EBI graduate students and postdocs have been actively educating each other via biweekly lunchtime seminar programs started at both Berkeley and Illinois. The seminars focus on work being conducted in the laboratories of EBI principal investigators.

The EBI recognizes its role in educating and training young researchers so that they are prepared for the coming bio-revolution.

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EBI Research Programs, Projects, and Research Personnel The following is a list of principal investigators and research staff in 50 programs and projects funded by the Energy Biosciences Institute during its first year. Detailed descriptions of the individual projects can be found on the EBI's public web site: www.energybiosciencesinstitute.org.

Feedstock Development Programs: Assessing the Potential Impact of Insect Pests and Plant Pathogens on Biomass Production of Miscanthus x Giganteus and Switchgrass Principal Investigator: Michael E. Gray, University of Illinois Co-PIs: Carl Bradley, Terry Niblack, and Kevin Steffey, University of Illinois; Shauna Somerville, UC Berkeley Postdocs: Bright Agindotan, Monday Ahonsi, Jeffrey Bradshaw, Tesfamariam Mekete, Jarrad Prasifka Technician: Michelle Averbeck

Postdocs: Tofael Ahamed, Hala Chaouui, Konstantinos Domdouzis, Ming-Che Hu, Qingting Liu, Zewei Miao, Yogendra Shastri

Cellulosomes Optimized for Biofuel Production Principal Investigator: Jamie H. D. Cate, UC Berkeley and Berkeley Lab

Co-PI: John Juvik, University of Illinois

Visiting Professor: Rafael Lamed

Feedstock Production/Agronomy Program

Postdoc: Olga Zernova

Principal Investigator: Thomas Voigt, University of Illinois

Graduate Student: Hyoung Kim

Postdocs: Corinne Hausmann, Sasa Jenko-Kokalj, Kai Zhang

Research Scientist: Vera Lozovaya

Graduate Students: Becky Arundale, Bosola Oladeinde, Ashley Spence, Andy Wycislo

Graduate Students: William Beeson, Padma Gunda, Chris Phillips, Veronica Zepeda, Elizabeth Znameroski

Biomass Depolymerization

Undergraduate Students: Valerie Chan, Duy Dao

Tech Specialists: Rich Pyter, Drew Schlumpf, Emily Thomas

Programs:

Co-PI: Stephen P. Long, University of Illinois

Postdocs: Madge Alabady, Cuixia Chen, Kankshita Swaminathan

Postdoc: Yuefeng Guan

Graduate Students: Adam Barling, Brandon James

Model Development to Predict Feedstock Production of Miscanthus and Switchgrass as Affected by Climate, Soils and Nitrogen

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Graduate Student: Sean Dee

Co-PIs: Michael A. Marletta, Haw Yang, Daniel A. Fletcher, Evan R. Williams, UC Berkeley and Berkeley Lab

Co-PIs: Matthew Hudson and Ray Ming, University of Principal Investigator: Sheila McCormick, UC Berkeley Illinois; Dan Rokhsar, UC Berkeley and Berkeley Lab

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Postdocs: Ting Chen, Chidam Mandan, Sasisanker Padmanabhan

Principal Investigator: Jack Widholm, University of Illinois

Reproductive Barriers in Miscanthus sinensis and Other Biofuel Plants

Co-PIs: Steven Eckhoff, Tony Grift, Alan Hansen, Luis Rodriguez, Lei Tian, Qin Zhang, University of Illinois

Postdoc: Yo Toma

Co-PI: Harvey W. Blanch, UC Berkeley and Berkeley Lab

Improvement of Bioenergy Crops

Principal Investigator: Stephen Moose, University of Illinois

Principal Investigator: KC Ting, University of Illinois

Co-PIs: German Bollero, Fabian G. Fernandez, University of Illinois; Toshihiko Yamada, Hokkaido University, Japan; Aya Nishiwaki, Miyazaki University, Japan

Principal Investigator: Alexis T. Bell, UC Berkeley and Berkeley Lab

Visiting Scholars: Yonghua Xiong, Jiang Yan, Yuliang Zhang, Qinyuan Zhu

Projects:

Engineering Solutions for Biomass Feedstock Production

Principal Investigator: J. Ryan Stewart, University of Illinois

Biomass Pretreatment and Chemical Synthesis of Transportation Fuels

Undergraduate Student: Jude Holscher

Genomics-Enabled Improvement of Andropogoneae Grasses as Feedstocks for Enhanced Biofuel Production

Undergraduate Students: Katie Boesche, Arthur Rudolph

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Germplasm Collection, Nutrient Cycling, Cold Hardiness, Photosynthetic Capacity, and Flowering Phenology of Miscanthus sacchariflorus, Miscanthus sinensis, and Their Natural Hybrids in Native Stands Ranging from Central to Northern Japan

Principal Investigator: German A. Bollero, University of Illinois Co-PIs: Stephen P. Long, Fabian G. Fernandez, University of Illinois

Research Associate: Bruno Martinez

Chemical Imaging of Plant Biomass with Microand Nano-Raman Spectroscopy

Thermophilic Microbes and Enzymes for Biofuel Production

Principal Investigator: Paul Adams, Berkeley Lab

Principal Investigator: Douglas S. Clark, UC Berkeley

Co-PI: Jim Schuck, Berkeley Lab

Co-PIs: Harvey W. Blanch, UC Berkeley and Berkeley Lab; Frank Robb, University of Maryland Biotechnology Institute

Postdoc: Martin Schmidt Cell Wall 3D Architecture at Nanometer Resolution Using High-Throughput TEM and EM Tomography Principal Investigator: Manfred Auer, Berkeley Lab Co-PIs: Kenneth Downing, Bahram Parvin, Berkeley Lab; Jan Liphardt, UC Berkeley

Postdocs: Harshal Chokhawala, Melinda Clark, Tae-Wan Kim, Seth Levine, Cong Trinh Junior Specialist: Paul Wolski Graduate Students: Craig Dana, Jerome Fox, Sarah Huffer, Priya Jayachandran, Dana Nadler

Postdocs: Phillip Jess, Purbasha Sarkar Specialist: Ju Han Associate Specialist: Elena Bosneaga

Postdoc: Fernando Miguez

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Engineering of Thermophilic Anaerobic Bacteria to Improve Biocatalysis of Plant Cell Wall Materials to Ethanol/Butanol Principal Investigator: Isaac Cann, University of Illinois Co-PIs: Roderick I. Mackie, M. Ashley Spies, Satish K. Nair, University of Illinois Research Associate: Wenze Li Postdocs: Yejun Han, Shinichi Kiyonari, Shosuke Yoshida Graduate Students: Richard Cozad, Dylan Dodd Undergraduate Students: Charles Hespan, Amara Hussain, Sana Jafri, Brad Jelinek, Jason Kim, Hussain Mithaiwala, Farhan Quader, Soe Tha Biochemistry, Structure and Engineering of Enzymes and Metabolic Pathways to Overcome Biomass Recalcitrance Principal Investigator: John Gerlt, University of Illinois

Biomass to Transportation Fuel via Hydrodeoxygenation

Ecology and Exploitation of Endophytic Diazotropic Bacteria in Biofuel Crops

Projects

Principal Investigator: Jonathan A. Ellman, UC Berkeley and Berkeley Lab

Principal Investigator: Angela Kent, University of Illinois

Bioengineering and Selection for Biodiesel Production in Bacteria

Co-PI: Robert G. Bergman, UC Berkeley and Berkeley Lab

Undergraduate Student: Neil Gottel

Postdoc: Jason Nichols

Principal Investigator: Thomas B. Rauchfuss, University of Illinois

Principal Investigator: Philip Hugenholtz, Berkeley Lab

Postdoc: Didier Morvan

Principal Investigator: Michelle Chang, UC Berkeley

Surface Kinetic Mechanisms of Enzymatic Cellulose Deconstruction

Graduate Student: Samuel Maurer

Enzyme-Inspired Catalysts for Enhancing Biofuels Production

Genomic Analysis of Bovine Rumen Microbiota Under Different Dietary Regimens

Principal Investigator: Alexander Katz, UC Berkeley

Principal Investigator: Eddy Rubin, Joint Genome Institute, Berkeley Lab

Principal Investigator: Dean Toste, UC Berkeley

Graduate Students: Zachariah Heiden, Aaron Royer

Postdoc: Falk Warnecke

Postdocs: Sudipta Majumdar, Jose Solbiati

Development of Novel Catalysts

Microbial Sugar Utilization

Enzymatic Lignin Degradation

Co-PIs: John Cronan, Satish Nair, University of Illinois

Postdocs: Tatiana Luts, Brandon McKenna

Postdoc: Maria Billini

Staff Scientist: Nikos Krypides

Principal Investigator: Clayton J. Radke, UC Berkeley and Berkeley Lab

Specialist: Andrew Solovyov

Researcher: Pilar Francino

Organometallic Catalytic Approaches to Delignification

Enzyme Discovery in Grass-Feeding Termites for the Depolymerization of Lignocellulosic Biomass

Research Scientist: Natalia Ivanova

Principal Investigators: Nikos Kyrpides, Athanasios Lykidis, Joint Genome Institute, Berkeley Lab

Co-PI: Susannah Tringe-Green, Joint Genome Institute, Berkeley Lab Postdocs: Tao Zhang, Matthias Hess

Postdocs: Francisco Santoro, Sunghee Son

Detoxification of Miscanthus Hydrolysates With a New Phase Separation Method

Graduate Student: Cole Witham

Principal Investigator: Hao Feng, University of Illinois

Junior Specialist: Vincent Chan

Co-PI: Bin Wang, Visiting Research Scientist Postdoc: Pradip B. Dhamole

Projects

Principal Investigator: Yong-Su Jin, University of Illinois Robustness to Environmental Heterogeneity— Engineering Strains Optimized for Large-Scale Fermentation

Graduate Student: Margaret Brown

Principal Investigator: Christopher V. Rao, University of Illinois

Biofuels Production

Co-PI: Ido Golding, University of Illinois Graduate Students: Tasha Desai, Michael Bednarz

Programs Systems Biology of Metabolism and its Regulation in Microbes Important to Biofuel Production

Environmental, Social and Economic Dimensions

Principal Investigator: Adam P. Arkin, UC Berkeley and Berkeley Lab

Programs

Co-PIs: Inna Dubchak, Terry Hazen, Berkeley Lab Postdoc: Anna Gersimova

Principal Investigators: Arpad Horvath and Thomas McKone, UC Berkeley and Berkeley Lab

Research Associate: Jordan Mar

Co-PIs: Maximilian Auffhammer, Peter Berck, Dan Kammen, William Nazaroff, Tim Lipman, Margaret Torn, UC Berkeley

Interest Group: Adam Deutschbauer, Paramvir Dehal, Jennifer Kuehl Engineering a Yeast Strain that Efficiently Utilizes C5/C6 Sugars Principal Investigator: Huimin Zhao, University of Illinois

Life-Cycle Environmental and Economic DecisionMaking for Alternative Biofuels

Lead Researchers: Agnes Lobscheid, Eric Masanet Graduate Students: Catherine Almirall, Joshua Apte, Surakshya Dhakal, Bret Strogen, Kevin Fingerman

Co-PIs: Nathan Price, Lucas Li, University of Illinois

Fungi and Deconstruction of Lignin and Other Components of Miscanthus Cell Walls

Fractionating Recalcitrant Miscanthus by a TwoStage Treatment Under Mild Reaction Conditions

Principal Investigator: John W. Taylor, UC Berkeley

Principal Investigator: Hao Feng, University of Illinois

Co-PIs: Thomas D. Bruns, N. Louise Glass, UC Berkeley

Graduate Student: Atilio de Frias

Postdoc: Tae Hee Lee Graduate Student: Jing Li

Visiting Research Scientist: Bin Wang

Postdoc: Chaoguang Tian Researcher: Tim Szaro 60

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EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL

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Economics of Biofuel Adoption and Impacts Principal Investigator: David Zilberman, UC Berkeley Co-PIs: Gordon Rauser, David Roland-Holst, UC Berkeley

Projects Development of Biofuel Productivity Potentials for Economic Analysis Under Changing Climate, Land Use, and Societal Demands

Postdoc: Gal Hochman

Principal Investigator: Norman L. Miller, UC Berkeley and Berkeley Lab

Graduate Students: Justine Lazaro, Maya Papineau, Deepak Rajagopal, Steve Sexton, Thomas Sproul

Co-PIs: David Sunding, UC Berkeley and Berkeley Lab; N. Maggi Kelly, David Zilberman, UC Berkeley

Administration: Amor Nolan

Faculty Collaborator: Steven W. Running, University of Montana

Subcontractor: Gregory Glass

Postdoc: Alan DiVittrio Ecosystem Impact and Sustainability of Feedstock Production Principal Investigator: Evan H. DeLucia, University of Illinois Co-PIs: Mary R. Berenbaum, Carl J. Bernacchi, Mark B. David, Roderick I. Mackie, and Donald R. Ort, University of Illinois Postdocs: Kristina Anderson-Teixeira, Sarah Davis, Candice Smith, Tony Yannarell, Art Zangeri, Marcelo Zeri Graduate Students: Joshua Burke, Terry Harrison, George Hickman, Mathew Nantie Research Technicians: Mike Masters, Corey Mitchell Collaborator: Bill Parton

Contextualizing Bioenergy Production: Life Cycles, History and Change in Brazil Principal Investigator: Dick Norgaard, UC Berkeley Co-PI: Alastair Iles, UC Berkeley

Principal Investigator: Carl J. Bernacchi, University of Illinois Co-PI: Tracy E. Twine, University of Minnesota Undergraduate Student: Christina Burke

Indirect Land Use Implications of Biofuels Programs

Graduate Student: Xiaolin Ren

Principal Investigator: Michael O’Hare, UC Berkeley

Graduate Students: Avery Cohn, Barbara Haya, Abigail Martin

Principal Investigator: Ximing Cai, University of Illinois Co-PIs: Siwa Msangi, Tingju Zhu, International Food Policy Research Institute Graduate Students: Yan Sun, Dingbao Wang

Principal Investigator: Ximing Cai, University of Illinois

Postdoc: Atsushi Oyama

Food Security Management in an Era of Biofuels

Co-PIs: John Braden, Wayland Eheart, George Czapar, University of Illinois

Graduate Students: Christopher J. Miller, Molly Novy

Principal Investigator: Brian Wright, UC Berkeley

Research Staff: Jody Endres

Italian Visiting Professor: Carlo Cafiero Graduate Students: Fei Han, Di Zheng

Economic and Environmental Impacts of Biofuels; Implications for Land Use and Policy Principal Investigator: Madhu Khanna, University of Illinois Co-PIs: Atul Jain, Hayri Onal, Yanfeng Ouyang, Jurgen Scheffran, University of Illinois Postdocs: Haixiao Huang, Seungmo Kang Graduate Students: William Bowser, Xiaoguang Chen, Matthew Erickson, Shahnila Islam, Christine Lasco, Deniz Tursun, Xiaojuan Yang ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT

Graduate Student: Alan Dafoe

Co-PIs: Madhu Khanna, Thomas Theis, University of Illinois

Researchers: Gary L. Andersen, Robert W. Dibble, J. R. Benemann, I. C. Woertz

Co-PI: A. Bryan Endres, University of Illinois

Postdoc: Regine Spector

Principal Investigator: John B. Braden, University of Illinois

Interactions Between Bioenergy, Carbon Allowances, and Water Quality BMPs: A Case Study of the Lake Bloomington Watershed

Principal Investigator: Jay P. Kesan, University of Illinois

Intellectual Property Protection and Contractual Relations for Biofuels Innovations

Co-PIs: Michael E. Gray, German Bollero, Maria Bonita Villamil, University of Illinois

Principal Investigator: Steve Weber, UC Berkeley

Regional Socioeconomic and Environmental Impacts of Alternative Biofuel Pathways

The Impact of Global Trade in Biofuels on Water Scarcity and Food Security in the World

Principal Investigator: Nigel W. T. Quinn, Berkeley Lab, UC Merced

Principal Investigator: Anne Heinze Silvis, University of Illinois

From a Global Oil Economy to a Global Biofuel Economy

Faculty Collaborators: Renata Andrade, Catholic University of Brasilia; Sergio Pacca, University of Sao Paolo

A Realistic Technology and Engineering Assessment of Algae Biofuel Production

Biofuels Research Initiatives and Extension: Synergizing Engagement With Stakeholders

Graduate Student: Andrew VanLoocke

Co-PI: Tryg J. Lundquist, Berkeley Lab, Cal Poly San Luis Obispo

Biofuels: Law and Regulation

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Regional Environmental Impacts of Biofuel Feedstock Production—Scaling Biogeochemical Cycles in Space and Time

Graduate Students: Tze Ling Ng, Aras Zygas, Jude Tate Market Context for Biofuels Microeconomics Principal Investigator: Hadi Esfahani, University of Illinois

Principal Investigator: Brian Wright, UC Berkeley

Co-PIs: Clifford Singer, John Vasquez, University of Illinois

Researcher: Josephine Mutugu

Graduate Students: Esra Ergul, Thorin Wright

Graduate Students: Kryiakos Drivas, Zhen Lei Undergraduate Student: Astrid Sky

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Biocatalysis The stimulation of a chemical reaction by a biochemical agent such as an enzyme.

A Glossary of Bioenergy Terms

Biodiesel A fuel that is chemically compatible with diesel refined from petroleum but is derived from biological sources such as rapeseed, soybean, and even waste oils, grease, and tallow.

Biofuel A fuel made from biological matter. The term usually refers to liquid fuels rather than materials such as wood.

Biomass Living or recently living biological materials that can be used as fuel; usually refers to plant matter.

Bioprospecting The process of searching for and extracting previously unknown compounds and plant-derived chemicals in organisms.

Carbon Neutral A product or process that does not add more carbon dioxide (CO2) to the atmosphere over its life cycle. For instance, a plant consumes CO2 when it grows, then releases it back out when it is transformed into and used as fuel.

Carbon Sequestration The capture and long-term storage of CO2 before it is emitted into the atmosphere, such as a system that separates CO2 out of coal-fuel emissions and pumps it deep underground.

Cellulases A class of enzymes produced chiefly by fungi and bacteria that catalyze the hydrolysis, or breakdown, of cellulose. 64

ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT

Cellulose

Feedstock

Intellectual Property

All higher plant cells are enclosed in cell walls composed primarily of polysaccharides (polymers of sugar) and lignin (a polymer of phenolics). The principal cell wall polysaccharide is cellulose, a fibrous material composed of hydrogen-bonded chains of the sugar glucose.

A raw material from nature that is in an unprocessed or minimally processed state and can be acted upon or used by organisms to create a product. Biofuel feedstock include grasses, wood, corn, sugarcane, sorghum, and other plant sources.

So-called “creations of the mind”— in the case of the EBI, inventions and new technologies—around which various rights are provided for the inventor. Legal protections give the patent holder the right to control reproduction or adaptation of such creations for a certain period of time.

Cellulosic Biomass The fibrous, woody, and generally inedible portions of plants that make up 75 percent or more of the plant material.

Cellulosomes Complexes of enzymes created by bacteria, but functioning outside the cell. They assist in digestion or degradation of molecules such as cellulose.

Deoxygenation The removal of dissolved oxygen from a substance.

Greenhouse Gases The gaseous constituents (water vapor, carbon dioxide, methane, nitrous oxide and ozone, among others) of the atmosphere, both natural and human-made, that absorb and emit radiation within the spectrum of thermal infrared radiation emitted by the Earth’s surface, the atmosphere itself, and clouds. While greenhouse gases are essential to maintaining the temperature of the Earth, an excess of greenhouse gases can raise its temperature, thus causing climate change and the resultant impacts on land and environment.

Life Cycle Analysis The investigation and valuation of the environmental impacts of a given product or service caused or necessitated by its existence. The term “life cycle” refers to the notion that a fair, holistic assessment of, for example, biofuel development, requires the assessment of raw material production, manufacture, distribution, use and disposal including all intervening transportation steps necessary or caused by the biofuel’s existence.

Lignin

A compound that accounts for roughly 25 percent of the plant material that provides rigidity, Heteropolymers (having many and together with cellulose and different sugar monomers, that hemicellulose forms the cell walls may include xylose, glucose, and the glue that binds them; an arabinose, and others) present in excellent fuel for providing heat, plant cell walls along with cellulose. steam, and electricity. While cellulose is crystalline, strong, and resistant to hydrolysis, hemicellulose has a random, Microbially Enhanced amorphous structure and is easily Hydrocarbon Recovery hydrolyzed by enzymes. (MEHR)

Hemicellulose Depolymerization Breaking down molecules into constituent parts. In biofuel feedstock, using the tools and techniques of biology and chemistry to convert polysaccharides like cellulose and lignocellulose into monosaccharides, or sugars, which then can be fermented into a fuel.

Energy Bioscience The field of scientific study that seeks to discover ways to adapt knowledge of biological processes and materials to the development of improved technologies for energy production.

Ethanol One of the most common types of biofuels, a liquid commonly produced by fermentation of sugar; also known as grain alcohol.

High-Throughput Genome Sequencing

Also called MEOR (oil recovery), using microbes to enhance recovery of fossil fuels.

Various technologies that are employed to lower the cost of gene library sequencing, allowing the large-scale production of thousands or millions of sequences at one time. DNA sequencing encompasses biochemical methods for determining the genetic “blueprint” of organisms by defining the order of their nucleotide bases.

A GLOSSARY OF BIOENERGY TERMS

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Miscanthus A genus of about 15 species of perennial grasses whose productivity, biomass yield, and growth capability on marginal lands makes it a prime candidate for development as a biofuel feedstock. The most widely used “species” is Miscanthus x giganteus, often referred to as “Miscanthus,” which is a sterile hybrid of Miscanthus sinensis and M. saccharifolius. These species can be found throughout East Asia, from Papua New Guinea to southern Siberia, and through Japan and Taiwan. Because of their stature and silver flowering heads, all three are popular garden plants found in gardens throughout North America and Europe.

Net Energy A fuel’s energy, minus what is required to produce or obtain it. For instance, the net energy of gasoline is reduced by the energy lost in extracting oil from the earth, refining it, and transporting it to consumers.

Polysaccharides Complex carbohydrates, such as starch and cellulose, consisting of a number of monosaccharides (sugars) joined together in long chains of molecules.

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Second Generation Biofuels First generation biofuels, like bioethanol, are produced by fermenting plant-derived sugars in a process similar to that used in making beer and wine. This requires the use of food crops like sugar cane and corn. Second generation biofuels, like cellulosic ethanol, are those produced sustainably with biomass comprised of the residual non-food parts of current crops and others, like grasses, grown for non-food purposes.

Sustainability The capacity to maintain a certain process or state indefinitely. To be sustainable, nature’s resources must only be used at a rate at which they can be replenished. A sustainable biofuel feedstock is one that requires little energy input and produces few byproducts that impact the environment.

Xylose

A sugar with five carbon atoms (“C5”) in each molecule, found in the cell walls of plants. Other sugars commonly found there include Synthetic Biology arabinose, mannose, galactose, The design and construction of new fucose, rhamnose, galacturonic biological entities such as enzymes, acid, and glucose, among others. genetic circuits, and cells, or the redesign of existing biological systems; builds upon advances in molecular cell and system biology.

Switchgrass A warm season grass (scientific name Panicum virgatum) that is one of the dominant species of the central North American tallgrass prairie. Properties that make it a strong candidate for biofuel production include survival in drought conditions, perennial habit, and low nitrogen requirement when harvested in the fall.

ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT