News Energy Biosciences Institute Funds First 49 Projects

BERKELEY, CA -- The Energy Biosciences Institute, the world’s largest public/private consortium dedicated to the application of biosciences to the energy sector, has announced an initial set of 49 research projects for funding during the first year of EBI’s 10-year program.

Projects are being supported at all three of the public partner institutions – the University of California, Berkeley; the University of Illinois at Urbana-Champaign; and Lawrence Berkeley National Laboratory. The international energy company BP is funding the decade of work with $500 million, about $20 million of which is supporting the first package of projects.

Research is being pursued in four categories related to exploring the opportunities for production of cellulosic biofuels – feedstock development, biomass depolymerization, biofuels production, and the socio-economic impacts of cellulosic biofuels development. A second initiative, concerned with fossil fuel bioprocessing, is expected to receive funding later this year.

By applying bioscience and biotechnology techniques to the energy industry, EBI will seek to develop the methods and technologies that will enable the transition from a fossil fuel-based energy economy to a balanced portfolio relying more upon renewables and cellulosic or algal biofuels with greatly reduced environmental impacts.

An initial thrust of EBI research will be the development of environmentally benign transportation fuels from non-food biomass (cellulosic biofuels). This involves identifying the most suitable species of plants for use as energy crops, and improving methods of breeding, propagation, harvesting, storage and processing of biomass to next-generation fuels. A central objective is to ensure that this is done in a sustainable way without negative impacts on food production or the environment. In this respect, a notable feature of the EBI research portfolio is an emphasis on investigation of the environmental and socioeconomic aspects of cellulosic biofuels.

Chris Somerville, a plant biochemist at UC Berkeley and EBI’s Director, said the establishment of the EBI represents a significant opportunity to explore solutions to the world’s most intractable and critical technology challenge. “We’ve embarked on a commitment to develop new solutions to global energy needs through the deployment of new technologies based on advances in knowledge about biological processes,” he said. “The enormous progress in understanding basic biological processes achieved during the past several decades have not previously been brought to bear in the energy sector, so we believe that there may be fundamentally new opportunities to reduce the environmental impacts of energy production and use.

“In addition,” he continued,“we believe that the multi-disciplinary approach in EBI, bringing together biology, chemistry, engineering and economics in the same building, will lead to completely new perspectives on how to approach these problems.”

Somerville is assisted by Steve Long, the Institute’s Deputy Director who oversees work at the University of Illinois, including a 340-acre Energy Farm, and by Paul Willems, the Associate Director who oversees the BP employees within the Institute.

From an initial list of more than 250 pre-proposals from researchers at the three institutions, EBI management employed a competitive peer review system to narrow the field to 49 high-priority research efforts that have received funding.  Awards were divided into two categories: programs and projects.  Programs are typically large integrated multi-investigator efforts with a single major target, 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 either too speculative at this stage to be a program or are on a single fixed task.   These average about $150,000 per year.

Program research is conducted mostly within the EBI, so that the post-doctoral and graduate student researchers from different disciplines will work side-by-side.  This will ensure 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 initial programs and projects are:


Feedstock Development

Eight projects and programs are seeking to identify and breed plant species that can maximize cellulosic biomass production on a global scale and to learn how to grow and harvest them sustainably. A primary goal is to discover plants that can produce more biomass, using minimal land, water and energy.



  • Assessing the Potential Impact of Insect Pests and Plant Pathogens on Biomass Production of Miscanthus x Giganteus and Switchgrass: These two plant species are highly promising biomass sources, and insects and pathogens can cause diseases that can have a serious impact on production. This project seeks to identify such threats and to study possible control strategies. Principal Investigator: Michael E. Gray, University of Illinois.
  • Genomics-Enabled Improvement of Andropogoneae Grasses as Feedstocks for EnhancedBiofuel Production: Four related plant species are leading biomass candidates due to their efficiencies in photosynthesis, nitrogen economy, and water use – sugar cane, Miscanthus, switchgrass and sorghum. Through genetic sequencing and bioinformatics, investigations into gene structure and function will seek ways to improve crop yield, quality and sustainability. Principal Investigator: Stephen Moose, University of Illinois.
  • Engineering Solutions for Biomass Feedstock Production: This project will study pre-harvest crop production, harvesting, transport, storage, and systems to develop the operational machinery, databases, and decision support tools required in the successful production of biomass feedstocks. Principal Investigator: K. C. Ting, University of Illinois.
  • Feedstock Production/Agronomy Program: Through field studies in Illinois and other locations around the globe, researchers will provide statistical information on feedstock yields, geographic variations, and agronomic requirements. The goal is to find the best combination of conditions and practices for high yield and sustainability. Principal Investigator: Thomas Voigt, University of Illinois.



  • Reproductive Barriers in Miscanthussinensis and Other Biofuel Plants: “Self-incompatibility” is a condition in many plant species, including grasses, which limits opportunities to improve productivity through breeding. Scientists will study the genetic basis of incompatibility in Miscanthus. Principal Investigator: Sheila McCormick, UC Berkeley.
  • Model Development to Predict Feedstock Production of Miscanthus and Switchgrass as Affected by Climate, Soils and Nitrogen: This mathematical modeling project will refine current knowledge about how crops are affected by environmental factors. For Miscanthus, in particular, such experimental data can more accurately assess its performance in the United States. Principal Investigator: German A. Bollero, University of Illinois.
  • Collection, Nutrient Cycling, Cold Hardiness, Photosynthetic Capacity, and Flowering Phenology of Miscanthussacchariflorus, Miscanthussinensis, and Their Natural Hybrids in Native Stands Ranging from Central to Northern Japan: Miscanthus, a promising biofuel crop, is native to Asia. It has its limitations, disadvantages and information gaps as a cultivar, so this project will study nutrient uptake and carbon sequestration of Japanese strains, some of which have been managed for hundreds of years. Thus long-term impacts of Miscanthus on biological sequestration and fertilizer requirements can be projected. Principal Investigators: J. Ryan Stewart and Fabian G. Fernandez, University of Illinois.
  • Genetic Improvement of Bionergy Crops: This project will develop tissue culture and stable genetic transformation systems for the sterile hybrid, but highly productive, Giant Miscanthus (Miscanthus x giganteus). This will provide a test-bed allowing the EBI to determine if specific genetic changes are of benefit -- for example, altered lignin contents. Principal Investigator: Jack Widholm, University of Illinois.


Biomass Depolymerization

Fashioning fuel from plants requires the use of individual sugar molecules that make up most of a plant’s body. Biofuel production requires isolating these molecules 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. These 19 projects are determined to find a less costly but effective depolymerization method, a requirement for ensuring that biofuels can be reasonably priced.



  • Chemical Imaging of Plant Biomass with Micro- and Nano-Raman Spectroscopy: One of the most expensive steps in biofuels processing is the conversion of cellulosic materials in plant cell walls, and critical to this conversion is the costly pretreatment of the biomass to make it amenable to generation of constituent sugar units. This work intends to create a high-resolution chemical map of plant cell walls, details of which will allow researchers to visualize the chemical and physical obstacles to the breakdown – vital to developing better pretreatment methods. Principal Investigator: Paul Adams, Berkeley Lab.
  • Cell Wall 3D Architecture at Nanometer Resolution Using Correlative Raman and Electron Tomography Imaging: This project seeks to obtain a comprehensive model of the cell wall, which is required to improve the efficiency of the conversion of plant material to biofuels. The molecular identity of the cell wall will be determined via the use of multiple complementary microscopy approaches. Principal Investigator: Manfred Auer, Berkeley Lab.
  • Biomass Pretreatment and Chemical Synthesis of Transportation Fuels: The highly ordered structure of cellulose in the plant cell wall, plus the linkages between lignin and hemicellulose, make the breakdown of the material into sugars, and subsequent conversion to fuels, extremely difficult. This project uses “ionic liquids,” a new class of solvents, for the dissolution and pretreatment of cellulose. Principal Investigator: Alexis T. Bell, UC Berkeley.
  • Cellulosomes Optimized for Biofuel Production: Understanding the molecular mechanisms of cellulose hydrolysis by cellulosomes is the goal of this work. This understanding may provide key insights needed to reconstruct “designer cellulosomes” optimized for depolymerization of the complex plant biomass envisioned as the feedstock for biofuels. Principal Investigator: Jamie H. D. Cate, UC Berkeley and Berkeley Lab.
  • Enhanced Conversion of Lignocellulose to Biofuels– Bioprocess Optimization from Cellulose Hydrolysis to Product Fermentation: This research addresses several bottlenecks impeding the production of biofuels and their potential solutions via microbe discovery and development. Goals include new organisms as effective enzyme sources, protein engineering of improved cellulases, and cell and bioprocess engineering for better solvent tolerance and fermentation. Principal Investigator: Douglas S. Clark, UC Berkeley.
  • Discovery and Characterization of Hydrolytic Enzymes to Improve Biocatalysis and Conversion of Plant Cell Wall Polysaccharides to Biofuels: A major limitation of microorganisms used in fermentation of carbohydrates to ethanol is their lack of enzymes required for the efficient conversion of cellulose to sugars. Nature, however, has evolved such enzymes that degrade cell walls in places like the stomach of cows. This work will identify the genes that encode for such enzymes, with a view to development of more highly active enzyme systems for use in the bioenergy-crops-to-fuels conversion. Principal Investigator: Isaac Cann, University of Illinois.
  • Biochemistry, Structure and Engineering of Enzymes and Metabolic Pathways to Overcome Biomass Recalcitrance: A major challenge in biofuel development is to reduce the energy expended in releasing cell wall polysaccharides so that the energy-rich cellulose and hemicellulose in plant cell walls can be more efficiently converted to fuels. This project will focus on the development of novel pathways for lignin hydrolysis. Genomes of bacteria that use lignocellulose as a carbon source will be sequenced and studied. Principal Investigator: John Gerlt, University of Illinois.
  • Enzyme-Inspired Catalysts for Enhancing Biofuels Production: Scientists will work on synthesizing new composite materials that are useful in the catalytic aspects ofbiofuels processing, such as hydrolysis and deoxygenation. Principal Investigator: Alexander Katz, UC Berkeley.
  • Development of Novel Catalysts: This program is aimed at the development of chemical catalysts for cellulose and lignin breakdown and modification. It incorporates high-throughput catalyst screening technology to discover and optimize these catalysts. Principal Investigator: Dean Toste, UC Berkeley.



  • Fungi and Deconstruction of Lignin and Other Components of Miscanthus Cell Walls: The objective is to identify novel cell wall deconstruction enzymes from the fungi that are best suited to decay Miscanthus cell walls, and to understand how the fungi coordinate their genomes to do this. This project seeks to identify new fungi that are capable of degrading lignocellulose and exploring the biochemical mechanisms used by these fungi. Principal Investigator: John W. Taylor, UC Berkeley.
  • Biomass to Transportation Fuel via Hydrodeoxygenation: New and efficient methods are needed to convert heavily oxygenated lignocellulosic biomass to higher energy-density hydrocarbon fuels. Catalysis research will be applied to develop new catalysts for this conversion and to better understand the mechanisms involved in transformations. Principal Investigator: Jonathan A. Ellman, UC Berkeley.
  • Enzyme Discovery in Grass-Feeding Termites for the Depolymerization of Lignocellulosic Biomass: Studying the natural systems that have evolved to decompose plant cell wall polymers – for example, the termite hindgut, which efficiently transforms plant biomass into sugars, fatty acids, hydrogen and methane – will offer insight into what is required for an effective synthetic process. The termite’s digestive system is like a miniature bioreactor, in which bacteria and archaea enable the energy transformation. Principal Investigator: Philip Hugenholtz, Berkeley Lab.
  • Surface Kinetic Mechanisms of Enzymatic Cellulose Deconstruction: The goal of this research is to provide an understanding of the cellulose decomposition in plant cell walls that leads to sugar production. Through the understanding of the molecular events that trigger key catalyzing enzymes, a framework can be developed upon which improved enzymes can be designed and synthesized. Principal Investigator: C. J. Radke, UC Berkeley.
  • Analysis of Bovine Rumen Microbiota Under Different Dietary Regimens for Identification of Feedstock-Targeted Cellulolytic Genes: Just as the termite is a model organism for the processing of plants into fuel, so the stomachs of cows and sheep offer a dense microbial community that enables the rapid digestion of high-fiber plants. This work will identify the enzymes produced by the microbes responsible for degradation of the plant cell wall polymers. This system can perhaps be co-opted for cellulose biomass conversion. Principal Investigator: Eddy Rubin, Joint Genome Institute (Berkeley Lab).
  • Detoxification of Miscanthus Hydrolysates With a New Phase Separation Method: This project will explore new methods for physically extracting chemicals which are toxic to the fermenting organisms on which biofuel processing depend. These degrading chemicals result from pretreatment of biomass and other processes. Principal Investigator: Hao Feng, University of Illinois.
  • Fractionating Recalcitrant Miscanthus by a Two-Stage Treatment Under Mild Reaction Conditions: A two-step process will first extract hemicellulose in Miscanthusand study it for value-added products following its separation from the plant, and then cellulose-rich solid byproducts will be pretreated for analysis of inhibiting compounds. The work seeks an environmentally friendly liquid for removal of lignin in biomass processing. Principal Investigator: Hao Feng, University of Illinois.
  • Ecology and Exploitation of EndophyticDiazotropic Bacteria in Biofuel Crops: This project will study the contribution of nitrogen-fixing bacteria to bioenergy crops and will design strategies to promote colonization of these bacteria. Methods are desired to increase the potential for plant-microbe interactions to enhance productivity and sustainability of biofuel crops. Principal Investigator: Angela Kent, University of Illinois.
  • Organometallic Chemistry Relevant to Delignification: The goal of this research is to uncover new transformations that will translate into improved process technologies either at the biomass pre-treatment stage or later. Organometallic chemistry focuses on the interaction of organic compounds with metal ions. The properties of organometallic catalysts that play major roles in biofuel processing will be the targets of analysis. Principal Investigator: Thomas B. Rauchfuss, University of Illinois.
  • New Approaches to Lignin Depolymerization: Biochemical studies will be conducted to understand how complex pathways interact with each other as lignin is deconstructed in plant cell walls. Environmental organisms with unique metabolism will be studied to guide the design and help describe the new chemistry that evolves inside the cell. The goal is to engineer living cells to carry out the synthesis of target compounds. Principal Investigator: Michelle Chang, UC Berkeley.


Biofuels Production

More productive ways of converting lignocellulose-derived sugars to fuels is the subject of these five projects. Methods used for biofuels today are similar to the fermentation practices used to make beer and wine, but they are not adequate for the large-scale production of cellulosic biofuels. EBI researchers seek ways to boost the concentration of fuel produced by the biofuel fermenting process. This could lead to a significant reduction in the cost of making biofuels.



  • Microbial Characterization Facility: Bacteria are an attractive alternative to yeast for industrial-level fuel production, and they can be engineered to greatly increase output. This requires a thorough systems-level understanding of how the bacterial metabolism, gene regulation, and stress response influence the process. This new facility will include an experimental and computational comparative microbial systems biology infrastructure that can identify, understand and engineer the central pathways in bacteria and fungi. Principal Investigator: Adam P. Arkin, UC Berkeley and Berkeley Lab.



  • Bioengineering and Selection for Biodiesel Production in Bacteria: The goal here is to improve the bio-oil production in engineered microbes, integrating introduced genes and pathways into their new genomic and cellular systems. The model organisms E. coli and Acinetobacter will be used. Principal Investigator: Nikos Kyrpides, Joint Genome Institute (Berkeley Lab).
  • Improvement of Xylose Fermentation By Recombinant Saccharomycescerevisiae Through Systematic and Combinatorial Approaches: Cellulosic biomass consists primarily of two fermentable sugars, glucose and xylose, and there is no optimal microorganism that can ferment both with high yield and productivity. Xylose utilization is essential for commercial bioconversion of lignocellulose into ethanol or other biofuels. This work seeks to understand regulation and control of xylose fermentation and to construct a yeast strain capable of enhancing biofuel production. Principal Investigator: Yong-Su Jin, University of Illinois.
  • Engineering a Yeast Strain that Efficiently Utilizes C5/C6 Sugars: Yeasts are currently used in fermentation of sugars to biofuel. This effort will focus on optimizing the pathways for sugar utilization by yeast, and studying the properties ofstrains currently used in fermentation in the production of ethanol. Principal Investigator: Huimin Zhao, University of Illinois.
  • Robustness to Environmental Heterogeneity – Engineering Strains Optimized for Large-Scale Fermentation: This work is focused on constructing a computational model of multiple-sugar utilization, which will facilitate the design of strains capable of efficiently metabolizing three sugars involved in plant fermentation. The dynamics of gene expression of cells as they transition from one sugar to the next will be characterized. Principal Investigator: Christopher V. Rao, University of Illinois.


Environmental, Social and Economic Dimensions

The EBI will seek to understand the potential environmental, economic and societal impacts of meeting a growing portion of the world’s energy needs through biofuels. This includes answering questions surrounding the amount of land globally available for biofuel production, the consequences of using land to grow biofuel crops, the effect of a biofuel industry on food crops, and the effects of production on the environment. The answers may assist policymakers as they attempt to regulate this transitioning industry. Seventeen projects have been funded to begin to find those answers.



  • Life-Cycle Environmental and Economic Decision-Making for Alternative Biofuels: The goal of this study is to analyze issues of cost, resource limitations, health risks, climate impacts, nutrient-cycle disruption, and other potential impacts of biofuel development. The results will inform key decisions in biofuels research and strategies for biofuels regulation. Principal Investigators: Arpad Horvath and Thomas McKone, UC Berkeley and Berkeley Lab.
  • Economics of Biofuel Adoption and Impacts: An economic understanding of fundamental issues associated with the introduction of biofuels is essential in order to develop tools to address them. This work will analyze impacts on the global economy, biofuel systems, energy resources and utilization, water allocation, and investment risk mitigation. Principal Investigator: David Zilberman, UC Berkeley.
  • Environmental Impact and Sustainability of Feedstock Production: Researchers will determine short- and long-term ecological impacts and sustainability issues of potential lignocellulosicfeedstocks. Through studies of Miscanthus and other plants, they will describe the environmental consequences of land conversion; capacity of feedstocks to sequester carbon, retain nitrogen and minimize water contamination; and effects of climate variables on ecosystem processes. Principal Investigator: Evan H. DeLucia, University of Illinois.
  • Biofuels: Law and Regulation: A comprehensive analysis of current legal and regulatory requirements (local, regional, international) will help determine potential hurdles to commercialization of biofuels in law and policy. This understanding is critical to developing a legal structure to support the industry. Principal Investigator: Jay P. Kesan, University of Illinois.
  • Economic and Environmental Impacts of Biofuels; Implications for Land Use and Policy: The project will examine the optimal allocation of existing cropland for feedstock production under several scenarios, site-specific impacts on yield and resources for each feedstock, biorefinery and transportation requirements, trade and subsidy policies, and impacts on farmers of crop transition. Principal Investigator: Madhu Khanna, University of Illinois.



  • Development of Biofuel Productivity Potentials for Economic Analysis Under Changing Climate, Land Use, and Societal Demands: Using economic analysis and numerical simulation of multiple scenarios, scientists will determine the most suitable biogeographic regions for biofuels, impacts of changes in soils and climate, impacts of the production to biofuels on natural habitats and food cropland, and impacts on economic and environmental conditions as cellulosic crops become widespread. Principal Investigator: Norman L. Miller, UC Berkeley and Berkeley Lab.
  • Explaining, Contextualizing and Comparing Bioenergy Life-Cycles in Brazil: Since Brazil has been an active producer of biofuels for 35 years and will greatly increase its production in the next decade, its biofuels model can be instructive to other nations. This work will assemble the first history of the Brazil program that links technological research and planning with environmental outcomes. Out of this analysis will come “best practices” to guide future activities in the industry. Principal Investigator: Dick Norgaard, UC Berkeley.
  • A Realistic Technology and Engineering Assessment of Algae Biofuel Production: This project evaluates the prospects for large-scale cultivation of algae, followed by its conversion to various biofuels. Scientists will make an assessment of the technological, engineering, and environmental aspects of algae-based biofuels and form recommendations about further research. Principal Investigator: Nigel W. T. Quinn, Berkeley Lab, UC Merced.
  • Food Security Management in an Era of Biofuels: Biofuels promise to change and expand the nature of the risks faced by food consumers. Modeling will help respond to the challenge of the integrated energy-biofuels market. Estimates will be developed for the world sugar market, and those will be applied to other agricultural crops. Policy alternatives, such as food storage enhancement and regional cooperation, will be assessed. Principal Investigator: Brian Wright, UC Berkeley.
  • Intellectual Property Protection and Contractual Relations for Biofuels Innovations: This survey of the global intellectual property (IP) landscape will provide information about the novelty of research outputs as they emerge from the project. It will include an assessment of the evolving effects of IP protection on scientists and their research as the biofuel industry matures. Principal Investigator: Brian Wright, UC Berkeley.
  • Regional Environmental Impacts of Biofuel Feedstock Production – Scaling Biogeochemical Cycles in Space and Time: This work will evaluate the impact of large-scale land conversion to biofuel feedstock production on energy, water and carbon resources. Numerical modeling will be applied to develop a global vegetation model, in particular studying feedstock production within the Amazon and Mississippi River basins. It will also identify “hot spots” in the United States and South America where feedstock production may maximize yield or where conditions may not be ideal for this land use. Principal Investigator: Carl J. Bernacchi, University of Illinois.
  • Regional Socioeconomic and Environmental Impacts of Alternative Biofuel Pathways: The goal here is to identify the mix of pathways that best balances economic and environmental considerations. A model will be applied that separates the world into four regions, each different in terms of biofuels, feedstocks, water quality, policies, and costs. From this analysis, decisions on the most efficient mix of biofuels and feedstocks, with sensitivity to policy measures and technological change, can be made. Principal Investigator: John B. Braden, University of Illinois.
  • The Impact of Global Trade in Biofuels on Water Scarcity and Food Security in the World: This research focuses on the food vs. fuel debate. It seeks to address which policies, technologies and investments are necessary to ensure that bioenergy is developed in ways that are economically efficient as well as compatible with reducing poverty and global warming. The modeling analysis will also study how large-scale biofuels production will influence water availability. Principal Investigator: Ximing Cai, University of Illinois.
  • Interactions Between Bioenergy, Carbon Allowances, and Water Quality BMPs: A Case Study of the Lake Bloomington Watershed: This central Illinois site will be used to gather useful information on how incentive-based water quality systems, energy crop production pressures, and opportunities for carbon sequestration interact to influence producers’ management decisions. This is especially applicable to corn, which is expected to be the primary biofuel feedstock over the next decade as other feedstocks are developed. Environmental impacts during the transition will be projected. Principal Investigator: Ximing Cai, University of Illinois.
  • Market Context for Biofuels Microeconomics: Researchers will develop a political economy framework for temporal variation of global energy and agriculture markets, which can then support studies of the economic realities of applying biotechnology to liquid fuel production. Included will be projected market price fluctuations of energy sources in different regions of the world, as well as relevant government policy considerations. Principal Investigator: Hadi Esfahani, University of Illinois.
  • Biofuels Research Initiatives and Extension: Synergizing Engagement With Stakeholders: A “learning community” that facilitates communication and collaborative problem-solving is desirable as the biofuel industry grows, and this work hopes to facilitate such a network between growers, consumers and researchers. A perceptions survey will be created, and data will be collected and disseminated broadly to stakeholders. Principal Investigator: Anne Heinze Silvis, University of Illinois.
  • From a Global Oil Economy to a Global Biofuel Economy: The goal of this project is to understand the international economic and political implications of even a partial shift to biofuels. Using historical examples such as the shift from coal to oil, the research will identify possible global consequences of a shift in fuel sources, which will be useful in formulating U.S. policy. Principal Investigator: Steve Weber, UC Berkeley.


Click here to read or download a copy of the contract.


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