Bioenergy Research Centers U.S. Department of Energy Office of Science
U.S. Department of Energy Office of Science

Suggested citation: U.S. DOE. 2010. U.S. Department of Energy’s Bioenergy Research Centers: An Overview of the Science, DOE/SC-0127. Office 

of Biological and Environmental Research within the DOE Office of 

Science (genomicscience.energy.gov/centers/brcbrochure.pdf).

Sources for cover images: Joint BioEnergy Institute photo by Jonathan Remis, Lawrence Berkeley National Laboratory. BioEnergy Science Center photo by Seokwon Jung and Arthur Ragauskas, Georgia 

Institute of Technology. Great Lakes Bioenergy Research Center photo 

by Kurt Stepnitz, Michigan State University.

Websites for DOE Bioenergy Research Centers

DOE Joint BioEnergy Institute

jbei.org

DOE BioEnergy Science Center

bioenergycenter.org

DOE Great Lakes Bioenergy 

Research Center

glbrc.org

Contact for DOE Bioenergy Research Centers

Sharlene Weatherwax

U.S. Department of Energy Office of Science

Office of Biological and Environmental Research

Sharlene.Weatherwax@science.doe.gov
Bioenergy Research Centers U.S. Department of Energy Office of Science i

U.S. DEPARTMENT OF ENERGY’S

Bioenergy Research Centers

An Overview of the Science

DOE/SC-0127

Prepared for the

U.S. Department of Energy Office of Science

Office of Biological and Environmental Research

July 2010

Web Address for this Document: genomicscience.energy.gov/centers/brcbrochure.pdf
ii U.S. Department of Energy Office of Science Bioenergy Research Centers

Introduction .................................................................................................................................................................................. 1

Biofuels: Research Strategies ..................................................................................................................................................... 2

Research Sidebar: Tapping Nature’s Strategies for Biomass Degradation ....................................................................... 2

DOE Bioenergy Research Center Strategies at a Glance................................................................................................... 4

Research Sidebar: Bridging the Gap from Fundamental Biology to Industrial Innovation for Bioenergy................... 6

Summaries of DOE Bioenergy Research Centers

 DOE Joint BioEnergy Institute................................................................................................................................................... 8

JBEI Research Highlights...................................................................................................................................................12

 DOE BioEnergy Science Center...............................................................................................................................................14

BESC Research Highlights.................................................................................................................................................18

 DOE Great Lakes Bioenergy Research Center........................................................................................................................20

GLBRC Research Highlights.............................................................................................................................................24

DOE Genomic Science Program..............................................................................................................................................26

DOE Biological and Environmental Research............................................................................................ Inside back cover

DOE Office of Science..................................................................................................................................... Inside back cover

Table of Contents

For More Information

DOE Bioenergy Research Centers

genomicscience.energy.gov/centers/

Joint BioEnergy Institute ( JBEI)

jbei.org

BioEnergy Science Center (BESC)

bioenergycenter.org

Great Lakes Bioenergy Research Center (GLBRC)

glbrc.org

DOE Genomic Science Program

genomicscience.energy.gov

DOE Mission Focus: Biofuels

genomicscience.energy.gov/biofuels/

DOE–USDA Plant Feedstock Genomics for Bioenergy

genomicscience.energy.gov/research/DOEUSDA/

DOE Joint Genome Institute

jgi.doe.gov

Breaking the Biological Barriers to Cellulosic Ethanol: 

A Joint Research Agenda

genomicscience.energy.gov/biofuels/b2bworkshop.shtml

DOE Office of Biological and Environmental Research

science.doe.gov/ober/

DOE Office of Science

science.doe.gov
Bioenergy Research Centers U.S. Department of Energy Office of Science 1

DOE Bioenergy Research Centers

Introduction

Alternative fuels from renewable cellulosic biomass—

plant stalks, trunks, stems, and leaves—are expected 

 to significantly reduce U.S. dependence on imported 

oil while enhancing national energy security and decreasing 

the environmental impacts of energy use. Ethanol and other 

advanced biofuels from cellulosic biomass are renewable 

alternatives that could increase domestic production of transportation fuels, revitalize rural economies, and reduce carbon 

dioxide and pollutant emissions. According to U.S. Secretary 

of Energy Steven Chu, “Developing the next generation of 

biofuels is key to our effort to end our dependence on foreign 

oil and address the climate crisis while creating millions of 

new jobs that can’t be outsourced.”

Although cellulosic ethanol production has been demonstrated on a pilot level, developing a cost-effective, commercial-scale cellulosic biofuel industry will require transformational science to significantly streamline current production 

processes. Woodchips, grasses, cornstalks, and other cellulosic biomass are widely abundant but more difficult to break 

down into sugars than corn grain—the primary source of U.S. 

ethanol fuel production today. Biological research is key to 

accelerating the deconstruction of cellulosic biomass into sugars that can be converted to biofuels (see figure below, From 

Biomass to Biofuels).

The Department of Energy (DOE) Office of Science continues to play a major role in inspiring, supporting, and guiding 

the biotechnology revolution over the past 30 years. The DOE 

Genomic Science program is advancing a new generation of 

research focused on achieving whole-systems understanding 

of biology. This program is bringing together scientists in 

diverse fields to understand the complex biology underlying 

solutions to DOE missions in energy production, environmental remediation, and climate change science. For more 

information on the Genomic Science program, see p. 26.

To focus the most advanced biotechnology-based resources 

on the biological challenges of biofuel production, DOE 

established three Bioenergy Research Centers (BRCs) in 

September 2007. Each center is pursuing the basic research 

underlying a range of high-risk, high-return biological solutions for bioenergy applications. Advances resulting from the 

BRCs are providing the knowledge needed to develop new 

biobased products, methods, and tools that the emerging 

biofuel industry can use (see sidebar, Bridging the Gap from 

Fundamental Biology to Industrial Innovation for Bioenergy, 

p. 6). The DOE BRCs have developed automated, highthroughput analysis pipelines that will accelerate scientific 

discovery for biology-based biofuel research.

The three centers, which were selected through a scientific peerreview process, are based in geographically diverse locations—

the Southeast, the Midwest, and the West Coast—with partners across the nation (see U.S. map, DOE Bioenergy Research 

Centers and Partners, on back cover). DOE’s Lawrence 

Berkeley National Laboratory leads the DOE Joint BioEnergy 

Institute ( JBEI) in California; DOE’s Oak Ridge National 

Laboratory leads the BioEnergy Science Center (BESC) in 

Tennessee; and the University of Wisconsin–Madison leads 

the Great Lakes Bioenergy Research Center (GLBRC). Each 

center represents a multidisciplinary partnership with expertise 

From Biomass to Biofuels
2 U.S. Department of Energy Office of Science Bioenergy Research Centers

DOE Bioenergy Research Centers

spanning the physical and biological sciences, including genomics, microbial and plant biology, analytical chemistry, computational biology and bioinformatics, and engineering. Institutional partners include DOE national laboratories, universities, 

private companies, and nonprofit organizations.

Biofuels: Research Strategies

The ultimate goal for the three DOE Bioenergy Research 

Centers is to better understand the biological mechanisms 

underlying biofuel production so that those mechanisms can 

be redesigned, improved, and used to develop novel, efficient 

bioenergy strategies that can be replicated on a mass scale. 

New strategies and findings emanating from the centers’ 

fundamental research ultimately will benefit all biological 

investigations and will create the knowledge underlying three 

grand challenges at the frontiers of biology:

•	 Development of next-generation bioenergy crops

•	 Discovery and design of enzymes and microbes with novel 

biomass-degrading capabilities

•	 Development of transformational microbe-mediated strategies for biofuel production

The extremely complex science needed to solve these challenges requires multiple interdisciplinary teams that approach 

the same problems from different directions to accelerate 

scientific progress (see table, DOE Bioenergy Research Center Strategies at a Glance, p. 4). The following sections explain 

some scientific issues related to these challenges.

Tapping Nature’s Strategies for Biomass Degradation

Nature has devised two types of enzyme-based strategies for breaking down plant cell walls. One strategy observed in 

oxygen-rich environments involves fungi and bacteria that secrete individual enzymes with complementary functions for degrading cell walls. These free enzymes work as a team to deconstruct plant cell-wall carbohydrates into simple 

sugars (see figure, Free-Enzyme Systems). Some of the most-studied free enzymes are cellulases secreted byTrichoderma 

reesei, a canvas-eating fungus isolated during World War II from tents and uniforms damaged by jungle rot. The DOE 

Bioenergy Research Centers are exploring natural environments to identify and produce new mixes of biomass-degrading 

enzymes that can substantially increase the efficiency of cellulosic biofuel production.

A second strategy, occurring in oxygen-free environments, is exhibited 

by bacteria that produce cellulosomes—large multiprotein complexes 

that degrade the cell wall by assembling several different enzymes 

into a single structure. Cellulosomes protrude from bacterial surfaces, latch onto plant cell walls, and tear carbohydrates into simple 

sugars. Clostridium thermocellum, a model bacterium for studying 

cellulosomes, can produce more than 25 different cell wall–degrading 

enzymes that it can “plug and play” into its large protein scaffold (see 

figure, The Cellulosome). By sensing the surrounding environment, 

C. thermocellum can modify the 

functionality of its cellulosomes 

on demand by assembling different combinations of enzymes to 

attack various compounds in the 

plant cell wall. The LEGO-like 

arrangement of enzymes in cellulosomes offers a unique opportunity to engineer “designer” 

multienzyme complexes targeted to specific biomass types 

or different stages of biomass 

deconstruction.

Free-Enzyme Systems

The Cellulosome
Bioenergy Research Centers U.S. Department of Energy Office of Science 3

DOE Bioenergy Research Centers

1. Development of Next-Generation 

Bioenergy Crops

Bioenergy crops include grasses, trees, and other plants grown 

specifically for energy production. These crops and other forms 

of cellulosic biomass provide the raw material for bioenergy. 

Cellulosic biomass primarily consists of cellulose and other 

complex cell-wall compounds, such as lignin, that strengthen 

and support plant structure. The main constituents of many 

plant cell-wall compounds are simple sugars amenable to 

fermentation, producing ethanol, other biofuels, and chemicals. The cell walls are so complex that several thousand genes 

are thought to be involved in their synthesis and maintenance. 

Many of these genes are now being characterized by the BRCs, 

and our knowledge of associated biological functions continues 

to expand as a result of this research.

By understanding the genes and mechanisms that control 

cell-wall synthesis in plants, scientists could develop new 

energy crops with altered biomass composition or modified links within and between cell-wall components. These 

“designer” bioenergy crops would retain robust growth in 

the field but could be triggered to break down rapidly in a 

biorefinery. Besides modification of plant cell walls, another 

approach to improving bioenergy crops is to increase the 

accumulation of starches and oils in plant tissues. Starches 

and oils can be converted into biofuels much more easily 

than cellulose.

Altering biomass composition is one approach to developing 

better bioenergy crops, but other important improvements 

include increasing biomass productivity per acre, increasing 

resistance to pests and drought, and decreasing applications of 

fertilizers and other inputs. Many potential energy crops are 

grasses or fast-growing trees that have not benefited from the 

years of agricultural research devoted to breeding traditional 

crops such as corn or wheat. Availability of more plant-genome 

sequence information can accelerate the development of DNA 

markers used to identify and isolate the many genes associated 

with traits that can improve energy crop yield, degradability, and 

sustainability. Having DNA markers and other new biological 

tools could significantly reduce the time required to identify 

desired genetic variants and produce new energy crops.

2. Discovery and Design of Enzymes 

and Microbes with Novel BiomassDegrading Capabilities

Nature uses both enzymes and multienzyme complexes, 

including those called “cellulosomes,” to break down cellulosic 

biomass (see sidebar, Tapping Nature’s Strategies for Biomass 

Degradation, p. 2). The biomass-degrading enzymes and 

cellulosomes studied thus far function slowly enough that 

scientists are optimistic that their activity and effectiveness can 

be improved significantly. Several factors—the nearly impenetrable architecture of plant cell walls, chemical and physical 

changes to biomass during pretreatment, and structural features 

of the enzymes—collectively contribute to the inefficiency of 

current biomass deconstruction approaches. Therefore, 

multiple strategies must be studied simultaneously and systematically at each DOE Bioenergy Research Center to illuminate 

the various biological and chemical processes at work.

Certain fungi and bacteria specialize in producing enzymes 

that degrade biological materials in natural environments. 

Discovering, harnessing, and enhancing the best biomassdegrading enzymes and microbes in nature ultimately will 

have a significant impact on increasing the efficiency and 

reducing the cost of cellulosic biofuel production. Scientists are just beginning to explore the staggering diversity of 

enzymes in environments such as the termite gut and cow 

rumen, and the vast majority of natural habitats are yet to be 

investigated. To accelerate the discovery of novel enzymes 

and microbes and to understand how their degradative 

processes work synergistically, each center is searching 

diverse biomass-degrading environments, from hot springs 

to rainforests to compost piles.

Discovering new biomass-degrading capabilities in nature 

is only part of the challenge. Molecular-level understanding of how enzymes and cellulosomes degrade biomass is a 

prerequisite to designing improved processes. Because no 

single research approach can provide this understanding, 

each center is integrating different combinations of methodologies. These include high-throughput screens for proteins 

and metabolites, chemical analyses, state-of-the-art imaging 

technologies, and computational modeling to identify and 

characterize important factors influencing the rapid deconstruction of plant materials into sugars and other energyrich components that can be converted to biofuels.
4 U.S. Department of Energy Office of Science Bioenergy Research Centers

Research Strategies: Development of Next-Generation Bioenergy Crops Center Strategies

• JBEI – Enhance lignin degradation in “model” plants by changing cross-links among lignin subunits; 

improve deconstruction and subsequent fermentation by altering linkages between lignin and other cell-wall 

components; translate genetic developments to switchgrass.

• BESC – Decrease or eliminate harsh chemical pretreatments by manipulating the composition and crosslinking of the plant cell-wall polymers in poplar and switchgrass; simultaneously increase total biomass 

produced per acre.

• GLBRC – Engineer “model” plants and potential energy crops to produce new forms of lignin and more 

starches and oils, which are more easily processed into fuels.

Research Strategies: Discovery and Design of Enzymes and Microbes with Novel Biomass-Degrading Capabilities Center Strategies

• JBEI – Develop new ionic liquid pretreatments that can completely solubilize and fractionate biomass 

components; improve performance and stability of enzymes obtained from the rainforest floor and other 

environments; engineer, through directed evolution, highly efficient cellulase enzymes.

• BESC – Screen natural thermal springs to identify enzymes and microbes that effectively break down and 

convert biomass at high temperatures; understand and engineer cellulosomes (multifunctional enzyme 

complexes for degrading cellulose).

• GLBRC – Identify combinations of enzymes and pretreatment needed to digest specific biomass types; 

express biomass-degrading enzymes in the stems and leaves of corn and other plants.

Research Strategies: Development of Transformational Microbe-Mediated Strategies for Biofuel Production Center Strategies

• JBEI – Connect diverse biological parts and pathways to create entirely new organisms that produce fuels 

other than ethanol; engineer organisms to produce and withstand high concentrations of biofuels; derive 

useful chemical products from lignin degradation.

• BESC – Start with a lignocellulose-degrading microbe and add ethanol- or butanol-producing capabilities 

to substantially reduce costs; develop a knowledgebase and pathway analysis tools to aid these manipulations; test degrading microbes on modified plants.

• GLBRC – Start with an ethanol-producing microbe and add lignocellulose-degrading capabilities to substantially reduce costs.

* JBEI: Joint BioEnergy Institute; BESC: BioEnergy Science Center; GLBRC: Great Lakes Bioenergy Research Center.

DOE Bioenergy Research Center Strategies at a Glance

The complexity of the three biological grand challenges that must be overcome to achieve industrial-scale 

bioenergy production requires the coordinated pursuit of numerous research approaches to ensure timely success. Collectively, the DOE Bioenergy Research Centers* provide a portfolio of diverse and complementary 

scientific strategies that address these challenges on a scale far greater than any effort to date. Some strategies 

are listed briefly in the table below.
Bioenergy Research Centers U.S. Department of Energy Office of Science 5

3. Development of Transformational 

Microbe-Mediated Strategies 

for Biofuel Production

In addition to cellulose, other carbohydrates (collectively 

called hemicelluloses) in plant cell walls are broken down 

into fermentable sugars when biomass is pretreated with heat 

and chemicals. Although cellulose is made of one type of 

6-carbon sugar (glucose) that is readily converted into ethanol and other products, microbial fermentation of the 5- and 

6-carbon sugar mix from hemicelluloses is less efficient and 

thus is a key area for improvement.

En route to the fermentation tank, biomass currently is 

subjected to physical, chemical, and enzymatic processing 

steps that can create by-products and conditions that might 

inhibit microbial conversion of sugars into biofuels. Ethanol 

and other biofuel products also inhibit microbial fermentation at high concentrations. Consequently, another important 

research area is developing microbes robust enough to withstand the stresses of industrial processing and tolerate higher 

ethanol concentrations.

An additional research target that could radically simplify 

the entire production process is consolidated bioprocessing 

(CBP). This scientific strategy combines cellulose deconstruction and sugar fermentation into a single step mediated 

by a “multitalented” microbe or mixed culture of microbes. 

CBP requires a redesign of microbial systems far more 

extensive than conventional genetic engineering approaches. 

For example, genetically engineering the microbial production of a single drug or other biochemical product might 

involve the modifications of only a few genes. A successful 

CBP microbe or specially designed microbial consortium 

may be required to produce a variety of biomass-degrading 

enzymes; produce only minimal amounts of molecules that 

inhibit the overall process; ferment both 5- and 6-carbon 

sugars; and thrive in industrial reactors with high temperature, low pH, and high concentrations of biofuel products. 

Simultaneously incorporating so many different capabilities 

into a single microbe or consortium requires an unprecedented understanding of microbial systems.

To accelerate development of the next generation of highenergy biofuels, the DOE Bioenergy Research Centers also 

are designing novel microbial systems that can produce biofuels other than ethanol. Some of these new fuels may be oily, 

petroleum-like products that are easily extracted from the 

watery solutions in biorefinery reactors and thus less inhibitory to biofuel-synthesizing microbes. These new biofuels 

also would be compatible with existing motor vehicles and 

fuel transportation infrastructure and contain as much energy 

per unit volume as gasoline or diesel.

DOE Bioenergy Research Centers
6 U.S. Department of Energy Office of Science Bioenergy Research Centers
Bioenergy Research Centers U.S. Department of Energy Office of Science 7
8 U.S. Department of Energy Office of Science Bioenergy Research Centers

DOE Joint BioEnergy Institute jbei.org

“DOE JBEI is designed to be an 

engine of ingenuity, dynamically 

organized with all the scientific 

teams working together in a single 

location to enable researchers to 

share ideas and address cellulosic 

biomass problems at a systems 

level. Within 60 miles of JBEI, we 

have available some of the world’s 

foremost authorities on energy, 

plant biology, systems and synthetic biology, imaging, nanoscience, and computation, plus the 

highest concentration of national 

laboratories and research universities in the nation.” 

 – Jay Keasling

Jay Keasling is the JBEI Chief Executive Officer and a University of California, Berkeley professor of chemical engineering. 

He also is an award-winning scientific researcher and one of 

the world’s leading authorities on synthetic biology.

JBEI Research Facility. JBEI researchers are located at a 

single site in Emeryville, California. [Photo by Roy Kaltschmidt, 

Lawrence Berkeley National Laboratory]

The DOE Joint BioEnergy Institute ( JBEI) is a sixinstitution partnership led by Lawrence Berkeley 

National Laboratory (Berkeley Lab). It is based in 

the San Francisco Bay Area, which is fast becoming a hub of 

renewable energy research and development, and is headquartered in a new facility in Emeryville, close to its partner 

institutions (see box, JBEI Partners, p. 11). JBEI researchers 

are engineering microbes and enzymes to process the complex sugars of lignocellulosic biomass into biofuels that can 

directly replace gasoline. Among the strategies they employ 

to produce these next-generation biofuels are the tools of 

synthetic biology. By developing new bioenergy crops, JBEI 

researchers will improve the fermentable content of biomass 

and transform lignin into a source of valuable new products.

JBEI’s research revolves around four interdependent 

efforts that focus on (1) developing new bioenergy crops, 

(2) enhancing biomass deconstruction, (3) producing new 

biofuels through synthetic biology, and (4) creating technologies that advance biofuel research. Some recent highlights 

of JBEI research are featured on pp. 12–13.

Research Strategy

1. Developing New Bioenergy Crops

To increase our understanding of genes and enzymes 

involved in the synthesis and modification of plant cell 

walls, JBEI researchers are using well-characterized 

genomes and genetic-engineering tools established for 

rice and Arabidopsis (a small flowering plant related to 

mustard). These two model systems are ideal for research 

because their development from seed to mature plant 

takes only weeks or months, rather than the year or more 

required for energy crops such as switchgrass and poplar. 

Genetic insights from rice (a model for grasses) and Arabidopsis (a model for trees) will accelerate the development 

of new energy crops (see figure, Bioenergy Crop Research 

at JBEI, p. 9).

In addition, JBEI scientists are investigating metabolic 

pathways involved in lignin biosynthesis. The research may 

lead to development of plants that can be deconstructed 

more easily. This unique basic research program also could 

help transform lignin into a valuable source of chemicals 

and polymers, while improving the economics of converting 

cellulosic biomass into fuels.

Jay Keasling

JBEI Chief Executive

Officer 
Bioenergy Research Centers U.S. Department of Energy Office of Science 9

2. Enhancing Biomass Deconstruction

Scientists at JBEI are developing new pretreatment 

approaches and enzymes that enhance cellulose conversion 

to sugars and minimize the formation of toxic by-products. A 

large focus is on the use of ionic liquids, salts that are liquid 

rather than crystalline at room or near-room temperatures. 

JBEI researchers are investigating both the effects of ionic 

liquids on biomass and the recovery of sugars from the liquid 

product through the use of solvents. They also are exploring 

a broad range of environments, from rainforests to compost, 

to discover and isolate new enzymes that more efficiently 

degrade cellulose and lignin. JBEI studies of the mechanisms 

of biomass deconstruction at the molecular level will enable 

new insights and approaches for the efficient conversion of all 

plant components to useful products.

3. Producing New Biofuels Through 

Synthetic Biology

JBEI researchers are applying synthetic biology techniques 

and mathematical models of metabolism and gene regulation 

to engineer microorganisms that convert the sugars released 

from biomass deconstruction into advanced biofuels, such as 

alcohols (e.g., butanol) and alkanes. These next-generation 

biofuels will yield almost as much energy per volume as gasoline and will be transportable through existing fuel pipelines 

(see sidebar, Synthetic Biology, p. 10). Biologically produced 

alkanes and other oil-like hydrocarbons could replace gasoline in today’s cars on a gallon-for-gallon basis.

4. Creating Technologies that Advance 

Biofuel Research

JBEI scientists are creating new, broadly applicable technologies to advance research that will speed biofuel development (see figure, JBEI Technology Development to 

Advance Biofuel Research, p. 10). Among these technologies is a novel chip-based system that can be used to identify 

new enzymes with cellulose- and lignin-degrading activities. 

In addition, the researchers are constructing automated 

microfluidic platforms that can screen hundreds of enzymatic reactions simultaneously to help identify the best 

enzymes for biomass deconstruction. Technologies also are 

being developed for rapid high-resolution imaging to visualize and characterize the effects of pretreatment protocols 

on plant biomass. These and other enabling technologies 

are generating large volumes of data that are collected and 

catalogued in a centralized database and then analyzed using 

new bioinformatic tools.

Industry Partnerships

To promote the transfer of JBEI inventions to private industry for commercial development that can benefit the nation, 

JBEI has established collaborations with companies that have 

relevant scientific and marketing capabilities in energy, agribusiness, and biotechnology. The JBEI Industry Partnership 

Program provides companies with opportunities to contribute to JBEI and become part of the JBEI community. To 

further help ensure that its science ultimately will be able to 

serve national needs, JBEI has established an advisory committee, with representatives from the entire spectrum of the 

biofuel industry. For more information on JBEI’S collaborations with industry, see jbei.org/for-industry/.

Bioenergy Crop Research at JBEI. JBEI’s director of Grass 

Genetics, Pam Ronald, in the Miscanthus plot at the University of California, Davis. [Photo courtesy of Dan Putnam, UC, Davis]
10 U.S. Department of Energy Office of Science Bioenergy Research Centers

JBEI

Synthetic Biology

Building Novel Biological Systems 

for Useful Purposes

Synthetic biologists design and build novel organisms 

to generate products not made by natural systems. This 

process may involve constructing entirely new biological 

systems from a set of standard parts—genes, proteins, and 

metabolic pathways—or redesigning existing biological 

systems. The tools of synthetic biology also can be used 

to study the interior of living cells at the molecular level, 

providing critical new information and insight into the 

machinery of life and the natural world. Synthetic biology 

holds promise for advances in many areas, including the 

development of renewable, carbon-neutral energy sources; 

nonpolluting biological routes for the production of chemicals; safer and more effective pharmaceuticals; and better 

environmental remediation technologies.

At JBEI, researchers are using synthetic biology to develop 

new platform hosts for producing enzymes and fuels and to 

create biomolecular parts and devices for constructing new 

fuel-generating organisms and improved plants. Among 

other advances, such goals will be achieved through the 

improved capabilities of fermentative organisms to tolerate 

processing conditions and inhibit unwanted by-products. 

Capabilities also will be engineered into fuel-producing 

organisms to convert 5-carbon sugars into fuel and make 

use of lignin monomers. Following the strategy that biological systems can be revamped more effectively or built from 

scratch if standardized parts are employed, investigators 

are assembling a catalog of well-characterized biosynthetic 

components to help in designing, testing, optimizing, and 

implementing integrated large-scale biosynthetic units. These 

tools and principles, used by JBEI Chief Executive Officer Jay 

Keasling to develop a relatively inexpensive microbial-based 

alternative for producing the antimalarial drug artemisinin, 

will aid in developing the next generation of biofuels.

[Image courtesy of Manfred Auer, Lawrence Berkeley National Laboratory]

Education and Outreach

Educational efforts at JBEI build on strong undergraduate, graduate, and postdoctoral training programs, plus 

nationally recognized K–12 and community college science outreach programs already in place at JBEI’s member 

institutions. In addition to starting a new student fellowship program, JBEI is collaborating with the University of 

California, Berkeley’s Management of Technology Program to enable young scientists and engineers to develop 

biofuel-related business plans. JBEI’s own education and 

outreach programs include internships, scientific academies, 

seminars, and collaborations with academic and industrybased science institutions. In addition to external education opportunities, JBEI also offers its researchers in-house 

seminars as resources for ongoing education.

JBEI Technology Development to Advance Biofuel 

Research. JBEI’s Chris Petzold and Alyssa Redding develop 

and apply mass spectrometry approaches to sort through 

the complex protein mixtures in biological cells and detect 

multiple target proteins in the same sample. [Photo by Dino 

Vournas, Sandia National Laboratories]
Bioenergy Research Centers U.S. Department of Energy Office of Science 11

JBEI Partners

DOE’s Lawrence Berkeley National Laboratory (Berkeley 

Lab), Berkeley, California (lead institution): Berkeley Lab, a 

multidisciplinary national laboratory, is home to the Advanced 

Light Source, the Molecular Foundry, the National Center 

for Electron Microscopy, and the National Energy Research 

Scientific Computing Center. It also is a founding partner of 

the DOE Joint Genome Institute, one of the world’s largest and most productive DNA sequencing centers. Berkeley 

Lab provides expertise in bioinformatics and analysis, data 

management, and biological modeling, in addition to being a 

world leader in advanced imaging, nanoscale biology, artificial 

photosynthesis, and technologies focused on energy efficiency 

and conservation.

DOE’s Sandia National Laboratories, Albuquerque, New 

Mexico, and Livermore, California: Sandia National Laboratories consist of multidisciplinary research institutes that provide expertise in systems engineering and integration function, 

microfluidics, computation, and robotics and materials development, as well as experience in manufacturing technologies.

University of California, Berkeley: UC Berkeley, ranked 

first for distinguished scholarship by the National Research 

Council, is home to the Energy Biosciences Institute, a 

partnership that includes Berkeley Lab and the University of 

Illinois, whose research complements that of JBEI. UC Berkeley provides a broad range of expertise in JBEI-related fields, 

including molecular and cellular biology, molecular genetics, 

proteomics, and environmental sciences.

University of California, Davis: UC Davis oversees the 

California Biomass Collaborative and is home to the Northern California Nanotechnology Center, the Western Regional 

Center of the National Institute for Global Environmental 

Change, and the UC Davis Genome Center. The university 

provides expertise in plant and environmental sciences, 

genetics, plant physiology, evolutionary biology, and environmental science.

Carnegie Institution for Science, Palo Alto, California:

The Carnegie Institution for Science is a private, nonprofit 

organization on the campus of Stanford University. It maintains TAIR, a comprehensive database on Arabidopsis thaliana, 

the model organism for plant molecular genetics, and provides 

expertise in photosynthesis, bioinformatics, and growth and 

developmental processes that enable plants to survive disease 

and environmental stress.

DOE’s Lawrence Livermore National Laboratory (LLNL), 

Livermore, California: LLNL is a multidisciplinary national 

laboratory that hosts the Center for Accelerator Mass Spectrometry and one of the world’s fastest supercomputers. LLNL 

also is one of the DOE Joint Genome Institute’s founding 

partners and provides expertise in genomics, bioinformatics, 

experimental protein production, advanced measurement 

technologies, and high-performance scientific computing.
12 U.S. Department of Energy Office of Science Bioenergy Research Centers

New Approach to Visualize Biomass Solubilization 

During Ionic Liquid Pretreatment

JBEI researchers have developed a technique, based on the 

natural autofluorescence of plant cell walls, that enables the 

dynamic imaging of biomass solubilization during ionic 

liquid pretreatment. Using this technique, researchers can 

accurately and quickly assess the ionic liquid’s performance 

without the need for labor-intensive and time-consuming 

chemical and immunological labeling. Working with switchgrass and using the ionic liquid known as 1-n-ethyl-3-methylimidazolium acetate (EmimAc), the researchers observed 

a rapid swelling of secondary plant cell walls (see figure)

within 10 minutes of exposure at relatively mild pretreatment 

temperatures (120°C). This reaction indicates a disruption 

of hydrogen bonding within cellulose and between cellulose and lignin. The swelling was followed by complete 

dissolution of biomass over 3 hours. By adding water to the 

solubilized biomass mixture, cellulose can be precipitated 

out and separated from the lignin, which remains in solution. 

This recovered cellulose was efficiently hydrolyzed into its 

sugar components by a commercial cellulase cocktail over a 

relatively short time interval. Currently, those ionic liquids 

that are most effective at dissolving plant cell-wall polymers 

are prohibitively expensive for use on a mass scale. Understanding how ionic liquids are able to dissolve lignocellulosic 

biomass could pave the way for finding new and better varieties for use in biofuel production. This research was reported 

in Singh, S., B. A. Simmons, and K. P. Vogel. 2009. “Visualization of Biomass Solubilization and Cellulose Regeneration 

During Ionic Liquid Pretreatment of Switchgrass,” Biotechnology and Bioengineering 104(1), 68–75.

Unique Database Provides Functional

and Phylogenomic Information 

for Rice Glycosyltransferases

JBEI researchers have made major advances in comprehensively identifying all rice glycosyltransferases (GT), an important class of enzymes involved in synthesizing polysaccharide 

sugars in plant cell walls. Because rice and other grasses such 

as switchgrass and Miscanthus share similar cell-wall characteristics, whole genome–scale analysis of rice has enabled 

the discovery of several candidate genes for more in-depth 

functional analysis that can help researchers understand 

and manipulate grass cell walls for biofuel production. This 

research has led to the development of JBEI’s Rice GT Database, a publicly available resource for integrating and displaying diverse sets of functional genomic information for GTs 

(ricephylogenomics.ucdavis.edu/cellwalls/gt/). The database 

contains information on 793 putative gene models for rice 

GTs, and the loci for these genes are distributed across all 12 

rice chromosomes. In addition to defining phylogenetic relationships among groups of rice GT genes based on sequence 

similarity, JBEI researchers also compared the number of 

different GT gene models identified for rice, Arabidopsis, and 

poplar (Populus trichocarpa). From the hundreds of possible 

GT genes that have been identified, scientists revealed 33 

rice-diverged GTs that are highly expressed in vegetative, 

aboveground tissues and that serve as prime targets for mutagenesis studies and enzyme activity screens. This database 

was reported in Cao, P. J., et al. 2008. “Construction of a Rice 

Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases,” Molecular Plant

1(5), 858–77.

Compost Microbes Adapted to Produce 

Switchgrass-Degrading Enzymes

By incubating switchgrass with a mix of microbes isolated from 

compost, JBEI researchers provided the selective pressure 

needed to grow a new microbial community enriched with 

enzymes that degrade cell-wall polymers specific to switchgrass. The sample was incubated in a bioreactor for 31 days 

under typical composting conditions. Metagenomic sequencing of the switchgrass-adapted compost (SAC) community on 

day 31 was carried out to investigate the sample’s diverse pool 

of glycoside hydrolases—enzymes that break bonds between 

carbohydrate molecules. The sample contained a high proportion of genes encoding enzymes that attack the branches and 

backbone of a major hemicellulose in grass cell walls. Analysis 

of the small-subunit ribosomal RNA (rRNA) isolated from 

the microbial community revealed dramatic changes in the 

JBEI Research Highlights

Dissolving Cell-Wall Compounds with Ionic Liquids. These 

confocal fluorescence images show switchgrass cell walls 

(A) before pretreatment with the EmimAc ionic liquid and 

(B) 10 minutes after treatment, in which the cell walls have 

swollen in size, a prelude to complete solubilization of cellulose, hemicellulose, and lignin. [Image courtesy of Seema Singh, 

Sandia National Laboratories]
Bioenergy Research Centers U.S. Department of Energy Office of Science 13

JBEI Research Highlights

Growth on Switchgrass Changes Microbial Community Composition. The populations 

of microbes present after 31 days of growth on switchgrass (indicated in red) are considerably different from those populations in the compost community (indicated in blue). 

This suggests a selection and enrichment of specific populations to degrade switchgrass. 

[Image from Allgaier et al. 2010]

community profile with more than a 20-fold increase for 

some bacterial populations in the SAC (see figure above). 

Although metagenomic DNA sequence is highly fragmented, 

making isolation of full genes from complex communities difficult, two full-length genes for cellulose-degrading enzymes 

were discovered, synthesized, expressed in Escherichia coli, 

and tested for enzyme activity. This research was reported in 

Allgaier, M., et al. 2010. “Targeted Discovery of Glycoside 

Hydrolases from a Switchgrass-Adapted Compost Community,” PLoS One 5(1), e8812.

Mass Spectrometry–Based Protein Detection 

Technique Speeds Optimization of Biofuel Protein 

Levels in Metabolically Engineered Microbes

JBEI researchers have developed a mass spectrometry–

based protein detection technique called multiple-reaction 

monitoring (MRM) for identifying microbial proteins that 

can convert cellulosic sugars into biofuels. With the MRM 

technique, researchers can detect multiple target proteins 

in the complex protein mixtures of native cells and rapidly 

change the specific proteins to be targeted, something not 

possible with conventional protein detection technology. 

When coupled to liquid chromatography, MRM analysis 

offers high selectivity and sensitivity. It eliminates background signal and noise even in the most complex protein 

mixtures by utilizing two 

targeted points—a peptide 

mass and a specific fragment 

mass generated by mass spectrometry. Since the entire mass 

range is not scanned and only 

combinations of peptide and 

fragment masses are monitored, MRM can be used to 

detect and quantify up to 10 

different proteins in a single 

liquid chromatography separation. The MRM technique is 

a valuable tool for analyzing 

enzyme complexes in a variety 

of JBEI projects such as the 

synthetic protein scaffold work 

reported in Dueber, J. E., et al. 

2009. “Synthetic Protein Scaffolds Provide Modular Control 

over Metabolic Flux,” Nature 

Biotechnology 27(8), 753–59.

Key Genes for Biosynthesis of Hydrocarbon 

Biofuels Identified in Bacterium Micrococcus luteus

JBEI researchers have elucidated the genes and a proposed 

biochemical pathway for the production of long-chain 

alkenes—key chemical components of petroleum-based 

gasoline and diesel fuels—in the bacterium Micrococcus 

luteus. Building on insights from microbial alkene research 

reported 4 decades ago, JBEI researchers hypothesized that 

a key mechanism for long-chain alkene biosynthesis would 

involve decarboxylation and condensation of fatty acids. By 

searching the genome of the alkene-producing bacterium 

M. luteus, researchers found three candidate genes with 

conserved sequences associated with condensing enzymes. 

Expression of these genes in E. coli resulted in long-chain 

alkene production, but additional research will be needed to 

reveal the specific biochemical role that each of the enzymes 

encoded by these genes plays in alkene synthesis. A wide 

range of bacteria has been found to contain genes similar to 

those that encode M. luteus alkene biosynthesis enzymes, 

so researchers will have an opportunity to learn more about 

these enzymes by exploring their diversity in nature. This 

research was reported in Beller, H. R., E. B. Goh, and J. D. 

Keasling. 2010. “Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus,” Applied and Environmental 

Microbiology 76(4), 1212–23.
14 U.S. Department of Energy Office of Science Bioenergy Research Centers

DOE BioEnergy Science Center bioenergycenter.org

BESC Headquarters. Oak Ridge National Laboratory’s 

Joint Institute for Biological Sciences facility in Oak Ridge, 

Tennessee, houses BESC administration and ORNL-based 

research staff. [Photo courtesy of Oak Ridge National Laboratory]

The DOE BioEnergy Science Center (BESC), led 

by Oak Ridge National Laboratory (ORNL) in 

Oak Ridge, Tennessee, focuses on the fundamental 

understanding and elimination of biomass recalcitrance—

the resistance of cellulosic biomass to enzymatic breakdown 

into sugars. BESC approaches the problem of biomass 

recalcitrance from two directions by closely linking (1) plant 

research to make cell walls easier to deconstruct and 

(2) microbial research to develop multitalented biocatalysts 

tailor-made to produce biofuels from this modified plant 

material in a single step.

Scientists at national laboratories, universities, and private 

companies that make up the BESC team have extensive 

experience with studying biomass recalcitrance, and they 

have made fundamental advances in a wide range of related 

sciences. The Joint Institute for Biological Sciences systems 

biology research facility at ORNL serves as the central hub 

for coordinating research among all BESC partners (see box, 

BESC Partners, p. 17).

BESC’s research is organized into three focus areas: (1) Biomass Formation and Modification, (2) Biomass Deconstruction and Conversion, and (3) Characterization and Modeling. Some recent highlights of BESC research are featured on 

pp. 18–19. By understanding the myriad factors that collectively determine biomass recalcitrance, BESC researchers 

are providing foundational knowledge that will streamline 

processing and reduce costs for many different approaches 

to plant feedstock and cellulosic biofuel production.

Research Strategy

1. Biomass Formation and Modification

BESC biomass formation and modification research 

involves understanding the genetics and biochemistry of 

plant cell-wall biosynthesis and working directly with two 

potential bioenergy crops—switchgrass and poplar—to 

develop varieties that are easier to break down into fermentable sugars. Computational models are being developed to 

help BESC researchers identify target genes and successful 

strategies for modifying biosynthetic pathways to generate cell walls that can be readily deconstructed into sugars 

for biofuel production. Target genes are turned on or off in 

thousands of poplar and switchgrass samples generated and 

studied by BESC, and then these samples are characterized 

“The BioEnergy Science Center is 

focused specifically on the challenge of overcoming biomass 

recalcitrance. If we can manage to 

understand and solve this challenge, 

we will not only improve our ability 

to generate cellulosic ethanol, but 

we also will open doors to a vast 

array of renewable and sustainable 

product pipelines that can serve 

many different missions. To address 

these important issues, we have 

assembled a team of world leaders 

in their fields from 20 different institutions and have built a 

culture of integration and collaboration that has significantly 

accelerated our rate of scientific discovery and application.” 

 – Paul Gilna

Paul Gilna, BESC director, also is deputy director of the 

Biosciences Division at Oak Ridge National Laboratory. An 

expert in computational biology, Gilna previously served as 

executive director of CAMERA (Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research 

and Analysis), a project providing researchers with bioinformatic tools and services.

Paul Gilna

BESC Director
Bioenergy Research Centers U.S. Department of Energy Office of Science 15

BESC Research on Biomass-Deconstructing Microbes. 

Isolated from decaying grass compost, Clostridium cellulolyticum degrades cellulosic biomass using multienzyme complexes called cellulosomes. This scanning electron micrograph shows C. cellulolyticum cells growing 

on switchgrass biomass. [Photo by Thomas Hass and Shi-You 

Ding, National Renewable Energy Laboratory]

Bioenergy Crop Research at BESC. Transformed 

Populus shoots grow in a greenhouse. These plants 

are altered in targeted cell-wall pathway genes. 

[Image courtesy of Oak Ridge National Laboratory] 

to assess how these modifications affect plant cell walls. 

These modified plants are growing in greenhouses and at 

several sites to help differentiate genetic versus environmental influences on plant trait development (see figure, Bioenergy Crop Research at BESC, this page). By understanding 

the synthesis and assembly of the polysaccharides and lignin 

in plant biomass, BESC researchers are reducing cell-wall 

recalcitrance using methods that can be applied to a wide 

range of woody and herbaceous plants.

2. Biomass Deconstruction 

and Conversion

Two key hypotheses drive biomass deconstruction and 

conversion research at BESC: (1) microorganisms can be 

engineered to enable consolidated bioprocessing (CBP)—

a game-changing, one-step, microbe-mediated strategy 

for directly converting plant biomass into ethanol and 

(2) enzymes and microbial biocatalysts can be understood 

and engineered to synergize with recalcitrance-reducing plant 

modifications to achieve better biomass deconstruction.

Model organisms for CBP development include species of 

Clostridia bacteria that rapidly degrade pure cellulose and then 

ferment the resulting sugars into ethanol (see figure, BESC 

Research on Biomass-Deconstructing Microbes, this page). 

These microbes deconstruct biomass using cellulosomes—

multifunctional enzyme complexes that specialize in degrading 

the mix of complex carbohydrates in cell walls. BESC is studying the structures and activities of these poorly understood 

multienzyme complexes to design new variants that are more 

efficient at deconstructing cell walls. 

BESC researchers also are investigating microbes that can 

rapidly degrade biomass at near-boiling temperatures, such as 

species of Caldicellulosiruptor isolated from hot springs at Yellowstone National Park. By developing genetic tools for these 

difficult-to-manipulate microbes, BESC is working to engineer 

novel microbes that add biofuel production capabilities to their 

native cellulose-degrading abilities. These microbes and their 

enzymes could provide new biomass-degrading capabilities 

resistant to the heat and stresses of industrial processing.
16 U.S. Department of Energy Office of Science Bioenergy Research Centers

BESC

3. Characterization and Modeling

Advancing BESC goals to develop improved plant materials 

and CBP methods that facilitate cost-effective conversion of 

biomass to fermentable sugars will require detailed knowledge of (1) the chemical and physical properties of biomass 

that influence recalcitrance, (2) how these properties can 

be altered by engineering plant biosynthetic pathways, and 

(3) how biomass properties change during pretreatment and 

how such changes affect biomass-biocatalyst interactions during deconstruction by enzymes and microorganisms.

To examine chemical and structural changes that occur in the 

modified plant cell walls of switchgrass and poplar, BESC analyzes thousands of native and modified biomass samples in a 

high-throughput screening pipeline that can perform compositional analysis, pretreatment, and enzyme digestibility studies. 

This screen already has revealed that a few native poplar 

samples can release most of their sugars using just a mild (hot 

water) pretreatment. Promising candidates selected from this 

screening pipeline are passed along to other partner institutions for a variety of detailed chemical, physical, and imaging 

analyses. The resulting data are incorporated into computational models and simulations used to predict relationships 

between biomass structure and recalcitrance.

Modeling and simulation tools are part of a knowledgebase 

BESC is establishing to maintain and share data, materials, 

experimental processes, and scientific insights across the 

distributed BESC community. One component of this 

knowledgebase is a comprehensive set of tools for discovering biomass recalcitrance genes in plant genomes and 

building pathways for cell-wall synthesis. By extracting and 

combining results from isolated experiments, this knowledgebase serves as a biological discovery platform for 

integrating diverse experimental, theoretical, and computational approaches that will help define the genomic and 

physical bases of plant cell-wall recalcitrance. A public 

version of the knowledgebase is at besckb.ornl.gov.

Translation of BESC Science 

into Commercial Applications

Translating BESC research results into the testing of applications and potential commercial deployment is an important 

step toward reaching DOE’s bioenergy objectives. BESC has 

formed a “commercialization council” of technology-transfer 

and intellectual property (IP) management professionals from 

partner institutions to evaluate the commercial potential of 

new inventions arising from BESC research and to promote 

and facilitate the licensing of BESC IP. Inventions are posted 

on the center’s website (bioenergycenter.org/licensing/). 

Some early inventions address techniques for plant and microbial genetic transformation, special microscopy methods, and 

innovations in biomass sample handling. To build external 

relationships that can promote commercialization of new 

technologies, BESC provides opportunities for companies 

to become BESC Industry Affiliates. Several BESC research 

partners and affiliates have pilot facilities for testing BESC 

improvements. The University of Tennessee–Genera Energy 

and Dupont Danisco Cellulosic Ethanol have established a 

demonstration plant for turning corn cobs and switchgrass 

into ethanol in Vonore, Tennessee. Mascoma, Verenium, 

Ceres, and ArborGen also have pilot and field sites.

Education and Outreach

To prepare the next generation of bioenergy scientists, BESC 

provides interdisciplinary research opportunities to graduate students, postdocs, and visiting scientists. In addition to 

these activities in higher education, BESC is teaming with the 

Creative Discovery Museum in Chattanooga, Tennessee, to 

raise awareness of cellulosic biofuels, carbon emissions from 

energy use, and obstacles to a successful biofuel economy. 

Targeting fifth-graders, BESC education and outreach efforts 

make information accessible to the general public and reach 

students when they still are excited about science. Lessons 

piloted to thousands of students at schools in Georgia and 

Tennessee are available to schools nationwide. BESC also 

began “Science Night” programs that build on these classroom lessons and are offered to students and their families. 

The National Geographic Jason Project featured BESC science in a program developed for high school students. The 

BESC website features announcements about BESC outreach and educational programs, seminars and presentations 

describing BESC research, and other resources.
Bioenergy Research Centers U.S. Department of Energy Office of Science 17

BESC Partners

DOE’s Oak Ridge National Laboratory (ORNL), Oak 

Ridge, Tennessee (lead institution): As DOE’s largest science and energy laboratory, ORNL features research programs 

in poplar genomics, computational science, bioenergy, and 

plant and microbial systems biology. The ORNL Spallation 

Neutron Source and supercomputers at the ORNL National 

Leadership Computing Facility will be used to investigate and 

simulate the activity of enzyme complexes.

University of Georgia, Athens (UGA): UGA’s Complex 

Carbohydrate Research Center maintains state-of-the-art 

capabilities in mass spectrometry, nuclear magnetic resonance 

spectroscopy, chemical and enzymatic synthesis, computer 

modeling, cell and molecular biology, and immunocytochemistry for studying the structures of complex carbohydrates and 

the genes and pathways controlling plant cell-wall biosynthesis.

DOE’s National Renewable Energy Laboratory (NREL), 

Golden, Colorado: NREL has more than 30 years of experience in biomass and biofuel research and houses premiere 

facilities for analyzing biomass surfaces. NREL also has a 

long and successful history of establishing biofuel pilot plants 

and partnering with industry for commercial development of 

technologies.

University of Tennessee, Knoxville (UT): UT conducts 

successful programs in bioenergy-crop genetic and field 

research (particularly switchgrass) and biotechnological applications of environmental microbiology.

Dartmouth College, Hanover, New Hampshire: Dartmouth’s Thayer School of Engineering is a leader in the 

fundamental engineering of microbial cellulose utilization and 

consolidated bioprocessing approaches.

Georgia Institute of Technology, Atlanta: Georgia Tech’s 

Institute for Paper Science and Technology provides BESC 

with expertise in biomass processing and instrumentation for 

high-resolution analysis of plant cell walls.

ArborGen, Summerville, South Carolina: ArborGen provides expertise in forest genetics research, tree development, 

and commercialization.

Verenium Corporation, Cambridge, Massachusetts: 

Verenium is a biofuels-focused biotechnology company and 

developer of specialty enzymes found in diverse natural environments and optimized for targeted applications.

Mascoma Corporation, Boston, Massachusetts: 

Mascoma develops microbes and processes for economical 

conversion of cellulosic feedstocks into ethanol.

The Samuel Roberts Noble Foundation, Ardmore, Oklahoma:This nonprofit research foundation is devoted to 

improving agricultural production and advancing the development of switchgrass and other grasses through genomic 

research. The foundation’s activities are conducted through programs in agriculture, plant biology, and forage improvement.

Ceres, Inc., Thousand Oaks, California: Ceres uses 

advanced plant breeding and biotechnology to develop and 

market low-carbon, nonfood crops for next-generation biofuels 

and biopower.

Individual Researchers: Specializing in biomass pretreatment, characterization of plant-associated microbes, cellulose 

and enzyme modeling, consolidated bioprocessing, and lignin 

biochemistry are researchers from the University of California, 

Riverside; DOE’s Brookhaven National Laboratory (Upton, 

New York); Cornell University (Ithaca, New York); Virginia 

Polytechnic Institute and State University (Blacksburg); 

University of Minnesota (St. Paul); North Carolina State 

University (Raleigh); Washington State University (Pullman); 

University of Californa, Los Angeles; and West Virginia University (Morgantown).
18 U.S. Department of Energy Office of Science Bioenergy Research Centers

BESC Research Highlights

Key Targets from a Complex Family of Lignin 

Biosynthesis Genes Identified in Switchgrass

Although lignin content and composition have been manipulated in several plant species by targeting the monolignol 

biosynthesis pathway, little is known about the genes and 

enzymes associated with this pathway in switchgrass. Cinnamoyl CoA reductase (CCR) catalyzes the first step in 

this pathway dedicated to monolignol synthesis. However, 

switchgrass contains numerous copies of CCR-like genes, 

complicating the selection of the best gene targets for altering lignin to reduce cell-wall recalcitrance. By analyzing the 

RNA of expressed CCR genes, BESC researchers show that 

one of the expressed genes (PvCCR1) encodes an enzyme 

actively involved in lignification and thus is a prime target 

for down-regulation to improve the degradability and sugar 

yield from switchgrass. Ongoing research is investigating how 

reducing the expression of the PvCCR1 gene impacts lignin 

composition and plant structure. This research was reported 

in Escamilla-Treviño, L. L., et al. 2009. “Switchgrass (Panicum 

virgatum) Possesses a Divergent Family of Cinnamoyl CoA 

Reductases with Distinct Biochemical Properties,” New Phytologist 185, 143–55.

Thousands of Proteins from Developing Xylem 

Cells in Poplar Are Identified

Woody biomass in trees primarily consists of the secondary 

cell walls of dead xylem tissue, so developing xylem cells are 

useful models for investigating secondary cell-wall formation. To provide subcellular context for identified protein 

functions and to enhance the detection of low-abundance 

proteins, subcellular fractionation techniques were used to 

obtain crude (soluble protein), pellet (insoluble protein), 

and nuclear protein fractions for analysis. Applying an 

automated approach known as MudPIT (Multidimensional 

Protein Identification Technology), BESC researchers 

successfully isolated and identified 6,000 different proteins 

from developing xylem cells in the stems of poplar plants. 

Results from this project greatly expanded the number of 

proteins that had been identified in previous poplar proteome studies. The protein products of several cell-wall synthesis genes (e.g., cellulose synthase, sucrose synthase, and 

polygalacturonase) were found to be associated with cellular 

membranes (see figure), and numerous new candidate genes 

for cell-wall synthesis were discovered—many are promising targets for further functional genomic analysis. Measuring differences in the whole proteomes of different poplar 

variations will increase understanding of the fundamental 

properties that underlie the recalcitrance of woody biomass 

to degradation. This research was reported in Kalluri, U. C., 

et al. 2009. “Shotgun Proteome Profile of Populus Developing Xylem,” Proteomics 9, 4871–80.

Heat-Tolerant Bacteria Efficiently Degrade 

Non-Pretreated Biomass

Presenting the possibility of eliminating the pretreatment step 

from cellulosic biofuel production, a hot springs bacterium 

known as Caldicellulosiruptor bescii has shown that it can efficiently degrade crystalline cellulose, xylan (a hemicellulose), 

and various types of non-pretreated biomass including hardwoods such as poplar, high-lignin grasses such as switchgrass, 

and low-lignin grasses such as Bermuda grass (see top figure, 

p. 19). With an optimal growth temperature of 75°C, C. bescii

was able to break down 65% of switchgrass biomass without 

pretreatment. This bacterium is the most heat-tolerant biomass 

degrader known (withstanding temperatures up to 90°C), and 

it primarily produces hydrogen as an end product when grown 

on plant biomass. BESC researchers have discovered another 

hot springs bacterium (Caldicellulosiruptor obsidiansis), isolated 

from Yellowstone National Park, that thrives at 78°C and can 

ferment all the simple sugars in cell-wall polysaccharides into 

diverse products including ethanol. Combining the functional capabilities of C. bescii and C. obsidiansis theoretically 

could yield organisms that both deconstruct and ferment plant 

biomass at temperatures above the boiling point of ethanol 

(78.4°C). Producing ethanol in the vapor phase could greatly 

reduce the inhibitory effects of ethanol on cell growth. C. bescii

(formerly called Anaerocellum thermophilum DSM 6725) findings are from Yang, S. J., et al. 2009. “Efficient Degradation of 

Lignocellulosic Plant Biomass, Without Pretreatment, by the 

Thermophilic Anaerobe ‘Anaerocellum thermophilum’ DSM 

Amount of Cellulose Synthase Proteins in Different Subcellular Fractions. The pellet fraction of extracted xylem 

proteins is enriched in membrane proteins. Significantly 

higher amounts of a key membrane protein, cellulose 

synthase, are associated with the pellet fraction relative to 

the other fractions. [Image from Kalluri et al. 2009]
Bioenergy Research Centers U.S. Department of Energy Office of Science 19

BESC Research Highlights

Validation of Gene Expression in 

Vascular Tissues. To confirm the 

expression of identified genes in vascular tissues, probes that specifically bind the 

mRNA of a small number of the identifed genes were applied to switchgrass tissue. 

The darker regions indicate the vascular bundles where the probes bound the abundant mRNA from the active expression of targeted genes in these regions. [Image 

courtesy of Elison Blancaflor, The Samuel Roberts Noble Foundation]

Caldicellulosiruptor bescii on Birchwood Xylan. [Image courtesy of Mike Adams, University of Georgia]

6725,” Applied and Environmental Microbiology 75(14), 4762–

69. The discovery of C. obsidiansis was reported in HamiltonBrehm, S. D., et al. 2010. “Caldicellulosiruptor obsidiansis sp. nov., 

an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium 

Isolated from Obsidian Pool, Yellowstone National Park,” 

Applied and Environmental Microbiology 76(4), 1014–20.

Researchers Target Expressed Genes in Vascular 

Tissues of Switchgrass

Using a laser-based technique for microdissecting plant tissues, 

BESC researchers have targeted and analyzed DNA that is 

actively expressed in switchgrass vascular tissues where secondary cell walls are synthesized and reinforced with lignin. A total 

of 2,766 unique genes were identified from 5,734 expressed 

DNA segments (known as expressed sequence tags or ESTs). A 

significant number of these expressed sequences are novel with 

no significant hits to existing EST data. A small subset of the 

identified genes was targeted with labeled probes to visualize the 

expression of these genes in live plant tissue (see figure below), 

and researchers found that several genes have much higher 

expression in the vascular bundles. The gene list generated from 

this study provides an important genomic resource for narrowing the range of molecular targets that could play key roles in 

modifying the lignin content of switchgrass and other related 

bioenergy crops. This research was reported in Srivastava, A. C., 

et al. 2010. “Collection and Analysis of Expressed Sequence Tags 

Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues,” BioEnergy Research, 

DOI: 10.1007/s12155-010-9080-8.

New Strategy Enhances Microbial Resistance 

to Inhibitory Pretreatment Chemicals

The chemical and physical processes for pretreating biomass 

help unravel the complex matrix of cell-wall components 

and enhance enzyme accessibility to these materials, but 

pretreatments also generate chemicals such as acetate that 

inhibit sugar fermentation to biofuels. Using a combination 

of adaptation, genetic engineering, and systems biology tools, 

BESC researchers have developed acetate-resistant strains of 

two industrial ethanol producers (the bacterium Zymomonas 

mobilis and the yeast Saccharomyces cerevisiae) by changing the 

expression of genes encoding transport proteins that move 

substances across the cell membrane. These proteins (called 

antiporters) transport proton and sodium ions and form gradients that are adversely impacted by the presence of acetate. 

By resequencing a Z. mobilis strain 

that had been adapted to withstand 

high acetate concentrations, BESC 

researchers discovered specific 

mutations in antiporter genes 

that enable acetate resistance. The 

specific antiporter mutations were 

validated using genetically engineered Z. mobilis and yeast showing 

the broad impact of these changes. 

This research is reported in Yang, S., 

et al. 2010. “Paradigm for Industrial Strain Improvement Identifies 

Sodium Acetate Tolerance Loci in 

Zymomonas mobilis and Saccharomyces cerevisiae,” Proceedings of 

the National Academy of Sciences

107(23), 10395-400.
20 U.S. Department of Energy Office of Science Bioenergy Research Centers

“We are proud of the pieces of 

the scientific puzzle we have 

assembled. The Great Lakes 

Bioenergy Research Center has 

brought together 400 handpicked scientists and staff and 

established core facilities for 

analyzing bioenergy microbes 

and plants in the lab or the field. 

The productivity of this team 

has resulted in more than 100 

peer-reviewed publications and 

patentable technologies that can 

serve as a foundation for a new 

renewable bioenergy future.” 

 – Tim Donohue

Tim Donohue is the GLBRC principal investigator and 

director as well as a professor of bacteriology at the University of Wisconsin–Madison. He is an expert in applying the latest genomic and systems biology approaches 

to understanding how genetic pathways and networks 

in microorganisms are used to generate cell biomass or 

biofuels from sunlight.

DOE Great Lakes Bioenergy Research Center glbrc.org

Tim Donohue

GLBRC Director

The DOE Great Lakes Bioenergy Research Center 

(GLBRC) is led by the University of Wisconsin–

Madison, in close partnership with Michigan State 

University (see box, GLBRC Partners, p. 23). Located in 

the world’s most productive agricultural region, the GLBRC 

is exploring scientifically diverse approaches to converting 

sunlight and various plant feedstocks—agricultural residues, 

wood chips, and grasses—into biofuels. In addition to its 

broad range of research projects, the GLBRC is collaborating 

with agricultural researchers and producers to help develop 

the most economically viable and environmentally sustainable practices for bioenergy production. A new facility is being 

designed to house GLBRC and other UW–Madison bioenergy programs.

The GLBRC scientific portfolio is organized into four core 

discovery programs: (1) Improved Plants, (2) Improved 

Processing, (3) Improved Catalysts, and (4) Sustainable Biofuels Practices. Each core discovery program has a targeted 

set of mutually supportive goals designed to develop biofuel 

technologies and transfer them to industry. The GLBRC’s sustainability projects span both basic science and applications. 

The center’s research activities are integrated so that data and 

models generated in one area inform research and technology development by the other core discovery programs. 

Research support activities that cut across all four discovery 

areas include the development of enabling technologies such 

as automated screens for genes and proteins in plants and 

microbes (see figure, Automated Microbial Colony Picker at 

GLBRC, p. 21), the creation and management of informatics and information technology tools, and education and 

outreach. Some recent highlights and successes of GLBRC 

research are featured on pp. 24–25.

Research Strategy

1. Improved Plants

In addition to investigating how genes affect cell-wall digestibility in model plants, cornstalks, and switchgrass, GLBRC 

researchers are using information from model and agronomic 

systems to breed plants that produce more or altered hemicelluloses, starches, oils, or new forms of lignin that are easier 

to process into fuels. Plant oils have twice the energy content 

of carbohydrates and require little energy to extract and 

convert into biodiesel. GLBRC researchers aim to increase 

the energy density of grasses and other nontraditional oil 

GLBRC Facility. University of Wisconsin–Madison’s new 

Microbial Sciences Building houses GLBRC administration 

and scientific research. [Photo by Wolfgang Hoffmann, University of Wisconsin–Madison]
Bioenergy Research Centers U.S. Department of Energy Office of Science 21

crops by understanding and manipulating the metabolic and 

genetic circuits that control accumulation of oils and other 

easily digestible, energy-rich compounds in plant tissues.

2. Improved Processing

Located at the intersection of America’s agricultural 

heartland and its abundant northern forest biomass, the 

GLBRC has access to a rich diversity of raw biomass 

for study. GLBRC biomass-processing research focuses 

on finding and improving natural cellulose-degrading 

enzymes extracted from diverse environments. Improved 

enzymes created by the GLBRC protein-production 

pipeline are tested with a range of plant materials and 

pretreatment conditions to identify the best combination 

of enzymes, chemicals, and physical processing for enhancing the digestibility of specific biomass sources. GLBRC 

researchers identify and quantify small molecules generated by different pretreatment methods and examine how 

these molecules impact biofuel yield.

To decrease the costs of producing and using enzymes to 

break down cellulose in plants, scientists in this discovery 

program are working with plant-biomass researchers. They 

are expressing biomass-degrading enzymes in the stems and 

leaves of corn and other plants—essentially designing plants 

to “self-destruct” on cue in a biofuel production facility.

3. Improved Catalysts

GLBRC biomass-conversion research is driven by the need 

to increase the quantity, diversity, and efficiency of energy 

products derived from plant biomass. Cellulosic ethanol 

is a major focus for GLBRC research, but the center also 

aims to improve both biological and chemical methods 

for converting plant material into intermediate chemicals 

that can be used to produce ethanol and other transportation fuels. In addition to producing new generations 

of cellulose-derived liquid transportation fuels, GLBRC 

researchers are improving the processes by which microbes 

directly convert a combination of biomass and sunlight 

into hydrogen or electricity. Another target is to develop a 

microbe capable of carrying out all biologically mediated 

biofuel production steps. The GLBRC strategy to reach this 

target is to start with efficient ethanol-producing microbes 

and enable them to produce enzymes and pathways for 

breaking down cellulose.

4. Sustainable Biofuels Practices

For the emerging cellulosic biofuel industry to have a positive impact on the United States, complex issues involving 

agricultural, industrial, and ecological systems as well as 

factors affecting human decision making and behaviors 

must be addressed. To create a better understanding of the 

Automated Microbial Colony 

Picker at GLBRC. GLBRC screening efforts begin with the 

automated selection of microbial 

colonies in multiwell plates—

selecting up to 7,000 colonies per 

hour. The robot then dispenses 

growth medium into the destination plates and seals the plates 

for analysis. [Photo by Wolfgang 

Hoffmann, University of Wisconsin–

Madison]
22 U.S. Department of Energy Office of Science Bioenergy Research Centers

larger context that ultimately influences the direction and 

acceptance of new biotechnologies, GLBRC scientists are 

examining the environmental and socioeconomic dimensions of converting biomass to biofuel.

To determine the best practices for biofuel production, 

GLBRC researchers are analyzing the impacts of issues such as 

minimizing energy and chemical inputs for bioenergy crop production and reducing greenhouse gas emissions from the entire 

biofuel production life cycle (see figure, GLBRC Research on 

Bioenergy Crop Sustainability, this page). They also are seeking 

to understand the environmental impacts of removing leftover 

stalks, stems, and leaves from food crops. Data from these and 

other studies will allow GLBRC scientists to make predictions 

on the social and financial incentives needed to promote the 

adoption of more environmentally beneficial practices.

Education and Outreach

The staff and partners of the GLBRC Education and Outreach 

area inform a variety of audiences about biofuels research, 

energy concerns, and sustainability issues affecting our planet. 

Their goal is to broaden the understanding of current issues 

in bioenergy for the general public as well as for students and 

educators at the K–12, undergraduate, and graduate levels. A 

GLBRC

strong emphasis is placed on using critical thinking, quantitative reasoning, and systems-based logic in the development of 

bioenergy-related K–12 classroom materials and other informational resources. Because bioenergy research and development 

are important contemporary issues, Education and Outreach 

members participate in various programs and events to present 

research from GLBRC laboratories in a way that is accessible 

and interesting to a broad array of audiences. Summer research 

experiences for undergraduates at UW–Madison and Michigan 

State University and other Education and Outreach projects are 

described in detail at glbrc.org/education/.

Industry Partnerships

The GLBRC employs a systems-driven, genome-informed, 

basic science approach within a project-management environment. Thus, the center operates primarily in the early research 

and development arena. The GLBRC is positioned to make key 

discoveries and major advances that will lead to breakthrough 

technologies for eventual large-scale conversion of biomass 

into biofuels. Once a technology is developed, the center works 

closely with industry partners through technology-transfer 

mechanisms or collaboratively to achieve commercial implementation. More information about collaborating with the 

GLBRC is available at glbrc.org/industry/.

GLBRC Research on Bioenergy Crop Sustainability. To 

improve the sustainability of 

crops and agricultural residues 

used for energy production, 

GLBRC researchers are studying the symbiotic associations 

of crop roots with arbuscular 

mycorrhizal (AM) fungi. Interactions with AM fungi benefit 

host plants by improving the 

uptake of nutrients, especially 

phosphorus, nitrogen, and 

potassium from the soil. Establishing these symbiotic associations in crops grown under 

suboptimal conditions has the 

potential to increase biomass 

production while limiting use 

of fertilizers and pesticides. 

[Photo courtesy of the Great Lakes 

Bioenergy Research Center]
Bioenergy Research Centers U.S. Department of Energy Office of Science 23

GLBRC

University of Wisconsin–Madison (lead institution): The 

GLBRC’s lead partner provides expertise in genome-enabled 

analysis of plant and microbial pathways, networks, and systems; computational analysis of bioenergy proteins, organisms, 

and ecosystems; biosynthesis and chemistry of lignin and cellwall cross-linking; and discovery, production, and improvement of bioenergy enzymes.

Michigan State University (MSU), East Lansing: MSU 

researchers are experts in the breakdown and biosynthesis of 

plant cell walls, oils, and other polymers; the breakdown of 

cellulose in plant stems, stalks, and leaves, including grasses, 

trees, and other woody plants; and the development of biofuel 

production practices that are environmentally and economically sustainable.

Cornell University, Ithaca, New York: Individual researchers 

at Cornell provide expertise in the design and creation of microorganisms with new or improved protein machinery, specifically 

extracellular secretion of cellulases by engineered bacteria.

Illinois State University, Normal: Researchers at Illinois 

State University work on the genetic and molecular analysis 

of switchgrass.

Iowa State University (ISU), Ames: ISU researchers are 

experts in constructing economic models of biomass practices.

GLBRC Partners

Lucigen Corporation, Middleton, Wisconsin: Lucigen 

provides valuable expertise in functional screening for cellulases and other enzymes, isolation and growth of thermophiles, 

ethanol production, and molecular cloning techniques.

DOE’s Oak Ridge National Laboratory (ORNL), Oak 

Ridge, Tennessee: ORNL will enable the GLBRC to evaluate 

biomass sustainability by modeling ecosystem changes that 

could result from the biofuel production cycle.

DOE’s Pacific Northwest National Laboratory (PNNL), 

Richland, Washington: PNNL enables the GLBRC to complete high-throughput analysis of bioenergy proteins and organisms and analyze the entire life cycle of bioenergy practices.

University of Minnesota, St. Paul: Individual researchers 

at the University of Minnesota provide expertise on complex 

global environmental systems and their interactions with 

human societies, focusing on the global land resource base for 

bioenergy feedstocks.

University of Missouri, Columbia: Individual researchers at 

the University of Missouri provide expertise in agricultural economics, specifically the impacts of Energy Independence and 

Security Act mandates on U.S. crop and livestock production.

University of Toledo, Ohio: Individual researchers at the 

University of Toledo provide expertise on biophysical constraints and resource use limitations in regards to maximizing biofuel production.
24 U.S. Department of Energy Office of Science Bioenergy Research Centers

GLBRC Research Highlights

Alterations in Poplar Lignin Could Enhance 

Pretreatment Efficiency

Alterations in lignin content or structure in plant cell walls can 

have a profound effect on chemical or enzymatic degradability and the efficiency by which certain pretreatment methods 

remove lignin from polysaccharides. GLBRC researchers 

found that overexpression of a particular gene [ferulate 

5-hydroxylase (F5H)] in the lignin biosynthetic pathway of 

a hybrid poplar created lignin with a structure and composition that can enhance lignin removal from cellulose, while still 

maintaining normal growth and development. When compared to wild-type poplar, the up-regulated F5H poplar has a 

much simpler lignin structure that is less branched and more 

homogeneous in its subunit composition, which makes the 

lignin easier to separate from cellulose during pretreatment. 

This and other poplar transgenic materials under investigation 

by GLBRC researchers have cell walls that release more sugar 

than wild-type poplar over a range of pretreatment methods. Ongoing work is examining the effect of ammonia fiber 

expansion pretreatment on these transgenic poplars. Details 

on the lignin structure of F5H up-regulated poplar were 

reported in Stewart, J. J., et al. 2009. “The Effects on Lignin 

Structure of Overexpression of Ferulate 5-Hydroxylase in 

Hybrid Poplar,” Plant Physiology 150(2), 621–35.

New Modeling Tool Combines Environmental 

and Economic Analysis of the Biorefinery 

in Agricultural Landscapes

GLBRC researchers have provided a direct simulation of 

different biorefinery configurations in realistic agricultural 

landscapes for diverse locations throughout the United 

States. Since no full-scale commercial examples of a cellulosic 

biorefinery yet exist, forecasting the risks and tradeoffs of 

the complete biofuel production chain requires the use of 

modeling tools. Developed at GLBRC, the Biorefinery and 

Farm Integration Tool (BFIT) enables a combined modeling 

approach, including both crop and animal production, for 

analyzing potential economic profitability as well as environmental impacts (see figure). Focusing on ethanol production from the two largest anticipated sources of cellulosic 

biomass—corn stover and switchgrass—BFIT simulated the 

farm-biorefinery interactions for nine different agricultural 

regions using county-specific data for soil, weather, and farm 

practice patterns. In all cases, cellulosic biofuel production 

was integrated into existing farmlands. Results from the simulated scenarios include projections for land area requirements, 

annual farm income, nitrogen loss, greenhouse gas emissions, 

total project investment, and minimum ethanol selling price. 

Based on these projections, GLBRC researchers show that 

introducing the cellulosic biorefinery and associated markets 

could improve farm economics and reduce emissions without 

additional clearing of lands for biofuels. BFIT research results 

are reported in Sendich, E. D., and B. E. Dale. 2009. “Environmental and Economic Analysis of the Fully Integrated 

Biorefinery,” GCB Bioenergy 1, 331–45.

Study Provides Insights on Maximizing 

Energy-Rich Lipid Content in Leaves

Energy-rich lipids—with two times more energy than carbohydrates or proteins—are life’s primary molecules for energy 

storage. Preventing the breakdown of lipids as leaves age 

during the process of senescence is estimated to increase the 

energy content of leaves by about 20%. GLBRC researchers systematically studied the age-dependent changes in the 

fatty acids of Arabidopsis, Brachypodium distachyon (a model 

grass), and switchgrass leaves during natural plant senescence. Researchers found that surface lipids were more stable 

during senescence than membrane lipids, thus a potential 

strategy for increasing the energy content of biofuel crops 

might be to enhance surface lipid production. This research 

was reported in Yang, Z., and J. B. Ohlrogge. 2009. “Turnover of Fatty Acids During Natural Senescence of Arabidopsis, Brachypodium, and Switchgrass and in Arabidopsis

β-Oxidation Mutants,” Plant Physiology 150, 1981–89.

Feed Manure

Crop

farming

Animal

farming

Fuels, chemicals,

and materials

Biorenery

Intermediates

Cogeneration

Water

Animal

feed

Farm

products

Steam

electricity

Sun, water,

and fuel

Integrated Biorefinery Concept. This figure shows the integrated system components analyzed by the Biorefinery and 

Farm Integration Tool. [Image from Sendich and Dale 2009]
Bioenergy Research Centers U.S. Department of Energy Office of Science 25

GLBRC Research Highlights

Sequencing Characterizes Bacterial Rhizosphere 

Communities of Biofuel Crops on Marginal Lands

Using a new high-capacity sequencing technology, GLBRC 

researchers characterized the structure of bacterial communities living in the rhizosphere (microscopic zone surrounding 

roots) of corn, soybean, canola, sunflower, and switchgrass. 

Samples were taken from agricultural sites and adjacent native 

forest in four locations with different soil types in Michigan. Three of the locations were marginal lands unsuitable 

for conventional agriculture, and a fourth site served as an 

experimental control to evaluate crop yield and quality on 

nonmarginal land. Although bacterial communities from biofuel crops and forest were clearly differentiated, the communities grouped mainly by location rather than by crop species, 

and soil environment and land management were key factors 

influencing community structure. Although more limited in 

plant diversity, greater bacterial diversity was observed in the 

biofuel crop samples than in the forest samples. Species of 

Acidobacteria were the most abundant community members 

in the rhizospheres of all plants, yet no strains have been 

isolated for cultivation and characterization in the laboratory. 

This research was reported in Jesus, E. C., et al. 2010. “Bacterial Communities in the Rhizosphere of Biofuel Crops Grown 

on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences,” Bioenergy Research 3, 20–27.

Chemical Process Produces Simple, Fermentable 

Sugars from Raw Biomass

A GLBRC research team has developed a promising new 

chemical method to liberate the sugar molecules trapped 

inside inedible plant biomass, a key step in the creation of 

cellulosic biofuels. The new chemical process combines 

ionic liquids and dilute acid to degrade cellulosic biomass 

without the use of cellulases. In this approach, ionic liquids 

make cell-wall polysaccharides accessible to chemical reactions by decrystallizing lignocellulosic biomass and dissolving cellulose. Then, dilute hydrochloric acid at 105°C is used 

to hydrolyze cellulose and hemicellulose into individual 

sugar subunits. Applying this process to pure cellulose 

resulted in nearly 90% yield of glucose (see figure), and 

applying it to raw corn stover achieved sugar yields of 70% to 

80%. By adding the right balance of water to the mixture, the 

researchers reduced the formation of unwanted by-products 

and demonstrated significant improvement in fermentable 

sugar yields from ionic liquid treatment of lignocellulose 

with yields comparable to those of enzymatic hydrolysis. Ionexclusion chromatography was used to separate sugars from 

the reaction mixture and recover the ionic liquids for reuse. 

Sugars recovered from the hydrolyzed stover were readily 

converted to ethanol by Escherichia coli and the yeast Pichia 

stipitis. This research was reported in Binder, J. B., and R. T. 

Raines. 2010. “Fermentable Sugars by Chemical Hydrolysis 

of Biomass,” Proceedings of the National Academy of Sciences

107, 4516–21.

Chemical Hydrolysis of Cellulose Achieves High Glucose 

Yields. Applying this new chemical approach to the hydrolysis of pure cellulose results in glucose yields approaching 

90% in just a few hours. Yields of unwanted by-products 

such as HMF (5-hydroxymethylfurfural, an inhibitor 

of microbial fermentation) and cellobiose (a molecule 

consisting of two linked glucose subunits) were minimal. 

[Image from Binder and Raines 2010]
26 U.S. Department of Energy Office of Science Bioenergy Research Centers

The Genomic Science program (formerly 

Genomics:GTL and Genomes to Life) is run by 

the DOE Office of Biological and Environmental 

Research (BER). This program aims to develop a predictive 

understanding of biological systems relevant to energy production and other DOE missions in environmental remediation 

and climate change mitigation (see box, Genomic Science Program Goal and Objectives, below). Genomic Science program 

research is conducted at national laboratories and universities 

and includes single-investigator projects, multi-institutional 

collaborations, and fundamental research centers. 

The DNA sequence of an organism’s complete genome is the 

starting point to understanding any biological system. Scientists from the three DOE Bioenergy Research Centers and 

other projects of the Genomic Science program are working with the DOE Joint Genome Institute to sequence the 

genomes of energy-related plants, as well as microbes and fungi 

that degrade biomass or impact plant productivity. Building 

on this foundation of genomic information, the whole-systems 

understanding of biology will enable scientists to redesign proteins, biochemical pathways, and even entire plants or microbes 

important to solving bioenergy challenges and meeting other 

DOE needs. Even though the specific functions of these systems vary, common fundamental principles control the behavior of all biological systems. Knowledge of these underlying 

principles will advance biological solutions to DOE missions.

Several developments have converged in recent years to suggest 

that systems biology research into microbes and plants may be 

able to overcome critical roadblocks to large-scale production 

of fuels from plant biomass. The ability to rapidly sequence the 

DNA of any organism is a critical but modest part of these new 

capabilities. Others include:

•	 Development of high-throughput techniques and commercially available reagents for protein production and 

characterization to test thousands of natural and engineered protein variations.

•	 Emergence of a range of new instrumentation for observing proteins and other cell constituents to determine, for 

example, how cell walls are constructed.

•	 Availability of technologies for high-resolution imaging—

spanning spatial scales from molecular to cellular to microbial community—that can be used to help understand, for 

example, why rates of cellulose degradation vary.

•	 Major advances in the integration of computational modeling, algorithm and software development, and modeldriven laboratory experimentation to enable solutions in 

bioenergy and systems biology.

In addition to these activities in the Genomic Science 

program, BER is supporting related genomic bioenergy 

collaborative research with other governmental agencies. 

A research program 

jointly sponsored 

by BER and the 

U.S. Department of 

Agriculture (USDA) 

National Institute of 

Food and Agriculture 

supports genomebased approaches 

to accelerate plantbreeding programs 

and improve potential 

bioenergy crops.

DOE Genomic Science Program

From Genome Sequences to Understanding genomicscience.energy.gov
DOE Biological and Environmental 

Research

The BER programs within the DOE Office of Science advance world-class research to understand 

complex biological and environmental systems and 

provide scientific user facilities to support DOE missions 

in scientific discovery and innovation, energy security, and 

environmental responsibility. BER’s interdisciplinary research 

programs engage scientists from national laboratories, universities, and the private sector in exploring the frontiers of 

genome-enabled biology; discovering the physical, chemical, and biological drivers of climate change; and seeking the 

geochemical, hydrological, and biological determinants of 

environmental sustainability. BER programs are managed 

within two divisions: the Biological Systems Science Division 

and the Climate and Environmental Sciences Division.

BER’s Biological Systems Science Division (BSSD) seeks to 

achieve a predictive understanding of biological systems with 

important roles in sustainable biofuels, climate science and 

carbon cycling, and subsurface biogeochemistry (see figure). 

BSSD research activities include using genomics and 

systems biology to understand plant and microbial 

systems, supporting DOE Bioenergy Research 

Centers to provide transformational breakthroughs in cellulosic biofuels, and developing real-time, high-resolution technologies 

(assisted by integration with computational 

modeling) for analyzing dynamic biological 

processes.

The Climate and Environmental Sciences 

Division (CESD) aims to achieve a 

predictive understanding of climate 

change, ecosystem response to climate change, and contaminant fate 

and transport in the subsurface. 

Projects supported by CESD programs are resolving the greatest 

uncertainties in climate change, 

improving the world’s most powerful climate models, providing the 

science to inform environmental 

remediation strategies, and working to 

understand carbon cycling in terrestrial 

vegetation and soils.

DOE Office of Science

The Office of Science manages fundamental research 

programs in basic energy sciences, high-energy 

physics, fusion, biological and environmental sciences, and computational science. In addition to being the 

federal government’s largest single funder of material and 

chemical sciences, the Office of Science supports unique 

and vital parts of U.S. research in climate change, geophysics, 

genomics, life sciences, and science education. About a third 

of Office of Science research funding supports projects at 

more than 300 colleges and universities nationwide.

The Office of Science also manages 10 world-class national 

laboratories with unmatched capabilities for solving complex 

interdisciplinary scientific problems and oversees the construction and operation of some of the nation’s most advanced 

scientific user facilities, located at national laboratories and 

universities. These include particle and nuclear physics accelerators, synchrotron light sources, neutron scattering facilities, 

and supercomputers and high-speed computer networks. 

Nearly 26,000 researchers from universities, 

national laboratories, industry, and international partners are expected to use 

the Office of Science scientific 

user facilities in FY 2011.