TABLE OF CONTENTS

Exploring the Applications of Modern Biology

to the Energy Sector
01 Message from the Director » 2-5
EBI Director Chris Somerville offers a personal perspective on the development
of the Institute: “We can look back at having successfully navigated a myriad of
typical startup challenges as well as a few that were unusual, if not unique.”

02 The EBI at 1 Year Old—a BP Perspective » 6-7

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

03 About the Energy Biosciences Institute » 8-19

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

04 An Introduction to Biofuels » 20-27

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

05 Feedstock: Agronomy, Engineering, and the Environment » 28-35

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

06 Bioconversion: Attacking Cellulosic » 36-41

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

07 Biofuels Production: Transforming Feedstock » 42-45

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

08 Societal and Economic Impacts of Biofuels » 46-53

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

09 Education and Outreach » 54-57

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

10 EBI Research Programs, Projects, and Research Personnel » 58-63

A listing of the first 50 funded projects in the Institute, including the teams
of principal investigators, research associates, postdocs, graduate, and
undergraduate students.
 Message from the Director
Translating the Vision into Reality
The creation of a new organization is inevitably
tumultuous and unfailingly exciting. Plans are tested
against reality, conflicts are resolved, people are
recruited to new roles, processes are put in place,
space and facilities are adapted and occupied,
and the activities of the organization begin to be
realized. As the first year of the Energy Biosciences
Institute’s formal existence as an organization draws
to a close, we can look back at having successfully
navigated a myriad of typical startup challenges as
well as a few that were unusual, if not unique.
The most important accomplishment of the startup
phase was the implementation of a broad research
portfolio within the three academic partner
institutions—the University of California at Berkeley,
Lawrence Berkeley National Laboratory, and the
University of Illinois at Urbana-Champaign. The EBI
is currently supporting 50 research groups composed
of approximately 130 faculty members and 160
graduate students, postdocs, and undergraduates. At
this juncture, the research topics encompassed by
this group are largely focused on understanding the
issues associated with the proposed development of
a cellulosic biofuels industry. Our goal is to probe all
aspects of the topic with the highest quality academic
research and to integrate knowledge from this broad
investigation into a coherent understanding of the
overall topic.
In pursuit of this goal, EBI investigators are engaging
in research in a wide range of academic disciplines
Our goal is to probe all aspects of the topic with the highest quality academic
research and to integrate knowledge from this broad investigation into a
coherent understanding of the overall topic.
Chris Somerville
2 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
that include agronomy, agricultural engineering,
biochemistry, chemistry, chemical engineering,
ecology and environmental science, economics,
geography, law, microbiology, plant breeding,
public policy, and systems biology. It is our hope
that by supporting a broad investigation within a
single framework, including common space, we
can facilitate interdisciplinary research that leads to
holistic understanding, innovation, and insight while
simultaneously minimizing the risks of pursuing
ideas that lead to dead ends.
The general thrust of the EBI research portfolio
was developed by a group of interested faculty in
response to a solicitation by BP in the summer of
2006. Following the selection by BP of the EBI
proposal in early 2007, and the appointment of
a leadership group charged with development of
the EBI as an operating unit within the academic
partnership, a competitive proposal process was
implemented to identify specific research topics.
Most of the current research programs and projects
were selected from approximately 250 pre-proposals.
Additionally, several projects have been implemented
outside the first general proposal process to support
recruitment of new faculty members who proposed
research topics of central importance to the EBI
mission, or to initiate research on timely concepts
that emerged after the proposal process.
A second call for proposals was issued recently in the
general area of microbially enhanced hydrocarbon
recovery. This solicitation was based on ideas that
emerged from an EBI-sponsored workshop held at
UC Berkeley in late 2007. Proposals were received
from 37 faculty who self-organized into several
consortia. These proposals are currently undergoing
external peer review, and we envision making
funding decisions shortly. Additional solicitations
are envisioned in 2009 and in subsequent years. In
2010, funding for the first round of projects expires,
and we anticipate new proposals will be submitted to
compete with current projects and programs.
An important component of EBI activities this year
has been sponsorship or co-sponsorship of a number
01
c h a p t e r
of workshops and seminars on topics related to
the EBI mission (listed on pages 54–57). Many of
these meetings were focused on illuminating issues
associated with environmental, economic, and social
consequences of potential land use changes that
may result from expanded production of biofuels.
We were pleased to be able to assist with meetings
sponsored by organizations that have included the
American Society for Plant Biologists, Ecological
Society of America, Environmental Defense Fund,
the Farm Foundation, Berkeley Energy Resources
Collaborative, and the UK Renewable Fuels
Association, in addition to supporting a series of
workshops developed by EBI investigators. Many
of these meetings were filled to the capacity of
the venues, and all engendered stimulating and
productive exchanges that helped to define the
research frontiers, compare the outcomes of various
models, and facilitate networking and data sharing
among experts.
My own conclusion from having participated in many
of the meetings was that the issues are complex,
but there are points of consensus. For example,
an important component of strategies to reduce
greenhouse gas emissions from human activities is
to prevent expansion of agriculture onto land, such
as native tropical forests, that currently supports
carbon-rich natural ecosystems. Cellulosic biofuels
will have the greatest environmental benefits if
produced on land that has been farmed in the past
but is no longer used for food production. Recent
studies have suggested that at least a billion acres of
land worldwide meet these criteria. EBI investigators
are using sophisticated crop models in conjunction
with detailed geographical information to evaluate
the productive potential of such lands.
A founding principle of the EBI was to develop
comprehensive research capabilities in the area of
energy biosciences with the three academic partners.
The partnership with the University of Illinois was
created with the specific goal of broadening the base
of expertise within the EBI beyond the range of
UC Berkeley and Lawrence Berkeley National Lab.
The collaboration with Illinois has been remarkably
MESSAGE FROM THE DIRECTOR 3
 smooth and enjoyable for everyone involved and conservative influences and financial limitations that
represents an unrivaled success. impair much federally funded research. Many brilliant

Not unexpectedly, several topics of central importance

and engaged people who had not previously worked The EBI at a Glance
on topics related to energy biosciences are now testing
to the field of energy biosciences are under- their ideas, and I expect an outpouring of innovation
represented in the EBI because no faculty member at
Comprehensive 4 research
and creativity. biofuels research partners
the partner institutions proposed a research program
in these areas. I expect that some of the topics will be A goal of the EBI management team is to develop
agenda
developed by newly recruited faculty. institutional capabilities and processes that will
support and facilitate bold and creative research by
An important aspect of the research program is the providing access to resources that might normally
co-location of a team of engineers and scientists be beyond the reach of an individual research group. $500 million grant 50 research groups
from BP within the EBI. At present, BP leases a small Towards this end, EBI investigators at Illinois are from BP and 130 faculty
amount of office space on the UC Berkeley campus developing a 320-acre energy farm where relatively
where a number of BP scientists and engineers are large-scale trials of prospective energy crops can
engaged in studying energy biosciences from an be tested in a wide variety of ways that include
industrial perspective. Unlike the academic members productivity studies, identification of pests and
of the EBI, who are focused on fundamental academic pathogens, carbon sequestration measurements,
questions, the BP fellows are engaged in envisioning greenhouse gas balances, and development of
how knowledge might be used in practice. The methods for harvesting and storage. We expect that
dialectic between those engaged in basic research the experience gained with this first test site will
and those charged with applied research is fertile inform the development of additional sites at locations
ground for the development of new questions and a around the world.
highly efficient way to translate basic research. Equally
importantly, the arrangement provides a wonderful We have also taken the first steps toward development
opportunity for education across both sides of the of an analytical laboratory at Berkeley that will provide Lab space at Illinois 144,000-sq-foot
basic/applied boundary. Standing-room-only seminars specialized services and characterized biomaterials and UC Berkeley Helios Building,
at EBI venues this year by BP chief economist Christof to EBI researchers, and several of the analytical complete in 2013
Ruehl and BP chief scientist Steve Koonin provided instruments that will facilitate the work have been
exceptional opportunities for the Berkeley and Illinois installed in Calvin Laboratory. The analytical team 160 postdoctoral
communities to understand perspectives on important will facilitate investigations of the composition researchers,
aspects of the world energy situation from people who and properties of biomass proposed by many EBI graduate, and
participate directly in providing energy. One-day tour- investigators. undergraduate 320-acre Energy
de-force workshops at Berkeley and Illinois on the students Farm
chemistry of fuels by BP engineer Frank Gerry were The EBI’s initial year has been filled with a hopeful
also sellout events. energy, tireless dedication of researchers and support
staff, and productive first steps on our journey as
" It is our hope that by supporting a broad
Looking forward, I expect many exciting discoveries to reflected in these pages. Deputy Director Steve Long,
emerge from EBI research. The exceptional resources Associate Director Paul Willems and I are privileged investigation within a single framework, we can
provided by BP have afforded a unique opportunity to lead the EBI forward. facilitate interdisciplinary research that leads to
to explore many new areas without some of the
holistic understanding, innovation, and insight..."
~ CHRIS SOMERVILLE

www.energybiosciencesinstitute.org
CHRIS SOMERVILLE
December 2008

4 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT MESSAGE FROM THE DIRECTOR 5

The EBI at 1 Year Old—
a BP Perspective
By PAUL WILLEMS
Associate Director, EBI
Technology Vice President, Energy Biosciences, BP
When BP decided to create the Energy Biosciences
Institute in partnership with the University of
California at Berkeley, the University of Illinois in
Urbana-Champaign, and the Lawrence Berkeley
National Laboratory, we had several objectives. As we
reach our first anniversary, it is a good time to reflect
on how we have done so far.
Our goals can be categorized in three groups: science,
collaboration, and people.
Let’s start with science. The creation of the EBI was
rooted in a belief that modern biology as a science
is ready to start making significant contributions to
energy problems. Lignocellulose-based biofuels have
come a long way, and the first commercially viable
processes (at least in the current environment of
high energy prices) are starting to emerge. However,
tremendous scope exists for further technical
innovation, and the processes we will employ in 10
years’ time likely will bear little resemblance to these
first installations.
We have chosen to engage in a broad research
portfolio, spanning the entire field addressing
dedicated energy crops, their management practices,
the technology used to convert them to fuels,
a variety of target fuel molecules, chemical and
biological conversion pathways, etc. In doing so,
we have assembled a great team of researchers, led
by distinguished faculty members at our partner
institutions. While these partners had some a priori
idea of faculty members interested in the field, we have
been pleasantly surprised at the level of engagement in
the community. Many faculty members are involved
with the EBI today who were not on the radar screen
initially.
Our investment in socio-economic research is one of
the features that makes the EBI unique: biofuels done
the right way is of crucial importance to us. A clear
focus on moving the debate in this arena from opinion-
based to fact-based is the mantra of the EBI. In our first
6 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
02
c h a p t e r
year, we have already seen the fruits of this philosophy
as we have been approached by various agencies
involved in policy-setting to provide assistance in
“getting to the bottom” of the various debates taking
place.
Next, collaboration. The EBI is a public/private
collaboration of unprecedented scale and scope. The
EBI is a mission-oriented, multidisciplinary, team-
science-based institute. These are new expectations
for most of our collaborators, as well as for the
partnering institutions. While change brings a certain
amount of uneasiness, it also brings excitement: new
possibilities, new relationships, new perspectives, new
innovations. Even as we are just getting under way
in our first year of operation, we have already seen
the kinds of examples we were hoping for: science
taking an unexpected turn, and new dialogue between
individuals who had never worked together leading to
new avenues of investigation.
And last but not least, people. Great people are the
foundation of great work. On the backs of our partner
institutions, we have been able to create a great
reputation for the EBI. Not a week goes by without an
important visitor to the EBI from somewhere around
the globe. Our reputation has allowed us to tap into the
great talent pool on our campuses. It is also our calling
card for attracting future students and researchers.
Part of the vision for the EBI was to create a talent
pool for a future energy biosciences-based industry.
This is obviously important to BP as we try to grow
our own internal technical capability in this area. It is
equally important to the wider world. We anticipate
that in due course this will result in a formal energy
biosciences curriculum, at both the undergraduate and
graduate level, at our partner institutions.
In summary, I would say we can be very proud of our
first year. We have a great portfolio of research projects
in place. We are continuing to create the collaborative
and multidisciplinary environment envisioned for the
EBI. We are positioned for successful collaboration
and delivery of great innovation in years ahead. We
couldn’t have asked for much more than this.
THE EBI AT 1 YEAR OLD—A BP PERSPECTIVE 7

About 87 percent of human energy use
is presently obtained by combustion of
fossil fuels. This dependence on fossil
fuel has increased the amount of carbon
dioxide in the atmosphere by about
one-third since the preindustrial era. It is
now apparent that continued dependence
on fossil fuels is causing climate change,
and that the consequences are both
uncertain and unwelcome. If global
climate models are correct, temperatures
will increase and rainfall patterns will
change with devastating effects on food
production in many areas of the world
along with the potential for attendant
societal disruptions. Also, many of the
world’s ecologically sensitive areas may
be unable to support the species that
currently define the ecological character
of the region and may be lost along
with potentially devastating effects of
biodiversity. These are the changes
forecast by the most recent Scientific
Assessment of the Intergovernmental
Panel on Climate Change (IPCC). The
realization that the polar ice caps are
currently melting at a faster rate than
forecast by this assessment underlines
the urgency of addressing net carbon
emissions.
THE ENERGY
BIOSCIENCES INSTITUTE
Empowering outstanding academic researchers to envision
and enable new approaches to the production of energy
8 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
ENTER BP
The multinational company BP was the
first major energy corporation to publicly
recognize that continued burning of fossil
fuels was problematic. In 1998 in a speech at
Stanford, BP Chief Executive Officer John
Browne committed the company to comply
internally with the Kyoto Protocol. “It would
be unwise and potentially dangerous to
ignore the mounting concern” about climate
change, said Browne. As a result, BP created
a renewable energy division that has grown
to become one of the largest photovoltaic
and wind energy producers in the world.
More recently, Browne’s successor, Tony
Hayward, has called for the implementation
of a cap-and-trade system in which emissions
of greenhouse gases are monetized so that
the environmental costs and benefits of
various energy options can be factored into
the cost of energy.
In 2006, as part of its overall strategy for
developing renewable energy sources, BP
issued an international call for proposals to
engage in a 10-year, $500 million research
partnership to explore the application of sci-
entific advances in basic biological sciences
to the energy sector. This bold concept was
based on the recognition that our under-
standing of biology is undergoing a revolu-
tion in which major discoveries are being
made on a daily basis. This is supported by a
series of technical and conceptual advances
in subjects such as genomics, computational
biology, synthetic biology and analytical
chemistry that have become the major tools
of discovery in many areas, especially in the
medical sciences. By contrast, the area of
“energy biosciences” is relatively unexplored
and underinvested compared with the vast
investment that has been made in health-
related aspects of the biosciences.
In 2007, following an international com-
petition involving about 20 major research
universities, BP selected a consortium
consisting of the University of California
at Berkeley, Lawrence Berkeley National
03
c h a p t e r
Laboratory and the University of Illinois at
Urbana-Champaign to host the new Energy
Biosciences Institute (EBI), and a new era of
groundbreaking public-private partnerships
was launched. Following a period of contrac-
tual negotiations, the EBI began operations
in November 2007.
AN INSTITUTE
OF COLLABORATIONS
An overriding goal of the EBI is to develop
an integrated holistic understanding of the
research topics related to energy biosciences.
The motivation for this arises from the
recognition that topics of interest such as
cellulosic biofuels are unusually complex and
involve research questions in subjects that
include agronomy, microbiology, mechanical
and chemical engineering, biochemistry,
chemistry, geography, economics, law and
policy analysis. Because advances in one area
may have important impacts in other areas,
the EBI’s goal is to create dynamic intellec-
tual bridges between the various disciplines
so that information and insights flow
efficiently, and new research initiatives can be
adopted based on a “big picture” view of the
overall topic. To this end, the EBI is working
toward placing the full-time researchers
that it supports into a common space on
each campus. This is facilitating horizontal
integration of disciplines, which range from
genomics and agronomy to environmental
sciences and economics.
This multidisciplinary approach will facilitate
discovery and will ultimately enable optimal
decision-making by the sectors in society
that are responsible for implementing
trade and regulatory policies and business
activities. In this respect, the close associa-
tion within the EBI of academics from the
partner institutions and industrial managers,
engineers and scientists from BP offers a rare
opportunity to accelerate the feed-forward
and feedback processes that are associated
with conversion of academic discovery into
real-world applications.
ABOUT THE ENERGY BIOSCIENCES INSTITUTE 9
 The Areas of Study
The primary initial thrust of EBI research is an exploration of the feasibility of commercially
viable, sustainable and environmentally benign transportation fuels from biomass. The most
promising opportunities are currently thought to be cellulosic biofuels, but the EBI is also
supporting a study on the feasibility of algal biofuels. The development of cellulosic fuels
involves identifying the most suitable species of plants for use as energy crops; improving
methods of breeding, propagation, planting, harvesting, storage and processing; and ensuring
that this is done in a sustainable way without negative impacts on food production or the
environment. Production of biofuels also involves the development of biomass-to-liquid
fuels technologies that yield major benefits in regard to both net energy output and net
greenhouse gas balance based on consideration of all inputs.
To accomplish this, research is divided into several areas of inquiry:
Societal and Economic Impacts of Biofuels
A major goal of the EBI is to understand the potential environmental, economic, and societal
impacts of meeting a growing portion of the world’s energy needs through cellulosic or
algal biofuels. Many in the world are concerned that the demand for energy is so large that
unrestrained conversion of land to biofuel production could have negative environmental
effects and could further disadvantage many poor people by increasing prices for food, feed,
and fiber. Therefore, the EBI is working to understand how land is used around the world and
to model the impacts of growing bioenergy crops on land that is not used for food production
or is providing key ecosystem services, such as carbon storage or biodiversity.
EBI investigators are also testing the environmental impacts of various bioenergy crops and
developing economic models that may help to understand the feasibility of bioenergy crop
production around the world. An important aspect of understanding the environmental
effects of cellulosic biofuels will include development of complete life cycle models that
incorporate both direct and indirect effects of the biofuels.
Feedstock: Agronomy, Engineering, and the Environment
Work in this area seeks to identify and characterize plant species that can maximize cellulosic
biomass production in various regions around the world, and to learn how to grow and
harvest them sustainably. A primary goal is to discover plants that maximize the production
of cellulosic biomass, using minimal land, water, and energy. Because of the importance of
soil carbon in the global greenhouse gas balance, the EBI is particularly interested in identify-
ing species that can be grown on the large amounts of minimally productive land around the
world. These considerations favor the use of perennial grasses and certain woody species.
However, the possible utility of algal species is also being explored.
Bioconversion: Attacking Cellulosic Degradation on Several Fronts
The main constituents of the body of higher plants are polysaccharides and lignin. Fashioning
fuel from plants requires conversion of the polysaccharides to sugars by severing the chemical
bond that holds them together, among the most critical and difficult steps in the process.
Today’s practices are costly and inefficient. EBI scientists are investigating nature’s methods
of releasing these sugars to achieve an effective and less costly method of breaking down
these substances. This will be key to ensuring that biofuels can be reasonably priced. The EBI
is examining the processes that take place in cow rumen, termites, compost heaps, and other
10 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
An overriding goal
of the EBI is to develop an
integrated holistic understanding
of the research topics related
to energy biosciences.
environments where biomass degradation takes place. In parallel, it is also
exploring the development of new synthetic catalysts that can accelerate
the degradation of polysaccharides and lignin.
Biofuels Production: Transforming Feedstock
to Fuel with Microbes
In order to convert sugars to liquid fuels, the proportion of oxygen
must be reduced. This can be accomplished by bioconversion, such as
fermentation, or by chemical transformations. With no clear front-runner
at the present time, the EBI is exploring several methods in parallel.
Methods used for production of biofuels today are similar to the
fermentation practices used to make beer and wine, but these traditional
methods are not optimized for the large-scale, energy-efficient produc-
tion of cellulosic biofuels. EBI researchers are exploring ways of improv-
ing bioconversion of sugars to next-generation fuels by using the methods
of systems biology to characterize new types of microbes and by testing
genetic modifications of promising organisms. They are particularly
interested in exploring ways of producing biofuels that will not require
major changes in the transportation infrastructure. This involves research-
ing chemical and fermentation routes to products more hydrophobic than
ethanol and butanol. The EBI is also interested in exploring alternatives to
bioconversion technologies, such as the use of non-biological catalysts to
transform biologically derived chemicals into fuels.
Microbiology of Fossil Fuel Reserves
During the past several decades, it has become apparent that significant
populations of microorganisms are found in both coal and petroleum
reservoirs deep underground. These microbial populations can contribute
to the properties of the reservoirs in deleterious ways, such as through
catalyzing the souring of petroleum, but they may also contribute
positively by activities such as altering the porosity of the reservoirs. This
could allow more efficient recovery of oil. In order to understand the
effects of these microbial populations, the EBI intends to support studies
into characterization of the organisms found in various reservoirs using
the tools of modern biology, such as high-throughput DNA sequencing
and analysis. By understanding the genomics of the reservoir microbes,
it may be possible to infer how their activities can be better controlled
toward useful purposes. The collaboration with BP provides a rare
opportunity for academic scientists to access deep-earth samples from
reservoirs that have been geologically characterized.
ABOUT THE ENERGY BIOSCIENCES INSTITUTE 11
 PROGRAMS AND PROJECTS
The EBI is a mission-oriented research organization. One approach to
realizing the EBI mission is to develop a consortium of comprehensive
expertise and research activities concerning energy biosciences within
the partner organizations. To achieve adequate breadth of scope, research
funds are allocated to various topics based on predefined targets.
Workshops are scheduled throughout the year to share data and to help
define key questions to be answered. Topical proposals that address
problems defined by the EBI are solicited from faculty and scientists in
the partner institutions. Thus, the EBI mandate defines the problem,
but the EBI investigators propose the research approaches to solutions.
A peer-review process narrows proposals drawn from solicitations to a
focused set of projects and programs for funding.
During the startup phase of the EBI in the summer of 2007, a very
broad solicitation was announced. From an initial list of more than 250
pre-proposals from researchers at the three partner institutions, EBI
management and advisors requested 85 full research proposals and,
following external peer review, narrowed the field to 50 high-priority
research efforts that received the first round of funding. A second
solicitation in the summer of 2008 was more narrowly focused. Awards
are divided into two categories: programs and projects. Programs are
typically large integrated multi-investigator efforts with broad goals,
funded at anywhere from about $400,000 per year up to about $1 million
per year, and may continue for the 10-year life of the institute. Projects
are smaller activities of 2-3 years in duration that are usually narrower in
scope. These average about $150,000 per year.
Program research is conducted mostly within EBI space so that post-
doctoral, support, and graduate student researchers from different
disciplines will work side-by-side, and so that space constraints will not
limit the ability of EBI investigators to participate in the EBI mission. This
will facilitate synergy across fields and will provide a training environment
and a broad appreciation of the scientific, technological, environmental,
economic, and policy issues that must all be addressed to achieve the
Institute’s goal of environmentally sustainable bioenergy.
12 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
THE RESEARCH ENTERPRISE—
PUBLIC AND PRIVATE
Openness of the research enterprise—and the
academic freedom of its faculty, graduate students, and
university researchers—is paramount for the three
public institutions in the EBI. Inventions made during
the course of research within the EBI are owned by
the academic institutions according to U.S. patent law,
and BP receives an automatic non-exclusive license
in return for funding the research. All four partners
have representation in the EBI’s two management
panels, with none having a majority or veto power
on the governing board, ensuring consensus in all
decisions. The Executive Committee, which provides
scientific direction and operational oversight, is mostly
composed of professors from the academic partners.
The Licensing Executives Society, a professional
organization for intellectual property specialists, chose
the EBI for its 2008 “Deal of Distinction” award for
being “an innovative model for collaboration between
academia, government labs, and industry.”
Collaborative research between universities and
industry yields new ideas and more effective pathways
for moving discoveries from the laboratory into com-
The close association within the EBI
of university academics and industrial
managers from BP offers a rare opportunity
to accelerate the processes that are
associated with conversion of academic
discovery into real-world applications.
mercial use. These collaborations also help prepare
students for non-academic careers and address the
need for real-world evaluation and implementation of
solutions science.
In the EBI, intellectual resources of leading research
institutions are being brought to bear on the quest for
sustainable, affordable, renewable energy. The exper-
tise of an international corporation is being employed
to ensure that commercialization and application can
happen as rapidly as the discoveries allow.
ABOUT THE ENERGY BIOSCIENCES INSTITUTE 13
 The Partners
It is an enticing formula—take the technical and intellectual strengths of three
internationally known public research institutions, add the successful commercial
legacy of one of the world’s leading energy companies, and blend together in a unique
partnership in which collaborations are forged and innovation is maximized. The sum is
greater than all of these impressive parts.
BP
BP, one of the world’s largest energy companies, is
the leading producer of oil and natural gas in the
United States, and the largest investor in U.S. energy
development. BP provides its customers with fuel for
transportation and energy for heat and light, employ-
ing more than 100,000 people worldwide and more
than 35,000 in the U.S. BP was the first major energy
company to acknowledge the need for precautionary
action to reduce greenhouse gas emissions, and today
it continues to lead the effort to meet the world’s
growing demand for sustainable, environmentally
responsible energy.
The University of Illinois
at Urbana-Champaign
The University of Illinois at Urbana-Champaign is a
world-class public university whose faculty, student,
and alumni honors have brought international
distinction. Home of the largest public university
library collection in the world, Illinois is also a
leader in supercomputing design and application
and boasts multi-disciplinary research excellence
in dozens of fields. The University has a pioneering
history of sustainability research as the originator of
no-till agriculture, and is home to the longest running
investigation of the impacts of varied crop manage-
ment methods on soil quality (1876, Morrow plots)
outside of Europe. Founded in 1867, Illinois enrolls
over 29,000 undergraduates in more than 150 fields
of study, and over 11,000 graduate and professional
students in over 100 programs. It is among the top
five universities in the United States in the number
of annual doctorates awarded. Among its array of
faculty honors, the U of I is one of only 11 campuses
worldwide to have been awarded two separate Nobel
Prizes in one year (2003).
14 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
The University of California, Berkeley
Founded in 1868, the University of California, Berkeley,
is the nation’s top-ranked public university and the flag-
ship of the 10-campus University of California system. It
enrolls over 24,000 undergraduates, distributed among
UC Berkeley
80 degree programs, and more than 10,000 graduate
students each year. The campus not only produces more
PhDs than any other university in the country, but a
greater number of its graduates go on to earn a PhD at
Berkeley or elsewhere than do graduates of any other
institution. The university is distinguished by its research
programs, which were funded in fiscal year 2006 by $469
million in contract and grant awards from outside spon-
sors. Berkeley faculty and researchers have won 20 Nobel
Prizes, 6 Pulitzer Prizes, 30 National Medals of Science
and 29 MacArthur “genius” Awards. Of its academic
staff, more than 130 are current members of the National
Academy of Sciences, and 85 belong to the National
Academy of Engineering.
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory (Berkeley Lab)
has been a leader in science and engineering research Berkeley Lab
for more than 75 years. Located on a 200-acre site in the
hills above UC Berkeley’s campus, the Lab is the oldest
of the U.S. Department of Energy’s national laboratories.
Managed by the University of California, it operates
with an annual budget of more than $550 million and
a staff of about 3,800 employees, including more than
500 students and 250 principal investigators with joint
appointments at UC Berkeley. It employs a “team”
concept to its research, as developed by founder Ernest
Orlando Lawrence, and boasts a legacy that has yielded
rich dividends in basic knowledge and applied technol-
ogy, and a profusion of awards. Berkeley Lab conducts
unclassified research across a wide range of scientific
disciplines, with key efforts in fundamental studies of the
universe, quantitative biology, nanoscience, new energy
systems and environmental solutions, and the use of
integrated computing as a tool for discovery. Its unique
user facilities include the Advanced Light Source, the
Molecular Foundry, the National Center for Electron
Microscopy, and the Joint Genome Institute. University of Illinois
ABOUT THE ENERGY BIOSCIENCES INSTITUTE 15
The Facilities
From the hills of Berkeley to
the farm fields of Illinois, EBI
research spans the nation—
and the world.
Research in the Energy Biosciences Institute is being conducted at two primary
locations—in California, at the historic Calvin Laboratory and the nearby Hildebrand
Hall chemistry building at UC Berkeley; and at the new Institute for Genomic Biology
building in the heart of the University of Illinois campus. A 320-acre Energy Farm, the
largest of its type (just south of the Illinois campus), includes land for demonstrations,
large-scale production, plant breeding and storage. In 2008, 120 acres of this farm were
planted, and another 160 are slated for development in the near future.

The Berkeley center includes dedicated biotechnology laboratories and specialized

facilities for high-throughput chemical synthesis and assays of many types. The
Illinois program is housed in a building specifically designed for integrated research
and development efforts, with a complete suite of microscopy, imaging, plant growth,
microfabrication, and bioanalysis facilities and tools. In addition, individual research-
ers have access to the offices, technical laboratories and user facilities of their home
campuses.
In 2013, the EBI is planning to move its permanent headquarters into a 144,000-
square-foot facility dedicated to renewable energy research to be built on UC Berkeley
land adjacent to Berkeley Lab. The “Helios” building, as it will be called, will have
office and laboratory space for 150 co-located institute staff, including the EBI
investigators, BP scientists, and laboratory personnel. The building will have space
and amenities that will promote a collegial and collaborative research environment,
including meeting and seminar rooms, lounges, and a café.
Architect's design of
proposed Helios Energy
Research Facility in
Berkeley, future home of
the EBI
EBI Leadership
Governance and leadership are critical components of the EBI agreement. Completed in 2007, the
EBI contract combines the resources of the partner institutions into an agreement that provides BP
a non-exclusive, royalty-free license to an invention.
The EBI operates as one of several research centers within the
partner institutions. The faculty and students that design and
carry out the research activities of the EBI have appointments
and academic responsibilities within the various academic
departments of the partners. The EBI administers the financial
and material resources and facilities supported by funding
from BP.
The EBI is managed on a day-to-day basis by a Director and a
small team of colleagues and advisors from the four partners
(the Executive Committee). This administrative team imple-
ments processes for deciding what research opportunities to
fund, for providing or facilitating research and administrative
support to EBI investigators, and for facilitating communica-
tions within the EBI and between EBI investigators and various
stakeholders and interested parties around the world.
The Governance Board has the responsibility to define, oversee
and review the implementation of EBI programs in the open
component of research. It also appoints the EBI Director and
Deputy Director. The Board has eight voting members, four
from the research partners—at least one each from the Berkeley
and Illinois campuses and one from Berkeley Lab—and four
appointed by BP. The EBI Director, Associate Director, and
Deputy Director are ex-officio members.
The EBI Director, Chris Somerville, manages the conduct of
research projects and EBI’s public communications, education,
and outreach activities. He works with the Executive Commit-
tee to develop an annual program plan with goals and mile-
stones, and he prepares the annual budget request. The EBI’s
Deputy Director, Steve Long, manages research conducted
at the Illinois EBI site and its integration into the Institute
as a whole. The Associate Director, Paul Willems, is the BP
representative on the EBI management team. He also leads the
team of BP employees who are located at the EBI.
The Executive Committee is the EBI’s program management
body, with Director Somerville as chair. He, the deputy and
associate directors, and five other professors from the partner
institutions (currently Adam Arkin, Dan Kammen, David
Zilberman, Evan DeLucia, Michael Marletta) comprise the
committee membership. This panel proposes the annual
strategic work plan, including priority research projects for
institute funding, for approval by the Governance Board.

16 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT ABOUT THE ENERGY BIOSCIENCES INSTITUTE 17
 The Directors
Chris Somerville, Director
Somerville is a professor in the Department of Plant
and Microbial Biology at UC Berkeley and a faculty
scientist at the Lawrence Berkeley National Labora-
tory. His research focuses on the characterization of
proteins implicated in plant cell wall synthesis and
modification. He has published more than 200 scien-
tific papers in plant and microbial genetics, genomics,
biochemistry and biotechnology. Somerville has served
on the scientific advisory boards of many corporations,
academic institutions and private foundations in Europe
and North America. He is a member of the U.S. National
Academy of Sciences, the Royal Society of London and
the Royal Society of Canada.
Stephen Long, Deputy Director
Long is the Robert Emerson Professor of Plant Biol-
ogy and Crop Sciences at the University of Illinois. He
is a researcher with the U of I’s Institute for Genomic
Biology and a resident scientist with the National Center
for Supercomputing Applications. Much of Long’s
research focuses on the effects of atmospheric change on
vegetation and ecosystems and on how certain perennial
crops might be used as biomass energy sources. He was a
contributing author and referee to the Intergovernmental
Panel on Climate Change, and he has served on com-
mittees worldwide that research global climate change.
He has been named one of the 250 most cited authors
in animal and plant biology and one of the 25 most cited
authors on global climate change. Long is a Fellow of the
American Association for the Advancement of Science.
Paul Willems, Associate Director
As Technology Vice President for Energy Biosciences in
BP, Willems is responsible for integrating biotechnology
into BP’s business activity. His duties include leading
the development and execution of an integrated
technology strategy which incorporates all of BP’s bio-
related activity and which is fully integrated with BP’s
company-wide business strategies. He has held a variety
of technical, manufacturing and commercial leadership
roles throughout his 20-year career, including business
technology manager for BP’s global PTA (purified
terephthalic acid, a polyester raw material) business,
and technology vice president for acetyls and aromatics.
Willems earned his PhD in Chemical Engineering from
the University of Ghent in Belgium.
18 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
EBI Administrators
and Managers
Assistant Director Susan Jenkins
manages the administrative team
for the EBI at Berkeley and oversees
all aspects of implementing
the activities sponsored by the
institute. Before joining the EBI,
she was the assistant chair of the
Department of Plant and Microbial
Biology at UC Berkeley. Deputy
Assistant Director Jenny Kokini
manages the implementation of
all EBI activities at the University
of Illinois. She moved to the EBI
from Princeton University, where
she was the departmental business
administrator for Mechanical
and Aerospace Engineering.
Professor Brad Moore, an emeritus
professor of chemistry, is the
manager for Strategic Planning.
He has extensive experience
in academic administration,
including most recently serving as
the vice president for research at
Northwestern University. Mitch
Altschuler manages processes
related to Intellectual Property. He
was formerly a professor of biology
at Northern Illinois University and
has also worked in the technology
transfer offices of the University
of Minnesota and Cargill,
Inc. Computing systems and
networking specialist Adam Cohen
moved from the UC Berkeley
web applications team to become
Information Technologies manager.
Ron Kolb is the communications
manager. Before joining the EBI,
he was communications director
for Lawrence Berkeley National
Laboratory. Melissa Edwards is
his counterpart at the University
of Illinois. Deputy Operations
Director Tim Mies manages the
From left, Willems, Somerville, and Long ABOUT THE ENERGY BIOSCIENCES INSTITUTE
construction, engineering, and
operation of the Energy Farm at
Illinois. He previously constructed
and managed SoyFACE, the largest
open-air facility for investigating
the effects of global atmospheric
change on crops, and before that
he ran the University of Maryland’s
controlled environment plant
growth facility. Safety and building
manager Zack Phillips was a
radiation safety officer at UC
Berkeley before joining the EBI’s
Berkeley staff. He is paralleled at
Illinois by Safety Officer John
Pingel, who coordinates safety
training and implementation
for the farm and laboratory. He
previously coordinated safety at
the U of I’s chemistry labs, is a
primary author of the “Science
Safety Handbook for Illinois
Schools,” and is principal lecturer
in the Illinois “Fundamentals of
Laboratory Safety” class. Stefan
Bauer manages the Analytical
Services group at the EBI. Before
joining the Institute, he was the
head of analytical chemistry at
Fresenius. Mara Bryant and
Rachel Knepp are laboratory
managers for the EBI at Berkeley
and Illinois, respectively. Bryant
recently completed postdoctoral
studies in biology at Michigan
State University, and Knepp
completed an MS in global change
impacts on forests and was a USDA
laboratory manager before joining
the EBI. Anne Krysiak and Trisha
Togonon at Berkeley and Becky
Heid and Connie Wilder at
Illinois provide a wide range of EBI
administrative services and assist
investigators in interactions with
other service providers within the
host institutions.
19
 04
c h a p t e r

Understanding the complex issues

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

First, the EBI is investigating how much land can

be used sustainably for cellulosic fuel production
An Introduction to Biofuels around the world without negatively impacting food
production or the environment. Because many aspects

Seeking an Understanding, of human economic activity are internationalized, it is

important to understand the issues on a global scale to
avoid displacement effects.

from Field to Fuel Tank Second, investigations are probing which types of
plants can be used for energy, how they can be grown
sustainably with minimal inputs, and how they can
be harvested, stored, and transported to the point
of utilization. This type of research involves aligning
models of the properties of different types of plants
with information from global geographic information
systems.

Third, the EBI is exploring new ways of converting

cellulosic biomass to liquid fuels. This involves a broad
investigation of how various types of organisms, rang-
ing from those found in compost heaps to the complex
systems in termite guts and cow rumen, degrade
biomass. Work is also proceeding on new chemical
catalysts that can convert the components of biomass
to novel fuels.

The rationale for this portfolio of research topics is sum-

marized in the following review, which is based upon an
article by EBI Director Chris Somerville published in
the journal Current Biology (17[4]R2).

20 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT AN INTRODUCTION TO BIOFUELS 21

 CORN AND CANE ETHANOL
...it would be possible to produce about At present, most biofuel is produced from cornstarch
and from sugar extracted from sugarcane using
half of all transportation fuels by growing a relatively mature technology and established
plant like Miscanthus on about 1 percent production practices. Research within the EBI is
generally not concerned with these sources of fuels
of the terrestrial surface area. but is directed toward next-generation opportunities
based on using the lignocellulose that comprises the
body of plants. But an understanding of the processes
WHY BIOFUELS?
involved in current biofuel production is important
The global energy market provides humans with about 370 exajoules of if improvement is to be achieved in the second
energy per year, which is equivalent to the energy content of about 170 generation.
million barrels of oil per day. Approximately 87 percent of energy pur-
Sugarcane (Saccharum sp.) is a highly productive
chased globally comes from fossil fuels. Although humans may eventually
tropical grass that accumulates sucrose in the stem
deplete reserves of fossil fuels, that moment is quite far off. In addition
tissues. The stalks are crushed to produce a sucrose
to substantial remaining reserves of oil and gas, abundant coal deposits
solution that can be fermented to produce a dilute
are projected to be adequate to meet human energy needs for several
ethanol solution. The crushed stalks or “bagasse” that
hundred years. Coal can be converted into a wide variety of liquid fuels
comprise the body of the plants are currently burned
that can substitute for petroleum. Thus, if concerns about greenhouse
to produce heat that is used to distill the ethanol
gas-induced climate change and energy are ignored, there is not a pressing
from the fermentation broth and to produce excess
need to develop biofuels.
electricity. It is possible that, with the development of
The linkage between climate change and biofuels arises from the fact that efficient technologies for conversion of lignocellulose
some types of biofuels can be substantially less carbon-intensive sources to fuels, a large proportion of the sugarcane bagasse
of energy than fossil fuels. Energy from sunlight is collected by the photo- will also be used to produce liquid fuels in the future.
synthetic system of plants and used to reduce and condense atmospheric
In Brazil, where land suitable for growing sugarcane
CO2 into the chemicals that comprise the body of plants. When plants
is abundant, about 4.2 billion gallons of cane ethanol
are burned, the energy is released as heat that can be used for work, such
was produced in 2005 on less than four million
as generating electricity, and the CO2 is recycled. With highly productive
hectares (a hectare is 2.47 acres) of land. Ethanol now
plants such as Miscanthus giganteus growing on good soils with adequate
comprises about 40 percent of all liquid transportation
rainfall and favorable mean temperature, such as is found in central Illi-
fuel used in Brazil. The automobile fleet is largely
nois, more than 1 percent of annual incident solar insolation (exposure to
composed of “flex-fuel” vehicles that can utilize widely
sunlight) is retained as chemical energy in biomass. If one uses a value for
varying ratios of ethanol and gasoline. By contrast,
total solar insolation of 120,000 TW (terawatts), 1 percent solar conver-
only about 2 percent of the fleet in the United States is
sion efficiency, and an energy recovery value of 50 percent, it would be
flex-fuel vehicles; the remainder cannot use alcohol/
possible to produce about half of all transportation fuels by growing a
gasoline mixtures containing more than 10 percent
plant like Miscanthus on about 1 percent of the terrestrial surface area.
ethanol without mechanical modifications.

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

22 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT AN INTRODUCTION TO BIOFUELS 23

 The technology required for cane sugar or cornstarch
ethanol production is mature, and most of the
technical issues concern improvements in engineering
related to the efficient use of heat and water. However,
unlike cane ethanol, which has an energy output-input
ratio of about 8-to-1, calculations of the life cycle
costs of making corn ethanol have stirred substantial
scientific debate. These calculations typically include
things such as the energy costs of producing and
distributing fertilizer, of planting and harvesting, of
making the farm machinery and the factories that
process the grain, in addition to the costs of converting
grain to ethanol. The results have been controversial
because of the uncertain assumptions about variables,
such as heat reuse.
"Cellulosic biofuels will have the greatest environmental benefits if produced on land
that has been farmed in the past but is
A recent analysis of all such calculations concluded
that corn ethanol provides about 25 percent more
no longer used for food production."
energy than is consumed in producing it if the process
heat is provided by natural gas or coal (versus burning
the cobs and stalks). Because of the low net energy
ratio, corn ethanol is generally not considered an
attractive long-term solution to meeting energy needs
in an environmentally sustainable way.
One development that may change this is carbon
sequestration. In fermenting sugars to fuels, about 33
percent of the carbon is released as pure CO2. Like a
number of other locations around the world, a large
area of the Midwest is underlain by deep saline aquifers
into which very large volumes of CO2 may be dissolved.
The aquifer is below shale and oil deposits that provide
additional seals against any release of “buried” CO2,
which is why Illinois was chosen for the “Futurgen”
clean coal plant. The U of I, together with Archer
Daniels Midland and the Department of Energy, is
now operating a pilot burial of the CO2 produced from
fermentation in making corn ethanol. Life cycle analyses
suggest manufacture of cellulosic ethanol from low
perennial grasses could achieve input:output energy
and carbon ratios of 1:5. Coupled with CO2 burial, this
raises the exciting possibility of being able to achieve a
carbon-negative biofuel.
There are also concerns that use of cropland for
biofuels, whether corn or perennial grasses, will
indirectly cause encroachment of agricultural
production onto ecologically sensitive land. A major
effort of the Institute seeks to identify opportunities
to grow a range of perennial feedstock on abandoned
agricultural and non-crop lands to avoid such effects.
24 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
BIODIESEL
A wide variety of chemicals or
mixtures of chemicals, including
biologically produced fatty acids
or lipids, undergo combustion
in conventional diesel engines.
The methyl or ethyl esters of
biologically derived fatty acids
are capable of being mixed with
petroleum-based diesel fuel. These
esters can be produced from
biological lipids or fatty acids
by very simple reactions. Thus,
establishing a commercial biodiesel
production facility is inexpensive
and technically simple.
The U.S. currently has a number
of small biodiesel production
facilities, many of which
include used cooking oils from
restaurants as feedstock. This
is an environmentally and
economically attractive use of a
material that would otherwise
be a waste disposal problem.
However, domestic biodiesel will
not become more than a niche
component of the liquid fuel
supply, because the amount of
lipid produced per acre of crop is
small relative to the total amount
of biomass. Thus, for instance,
the average soybean crop yields
only about 63 gallons of biodiesel
per acre. Contrast this with the
much higher yields of cellulosic
biomass that could be grown on
the same acres—estimated at more
than 1,500 gallons of cellulosic
ethanol. Additionally, vegetable
oils are a quantitatively important
component of human diets
and, therefore, relatively small
disruptions in supply result in
large increases in price because of
inelasticity of food demand.
The U.S. Congressional Research
Service conducted a study that
concluded if every ounce of plant
and animal lipid produced in
the United States was used for
biodiesel production, the total
~ CHRIS SOMERVILLE
amount would be about four
billion gallons. When compared
with the roughly 200 billion
gallons of liquid fuels used in the
U.S. each year, domestic biodiesel
derived from seeds and fruit
is not likely to be a significant
contributor to transportation fuels
in the developed world, nor an
effective use of land.
In contrast to annual oilseeds,
several tropical plants are used to
produce relatively large amounts
of lipids in tropical countries. Oil
palm (Elaeis sp.), which grows
in high rainfall zones within 15
degrees of the equator, produces
clusters of oil-rich fruits that are
similar to small avocados. Yields
of up to seven metric tons of oil
per hectare per year have been
recorded, although the average is
lower. The plants have very long
life cycles and do not require
significant energy inputs for
production. In addition, mature
plantations reportedly produce
up to ten metric tons per hectare
per year of cellulosic biomass (e.g.,
senescent fronds) that can also
be used for fuel production. Thus
oil palm acreage has continued to
expand due to increasing demand
for edible oil and for projected use
in biodiesel.
However, the expansion of palm
production is generally considered
undesirable from an environmental
perspective, because the expansion
is associated with clearing of
tropical forests that are some of the
richest reservoirs of biodiversity.
Additionally, clearing of tropical
forests causes large emissions of
greenhouse gases from both soil
emissions and from the burning of
the biomass, resulting in negative
greenhouse gas balances for biofuel
production.
Recent interest has been shown in
a drought-tolerant bush, Jatropha
curcus, which reportedly yields
up to several metric tons of oil
per hectare per year with little or
no input. This plant may allow
production of oil on land that is
too drought-prone for food crop
production, and acreage has been
expanding rapidly in Africa, India,
and Southeast Asia.
CELLULOSIC ETHANOL
All higher plant cells are enclosed in cell walls
composed primarily of polysaccharides (polymers of
sugar) and lignin (polymer of phenolics) that, in many
plant species, comprise more than 90 percent of the
dry body mass. The principal cell wall polysaccharide
is cellulose, a fibrous material composed of hydrogen-
bonded chains of the sugar glucose. Cellulose is coated
with another class of polysaccharides called hemicellu-
lose, the most abundant of which is xylan, a polymer of
xylose that may, depending on the plant species, have
branches containing other sugars such as arabinose or
glucuronic acid. The principal sugars in most tissues
that are useful for biofuels are glucose and xylose,
but many other sugars are also present in significant
amounts. Cell walls from vascular tissues usually also
contain lignin, a complex polymer.
These structural polysaccharides are less readily
hydrolyzed to sugars than storage polysaccharides such
as starch. Acids are being used to obtain sugars from
celluloses, but this is inefficient. Efficient hydrolysis
occurs in nature, for example by bacteria and fungi in
the digestive systems of animals, such as ruminants
and termites, who derive their energy from the sugars
released from cellulose and hemicellulose. Replicat-
ing this in industrial processing facilities would then
provide sugars that can be converted to ethanol or
other fuels by fermentation in much the same way
as cornstarch. However, because the whole plant can
be used, the yield of sugar per unit of land per year is
much higher than can be obtained using only corn
grain.
No large-scale cellulosic ethanol facilities are yet in
commercial production, although several companies
have small-scale test production facilities. A typical
pilot-scale process involves treatment of pulverized
biomass with hot acid, which partially hydrolyzes
hemicellulose and other polysaccharides and disrupts
the association of lignin with the polysaccharides.
The hydrolysate is neutralized, separated from the
insolubles, and fermented to produce ethanol. The
insoluble fraction is then treated with cellulase and
glycosidases to release glucose, which is also fermented
to produce ethanol. The residual insoluble material,
mostly lignin, could then be burned to generate energy
for the overall process. The fermentation process pro-
duces a nutrient-rich microbial cell mass that can be
deactivated and used as fertilizer to recycle the mineral
nutrients to the land.
AN INTRODUCTION TO BIOFUELS 25
 Many components of the cellulosic ethanol bioconver- organisms, by altering the chemical composition of the
sion process are not yet optimized for commercial biomass, or by process improvements.
production. For instance, the strains of yeast that are
used for industrial fermentations do not normally The development of a biofuel industry is only feasible
utilize sugars other than glucose. Strains of yeast in regions where land and water resources are available
(Saccharomyces cerevisiae) and Eschericia coli have been to support the growth of plant biomass that is excess No miracles are
engineered to ferment xylose to ethanol, but additional to other needs. The Departments of Energy and Agri-
culture conducted a study of biomass availability and required to develop
work needs to be done to adapt such lines to industrial
conditions, to optimize metabolic control of the path- concluded that approximately 1.3 billion dry metric cost-effective cellulosic
ways, and to enable fermentation of other sugars. tons of excess cellulosic biomass is available each biofuels; however,
year in the U.S. This includes half the corn stover (the
implementing rational
Another problem is that large amounts of cellulase leaves and stalks of the corn plant) and wheat straw,
are required to hydrolyze cellulose. Process improve- and about 40 million acres of set-aside land to grow improvements in the
ments during the past decade have reduced the cost of perennial grasses such as switchgrass and Miscanthus. overall process is
cellulase per gallon of ethanol from about $5 to about At a conversion value of about 100 gallons of ethanol challenging.
50 cents but that is still considered too expensive per ton of lignocellulosic biomass, this would be
compared to other enzyme-based processes. There is equivalent to about 130 billion gallons of ethanol, or
widespread interest in finding enzymes with higher about 40 percent of U.S. liquid fuel consumption on an
activity than current cellulases by surveying the prop- energy-equivalent basis.
erties of enzymes from poorly explored sources such
as termite guts, rumen, compost heaps, and tropical Based upon the proportion of transportation fuel
forests. Alternatively, it may be possible to improve the already produced by Brazil, it seems likely that South
activity of industrial cellulases by protein engineering. America could meet all its needs for transportation
It is also important to understand the structure and fuels with biofuels. A recent analysis of the 15 coun-
function of cellulosomes, extracellular enzyme com- tries in the European Union concluded that Europe
plexes that catalyze hydrolysis of cellulose and other could produce approximately 11.7 exajoules (units of
polysaccharides. Industrial ethanol production has energy) per year of biofuels, an amount similar to the
used yeasts that ferment glucose. To make use of the U.S. goal of 30 percent of transportation fuels (11.6
sugars derived from hemicelluloses, yeasts and other exajoules).
organisms are being engineered to use these sugars
A recent study by ecologists at Stanford concluded that
as well as glucose. The holy grail of cellulosic ethanol
about a billion acres of land around the world that was
production is to incorporate improvements in both
farmed in the past has been abandoned. It seems likely
cellulases and fermentation into a single organism that
that much of this land could be used for production
would secrete all of the necessary enzymes and utilize
of energy crops without impacts on food production
all of the available sugars in a process referred to as
and without incurring production of greenhouse gases
“integrated bioprocessing.”
from land conversion. Although cellulosic fuels will
Many other problems may have multiple solutions, but not completely meet global needs for transportation
relatively little progress has been made. For instance, fuels anytime soon, they are expected to become a
many plant polysaccharides, during biomass hydroly- significant component worldwide. The widespread
sis, release acetic acid that inhibits the growth of the implementation of trading in carbon credits could
fermentative organisms. Similarly, furfural, an organic accelerate progress toward that goal and could encour-
liquid compound produced by a side reaction during age best practices in terms of land management and
acid-catalyzed polysaccharide hydrolysis, inhibits fuel production.
microbial growth. In principle, these and related
problems may be overcome by developing resistant
OTHER BIOFUELS
Ethanol is not an ideal fuel in several respects and may not be the
major biofuel in 20 years. The main problem is its ability to mix with
water, which imposes an energy cost for distillation, creates problems
in transporting the fuel via pipelines, and leads to poisoning of the
microorganisms that produce it. Thus there is interest in developing
biofuels that are more hydrophobic and spontaneously partition out of
the aqueous phase. For instance, butanol dehydrates spontaneously at
about 9 percent solution, has very low vapor pressure, and has a latent
heat similar to octane so that fuel-air mixing at low temperature is not a
problem. When added to ethanol-gasoline mixtures, small amounts of
butanol depress the vapor pressure, reducing the hazards of explosions
during fuel handling. Unfortunately, butanol is toxic to organisms that
produce it at concentrations very much lower than 9 percent solution.
Several companies have recently announced plans to produce butanol by
fermentation of sugars from biomass. Some microorganisms have been
reported to secrete alkanes, which do not mix with water. Plants and
other organisms have a wide array of lipid synthetic pathways, raising
the opportunity for engineering these pathways into bacteria or yeasts.
It seems likely that additional types of biofuels with physical properties
similar to those in current use will be developed.
Although much of the current research on cellulosic fuels is focused
on bioconversion technologies, other approaches are being explored
within the EBI. In particular, it is possible to convert biomass to liquid
fuels by direct chemical conversions using either gasification followed by
re-forming of the gaseous products to fuels, or by chemically catalyzed
conversion of biomass to fuels. Because the mandate of the EBI is to
explore biological technologies, it is not pursuing research based on
gasification technologies. However, a number of EBI research groups are
exploring the development of new catalysts for hydrolysis of biomass to
soluble molecules and conversion of such molecules to liquid fuels.
COORDINATION, INTEGRATION
The major opportunity to expand the use of biofuels will be found in
improving the various components of cellulosic biofuels production. No
miracles are required to develop cost-effective cellulosic biofuels; a series
of two-fold improvements in the efficiency of various steps could make
biofuels less expensive than liquid fossil fuels. However, implementing
rational improvements in the overall process is challenging. Managing
the various components will have to be coordinated, integrating
knowledge from many scientific and engineering disciplines. Integration
is encouraged through the placement of researchers from different
disciplines in shared space. This is what the EBI was established to do.

26 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT AN INTRODUCTION TO BIOFUELS 27

 05
c h a p t e r

Can microbes be superheroes? Can crops grown

for biofuels actually help the environment? Can a
giant Asian grass really power a biofuels revolution?
Perhaps. EBI scientists are quite literally on the ground
level of the search for the most productive biofuels
plants, conducting field trials, studying essential farm
machinery, searching for sustainable fertilizers, and
exploring the issues surrounding agro-ecosystem
diversity that may make second-generation biofuels a
boon for the environment.

Most fuel ethanol today is produced to achieve sufficient feedstock

from cornstarch. The Energy while ensuring environmental and
Biosciences Institute is looking economic sustainability.
beyond the major food crops as the
feedstock for biofuels, with a focus If the use of lignocellulose opens
on sustainable crops that could be up all plants as potential feedstock,
grown on land unsuited for food how has the EBI narrowed this
production. down to a manageable task?
Examination of yields in terms of
Dried stems, roots and leaves of conversion of incident solar energy
most plants are made up largely of into biomass has shown a group
three types of polymers: cellulose, of grasses, the Androponodae, to
hemicelluloses and lignin. This appear particularly efficient. This
mixture of the three polymers, group includes sugarcane, sorghum
termed lignocellulose, comprises and Miscanthus. The EBI Feedstock
most of the structural mass of all Program, and those looking at
plants. utilization, have chosen these plants
as their first targets for detailed
Tree trunks, crop residues, and investigations. These species are
fall-harvested shoots of perennials also of primary interest to the
such as switchgrass and Miscanthus Feedstock Genomics group led by
are predominantly lignocellulose. the University of Illinois’ Stephen
If the sugars of the cellulose and Moose, since sorghum has now
hemicellulose can be efficiently been sequenced and many molecu-
released, then these can be lar markers have been developed for
fermented or chemically converted sugarcane. This allows the program
to ethanol and other fuels. This a jump-start with Miscanthus,
makes any plant material a potential since the DNA sequences in the
feedstock for the manufacture of protein-coding regions appear
“cellulosic biofuels.” highly homologous with its close
relatives, sorghum and sugarcane.
The ideal cellulosic biofuel
Genetic similarity among grasses
feedstock will vary with location,
may also facilitate mechanistic

FEEDSTOCK:
but as a general rule they will all
studies by Berkeley scientist Sheila
provide high productivity with a
McCormick of self-incompatibility
minimum of inputs. Such crops will
mechanisms that impede breeding
minimize the footprint required
in Miscanthus and other grasses
Agronomy, Engineering, and the Environment

28 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 29
 such as switchgrass. The develop- costs? The Agricultural Engineering
ment of transformation technology Program, led by KC Ting at Illinois,
for grasses by Jack Widholm, Don is developing and testing machin- STEVE LONG:
Duvick and colleagues in Illinois is
expected to facilitate direct tests of
ery that can improve efficiency
in production and transport. For
Passionate About Plants and Their Potential
hypotheses about the mechanists example, harvesting can today
basis of important traits such as require three operations. The EBI It all begins with the feedstock, the spoken, British-born Long. “And enable the production of plant-
self-incompatibility program has tested a machine that source plant material. Commercial I’ve been curious about how we can based transportation fuels. The
may integrate the three into one. It biofuel production will require lots maximize the efficiency with which two colleagues had never met, but
The Agronomy Program led by is also looking at the cost/benefit of it, preferably grown they convert solar energy into when the Berkeley leadership team
Tom Voigt at Illinois is in the of on-farm compaction to facilitate where food crops can’t, biomass, to achieve more yield per introduced the prospect of compet-
process of establishing comparative transport. and in quantities that acre.” When the opportunity arose ing for the BP-funded EBI, together
trials of Miscanthus and switch- yield huge amounts of to apply his expertise to a potential they jumped at the chance.
grass around North America. All these options are evaluated in a biomass. solution to the world energy crisis,
This includes comparisons with systems analysis context to identify he seized it. Long, the feedstock expert, has
sorghum and sugarcane at more the key bottlenecks—engineering, Meet Steve Long. He already reported research results
southern locations and with prairie environmental and economic— was looking through After a productive 23-year career as that indicate Miscanthus is a supe-
plants at other locations. About from planting to delivery to old family photographs scientist and professor at England’s rior crop in terms of biomass yield
half of the spectacular gain in biofuel synthesis. While Miscan- the other day, and he University of Essex, he decided to and sustainability in poor soils. But
yields of the major food crops has thus, switchgrass, sorghum and came upon one in which he was pull up roots in 1999 and headed the search is far from over.
been achieved through improved sugarcane are the current program teaching a college course in 1978. overseas, to Illinois, where “there
agronomy, and it is expected that focus, it will certainly expand into The subject of his lecture? Biofuels. was a much larger concentration “What the EBI allows us to do is
agronomy will be similarly impor- trees, such as poplar and willow, “I was surprised it was that long of plant biologists, as befitted the to explore options, to look at many
tant for optimizing production of for locations where trees will be ago,” he says. land-grant schools in the United more plants than we have before,”
energy crops. The agronomy group more appropriate feedstocks—e.g. The answer might be found States. There were broad intel- he says. “We are open to the pos-
is examining how plant spacing, on terrain that is too irregular for Since that prescient moment, Long lectual resources, and access to the sibility that there might be other
weed control and fertilizers can be conventional machine harvesting. in crops not currently known. has become one of the world’s farm.” possible feedstocks. There will not
optimized to increase yields and A wide range of other perennials is foremost experts on the so-called be one solution. For example, in
“C4” perennial grasses like Miscan- “The farm” is UIUC’s vast acreage drier areas, switchgrass might be
minimize inputs. A project lead by also being tested on the EBI Energy He will be looking at over 20 thus, which has emerged as a major of experimental croplands, in the better option, and in the driest
German Bollero at Illinois is devel- Farm at Illinois.
bioenergy crop in the United King- which he could test cultivation Agaves.”
oping a computer model that will different grasses at the farm, dom, where he conducted some of and nutrition techniques on the
be able to predict how energy crops The Engineering, Agronomy,
the first analyses of this crop. His carbon-fixing grasses he had been Or, he says, the answer might
respond to factors such as climate, and Genomics groups are also and many more variants within work in the U.S. has now shown studying in Europe—Miscanthus be found in crops not currently
soils and nutrients. The plants used collaborating on the development
of remote sensing methods of track- it to be a promising candidate as x giganteus, found naturally in the known. With others he will be
in the sustainability trials are also those species. a dedicated biofuel feedstock. He highland areas of Japan and China, looking at over 20 different grasses
being used by the Biotic Stress ing plant growth and production,
Program, under Illinois’ Mike Gray, which will allow rapid assessment is deputy director of the EBI and and switchgrass, a variety on which at the EBI Energy Farm in Illinois
to identify the diseases and pests of thousands of different genetic the Robert Emerson Professor of American agronomists were focus- and many more variants within
lines non-destructively. Methods Crop Sciences and Plant Biology at ing for fuel conversion. those species. He is also interested
that may emerge with these new
the University of Illinois Urbana- in pursuing salt-tolerant plants
crops, and strategies for protecting are currently being tested that
promise far more rapid identifica- Champaign. And he is passionate When Lawrence Berkeley National that could thrive on saline lands—
them. The group is monitoring
about plants, in particular about Laboratory Director Steve Chu salinated through geology, past
insects, nematodes, fungi, bacteria tion of the most promising materi-
als. In parallel, Michael Dietze the impacts of global atmospheric invited him in 2006 to join a panel irrigation practices or hydrated
and viruses.
in Illinois is building a database change on photosynthesis. of experts to brainstorm alternative with sea water.
New crops present on-farm engi- of the broad basket of potential fuels, he traveled to Berkeley and
neering challenges. In particular, cellulosic feedstocks coupled with “I’ve always been fascinated about listened to Chris Somerville talk
how can these crops be planted, the development of mechanistic how plants work,” says the soft- about the potential of biology to
harvested, stored and transported models of growth, production and
efficiently, and without large energy ecosystems services.

30 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 31
ANGELA KENT:
Looking to Microscopic ‘Superpowers’
to Sustain Plant Growth
Forgive Angela Kent if she’s biased, but she
believes that microbes are the most important
organisms in the world. She is especially high
on bacteria, the most abundant group of
organisms on the planet. And she thinks they
could be key to the efficient productivity of
future biofuel feedstocks.
“Microbes have the greatest reservoir of
genetic diversity on earth,” says the young
microbial ecologist at the University of Illinois,
Urbana-Champaign. “They can do incredible
things. It’s almost like they have superpowers.
They can find a way to make a living with any
kind of compound.”
The EBI believes in Kent and her bacterial
troops, supporting a project that seeks to
exploit the nitrogen-fixing capabilities of
microbes to enhance the sustainability of
bioenergy crops.
“Production of nitrogen fertilizer requires a lot
of energy input from fossil fuel,” Kent says. “It
takes chemicals to make and farm machinery
to apply. But microbes can do that essentially
for free. If we can find conditions that favor
bacterial nitrogen fixation in the plants, we can
influence their long-term sustainability.”
The first step is to understand how the
association of certain bacteria with targeted
biofuel grasses will work, and then how that
association is affected by environmental
factors—water, climate, soil texture and
fertility, etc. Then there is the task of analyzing
the characteristics of individual microbes
through genetic phenotyping, searching for
the genes that are involved in the nitrogen
production. Considering that there can be
millions of microbes in a gram of soil (such
as the samples seen at right), Kent’s task is
daunting.
There’s no guarantee that inoculations of
naturally occurring nitrogen-fixing bacteria will
improve the growth of crops like Miscanthus,
32 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
but Kent thinks the prospects
are high. With the assistance
of two postdocs and two
undergraduate students in her
laboratory, she hopes to build
a library of relevant bacteria
and then apply them to
Miscanthus and other plants
in the EBI Energy Farm.
She says she suspects that both growth and
sustainability will be improved.
Kent’s early studies at the University of
Wisconsin focused on a medical career,
her fascination about microbes leading her
" They can do incredible things. It’s
almost like they have superpowers.
They can find a way to make a living
with any kind of compound."
into the study of pathogens and their role in
causing disease. But applications to human
health were long-term, and she admits to
looking for something more immediate.
Environmental microbiology “felt much
more applied to me, looking at microbes
involved in plant health. I knew I could make “In three years, we should have a pretty good idea of the inventory
a difference,” she recalls. of microbes that work on Miscanthus, and we will be able to
demonstrate whether nitrogen fixation plays an important role.”
Now that difference might be the application
of microbiology, and her “super” microbes,
to the development and nurturing of a new
class of plant-based transportation fuels.
“In three years,” Kent says, “we should
have a pretty good idea of the inventory of
microbes that work on Miscanthus, and we
will be able to demonstrate whether nitrogen
fixation plays an important role, as well as
what traits contribute to the colonization of
the plant.”
FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 33
 Environmental and Life
Cycle Analysis
The Environment Program is using the trials established by the
Agronomy Program to provide the first actual measurements, as
opposed to projections, of greenhouse gas balances and impacts
on water availability and quality.
In 2008, large-scale (up to 10 acres each) replicated trials of Mis-
canthus x giganteus, switchgrass, mixed species restored prairie,
and continuous corn were established on the energy farm above
instrumented field drains that monitor the volumes of water,
nutrients and carbon draining out of each crop. Simultaneously,
using a technique known as eddy-covariance, the net fluxes of
gases containing carbon and nitrogen emitted and absorbed
by these plots are being monitored continuously. This will be a
unique data set, critical to constraining Life Cycle Assessment
models and greenhouse gas balance models of the ecosystems
services provided by different biofuel cropping systems. It will
also test the predictions that the group has already made using
the state-of-the-art models of soil carbon balance in conjunction
with consultant Bill Parton.
These studies will also be vital to gaining informed Life Cycle
Assessments (LCAs), an activity that is the focus of research by
Arpad Horvath and Thomas McKone at Berkeley. A key motiva-
tion for developing second-generation biofuels is to provide
truly renewable liquid transportation fuel—fuel that may be
made without degrading the ability of the land to produce the
feedstock, and with a minimum of greenhouse gas emissions in
their production, utilization and indirect impacts compared to
fossil fuels. Any new activity that is likely to impact the environ-
ment, for better or worse, is typically subject to an LCA. An
LCA examines, in the case of a second-generation biofuel, the
environmental costs and benefits at each step from the conver-
sion of land and planting of the crop through the combustion of
the fuel. What are the inputs and outputs of carbon, energy and
other resources at each stage? Projections around farm opera-
tions are currently hypothetical, because there have been no
thorough measurements of greenhouse gas balances over these
new cropping systems and conversion operations. This is further
complicated by the fact that, as with any new technology in its
infancy, there is uncertainty as to the appearance of the mature
technology. The experience gained on the energy farm will be
critical to adding more substance and reality to LCAs
Two major tasks of the Feedstock Programs on Agronomy,
Engineering, and Environment are 1) to actually measure
greenhouse gas and energy balances; and 2) to define the
most sustainable farm operations and opportunities for land
conversion that would maximize opportunities for sequestering
carbon from the atmosphere, as opposed to releasing carbon.
34 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
EVAN DELUCIA:
Reviving Depleted Agricultural Land—
A Biofuel Bonus?
Biofuels are often touted as a solution to rising oil prices and global climate change—but they could also help
solve agricultural problems caused by centuries of land abuse. That possibility is being put to the test in the EBI
research program being conducted by University of Illinois Professor Evan DeLucia, who is heading an investi-
gation of the impact and sustainability of feedstock production. “I am hopeful,” says DeLucia,
“that not only will biofuel crops provide sustainable energy, but that they will diversify and
improve the health of our agricultural ecosystem.”
Such an improvement is long overdue. Years of corn-
soybean rotation in the Midwest have eroded soil,
polluted water, and disrupted carbon and nitrogen
cycles. Continuing that cycle could spell disaster for
farmland, while introducing new, low-maintenance
crops like Miscanthus or switchgrass could replenish
the nutrients that have been leached from the soil.
DeLucia’s team is trying to turn these hypotheticals
into hard facts. They have planted plots of four bio-
mass crops at Illinois’ new EBI Energy Farm—corn,
Miscanthus, switchgrass, and mixed restored prairie
grass. “This is the first time that side-by-side compari-
sons of the ecology of different biofuel feedstocks will
be conducted under realistic field conditions,” says
DeLucia. As the crops continue to grow over their
three-year establishment period, high-tech instrumen-
tation will carefully monitor the plants’ effects on the
A complementary project led by Ryan Stewart at Illinois is environment.
focused on studying the effects on soil quality of stands of
Miscanthus in Japan that are more than 1,000 years old. And that effect is complex, to say the least. To provide
a full sense of the crops’ impact, tests range from soil
One of the key environmental issues surrounding production carbon measurements to energy exchange readings
of biofuels concerns effects on water quality and availability. to analysis of arthropod activity. The variety of data
Plants transpire enormous amounts of water during growth, requires researchers with all kinds of specialties: the
and such water emissions can affect soil moisture and the EBI team includes ecologists, entomologists, physiolo-
amount of water runoff that may support streams and lakes. The gists, and many others. Their program reflects the
potential effects of cellulosic crops on water are being modeled unique interdisciplinary nature of EBI research. DeLu-
using climate and soil data in a collaboration between Carl cia, a plant biologist, calls working with scientists from
Bernacchi at Illinois and Tracy Twine at the University of Min- such diverse fields “invigorating and exciting” and says
nesota. In addition, a detailed analysis of the potential effects this breadth of experience can “provide deep insight
on the well-characterized Lake Bloomington watershed is being into the sustainability of biofuel crops.”
carried out by Ximing Cai, John Braden, Wayland Eheart and
George Czapar at Illinois. This isn’t the first foray into environmental research
for DeLucia, who has spent his career studying global
Concerns about water and land use have stimulated interest in carbon cycles, climate change, forest preservation,
the possibility of using algae to produce biofuels. Preliminary and pollution. His previous research has shown him
analyses of the costs of fuels produced from algae indicate the pressing need for sustainable biofuels, and now
that there are challenges associated with bringing the costs of he hopes that biofuels could solve more than one
production in line with alternatives. To understand the oppor- environmental problem.
tunity, the EBI is supporting a feasibility study by a large group
of algal biologists led by Berkeley Lab scientist Nigel Quinn.
FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 35

BIOCONVERSION:
Attacking Cellulosic Degradation on Several Fronts
36 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
06
c h a p t e r
Bioconversion research at the EBI is addressing several of
the major bottlenecks impeding the practical production
of biofuels, such as ethanol and butanol, from lignocel-
lulosic feedstocks. These programs have several inter-
related components—the discovery and characterization
of fungi and thermophiles that produce new enzymes for
lignin and cellulose deconstruction; protein engineering
and kinetic modeling of improved cellulases; new organism
discovery and cellular engineering for enhanced biofuel
production and improved tolerance of the biofuel product;
and bioprocess engineering to optimize fermentation.
VISUALIZING LIGNOCELLULOSE
Lignocellulose is a composite material made up of a variety of polymers
that are tightly bound to one another. Because the polymers are too small
to be seen by most types of microscopy, the exact molecular structure
of the cell walls that comprise plant biomass is not known. Berkeley Lab
scientist Manfred Auer and colleagues are using new methods of electron
microscopy to visualize biomass at nanometer resolution. His colleagues
Paul Adams and Jim Schuck are building a novel Raman microscope
that they expect will provide spatially resolved chemical information
about cell walls that will be complementary to other types of imaging.
Used together, these types of imaging provide insights into how various
treatments affect the structure of biomass and facilitate improvements in
the overall conversion process.
BIOPROSPECTING AND DISCOVERY OF NOVEL
ORGANISMS AND ENZYMES FOR BIOMASS
DEPOLYMERIZATION AND CONVERSION TO
BIOFUELS
The ability to carry out biomass processing or fermentation at relatively
high temperatures has several advantages. In addition to lower risk of
microbial contamination, a higher temperature accelerates enzyme-cata-
lyzed reactions and would reduce cooling costs and facilitate ethanol (or
butanol) removal and recovery. To enable translation of these advantages
to practice, EBI investigators are seeking to isolate and characterize
enzymes from several extremely thermophilic bacterial strains specifically
adapted for cellulose and hemicellulose degradation.
For example, Doug Clark, Harvey Blanch, and co-workers at UC Berke-
ley, in collaboration with the Frank Robb laboratory at the University of
Maryland, are cultivating communities of organisms from hot springs
with cellulosic substrates with the aim of enriching for, and isolating, novel
thermophiles that produce biofuels and/or thermostable cellulolytic
BIOCONVERSION: ATTACKING CELLULOSIC DEGRADATION ON SEVERAL FRONTS 37
 enzymes. Bioprospecting for cellulose/hemicellulose segments, and fecal pellets of grass-feeding termites.
degradation systems is assisted by whole genome Thus, today’s wood-chomping pests may prove to be
sequencing of novel isolates. important players in tomorrow’s biofuel-producing
technology.
Efforts to exploit the advantages of thermophilic
microorganisms for biofuels production are also In addition to cellulose, a particularly problematic
underway at the University of Illinois in a program component of plant biomass is lignin. Lignin is a
led by Isaac Cann (photo, page 36), Rob Mackie, and complex, decay-resistant, highly cross-linked aromatic
co-workers. Research in their laboratory has resulted polymer. Almost all research on lignin and lignocel-
in isolation and characterization of three novel ther- lulose biological degradation has so far focused on PROTEIN ENGINEERING wall. The goal of research carried out by Jamie Cate,
mophilic bacteria with maximum growth temperatures fungi that decay wood. However, grass cell walls OF IMPROVED CELLULASES Michael Marletta, and co-workers at UC Berkeley is to
of about 70°C. are very different from the walls of conifers, and in develop new experimental systems to study cellulo-
nature, none of the wood-decaying fungi are known Protein engineering has proven to be a powerful tool some degradation of cellulosic biomass. The Cate and
They are also turning to ruminant animals as a promis- to decompose grasses. To find the fungal enzymes in creating enzymes with new and improved proper- Marletta team aims to develop model systems that will
ing source of cellulolytic microorganisms that function best adapted to deconstruction of grass cell walls, ties. However, designing and employing methods to enable them to study the enzymatic properties of cel-
efficiently at more moderate temperatures. Ruminant the Berkeley team headed by John Taylor, N. Louise screen or select cellulase mutants using solid cellulosiclulosomes at a fundamental level. Understanding the
animals are specialized in the utilization of grasses as Glass, and Tom Bruns aims to discover and bring into substrates remains a largely unmet challenge. Research molecular mechanisms may provide the key insights
a source of feed. Both switchgrass and Miscanthus, in cultivation the fungi that decompose the litter that by Clark, Blanch, and co-workers aims to overcome needed to reconstitute “designer cellulosomes”
mesh bags, have been placed in the rumen of fistulated has been accumulated at Illinois under the feedstock this challenge as well as that of developing more cost- optimized for depolymerization of plant biomass.
cattle at the University of Illinois. These have then of choice—Miscanthus giganteus, a C4 grass closely effective cellulases, by developing high-throughput
been recovered and the attached microbes investigated related to sugarcane. solid substrate assays and applying them in the directed
by Eddy Rubin (photo, page 39) and co-workers at evolution of thermophilic cellulases and of cellulases MODELING FOR OPTIMAL CELLULASE
Berkeley Lab’s DOE Joint Genome Institute to identify Using modern high-throughput culture methods with high activity in ionic liquids. The methodology DESIGN AND CELLULOSE HYDROLYSIS
possible sources of robust cellulolytic enzymes for developed by the pharmaceutical industry, among developed will be applicable to the generation and
efficient conversion of cellulosic biomass into ferment- other techniques, fungi capable of deconstructing Mis- study of improved cellulases that can be used in various Accurate kinetic models of cellulose hydrolysis by
able sugars. These two complementary programs canthus cell walls will be identified and considered for process configurations for the production of biofuels cellulases are of critical importance for evaluating
aim to identify enzymes produced by the abundant relevant enzyme production. The Taylor team is also from cellulosic biomass. cellulase-component compositions and for designing
microbes responsible for degradation of plant cell using transcriptional profiling and lignocellulolytic and optimizing processes for cellulose conversion to
wall polymers in the rumen of forage-feeding animals enzyme characterization of the filamentous fungus, Enzyme and metabolic pathway engineering are also biofuels. Such models will also aid in the development
that can potentially be co-opted for cellulosic biomass Neurospora crassa, growing on Miscanthus cell walls to among the tools being used by the Illinois group and characterization of improved cellulolytic systems

Understanding the molecular mechanisms (of degradation of cellulosic

biomass) may provide the key insights needed to reconstitute "designer
cellulosomes..."

conversion. A related goal is to develop tailor-made
enzyme “cocktails” optimized for saccharification of
specific bioenergy crops with their subsequent conver-
sion to alcohol fuels.
Another natural bioconverter that efficiently breaks
down and transforms plant biomass is the termite
hindgut. In a program aimed at discovering novel
enzymes capable of degrading wood lignocellulose,
Phil Hugenholtz and co-workers at the DOE Joint
Genome Institute are performing metagenomic and
bioinformatic analyses of several species of wood-
feeding and grass-feeding termites. These studies
will be complemented by functional screening of
selected enzymes and characterization of the plant cell
wall polymers present in the food sources, hindgut
learn how a fungus regulates genes responsible for cell
wall deconstructing enzymes.
Berkeley chemist Michelle Chang is taking a different
approach—in order to explore mechanistic aspects of
how certain organisms degrade lignin, she is exploring
how to modify yeast and bacteria that are normally
unable to degrade lignin so that they are able to carry
out the chemical transformations associated with
lignin breakdown. In this way she will test whether
our understanding of the pathway is correct and
also whether there may be opportunities to alter the
pathway for increased activity in industrial conditions.
led by principal investigators John Gerlt and John
Cronan in a program directed toward overcoming
biomass recalcitrance as a key obstacle in biofuel
production. The objectives of their program are to
identify and characterize degradation pathways for
lignin, characterize the enzymes that are involved in
those pathways, engineer these enzymes so that they
will have enhanced catalytic properties, and design
new metabolic pathways in organisms so that biofuel
production can be enhanced.
In addition to soluble cellulases, some organisms
degrade cellulose using cellulosomes, which are com-
prised of cellulases organized in a complex assembly
of enzymes and scaffolding on the bacterial cell
generated by protein engineering and synthetic
biology.
Projects under way at UC Berkeley headed by
Clark, Blanch, and Clayton Radke aim to develop
a comprehensive model of cellulose hydrolysis that
can be used to predict cellulase performance, guide
cellulase design, and optimize the hydrolysis of various
cellulosic substrates, including those obtained from
EBI investigators.
As an important first step toward modeling cellulose
hydrolysis and engineering improved cellulases, Clark,
Blanch, and co-workers have isolated the individual
components of the cellulase mixture secreted by the

38 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT BIOCONVERSION: ATTACKING CELLULOSIC DEGRADATION ON SEVERAL FRONTS 39
 JAMIE CATE:
fungus Trichoderma reesei. Determining the kinetics CHEMICAL TRANSFORMATIONS— Quest for Reliable, Responsible Biofuel
of these enzymes toward various recalcitrant sub- ALTERNATIVES TO BIOCONVERSION Runs Through Biochemist's Lab
strates, with and without pretreatment, including
cellulosic substrates dissolved in ionic liquids, will An alternative approach to bioconversion of biomass
provide a useful baseline against which the activities to fuels is to use synthetic chemical catalysts to either What’s an RNA biochemist like Jamie Cate doing in a place like this?
of newly discovered and developed cellulases can hydrolyze biomass or convert hydrolysis products
be compared. Up until a few years ago, the UC Berkeley associate professor was totally
to fuels, or both. This relatively undeveloped area is
preoccupied with the mechanisms of protein synthesis, how antibiotics stop the
being explored on several fronts. Berkeley chemical
bacterial ribosome and how viruses take over protein synthesis in human cells.
engineers Alexis Bell, Berend Smit, John Prausnitz and
Then, as he recalls, “I started thinking about climate change and the fossil fuel
ALLEVIATING PRODUCT TOXICITY Harvey Blanch are analyzing the utility of ionic liquids
issue.”
IN BIOFUEL PRODUCTION to solubilize biomass as a prelude to subsequent
chemical or enzyme-catalyzed hydrolysis. They are He says he installed solar panels on his house and bought a Prius, but it wasn’t
The development of new microbes with greater also looking into the possibility of using synthetic enough. “What can I do with my science?” he asked himself. And the answer was found in
tolerance toward the final fuel product, such as catalysts to directly reform sugars released from an Energy Biosciences Institute program that three graduate students—Veronica Zepeda,
butanol, could lead to substantial improvements in the biomass hydrolysis to fuels. Berkeley chemist Dean Padma Gunda, and Will Beeson—helped him to develop.
cost-effectiveness of producing biofuels from cellulosic Toste is exploring the development of novel synthetic
biomass. To this end, the Clark/Blanch program homogeneous catalysts for polysaccharide hydrolysis, Cate and his team—the students, plus four subject matter expert colleagues from the campus
is working to engineer enhanced tolerance toward and Berkeley chemical engineer Alex Katz is studying and Lawrence Berkeley National Laboratory—are studying how organisms like bacterial
butanol into bacteria, yeast and Clostridia. The group the use of heterogeneous catalysts. Lignin cleavage by microbes make the enzymes that break down plant biomass into fermentable sugars. His
is also exploring the design of extractive fermentation synthetic catalysts is also being researched by Berkeley experience with the tools of structural biology research are being put to use as probes
systems that may be used to minimize inhibition of chemists Jonathan Ellman and Robert Bergman and into the workings of cellulosomes; that is, clusters of protein enzymes, or catalysts, whose
cultures by the products of fermentation. The use of Illinois chemist Tom Rauchfuss. The promise of this interactions enable the decomposition of complex plant infrastructure.
additives that reduce toxicity of fuels during fermenta- new line of research is that entirely novel ways of trans-
tion is being explored by Illinois engineer Hao Feng. forming biomass to fuels may be discovered. This work “We ultimately want to get to a designer cellulosome,” Cate says, “whose enzymes can work
He is also researching novel biomass pretreatment also opens up the possibility of finding routes to types of as well or better than nature to degrade plant material.” He explains it as a “combinatorial”
methods that reduce production of toxic byproducts. fuels that cannot be produced by bioconversions. challenge, in which a central protein called scaffoldin has six sites on which enzymes can
bind, and 70 different enzymes to choose from. So, which enzymes go to which sites, and
Another component of the proposed effort is the why?
development of a simultaneous saccharification
and fermentation process that can operate near the The team’s model organism is a Clostridium species, an anaerobic bacterium that degrades
boiling point of ethanol. Ethanol production during cellulose. And their strategy of study involves multiple approaches: analysis of the genomic
saccharification of cellulose/hemicellulose at 75º will sequence; surface enzymology using mass spectrometry, in which electrically charge samples
increase process efficiency, minimize contamination, are accelerated through a magnetic field and “fingerprinted” on a screen; and atomic force
and facilitate removal of the fuel product. microscopy, which can sense the surfaces of biomass as it’s broken down.

One of the disadvantages of low-mass alcohols like “Eventually, we will begin to focus our attention on breaking down increasingly complex
ethanol and butanol is that they are miscible with potential feedstock for biofuel production, like corn stover, switchgrass, and Miscanthus
water. This feature contributes to the toxicity of such giganteus,” Cate says. “So for the first three years, our goal is to set up an integrated
fuels to the producing organisms and also imposes experimental system to predict and test properties of our ‘designer
energy costs in dehydrating the fuels by distillation. cellulosomes’ and, eventually, to optimize the deploymerization of
Berkeley engineer Nitash Balsara is exploring the feedstock for biofuel production.”
development of advanced membranes that can
selectively separate fuels from the aqueous phase. The work is a graphic example of how the techniques of modern
The successful development of membrane separation biology can be applied to solving one of society’s most challenging
technologies could facilitate the implementation of problems—finding a sustainable, environment-friendly alternative
much more efficient processes than are currently to fossil fuels for transportation energy.
possible.

40 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT BIOCONVERSION: ATTACKING CELLULOSIC DEGRADATION ON SEVERAL FRONTS 41
 07
c h a p t e r

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

A number of molecules of biological origin can serve as fuels. Ethanol is

perhaps the most industrially successful biologically produced fuel. Other
molecules—ranging from more complex branched-chain alcohols to fatty
acids and hydrocarbons—have a variety of properties that make them
more or less attractive as targets for production. And they can be made in
plants and microbes. Some burn cleaner than others; some have higher
energy density, possess different octane ratings, or can be physically
transported or produced more cost-effectively and reliably with less
energy input. Those closer in form to what is found in gasoline, diesel and
jet fuel may prove superior.

The routes to biological production of fuel molecules are numerous and

include sources such as plant oils or algae. However, one of the most
effective routes is through microbial fermentation and synthesis. Decon-
struction of feedstocks leads to hydrolysates rich in 5- and 6-carbon
sugars such as glucose, xylose, and arabinose along with other compounds
that can be toxic. Natural or engineered yeast and bacteria can metabolize
the sugars into different variants of the possible fuel molecules but are
inhibited to various extents by toxins and the fuel products themselves.

Nonetheless, the relative success of this approach derives from a number

of factors. Microbes express an amazing array of natural abilities to
consume simple feed molecules and create complex organic chemicals.
The revolutions in molecular biology and genomics have enabled
scientists to discover the genes responsible for these capabilities and to
transplant their function into industrially robust host microbes. Advances
in quantitative and genome-scale measurement of cellular physiology
down to the single-cell level give unprecedented insight into the factors
that restrict optimal production by limiting metabolic flux and microbial
growth. These tools have only just begun to be applied systematically to
improve microbial fuel production and, despite some early successes,
there remains much room for improvement.

The Energy Biosciences Institute has initiated a cutting-edge microbial

engineering program combining both synthetic biology and metabolic
engineering approaches to create new routes to fuels in bacteria and fungi
as well as systems biology and genomics approaches to measure and
diagnose function.

42 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT BIOFUELS PRODUCTION: TRANSFORMING FEEDSTOCK TO FUEL WITH MICROBES 43

THE MICROBIAL
CHARACTERIZATION PROGRAM
Researchers at UC Berkeley and Lawrence Berkeley
National Laboratory have established a high-
throughput genetics and genomics capability and
are developing an experimental and computational
program to determine the genetic mediators of
optimal fuel production in microbes. Using the
ethanol-producing bacterium Zymomonas mobilis as a
model system, program scientists headed by Berkeley
bioengineer Adam Arkin will screen large-scale genetic
knockout libraries and generate high-resolution whole-
genome gene expression compendia of the bacterium
exposed to different feedstock hydrolysates, their
purified inhibitors and sugars, and the various possible
fuel products. This data will allow dissection of the
mechanisms that impact the ability of Zymomonas
to grow and metabolize sugars into fuel and suggest
routes for engineering more efficient production. The
computational framework and experimental facility
created as part of this program will ultimately scale
to aid the engineering of resistance and fuel molecule
synthesis in this organism and the others being
pursued at the EBI.
44 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
ENGINEERING YEAST
FOR SUGAR UTILIZATION
Two research groups at the University of Illinois
seek to improve the utilization of the different sugars
present in hydrolysates. Most microbes used for fuel
production cannot effectively use both the 5 (like
xylose and arabinose) and 6-carbon sugars (such as
mannose and glucose) that are the most abundant
products from the feedstock deconstruction.
Complete fermentation of all these sugars to biofuels
is necessary to maximize yield and minimize waste in
the production process. Investigators led by chemical
engineer Huimin Zhao and microbial geneticist Yong-
Su Jin will identify genes that transport the sugars into
the cell and metabolize them into common precursors
for fuel synthesis in a number of different fungi.
These will be transplanted into industrially important
host cells starting with the ethanol-producing yeast
Saccharomyces cerevisiae. Advanced approaches for
metabolic analysis and engineering will be employed
to optimize yield and rate of production.
ELUCIDATING THE IMPACT OF
REGULATION AND HETEROGENEITY
ON SUGAR METABOLISM
IN BACTERIA
Engineered pathways are usually dependent upon the
normal metabolism of the host. The endogenous regu-
latory machinery often hampers fuel yields. Metabolic
regulation is evolved to sense environmental condi-
tions and deploy the right pathways to allow organisms
to survive in an uncertain and competitive world.
However, they may be triggered by the particular con-
ditions found in industrial bioreactors and lead to poor
sugar utilization and production. These effects are
further complicated in large-scale fermentations where
cells experience fluctuating nutrient conditions due
to imperfect mixing. The populations will be physi-
ologically heterogeneous, and thus not all individuals
will be producing optimally. EBI scientists in Illinois
under biochemical engineers Christopher Rao and Ido
Golding seek to overcome this problem in Escherichia
coli by creating a quantitative model of the system that
will facilitate the design of strains capable of homoge-
neously, simultaneously and efficiently metabolizing
the arabinose, xylose, and glucose.
PRODUCING DIESEL SUBSTITUTES
IN BACTERIA
While ethanol production is an initial target for the
EBI, other fuel molecules may prove to have superior
properties. Biodiesel is an alternative fuel, widely
used in the alternative energy economy. It is usually
composed mostly of fatty acid alkyl esters (FAAE).
These molecules are often produced by catalyzed
reaction of methanol with fatty acids from plants,
tallow and used cooking oils. Current estimates
predict that production costs for this fuel will remain
substantially higher than petroleum-based products.
Berkeley Lab scientists led by Nikos Krypides and
Athanasios Lykidis are therefore applying biochemical
and metabolic engineering approaches, similar to
those above, augmented with experimental evolution
to generate bacteria with enhanced production of free
fatty acids, triacylglycerols, or FAAE.
Together these programs and projects are creating
an integrated engineering framework for designing
microbes for transformation of feedstock into fuels.
In the next few years, the EBI will add synergetic
programs to the Biofuels Production effort that will
push the frontiers even farther.
These programs and projects are creating
an integrated engineering framework for
designing microbes for transfromation
of feedstock into fuels.
ALEX BELL:
Finding Chemical Keys
to Open the Cellulose Lock
Cellulose, that tough organic
component of all plant cell walls, is
itself constructed of complex chains
of sugars that hold the key to biofuel
development. Unless cellulose and the
related polysaccharide, hemicellulose,
are effectively liberated from their lignin
seal, then broken down and dissolved,
sugars for fuel fermentation will not be
released.
Enter chemical engineer Alex Bell, whose EBI
program challenge is to pretreat the biomass in a way
that can efficiently dissolve cellulose and process the
residue through depolymerization into sugars. He
thinks the answer might lie in inorganic solvents called
ionic liquids—salts in liquid form. They have the
benefits of functioning at room temperature, rather
than requiring heat, and they are inert, meaning they
won’t interfere chemically with the reaction.
“The challenge is in understanding what properties
ionic fluids require to dissolve crystalline cellulose,”
says Bell, an expert on the form and function
of catalysts. He’s certain his team will solve the
dissolution and depolymerization puzzles; he’s less
sure about controlling the chemical transformation of
the sugars into transportation fuels.
The search is both practical and theoretical. While
a half-dozen lab researchers, mostly postdocs and
graduate students, employ high-throughput screening
of candidate solvents (almost 100 reactions at a
time on automated assay machines), Bell’s faculty
colleagues will be looking at the theoretical aspects of
cellulose and carbohydrate dissolution in ionic liquids.
They have a three-year commitment to find the
answers, in order to determine whether or not this
process will successfully lead to commercialization
and industrial application. That’s where the BP
partnership comes in handy. “Having BP’s experts
in residence, to interact with us, will be invaluable in
determining which of the approaches will be fruitful,”
says Bell.
BIOFUELS PRODUCTION: TRANSFORMING FEEDSTOCK TO FUEL WITH MICROBES 45
 08
c h a p t e r

How much land globally is available for

the production of biofuels? What might
be the consequences of devoting vast
amounts of land for raising crops used to
produce biofuels? Will food production be
affected? What impact would a dynamic
biofuels market have on the environment?
As we transition to a sustainable energy
system, EBI scientists are scrutinizing the
potential impacts of these issues on our
society.

The socio-economic program in the Energy

Biosciences Institute is developing modeling
frameworks and applying them using extensive
economic and biophysical data to investigate the
socio-economic, environmental and intellectual
property issues associated with the introduction
of the next generation of biofuels. Researchers are
using both a micro-economic (bottom-up) approach
to assess impacts on land use, food production and
carbon emissions at the local and regional level
and then aggregate them to a national level; and a
macroeconomic (top-down) approach that examines
national and global impacts of biofuels on food and
fuel markets, welfare of consumers and producers and
the environment. In particular, teams are conducting
research in the following areas:

ASSESSMENT OF LAND USE

CHANGES
Madhu Khanna’s program at Illinois is developing an
integrated, interdisciplinary framework to investigate
the effects of large-scale production of cellulosic

SOCIETAL AND ECONOMIC biofuels in the U.S. on land use, crop production,
farm income and carbon mitigation over a 15-year

IMPACTS OF BIOFUELS:
horizon. A key component of this framework is
the application of a mechanistic crop productivity
model (MISCANMOD) by Fernando Miguez and
German Bollero to simulate the yields of switchgrass
Implications for Land Use, Markets, and Miscanthus in the U.S. The model projects
and the Environment daily crop growth with detailed spatial data at a
0.1-by-0.1-degree level on temperature, precipitation,
and solar radiation and soil moisture limitations. Its
mechanistic base allows seamless integration with
improvements identified by the Feedstock Programs.

46 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT SOCIETAL AND ECONOMIC IMPACTS OF BIOFUELS: IMPLICATIONS OF LAND USE, MARKETS, AND THE ENVIRONMENT 47
 Simulated growth and crop yields are within 10 percent of observed
values for Illinois and the Midwest, and for a range of sites in Europe.
Ecosystem services, including soil moisture and carbon balances, are
determined by integrating this model and the CENTURY model used
by the Environment Program in the Integrated Science Assessment
Model (ISAM) developed by Atul Jain as one of the three key models
for projecting global carbon balances for the Intergovernmental Panel on
Climate Change.
Madhu Khanna and Hayri Onal have developed an economic model that
integrates these findings to examine the economically viable land use
allocation among various food and fuel crops and the costs of meeting
biofuel production targets. But it is also capable of assessing the impacts
of systems of crediting carbon storage. Initial application of this model
to Illinois shows that there is considerable spatial heterogeneity in the
competitiveness of various feedstock for biofuel production and that
per-acre yields of biofuel crops as well as the cost of the land are key
determinants of that competitiveness. They find that a mix of cellulosic
feedstock is likely to be more economically viable than a single feedstock,
and this mix is expected to evolve from greater reliance on crop residues
initially, then to reliance on energy crops, like Miscanthus, over time.
They are currently working on applying this model to the Midwestern
states and then to other states where energy crop production is likely to
be viable.
A related approach to a global assessment of land use is being developed
by UC Berkeley and Berkeley Lab scientists Norm Miller, David
Sunding, Maggi Kelly, and David Zilberman. They are integrating
production models for a variety of potential energy crops with spatially
and temporally defined global geographic and economic data in order to
develop an assessment of global potential for cellulosic fuels. A key feature
of such studies is an assessment of how land use is expected to change in
response to changing climate and population density.
48 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Researchers
are examining
national and global
impacts of biofuels
on food and fuel
markets, welfare
of consumers and
producers, and the
environment. LOGISTICS, POLICY, AND INFRASTRUCTURE
The group led by Jürgen Scheffran is developing a framework to
determine the optimal capacity and location of biorefineries as a function
of the regional distribution of bioenergy feedstocks in the Midwest,
the costs of transportation of feedstocks and biofuels, and the demand
centers for biofuels. Mathematical programming tools are used to identify
location of biorefineries that minimize the costs, including transportation
to and processing of bioenergy crops at refineries, transportation of
fuel from refineries to the demand destinations, capital investment of
refineries, with a net of by-product credits. A multi-year transshipment
and facility location model determines the optimal time to build each
plant in the system, water needs and availability, the amount of raw
material processed by individual plants, and the distribution patterns of
inputs from crop-producing regions to the refineries and shipment of
ethanol to the demand destinations.
Illinois legal scholars Jay Kesan and Brian Endres are examining how the
regulatory framework in various regions may impact the establishment
of a cellulosic fuels industry in the U.S. The group is also investigating
the implications of the new Renewable Fuels Standard that the
Environmental Protection Agency is expected to release early in 2009.
Further afield, UC Berkeley’s Dick Norgaard and Alastair Iles are studying
the structure of the existing biofuel industry in Brazil in order to develop
a basis for evaluating how future development of the industry may occur.
Berkeley political scientist Steve Weber is developing an analysis of
how previous transitions in the energy sector have occurred with a view
to understanding the impacts of current and future energy policies on
emergence of a biofuels industry.
SOCIETAL AND ECONOMIC IMPACTS OF BIOFUELS: IMPLICATIONS OF LAND USE, MARKETS, AND THE ENVIRONMENT 49
 FOOD AND FUEL MARKET IMPACTS ROLE OF INNOVATION, INTELLECTUAL
PROPERTY RIGHTS, AND
David Zilberman’s Berkeley team is developing
quantitative models and measures to assess the impact TECHNOLOGY ADOPTION AND LAW
of different kinds of biofuels on food and energy
Zilberman and colleagues are analyzing the
prices, farmers, consumers, and overall economic
potential role of productivity-enhancing agricultural
welfare. Analyzing the impact of corn ethanol in 2006-
biotechnology in the growth of the biofuel sector.
07, they find that biofuels reduced the average price of
Early results suggest that the capacity of biofuel to
fuel between 1 and 3 percent and increased corn price
meet energy demand largely depends on the increased
by between 5 and 20 percent in the U.S. This saved
productivity of traditional crops that may partially
up to $45 billion in fuel costs, increased the food bill
compete with biofuel for land, water, and other
by up to $20 billion, and raised farm income by up to
resources.
$18 billion. The Berkeley group is also developing a
model to explain global oil prices, which suggests that UC Berkeley economist Brian Wright is assessing the
OPEC does not behave like an “economic cartel” that intellectual property (IP) issues relevant to biofuels
maximizes profit but rather as a political cartel that research beyond current ethanol production. An
maximizes the overall welfare of oil-exporting nations. initial assessment of the landscape indicates that IP
This will be used to make quantitative assessments ownership is fragmented and that over 50 assignees are
of resource allocation and pricing in fuel, food, and active in this technology arena, with Genencor holding
biofuel markets. the largest portfolio. His analysis shows that the public
sector is highly active in biofuels research, and it points
Zilberman’s work analyzing the profitability of
to the need to understand public/private relationships
corn ethanol incorporates stochastic influences on
in this area. He plans to measure and assess the
economic decisions arising from randomness in
evolving effects of intellectual property protection of
natural phenomena and economic processes. Early
inputs and outputs of research and of some relevant
results indicate that there may be significant losses
regulatory constraints, from the viewpoints of the EBI
in the biofuel industry during periods of low supply
scientists involved in activities relevant to the initiative.
inventories of corn and large profits during periods of
Work is also proceeding on a study of the relationship
abundant corn supply and high oil prices. His work is
between the terms of research sponsorship and
currently analyzing the implications of this “boom-
subsequent patenting and licensing at the UC Office of
bust” nature of corn biofuel for the design of contracts
Technology Transfer. This has generated interest and
and will be extended to analyze the effect of random
an offer of modest support at the National Academies.
forces on the economics of cellulosic biofuels.
Zilberman is also developing a conceptual framework
Khanna is also analyzing the effects of liberalizing
to explain adoption of biofuel technologies while
trade in biofuels with Brazil on food and fuel prices,
incorporating the interdependencies between the
consumer and producer well-being, and greenhouse
farmer, processor and oil marketers and to analyze
gas emissions. She finds that the current biofuel
the types of production contracts needed to induce
policy of an import tariff and a subsidy on ethanol Work will seek to understand how adoption adoption. The Illinois team of Anne Heinze Silvis,
imposes an economic cost of over $3 billion annually
Michael Gray, German Bollero and Maria Villamil is
and results in significantly higher corn and ethanol of biofuel technologies can incorporate engaged in surveys of farmers and investors in ethanol
prices in the U.S. with negligible current reductions in
plants to examine the factors that will influence their
carbon emissions as compared to those with no policy
intervention.
the interdependencies between farmer, decisions to produce and use cellulosic feedstock.

processor, and oil marketers

50 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT SOCIETAL AND ECONOMIC IMPACTS OF BIOFUELS: IMPLICATIONS OF LAND USE, MARKETS, AND THE ENVIRONMENT 51
 The EBI is developing collaborations with other organizations
around the world to increase the critical mass of
researchers with expertise and access to data
that is relevant to understanding core issues.
ENVIRONMENTAL AND SOCIETAL
IMPACTS OF BIOFUELS
Several research teams within the socio-economic program are assessing various aspects of
the environmental and societal impacts of biofuels from an economic perspective. Atul Jain
is using biophysical models to assess the soil carbon sequestration potential and nitrogen
requirements of biofuel crops. Khanna’s team is analyzing data on life cycle emissions in
conjunction with detailed spatial data on production methods and land use to determine the
potential for biofuel-driven land use changes and displacement of gasoline to mitigate carbon
and the costs of achieving mitigation. They find that biofuel production in Illinois, to meet 20
percent of the ethanol mandate by 2022, has the potential to reduce cumulative greenhouse
gas emissions by 45 percent relative to baseline levels over the next 15 years by displacing
energy equivalent gasoline, but that the enhanced production of corn ethanol to meet a part
of the mandate increases nitrogen use by 27 percent over this period.
Using a macro-economic computable general equilibrium model of the U.S., John Braden’s
Illinois group is analyzing the efficient mix of biofuel pathways based on their economic and
environmental impacts which considers the trade-offs between reduced carbon emissions
due to biofuels and water quality degradation due to greater fertilizer use for some feedstock,
such as corn. Zilberman’s team is developing ways to integrate economics into the methods
currently used to assess life cycle carbon emissions of biofuels. The group is developing
measures that modify the standard life cycle analysis to reflect the effects of changing market
conditions and policies on choice of production methods and carbon emissions.
One of the complexities of understanding the life cycle aspects of various types of biofuels
is the recent recognition of potential indirect land use effects. The concept is that, because
demand for food is inelastic, if land is converted from food production to fuel production,
previously unused land will be converted to food production with attendant releases of
greenhouse gases. However, the situation is complex because demand for food can also be
satisfied by increasing production on fewer acres in response to price signals. Michael O’Hare
and his Berkeley colleagues are working to develop economic models that can be used to
understand this issue quantitatively. Their findings may have important implications for
future policies that place economic value on greenhouse gas emissions.
Another matter of potential concern regarding biofuels is the possibility that diversion of land
to production of biofuels could negatively impact food availability for disadvantaged people
around the world. This is a complex issue that appears to be more related to the structure
and operation of markets rather than about the availability of land. Berkeley economist Brian
Wright and colleagues are studying this issue, as are Ximing Cai at Illinois and collaborators
Siwa Msangi and Tingju Zhu at the International Food Policy Institute. Much of the other
economics research in the EBI also impinges on this important question from various
perspectives. This topic is so important that the EBI is developing collaborations with other
organizations around the world to increase the critical mass of researchers with expertise and
access to data that is relevant to understanding the core issues.
52 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
MADHU KHANNA:
Seeking a Biofuels Policy
Where Everybody Wins
Creating a national biofuels policy is tricky because it has to
work for diverse interests. Ideally, such a policy would cut oil
imports, curtail greenhouse gas emissions, and be profitable
for agriculture. And, the biofuels policy can’t act as a drag on
the economy or limit food production.
That’s a tall order. Nonetheless, an EBI research team has
waded into the debate by undertaking a massive study of the
economic issues related to biofuel development.
“We should be able to assess the benefits and unintended consequences
of biofuels policies as they stand today, particularly for the environment,”
said Madhu Khanna, an environmental economist at the University of
Illinois at Urbana-Champaign and lead investigator for the EBI team.
“And we should be able to determine how those policies might be better
designed to achieve social goals.”
To come up with a broadly acceptable biofuels policy, she and her
colleagues must collect huge amounts of research data, much of it dealing
with the logistics of creating a massive new industry. “We need to know
how much switchgrass, Miscanthus, and crop residues can be grown or
collected in different parts of the country,” said Khanna. “We don’t know
because we’ve never done it. We want to know how much carbon each of
those biofuel crops is going to sequester in the soil. And we want to know
how much carbon will be produced (by) each crop.”
One complicating factor is a federal mandate that requires production of
36 billion gallons of biofuel annually by 2022. Of that, 21 billion gallons
must come from advanced biofuels—fuels which produce no more than
half as much greenhouse gas as gasoline. “We want to find the lowest-cost
way we could meet that mandate,” Khanna said. “The first step is to figure
out where to grow corn, where to grow Miscanthus, and where to grow
switchgrass in order to meet the 36-billion-gallon mark.”
Ultimately, the team expects to give policymakers the information
they need to help craft a national biofuels policy that works for the
environment, the economy, and farmers.
“Farmers won’t do this unless they see the right price signals,” Khanna
added. “The price signals provided by the market may not reflect the
various environmental effects of biofuels produced from different
feedstocks. So the government may have to provide appropriate
incentives so that farmers produce a sustainable mix of biofuel crops.”
SOCIETAL AND ECONOMIC IMPACTS OF BIOFUELS: IMPLICATIONS OF LAND USE, MARKETS, AND THE ENVIRONMENT 53
 Education and Outreach 09
c h a p t e r

Conferences, Symposia, Workshops, Seminars Greenhouse Gas Emissions from Biofuels Measuring and Modeling the Life Cycle GHG
June 8-9, 2008 Impacts of Transportation Fuels
From a symposium on using microbes to recover earth-bound oil supplies, held in October In this workshop, participants discussed the current July 1-2, 2008
of 2007, to an economic modeling conference on biofuels in November 2008, the EBI has state of knowledge of greenhouse gas emissions This Berkeley workshop explored the differences
sponsored or co-sponsored a wide range of workshops and meetings during its first year of associated with biofuel crops and new research needed among the fuel life cycle Greenhouse Gas (GHG)
operations. The knowledge shared by participants broadened and enriched the global quality to understand mechanisms of greenhouse gas release, estimates from leading models, including system
of scientific inquiry within and about bioenergy. Of special note was the EBI-sponsored Pan sensitivity of that release to land use management and boundaries and other judgments about land-use
American Plants and Bioenergy Symposium at Merida, Mexico, co-organized by Deputy Director farming practices, and strategies for extrapolation of change. Experts from the academic and fuels analysis
Steve Long. This brought together groups working on feedstock improvement from the EBI and greenhouse gas emissions to the global scale. communities addressed both current and emerging
many institutes throughout the Americas, and in particular teams from São Paulo advancing biofuels and other options for reducing the carbon
the use of sugarcane. Pan American Congress on Plants footprint of motor fuels. The Environmental Defense
and Bioenergy Fund was primary sponsor.
Within EBI, investigators benefitted from three seminar series launched in Berkeley and two in
June 22-25, 2008
Illinois to provide forums for the exchange of project information and the prospective collabora- Biofuels and Sustainability
tions between research units. This international conference in Merida, Mexico
featured plant biologists meeting with government October 21-22, 2008
policy makers, agronomists, microbiologists, econo- EBI joined with the Illinois Sustainable Technology
mists and ecologists to forge a path toward Western Center to convene this conference in Champaign,
In chronological order, the meetings included: Hemisphere bioenergy security that is sustainable and dedicated to issues and innovations that can improve
environmentally and economically sound. EBI Deputy the sustainability of biofuels. Discussions focused on
Research Priorities in Microbially Enhanced 5th Annual Bioenergy Feedstocks Symposium Director Steve Long was co-organizer of the confer- the economic, social, and environmental feasibility
Hydrocarbon Recovery (MEHR) January 9-10, 2008 ence and gave the opening lecture. and ethics of biofuels options for meeting energy
This symposium at the University of Illinois was needs.
October 24, 2007
part of a series established with the State Program Transition to a Bioeconomy: Risk, Infrastructure
Microbially Enhanced Hydrocarbon Recovery
on Bioenergy Feedstocks. The symposium has and Industry Evolution Linking Biophysical and Economic Models of
involves using microbes in the subsurface to recover
grown from 20 participants in 2004 to 300 from four June 24-25, 2008 Biofuel Production and Environmental Impacts
additional oil or hydrocarbon gas from conventional
continents in 2008. It brought together agronomists, November 13-14, 2008
oil and gas reservoirs, or to liberate methane from Co-sponsored by EBI, this Farm Foundation confer-
environmentalists, industry and pioneering farmers
other hydrocarbon-rich environments (e.g., coal ence in Berkeley focused on risk and infrastructure This workshop in Chicago focused on the need to
experimenting with potential cellulosic feedstocks.
beds, tar sands, oil shales). This workshop defined the for the biofuel industry of the future. Participants develop simulation models to understand how much
Beside reports on five years of trials with Miscanthus
research parameters for a project solicitation that will examined such issues as finances, business models, and cellulose biofuel crops would yield under alterna-
and switchgrass in Illinois, a highlight was the
lead to EBI funding of research in this area. transportation infrastructure. tive growing conditions and what would be their
agronomic approaches and business model being
implications for water quality, climate change and
adopted in Ireland to achieve self-sufficiency in
Biologically Enhanced Carbon Sequestration: biodiversity. Participants reviewed recent develop-
fuels, via feedstocks that include Miscanthus, and
Research Needs and Opportunities ments in biophysical models of bioenergy feedstocks
a parallel program in SW Ontario. This has led to
October 29, 2007 and their integration with economic models to study
valuable interactions between the EBI Agronomy and
Fossil fuel combustion, deforestation and biomass the economic and environmental impacts of bioenergy
Engineering Programs and these activities in Ireland
burning are the dominant contributors to increasing crops. The meeting was co-sponsored by the B-Basic
and Canada.
atmospheric carbon dioxide concentrations and global program at Delft University of The Netherlands and
warming. This workshop explored the promising the Great Lakes Bioenergy Center sponsored by the
current approaches and research roadmaps to Berkeley Energy and Resources Collaborative U.S. Department of Energy.
mitigating CO2 emissions in both terrestrial and (BERC) Symposium
geologic carbon sequestration. Advances in ecology March 7, 2008
and microbial biology offer new possibilities for The symposium featured leaders in research and
enhanced sequestration. technology, industry and academia, and economic and
political organizations, who discussed the need for
concerted global action to address climate change and
sustainable solutions to energy needs. EBI supported
this student-run program and participated through
talks and panel discussions.

54 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT EDUCATION AND OUTREACH 55

 In addition to the aforementioned programs,
EBI investigators attended national and
international symposia on relevant topics and
gave talks and poster sessions on the work
being conducted in the Institute. They also
accepted invitations as lecturers in university
classrooms and at industry conferences.
EBI in Education
In the decades ahead, the students of today will help
to establish and maintain this new industry as well as
manage its impacts on global society. The EBI recog-
nizes its role in educating and training these young
researchers so that they are prepared for the coming
bio-revolution. Nearly 200 graduate and undergradu-
ate students and postdoctoral scientists were engaged
in EBI programs during its first year in laboratories and
offices at both Berkeley and Illinois campuses.
Partnership with India
Five top undergraduates from the Indian Institute of
Technology (IIT) at Kharagpur spent eight weeks
during the summer of 2008 conducting research with
EBI faculty as part of a new Berkeley-IIT Kharagpur
collaboration in biofuels sponsored by the EBI. The
scientific partnership was brokered by UC Berkeley
Deans Mark Richards, of the College of Letters and
Science, and of Physical and Mathematical Sciences;
and Geoff Owen, of Biological Sciences. The EBI
and its Director, Chris Somerville, are supporting
sponsors.
The collaboration involves two phases. The first seeks
to build relationships among faculty and students of
both institutions while increasing the pool of research-
ers focused on addressing the energy challenge. The
second phase will focus on joint targeted research
projects. As part of the first phase, five IIT Kharagpur
students were mentored by, and assisted, UC Berkeley
and Lawrence Berkeley National Laboratory principal
investigators in the EBI research program—Poulami
Mondal, with Paul Adams; Shailabh Kumar, with
Manfred Auer; Akhilesh Jain, with Alex Bell; Aniket,
with Doug Clark; and Raj Shekhar Singh, with Norm
Miller.
56 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Elementary and Middle Schools Bioenergy Crop Modeling and Land Use
At the other end of the spectrum, EBI graduate October 9-10, 2008
student Becky Arundale and office manager Becky To understand bioenergy crop production potential
Heid in Illinois have developed resources in col- in marginal and abandoned lands, a well-planned
laboration with a local teacher to explain the EBI to modeling and data analysis strategy is required. This
elementary school students. EBI graduate student workshop was conducted to design a crop modeling
Ashley Spence developed and presented a program of validation exercise and to define methods for
EBI mission-based activities for girls from area middle quantifying targeted land distributions.
schools at Illinois for GAMES (Girls Adventures in
Math, Engineering, and Science). Biofuels Research Seminar Series
Recognizing the need for interdisciplinary information
Cal Day “Voyage” exchange as well as collegial partnerships with parallel
Berkeley students, as well as campus visitors during the groups, EBI management launched two internal
annual spring Cal Day open house program, learned seminar series in 2008 addressing the challenges,
about Robert Swan’s “Voyage for Clean Energy” in two progress, and promise of biofuels research.
talks sponsored by the EBI. Explorer Swan, one of the
Biweekly presentations from researchers in EBI-
few to have successfully walked to both the north and
supported programs and projects have been held in
south poles, was kicking off his next venture, a five-year
Berkeley’s Calvin Laboratory since debuting with
sail around the world to raise awareness about climate
EBI Intellectual Property Manager Mitch Altschuler
change and saving the environment.
on Aug. 26. A second series of monthly talks jointly
Two Berkeley graduate students actually took Swan up sponsored by EBI and the U.S. Department of
on his offer to work on his BP-sponsored biofuel-pow- Energy’s Joint BioEnergy Institute ( JBEI), located in
ered sailboat during its West Coast journey—Vasanth Emeryville, CA, debuted on Sept. 10 with a seminar
Mohan, a graduating MBA student in the Haas School by University of Illinois microbiologist Roderick I.
of Business, and Bret Strogen, a second-year doctoral Mackie. This series will resume in the first quarter
student in environmental engineering. Strogen is of 2009.
currently working on an EBI program headed by
Arpad Horvath and Tom McKone entitled “Life Cycle
Environmental and Economic Decision-Making for
Alternative Biofuels.”
EBI graduate students and postdocs have been actively
educating each other via biweekly lunchtime seminar
programs started at both Berkeley and Illinois. The
seminars focus on work being conducted in the
laboratories of EBI principal investigators.
The EBI recognizes its role in educating
and training young researchers so that they
are prepared for the coming bio-revolution.
EDUCATION AND OUTREACH 57
 EBI Research Programs,
Projects, and Research Personnel
The following is a list of principal investigators and research staff in 50
programs and projects funded by the Energy Biosciences Institute during its
first year. Detailed descriptions of the individual projects can be found on the
EBI's public web site: www.energybiosciencesinstitute.org.
Feedstock Development
Programs:
Assessing the Potential Impact of Insect Pests
and Plant Pathogens on Biomass Production of
Miscanthus x Giganteus and Switchgrass
Principal Investigator: Michael E. Gray, University
of Illinois
Co-PIs: Carl Bradley, Terry Niblack, and Kevin
Steffey, University of Illinois; Shauna Somerville,
UC Berkeley
Postdocs: Bright Agindotan, Monday Ahonsi, Jeffrey
Bradshaw, Tesfamariam Mekete, Jarrad Prasifka
Technician: Michelle Averbeck
Genomics-Enabled Improvement of
Andropogoneae Grasses as Feedstocks for
Enhanced Biofuel Production
Principal Investigator: Stephen Moose, University
of Illinois
Co-PIs: Matthew Hudson and Ray Ming, University of Principal Investigator: Sheila McCormick, UC
Illinois; Dan Rokhsar, UC Berkeley and Berkeley Lab Berkeley
Postdocs: Madge Alabady, Cuixia Chen, Kankshita
Swaminathan
Graduate Students: Adam Barling, Brandon James
Undergraduate Students: Katie Boesche, Arthur
Rudolph
Engineering Solutions for Biomass Feedstock
Production
Principal Investigator: KC Ting, University of Illinois
Co-PIs: Steven Eckhoff, Tony Grift, Alan Hansen,
Luis Rodriguez, Lei Tian, Qin Zhang, University of
Illinois
58 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Postdocs: Tofael Ahamed, Hala Chaouui,
Konstantinos Domdouzis, Ming-Che Hu, Qingting
Liu, Zewei Miao, Yogendra Shastri
Undergraduate Student: Jude Holscher
Visiting Scholars: Yonghua Xiong, Jiang Yan, Yuliang
Zhang, Qinyuan Zhu
Feedstock Production/Agronomy Program
Principal Investigator: Thomas Voigt, University
of Illinois
Co-PI: Stephen P. Long, University of Illinois
Graduate Students: Becky Arundale, Bosola
Oladeinde, Ashley Spence, Andy Wycislo
Tech Specialists: Rich Pyter, Drew Schlumpf,
Emily Thomas
Projects:
Reproductive Barriers in Miscanthus sinensis
and Other Biofuel Plants
Postdoc: Yuefeng Guan
Model Development to Predict Feedstock
Production of Miscanthus and Switchgrass as
Affected by Climate, Soils and Nitrogen
Principal Investigator: German A. Bollero,
University of Illinois
Co-PIs: Stephen P. Long, Fabian G. Fernandez,
University of Illinois
Postdoc: Fernando Miguez
Germplasm Collection, Nutrient Cycling,
Cold Hardiness, Photosynthetic Capacity,
and Flowering Phenology of Miscanthus
sacchariflorus, Miscanthus sinensis, and Their
Natural Hybrids in Native Stands Ranging from
Central to Northern Japan
Principal Investigator: J. Ryan Stewart, University
of Illinois
Co-PIs: German Bollero, Fabian G. Fernandez,
University of Illinois; Toshihiko Yamada, Hokkaido
University, Japan; Aya Nishiwaki, Miyazaki University,
Japan
Postdoc: Yo Toma
Improvement of Bioenergy Crops
Principal Investigator: Jack Widholm, University
of Illinois
Co-PI: John Juvik, University of Illinois
Postdoc: Olga Zernova
Graduate Student: Hyoung Kim
Research Scientist: Vera Lozovaya
Biomass Depolymerization
Programs:
Chemical Imaging of Plant Biomass with Micro-
and Nano-Raman Spectroscopy
Principal Investigator: Paul Adams, Berkeley Lab
Co-PI: Jim Schuck, Berkeley Lab
Postdoc: Martin Schmidt
Cell Wall 3D Architecture at Nanometer
Resolution Using High-Throughput TEM and EM
Tomography
Principal Investigator: Manfred Auer, Berkeley Lab
Co-PIs: Kenneth Downing, Bahram Parvin, Berkeley
Lab; Jan Liphardt, UC Berkeley
Postdocs: Phillip Jess, Purbasha Sarkar
Specialist: Ju Han
Associate Specialist: Elena Bosneaga
EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL
Biomass Pretreatment and Chemical Synthesis
10
c h a p t e r
of Transportation Fuels
Principal Investigator: Alexis T. Bell, UC Berkeley
and Berkeley Lab
Co-PI: Harvey W. Blanch, UC Berkeley and Berkeley
Lab
Postdocs: Ting Chen, Chidam Mandan, Sasisanker
Padmanabhan
Graduate Student: Sean Dee
Cellulosomes Optimized for Biofuel Production
Principal Investigator: Jamie H. D. Cate, UC Berkeley
and Berkeley Lab
Co-PIs: Michael A. Marletta, Haw Yang, Daniel A.
Fletcher, Evan R. Williams, UC Berkeley and Berkeley
Lab
Visiting Professor: Rafael Lamed
Postdocs: Corinne Hausmann, Sasa Jenko-Kokalj,
Kai Zhang
Graduate Students: William Beeson, Padma
Gunda, Chris Phillips, Veronica Zepeda, Elizabeth
Znameroski
Undergraduate Students: Valerie Chan, Duy Dao
Research Associate: Bruno Martinez
Thermophilic Microbes and Enzymes for Biofuel
Production
Principal Investigator: Douglas S. Clark, UC Berkeley
Co-PIs: Harvey W. Blanch, UC Berkeley and Berkeley
Lab; Frank Robb, University of Maryland Biotechnology
Institute
Postdocs: Harshal Chokhawala, Melinda Clark,
Tae-Wan Kim, Seth Levine, Cong Trinh
Junior Specialist: Paul Wolski
Graduate Students: Craig Dana, Jerome Fox, Sarah
Huffer, Priya Jayachandran, Dana Nadler
59
 Engineering of Thermophilic Anaerobic Bacteria
to Improve Biocatalysis of Plant Cell Wall
Materials to Ethanol/Butanol
Principal Investigator: Isaac Cann, University
of Illinois
Co-PIs: Roderick I. Mackie, M. Ashley Spies, Satish
K. Nair, University of Illinois
Research Associate: Wenze Li
Postdocs: Yejun Han, Shinichi Kiyonari, Shosuke
Yoshida
Graduate Students: Richard Cozad, Dylan Dodd
Undergraduate Students: Charles Hespan, Amara
Hussain, Sana Jafri, Brad Jelinek, Jason Kim, Hussain
Mithaiwala, Farhan Quader, Soe Tha
Biochemistry, Structure and Engineering of
Enzymes and Metabolic Pathways to Overcome
Biomass Recalcitrance
Principal Investigator: John Gerlt, University
of Illinois
Co-PIs: John Cronan, Satish Nair, University of Illinois
Postdocs: Sudipta Majumdar, Jose Solbiati
Enzyme-Inspired Catalysts for Enhancing Biofuels
Production
Principal Investigator: Alexander Katz, UC Berkeley
Specialist: Andrew Solovyov
Postdocs: Tatiana Luts, Brandon McKenna
Development of Novel Catalysts
Principal Investigator: Dean Toste, UC Berkeley
Postdocs: Francisco Santoro, Sunghee Son
Graduate Student: Cole Witham
Junior Specialist: Vincent Chan
Projects
Fungi and Deconstruction of Lignin and Other
Components of Miscanthus Cell Walls
Principal Investigator: John W. Taylor, UC Berkeley
Co-PIs: Thomas D. Bruns, N. Louise Glass, UC
Berkeley
Postdoc: Chaoguang Tian
Researcher: Tim Szaro
60 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Biomass to Transportation Fuel via
Hydrodeoxygenation
Principal Investigator: Jonathan A. Ellman, UC
Berkeley and Berkeley Lab
Co-PI: Robert G. Bergman, UC Berkeley and Berkeley
Lab
Postdoc: Jason Nichols
Enzyme Discovery in Grass-Feeding Termites for
the Depolymerization of Lignocellulosic Biomass
Principal Investigator: Philip Hugenholtz,
Berkeley Lab
Research Scientist: Natalia Ivanova
Staff Scientist: Nikos Krypides
Postdoc: Falk Warnecke
Surface Kinetic Mechanisms of Enzymatic
Cellulose Deconstruction
Principal Investigator: Clayton J. Radke, UC Berkeley
and Berkeley Lab
Graduate Student: Samuel Maurer
Genomic Analysis of Bovine Rumen Microbiota
Under Different Dietary Regimens
Principal Investigator: Eddy Rubin, Joint Genome
Institute, Berkeley Lab
Co-PI: Susannah Tringe-Green, Joint Genome
Institute, Berkeley Lab
Postdocs: Tao Zhang, Matthias Hess
Detoxification of Miscanthus Hydrolysates With a
New Phase Separation Method
Principal Investigator: Hao Feng, University of Illinois
Co-PI: Bin Wang, Visiting Research Scientist
Postdoc: Pradip B. Dhamole
Fractionating Recalcitrant Miscanthus by a Two-
Stage Treatment Under Mild Reaction Conditions
Principal Investigator: Hao Feng, University of Illinois
Visiting Research Scientist: Bin Wang
Graduate Student: Atilio de Frias
Ecology and Exploitation of Endophytic
Diazotropic Bacteria in Biofuel Crops
Principal Investigator: Angela Kent, University
of Illinois
Undergraduate Student: Neil Gottel
Organometallic Catalytic Approaches to
Delignification
Principal Investigator: Thomas B. Rauchfuss,
University of Illinois
Postdoc: Didier Morvan
Graduate Students: Zachariah Heiden, Aaron Royer
Enzymatic Lignin Degradation
Principal Investigator: Michelle Chang, UC Berkeley
Graduate Student: Margaret Brown
Biofuels Production
Programs
Systems Biology of Metabolism and its
Regulation in Microbes Important to Biofuel
Production
Principal Investigator: Adam P. Arkin, UC Berkeley
and Berkeley Lab
Co-PIs: Inna Dubchak, Terry Hazen, Berkeley Lab
Postdoc: Anna Gersimova
Research Associate: Jordan Mar
Interest Group: Adam Deutschbauer, Paramvir
Dehal, Jennifer Kuehl
Engineering a Yeast Strain that Efficiently Utilizes
C5/C6 Sugars
Principal Investigator: Huimin Zhao, University
of Illinois
Co-PIs: Nathan Price, Lucas Li, University of Illinois
Postdoc: Tae Hee Lee
Graduate Student: Jing Li
EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL
Projects
Bioengineering and Selection for Biodiesel
Production in Bacteria
Principal Investigators: Nikos Kyrpides, Athanasios
Lykidis, Joint Genome Institute, Berkeley Lab
Researcher: Pilar Francino
Postdoc: Maria Billini
Microbial Sugar Utilization
Principal Investigator: Yong-Su Jin, University
of Illinois
Robustness to Environmental Heterogeneity—
Engineering Strains Optimized for Large-Scale
Fermentation
Principal Investigator: Christopher V. Rao, University
of Illinois
Co-PI: Ido Golding, University of Illinois
Graduate Students: Tasha Desai, Michael Bednarz
Environmental, Social and Economic
Dimensions
Programs
Life-Cycle Environmental and Economic Decision-
Making for Alternative Biofuels
Principal Investigators: Arpad Horvath and Thomas
McKone, UC Berkeley and Berkeley Lab
Co-PIs: Maximilian Auffhammer, Peter Berck, Dan
Kammen, William Nazaroff, Tim Lipman, Margaret
Torn, UC Berkeley
Lead Researchers: Agnes Lobscheid, Eric Masanet
Graduate Students: Catherine Almirall, Joshua Apte,
Surakshya Dhakal, Bret Strogen, Kevin Fingerman
61
 Economics of Biofuel Adoption and Impacts
Principal Investigator: David Zilberman,
UC Berkeley
Co-PIs: Gordon Rauser, David Roland-Holst,
UC Berkeley
Postdoc: Gal Hochman
Graduate Students: Justine Lazaro, Maya Papineau,
Deepak Rajagopal, Steve Sexton, Thomas Sproul
Administration: Amor Nolan
Subcontractor: Gregory Glass
Projects
Development of Biofuel Productivity Potentials
for Economic Analysis Under Changing Climate,
Land Use, and Societal Demands
Principal Investigator: Norman L. Miller, UC
Berkeley and Berkeley Lab
Co-PIs: David Sunding, UC Berkeley and Berkeley
Lab; N. Maggi Kelly, David Zilberman, UC Berkeley
Faculty Collaborator: Steven W. Running, University
of Montana
Postdoc: Alan DiVittrio
Regional Environmental Impacts of Biofuel
Feedstock Production—Scaling Biogeochemical
Cycles in Space and Time
Principal Investigator: Carl J. Bernacchi, University
of Illinois
Co-PI: Tracy E. Twine, University of Minnesota
Graduate Student: Andrew VanLoocke
Undergraduate Student: Christina Burke
Regional Socioeconomic and Environmental
Impacts of Alternative Biofuel Pathways
Biofuels Research Initiatives and Extension:
Synergizing Engagement With Stakeholders
Principal Investigator: Anne Heinze Silvis, University
of Illinois
Co-PIs: Michael E. Gray, German Bollero, Maria
Bonita Villamil, University of Illinois
From a Global Oil Economy to a Global Biofuel
Economy
Principal Investigator: Steve Weber, UC Berkeley
Postdoc: Regine Spector

Ecosystem Impact and Sustainability of
Feedstock Production
Principal Investigator: Evan H. DeLucia, University
of Illinois
Co-PIs: Mary R. Berenbaum, Carl J. Bernacchi, Mark
B. David, Roderick I. Mackie, and Donald R. Ort,
University of Illinois
Postdocs: Kristina Anderson-Teixeira, Sarah Davis,
Candice Smith, Tony Yannarell, Art Zangeri, Marcelo
Zeri
Graduate Students: Joshua Burke, Terry Harrison,
George Hickman, Mathew Nantie
Research Technicians: Mike Masters, Corey Mitchell
Collaborator: Bill Parton
Biofuels: Law and Regulation
Principal Investigator: Jay P. Kesan, University
of Illinois
Co-PI: A. Bryan Endres, University of Illinois
Contextualizing Bioenergy Production: Life Cycles,
History and Change in Brazil
Principal Investigator: Dick Norgaard, UC Berkeley
Co-PI: Alastair Iles, UC Berkeley
Faculty Collaborators: Renata Andrade, Catholic
University of Brasilia; Sergio Pacca, University of Sao
Paolo
Graduate Students: Avery Cohn, Barbara Haya,
Abigail Martin
A Realistic Technology and Engineering
Assessment of Algae Biofuel Production
Principal Investigator: Nigel W. T. Quinn, Berkeley
Lab, UC Merced
Co-PI: Tryg J. Lundquist, Berkeley Lab, Cal Poly San
Luis Obispo
Researchers: Gary L. Andersen, Robert W. Dibble, J.
R. Benemann, I. C. Woertz
Principal Investigator: John B. Braden, University Graduate Student: Alan Dafoe
of Illinois
Co-PIs: Madhu Khanna, Thomas Theis, University Indirect Land Use Implications of Biofuels
of Illinois Programs
Graduate Student: Xiaolin Ren Principal Investigator: Michael O’Hare, UC Berkeley
The Impact of Global Trade in Biofuels on Water
Scarcity and Food Security in the World
Principal Investigator: Ximing Cai, University
of Illinois
Co-PIs: Siwa Msangi, Tingju Zhu, International
Food Policy Research Institute
Graduate Students: Yan Sun, Dingbao Wang
Interactions Between Bioenergy, Carbon
Allowances, and Water Quality BMPs: A Case
Study of the Lake Bloomington Watershed
Principal Investigator: Ximing Cai, University
of Illinois

Research Staff: Jody Endres
Postdoc: Atsushi Oyama
Graduate Students: Christopher J. Miller, Molly
Novy
Economic and Environmental Impacts of Biofuels;
Implications for Land Use and Policy
Principal Investigator: Madhu Khanna, University
of Illinois
Co-PIs: Atul Jain, Hayri Onal, Yanfeng Ouyang,
Jurgen Scheffran, University of Illinois
Postdocs: Haixiao Huang, Seungmo Kang
Graduate Students: William Bowser, Xiaoguang
Chen, Matthew Erickson, Shahnila Islam, Christine
Lasco, Deniz Tursun, Xiaojuan Yang
62 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Food Security Management in an Era of Biofuels
Principal Investigator: Brian Wright, UC Berkeley
Italian Visiting Professor: Carlo Cafiero
Graduate Students: Fei Han, Di Zheng
Intellectual Property Protection and Contractual
Relations for Biofuels Innovations
Principal Investigator: Brian Wright, UC Berkeley
Researcher: Josephine Mutugu
Graduate Students: Kryiakos Drivas, Zhen Lei
Undergraduate Student: Astrid Sky
Co-PIs: John Braden, Wayland Eheart, George
Czapar, University of Illinois
Graduate Students: Tze Ling Ng, Aras Zygas,
Jude Tate
Market Context for Biofuels Microeconomics
Principal Investigator: Hadi Esfahani, University
of Illinois
Co-PIs: Clifford Singer, John Vasquez, University
of Illinois
Graduate Students: Esra Ergul, Thorin Wright
EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL 63
 Biocatalysis Cellulose Feedstock Intellectual Property
The stimulation of a chemical
reaction by a biochemical agent
A Glossary of Bioenergy Terms All higher plant cells are enclosed
in cell walls composed primarily
A raw material from nature that is
in an unprocessed or minimally
So-called “creations of the mind”—
in the case of the EBI, inventions
such as an enzyme. of polysaccharides (polymers processed state and can be acted and new technologies—around
of sugar) and lignin (a polymer upon or used by organisms to which various rights are provided
of phenolics). The principal cell create a product. Biofuel feedstock for the inventor. Legal protections
Biodiesel wall polysaccharide is cellulose, include grasses, wood, corn, give the patent holder the right to
A fuel that is chemically a fibrous material composed of sugarcane, sorghum, and other control reproduction or adaptation
compatible with diesel refined hydrogen-bonded chains of the plant sources. of such creations for a certain
from petroleum but is derived sugar glucose. period of time.
from biological sources such as
rapeseed, soybean, and even waste Greenhouse Gases
oils, grease, and tallow. Cellulosic Biomass The gaseous constituents (water Life Cycle Analysis
The fibrous, woody, and generally vapor, carbon dioxide, methane, The investigation and valuation
inedible portions of plants that nitrous oxide and ozone, among of the environmental impacts of a
Biofuel make up 75 percent or more of the given product or service caused or
others) of the atmosphere, both
A fuel made from biological plant material. natural and human-made, that necessitated by its existence. The
matter. The term usually refers to term “life cycle” refers to the notion
absorb and emit radiation within
liquid fuels rather than materials that a fair, holistic assessment of,
Cellulosomes the spectrum of thermal infrared
such as wood. for example, biofuel development,
radiation emitted by the Earth’s
Complexes of enzymes created by surface, the atmosphere itself, and requires the assessment of raw
Biomass bacteria, but functioning outside clouds. While greenhouse gases material production, manufacture,
the cell. They assist in digestion or are essential to maintaining the distribution, use and disposal
Living or recently living biological degradation of molecules such as including all intervening transpor-
materials that can be used as fuel; temperature of the Earth, an excess
cellulose. of greenhouse gases can raise its tation steps necessary or caused by
usually refers to plant matter. the biofuel’s existence.
temperature, thus causing climate
Deoxygenation change and the resultant impacts
Bioprospecting on land and environment. Lignin
The removal of dissolved oxygen
The process of searching for and from a substance. A compound that accounts for
extracting previously unknown roughly 25 percent of the plant
compounds and plant-derived Hemicellulose
material that provides rigidity,
chemicals in organisms. Depolymerization Heteropolymers (having many
and together with cellulose and
Breaking down molecules into con- different sugar monomers, that
hemicellulose forms the cell walls
stituent parts. In biofuel feedstock, may include xylose, glucose,
Carbon Neutral arabinose, and others) present in
and the glue that binds them; an
using the tools and techniques of excellent fuel for providing heat,
A product or process that does not biology and chemistry to convert plant cell walls along with cellulose.
add more carbon dioxide (CO2) to steam, and electricity.
polysaccharides like cellulose and While cellulose is crystalline,
the atmosphere over its life cycle. lignocellulose into monosaccha- strong, and resistant to hydrolysis,
For instance, a plant consumes rides, or sugars, which then can be hemicellulose has a random, Microbially Enhanced
CO2 when it grows, then releases fermented into a fuel. amorphous structure and is easily Hydrocarbon Recovery
it back out when it is transformed hydrolyzed by enzymes. (MEHR)
into and used as fuel.
Energy Bioscience Also called MEOR (oil recovery),
High-Throughput using microbes to enhance recovery
Carbon Sequestration The field of scientific study that of fossil fuels.
seeks to discover ways to adapt Genome Sequencing
The capture and long-term storage Various technologies that are
knowledge of biological processes
of CO2 before it is emitted into employed to lower the cost of
and materials to the development
the atmosphere, such as a system gene library sequencing, allowing
of improved technologies for
that separates CO2 out of coal-fuel the large-scale production of
energy production.
emissions and pumps it deep thousands or millions of sequences
underground. at one time. DNA sequencing
Ethanol encompasses biochemical
Cellulases One of the most common types methods for determining the
of biofuels, a liquid commonly genetic “blueprint” of organisms
A class of enzymes produced
produced by fermentation of sugar; by defining the order of their
chiefly by fungi and bacteria
also known as grain alcohol. nucleotide bases.
that catalyze the hydrolysis, or
breakdown, of cellulose.

64 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT A GLOSSARY OF BIOENERGY TERMS 65

 Miscanthus
A genus of about 15 species
of perennial grasses whose
productivity, biomass yield, and
growth capability on marginal lands
makes it a prime candidate for
development as a biofuel feedstock.
The most widely used “species”
is Miscanthus x giganteus, often
referred to as “Miscanthus,” which
is a sterile hybrid of Miscanthus
sinensis and M. saccharifolius. These
species can be found throughout
East Asia, from Papua New Guinea
to southern Siberia, and through
Japan and Taiwan. Because of their
stature and silver flowering heads,
all three are popular garden plants
found in gardens throughout North
America and Europe.
Net Energy
A fuel’s energy, minus what is
required to produce or obtain it.
For instance, the net energy of
gasoline is reduced by the energy
lost in extracting oil from the earth,
refining it, and transporting it to
consumers.
Polysaccharides
Complex carbohydrates, such as
starch and cellulose, consisting
of a number of monosaccharides
(sugars) joined together in long
chains of molecules.
66 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT
Second Generation Sustainability
Biofuels The capacity to maintain a certain
First generation biofuels, like process or state indefinitely. To
bioethanol, are produced by be sustainable, nature’s resources
fermenting plant-derived sugars must only be used at a rate at
in a process similar to that used in which they can be replenished. A
making beer and wine. This requires sustainable biofuel feedstock is
the use of food crops like sugar one that requires little energy input
cane and corn. Second generation and produces few byproducts that
biofuels, like cellulosic ethanol, are impact the environment.
those produced sustainably with
biomass comprised of the residual
non-food parts of current crops Xylose
and others, like grasses, grown for A sugar with five carbon atoms
non-food purposes. (“C5”) in each molecule, found in
the cell walls of plants. Other sugars
commonly found there include
Synthetic Biology arabinose, mannose, galactose,
The design and construction of new fucose, rhamnose, galacturonic
biological entities such as enzymes, acid, and glucose, among others.
genetic circuits, and cells, or the
redesign of existing biological
systems; builds upon advances in
molecular cell and system biology.
Switchgrass
A warm season grass (scientific
name Panicum virgatum) that
is one of the dominant species
of the central North American
tallgrass prairie. Properties that
make it a strong candidate for
biofuel production include
survival in drought conditions,
perennial habit, and low nitrogen
requirement when harvested in
the fall.