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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
01
c h a p t e r

Translating the Vision into Reality


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

Chris Somerville

2 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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
02
c h a p t e r

The EBI at 1 Year Old—


a BP Perspective
By PAUL WILLEMS
Associate Director, EBI year, we have already seen the fruits of this philosophy
Technology Vice President, Energy Biosciences, BP as we have been approached by various agencies
When BP decided to create the Energy Biosciences involved in policy-setting to provide assistance in
Institute in partnership with the University of “getting to the bottom” of the various debates taking
California at Berkeley, the University of Illinois in place.
Urbana-Champaign, and the Lawrence Berkeley Next, collaboration. The EBI is a public/private
National Laboratory, we had several objectives. As we collaboration of unprecedented scale and scope. The
reach our first anniversary, it is a good time to reflect EBI is a mission-oriented, multidisciplinary, team-
on how we have done so far. science-based institute. These are new expectations
Our goals can be categorized in three groups: science, for most of our collaborators, as well as for the
collaboration, and people. partnering institutions. While change brings a certain
amount of uneasiness, it also brings excitement: new
Let’s start with science. The creation of the EBI was possibilities, new relationships, new perspectives, new
rooted in a belief that modern biology as a science innovations. Even as we are just getting under way
is ready to start making significant contributions to in our first year of operation, we have already seen
energy problems. Lignocellulose-based biofuels have the kinds of examples we were hoping for: science
come a long way, and the first commercially viable taking an unexpected turn, and new dialogue between
processes (at least in the current environment of individuals who had never worked together leading to
high energy prices) are starting to emerge. However, new avenues of investigation.
tremendous scope exists for further technical
innovation, and the processes we will employ in 10 And last but not least, people. Great people are the
years’ time likely will bear little resemblance to these foundation of great work. On the backs of our partner
first installations. institutions, we have been able to create a great
reputation for the EBI. Not a week goes by without an
We have chosen to engage in a broad research important visitor to the EBI from somewhere around
portfolio, spanning the entire field addressing the globe. Our reputation has allowed us to tap into the
dedicated energy crops, their management practices, great talent pool on our campuses. It is also our calling
the technology used to convert them to fuels, card for attracting future students and researchers.
a variety of target fuel molecules, chemical and Part of the vision for the EBI was to create a talent
biological conversion pathways, etc. In doing so, pool for a future energy biosciences-based industry.
we have assembled a great team of researchers, led This is obviously important to BP as we try to grow
by distinguished faculty members at our partner our own internal technical capability in this area. It is
institutions. While these partners had some a priori equally important to the wider world. We anticipate
idea of faculty members interested in the field, we have that in due course this will result in a formal energy
been pleasantly surprised at the level of engagement in biosciences curriculum, at both the undergraduate and
the community. Many faculty members are involved graduate level, at our partner institutions.
with the EBI today who were not on the radar screen
initially. In summary, I would say we can be very proud of our
first year. We have a great portfolio of research projects
Our investment in socio-economic research is one of in place. We are continuing to create the collaborative
the features that makes the EBI unique: biofuels done and multidisciplinary environment envisioned for the
the right way is of crucial importance to us. A clear EBI. We are positioned for successful collaboration
focus on moving the debate in this arena from opinion- and delivery of great innovation in years ahead. We
based to fact-based is the mantra of the EBI. In our first couldn’t have asked for much more than this.

6 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT THE EBI AT 1 YEAR OLD—A BP PERSPECTIVE 7
03
c h a p t e r

ENTER BP Laboratory and the University of Illinois at


Urbana-Champaign to host the new Energy
The multinational company BP was the Biosciences Institute (EBI), and a new era of
first major energy corporation to publicly groundbreaking public-private partnerships
recognize that continued burning of fossil was launched. Following a period of contrac-
fuels was problematic. In 1998 in a speech at tual negotiations, the EBI began operations
About 87 percent of human energy use
Stanford, BP Chief Executive Officer John in November 2007.
is presently obtained by combustion of
Browne committed the company to comply
fossil fuels. This dependence on fossil
internally with the Kyoto Protocol. “It would
fuel has increased the amount of carbon AN INSTITUTE
be unwise and potentially dangerous to
dioxide in the atmosphere by about ignore the mounting concern” about climate OF COLLABORATIONS
one-third since the preindustrial era. It is change, said Browne. As a result, BP created
now apparent that continued dependence a renewable energy division that has grown An overriding goal of the EBI is to develop
on fossil fuels is causing climate change, to become one of the largest photovoltaic an integrated holistic understanding of the
and that the consequences are both and wind energy producers in the world. research topics related to energy biosciences.
uncertain and unwelcome. If global More recently, Browne’s successor, Tony The motivation for this arises from the
climate models are correct, temperatures Hayward, has called for the implementation recognition that topics of interest such as
will increase and rainfall patterns will of a cap-and-trade system in which emissions cellulosic biofuels are unusually complex and
change with devastating effects on food of greenhouse gases are monetized so that involve research questions in subjects that
production in many areas of the world the environmental costs and benefits of include agronomy, microbiology, mechanical
various energy options can be factored into and chemical engineering, biochemistry,
along with the potential for attendant
the cost of energy. chemistry, geography, economics, law and
societal disruptions. Also, many of the
policy analysis. Because advances in one area
world’s ecologically sensitive areas may may have important impacts in other areas,
In 2006, as part of its overall strategy for
be unable to support the species that the EBI’s goal is to create dynamic intellec-
developing renewable energy sources, BP
currently define the ecological character tual bridges between the various disciplines
issued an international call for proposals to
of the region and may be lost along engage in a 10-year, $500 million research so that information and insights flow
with potentially devastating effects of partnership to explore the application of sci- efficiently, and new research initiatives can be
biodiversity. These are the changes entific advances in basic biological sciences adopted based on a “big picture” view of the
forecast by the most recent Scientific to the energy sector. This bold concept was overall topic. To this end, the EBI is working
Assessment of the Intergovernmental based on the recognition that our under- toward placing the full-time researchers
Panel on Climate Change (IPCC). The standing of biology is undergoing a revolu- that it supports into a common space on
realization that the polar ice caps are tion in which major discoveries are being each campus. This is facilitating horizontal
currently melting at a faster rate than made on a daily basis. This is supported by a integration of disciplines, which range from
forecast by this assessment underlines series of technical and conceptual advances genomics and agronomy to environmental
the urgency of addressing net carbon in subjects such as genomics, computational sciences and economics.
emissions. biology, synthetic biology and analytical
chemistry that have become the major tools This multidisciplinary approach will facilitate
of discovery in many areas, especially in the discovery and will ultimately enable optimal

THE ENERGY medical sciences. By contrast, the area of decision-making by the sectors in society
“energy biosciences” is relatively unexplored that are responsible for implementing
and underinvested compared with the vast trade and regulatory policies and business

BIOSCIENCES INSTITUTE investment that has been made in health-


related aspects of the biosciences.
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
Empowering outstanding academic researchers to envision In 2007, following an international com-
opportunity to accelerate the feed-forward
petition involving about 20 major research
and enable new approaches to the production of energy universities, BP selected a consortium and feedback processes that are associated
consisting of the University of California with conversion of academic discovery into
at Berkeley, Lawrence Berkeley National real-world applications.

8 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT ABOUT THE ENERGY BIOSCIENCES INSTITUTE 9
The Areas of Study
environments where biomass degradation takes place. In parallel, it is also
The primary initial thrust of EBI research is an exploration of the feasibility of commercially exploring the development of new synthetic catalysts that can accelerate
viable, sustainable and environmentally benign transportation fuels from biomass. The most the degradation of polysaccharides and lignin.
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 Biofuels Production: Transforming Feedstock
methods of breeding, propagation, planting, harvesting, storage and processing; and ensuring An overriding goal to Fuel with Microbes
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 of the EBI is to develop an In order to convert sugars to liquid fuels, the proportion of oxygen
fuels technologies that yield major benefits in regard to both net energy output and net must be reduced. This can be accomplished by bioconversion, such as
integrated holistic understanding fermentation, or by chemical transformations. With no clear front-runner
greenhouse gas balance based on consideration of all inputs.
at the present time, the EBI is exploring several methods in parallel.
To accomplish this, research is divided into several areas of inquiry:
of the research topics related
Methods used for production of biofuels today are similar to the
to energy biosciences. fermentation practices used to make beer and wine, but these traditional
Societal and Economic Impacts of Biofuels
methods are not optimized for the large-scale, energy-efficient produc-
A major goal of the EBI is to understand the potential environmental, economic, and societal tion of cellulosic biofuels. EBI researchers are exploring ways of improv-
impacts of meeting a growing portion of the world’s energy needs through cellulosic or ing bioconversion of sugars to next-generation fuels by using the methods
algal biofuels. Many in the world are concerned that the demand for energy is so large that of systems biology to characterize new types of microbes and by testing
unrestrained conversion of land to biofuel production could have negative environmental genetic modifications of promising organisms. They are particularly
effects and could further disadvantage many poor people by increasing prices for food, feed, interested in exploring ways of producing biofuels that will not require
and fiber. Therefore, the EBI is working to understand how land is used around the world and major changes in the transportation infrastructure. This involves research-
to model the impacts of growing bioenergy crops on land that is not used for food production ing chemical and fermentation routes to products more hydrophobic than
or is providing key ecosystem services, such as carbon storage or biodiversity. ethanol and butanol. The EBI is also interested in exploring alternatives to
bioconversion technologies, such as the use of non-biological catalysts to
EBI investigators are also testing the environmental impacts of various bioenergy crops and transform biologically derived chemicals into fuels.
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 Microbiology of Fossil Fuel Reserves
incorporate both direct and indirect effects of the biofuels.
During the past several decades, it has become apparent that significant
populations of microorganisms are found in both coal and petroleum
Feedstock: Agronomy, Engineering, and the Environment reservoirs deep underground. These microbial populations can contribute
to the properties of the reservoirs in deleterious ways, such as through
Work in this area seeks to identify and characterize plant species that can maximize cellulosic catalyzing the souring of petroleum, but they may also contribute
biomass production in various regions around the world, and to learn how to grow and positively by activities such as altering the porosity of the reservoirs. This
harvest them sustainably. A primary goal is to discover plants that maximize the production could allow more efficient recovery of oil. In order to understand the
of cellulosic biomass, using minimal land, water, and energy. Because of the importance of effects of these microbial populations, the EBI intends to support studies
soil carbon in the global greenhouse gas balance, the EBI is particularly interested in identify- into characterization of the organisms found in various reservoirs using
ing species that can be grown on the large amounts of minimally productive land around the the tools of modern biology, such as high-throughput DNA sequencing
world. These considerations favor the use of perennial grasses and certain woody species. and analysis. By understanding the genomics of the reservoir microbes,
However, the possible utility of algal species is also being explored. 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
Bioconversion: Attacking Cellulosic Degradation on Several Fronts reservoirs that have been geologically characterized.
The main constituents of the body of higher plants are polysaccharides and lignin. Fashioning
fuel from plants requires conversion of the polysaccharides to sugars by severing the chemical
bond that holds them together, among the most critical and difficult steps in the process.
Today’s practices are costly and inefficient. EBI scientists are investigating nature’s methods
of releasing these sugars to achieve an effective and less costly method of breaking down
these substances. This will be key to ensuring that biofuels can be reasonably priced. The EBI
is examining the processes that take place in cow rumen, termites, compost heaps, and other

10 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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
THE RESEARCH ENTERPRISE—
funds are allocated to various topics based on predefined targets. PUBLIC AND PRIVATE
Workshops are scheduled throughout the year to share data and to help
define key questions to be answered. Topical proposals that address Openness of the research enterprise—and the
problems defined by the EBI are solicited from faculty and scientists in academic freedom of its faculty, graduate students, and
the partner institutions. Thus, the EBI mandate defines the problem, university researchers—is paramount for the three
but the EBI investigators propose the research approaches to solutions. public institutions in the EBI. Inventions made during
A peer-review process narrows proposals drawn from solicitations to a the course of research within the EBI are owned by
focused set of projects and programs for funding. the academic institutions according to U.S. patent law,
and BP receives an automatic non-exclusive license
During the startup phase of the EBI in the summer of 2007, a very in return for funding the research. All four partners
broad solicitation was announced. From an initial list of more than 250 have representation in the EBI’s two management
pre-proposals from researchers at the three partner institutions, EBI panels, with none having a majority or veto power
management and advisors requested 85 full research proposals and, on the governing board, ensuring consensus in all
following external peer review, narrowed the field to 50 high-priority decisions. The Executive Committee, which provides
research efforts that received the first round of funding. A second scientific direction and operational oversight, is mostly
solicitation in the summer of 2008 was more narrowly focused. Awards composed of professors from the academic partners.
are divided into two categories: programs and projects. Programs are
typically large integrated multi-investigator efforts with broad goals, The Licensing Executives Society, a professional
funded at anywhere from about $400,000 per year up to about $1 million organization for intellectual property specialists, chose
per year, and may continue for the 10-year life of the institute. Projects the EBI for its 2008 “Deal of Distinction” award for
are smaller activities of 2-3 years in duration that are usually narrower in being “an innovative model for collaboration between
scope. These average about $150,000 per year. academia, government labs, and industry.”

Program research is conducted mostly within EBI space so that post- Collaborative research between universities and
doctoral, support, and graduate student researchers from different industry yields new ideas and more effective pathways
disciplines will work side-by-side, and so that space constraints will not for moving discoveries from the laboratory into com-
limit the ability of EBI investigators to participate in the EBI mission. This
will facilitate synergy across fields and will provide a training environment The close association within the EBI
and a broad appreciation of the scientific, technological, environmental, of university academics and industrial
economic, and policy issues that must all be addressed to achieve the managers from BP offers a rare opportunity
Institute’s goal of environmentally sustainable bioenergy.
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.

12 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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 The University of California, Berkeley


BP, one of the world’s largest energy companies, is Founded in 1868, the University of California, Berkeley,
the leading producer of oil and natural gas in the is the nation’s top-ranked public university and the flag-
United States, and the largest investor in U.S. energy ship of the 10-campus University of California system. It
development. BP provides its customers with fuel for enrolls over 24,000 undergraduates, distributed among
transportation and energy for heat and light, employ- UC Berkeley
80 degree programs, and more than 10,000 graduate
ing more than 100,000 people worldwide and more students each year. The campus not only produces more
than 35,000 in the U.S. BP was the first major energy PhDs than any other university in the country, but a
company to acknowledge the need for precautionary greater number of its graduates go on to earn a PhD at
action to reduce greenhouse gas emissions, and today Berkeley or elsewhere than do graduates of any other
it continues to lead the effort to meet the world’s institution. The university is distinguished by its research
growing demand for sustainable, environmentally programs, which were funded in fiscal year 2006 by $469
responsible energy. 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
The University of Illinois and 29 MacArthur “genius” Awards. Of its academic
at Urbana-Champaign staff, more than 130 are current members of the National
Academy of Sciences, and 85 belong to the National
The University of Illinois at Urbana-Champaign is a
Academy of Engineering.
world-class public university whose faculty, student,
and alumni honors have brought international
distinction. Home of the largest public university Lawrence Berkeley National Laboratory
library collection in the world, Illinois is also a
leader in supercomputing design and application Lawrence Berkeley National Laboratory (Berkeley Lab)
and boasts multi-disciplinary research excellence has been a leader in science and engineering research Berkeley Lab
in dozens of fields. The University has a pioneering for more than 75 years. Located on a 200-acre site in the
history of sustainability research as the originator of hills above UC Berkeley’s campus, the Lab is the oldest
no-till agriculture, and is home to the longest running of the U.S. Department of Energy’s national laboratories.
investigation of the impacts of varied crop manage- Managed by the University of California, it operates
ment methods on soil quality (1876, Morrow plots) with an annual budget of more than $550 million and
outside of Europe. Founded in 1867, Illinois enrolls a staff of about 3,800 employees, including more than
over 29,000 undergraduates in more than 150 fields 500 students and 250 principal investigators with joint
of study, and over 11,000 graduate and professional appointments at UC Berkeley. It employs a “team”
students in over 100 programs. It is among the top concept to its research, as developed by founder Ernest
five universities in the United States in the number Orlando Lawrence, and boasts a legacy that has yielded
of annual doctorates awarded. Among its array of rich dividends in basic knowledge and applied technol-
faculty honors, the U of I is one of only 11 campuses ogy, and a profusion of awards. Berkeley Lab conducts
worldwide to have been awarded two separate Nobel unclassified research across a wide range of scientific
Prizes in one year (2003). 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

14 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT ABOUT THE ENERGY BIOSCIENCES INSTITUTE 15
The Facilities 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
From the hills of Berkeley to building in the heart of the University of Illinois campus. A 320-acre Energy Farm, the
the farm fields of Illinois, EBI largest of its type (just south of the Illinois campus), includes land for demonstrations,
research spans the nation— large-scale production, plant breeding and storage. In 2008, 120 acres of this farm were
and the world. planted, and another 160 are slated for development in the near future.

The Berkeley center includes dedicated biotechnology laboratories and specialized


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

16 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT ABOUT THE ENERGY BIOSCIENCES INSTITUTE 17
The Directors
EBI Administrators construction, engineering, and
Chris Somerville, Director and Managers operation of the Energy Farm at
Illinois. He previously constructed
Somerville is a professor in the Department of Plant Assistant Director Susan Jenkins and managed SoyFACE, the largest
and Microbial Biology at UC Berkeley and a faculty manages the administrative team open-air facility for investigating
scientist at the Lawrence Berkeley National Labora- for the EBI at Berkeley and oversees the effects of global atmospheric
tory. His research focuses on the characterization of all aspects of implementing change on crops, and before that
proteins implicated in plant cell wall synthesis and the activities sponsored by the he ran the University of Maryland’s
modification. He has published more than 200 scien- institute. Before joining the EBI, controlled environment plant
tific papers in plant and microbial genetics, genomics, she was the assistant chair of the growth facility. Safety and building
biochemistry and biotechnology. Somerville has served Department of Plant and Microbial manager Zack Phillips was a
on the scientific advisory boards of many corporations, Biology at UC Berkeley. Deputy radiation safety officer at UC
academic institutions and private foundations in Europe Assistant Director Jenny Kokini Berkeley before joining the EBI’s
and North America. He is a member of the U.S. National manages the implementation of Berkeley staff. He is paralleled at
Academy of Sciences, the Royal Society of London and all EBI activities at the University Illinois by Safety Officer John
the Royal Society of Canada. of Illinois. She moved to the EBI Pingel, who coordinates safety
from Princeton University, where training and implementation
she was the departmental business for the farm and laboratory. He
Stephen Long, Deputy Director administrator for Mechanical previously coordinated safety at
and Aerospace Engineering. the U of I’s chemistry labs, is a
Long is the Robert Emerson Professor of Plant Biol- Professor Brad Moore, an emeritus primary author of the “Science
ogy and Crop Sciences at the University of Illinois. He professor of chemistry, is the Safety Handbook for Illinois
is a researcher with the U of I’s Institute for Genomic manager for Strategic Planning. Schools,” and is principal lecturer
Biology and a resident scientist with the National Center He has extensive experience in the Illinois “Fundamentals of
for Supercomputing Applications. Much of Long’s in academic administration, Laboratory Safety” class. Stefan
research focuses on the effects of atmospheric change on including most recently serving as Bauer manages the Analytical
vegetation and ecosystems and on how certain perennial the vice president for research at Services group at the EBI. Before
crops might be used as biomass energy sources. He was a Northwestern University. Mitch joining the Institute, he was the
contributing author and referee to the Intergovernmental Altschuler manages processes head of analytical chemistry at
Panel on Climate Change, and he has served on com- related to Intellectual Property. He Fresenius. Mara Bryant and
mittees worldwide that research global climate change. was formerly a professor of biology Rachel Knepp are laboratory
He has been named one of the 250 most cited authors at Northern Illinois University and managers for the EBI at Berkeley
in animal and plant biology and one of the 25 most cited has also worked in the technology and Illinois, respectively. Bryant
authors on global climate change. Long is a Fellow of the transfer offices of the University recently completed postdoctoral
American Association for the Advancement of Science. of Minnesota and Cargill, studies in biology at Michigan
Inc. Computing systems and State University, and Knepp
networking specialist Adam Cohen completed an MS in global change
Paul Willems, Associate Director moved from the UC Berkeley impacts on forests and was a USDA
As Technology Vice President for Energy Biosciences in web applications team to become laboratory manager before joining
BP, Willems is responsible for integrating biotechnology Information Technologies manager. the EBI. Anne Krysiak and Trisha
into BP’s business activity. His duties include leading Ron Kolb is the communications Togonon at Berkeley and Becky
the development and execution of an integrated manager. Before joining the EBI, Heid and Connie Wilder at
technology strategy which incorporates all of BP’s bio- he was communications director Illinois provide a wide range of EBI
related activity and which is fully integrated with BP’s for Lawrence Berkeley National administrative services and assist
company-wide business strategies. He has held a variety Laboratory. Melissa Edwards is investigators in interactions with
of technical, manufacturing and commercial leadership his counterpart at the University other service providers within the
roles throughout his 20-year career, including business of Illinois. Deputy Operations host institutions.
technology manager for BP’s global PTA (purified Director Tim Mies manages the
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 From left, Willems, Somerville, and Long ABOUT THE ENERGY BIOSCIENCES INSTITUTE 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 Corn (Zea mays) is the largest U.S. crop with about
81 million acres planted in 2005, yielding about
involved in current biofuel production 11.1 billion bushels of corn seed. Approximately 60
percent of the mass of corn seed is starch. The starch
is important if improvement is to be is released by grinding the seed in either a dry or wet
process, cooked to gelatinize the starch, hydrolyzed
achieved in the second generation. 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 BIODIESEL than 1,500 gallons of cellulosic significant energy inputs for CELLULOSIC ETHANOL
ethanol production is mature, and most of the ethanol. Additionally, vegetable production. In addition, mature
technical issues concern improvements in engineering A wide variety of chemicals or oils are a quantitatively important plantations reportedly produce All higher plant cells are enclosed in cell walls
related to the efficient use of heat and water. However, mixtures of chemicals, including component of human diets up to ten metric tons per hectare composed primarily of polysaccharides (polymers of
unlike cane ethanol, which has an energy output-input biologically produced fatty acids and, therefore, relatively small per year of cellulosic biomass (e.g., sugar) and lignin (polymer of phenolics) that, in many
ratio of about 8-to-1, calculations of the life cycle or lipids, undergo combustion disruptions in supply result in senescent fronds) that can also plant species, comprise more than 90 percent of the
costs of making corn ethanol have stirred substantial in conventional diesel engines. large increases in price because of be used for fuel production. Thus dry body mass. The principal cell wall polysaccharide
scientific debate. These calculations typically include The methyl or ethyl esters of inelasticity of food demand. oil palm acreage has continued to is cellulose, a fibrous material composed of hydrogen-
things such as the energy costs of producing and biologically derived fatty acids expand due to increasing demand bonded chains of the sugar glucose. Cellulose is coated
distributing fertilizer, of planting and harvesting, of are capable of being mixed with The U.S. Congressional Research for edible oil and for projected use with another class of polysaccharides called hemicellu-
making the farm machinery and the factories that petroleum-based diesel fuel. These Service conducted a study that in biodiesel. lose, the most abundant of which is xylan, a polymer of
process the grain, in addition to the costs of converting esters can be produced from concluded if every ounce of plant xylose that may, depending on the plant species, have
grain to ethanol. The results have been controversial biological lipids or fatty acids and animal lipid produced in However, the expansion of palm branches containing other sugars such as arabinose or
because of the uncertain assumptions about variables, by very simple reactions. Thus, the United States was used for production is generally considered glucuronic acid. The principal sugars in most tissues
such as heat reuse. establishing a commercial biodiesel biodiesel production, the total undesirable from an environmental that are useful for biofuels are glucose and xylose,
but many other sugars are also present in significant
"Cellulosic biofuels will have the greatest environmental benefits if produced on land amounts. Cell walls from vascular tissues usually also
that has been farmed in the past but is contain lignin, a complex polymer.
A recent analysis of all such calculations concluded
that corn ethanol provides about 25 percent more
no longer used for food production." These structural polysaccharides are less readily
energy than is consumed in producing it if the process hydrolyzed to sugars than storage polysaccharides such
heat is provided by natural gas or coal (versus burning ~ CHRIS SOMERVILLE as starch. Acids are being used to obtain sugars from
the cobs and stalks). Because of the low net energy celluloses, but this is inefficient. Efficient hydrolysis
ratio, corn ethanol is generally not considered an production facility is inexpensive amount would be about four perspective, because the expansion occurs in nature, for example by bacteria and fungi in
attractive long-term solution to meeting energy needs and technically simple. billion gallons. When compared is associated with clearing of the digestive systems of animals, such as ruminants
in an environmentally sustainable way. with the roughly 200 billion tropical forests that are some of the and termites, who derive their energy from the sugars
The U.S. currently has a number gallons of liquid fuels used in the richest reservoirs of biodiversity. released from cellulose and hemicellulose. Replicat-
One development that may change this is carbon of small biodiesel production U.S. each year, domestic biodiesel Additionally, clearing of tropical ing this in industrial processing facilities would then
sequestration. In fermenting sugars to fuels, about 33 facilities, many of which derived from seeds and fruit forests causes large emissions of provide sugars that can be converted to ethanol or
percent of the carbon is released as pure CO2. Like a include used cooking oils from is not likely to be a significant greenhouse gases from both soil other fuels by fermentation in much the same way
number of other locations around the world, a large restaurants as feedstock. This contributor to transportation fuels emissions and from the burning of as cornstarch. However, because the whole plant can
area of the Midwest is underlain by deep saline aquifers is an environmentally and in the developed world, nor an the biomass, resulting in negative be used, the yield of sugar per unit of land per year is
into which very large volumes of CO2 may be dissolved. economically attractive use of a effective use of land. greenhouse gas balances for biofuel much higher than can be obtained using only corn
The aquifer is below shale and oil deposits that provide material that would otherwise production. grain.
additional seals against any release of “buried” CO2, be a waste disposal problem. In contrast to annual oilseeds,
which is why Illinois was chosen for the “Futurgen” However, domestic biodiesel will several tropical plants are used to Recent interest has been shown in No large-scale cellulosic ethanol facilities are yet in
clean coal plant. The U of I, together with Archer not become more than a niche produce relatively large amounts a drought-tolerant bush, Jatropha commercial production, although several companies
Daniels Midland and the Department of Energy, is component of the liquid fuel of lipids in tropical countries. Oil curcus, which reportedly yields have small-scale test production facilities. A typical
now operating a pilot burial of the CO2 produced from supply, because the amount of palm (Elaeis sp.), which grows up to several metric tons of oil pilot-scale process involves treatment of pulverized
fermentation in making corn ethanol. Life cycle analyses lipid produced per acre of crop is in high rainfall zones within 15 per hectare per year with little or biomass with hot acid, which partially hydrolyzes
suggest manufacture of cellulosic ethanol from low small relative to the total amount degrees of the equator, produces no input. This plant may allow hemicellulose and other polysaccharides and disrupts
perennial grasses could achieve input:output energy of biomass. Thus, for instance, clusters of oil-rich fruits that are production of oil on land that is the association of lignin with the polysaccharides.
and carbon ratios of 1:5. Coupled with CO2 burial, this the average soybean crop yields similar to small avocados. Yields too drought-prone for food crop The hydrolysate is neutralized, separated from the
raises the exciting possibility of being able to achieve a only about 63 gallons of biodiesel of up to seven metric tons of oil production, and acreage has been insolubles, and fermented to produce ethanol. The
carbon-negative biofuel. per acre. Contrast this with the per hectare per year have been expanding rapidly in Africa, India, insoluble fraction is then treated with cellulase and
much higher yields of cellulosic recorded, although the average is and Southeast Asia. glycosidases to release glucose, which is also fermented
There are also concerns that use of cropland for biomass that could be grown on lower. The plants have very long to produce ethanol. The residual insoluble material,
biofuels, whether corn or perennial grasses, will the same acres—estimated at more life cycles and do not require mostly lignin, could then be burned to generate energy
indirectly cause encroachment of agricultural for the overall process. The fermentation process pro-
production onto ecologically sensitive land. A major duces a nutrient-rich microbial cell mass that can be
effort of the Institute seeks to identify opportunities deactivated and used as fertilizer to recycle the mineral
to grow a range of perennial feedstock on abandoned nutrients to the land.
agricultural and non-crop lands to avoid such effects.

24 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT AN INTRODUCTION TO BIOFUELS 25


Many components of the cellulosic ethanol bioconver- organisms, by altering the chemical composition of the OTHER BIOFUELS
sion process are not yet optimized for commercial biomass, or by process improvements.
production. For instance, the strains of yeast that are Ethanol is not an ideal fuel in several respects and may not be the
used for industrial fermentations do not normally The development of a biofuel industry is only feasible major biofuel in 20 years. The main problem is its ability to mix with
utilize sugars other than glucose. Strains of yeast in regions where land and water resources are available water, which imposes an energy cost for distillation, creates problems
(Saccharomyces cerevisiae) and Eschericia coli have been to support the growth of plant biomass that is excess No miracles are in transporting the fuel via pipelines, and leads to poisoning of the
engineered to ferment xylose to ethanol, but additional to other needs. The Departments of Energy and Agri- microorganisms that produce it. Thus there is interest in developing
culture conducted a study of biomass availability and required to develop biofuels that are more hydrophobic and spontaneously partition out of
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 the aqueous phase. For instance, butanol dehydrates spontaneously at
ways, and to enable fermentation of other sugars. tons of excess cellulosic biomass is available each biofuels; however, about 9 percent solution, has very low vapor pressure, and has a latent
year in the U.S. This includes half the corn stover (the heat similar to octane so that fuel-air mixing at low temperature is not a
implementing rational
Another problem is that large amounts of cellulase leaves and stalks of the corn plant) and wheat straw, problem. When added to ethanol-gasoline mixtures, small amounts of
are required to hydrolyze cellulose. Process improve- and about 40 million acres of set-aside land to grow improvements in the butanol depress the vapor pressure, reducing the hazards of explosions
ments during the past decade have reduced the cost of perennial grasses such as switchgrass and Miscanthus. overall process is during fuel handling. Unfortunately, butanol is toxic to organisms that
cellulase per gallon of ethanol from about $5 to about At a conversion value of about 100 gallons of ethanol challenging. produce it at concentrations very much lower than 9 percent solution.
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 Several companies have recently announced plans to produce butanol by
widespread interest in finding enzymes with higher about 40 percent of U.S. liquid fuel consumption on an fermentation of sugars from biomass. Some microorganisms have been
activity than current cellulases by surveying the prop- energy-equivalent basis. reported to secrete alkanes, which do not mix with water. Plants and
erties of enzymes from poorly explored sources such other organisms have a wide array of lipid synthetic pathways, raising
as termite guts, rumen, compost heaps, and tropical Based upon the proportion of transportation fuel the opportunity for engineering these pathways into bacteria or yeasts.
forests. Alternatively, it may be possible to improve the already produced by Brazil, it seems likely that South It seems likely that additional types of biofuels with physical properties
activity of industrial cellulases by protein engineering. America could meet all its needs for transportation similar to those in current use will be developed.
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 Although much of the current research on cellulosic fuels is focused
plexes that catalyze hydrolysis of cellulose and other could produce approximately 11.7 exajoules (units of on bioconversion technologies, other approaches are being explored
polysaccharides. Industrial ethanol production has energy) per year of biofuels, an amount similar to the within the EBI. In particular, it is possible to convert biomass to liquid
used yeasts that ferment glucose. To make use of the U.S. goal of 30 percent of transportation fuels (11.6 fuels by direct chemical conversions using either gasification followed by
sugars derived from hemicelluloses, yeasts and other exajoules). re-forming of the gaseous products to fuels, or by chemically catalyzed
organisms are being engineered to use these sugars conversion of biomass to fuels. Because the mandate of the EBI is to
A recent study by ecologists at Stanford concluded that explore biological technologies, it is not pursuing research based on
as well as glucose. The holy grail of cellulosic ethanol
about a billion acres of land around the world that was gasification technologies. However, a number of EBI research groups are
production is to incorporate improvements in both
farmed in the past has been abandoned. It seems likely exploring the development of new catalysts for hydrolysis of biomass to
cellulases and fermentation into a single organism that
that much of this land could be used for production soluble molecules and conversion of such molecules to liquid fuels.
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 COORDINATION, INTEGRATION
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 The major opportunity to expand the use of biofuels will be found in
many plant polysaccharides, during biomass hydroly- significant component worldwide. The widespread improving the various components of cellulosic biofuels production. No
sis, release acetic acid that inhibits the growth of the implementation of trading in carbon credits could miracles are required to develop cost-effective cellulosic biofuels; a series
fermentative organisms. Similarly, furfural, an organic accelerate progress toward that goal and could encour- of two-fold improvements in the efficiency of various steps could make
liquid compound produced by a side reaction during age best practices in terms of land management and biofuels less expensive than liquid fossil fuels. However, implementing
acid-catalyzed polysaccharide hydrolysis, inhibits fuel production. rational improvements in the overall process is challenging. Managing
microbial growth. In principle, these and related the various components will have to be coordinated, integrating
problems may be overcome by developing resistant 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 but Kent thinks the prospects
believes that microbes are the most important are high. With the assistance
organisms in the world. She is especially high of two postdocs and two
on bacteria, the most abundant group of undergraduate students in her
organisms on the planet. And she thinks they laboratory, she hopes to build
could be key to the efficient productivity of a library of relevant bacteria
future biofuel feedstocks. and then apply them to
Miscanthus and other plants
“Microbes have the greatest reservoir of in the EBI Energy Farm.
genetic diversity on earth,” says the young She says she suspects that both growth and
microbial ecologist at the University of Illinois, sustainability will be improved.
Urbana-Champaign. “They can do incredible
things. It’s almost like they have superpowers. Kent’s early studies at the University of
They can find a way to make a living with any Wisconsin focused on a medical career,
kind of compound.” her fascination about microbes leading her

The EBI believes in Kent and her bacterial " They can do incredible things. It’s
troops, supporting a project that seeks to
exploit the nitrogen-fixing capabilities of almost like they have superpowers.
microbes to enhance the sustainability of They can find a way to make a living
bioenergy crops.
with any kind of compound."
“Production of nitrogen fertilizer requires a lot
into the study of pathogens and their role in
of energy input from fossil fuel,” Kent says. “It
causing disease. But applications to human
takes chemicals to make and farm machinery
health were long-term, and she admits to
to apply. But microbes can do that essentially
looking for something more immediate.
for free. If we can find conditions that favor
Environmental microbiology “felt much
bacterial nitrogen fixation in the plants, we can
more applied to me, looking at microbes
influence their long-term sustainability.”
involved in plant health. I knew I could make “In three years, we should have a pretty good idea of the inventory
The first step is to understand how the a difference,” she recalls. of microbes that work on Miscanthus, and we will be able to
association of certain bacteria with targeted demonstrate whether nitrogen fixation plays an important role.”
Now that difference might be the application
biofuel grasses will work, and then how that
of microbiology, and her “super” microbes,
association is affected by environmental
to the development and nurturing of a new
factors—water, climate, soil texture and
class of plant-based transportation fuels.
fertility, etc. Then there is the task of analyzing
the characteristics of individual microbes “In three years,” Kent says, “we should
through genetic phenotyping, searching for have a pretty good idea of the inventory of
the genes that are involved in the nitrogen microbes that work on Miscanthus, and we
production. Considering that there can be will be able to demonstrate whether nitrogen
millions of microbes in a gram of soil (such fixation plays an important role, as well as
as the samples seen at right), Kent’s task is what traits contribute to the colonization of
daunting. the plant.”
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 FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 33
Environmental and Life EVAN DELUCIA:
Cycle Analysis Reviving Depleted Agricultural Land—
A Biofuel Bonus?
The Environment Program is using the trials established by the Biofuels are often touted as a solution to rising oil prices and global climate change—but they could also help
Agronomy Program to provide the first actual measurements, as solve agricultural problems caused by centuries of land abuse. That possibility is being put to the test in the EBI
opposed to projections, of greenhouse gas balances and impacts research program being conducted by University of Illinois Professor Evan DeLucia, who is heading an investi-
on water availability and quality. 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
In 2008, large-scale (up to 10 acres each) replicated trials of Mis-
improve the health of our agricultural ecosystem.”
canthus x giganteus, switchgrass, mixed species restored prairie,
and continuous corn were established on the energy farm above Such an improvement is long overdue. Years of corn-
instrumented field drains that monitor the volumes of water, soybean rotation in the Midwest have eroded soil,
nutrients and carbon draining out of each crop. Simultaneously, polluted water, and disrupted carbon and nitrogen
using a technique known as eddy-covariance, the net fluxes of cycles. Continuing that cycle could spell disaster for
gases containing carbon and nitrogen emitted and absorbed farmland, while introducing new, low-maintenance
by these plots are being monitored continuously. This will be a crops like Miscanthus or switchgrass could replenish
unique data set, critical to constraining Life Cycle Assessment the nutrients that have been leached from the soil.
models and greenhouse gas balance models of the ecosystems
services provided by different biofuel cropping systems. It will DeLucia’s team is trying to turn these hypotheticals
also test the predictions that the group has already made using into hard facts. They have planted plots of four bio-
the state-of-the-art models of soil carbon balance in conjunction mass crops at Illinois’ new EBI Energy Farm—corn,
with consultant Bill Parton. Miscanthus, switchgrass, and mixed restored prairie
grass. “This is the first time that side-by-side compari-
These studies will also be vital to gaining informed Life Cycle sons of the ecology of different biofuel feedstocks will
Assessments (LCAs), an activity that is the focus of research by be conducted under realistic field conditions,” says
Arpad Horvath and Thomas McKone at Berkeley. A key motiva- DeLucia. As the crops continue to grow over their
tion for developing second-generation biofuels is to provide three-year establishment period, high-tech instrumen-
truly renewable liquid transportation fuel—fuel that may be tation will carefully monitor the plants’ effects on the
made without degrading the ability of the land to produce the A complementary project led by Ryan Stewart at Illinois is environment.
feedstock, and with a minimum of greenhouse gas emissions in focused on studying the effects on soil quality of stands of
their production, utilization and indirect impacts compared to Miscanthus in Japan that are more than 1,000 years old. And that effect is complex, to say the least. To provide
fossil fuels. Any new activity that is likely to impact the environ- a full sense of the crops’ impact, tests range from soil
ment, for better or worse, is typically subject to an LCA. An One of the key environmental issues surrounding production carbon measurements to energy exchange readings
LCA examines, in the case of a second-generation biofuel, the of biofuels concerns effects on water quality and availability. to analysis of arthropod activity. The variety of data
environmental costs and benefits at each step from the conver- Plants transpire enormous amounts of water during growth, requires researchers with all kinds of specialties: the
sion of land and planting of the crop through the combustion of and such water emissions can affect soil moisture and the EBI team includes ecologists, entomologists, physiolo-
the fuel. What are the inputs and outputs of carbon, energy and amount of water runoff that may support streams and lakes. The gists, and many others. Their program reflects the
other resources at each stage? Projections around farm opera- potential effects of cellulosic crops on water are being modeled unique interdisciplinary nature of EBI research. DeLu-
tions are currently hypothetical, because there have been no using climate and soil data in a collaboration between Carl cia, a plant biologist, calls working with scientists from
thorough measurements of greenhouse gas balances over these Bernacchi at Illinois and Tracy Twine at the University of Min- such diverse fields “invigorating and exciting” and says
new cropping systems and conversion operations. This is further nesota. In addition, a detailed analysis of the potential effects this breadth of experience can “provide deep insight
complicated by the fact that, as with any new technology in its on the well-characterized Lake Bloomington watershed is being into the sustainability of biofuel crops.”
infancy, there is uncertainty as to the appearance of the mature carried out by Ximing Cai, John Braden, Wayland Eheart and
technology. The experience gained on the energy farm will be George Czapar at Illinois. This isn’t the first foray into environmental research
critical to adding more substance and reality to LCAs 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,
Two major tasks of the Feedstock Programs on Agronomy, the possibility of using algae to produce biofuels. Preliminary and pollution. His previous research has shown him
Engineering, and Environment are 1) to actually measure analyses of the costs of fuels produced from algae indicate the pressing need for sustainable biofuels, and now
greenhouse gas and energy balances; and 2) to define the that there are challenges associated with bringing the costs of he hopes that biofuels could solve more than one
most sustainable farm operations and opportunities for land production in line with alternatives. To understand the oppor- environmental problem.
conversion that would maximize opportunities for sequestering tunity, the EBI is supporting a feasibility study by a large group
carbon from the atmosphere, as opposed to releasing carbon. of algal biologists led by Berkeley Lab scientist Nigel Quinn.

34 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT FEEDSTOCK: AGRONOMY, ENGINEERING, AND THE ENVIRONMENT 35
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

BIOCONVERSION: enzymes from several extremely thermophilic bacterial strains specifically


adapted for cellulose and hemicellulose degradation.

Attacking Cellulosic Degradation on Several Fronts 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

36 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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 learn how a fungus regulates genes responsible for cell led by principal investigators John Gerlt and John generated by protein engineering and synthetic
enzyme “cocktails” optimized for saccharification of wall deconstructing enzymes. Cronan in a program directed toward overcoming biology.
specific bioenergy crops with their subsequent conver- biomass recalcitrance as a key obstacle in biofuel
sion to alcohol fuels. Berkeley chemist Michelle Chang is taking a different production. The objectives of their program are to Projects under way at UC Berkeley headed by
approach—in order to explore mechanistic aspects of identify and characterize degradation pathways for Clark, Blanch, and Clayton Radke aim to develop
Another natural bioconverter that efficiently breaks how certain organisms degrade lignin, she is exploring lignin, characterize the enzymes that are involved in a comprehensive model of cellulose hydrolysis that
down and transforms plant biomass is the termite how to modify yeast and bacteria that are normally those pathways, engineer these enzymes so that they can be used to predict cellulase performance, guide
hindgut. In a program aimed at discovering novel unable to degrade lignin so that they are able to carry will have enhanced catalytic properties, and design cellulase design, and optimize the hydrolysis of various
enzymes capable of degrading wood lignocellulose, out the chemical transformations associated with new metabolic pathways in organisms so that biofuel cellulosic substrates, including those obtained from
Phil Hugenholtz and co-workers at the DOE Joint lignin breakdown. In this way she will test whether production can be enhanced. EBI investigators.
Genome Institute are performing metagenomic and our understanding of the pathway is correct and
bioinformatic analyses of several species of wood- also whether there may be opportunities to alter the In addition to soluble cellulases, some organisms As an important first step toward modeling cellulose
feeding and grass-feeding termites. These studies pathway for increased activity in industrial conditions. degrade cellulose using cellulosomes, which are com- hydrolysis and engineering improved cellulases, Clark,
will be complemented by functional screening of prised of cellulases organized in a complex assembly Blanch, and co-workers have isolated the individual
selected enzymes and characterization of the plant cell of enzymes and scaffolding on the bacterial cell components of the cellulase mixture secreted by the
wall polymers present in the food sources, hindgut

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

48 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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
MADHU KHANNA:
researchers with expertise and access to data Seeking a Biofuels Policy
Where Everybody Wins
that is relevant to understanding core issues.
Creating a national biofuels policy is tricky because it has to
ENVIRONMENTAL AND SOCIETAL work for diverse interests. Ideally, such a policy would cut oil
imports, curtail greenhouse gas emissions, and be profitable
IMPACTS OF BIOFUELS for agriculture. And, the biofuels policy can’t act as a drag on
Several research teams within the socio-economic program are assessing various aspects of the economy or limit food production.
the environmental and societal impacts of biofuels from an economic perspective. Atul Jain That’s a tall order. Nonetheless, an EBI research team has
is using biophysical models to assess the soil carbon sequestration potential and nitrogen waded into the debate by undertaking a massive study of the
requirements of biofuel crops. Khanna’s team is analyzing data on life cycle emissions in economic issues related to biofuel development.
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 “We should be able to assess the benefits and unintended consequences
and the costs of achieving mitigation. They find that biofuel production in Illinois, to meet 20 of biofuels policies as they stand today, particularly for the environment,”
percent of the ethanol mandate by 2022, has the potential to reduce cumulative greenhouse said Madhu Khanna, an environmental economist at the University of
gas emissions by 45 percent relative to baseline levels over the next 15 years by displacing Illinois at Urbana-Champaign and lead investigator for the EBI team.
energy equivalent gasoline, but that the enhanced production of corn ethanol to meet a part “And we should be able to determine how those policies might be better
of the mandate increases nitrogen use by 27 percent over this period. designed to achieve social goals.”
Using a macro-economic computable general equilibrium model of the U.S., John Braden’s To come up with a broadly acceptable biofuels policy, she and her
Illinois group is analyzing the efficient mix of biofuel pathways based on their economic and colleagues must collect huge amounts of research data, much of it dealing
environmental impacts which considers the trade-offs between reduced carbon emissions with the logistics of creating a massive new industry. “We need to know
due to biofuels and water quality degradation due to greater fertilizer use for some feedstock, how much switchgrass, Miscanthus, and crop residues can be grown or
such as corn. Zilberman’s team is developing ways to integrate economics into the methods collected in different parts of the country,” said Khanna. “We don’t know
currently used to assess life cycle carbon emissions of biofuels. The group is developing because we’ve never done it. We want to know how much carbon each of
measures that modify the standard life cycle analysis to reflect the effects of changing market those biofuel crops is going to sequester in the soil. And we want to know
conditions and policies on choice of production methods and carbon emissions. how much carbon will be produced (by) each crop.”
One of the complexities of understanding the life cycle aspects of various types of biofuels One complicating factor is a federal mandate that requires production of
is the recent recognition of potential indirect land use effects. The concept is that, because 36 billion gallons of biofuel annually by 2022. Of that, 21 billion gallons
demand for food is inelastic, if land is converted from food production to fuel production, must come from advanced biofuels—fuels which produce no more than
previously unused land will be converted to food production with attendant releases of half as much greenhouse gas as gasoline. “We want to find the lowest-cost
greenhouse gases. However, the situation is complex because demand for food can also be way we could meet that mandate,” Khanna said. “The first step is to figure
satisfied by increasing production on fewer acres in response to price signals. Michael O’Hare out where to grow corn, where to grow Miscanthus, and where to grow
and his Berkeley colleagues are working to develop economic models that can be used to switchgrass in order to meet the 36-billion-gallon mark.”
understand this issue quantitatively. Their findings may have important implications for
future policies that place economic value on greenhouse gas emissions. Ultimately, the team expects to give policymakers the information
they need to help craft a national biofuels policy that works for the
Another matter of potential concern regarding biofuels is the possibility that diversion of land environment, the economy, and farmers.
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 “Farmers won’t do this unless they see the right price signals,” Khanna
and operation of markets rather than about the availability of land. Berkeley economist Brian added. “The price signals provided by the market may not reflect the
Wright and colleagues are studying this issue, as are Ximing Cai at Illinois and collaborators various environmental effects of biofuels produced from different
Siwa Msangi and Tingju Zhu at the International Food Policy Institute. Much of the other feedstocks. So the government may have to provide appropriate
economics research in the EBI also impinges on this important question from various incentives so that farmers produce a sustainable mix of biofuel crops.”
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 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, Elementary and Middle Schools Bioenergy Crop Modeling and Land Use
EBI investigators attended national and At the other end of the spectrum, EBI graduate October 9-10, 2008
international symposia on relevant topics and student Becky Arundale and office manager Becky To understand bioenergy crop production potential
gave talks and poster sessions on the work Heid in Illinois have developed resources in col- in marginal and abandoned lands, a well-planned
being conducted in the Institute. They also laboration with a local teacher to explain the EBI to modeling and data analysis strategy is required. This
accepted invitations as lecturers in university elementary school students. EBI graduate student workshop was conducted to design a crop modeling
classrooms and at industry conferences. 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
EBI in Education
Recognizing the need for interdisciplinary information
In the decades ahead, the students of today will help
Cal Day “Voyage” exchange as well as collegial partnerships with parallel
to establish and maintain this new industry as well as
Berkeley students, as well as campus visitors during the groups, EBI management launched two internal
manage its impacts on global society. The EBI recog-
annual spring Cal Day open house program, learned seminar series in 2008 addressing the challenges,
nizes its role in educating and training these young
about Robert Swan’s “Voyage for Clean Energy” in two progress, and promise of biofuels research.
researchers so that they are prepared for the coming
bio-revolution. Nearly 200 graduate and undergradu- talks sponsored by the EBI. Explorer Swan, one of the
Biweekly presentations from researchers in EBI-
ate students and postdoctoral scientists were engaged few to have successfully walked to both the north and
supported programs and projects have been held in
in EBI programs during its first year in laboratories and south poles, was kicking off his next venture, a five-year
Berkeley’s Calvin Laboratory since debuting with
offices at both Berkeley and Illinois campuses. 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
Partnership with India Two Berkeley graduate students actually took Swan up sponsored by EBI and the U.S. Department of
Five top undergraduates from the Indian Institute of on his offer to work on his BP-sponsored biofuel-pow- Energy’s Joint BioEnergy Institute ( JBEI), located in
Technology (IIT) at Kharagpur spent eight weeks ered sailboat during its West Coast journey—Vasanth Emeryville, CA, debuted on Sept. 10 with a seminar
during the summer of 2008 conducting research with Mohan, a graduating MBA student in the Haas School by University of Illinois microbiologist Roderick I.
EBI faculty as part of a new Berkeley-IIT Kharagpur of Business, and Bret Strogen, a second-year doctoral Mackie. This series will resume in the first quarter
collaboration in biofuels sponsored by the EBI. The student in environmental engineering. Strogen is of 2009.
scientific partnership was brokered by UC Berkeley currently working on an EBI program headed by
Deans Mark Richards, of the College of Letters and Arpad Horvath and Tom McKone entitled “Life Cycle
Science, and of Physical and Mathematical Sciences; Environmental and Economic Decision-Making for
and Geoff Owen, of Biological Sciences. The EBI Alternative Biofuels.”
and its Director, Chris Somerville, are supporting
sponsors. EBI graduate students and postdocs have been actively
educating each other via biweekly lunchtime seminar
The collaboration involves two phases. The first seeks programs started at both Berkeley and Illinois. The
to build relationships among faculty and students of seminars focus on work being conducted in the
both institutions while increasing the pool of research- laboratories of EBI principal investigators.
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
The EBI recognizes its role in educating
Miller. and training young researchers so that they
are prepared for the coming bio-revolution.

56 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT EDUCATION AND OUTREACH 57


EBI Research Programs, Germplasm Collection, Nutrient Cycling, Biomass Pretreatment and Chemical Synthesis
10
c h a p t e r

Projects, and Research Personnel Cold Hardiness, Photosynthetic Capacity,


and Flowering Phenology of Miscanthus
of Transportation Fuels
Principal Investigator: Alexis T. Bell, UC Berkeley
sacchariflorus, Miscanthus sinensis, and Their
and Berkeley Lab
The following is a list of principal investigators and research staff in 50 Natural Hybrids in Native Stands Ranging from
programs and projects funded by the Energy Biosciences Institute during its Central to Northern Japan Co-PI: Harvey W. Blanch, UC Berkeley and Berkeley
Lab
first year. Detailed descriptions of the individual projects can be found on the Principal Investigator: J. Ryan Stewart, University
of Illinois Postdocs: Ting Chen, Chidam Mandan, Sasisanker
EBI's public web site: www.energybiosciencesinstitute.org. Padmanabhan
Co-PIs: German Bollero, Fabian G. Fernandez,
University of Illinois; Toshihiko Yamada, Hokkaido Graduate Student: Sean Dee
University, Japan; Aya Nishiwaki, Miyazaki University,
Japan
Feedstock Development Postdocs: Tofael Ahamed, Hala Chaouui, Cellulosomes Optimized for Biofuel Production
Konstantinos Domdouzis, Ming-Che Hu, Qingting Postdoc: Yo Toma
Principal Investigator: Jamie H. D. Cate, UC Berkeley
Programs: Liu, Zewei Miao, Yogendra Shastri
and Berkeley Lab
Undergraduate Student: Jude Holscher Improvement of Bioenergy Crops
Assessing the Potential Impact of Insect Pests Co-PIs: Michael A. Marletta, Haw Yang, Daniel A.
and Plant Pathogens on Biomass Production of Visiting Scholars: Yonghua Xiong, Jiang Yan, Yuliang Principal Investigator: Jack Widholm, University Fletcher, Evan R. Williams, UC Berkeley and Berkeley
Miscanthus x Giganteus and Switchgrass Zhang, Qinyuan Zhu of Illinois Lab
Principal Investigator: Michael E. Gray, University Co-PI: John Juvik, University of Illinois Visiting Professor: Rafael Lamed
of Illinois Feedstock Production/Agronomy Program Postdoc: Olga Zernova Postdocs: Corinne Hausmann, Sasa Jenko-Kokalj,
Co-PIs: Carl Bradley, Terry Niblack, and Kevin Principal Investigator: Thomas Voigt, University Kai Zhang
Graduate Student: Hyoung Kim
Steffey, University of Illinois; Shauna Somerville, of Illinois Graduate Students: William Beeson, Padma
UC Berkeley Research Scientist: Vera Lozovaya Gunda, Chris Phillips, Veronica Zepeda, Elizabeth
Co-PI: Stephen P. Long, University of Illinois
Postdocs: Bright Agindotan, Monday Ahonsi, Jeffrey Znameroski
Graduate Students: Becky Arundale, Bosola
Bradshaw, Tesfamariam Mekete, Jarrad Prasifka Biomass Depolymerization Undergraduate Students: Valerie Chan, Duy Dao
Oladeinde, Ashley Spence, Andy Wycislo
Technician: Michelle Averbeck Research Associate: Bruno Martinez
Tech Specialists: Rich Pyter, Drew Schlumpf,
Emily Thomas
Programs:
Genomics-Enabled Improvement of Chemical Imaging of Plant Biomass with Micro- Thermophilic Microbes and Enzymes for Biofuel
Andropogoneae Grasses as Feedstocks for and Nano-Raman Spectroscopy Production
Enhanced Biofuel Production
Projects:
Principal Investigator: Paul Adams, Berkeley Lab Principal Investigator: Douglas S. Clark, UC Berkeley
Principal Investigator: Stephen Moose, University Reproductive Barriers in Miscanthus sinensis
Co-PI: Jim Schuck, Berkeley Lab Co-PIs: Harvey W. Blanch, UC Berkeley and Berkeley
of Illinois and Other Biofuel Plants
Postdoc: Martin Schmidt Lab; Frank Robb, University of Maryland Biotechnology
Co-PIs: Matthew Hudson and Ray Ming, University of Principal Investigator: Sheila McCormick, UC Institute
Illinois; Dan Rokhsar, UC Berkeley and Berkeley Lab Berkeley
Postdocs: Harshal Chokhawala, Melinda Clark,
Postdocs: Madge Alabady, Cuixia Chen, Kankshita Postdoc: Yuefeng Guan Cell Wall 3D Architecture at Nanometer Tae-Wan Kim, Seth Levine, Cong Trinh
Swaminathan Resolution Using High-Throughput TEM and EM
Tomography Junior Specialist: Paul Wolski
Graduate Students: Adam Barling, Brandon James Model Development to Predict Feedstock
Principal Investigator: Manfred Auer, Berkeley Lab Graduate Students: Craig Dana, Jerome Fox, Sarah
Undergraduate Students: Katie Boesche, Arthur Production of Miscanthus and Switchgrass as Huffer, Priya Jayachandran, Dana Nadler
Rudolph Affected by Climate, Soils and Nitrogen Co-PIs: Kenneth Downing, Bahram Parvin, Berkeley
Lab; Jan Liphardt, UC Berkeley
Principal Investigator: German A. Bollero,
University of Illinois Postdocs: Phillip Jess, Purbasha Sarkar
Engineering Solutions for Biomass Feedstock
Production Co-PIs: Stephen P. Long, Fabian G. Fernandez, Specialist: Ju Han
University of Illinois Associate Specialist: Elena Bosneaga
Principal Investigator: KC Ting, University of Illinois
Postdoc: Fernando Miguez
Co-PIs: Steven Eckhoff, Tony Grift, Alan Hansen,
Luis Rodriguez, Lei Tian, Qin Zhang, University of
Illinois

58 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL 59
Engineering of Thermophilic Anaerobic Bacteria Biomass to Transportation Fuel via Ecology and Exploitation of Endophytic Projects
to Improve Biocatalysis of Plant Cell Wall Hydrodeoxygenation Diazotropic Bacteria in Biofuel Crops
Materials to Ethanol/Butanol Bioengineering and Selection for Biodiesel
Principal Investigator: Jonathan A. Ellman, UC Principal Investigator: Angela Kent, University
Production in Bacteria
Principal Investigator: Isaac Cann, University Berkeley and Berkeley Lab of Illinois
of Illinois Principal Investigators: Nikos Kyrpides, Athanasios
Co-PI: Robert G. Bergman, UC Berkeley and Berkeley Undergraduate Student: Neil Gottel
Lykidis, Joint Genome Institute, Berkeley Lab
Co-PIs: Roderick I. Mackie, M. Ashley Spies, Satish Lab
K. Nair, University of Illinois Researcher: Pilar Francino
Postdoc: Jason Nichols Organometallic Catalytic Approaches to
Research Associate: Wenze Li Postdoc: Maria Billini
Delignification
Postdocs: Yejun Han, Shinichi Kiyonari, Shosuke Enzyme Discovery in Grass-Feeding Termites for Principal Investigator: Thomas B. Rauchfuss,
Yoshida the Depolymerization of Lignocellulosic Biomass University of Illinois Microbial Sugar Utilization
Graduate Students: Richard Cozad, Dylan Dodd Principal Investigator: Philip Hugenholtz, Postdoc: Didier Morvan Principal Investigator: Yong-Su Jin, University
Undergraduate Students: Charles Hespan, Amara Berkeley Lab of Illinois
Graduate Students: Zachariah Heiden, Aaron Royer
Hussain, Sana Jafri, Brad Jelinek, Jason Kim, Hussain Research Scientist: Natalia Ivanova
Mithaiwala, Farhan Quader, Soe Tha
Staff Scientist: Nikos Krypides Enzymatic Lignin Degradation
Robustness to Environmental Heterogeneity—
Engineering Strains Optimized for Large-Scale
Postdoc: Falk Warnecke Principal Investigator: Michelle Chang, UC Berkeley
Biochemistry, Structure and Engineering of Fermentation
Enzymes and Metabolic Pathways to Overcome Graduate Student: Margaret Brown Principal Investigator: Christopher V. Rao, University
Biomass Recalcitrance Surface Kinetic Mechanisms of Enzymatic of Illinois
Principal Investigator: John Gerlt, University Cellulose Deconstruction
Biofuels Production Co-PI: Ido Golding, University of Illinois
of Illinois Principal Investigator: Clayton J. Radke, UC Berkeley
Graduate Students: Tasha Desai, Michael Bednarz
Co-PIs: John Cronan, Satish Nair, University of Illinois and Berkeley Lab
Programs
Postdocs: Sudipta Majumdar, Jose Solbiati Graduate Student: Samuel Maurer
Systems Biology of Metabolism and its Environmental, Social and Economic
Regulation in Microbes Important to Biofuel Dimensions
Enzyme-Inspired Catalysts for Enhancing Biofuels Genomic Analysis of Bovine Rumen Microbiota Production
Production Under Different Dietary Regimens Programs
Principal Investigator: Adam P. Arkin, UC Berkeley
Principal Investigator: Alexander Katz, UC Berkeley Principal Investigator: Eddy Rubin, Joint Genome and Berkeley Lab
Institute, Berkeley Lab Life-Cycle Environmental and Economic Decision-
Specialist: Andrew Solovyov Co-PIs: Inna Dubchak, Terry Hazen, Berkeley Lab Making for Alternative Biofuels
Co-PI: Susannah Tringe-Green, Joint Genome
Postdocs: Tatiana Luts, Brandon McKenna Institute, Berkeley Lab Postdoc: Anna Gersimova Principal Investigators: Arpad Horvath and Thomas
Research Associate: Jordan Mar McKone, UC Berkeley and Berkeley Lab
Postdocs: Tao Zhang, Matthias Hess
Development of Novel Catalysts Interest Group: Adam Deutschbauer, Paramvir Co-PIs: Maximilian Auffhammer, Peter Berck, Dan
Dehal, Jennifer Kuehl Kammen, William Nazaroff, Tim Lipman, Margaret
Principal Investigator: Dean Toste, UC Berkeley Detoxification of Miscanthus Hydrolysates With a Torn, UC Berkeley
Postdocs: Francisco Santoro, Sunghee Son New Phase Separation Method Lead Researchers: Agnes Lobscheid, Eric Masanet
Graduate Student: Cole Witham Principal Investigator: Hao Feng, University of Illinois Engineering a Yeast Strain that Efficiently Utilizes
C5/C6 Sugars Graduate Students: Catherine Almirall, Joshua Apte,
Junior Specialist: Vincent Chan Co-PI: Bin Wang, Visiting Research Scientist Surakshya Dhakal, Bret Strogen, Kevin Fingerman
Principal Investigator: Huimin Zhao, University
Postdoc: Pradip B. Dhamole of Illinois
Projects Co-PIs: Nathan Price, Lucas Li, University of Illinois
Fungi and Deconstruction of Lignin and Other Fractionating Recalcitrant Miscanthus by a Two- Postdoc: Tae Hee Lee
Components of Miscanthus Cell Walls Stage Treatment Under Mild Reaction Conditions
Graduate Student: Jing Li
Principal Investigator: John W. Taylor, UC Berkeley Principal Investigator: Hao Feng, University of Illinois

Co-PIs: Thomas D. Bruns, N. Louise Glass, UC Visiting Research Scientist: Bin Wang
Berkeley Graduate Student: Atilio de Frias
Postdoc: Chaoguang Tian
Researcher: Tim Szaro

60 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT EBI RESEARCH PROGRAMS, PROJECTS, AND RESEARCH PERSONNEL 61
Economics of Biofuel Adoption and Impacts Projects Regional Environmental Impacts of Biofuel Biofuels Research Initiatives and Extension:
Principal Investigator: David Zilberman, Feedstock Production—Scaling Biogeochemical Synergizing Engagement With Stakeholders
Development of Biofuel Productivity Potentials Cycles in Space and Time
UC Berkeley Principal Investigator: Anne Heinze Silvis, University
for Economic Analysis Under Changing Climate,
Co-PIs: Gordon Rauser, David Roland-Holst, Principal Investigator: Carl J. Bernacchi, University of Illinois
Land Use, and Societal Demands
UC Berkeley of Illinois Co-PIs: Michael E. Gray, German Bollero, Maria
Principal Investigator: Norman L. Miller, UC
Postdoc: Gal Hochman Co-PI: Tracy E. Twine, University of Minnesota Bonita Villamil, University of Illinois
Berkeley and Berkeley Lab
Graduate Students: Justine Lazaro, Maya Papineau, Graduate Student: Andrew VanLoocke
Co-PIs: David Sunding, UC Berkeley and Berkeley
Deepak Rajagopal, Steve Sexton, Thomas Sproul Lab; N. Maggi Kelly, David Zilberman, UC Berkeley Undergraduate Student: Christina Burke From a Global Oil Economy to a Global Biofuel
Administration: Amor Nolan Economy
Faculty Collaborator: Steven W. Running, University
Subcontractor: Gregory Glass of Montana Regional Socioeconomic and Environmental Principal Investigator: Steve Weber, UC Berkeley
Postdoc: Alan DiVittrio Impacts of Alternative Biofuel Pathways Postdoc: Regine Spector

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

Research Staff: Jody Endres Co-PIs: John Braden, Wayland Eheart, George
Czapar, University of Illinois
Postdoc: Atsushi Oyama Food Security Management in an Era of Biofuels
Graduate Students: Tze Ling Ng, Aras Zygas,
Graduate Students: Christopher J. Miller, Molly Principal Investigator: Brian Wright, UC Berkeley
Jude Tate
Novy Italian Visiting Professor: Carlo Cafiero
Graduate Students: Fei Han, Di Zheng
Market Context for Biofuels Microeconomics
Economic and Environmental Impacts of Biofuels;
Implications for Land Use and Policy Principal Investigator: Hadi Esfahani, University
Intellectual Property Protection and Contractual of Illinois
Principal Investigator: Madhu Khanna, University Relations for Biofuels Innovations
of Illinois Co-PIs: Clifford Singer, John Vasquez, University
Principal Investigator: Brian Wright, UC Berkeley of Illinois
Co-PIs: Atul Jain, Hayri Onal, Yanfeng Ouyang,
Researcher: Josephine Mutugu Graduate Students: Esra Ergul, Thorin Wright
Jurgen Scheffran, University of Illinois
Graduate Students: Kryiakos Drivas, Zhen Lei
Postdocs: Haixiao Huang, Seungmo Kang
Undergraduate Student: Astrid Sky
Graduate Students: William Bowser, Xiaoguang
Chen, Matthew Erickson, Shahnila Islam, Christine
Lasco, Deniz Tursun, Xiaojuan Yang
62 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT 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 Second Generation Sustainability
A genus of about 15 species Biofuels The capacity to maintain a certain
of perennial grasses whose First generation biofuels, like process or state indefinitely. To
productivity, biomass yield, and bioethanol, are produced by be sustainable, nature’s resources
growth capability on marginal lands fermenting plant-derived sugars must only be used at a rate at
makes it a prime candidate for in a process similar to that used in which they can be replenished. A
development as a biofuel feedstock. making beer and wine. This requires sustainable biofuel feedstock is
The most widely used “species” the use of food crops like sugar one that requires little energy input
is Miscanthus x giganteus, often cane and corn. Second generation and produces few byproducts that
referred to as “Miscanthus,” which biofuels, like cellulosic ethanol, are impact the environment.
is a sterile hybrid of Miscanthus those produced sustainably with
sinensis and M. saccharifolius. These biomass comprised of the residual
species can be found throughout non-food parts of current crops Xylose
East Asia, from Papua New Guinea and others, like grasses, grown for A sugar with five carbon atoms
to southern Siberia, and through non-food purposes. (“C5”) in each molecule, found in
Japan and Taiwan. Because of their the cell walls of plants. Other sugars
stature and silver flowering heads, commonly found there include
all three are popular garden plants Synthetic Biology arabinose, mannose, galactose,
found in gardens throughout North The design and construction of new fucose, rhamnose, galacturonic
America and Europe. biological entities such as enzymes, acid, and glucose, among others.
genetic circuits, and cells, or the
redesign of existing biological
Net Energy systems; builds upon advances in
A fuel’s energy, minus what is molecular cell and system biology.
required to produce or obtain it.
For instance, the net energy of
gasoline is reduced by the energy Switchgrass
lost in extracting oil from the earth, A warm season grass (scientific
refining it, and transporting it to name Panicum virgatum) that
consumers. is one of the dominant species
of the central North American
tallgrass prairie. Properties that
Polysaccharides make it a strong candidate for
Complex carbohydrates, such as biofuel production include
starch and cellulose, consisting survival in drought conditions,
of a number of monosaccharides perennial habit, and low nitrogen
(sugars) joined together in long requirement when harvested in
chains of molecules. the fall.

66 ENERGY BIOSCIENCES INSTITUTE // 2008 ANNUAL REPORT