Genomic Science Program. Click to return to home page.
Department of Energy Office of Science. Click to visit main DOE SC site.

Genomic Science Program

Archival Information About the First DOE Bioenergy Research Centers (2007-2017)

In July 2017, the U.S. Department of Energy (DOE) provided $40 million for four DOE Bioenergy Research Centers. See more about those centers and the next phase of bioenergy research here.

Below is archival information about DOE's first three Bioenergy Centers (BRCs) that were funded from 2007-2017.

These initial BRCs were supported by the Genomic Science program within DOE’s Office of Science Office of Biological and Environmental Research (BER). They made significant advances toward a new biobased economy. They produced multiple breakthroughs in the form of deepened understanding of sustainable biomass production practices, targeted reengineering of biomass feedstocks, development of new methods for deconstructing feedstocks, and engineering of microbes for more effective production of a diverse range of biofuels.

In all, these three BRCs produced 2,696 peer-reviewed publications, 619 invention disclosures, 397 patent applications, 199 licenses or options, 101 patents, and 14 company startups (see figure below). Through this work, they transferred substantial insight and expertise to industry through cooperation with both large and small companies.

Focus of Previous DOE Bioenergy Centers

Each of the previous centers represented an integrative, multidisciplinary partnership with expertise spanning the physical, chemical, biological, and computational sciences, including genomics, microbial and plant biology, analytical chemistry, computational biology and bioinformatics, and engineering. The scientific rationale for these centers and for other fundamental genomic research critical to the biofuel industry was established at a DOE workshop involving members of the research community.

These BRCs were structured to facilitate knowledge sharing among multiple disciplines so that breakthroughs in one area could be capitalized on and translated to other areas of emphasis. In these integrated and collaborative environments, the BRCs pursued the necessary fundamental research to improve the processes needed for large-scale, cost-effective production of advanced biofuels from cellulosic biomass. Additionally, as each center approached biofuel production challenges from different angles, the types of knowledge gained were multiplied, new questions opened up, and new avenues of research pursued, ultimately accelerating the pathway to improving and scaling up biofuel production processes.

The ultimate goal for the three DOE BRCs was to provide the fundamental science to underpin a cost-effective, advanced cellulosic biofuels industry. Using systems biology approaches, the BRCs focused on new strategies to reduce the impact of key cost-driving processes in the overall production of cellulosic biofuels from biomass. For these biofuels to be adopted on a large scale, they represented environmentally sustainable and economically competitive alternatives to existing fuel systems. New strategies and findings emanating from the centers' fundamental research addressed three grand challenges for cost-effective advanced biofuels production:

  • Develop next-generation bioenergy crops by unraveling the biology of plant development.
  • Discover and design enzymes and microbes with novel biomass-degrading capabilities.
  • Develop transformational microbe-mediated strategies for advanced biofuels production.

DOE BRC Partners

Map of DOE Bioenergy Research Centers and Partners (2007-2017).

The Three Centers (2007-2017)

The Centers were supported by multidisciplinary teams of top scientists from the nation’s leading universities, national laboratories, nonprofit organizations, and a range of private companies. The three Centers were located in geographically distinct areas and used different plants both for laboratory research and for improving feedstock crops.

The complexity of the three biological grand challenges to be overcome to achieve industrial-scale bioenergy production required the coordinated pursuit of numerous research approaches to ensure timely success. Collectively, the DOE Bioenergy Research Centers provided a portfolio of diverse and complementary scientific strategies that addressed these challenges on a scale far greater than any effort to date.

DOE BRC Research Strategies at a Glance (2007-2017)

The science needed to solve these complex challenges required multiple, coordinated, multidisciplinary teams approaching problems from varied perspectives to accelerate scientific progress. Some key scientific approaches to these challenges are described below.

1. Develop Next-Generation Bioenergy Crops by Unraveling the Biology of Plant Development

The raw material for biofuel production is cellulose, which is derived primarily from the cell walls of plants. Cellulose is a polymer of glucose that is easily broken down and converted into biofuels, hence the term cellulosic biofuels. However, the recovery of cellulose from plant biomass is an energy-intensive (and costly) process. In addition to cellulose, plant cell walls also contain hemicellulose and other complex cell wall compounds, such as lignin, that together give plant tissues their structural strength. These other plant cell wall constituents are less amenable to breakdown and fermentation and impede cost-efficient biomass conversion to biofuels.

Many potential bioenergy crops are grasses or fast-growing trees that have not benefited from the years of agricultural research devoted to breeding traditional crops such as corn or wheat. However, the availability of plant genome sequences has greatly accelerated bioenergy crop research, enabling scientists to more rapidly develop DNA markers to identify and isolate genes associated with beneficial traits that could improve crop yield, degradability, and sustainability. Mapping DNA markers and developing new tools for high-throughput genetic modification in plants are significantly reducing the time required to identify desired genetic variants and produce new energy crops.

The BRCs used genome-enabled approaches to gain a better fundamental understanding of plant cell wall synthesis to improve the bioenergy attributes of potential bioenergy crops. Genome-enabled studies have yielded the identity of key genes thought to be involved in cell wall synthesis and maintenance. Many of these genes were under intense BRC investigation as potential targets for influencing cell wall composition via metabolic engineering approaches, for example. By understanding the genes and mechanisms that control cell wall synthesis, scientists developed new energy crops with altered cellulose (or lignin) composition and modified linkages within and between cell wall components. These new bioenergy crops retain robust growth characteristics in the field but can be broken down to cellulose in a biorefinery much more cost effectively than the most prominent bioenergy crops currently in use. Other genome-enabled approaches focused on increasing the accumulation in plant tissues of starches or oils that can be converted into biofuels even more easily than cellulose. These same approaches also were used to investigate other important cost-saving enhancements such as increasing biomass productivity per acre, increasing resistance to pests and drought, and decreasing the need for fertilizer applications and other inputs crucial to improving the sustainability of bioenergy crop production on marginal lands.

2. Discover and Design Enzymes and Microbes with Novel Biomass-Degrading Capabilities

Nature uses both cellulases and multienzyme complexes known as cellulosomes to break down cellulosic biomass. In nature, biomass breakdown is relatively slow. For example, a fallen tree in the forest persists for quite some time before it completely degrades and disappears. BRC scientists studied the activity of cellulases and cellulosomes were optimistic that this process could be accelerated significantly by modifying known biomass-degrading enzymes and discovering new ones. Several factors govern the enzymatic deconstruction of plant polymers, including the (1) recalcitrant architecture of plant cell walls, (2) chemical and physical changes to biomass during pretreatment, and (3) structural features of the enzymes. Collectively, these factors and the high cost of commercially producing biomass-degrading enzymes contribute to the inefficiency and high cost of current enzyme-based biomass deconstruction approaches. Multiple strategies were under BRC investigation to address each of these factors, combining detailed understanding of the deconstruction process with the discovery or development of new or improved enzymatic approaches to biomass degradation.

Nature harbors a staggering diversity of microorganisms in environments such as the termite gut, cow rumen, compost piles, rainforests, hot springs, and other natural habitats where enzymatic breakdown of plant material drives these ecosystems. The BRCs "mined" these environments for new, natural capabilities for efficient biomass breakdown. Each center discovered, characterized, evaluated, and developed new enzymes from these environments for biofuel production purposes.

Discovering new biomass-degrading capabilities in nature was only part of the challenge. Molecular-level understanding of how enzymes degrade biomass is a prerequisite to designing improved processes. Because no single research approach can provide this understanding, each center integrated different combinations of methodologies. These included high-throughput screens for genes, proteins, and metabolites; chemical and structural analyses; state-of-the-art imaging technologies; and computational modeling to identify and characterize important factors influencing the rapid deconstruction of plant materials into sugars and other energy-rich components that can be converted to biofuels.

3. Develop Transformational Microbe-Mediated Strategies for Advanced Biofuels Production

Microorganisms can convert sugars derived from plant biomass to a range of different biofuels and bioproducts, but this activity can be altered by inhibitory and toxic compounds present in extracted biomass. These inhibitory conditions are created by the physical, chemical, and enzymatic processing steps that biomass is subjected to prior to fermentation. Biofuels themselves also can inhibit microbial fermentation at high concentrations. Costly extraction steps often must be incorporated into the treatment process to remove these inhibitory compounds. One method to reduce the overall cost of the biofuel production process is to develop robust microorganisms that can tolerate biorefinery conditions and still produce the desired biofuel. Consequently, the BRCs used genome-enabled methods to understand stress-tolerance mechanisms in a variety of microbial strains used in biofuel production. These studies led to the re-engineering of several cellular processes, including cross-membrane transport pathways to increase the tolerance of fermentative microbes to conditions found in a biorefinery process train and decrease the impact of biofuel product inhibition.

BRC research also explored alternative microbial methods to use plant biomass more efficiently. Plant cell walls contain cellulose, the prime target for biofuel production purposes, but they also contain hemicellulose and lignin. Together, these polymers impart rigidity to plant cells and serve as the structural backbone of plants, thereby comprising a significant percentage of the total terrestrial plant biomass. To use these materials more efficiently, the BRCs investigated the recovery, breakdown, and conversion of other cell wall components such as hemicellulose. Unlike cellulose, hemicellulose is comprised of both 5- and 6-carbon sugars that are less easily broken down into fermentable sugars. BRC researchers targeted new processes to break down hemicellulose into its component sugars and developing new microbial strains to convert these sugars to biofuel products, as well as altering the nature of the hemicellulose incorporated into cell walls. These methods target more efficient uses of bulk plant biomass used for biofuel feedstocks and help increase biofuel yields from bioenergy plants on a per weight basis.

The BRCs also developed ways to combine unit processes into consolidated bioprocessing (CBP) to further decrease costs and increase the overall efficiency of biofuels production. The CBP strategy combines cellulose deconstruction and sugar fermentation into advanced biofuels in a single step mediated by a "multitalented" microbe or mixture of microbes (called a microbial consortium). Approaches that use a CBP microbe or microbial consortium combine knowledge of microbial stress tolerance and fermentative pathways with genome-enabled techniques to incorporate the enzymatic machinery (developed from other organisms) necessary to break down cellulose polymers into component sugars. Unprecedented understanding of microbial systems is required to incorporate and optimize expression of numerous non-native genetic elements that catalyze the conversion of plant polymers to biofuels in one step.

BRC researchers took CBP a step further by determining the necessary metabolic pathway modifications to develop a range of high-energy "drop-in" biofuels as substitutes for gasoline and petroleum-derived diesel fuel. These advanced biofuels are compatible with existing internal combustion engines and fuel transportation infrastructure and contain as much energy per unit volume as gasoline or diesel. Jet fuel components have even been produced via metabolic engineering of microbes. Production of these fuels drew on remarkable developments in metabolic engineering, enabling BRC researchers to "borrow" enzymatic capabilities from other plants and microbes found in nature and express these traits in a modified host microbe engineered for biofuel production. These techniques were at the very forefront of biotechnological innovation and laid the scientific foundation for developing numerous beneficial products, in addition to biofuels, from renewable biomass.


Plant Feedstock Genomics for Bioenergy Abstracts [9/16]

Bioenergy Research Centers
Key Advances Update: 2014-2016 [06/16]

Systems Biology Research to Advance Sustainable Bioenergy Crop Development (Summary of Funded Projects) [9/15]

Lignocellulosic Biomass for Advanced Biofuels and Bioproducts: Workshop Report [2/15]

Systems Biology-Enabled Research for Microbial Production of Advanced Biofuels (Summary of Funded Projects) [9/14]

Sustainable Bioenergy [05/14]

BRC cover

Bioenergy Research Centers [02/14]