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DOE BRC Research Strategies

DOE Bioenergy Research Centers' Research Strategies

The ultimate goal for the three DOE Bioenergy Research Centers is to better understand the biological mechanisms underlying biofuel production so that those mechanisms can be redesigned, improved, and used to develop novel, efficient bioenergy strategies that can be replicated on a mass scale. New strategies and findings emanating from the centers’ fundamental research ultimately will benefit all biological investigations and will create the knowledge underlying three grand challenges at the frontiers of biology:

  • Development of next-generation bioenergy crops
  • Discovery and design of enzymes and microbes with novel biomass-degrading capabilities
  • Development of transformational microbe-mediated strategies for biofuel production

The extremely complex science needed to solve these challenges requires multiple interdisciplinary teams that approach the same problems from different directions to accelerate scientific progress. The following sections explain some scientific issues related to these challenges.

1. Development of Next-Generation Bioenergy Crops

Bioenergy crops include grasses, trees, and other plants grown specifically for energy production. These crops and other forms of cellulosic biomass provide the raw material for bioenergy. Cellulosic biomass primarily consists of cellulose and other complex cell-wall compounds, such as lignin, that strengthen and support plant structure. The main constituents of many plant cell-wall compounds are simple sugars amenable to fermentation, producing ethanol, other biofuels, and chemicals. The cell walls are so complex that several thousand genes are thought to be involved in their synthesis and maintenance. Many of these genes are now being characterized by the BRCs, and our knowledge of associated biological functions continues to expand as a result of this research.

By understanding the genes and mechanisms that control cell-wall synthesis in plants, scientists could develop new energy crops with altered biomass composition or modified links within and between cell-wall components. These “designer” bioenergy crops would retain robust growth in the field but could be triggered to break down rapidly in a biorefinery. Besides modification of plant cell walls, another approach to improving bioenergy crops is to increase the accumulation of starches and oils in plant tissues. Starches and oils can be converted into biofuels much more easily than cellulose.

Altering biomass composition is one approach to developing better bioenergy crops, but other important improvements include increasing biomass productivity per acre, increasing resistance to pests and drought, and decreasing applications of fertilizers and other inputs. Many potential energy crops are grasses or fast-growing trees that have not benefited from the years of agricultural research devoted to breeding traditional crops such as corn or wheat. Availability of more plant-genome sequence information can accelerate the development of DNA markers used to identify and isolate the many genes associated with traits that can improve energy crop yield, degradability, and sustainability. Having DNA markers and other new biological tools could significantly reduce the time required to identify desired genetic variants and produce new energy crops.

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

Nature uses both enzymes and multienzyme complexes, including those called “cellulosomes,” to break down cellulosic biomass (see sidebar, Tapping Nature’s Strategies for Biomass Degradation, p. 2). The biomass-degrading enzymes and cellulosomes studied thus far function slowly enough that scientists are optimistic that their activity and effectiveness can be improved significantly. Several factors—the nearly impenetrable architecture of plant cell walls, chemical and physical changes to biomass during pretreatment, and structural features of the enzymes—collectively contribute to the inefficiency of current biomass deconstruction approaches. Therefore, multiple strategies must be studied simultaneously and systematically at each DOE Bioenergy Research Center to illuminate the various biological and chemical processes at work.

Certain fungi and bacteria specialize in producing enzymes that degrade biological materials in natural environments. Discovering, harnessing, and enhancing the best biomassdegrading enzymes and microbes in nature ultimately will have a significant impact on increasing the efficiency and reducing the cost of cellulosic biofuel production. Scientists are just beginning to explore the staggering diversity of enzymes in environments such as the termite gut and cow rumen, and the vast majority of natural habitats are yet to be investigated. To accelerate the discovery of novel enzymes and microbes and to understand how their degradative processes work synergistically, each center is searching diverse biomass-degrading environments, from hot springs to rainforests to compost piles.

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

3. Development of Transformational Microbe-Mediated Strategies for Biofuel Production

In addition to cellulose, other carbohydrates (collectively called hemicelluloses) in plant cell walls are broken down into fermentable sugars when biomass is pretreated with heat and chemicals. Although cellulose is made of one type of 6-carbon sugar (glucose) that is readily converted into ethanol and other products, microbial fermentation of the 5- and 6-carbon sugar mix from hemicelluloses is less efficient and thus is a key area for improvement.

En route to the fermentation tank, biomass currently is subjected to physical, chemical, and enzymatic processing steps that can create by-products and conditions that might inhibit microbial conversion of sugars into biofuels. Ethanol and other biofuel products also inhibit microbial fermentation at high concentrations. Consequently, another important research area is developing microbes robust enough to withstand the stresses of industrial processing and tolerate higher ethanol concentrations.

An additional research target that could radically simplify the entire production process is consolidated bioprocessing (CBP). This scientific strategy combines cellulose deconstruction and sugar fermentation into a single step mediated by a “multitalented” microbe or mixed culture of microbes. CBP requires a redesign of microbial systems far more extensive than conventional genetic engineering approaches. For example, genetically engineering the microbial production of a single drug or other biochemical product might involve the modifications of only a few genes. A successful CBP microbe or specially designed microbial consortium may be required to produce a variety of biomass-degrading enzymes; produce only minimal amounts of molecules that inhibit the overall process; ferment both 5- and 6-carbon sugars; and thrive in industrial reactors with high temperature, low pH, and high concentrations of biofuel products. Simultaneously incorporating so many different capabilities into a single microbe or consortium requires an unprecedented understanding of microbial systems.

To accelerate development of the next generation of highenergy biofuels, the DOE Bioenergy Research Centers also are designing novel microbial systems that can produce biofuels other than ethanol. Some of these new fuels may be oily, petroleum-like products that are easily extracted from the watery solutions in biorefinery reactors and thus less inhibitory to biofuel-synthesizing microbes. These new biofuels also would be compatible with existing motor vehicles and fuel transportation infrastructure and contain as much energy per unit volume as gasoline or diesel.

Grand Challenge: Development of Next-Generation Bioenergy Crops
Center Strategies
  • GLBRC – Engineer “model” plants and potential energy crops to produce new forms of lignin and more starches and oils, which are more easily processed into fuels.
  • JBEI – Enhance lignin degradation in “model” plants by changing cross-links among lignin subunits; improve deconstruction and subsequent fermentation by altering linkages between lignin and other cell-wall components; translate genetic developments to switchgrass.
  • BESC – Decrease or eliminate harsh chemical pretreatments by engineering plant cell walls in poplar and switchgrass to be less recalcitrant; simultaneously increase total biomass produced per acre.
Grand Challenge: Discovery and Design of Enzymes and Microbes with Novel Biomass-Degrading Capabilities
Center Strategies
  • GLBRC – Identify combinations of enzymes and pretreatment needed to digest specific biomass types; express biomass-degrading enzymes in the stems and leaves of corn and other plants.
  • JBEI – Develop new ionic liquid pretreatments that can completely solubilize and fractionate biomass components; improve performance and stability of enzymes obtained from the rainforest floor and other environments; engineer, through directed evolution, highly efficient cellulase enzymes.
  • BESC – Screen natural thermal springs to identify enzymes and microbes that effectively break down and convert biomass at high temperatures; understand and engineer cellulosomes (multifunctional enzyme complexes for degrading cellulose).
Grand Challenge: Development of Transformational Microbe-Mediated Strategies for Biofuel Production
Center Strategies
  • GLBRC – Start with an ethanol-producing microbe and add lignocellulose-degrading capabilities to substantially reduce costs.
  • JBEI – Connect diverse biological parts and pathways to create entirely new organisms that produce fuels other than ethanol; engineer organisms to produce and withstand high concentrations of biofuels; derive useful chemical products from lignin degradation.
  • BESC – Start with a lignocellulose-degrading microbe and add ethanol-producing capabilities to substantially reduce costs; develop a knowledgebase and pathway analysis tools to aid this manipulation.
BESC: BioEnergy Science Center; GLBRC: Great Lakes Bioenergy Research Center; JBEI: Joint BioEnergy Institute.

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