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Systems Biology for Bioenergy

The vast majority of liquid transportation fuel used in the United States currently is derived from petroleum. In addition to the significant problems associated with security and renewability of these resources, their continued use results in massive releases of carbon dioxide and other greenhouse gases that drive global climate change. In recent years, the expanded availability of ethanol from corn starch and of biodiesel from soybeans has supplemented the transportation fuel supply but raised concerns regarding competition between biofuel production and the food supply. Also, given the energyintensive agricultural practices normally used to produce these crops, the degree to which a shift to these types of biofuels would actually reduce overall greenhouse gas emissions has been the subject of much debate.

From Biomass to Cellulosic Ethanol. Depicts the process used to convert biomass (plant matter) into cellulosic ethanol and the improvements needed to optimize these processes. (see Biofuels Primer)

Cellulosic plant biomass (i.e., fibrous or woody plant materials such as stems and leaves) can be broken down into its component sugars by a combination of physical, chemical, and enzymatic treatments. These sugars can then be converted into ethanol or other liquid biofuels by fermentative microbes or other chemical processes. Biofuels derived in this manner have the potential to provide a secure, renewable source of energy that will reduce dependence on fossil fuels and emissions of greenhouse gases. Agricultural residues (i.e., nonedible parts of crop plants) represent one current source of biomass carbon available for fuel production, but supply of this material is unlikely to meet total demands. Every year, a significant percentage of biomass must be left to decay in fields to maintain soil stock composition; furthermore, food crops are limited in their ability to grow on marginal lands, which comprise most of the landscape available for bioenergy production.

Dedicated biomass crops (i.e., switchgrass, poplar, energy cane, and a variety of other plant species) offer one possible route toward sustainable biofuels production that does not directly compete with food crops and could be grown on lands unsuitable for food agriculture. Dedicated biomass feedstocks potentially could yield much greater amounts of cellulosic material and have decreased water and fertilizer requirements and greater tolerance to pests and disease.

In addition to using dedicated biomass plants to produce sugars suitable for biofuels production, photosynthetic microbes such as algae and cyanobacteria potentially offer direct capture of atmospheric carbon dioxide and conversion to biofuels in a single step.

Despite these possible advantages, biofuels produced from cellulosic biomass or via direct microbial photosynthesis are not yet widely available. Compared with the relatively simple sugar chain of starch, cellulosic biomass is a complex, heterogeneous material that is much more difficult to degrade into its component sugars and currently requires expensive chemical pretreatments and enzyme cocktails. This recalcitrance of cellulosic biomass to degradation is due to the crystalline structure of cellulose in plant cell walls, as well as to the presence of covalently bound lignin polymers, which make lignocellulose a very stable material. As such, most cellulosic biofuels are not yet cost competitive with either fossil fuels or ethanol produced from corn starch. Ethanol, whether produced from corn or cellulosic materials, has considerably lower energy density than gasoline or diesel fuel and is more difficult to transport via current distribution infrastructures or use as the primary fuel constituent in most existing vehicle engines. Attempts at commercially viable biofuels production by photosynthetic microbes have been hampered by the significant front-end costs required to establish and maintain scalable microbial cultivation systems and difficulties in engineering production of biofuel compounds by these organisms.

A variety of significant research and development barriers need to be addressed before cellulosic biofuels can be more broadly adopted for use. Technical hurdles particularly relevant to the core strengths of the Genomic Science program include:

  • Limited understanding of plant cell wall structural properties that impart strength and resistance to degradation, hindering the development of better biomass deconstruction strategies.
  • Inefficiency and high cost associated with currently available physical, chemical, and enzymatic treatments for breakdown of cellulosic biomass and conversion of the resulting sugars to biofuel compounds.
  • Gaps in fundamental understanding of systems biology properties of (1) plant species with the potential to serve as biomass feedstock crops and (2) microorganisms capable of mediating deconstruction of complex plant biomass, photosynthetic capture of atmospheric carbon dioxide, and synthesis of advanced biofuel compounds.
  • Limitations in currently available approaches for genomescale engineering and targeted biodesign aimed at improving biomass feedstock crop yields or microbial conversion of biomass and synthesis of advanced biofuels compatible with existing distribution pipelines and engines.

Systems Biology Approaches

DOE's Genomic Science program is uniquely well suited to address the fundamental research challenges embedded within these technical barriers, and the integrative systems biology approach pioneered by the program lends itself to the multidisciplinary nature of the problems. For example, significant advances in breeding, molecular genetics, and genomic technologies provide new opportunities to (1) build on existing knowledge of plant biology and (2) more confidently predict and manipulate functional properties of potential biomass feedstock plant species. Applying a systems biology approach permits highthroughput characterization of the genes, proteins, and molecular interactions that influence cellulosic biomass production and enables accelerated improvement of biomass feedstocks for enhanced yields and growth properties. Specific targets include:

  • Elucidation of the regulation of gene networks, proteins, and metabolites to improve plant feedstock productivity and sustainability and to advance understanding of carbon partitioning and nutrient cycling.
  • Comparative approaches to enhance knowledge of the structure, function, and organization of plant genomes, leading to innovative strategies for feedstock characterization, breeding, manipulation, and improvement.
  • Characterization of plant germplasm collections and advanced breeding lines of bioenergy crops to discover and deploy valuable alleles for key bioenergy traits.
  • Development of new cultivars of regionally adapted bioenergy feedstock crops in public breeding programs using innovative approaches to identify desirable traits and accelerate trait integration.
  • Research into the complex interactions between bioenergy feedstock plants and their environment and how these processes influence plant growth and development, expression of bioenergy-relevant traits, and adaptation to changing environments.

Similarly, continuing advances in genome-enabled systems biology approaches for microorganisms relevant to biofuels production provide a number of opportunities to address key barriers. Only a limited number of microbes that are capable of complex biomass breakdown, photosynthetic capture of carbon dioxide, or synthesis of potential biofuels have been studied sufficiently to be considered "model organisms" that can be reliably manipulated for experiments. The subset of those with potential to serve as "chassis organisms" for industrial biotechnology applications is even smaller. Systems biology research on microbes with these capabilities will not only advance our knowledge of the fundamental nature of these functional processes but also facilitate engineering of microbes having these traits:

  • Increased rates of biomass degradation and expanded utilization of biomass components (i.e., hemicellulose and lignin monomers).
  • Decreased susceptibility to product inhibition by toxins released during biomass breakdown or high titers of synthesized biofuels, thus increasing the efficiency and yield of biofuel production.
  • Increased tolerance to physicochemical stresses associated with industrial-scale biofuels production (i.e., elevated temperature, altered pH levels, or fuel toxicity).
  • Modified functional properties that result in increased yield of biofuel compounds or synthesis of a broader range of molecules that can be used as next-generation biofuels and related bioproducts.

In addition, coupling these results with systems biology work on biomass-degrading microbes potentially could enable development of new consolidated biomass-processing approaches, in which a single organism (or assemblage of organisms) performs coupled deconstruction of biomass and synthesis of biofuel compounds. DOE's Bioenergy Research Centers are spearheading these research efforts.

Bioenergy Research Centers

To focus the most advanced biotechnology-based resources on the biological challenges of biofuel production, DOE established three Bioenergy Research Centers (BRCs) in September 2007. Each center is pursuing the basic research underlying a range of high-risk, high-return biological solutions for bioenergy applications. Advances resulting from the BRCs will provide the knowledge needed to develop new biobased products, methods, and tools that the emerging biofuel industry can use. The scientific rationale for these centers and for other fundamental genomic research critical to the biofuel industry was established at a DOE workshop on Biomass to Biofuels involving members of the research community.

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

USDA - DOE Plant Feedstock Genomics for Bioenergy

DOE and the USDA began a competitive grant program in 2006 that is committed to fundamental research in biomass genomics, providing the scientific foundation to facilitate use of lignocellulosic materials for bioenergy and biofuels. Since lignocellulosic crop plants are less intensive to produce and can grow on poorer quality land, competition with crops grown for food production is avoided. See current and previous awards.

Systems Biology—Enabled Research for Microbial Production of Advanced Biofuels

In 2014, DOE awarded grants for systems biology—driven basic research in three areas of development focused on enabling advanced biofuels production: 1) promising new model organisms relevant to biofuels production, 2) novel microbial functional capabilities and biosynthetic pathways relevant to advanced biofuels production and strategies to overcome associated metabolic challenges resulting from pathway modification, and 3) novel analytical technologies or high-throughput screening approaches. See current awards. See corresponding FOA.

Additional Information

Featuring

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


Plant Feedstock Genomics for Bioenergy Abstracts [09/14]


Sustainable Bioenergy [05/14]


BRC cover

Bioenergy Research Centers [02/14]


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