BER Research Highlights

Search Date: June 28, 2017

72 Records match the search term(s):


December 18, 2011

Understanding Impacts of Climate Change on Carbon Cycling by Soil Microbes

Quantifying feedbacks between terrestrial carbon cycling and changing climate conditions remains one of the major sources of uncertainty in predicting climate change impacts. A lack of mechanistic understanding of biogeochemical processes mediated by soil microbes and how they are affected by climate change variables is a significant element of this problem. New 'omics techniques for high-throughput characterization of microbial community structure and function are now providing powerful tools to examine these processes in intact ecosystems. Researchers at the University of Oklahoma have studied the impacts of long-term warming experiments (10+ years) on soil microbes at a grassland field site. The study describes compositional and functional shifts in the microbial communities related to elevated temperature and resulting changes in overlying vegetation and soil moisture. These effects were correlated with an increase in CO2 efflux from soils, which was tied to stimulation of microbial community members and enzyme activities associated with degradation of labile (but not recalcitrant) soil carbon sources. The team also observed an accelerated microbial cycling of nitrogen, phosphorous, and other soil nutrients that appeared to help stimulate plant growth and at least partially ameliorate the net loss of carbon from the system. These findings point to the complex role of microbial communities in climate impacted ecosystem processes. Further study will be needed to tease apart their net effects on carbon feedbacks.

Reference: Zhou, J., K. Xue, J. Xie, Y. Deng, L. Wu, X. Cheng, S. Fei, S. Deng, Z. He, J. D. Van Nostrand, and Y. Luo. 2011. "Microbial Mediation of Carbon-Cycle Feedbacks to Climate Warming," Nature Climate Change 2, 106-10. DOI: 10.1038/nclimate1331. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 12, 2011

Understanding Winter Hardiness in Switchgrass

The nation's dependence on imported fossil fuels could be alleviated, at least in part, by the domestication of dedicated bioenergy crops such as native perennial switchgrass for lignocellulosic ethanol production. Switchgrass is a promising feedstock candidate because it produces high yields of biomass on marginal lands unsuitable for production of food crops. In addition, perenniality (the ability of a plant to survive over winter and resume growth in the spring) is important for sustainability, since the unharvested below-ground tissues help maintain the integrity and nutrient status of the soil. Perennial biomass cultivars will need to tolerate fluctuations in temperature and rainfall, traits influenced by the overall health of below-ground tissues. Research¬ers at the USDA-ARS in Lincoln, Nebraska, with funding from the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy Program, analyzed changes in gene expression patterns in below-ground tissues (crowns and rhizomes) of the switchgrass cultivar 'Summer' to gain insight into the genetic mechanisms regulating these processes. The results revealed that these tissues are metabolically active, including pathways involved in basal cell metabolism and stress response. In addition, several novel gene sequences of unknown function were identified, which may represent genes specific to these tissues and with unique functions. These analyses should yield further insights into perenniality that will improve switchgrass as a sustainable bioenergy feedstock.

Reference: Palmer, N. A., A. J. Saathoff, J. Kim, A. Benson, C. M. Tobias, P. Twigg, K. P. Vogel, S. Madhavan, and G. Sarath. 2011. "Next-Generation Sequencing of Crown and Rhizome Transcriptome from Upland, Tetraploid Switchgrass," BioEnergy Research, DOI: 10.1007/s12155-011-9171-1. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 09, 2011

Microbial Carboxysomes: Key to Understanding Ocean Carbon Cycle

Bacteria play a key role in sequestering carbon dioxide (CO2) in the oceans. In particular, Prochlorococcus cyanobacteria are considered the world's most abundant photosynthetic organisms, able to convert sunlight to energy at ocean depths of up to 200 meters. Despite their small size, they are estimated to contribute up to half of all marine biological carbon sequestration. This microbe's ability to use carbon is attributed in part to the RuBisCO enzymes that fix CO2 and are stored in microcompartments known as carboxysomes. Learning about these tiny cellular structures can help researchers understand how their composition and design support their function, contributing to a better understanding of the ocean carbon cycle. Scientists at the University of Mississippi, the DOE Joint Genome Institute (JGI), and University of California at Berkeley report the first successful purification and characterization of these carboxysomes from a strain of P. marinus. Comparisons against 29 cyanobacterial genomes in a phylogenetic assay suggested, based on the numbers and types of genes that the team identified, that the carboxysome's structure is more complex than had been previously assumed. "Our findings have important implications for the structure, function, and regulation of α-carboxysomes and suggest that the protein composition of these important bacterial organelles warrants a closer look beyond what was assumed to be a solved problem," the team concluded.

Reference: Roberts, E. J., et al. 2012. "Isolation and Characterization of the Prochlorococcus Carboxysome Reveal the Presence of the Novel Shell Protein CsoS1D," Journal of Bacteriology 194(4), 787-95. DOI: 10.1128/JB.06444-11. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 02, 2011

Genome-Scale Modeling of Methane-Producing Microbes

Methane-producing microbes (i.e., methanogens) play a key role in the global carbon cycle and could significantly contribute to climate change due to the potent greenhouse gas properties of methane. These organisms occupy a central place in the biogeochemistry of soils, wetlands, and permafrost. However, it remains difficult to predict how they may respond to changing environmental conditions due to limited understanding of their biology. In a new study by DOE investigators at the University of Illinois, the first fully curated genome-scale metabolic model has been assembled for the methanogen Methanosarcina acetivorans. M. acetivorans is unique among methanogens in its ability to convert organic compounds such as acetate to methane, but it cannot perform the more traditional conversion of hydrogen and CO2. The new model's predictions have been validated using flux balance analysis and gene knockouts. The model provides new information on the integration of central and peripheral metabolic pathways, an important step in developing a systems biology approach to understanding this methanogen's behavior. These findings significantly increase our predictive understanding of this important class of microbes providing a powerful new tool to test hypotheses on their potential roles in climate change.

Reference: Benedict, M. N., M. C. Gonnerman, W. W. Metcalf, and N. D. Price. 2012. "Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A," Journal of Bacteriology 194, 855-65, DOI: 10.1128/JB.06040-11. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 30, 2011

Protein Complex Within Plant Cell Wall Associated with Secondary Cell-Wall Synthesis

The plant cell wall polysaccharide pectin is often associated with the tissue softening that occurs during fruit ripening. However, this complex compound is also involved in secondary cell-wall synthesis in grasses and woody plants, helping to give the plant rigidity, but also impeding the deconstruction of plant biomass and hence its conversion into biofuels. Researchers at the DOE BioEnergy Research Center (BESC) have discovered that the pectin-synthesizing enzyme GAUT1 forms an unusual, two-protein complex with a similar protein (GAUT7) that constitutes a critical part of a pectin-synthesizing protein complex. They also showed that this complex plays a role in secondary cell-wall synthesis. Manipulating the formation of this complex may provide a way to modify secondary cell walls, which could either increase available biomass or improve its digestibility for biofuel production.

Reference: Atmodjo, M. A., Y. Sakuragi, X. Zhu, A. J. Burrell, S. S. Mohanty, J. A. Atwood III, R. Orlando, H. V. Scheller, and D. Mohnen. 2011. "Galacturonosyltransferase (GAUT)1 and GAUT7 Are the Core of a Plant Cell Wall Pectin Biosynthetic Homogalacturonan: Galacturonosyltransferase Complex," Proceedings of the National Academy of Sciences of the United States of America 108(50), 20225-230. DOI: 10.1073/pnas.11128116108. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 28, 2011

Designing Low Lignin, High Biomass Yielding Plants

The major barrier to the efficient conversion of biomass from plant feedstocks to biofuels is breaking down the plant cell wall so that the sugars locked within can be released. This barrier is due to the presence of lignin, a complex compound that cross links the walls and provides rigidity to the plant. Plants that are genetically modified to have less lignin can be broken down more easily, but often these plants show severely stunted growth. Plants have a stress hormone (salicylic acid (SA)) that is known to impact plant growth and development and whose levels are inversely proportional to lignin levels. Researchers at the DOE BioEnergy Science Center (BESC) have found that genetically removing SA from Arabidopsis plants that were also modified to produce low levels of lignin restores normal growth to these plants while maintaining low lignin content. These results support the hypothesis that low lignin, high biomass yielding plants can be engineered to produce sustainable biofeedstocks for biofuel production.

Reference: Gallego-Giraldo, L., L. Escamilla-Trevino, L. A. Jackson, and R. A. Dixon. 2011. "Salicylic Acid Mediates the Reduced Growth of Lignin Down-Regulated Plants," Proceedings of the National Academy of Sciences of the United States of America 108(51), 20814-19. DOI: 10.1073/pnas.1117873108. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 28, 2011

Microbial Conversion of Switchgrass to Multiple Drop-In Biofuels

The low efficiency and high cost of enzymes used to break down plant material into sugars remains a major barrier to economically competitive production of cellulosic biofuels. Consolidated biomass processing, in which a single microorganism both produces cellulose-degrading enzymes and converts the resulting sugars to a desired biofuel, presents a promising alternative to improve efficiency and reduce costs, but few organisms naturally possess both capabilities. Researchers at the Joint Bioenergy Institute (JBEI) have now engineeered a modified strain of the workhorse industrial microbe E. coli that expresses a tailored set of cellulases, allowing it to degrade both the cellulose and hemicellulose chains released from switchgrass pretreated with ionic liquid. This was accomplished by cloning cellulase genes from Cellvibrio japonicus, a soil microbe with similar protein secretion systems to E. coli, and modifying the genes to allow proper timing and level of cellulase expression in the host. The team then added metabolic pathways that allowed E. coli to convert resulting sugars to either of two drop-in automotive biofuels (biodiesel and butanol) or a jet fuel precursor terpene compound. This presents a promising new advance in consolidated biomass processing, and, given the relative ease of genetic modification in E. coli, offers tremendous potential for subsequent engineering to increase conversion efficiency or synthesize a broader range of fuels.

Reference: Bokinsky, G., P. P. Peralta-Yahyn, A. George, B. M. Holmes, E. J. Steen, J. Dietrich, T. S. Lee, D. Tullman-Ercek, C. A. Voigt, B. A. Simmons, and J. D. Keasling. 2011. "Synthesis of Three Advanced Biofuels from Ionic Liquid-Pretreated Switchgrass Using Engineered Escherichia coli," Proceedings of the National Academy of Sciences of the United States 108(50), 19949-54. DOI: 10.1073/pnas.1106958108. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 23, 2011

Structure of Essential Malaria Parasite Enzyme Determined

The three-dimensional structures of proteins and other macromolecules often provide a starting point for designing new approaches to solving problems in a wide range of applications from bioenergy to medicine. The high-resolution structure of a specific protein can be used to identify small molecules that would bind to the protein and increase or decrease its activity to achieve a desired change in a biological system. A new study has determined the structures of an enzyme found in the malaria parasite (Plasmodium falciparum). The enzyme is not found in humans but is required by the parasite for the formation of its outer membrane. Several high-resolution structures were obtained for the enzyme in several stages of its functioning as well as with a small molecule that inhibits it. The structural information helped identify the enzyme’s active site and will be used as a starting point to seek drugs to treat infections by the malaria parasite. The results, published in the Journal of Biological Chemistry, were obtained by scientists from Washington University at the highly productive beamline 19ID of the DOE Structural Biology Center at Argonne National Laboratory’s Advanced Photon Source.

Reference: Lee, S. G., Y. Kim, T. D. Alpert, A. Nagata, and J. M. Jez. 2012. "Structure and Reaction Mechanism of Phosphoethanolamine Methyltransferase from the Malaria Parasite Plasmodium falciparum," Journal of Biological Chemistry 287, 1426-1434, DOI: 10.1074/jbcM111.315267. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2011

How do Microbes Adapt to Diverse Environments?

Earth's microbes live in staggeringly diverse environments, colonizing habitats with extremes of temperature, pH, salt concentration, or presence of toxic compounds. Archaea, a domain of single-celled microbes sharing traits with bacteria and simple eukaryotes, are well known for their ability to thrive in harsh environments. How this impressive adaptive capability is achieved has remained a mystery. Now, a team of investigators at the Institute for Systems Biology has completed a groundbreaking study on the role of gene regulation in environmental niche adaptation by Halobacterium salinarum, an archaeal microbe that grows in high salt environments. Using a combination of comparative genomics and hypothesis-driven molecular biology experiments, the team found that a specific class of regulatory genes had been duplicated during the archaea's evolution and controls a nested set of "niche adaptation programs." These programs control cascades of gene expression essential for adaptation to particular environments. Diversification of these control elements has resulted in a "division of labor" such that overlapping regulatory networks flexibly balance large-scale functional shifts under changing conditions, where rapid adaptation increases fitness. Describing mechanisms that control niche adaptation in microbes allows us to better understand how microbial communities function in natural environments, and provides an intriguing glimpse into fundamental design rules governing biological systems.

Reference: Turkarslan, S., D. J. Reiss, G. Gibbins, W. L. Su, M. Pan, J. C. Bare, C. L. Plaisier, and N. S. Baliga. 2011. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors,” Molecular Systems Biology 7, Article 554. DOI:10.1038/msb.2011.87. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 18, 2011

Microbes Solve Environmental Contamination Problems

Microbes carry out a wide range of chemical transformations. Understanding the mechanisms of these processes can lead to new biological insights and practical applications. For example, removal of polycyclic aromatic hydrocarbons (PAHs) from contaminated soils is facilitated by microbial degradation. The PAH phenanthrene can be broken down by Arthrobacter phenanthrenivorans, a bacterium isolated from a creosote-polluted site in Greece and that uses phenanthrene as a carbon and energy source. A team of researchers, including a collaborator from the DOE Joint Genome Institute, has purified and analyzed two phenanthrene-breakdown enzymes from this microbe. Based on the similarity of the two genes' sequences and their common expression in the presence of the PAH, the authors suggest that one of the genes is a duplication of the other even though they are located in very different parts of the genome. Similar results are found in other related bacteria. These types of comparative studies may aid in the design of strategies using microbes for DOE missions or other applications, such as wastewater treatment, biodegradation, and biocatalysis.

References: Vandera, E., K. Kavakiotis, A. Kallimanis, N. Kyrpides, C. Drainas, and A. Koukkoua. 2012. "Heterologous Expression and Characterization of Two 1-Hydroxy-2-Naphthoic Acid Dioxygenases from Arthrobacter phenanthrenivorans," Applied and Environmental Microbiology 78(3), 621-27. DOI: 10.1128/AEM.07137-11. (Reference link)

Kallimanis, A., et al. 2011. "Complete Genome Sequence of Arthrobacter phenanthrenivorans Type Strain (Sphe3)," Standards in Genomic Sciences 4, 123-30. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 06, 2011

Permafrost Microbes Could Make Impacts of Arctic Warming Worse

In Earth’s Arctic regions, frozen soils (permafrost) sequester an estimated 1.6 trillion metric tons of carbon, more than 250 times the amount of greenhouse gas emissions attributed to the United States in 2009. Concerns are growing about the potential impact on the global carbon cycle when rising temperatures thaw the permafrost and release the trapped carbon. Microbes may significantly influence the eventual outcome through their involvement in carbon cycling. New research on permafrost microbes has discovered a previously unknown, yet abundant microbe that produces methane, a far more potent greenhouse gas than carbon dioxide. A draft of this microbe’s genome was determined by assembling DNA fragments isolated from permafrost. The DOE Joint Genome Institute (JGI) had previously identified several microbes that produced methane ("methanogens") as a metabolic byproduct, and used this knowledge to identify enough fragments of the new microbe’s DNA to assemble a draft of its genome. The abundance of this novel methanogen implies that it could be an important factor in methane production under permafrost thawing conditions. The research, published in Nature, was carried out by scientists at JGI, Lawrence Berkeley National Laboratory, and U.S. Geological Survey.

Reference: Mackelprang, R., et al. 2011. “Metagenomic Analysis of a Permafrost Microbial Community Reveals a Rapid Response to Thaw,” Nature 480, 368-71. DOI: 10.1038/nature10576. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 19, 2011

DOE User Facilities Help Explain Workings of Key Metabolic Enzyme

Carbonic anhydrase (CA) converts bicarbonate ion to carbon dioxide and back. It is a key part of the metabolism of humans, animals, plants, and microbes that involves carbon dioxide. Engineered and stabilized forms of CA are being studied for use to capture CO2 from flue gas at coal-fired power plants and as part of algal biofuel production. Three recent publications improve our understanding of how CA works using the unique capabilities of DOE's National Synchrotron Light Source (NSLS) and Los Alamos Neutron Science Center (LANSCE). X-ray crystallography at the NSLS was used to show how human CA recognizes molecules to which it might bind. These data support the authors' hypothesis from thermodynamic considerations that "the shape of the water in the (HA) binding cavity may be as important as the shape of the cavity." The second study, used neutron diffraction of human CA at LANSCE to show that the catalytic site CA changes when the pH of the water around it decreases from 10.0 to 7.8. This observation, the first of its kind, enabled the authors to define more clearly the proton transfer that occurs when CA catalyzes the carbon dioxide—bicarbonate conversion. These studies will help scientists re-engineering CA designs for CO2 capture, biofuel production, and other applications.

The NSLS studies were carried out by scientists at Brookhaven’s Macromolecular Crystallography Research Resource jointly with scientists from Harvard University, while the LANSCE experiments were carried out by scientists at Los Alamos’ Protein Crystallography Station in collaboration with scientists from the University of Florida.

Reference: Snyder, P.W., et al. 2011. "Mechanism of the Hydrophobic Effect in the Biomolecular Recognition of Arylsulfonamides by Carbonic Anhydrase," Proceedings of the National Academy of Sciences (USA), DOI: 10.1073/pnas.1114107108. (Reference link)
[Discussed in Ball, P. 2011. "Biophysics: More Than a Bystander," Nature 478, 467-68. (DOI:10.1038/478467a) (Reference link)]

Mecinovic, J., et al. 2011. "Fluoroalkyl and Alkyl Chains Have Similar Hydrophobicities in Binding to the 'Hydrophobic Wall' of Carbonic Anhydrase," Journal of the American Chemical Society 133, 14017. DOI: 10.1021/ja2045293. (Reference link)

Fisher, Z., et al. 2011 "Neutron Structure of Human Carbonic Anhydrase II: A Hydrogen-Bonded Water Network "Switch" Is Observed Between pH 7.8 and 10.0," Biochemistry 50, 9421-23. DOI: 10.1021/bi201487b. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 18, 2011

Genomic Science Program Scientist To Become Editor of Analytical Chemistry

Jonathan Sweedler of the University of Illinois, Urbana-Champaign, has been named the new editor of the American Chemical Society journal Analytical Chemistry, the most widely read journal in this field. His research has focused on bioanalytical chemistry, specifically on small volume peptidomics and metabolomics. Sweedler has been funded since the late 1990s for the development and application to DOE missions of a variety of analytical techniques, initially for genome sequencing and currently for genomic applications of mass spectrometry. He has a current Office of Biological and Environmental Research award with his collaborator Paul Bohn of Notre Dame to study the molecular interactions among microbes, and between microbes and plants. The objective of this work is to develop correlated chemical and spatial information, employing mass spectrometry and confocal Raman imaging to characterize key molecular species and events in multicellular processes. Sweedler is a chemistry professor and director of the Roy J. Carver Biotechnology Center at the University of Illinois.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 12, 2011

Mapping Sensory Systems in Sulfate-Reducing Bacteria

Sulfate-reducing bacteria (SRBs) play important roles in the decomposition of organic matter, cycling of nutrients, and transformation of heavy metals in subsurface environments. Sensing and responding to minute shifts in nutrient levels, potentially damaging or toxic conditions, and the presence of other microbes is critical to their lifestyle. Systems involving two components, paired sets of sensor and regulator proteins that control gene expression, are an important sense/response mechanism in bacteria, but it remains extremely difficult to establish relationships between the systems and larger networks of regulated genes. Researchers at Lawrence Berkeley National Laboratory have now completed the first-ever map of two-component regulatory systems for the model microbe SRB Desulfovibrio vulgaris using a cell-free approach based on direct binding of purified regulator proteins to genome fragments. Genes involved in nutrient acquisition, growth, stress response, and community assembly were mapped onto specific response regulators, providing a greatly enhanced understanding of how SRBs react to changing environmental conditions and mediate key processes in the subsurface.

Reference: Rajeev, L., E. G. Luning, P. S. Dehal, M. N. Price, A. P. Arkin, and A. Mukhopadhyay. 2011. “Systematic Mapping of Two Component Response Regulators to Gene Targets in a Model Sulfate Reducing Bacterium,” Genome Biology 12:R99. DOI:10.1186/gb-2011-12-10-r99. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 10, 2011

Maize Juvenility Gene Enhances Biofuel Production from Bioenergy Crops

The sugars in plant cell walls have the potential to be converted on a large scale to biofuels; however, these sugars are locked in a rigid lignin matrix, inhibiting their extraction and conversion into biofuels. Researchers have now discovered a potential way around this obstacle through studies of the maize Corngrass1 (Cg1) gene, which promotes maintenance of juvenility in maize plants. Since juvenile plant material contains less lignin, they hypothesized that this mutant might produce plants whose sugars would be more easily extracted and converted into biofuels. When the Cg1 gene was transferred into other plants, including the potential bioenergy crop switchgrass, the amount of starch and subsequent glucose release was significantly higher than from the wild type plants even without expensive pretreatment. These results offer a promising new approach for the improvement of dedicated bioenergy crops. The research was carried out at the USDA-ARS, University of California, Berkeley, DOE's Joint BioEnergy Institute, and the Energy Biosciences Institute, and supported in part by the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy program. It is published in the Proceedings of the National Academy of Sciences.

Reference: Chuck, G. S., C. Tobias, L. Sun, F. Kraemer, C. Li, D. Dibble, R. Arora, J. N. Bragg, J. P. Vogel, S. Singh, B. A. Simmons, M. Pauly, and S. Hake. 2011. "Overexpression of the Maize Corngrass1 MicroRNA Prevents Flowering, Improves Digestibility, and Increases Starch Content of Switchgrass," Proceedings of the National Academy of Sciences (USA) 108(42), 17550-55. DOI:10.1073/pnas.1113971108. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 27, 2011

Microbial Production of Bisabolane, a New Terpene-Based Biofuel

Development of next-generation biofuels will require economical production of high-energy compounds that are compatible with existing vehicle engines and fuel distribution infrastructures. To this end, researchers at the DOE Joint Bioenergy Institute (JBEI) have been exploring potential fuel properties of molecules in the terpene family. Many terpene molecules possess properties similar to petroleum-derived fuel compounds, and industrial microbes such as yeast and E. coli have been previously engineered for terpene compound synthesis for pharmaceutical production. In a new study published in Nature Communications, JBEI scientists describe production of the terpene bisabolane, a molecule with fuel properties similar to D2 diesel. After identifying bisabolane as a promising biofuel, the team embarked on a series of targeted genetic modifications to terpene synthesizing E. coli and yeast strains, resulting in microbial production of the compound using simple sugars as the starting material. Unlike other biofuels such as ethanol and isobutanol, bisabolane was found to be relatively nontoxic to the microbes and thus could potentially be produced at higher yields. Efforts are currently underway to screen the fuel properties of biologically produced bisabolane and develop improved fermentation strategies that would enable scaling of production to commercial levels.

Reference: Peralta-Yahya, P. P., M. Ouellet, R. Chan, A. Mukhopadhyay, J. D. Keasling, and T. S. Lee. 2011. "Identification and Microbial Production of a Terpene-Based Advanced Biofuel," Nature Communications 2:483. (DOI: 10.1038/ncomms1494) (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 16, 2011

Engineering Microbes to Produce Biodiesel Precursors

Biodiesel production typically starts with oil-rich energy crops such as soybean, palm, or rapeseed, which are harvested and converted into fatty acids from which biodiesels or other fuels are derived. The cost of expanding crop production is a limiting factor in allowing biodiesel to compete with fossil fuel sources. One alternative is to avoid the plant entirely and directly synthesize the precursor fatty acids in bacteria, bypassing several upstream steps, reducing production costs, and raising final yields. A team of researchers, including members of the DOE Joint Genome Institute, now has developed a process to engineer bacteria to produce biodiesel with the help of a novel fatty acid synthesis enzyme. The enzyme, identified and characterized from several bacterial sequences, was inserted into the commonly used model microbe E. coli to prove that it was involved in fatty acids synthesis. The fatty acid pathway was further engineered to improve the generation of biodiesel precursors. This new work provides an alternative route for the synthesis of biofuel molecules. The pathway they describe is a first step in the generation of biodiesel and, with further optimization, may lead to the production of a cost-efficient, next-generation biofuel. The results have just been published in Applied and Environmental Microbiology.

Reference: Nawabi, P., S. Bauer, N. Kyrpides, and A. Lykidis. 2011. "Engineering Escherichia coli for Biodiesel Production Utilizing a Bacterial Fatty Acid Methyltransferase," Applied and Environmental Microbiology 77(22), 8052-61. DOI:10.1128/AEM.05046-11

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 12, 2011

Understanding How Environmental Microbes Make Uranium Less Soluble

Uranium is one of the major contaminants at DOE cleanup sites. It was usually released into the environment as the highly soluble uranyl ion (uranium (VI)). This ion interacts with bacteria and minerals in the ground to form reduced uranium (IV), notably in the mineral uraninite, a form that is much less soluble than uranium (VI). Less soluble uranium (IV) species are less likely to be moved out of the initially contaminated zone and into nearby rivers or aquifers by groundwater. New research has shown that biologically produced uraninite in a natural underground environment dissolves much more slowly than uraninite prepared in the laboratory. Researchers have developed a model showing that the slower dissolution is due to the presence of biomass that limits the reoxidation rate of the uranium (IV) in uraninite and diffusion of oxidized uranium into the groundwater. This understanding will be used in developing improved models of uranium transport in contaminated environments. Field studies were carried out at the Old Rifle, Colorado, Integrated Field Research Challenge site, while experiments to determine the forms of uranium present were conducted at the Stanford Synchrotron Radiation Lightsource.

Reference: Campbell, K. M., et al. 2011. "Oxidative Dissolution of Biogenic Uraninite in Groundwater at Old Rifle, CO," Environmental Science and Technology 45, 8748–54. DOI: 10.1021/es200482f. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 02, 2011

Capturing Carbon in the Dark Ocean

Contributions to the carbon cycle in the ocean's water column below the penetration of sunlight have not yet been explained either mechanistically or quantitatively, although a significant part of ocean carbon fixation is known to be due to microbial activities. Current oceanographic models suggest that archaea, the prevalent microbial domain in the oceans, do not adequately account for the carbon that is being fixed in the dark ocean. New research using sequencing technology has identified microbes involved in capturing carbon in the twilight zone, the region of the ocean that lies between 200 meters and 1,000 meters beneath the surface. This study discovered specific types of bacteria (the other domain of prokaryotic microbes besides the archaea) that may be responsible for this major, previously unrecognized component of the dark ocean carbon cycle. The report's authors isolated and identified bacteria from water samples collected in the South Atlantic and North Pacific oceans. They found that "...previously unrecognized metabolic types of dark ocean bacteria may play an important role in global biogeochemical cycles, and their activities may in part reconcile current discrepancies in the dark ocean's carbon budget." A better model of carbon cycling in the oceans will help experts predict future CO2 concentrations in the atmosphere and oceans and impacts of altered CO2 fluxes on ocean biogeochemistry. This work involved researchers from the DOE Joint Genome Institute.

Reference: Swan, B., et al. 2011. "Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean," Science 333, 1296-1300. DOI: 10.1126/science.1203690. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 01, 2011

Direct Mass Spectrometric Imaging of Cellulose and Hemicellulose in Populus Tissue

Pretreatment of bioenergy feedstocks produces complex chemical changes that need to be understood to evaluate the effectiveness of different pretreatment regimens. Feedstock imaging can provide useful information, but high molecular specificity is required to identify components such as cellulose and hemicellulose and to produce useful spatial images. Simple mass spectrometry (MS) is limited by the complexity of the plant tissue. University of Florida researchers have successfully overcome this difficulty by applying matrix-assisted laser desorption/ionization mass spectrometry (MALDI) linear ion trap tandem MS technology. In tandem MS, the material goes through two consecutive rounds of MS instead of one. While single MALDI MS images of young Populus wood stems show an even distribution of both cellulose and hemicellulose, tandem MS produces very different images of the distribution of the two plant components. The new strategy offers the high molecular specificity needed for analyzing complex lignocellulosic biomass and will be applicable to many plant species that are potential bioenergy resources.

Reference: Lunsford, K. A., G. Peter, and R. Yost. 2011. "Direct Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Imaging of Cellulose and Hemicellulose in Populus Tissue," Analytical Chemistry 83(17), 6722-30. (DOI: 10.1021/ac2013527) (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 01, 2011

Engineering Microbes for Optimized Biofuel Production

Redirecting a microbe's metabolic pathways to make desired products frequently results in slower growth, lower yield, and other negative impacts that reduce production efficiency. This is often related to the accumulation of toxic intermediates at metabolic "bottlenecks" in microbes lacking natural pathways to use, redirect, or dispose of these compounds. Researchers at the DOE Joint Bioenergy Institute (JBEI) have observed this phenomenon in E. coli strains expressing an engineered pathway for the synthesis of terpene, a precursor of several different hydrocarbon biofuels. To alleviate this toxicity, the team screened genome databases to identify variants of the enzyme in other organisms that are able to process the problematic compound. The enzymes were expressed in vitro and assayed for activity, and genes encoding the most promising candidates were engineered into E. coli. This produced a set of strains with varying synthesis properties under different growth conditions. Subsequent manipulation of gene expression levels, cofactor pools, and redox conditions resulted in a 120% improvement in terpene production over the initial strain. These results further improve an already promising industrial microbe and demonstrate the potential of coupled systems biology and targeted metabolic engineering for enhancing biofuel production.

Reference: Maa, S. M., D. E. Garcia, A. M. Redding-Johanson, G. D. Friedland, R. Chan, T. S. Batth, J. R. Haliburton, D. Chivian, J. D. Keasling, C. J. Petzold, T. Lee, and S. R. Chhabra. 2011. "Optimization of a Heterologous Mevalonate Pathway Through the Use of Variant HMG-CoA Reductases," Metabolic Engineering 13(5), 588-97. (DOI: 10.1016/j.ymben.2011.07.001) (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 01, 2011

Improving Understanding of Microbial Interactions with the Environment

Transporter proteins control the flow of large and small molecules in and out of the cell and are a primary means for organisms to interface with the environment. Transporters affect cellular metabolic capabilities and influence signaling pathways and regulatory networks that are key to the cell’s behavior. DOE researchers have confirmed the efficacy of a high-throughput methodology to rapidly and specifically identify the molecules transported by these proteins. The new technique measures the change in the melting temperature of proteins. Using Rhodopseudomonas palustris as a test case, they found a variety of compounds bound to the transporters studied that were not predicted using standard computational methods. These findings illustrate the potential of this method to expand our ability to predict the response of microbes and cells to environmental changes, such as the utilization of environmental nutrients and the ejection of toxic compounds.

Reference: Giuliani, S. E., A. M. Frank, D. M. Corgliano, C. Seifert, L. Hauser, and F. R. Collart. 2011. "Environment Sensing and Response Mediated by ABC Transporters," BMC Genomics 12(Supplement 1), S8. (DOI: 10.1186/1471-2164-12-S1-S8) (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 01, 2011

Poplar Roots Influence Microbial Community Composition

Poplar, a model organism for woody perennials, is a promising bioenergy feedstock for producing cellulosic biofuels. Poplar roots establish intimate associations with various microorganisms, both bacterial and fungal, that are beneficial to both plant and microbe. However, these associations are still poorly understood. Researchers at Oak Ridge National Laboratory have published the first results of a comprehensive study of the poplar rhizosphere (soil in direct contact with plant roots) and endophytic (living within plant tissues without causing harm) microbial communities from mature, natural poplar stands. They investigated microbial diversity among root endophyte and associated rhizosphere communities from two poplar populations differing in soil and stand characteristics near the Caney Fork River in central Tennessee. Although soil was not a major determinant of microbial distribution and diversity, the rhizosphere and endophyte communities of both bacteria and fungi were distinct. The results suggest that tissues within naturally occurring poplar roots provide a unique niche for these microorganisms. The research has implications for the growth and management of poplar plantations established for biofuel production.

Reference: Gottel, N. R., H. F. Castro, M. Kerley, Z. Yang, D. A. Pelletier, M. Podar, T. Karpinets, E. Uberbacher, G. A. Tuskan, R. Vilgalys, M. J. Doktycz, and C. W. Schadt. 2011. "Distinct Microbial Communities Within the Endosphere and Rhizosphere of Populus deltoides Roots Across Contrasting Soil Types," Applied and Environmental Microbiology 77(17), 5934-44. (DOI:10.1128/AEM.05255-11) (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 21, 2011

New Microfluidic Device Enables Characterization of Environmental Microbes

Microbes play critical roles in global scale environmental processes such as carbon cycling and the movement and degradation of environmental contaminants at waste sites. Understanding and predicting the roles of particular types of microbes in these processes remains extremely challenging, since over 90% of environmental microbes cannot be grown in the lab and existing approaches do not allow identification of specific cell types or quantification of their abundance. Researchers at Lawrence Berkeley National Laboratory and Sandia National Laboratories have now developed a new microfluidic device called µFlowFISH that enables the high-throughput identification of the types and abundance of microbes from environmental samples. Microbial cells are moved through the chip-mounted device using electrical currents, fluorescently labeled using diagnostic probes, and counted in a flow cytometry chamber. After initial testing with microbes that could be cultured, µFlowFISH was used to analyze microbes in groundwater samples from the DOE Hanford 100H cleanup site, targeting organisms known to be involved in uranium immobilization. Results from the device were in good agreement with more cumbersome and time-intensive techniques, requiring 100-fold less sample and far less time. Coupled to "omics" methods for comprehensive microbial community analysis, µFlowFISH presents a powerful new tool for dissecting microbial community structure and function in a variety of environments. Reference: Peng, L., R. J. Meagher, Y. K. Light, S. Yilmaz, R. Chakraborty, A. P. Arkin, T. C. Hazen, and A. K. Singh. 2011. "Microfluidic Fluorescence In Situ Hybridization and Flow Cytometry (µFlowFISH)," Lab on a Chip 11, 2673-79. DOI: 10.1039/c1lc20151d.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 18, 2011

A "Meraculous" Algorithm for Whole-Genome Assemblies

DNA sequencing technologies generate a tremendous amount of genomic data compared to just a few years ago. Today, however, most genomic data is for small DNA fragments that need to be assembled back into a whole genome to elucidate the biological function of the parent organism. This represents a computational challenge for the sequencing community, in particular when the amount of genomic data reaches more than a hundred million fragments. DOE Joint Genome Institute researchers have now developed an efficient algorithm, Meraculous, to assemble the short genomic fragments into whole genome sequences. Meraculous can quickly and accurately assemble microbial genomes with a fraction of the computer memory required for more traditional methods, thanks to the use of novel techniques in graph theory and in memory-efficient hashing schemes. JGI staff have tested this method on Pichia stipiti, a microbe that efficiently produces ethanol from the five-carbon sugar xylose and found that they were able to quickly reconstruct 95% of the genome, error free. Research at JGI continues to advance this algorithm with applications to more complex plant genomes planned.

Reference: Chapman, J. A., I. Ho, S. Sunkara, S. Luo, G. P. Schroth, and D. S. Rokhsar. 2011. "Meraculous: De Novo Genome Assembly with Short Paired-End Reads," PLoS ONE 6(8), e23501. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 16, 2011

Assessing Carbon Impacts of Land-Use Choices for Bioenergy Crops

The Conservation Reserve Program (CRP) contains over 13 million hectares of former croplands now in grasslands, providing a reservoir of biodiversity, water quality, and carbon sequestration benefits. However, these benefits could be lost if the land is converted back to agricultural use for biofuel production. Scientists from the DOE Great Lakes Bioenergy Research Center analyzed the effects that converting CRP lands to annual crops for biofuel production (continuous corn and corn-soybean rotation, each either tilled or permanent no-till) would have on greenhouse gas (GHG) emissions as compared with directly harvesting perennial grasses on these lands for cellulosic ethanol. They report that although a no-till management regime of an annual bioenergy crop would reduce the carbon debt significantly compared with tilling, harvesting perennial grasses would result in virtually no GHGs lost, because the disruption required when converting to annual crops would be avoided. This is the first time field trials have been used instead of model predictions. The trials show that carbon debt can be avoided and climate change mitigated by directly using unconverted CRP grasslands for cellulosic feedstock production. The results will be helpful in developing strategies for producing bioenergy crop systems.

Reference: Gelfand, I., T. Zenone, P. Jasrotia, J. Chen, S. K. Hamilton, and G. P. Robertson. 2011. "Carbon Debt of Conservation Reserve Program (CRP) Grasslands Converted to Bioenergy Production," Proceedings of the National Academy of Sciences of the United States of America 108(33), 13864-69. (DOI: 10.1073/pnas.1017277108) ( (Reference link)

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 08, 2011

Key Ethanol Tolerance Gene Identified in Biomass-Degrading Bacteria

If a single organism could breakdown cellulosic biomass and synthesize biofuels, a process known as consolidated bioprocessing, it could significantly increase the efficiency and reduce the costs of biofuel production. Some biomass-degrading microbes such as Clostridium thermocellum can also synthesize ethanol, but they are poisoned by relatively low ethanol concentrations compared to sugar fermenters such as yeast or E. coli. Researchers at the DOE Bioenergy Science Center (BESC) have now identified a key gene in C. thermocellum that is related to enhanced ethanol tolerance. The team analyzed genomes of C. thermocellum mutants that could tolerate higher than normal ethanol concentrations, and found a consistently modified gene involved in alcohol metabolism. By analyzing the structure of the encoded protein, it was determined that the mutation causes significant alterations to central ethanol metabolism. The identification of this gene will enable more targeted metabolic engineering approaches to improve production of ethanol and other biofuels in C. thermocellum and other biomass-degrading microbes useful for consolidated bioprocessing.

Reference: Brown, S. D., A. M. Guss, T. V. Karpinets, J. M. Parks, N. Smolin, S. Yang, M. L. Land, D. M. Klingeman, A. Bhandiwad, M. Rodriguez, Jr., B. Raman, X. Shao, J. R. Mielenz, J. C. Smith, M. Keller, and L. R. Lynd. 2011. "Mutant Alcohol Dehydrogenase Leads to Improved Ethanol Tolerance in Clostridium thermocellum," Proceedings of the National Academy of Sciences of the United States of America 108, 13752-57. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 05, 2011

Conifer-Rotting Fungus Offers Potential New Strategy for Lignocellulose Degradation

Due to its abundance and high cellulose content, wood has great potential as raw material for the production of biofuels. However, wood also contains lignin, a hard-to-degrade polymer that poses a major obstacle to converting its cellulose into liquid fuels. White rot fungi have evolved mechanisms to digest lignin and cellulose, and scientists are trying to take advantage of these capabilities. Now, new research using genome sequencing and comparative analysis of the brown rot fungus Serpula lacrymans has discovered a different strategy used by this boreal forest fungus to extract the energy-rich cellulose from conifer wood. A comparison of the gene content in white and brown rot fungi indicates that the enzymatic machinery to degrade lignin has been eliminated in brown rot fungi, enabling it to specifically target cellulose, separating it from the recalcitrant lignin. The researchers also discovered that in the presence of wood, S. lacrymans produces variegatic acid, a phenolate compound that helps in reducing iron ions to Fe+2, which are required for the initial non-enzymatic steps in cellulose degradation upon wood colonization by the fungus. These insights provide researchers with new strategies to potentially bypass the problem of eliminating lignin from renewable woody feedstocks for transportation fuel production. The research has just been published in Science and was carried out by an international consortium including researchers at DOE's Joint Genome Institute in Walnut Creek, CA, and its partners HudsonAlpha Institute for Biotechnology (Huntsville, AL) and Pacific Northwest National Lab (Richland, WA).

Reference: D. C. Eastwood, et al. 2011. "The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi", Science, 333, 762-65. DOI:10.1126/science.1205411. (Reference link)

Contact: Pablo Rabinowicz, SC-23.2 (301) 903-0379
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 02, 2011

New Insights on Algal Metabolism

Photosynthetic algae are a potential bioenergy source; however, significant unknowns about their basic metabolic properties have hindered development of algae for biofuel production. DOE researchers now present a new metabolic network reconstruction and a genome-scale model of light-driven metabolism for the alga Chlamydomonas reinhardtii. This approach represents a significant advance over previous metabolic models for this organism since it incorporates greatly improved functional gene annotations, experimental validation of gene expression, and quantitative reaction measurements under different light conditions. This model allows enhanced understanding and prediction of photosynthetic growth properties (including lipid synthesis) under varying conditions and provides a broad knowledgebase of potential targets for directed metabolic engineering. This publication was featured in the Editor’s Choice section of the August 12th issue of Science.

Reference: Chang, R. L., L. Ghamsari, A. Manichaikul, E. F. Hom, S. Balaji, W. Fu, Y. Shen, T. Hao, B. Palsson, K. Salehi-Ashtiani, and J. A. Papin. 2011. "Metabolic Network Reconstruction of Chlamydomonas Offers Insight into Light-Driven Algal Metabolism," Molecular Systems Biology 7:518. DOI:10.1038/msb.2011.52. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 26, 2011

Symbiotic Relationship with Fungi Benefits Bioenergy Feedstock Poplar

The forest soil environment is teeming with microbial communities, including a group of mutualistic fungi known as the ectomycorrhizae. These organisms develop a close association with tree roots, establishing an exchange of nutrients and sugars essential for the health of both plant and microbe. While this phenomenon has been known for a long time, the signaling and regulatory mechanisms of this exchange are poorly understood. Researchers at the DOE Oak Ridge National Laboratory, as part of an international collaboration, have identified and characterized a protein called Mycorrhizal Induced Small Secreted Protein 7 (MiSSP7) that is secreted from the ectomycorrhizal fungus Laccaria bicolor in response to signals diffused from the roots of poplar trees, a promising bioenergy feedstock. They found that this very small protein is imported into the nucleus of the host plant cell where it alters the expression of certain plant genes, similar to the manner in which fungal pathogens work. The result is a "reprogram-ming" of plant cells, through which a beneficial, symbiotic relationship between fungus and plant is established. This relationship enhances growth and productivity of the tree. Understanding the underlying mechanism will help address diverse DOE missions, including bioenergy production, environmental remediation, and carbon cycling and sequestration.

Reference: Plett, J. M., M. Kemppainen, S. D. Kale, A. Kohler, V. Legué, A. Brun, B. M. Tyler, A. G. Pardo, and F. Martin. 2011. "A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development," Current Biology 21, 1197&ndash1203. DOI:10.1016/j.cub.2011.05.033. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 12, 2011

Impact of Bioenergy Feedstocks on Agricultural Landscapes

Simplification of the agricultural landscape due to expansive monocultures of individual crops reduces habitat diversity and has long been believed to increase insect pest pressure with a resulting need for more insecticides. This assumption seems logical, but has lacked supporting scientific evidence, evidence needed to establish a science-based land-use policy that includes dedicated bioenergy crops. Now, researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) have reported an analysis of cropping systems across 562 counties in seven Midwestern states. They found a significant correlation between insecticide use and land simplification (i.e., less natural habitat). The results suggest that plantings of more minimally managed perennial bioenergy crops requiring less insecticide use may mitigate some of the negative effects associated with continued simplification. This study provides a scientific basis for understanding the impact that the greater demand for bioenergy feedstocks will have on the agricultural landscape.

Reference: Meehan, T. D., B. P. Werling, D. A. Landis, and C. Gratton. 2011. "Agricultural Landscape Simplification and Insecticide Use in the Midwestern United States," Proceedings of the National Academy of Sciences of the United States of America 108, 11500–505. DOI: 10.1073/pnas.1100751108.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 11, 2011

Engineering a Better Switchgrass

Perennial grasses such as switchgrass are considered prime candidates for bioenergy feedstocks because of their potential for substantial biomass yields on marginal lands. An approach that promises further improvement in this species is genetic transformation, the introduction and expression of desirable genes from other sources to increase yields and reduce recalcitrance. Current transformation technology, however, uses promoters (segments of DNA that control the expression of desired genes) from other plants making them inefficient for use in switchgrass. Researchers from the DOE BioEnergy Science Center (BESC) now report the identification of novel promoter regions from a specific switchgrass gene that is found in all eukaryotes and that can be used for efficient genetic transformation in switchgrass. A variety of transgenic plants constructed with these promoters exhibited significantly higher gene expression levels than observed using the non-switchgrass promoters, showing great potential for driving transgenic expression in switchgrass and other plants. This is the first characterization of native switchgrass promoter sequences for transgene expression. The results will facilitate improvement of switchgrass and other bioenergy feedstocks through engineering of key bioenergy-relevant traits.

Reference: Mann, D. G. J., Z. R. King, W. Liu, B. L. Joyce, R. J. Percifield, J. S. Hawkins, P. R. LaFayette, B. J. Artelt, J. N. Burris, M. Mazarei, J. L. Benentzen, W. A. Parrott, and C. N. Stewart. 2011. "Switchgrass (Panicum virgatum L.) Ubiquitin Gene (PvUbi1 and PvUbi2) Promoters for Use in Plant Transformation," BMC Biotechnology 11, DOI: 10.1186/1472-6750-11-74. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 30, 2011

In Search of Enzymes for Biofuel Production

Some microbes contain enzymes that can break down lignocellulosic biomass, such as that found in switchgrass or Miscanthus. But there are few suitable methods for finding these enzymes in complex microbial communities. Researchers at the DOE Joint BioEnergy Institute (JBEI) have developed a new method that uses nanostructure initiator mass spectroscopy (NIMS). It enables rapid and accurate characterization of enzymes in complex microbial and environmental samples (e.g., microbial compost). Using this new technology, JBEI researchers have characterized a broad range of environmental and purified microbial samples, further optimizing selected samples for enzymatic activity and stability in the presence of ionic liquids, which are being tested by JBEI for use in biofuel production. This new NIMS-based approach may aid in finding more efficient ways to convert biomass into lignocellulosic biofuels.

Reference: Reindl, W., K. Deng, J. M. Gladden, G. Cheng, A. Wong, S. W. Singer, S. Singh, J.-C. Lee, C.-H. Yao, T. C. Hazen, A. K. Singh, B. A. Simmons, P. D. Adams, and T. R. Northen. 2011. "Colloid-Based Multiplexed Screening for Plant Biomass-Degrading Glycoside Hydrolase Activities in Microbial Communities," Energy and Environmental Science 4, 2884–93. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 23, 2011

Special "Biofuels Outlook" Section in Nature

The June 23, 2011, issue of the journal Nature features a special supplementary section that outlines the current state of biofuels research, highlights recent advances, and discusses potential issues associated with the expanded use of biomass-derived transportation fuels. Articles in the supplement discuss development of advanced drop-in biofuels compatible with existing engines, new approaches to economically break down tough lignocellulosic plant material into fermentable sugars, the potential of dedicated biomass feedstocks to reduce “food vs fuel” and water demand issues, and a variety of other topics relevant to biofuels development. Researchers involved in all three DOE Bioenergy Research Centers, as well as numerous scientists pursuing independent biofuels research supported by DOE’s Genomic Science program, discuss their work in the supplement. The collected articles provide a valuable resource for communicating the current state of biofuels R&D to the broader scientific community and the general public.

Reference: Grayson, M., et al. 2011. "Nature Outlook: Biofuels," Nature 474 (7352), supp S1–S43.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 17, 2011

What Makes a Plant a Plant?

DNA sequencing has generated vast collections of genes for all types of organisms; however, determining the roles of the proteins coded within those genes is a difficult task and the functions of many of those proteins are still unknown. Researchers at the UCLA-DOE Institute for Genomics and Proteomics and at the DOE Joint Genome Institute in Walnut Creek, California, have now provided new information on the function of genes that are uniquely found in plants and green algae. Comparing the genes present in the genomes of 20 photosynthetic organisms with those of non-photosynthetic organisms, the investigators compiled GreenCut2, an inventory of nearly 600 plant-specific genes. As the function of more than half of those 600 genes is not known, this work sheds new light on genes needed for plant-specific processes, including those related to the chloroplast (the photosynthetic organelle of plant cells). Further analysis of those proteins of unknown function showed that many of them are likely involved in protein modification, gene regulation, and transport of molecules to the chloroplast. This new knowledge provides insights on plant evolution and will help researchers better understand how plants work, enabling them to harness their potential to provide alternative energy sources.

Reference: Karpowicz, S., S. E. Prochnik, A. R. Grossman, and S. S. Merchant. 2011. "The GreenCut2 Resource: A Phylogenomically-Derived Inventory of Proteins Specific to the Plant Lineage," Journal of Biological Chemistry 286, 21427–439.

Contact: Pablo Rabinowicz, SC-23.2, (301) 903-0379; Susan Gregurick, SC-23.2, (301) 903- 7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 16, 2011

A Step Closer to the "Greening" of Commercial Biofuel Production

Ionic liquids, a relatively new class of "green" solvents, can break down a wide range of feedstocks for biofuels, producing high yields of sugar and relatively pure lignin with short treatment times. However, even after scale up, ionic liquids are expensive compared with other pretreatment options. To determine which biofuel production parameters have the greatest impact on total cost, DOE's Joint BioEnergy Institute (JBEI) conducted a techno-economic analysis. A publically available techno-economic model of a biofuel refinery was developed, using ionic liquid pretreatment, to show a prioritized research path for fundamental understanding, process engineering, and operational improvements that would enable the use of ionic liquids in a commercial setting. The model results indicate, in decreasing order of significance, the importance of high prices for lignin byproducts, reducing the cost of the ionic liquid solvents and the concentration of the solvent used, and increasing the rate of solvent recovery. This analysis will lead to improvements in the cost effectiveness of biofuel production using ionic liquid-based processes.

Reference: Klein-Marcuschamer, D., B. A. Simmons, and H. W. Blanch. 2011. "Techno-Economic Analysis of a Lignocellulosic Ethanol Biorefinery with Ionic Liquid Pretreatment," Biofuels, Bioproducts and Biorefining, DOI: 10.1002/bbb.303.

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 15, 2011

Exploring the Cellulose Degradation Machinery of Hot Springs Bacteria

Members of the Caldicellulosiruptor genus of bacteria, originally discovered in terrestrial hot springs, are unique in their ability to efficiently degrade cellulosic plant biomass at temperatures over 70°C. Researchers at the DOE Bioenergy Science Center (BESC) at Oak Ridge National Laboratory previously sequenced the genomes of several Caldicellulosiruptor species and characterized their abilities to degrade corn stover, switchgrass, and other biomass feedstocks. In a new study, BESC scientists used mass spectrometry-based proteomics to compare the complex mixture of enzymes secreted by two Caldicellulosiruptor species during cellulose degradation. Both of the organisms deployed carefully regulated configurations of multifunctional cellulase modules, tethered cellulose binding elements, and proteins that bind released sugars and return them to the cell. All of these elements were traced back to encoding genes on sequenced genomes. The secreted cellulase fractions from the Caldicellulosiruptors were found to work optimally at 85°C and pH 5, indicating significantly higher thermal stability and acid tolerance than current commercially available cellulase cocktails. These results present a promising source of novel cellulase enzymes for industrial development and provide new insights into the diversity of tools that microbes have at their disposal for biomass breakdown.

Reference: Lochner, A., R. J. Giannone, M. Rodriguez, Jr., M. B. Shah, J. R. Mielenz, M. Keller, G. Antranikian, D. E. Graham, and R. L. Hettich. 2011. “Use of Label-Free Quantitative Proteomics To Distinguish the Secreted Cellulolytic Systems of Caldicellulosiruptor bescii and Caldicellulosiruptor obsidiansis,” Applied and Environmental Microbiology 77, 4042–54.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 09, 2011

Circadian-Controlled Pathways Facilitate Adaptation to a Changing Environment

Plants and other organisms synchronize their internal processes with the environment through circadian clocks to cope with natural cycles of light and temperature. These temporal rhythms coordinate physiological and metabolic processes with daily and seasonal changes by helping coordinate gene expression that enable organisms to adapt. Researchers at Oregon State University and collaborators used a combination of genomics and bioinformatics technologies to investigate daily rhythms in gene expression in the monocot plant rice and the dicot plant poplar. They compared their findings to work previously performed in the model plant Arabidopsis. They found a high degree of conservation across the three species among the cycling patterns of many circadian clock genes. This new research indicates that a core regulatory network is conserved across higher plants, although some cases of species-specific diurnal/circadian-associated regulatory circuits were observed. The findings have implications for engineering plants with enhanced vigor, fitness, and adaptation to changing environments. The research was supported in part by the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy program.

Reference: Filichkin, S. A., G. Breton, H. D. Priest, P. Dharmawardhana, P. Jaiswal, S. E. Fox, T. P. Michael, J. Chory, S. A. Kay, and T. C. Mockler. 2011. "Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and cis-Regulatory Modules," PLoS ONE 6(6):e16907. (DOI: 10.1371/journal.pone.0016907) (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 02, 2011

Solving the Mysteries of Cellobiose Stability Using High-Performance Computing

Cellobiose, a two glucose basic repeat unit of cellulose, is formed in enzymatic or acidic hydrolysis of plant biomass and is the precursor compound that microbes digest to produce cellulosic biofuels. Because this process happens outside of the microbial cell, understanding the structure and stability of cellobiose in solution provides a framework for improving microbial biofuel production. Interestingly, the low-temperature, gas-phase stable, preferred structure of cellobiose is cis, while the high temperature structure is trans. However, in cellulose itself, cellobiose is always in the trans state. Researchers believe that the stability of trans-cellobiose could be due to the water environment that surrounds it. Now, an international collaborative study has found that water molecules hydrate cellobiose collectively instead of binding to cellobiose separately and sequentially as was previously assumed. The team used DOE’s National Energy Research Scientific Computing Center, a high-performance computing facility, to simulate cellobiose dynamics together with vibrational spectroscopy experiments. Their results suggest that water dynamics could play a critical role in determining the most stable structure of cellobiose. The next step in this research will be to produce a simulation of cellobiose that includes the quantum and dynamically polar nature of water. It is anticipated that this new research will provide insight into how to optimize the hydrolysis of plant-derived cellulose, a key step in the production of biofuels. The computational aspects of the research were funded by DOE's SciDAC program.

Reference: Pincu, M., et al. 2011. "Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations," Journal of Physical Chemistry A, DOI: 10.1021/jp112109p. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 25, 2011

Biological Impacts of Climate Change on Coral Reefs

Over the past two decades, scientists have linked the decrease in the pH levels of the global oceans and the corresponding slowdown in coral growth to the increasing levels of carbon dioxide trapped in the atmosphere and which, in turn, are being absorbed in the ocean. As coral reefs are the primary habitat for several marine organisms, their decline has significant impacts on the health of the marine ecosystems and ocean productivity. To better understand how corals contribute to the global carbon cycle, the DOE Joint Genome Institute (JGI) generated a dataset of expressed sequence tags or ESTs, small portions of a genome that can be used to help identify unknown genes and chart their locations along the sequence, from the reef-building coral Acropora palmate. In a study published online May 25, 2011, in PLoS ONE, a team of researchers including DOE JGI’s Erika Lindquist compared the A. palmate EST dataset to an EST dataset of another reef-building coral to identify the proteins involved in helping corals adapt to global climate change. The comparative analysis identified several proteins evolving at an accelerated rate, such as those involved in immunity, reproduction and sensory perception. “The category that was the most enriched with rapidly evolving proteins —cell adhesion—may also be related to symbiosis,” noted the study authors in their paper. These proteins are expected to evolve under positive selection due to the need for readjustments, e.g., due to the “arms race” between the coral and the bacterial symbionts. This research provides insights into the impacts of climate change at the biological level.

Reference: Voolstra, C. R., S. Sunagawa, M. V. Matz, T. Bayer, M. Aranda, et al. 2011. “Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment,” PLoS ONE 6(5),e20392. DOE:10.1371/journal.pone.0020392.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Acropora table coral on the Great Barrier Reef (Image (c) Pete Faulkner, Mission:awareness/Marine Photobank).



May 19, 2011

Using New Computational Methods To Improve Biofuel Production

Lignin gives plants their strength and helps make them resistant to diseases, but it also complicates the use of plant material for biofuel production because of its recalcitrance to deconstruction. Researchers have successfully manipulated the lignin biosynthetic pathway in biofuel-producing plant species; however, the modified plants often have unexplained or undesirable biological features. It is difficult to predict, given our current ability to model plant metabolic processes, how individual biosynthetic pathways connect together, influence each other, and are controlled. To address this challenge, Yun Lee and co-workers at DOE’s BioEnergy Research Center (BESC) have developed a new computational method that combines metabolic modeling with Monte Carlo (random sampling) simulations to enable the analysis of many biological pathways simultaneously. When this method was applied to the prediction of lignin biosynthesis in alfalfa, BESC researchers found that lignin generation was not due to a single process but involved many pathways. In addition, the researchers predicted, and later confirmed, that a possible control for lignin biosynthesis was the signaling molecule salicylic acid. This work addresses the complexity of plant biosynthetic pathways and provides a computational method that can help researchers decipher them, providing new tools that can be used to improve biofuel production.

Reference: Lee, Y., F. Chen, L. Gallego-Giraldo, R. A. Dixon, and E. O. Voit. 2011. "Integrative Analysis of Transgenic Alfalfa (Medicao sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis," PLoS Computational Biology 7(5), e1002047.

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 16, 2011

Fungal Lesson in Improving Large-Scale Chemical Production

The chemical compound citric acid has been produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger. The fungus also has enzymes that can be used to help break down plant cell walls for biofuel production, and it plays a key role in the carbon cycle.

For biofuels, A. niger is a highly relevant organism since it has already been scaled up, shown to be safe, and used for enzyme production. An A. niger strain was selected for sequencing by the DOE Joint Genome Institute (JGI) in 2005.

In a recent paper, an international team of collaborators including JGI compared the genome of the citric-acid producing A. niger strain with another strain that had undergone mutagenesis for enzyme production. The fungal genomes are expected to help industry generate green chemicals and fuels from sustainable sources. The comparative analysis allowed the team to identify the key genes to each strain’s predominant characteristics. This information, along with genomic data from additional Aspergillus strains being sequenced at the DOE JGI should facilitate further optimization of these strains for different bio-products.

Reference: Andersen, M. R., et al. 2011. “Comparative Genomics of Citric-Acid-Producing Aspergillus niger ATCC 1015 Versus Enzyme-Producing CBS 513.88,” Genome Research. Published online May 4, 2011, DOI:10.1101/gr.112169.110.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Aspergillus niger. (Image: Sue Karagiosis, PNNL)



May 16, 2011

Quantum Dot Thermometers Measure Temperatures Inside Single Living Cells

Small temperature differences inside individual cells affect kinetics and shift chemical equilibria, but also alter the physical state of biomaterials such as DNA and proteins. Technology for detecting such temperature variations could lead to insights into biological mechanisms related to a wide range of metabolic processes in bioenergy-relevant systems. New research has shown that quantum dots can serve as nano thermometers to measure local temperature responses inside single living cells following exposure to external chemical and physical stimuli. Quantum dots are semiconductors in the form of crystals that fluoresce with colors determined by crystal size and chemical composition. The spectral shifts in the photoluminescence produced by the quantum dots were used to map intracellular heat generation from different organelles and compartments in cells following exposure to stress from high calcium levels and cold shock. These results are the first experimental evidence for inhomogeneous intracellular temperature progression in cells. The research was carried out at the Berkeley Lab and Princeton University and published in ACS Nano.

Reference: Yang, J.-M., H. Yang, and L. Lin. 2011. "Quantum Dot Nano Thermometers Reveal Heterogeneous Local Thermogenesis in Living Cells," ACS Nano 5(6), 5067-71. (DOI: 10.1021/nn201142f) (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 09, 2011

Spikemoss Genome Aids Biofuels Researchers

The genome of a small plant is providing biofuels researchers with information that could influence the development of candidate biofuel feedstock plants and offering botanists long-awaited insights into plant evolution. A team of researchers, including from DOE’s Joint Genome Institute (JGI), used a comparative genomics approach on Selaginella moellendorffii and 14 other plants up and down the phylogenetic tree to identify the core genes likely to be present in a common ancestor to land plants.

“When you burn coal, you’re burning Selaginella’s ancestors,” said Purdue University botanist Jody Banks, who led the 2005 DOE JGI Community Sequencing Program project. The Selaginella research community has grown up around the availability of the genome since 2009 through the DOE JGI’s plant portal Phytozome. The spikemoss genome has revealed the transition from mosses to plants with vascular systems involving fewer genes than going from a non flower-producing vascular plant to one that does.

The spikemoss genome is already proving useful for biofuels researchers. For example, Banks’ colleague Clint Chapple, a coauthor on the paper and a Purdue colleague, has been using the Selaginella genome to study the pathways by which the three different types of lignin are synthesized in plants. He and his team have used enzymes from the lignin-synthesizing pathway in Selaginella to modify the canonical lignin-producing pathway in Arabidopsis to produce the polymer.

Reference: Banks, J. A., et al. 2011. “The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants,” Science 332, 960–63. Published online May 5, 2011, DOI:10.1126/science.1203810.

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Selaginella moelledorffii. (Image by Jing-Ke Weng, Salk Institute)



May 06, 2011

Wood Degrading Fungi Use Specialized Systems for Degrading Different Plant Types

“Brown rot” and “white rot” fungi from forest floors are among the few organisms on Earth that can fully degrade both the long, repeated sugar chains (cellulose and hemicellulose) and the complex, interlinked network of aromatic compounds (lignin) that make up woody plant material. The two classes of fungi use distinct (but poorly understood) enzyme systems to break down biomass and show strong preferences for particular types of wood. A collaborative team of researchers at the DOE Great Lakes Bioenergy Research Center and the DOE Joint Genome Institute have examined representative species of brown and white fungi to determine which specific genes involved in biomass deconstruction are deployed to attack aspen or pine wood. These studies revealed that the two types of fungi used distinct deconstruction systems, and the expression of these systems was heavily influenced by the type of wood being degraded. Many genes identified in the study correspond to known biomass degradation enzymes, but a significant fraction have no currently known catalytic function and will be the subject of further investigation. The results of this study increase our understanding of molecular mechanisms that allow degradation of biomass and could lead to the identification of new systems for plant deconstruction and biofuels production.

Reference: Wymelenberg, A. V., et al. 2011 “Gene Expression of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium is Significantly Altered by Plant Species,” Applied and Environmental Microbiology, doi:10.1128/AEM.00508-11.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 05, 2011

Poplar Rust Fungus Is First Tree Pathogen Sequenced

Rust plant pathogens make up a large fungal group that cannot survive on their own, so they use crops as hosts, leading to reduced yields and potentially hindering efforts to grow biomass for fuel. To learn more about these pathogens, a 2006 Community Sequencing Program project at the DOE Joint Genome Institute (JGI) generated the 101-million base pair genome of the poplar leaf rust fungus Melampsora larici-populina, the first tree pathogen sequenced.

The fungal project complements work as poplar leaf rust outbreaks weaken poplar trees, a candidate bioenergy feedstock whose genome sequence was published by JGI in 2007. A new study that involved a JGI researcher compares the genomes of poplar leaf rust and wheat stem rust fungi, the latter sequenced by the Broad Institute, in order to develop better biocontrol methods. In combination with the genome sequence of Populus, published in 2006, researchers will be able to compare and dissect the molecular interactions that lead to symbiotic versus pathogenic responses in the host plant.

Reference: Duplessis, S., et al. 2011. "Obligate Biotrophy Features Unraveled by the Genomic Analysis of Rust Fungi," PNAS Early Edition, www.pnas.org/content/108/22/9166

Contact: SC-23.2, (301) 903-4742, Dan Drell
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Original confocal microscopy image of infected leaves from poplar cv. (Image by Stéphane Hacquard, INRA Nancy)



April 25, 2011

Comparative Genomics of Social Amoebae

Found in soils worldwide, slime molds such as Dictyostelium discoideum are perhaps best known by their behavior in the presence or absence of food. When food is plentiful, the social amoeba behave as individuals, but when food is scarce, they come together to form multicellular “fruiting bodies” that look like a flower bud atop a single stalk or foot composed of a fifth of the amoebae that have sacrificed themselves for the group.

Studying social amoebae allows researchers to learn more about multicellularity because these amoebae can exist in both single-cell and multicellular states. From a bioremediation perspective however, slime molds are important candidates in cleaning up sites contaminated with chemicals and radioactive materials.

In a recent paper, researchers from DOE’s Joint Genome Institute and Baylor College offer a second Dictyostelium genome, and compare the 33-million base draft sequence produced using the Sanger platform with the finished genome of the model organism D. discoideum.

Separated by 400 million years of evolution, Dictyostelium purpureum is a close relative of D. discoideum and shares many of the same characteristics. Aside from their food-related behaviors, they also have a highly sophisticated recognition system that allows them to distinguish same-species Dictyostelium from others. The researchers found that the genes involved in sociality evolve more rapidly, probably due to continuous adaptation and counter-adaptation.

Reference: Sucgang, R., et al. 2011. “Comparative Genomics of the Social Amoebae Dictyostelium discoideum and Dictyostelium purpureum,” Genome Biology 12:R20, DOI:10/1186/gb-2011-12-2-r20, reference link

Contact: Dan Drell, SC-23.2, (301) 903-4742, Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



D. purpureum. (Photo by Chandra Jack, Rice University)



April 14, 2011

Understanding the Role of Microbes in Greenhouse Gas Production in Agricultural Soils

It is critical to understand the role of agricultural practices on soil greenhouse gas (GHG) emissions as expanded collections of agricultural residues are considered for bioenergy production and shifts are made to farming dedicated bioenergy crops. Production and consumption of carbon dioxide, methane, and other GHGs are predominantly mediated by soil microbes, yet the relationship between functional processes and microbial diversity in these systems is poorly understood. Researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) have examined agricultural GHG production, linking these processes to microbial community activities. The study included agricultural soils under various management practices, both successional grasslands on abandoned agricultural land and mature forests or grasslands that had never been farmed. GHG production and consumption rates were correlated to soil microbial community composition. Rates of methane consumption were found to be highest in non-agricultural forests and grasslands, which also showed the greatest diversity of methane-consuming microbes (i.e., methanotrophs). Successional sites were intermediate in terms of both methane consumption and methanotroph diversity, suggesting a gradual recovery process following disruption by traditional tillage agriculture. These results have important implications in considering sustainable establishment and long-term management of bioenergy landscapes and predictive modeling of GHG emissions.

Reference: Levine, U. Y., T. K. Teal, G. P. Robertson, and T. M. Schmidt. 2011. "Agriculture's Impact on Microbial Diversity and Associated Fluxes of Carbon Dioxide and Methane," The ISME Journal, DOI:10.1038/ismej.2011.40. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 07, 2011

Probing the Natural Variation in Poplar Trees to Increase the Yield of Sugars for Biofuels

A promising source of renewable “next generation” fuels is from the lignocellulosic biomass of poplar trees, from which sugars can be extracted and fermented to produce biofuels. These sugars, in the form of cellulose and hemicellulose, are embedded within lignin, a complex polymer composed of varying ratios of phenylpropanoid subunits. The rigid structure of lignin is a critical component of the plant cell wall, but this same trait impedes extraction of the sugars. Researchers at the DOE BioEnergy Research Center (BESC) at Oak Ridge National Laboratory measured lignin content and composition in a large (1100 individual) sample of undomesticated poplar trees and found that variation between individuals was large and significant. Using a high-throughput screening method, samples were tested for total sugar release with or without various pretreatments. The total amounts of sugars released varied widely among samples, and, as expected, a strong negative correlation between sugar release and lignin content was observed. However, the large data set allowed the researchers to discover critical exceptions to the overall correlation. The negative correlation did not apply to trees with a certain composition of lignin, and, for some trees with typical lignin content and composition, a very high volume of sugars were released. These results indicate that although recalcitrance to sugar release is partly determined by lignin content, lignin composition and other factors are also critical, and underscores the need for further research on cell wall structure in order to rationally design high-yielding bioenergy feedstocks for large-scale industrial use. The research has just been published in the Proceedings of the National Academy of Sciences (USA).

Reference: Studer, M.H., M.F. Davis, R.W. Sykes, B.H. Davison, M. Keller , G.A. Tuskan, and C.E. Wyman. 2011. Lignin Content in Natural Populus Variants Affects Sugar Release." PNAS doi:10.1073/pnas.1009252108.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 21, 2011

Correlating Biomolecular Experimental Measurements with Computational Simulations

Understanding the structural changes a biomolecule undergoes during processing is important in the design of, for example, new routes to convert biomass to biofuels. However, when studying these processes it often is difficult to correlate kinetic experiments with computer simulations. Both the experiments and the simulations provide a time-ordered understanding of the biological process at hand, but the results are often hard to compare. Research by an international consortium that includes Jeremy Smith of Oak Ridge National Laboratory has developed a new mathematical method, “Dynamical Fingerprints,” that allows researchers to visualize the essential kinetic features of an experiment and compare these features directly to computational simulation results. Structural changes present in the simulation can be assigned to experimentally observed processes. The new method enables enhanced interpretation of experiments ranging from neutron scattering to fluorescence correlation spectroscopy and Förster resonance energy transfer efficiency. Combining simulations and experiments will enable progress in areas such as biofuel production and design of advanced materials, which require a clear understanding of how molecules move and interact. The research was supported by DOE SciDAC funding and was just published online in the Proceedings of the National Academy of Sciences (USA).

Reference: Noe, F., S. Doose, I. Daidone, M. Löllmann, M. Sauer, J. Chodera and J. Smith. 2011. “Dynamical Fingerprints for Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiment,” Proceedings of the National Academy of Sciences (USA), Early Edition March 2, 2011 (DOI: 10.1073/pnas.1004646108).

Contact: Christine Chalk, SC-21.1, (301) 903-5152, Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 21, 2011

Finding “Small” Proteins and Discovering How They Affect Plant Biomass Growth

Proteins less than 200 amino acids in length are commonly called “small proteins.” They have recently been found to have important roles in regulating biological processes such as stress response, flowering, and cell-to-cell communication in plants. However, identification of short open reading frames (sORFs), the genes that encode small proteins, has been a problem because their small size makes accurate prediction difficult. Researchers at Oak Ridge National Laboratory, working with scientists at the DOE BioEnergy Research Center, have applied computational biology to gene expression and protein data to discover sORFs encoding small proteins in the promising bioenergy feedstock Populus deltoids (poplar). Using the capacity of the DOE Joint Genome Institute for deep RNA sequencing, they reconstructed high-quality, full-length genes directly from the set of genes expressed in poplar (transcriptome), thus avoiding the uncertainty of prediction from genome sequence. The team then applied three computational filters to enrich for protein-encoding sORFs: prediction based on known protein sequences, evolutionary conservation between poplar and other plants, and protein family clustering. The results demonstrated the efficacy of this strategy in discovering candidate sORFs in sequenced as well as yet unannotated genomes. This method will greatly enhance understanding of the regulatory mechanisms underlying processes such as growth and stress response, features important to the development of high-yielding, sustainable bioenergy feedstocks.

Reference: Yang, X., T. J. Tschaplinski, G. B. Hurst, S. Jawdy, P. E. Abraham, P. K. Lankford, R. M. Adams, M. B. Shah, R. L. Hettich, E. Lindquist, U. C. Kalluri, L. E. Gunter, C. Pennacchio, and G. A. Tuskan. 2011. “Discovery and Annotation of Small Proteins Using Genomics, Proteomics, and Computational Approaches,” Genome Research doi:10.1101/gr.109280.110. Published online March 2, 2011.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 21, 2011

Improved Pretreatment of Biomass by Ionic Liquids Pretreatment

Pretreatment is a critical yet expensive stage in the biomass to biofuels pathway. However, pretreatment can reduce the overall biofuel production cost by facilitating conversion of the raw lignocellulosic biomass material into fermentable sugars and other valuable components. Pretreatment is thought to disrupt the lignin-carbohydrate complex in the cellulose microfibrils. Researchers at the DOE Joint BioEnergy Institute (JBEI) applied X-ray diffraction and small-angle neutron scattering to better understand ionic liquid pretreatment of these materials. The techniques were used to determine structural and surface changes in the biomass as a function of pretreatment conditions. Compared with other biomass samples studied, the ionic liquid pretreatment of switchgrass facilitated a more rapid expansion and conversion of the crystalline cellulose structure into a form more susceptible to enzymatic hydrolysis. The researchers also found that the degree to which lignin is intermixed within the cellulose microfibrils influences the required temperature and duration of an effective ionic liquid pretreatment.

Reference: Cheng, G., P. Varanasi, C. Li, H. Liu, Y. B. Melnichenko, B. A. Simmons, M. S. Kent, and S. Singh. 2011. “Transition of Cellulose Crystalline Structure and Surface Morphology of Biomass as a Function of Ionic Liquid Pretreatment, and Its Relation to Enzymatic Hydrolysis,” Biomacromolecules, dx.doi.org/10.1021/bm101240z.

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 07, 2011

Complex Sugar Diet Makes Microbe a Good Candidate for Producing Biofuels

Many current biofuel production scenarios involve breaking down biomass into its component sugars and using microbes to convert these sugars into liquid biofuels. However, plant biomass contains long chains of both six- and five-carbon sugars (cellulose and hemicelluloses, respectively) and the commonly used biofuel-producing microbes such as the yeast Saccharomyces cerevisiae or the bacterium Escherichia coli cannot use both sugars simultaneously. Thus, substantial effort and expense is required to separate the sugars prior to conversion to fuels, resulting in reduced overall process efficiency. Now, researchers at the DOE Joint Bioenergy Institute (JBEI) have demonstrated that the microbe Sulfolobus acidocaldarius can simultaneously consume both types of sugars, efficiently consuming even complex substrate mixtures. S. acidocaldarius is an extremophile capable of growing at high temperatures in acidic conditions with an unusually high degree of genome stability. Altogether, these traits make this organism an attractive candidate for metabolic engineering and further development as industrial biofuel producer.

Reference: Joshua, C. J., R. Dahl, P. I. Benke, and J. D. Keasling. 2011. “Absence of Diauxie During Simultanteous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius,” Journal of Bacteriology 193, 1293–1301.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 07, 2011

Engineering Production of Biofuels From Proteins

Biofuels currently are produced either from carbohydrates (e.g., ethanol from starch or sugar) or lipids (e.g., biodiesel from oils or fats). Both have serious shortcomings, requiring processes that have limited net energy efficiency and yielding byproducts such as nitrous oxide, a potent greenhouse gas. Research has now shown that the third major component of living organisms, proteins, could provide a large-scale source of biofuels without these limitations. Scientists at the UCLA-DOE Institute for Genomics and Proteomics have demonstrated that proteins produced in yeasts, bacteria, and algae can be converted efficiently into long-chain alcohols that are readily used in liquid fuels. The critical step in this research was to engineer metabolic processes into cells that convert the amino acids making up proteins into fuel molecules. These processes enable efficient deamination, or removal of the nitrogen-containing group from the amino acids and conversion of the resulting molecules into fuel alcohols. The nitrogen-containing byproducts are readily captured and recycled to fertilize growth of more of the photosynthetic cells, such as algae. The process can make effective use of sunlight as an energy source and CO2 as a carbon source, as proteins are the principal product of rapid growth in photosynthetic microorganisms. The research was led by James C. Liao and was just published in Nature Biotechnology.

Reference: Huo, Y.-X., K. M. Cho, J. G. Lafontaine Rivera, E. Monte, C. R. Shen, Y. Yan, and J. C. Liao. 2011. “Conversion of Proteins into Biofuels by Engineering Nitrogen Flux,” Nature Biotechnology, published online March 6, 2011, (doi:10.1038/nbt.1789).

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 07, 2011

Making Better Feedstocks for Bioenergy by “Cracking” Switchgrass’s “Backbone”

The perennial grass switchgrass is considered one of the most promising biofuel feedstocks because of its high yield potential and ability to thrive on lands poorly suited for conventional agriculture. However, the presence of lignin within the cell walls, which provides rigidity and pathogen resistance to the plant, also confers resistance to breakdown into constituent sugars. This recalcitrance to cell wall deconstruction limits current efforts to convert these sugars into biofuels. Now researchers at the U.S. Department of Agriculture’s Agricultural Research Service (USDA-ARS), with funding from the joint USDA-DOE Plant Feedstock Genomics for Bioenergy Program, have re-engineered switchgrass to produce a modified lignin that, when subjected to alkaline pretreatment, released a modest but significant increase in glucose compared to control plants. These modified plants have a reduced function of the gene catalyzing the last step in the lignin biosynthetic pathway (cinnamyl-alcohol dehydrogenase, or CAD). These results demonstrate the promise of this approach in developing high-yielding switchgrass lines for biofuel production.

Reference: Saathoff, A. J., G. Sarath, E. K. Chow, B. S. Dien, and C. M. Tobias. 2011. “Downregulation of Cinnamyl-Alcohol Dehydrogenase in Switchgrass by RNA Silencing Results in Enhanced Glucose Release after Cellulase Treatment,” PLoS ONE 6(1): 16416.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 07, 2011

New Metabolic Mapping Capabilities May Lead to Design of More Useful Microbes

The recent development of metabolic flux analysis has enabled better understanding of the physiological state of microbes by tracing the molecules involved in cellular metabolism. Typically, however, metabolic flux analysis requires that molecular reactions be lumped together because it is too difficult to map all of the atoms involved in cellular processes. DOE researchers at Penn State University have tackled this problem head on by using techniques from pattern recognition and graph theory combined with conventional metabolic flux analysis and high-performance computing. They can now automatically trace the path of all atoms (C, O, N, P, S, metals and their ions) as these atoms move through metabolic reactions in E. coli. Thanks to the database they developed as part of this project, this process can be applied to other organisms so that researchers can quickly design and analyze isotopic labeling experiments. This new approach will allow researchers to better understand the physiological state of a microbe and then to design or enhance metabolic processes, such as for bioenergy production or carbon sequestration.

Reference: Ravikirthi, P., P. Suthers, and C. Maranas. 2011."Construction of an E. Coli Genome-Scale Atom Mapping Model for MFA Calculations," Biotechnology and Bioengineering, available online February 2011 (DOI: 10.1002/bit.23070). PubMed.

Contact: (301) 903-7672, SC-23.2, Susan Gregurick
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 07, 2011

One-Stop “Shopping” for Biofuels: A Breakthrough in Consolidated Bioprocessing

In most current biomass-to-biofuel strategies, plant material must be first broken down into its component sugars and then converted to ethanol in a separate step, resulting in a costly and inefficient process. Researchers at the DOE Bioenergy Science Center (BESC) and the University of California, Los Angeles, have now successfully engineered the cellulose-degrading bacterium Clostridium cellulolyticum to convert cellulose directly to isobutanol, a liquid fuel with much higher energy density than ethanol and, unlike ethanol, with the potential to be directly used in current engines. This consolidated bioprocessing (CBP) approach, in which a single organism both deconstructs plant cellulose and converts it to a biofuel in one step, significantly improves overall process efficiency. Until now no single microbe was known to possess the necessary combination of biomass degradation and fuel synthesis properties, and the most promising organisms are extremely challenging to genetically manipulate. This breakthrough thus provides a promising new avenue to engineer similar organisms for single-step conversion of plant biomass to fuels.

Reference: Higashide, W., Y. Li, Y. Yang, and J. C. Liao. 2011. “Metabolic Engineering of Clostridium cellulolyticumfor Isobutanol Production from Cellulose,” Applied and Environmental Microbiology, published online March 4, 2011 (doi:10.1128/AEM.02454-10).

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 03, 2011

New Insight into the Mechanism of Plutonium Transport in the Environment

The potential migration of plutonium in the environment is a concern at DOE sites such as the Hanford Nuclear Reservation and the Nevada Test Site, as well as an issue in nuclear waste disposal for nuclear energy development. Using a number of transmission electron microscopy techniques Lawrence Livermore National Laboratory researchers and collaborating Clemson University scientists have provided important new understanding of the formation and the biogeochemical mechanisms controlling plutonium migration. Once thought immobile in the subsurface, it has been recently recognized that plutonium is capable of being transported with the colloidal faction of groundwater. The researchers examined the interaction of plutonium nanocolloids with environmentally relevant minerals such as iron-containing goethite and silicon-containing quartz. The studies revealed the molecular basis of potential binding through epitaxial growth between the plutonium nanocolloids and colloid goethite that may be a possible mechanism for enhanced plutonium transport. The results improve our understanding of how molecular-scale behavior at the mineral-water interface may facilitate transport of plutonium at the field scale, providing important molecular-level input to improve contaminant transport models and the prediction of plutonium behavior.

Reference: Powell, B. A., Z. Dai, M. Zavarin, P. Zhao, and A. B. Kersting. 2011. "Stabilization of Plutonium Nano-Colloids by Epitaxial Distortion on Mineral Surfaces," Environmental Science and Technology 45, 2698–2703. DOI:dx.doi.org/10.1021/es1033487. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.1 Climate and Environmental Sciences Division, BER


March 01, 2011

Assembly Path of Multi-Metal Catalysis Clusters in [FeFe]-Hydrogenases Revealed

Complex enzymes containing iron-sulfur (Fe-S) clusters are ubiquitous in nature where they are involved in a number of reactions fundamental for life, including carbon dioxide and nitrogen fixation and hydrogen metabolism. Because these enzymes have high catalytic rates of hydrogen production, their potential for improving hydrogen–fuel cell technologies is the focus of much interest. One type of such enzymes, the [FeFe]-hydrogenases, is being investigated as an alternative biological catalyst to enzymes containing precious metals such as platinum. The active site of this hydrogenase, the H-cluster, has a [4Fe-4S] subcluster bridged to a 2Fe subcluster. Advancements in understanding how this H-cluster is synthesized in nature could contribute significantly to both the genetic engineering of hydrogen-producing microorganisms and the synthesis of biomimetic hydrogen-production catalysts. X-ray crystallography data from an intermediate, not-yet-mature form of [FeFe]-hydrogenase present insights into how the H-cluster (bio)synthesis occurs. This research was conducted at the Stanford Synchrotron Radiation Lightsource.

Reference: Mulder, D. W., et al. 2010. “Stepwise [FeFe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of HydAΔEFG,” Nature 465, 248–51.

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

Improving Access to Cellulose in Biomass for Biofuel Production

The conversion of cellulosic biomass to fermentable sugars usually requires costly, time-consuming pretreatment to increase the material’s porosity, decrease its crystallinity, and reduce the amount of structural lignin in the cell wall. Researchers used small-angle neutron scattering at the High-Flux Isotope Reactor to probe the morphological changes of switchgrass cell walls during dilute acid pretreatment, elucidating the interplay of different biomolecular components in the breakdown process. The results are important for the development of efficient strategies to convert biomass to biofuel.

Reference: Pingali, S. V., et al. 2010. “Breakdown of Cell Wall Nanostructure in Dilute Acid Pretreated Biomass,” Biomacromolecules 11, 2329–35.

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Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

Key Plant Receptors Discovered

The phytohormone abscisic acid (ABA) plays important regulatory roles in physiological pathways for plant growth and development and enables adaptation to environmental stresses, yet the protein recognition mechanisms for this hormone have eluded plant biologists. Crystallographic and small-angle X-ray scattering capabilities at the Advanced Light Source enabled researchers to determine the atomic resolution of the ABA receptor and identify conformational changes on the ABA binding site. Elucidating the structural mechanisms mediating ABA receptor recognition and signaling is essential for understanding and manipulating abiotic stress resistance. These results were listed as one of the top 10 scientific breakthroughs of the year in 2009 by Science.

Reference: Nishimura, N., et al. 2009. “Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1,” Science 326, 1373–79.

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Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

Measuring Chemical Changes Inside Living Cells

Understanding how microbes adapt to changing chemical environments is a critical aspect of using them to solve DOE challenges. With synchrotron radiation-based Fourier transform infrared microscopy at the Advanced Light Source, researchers tracked the chemistry of living Desulfovibrio vulgaris cells in real time. The ability to make these dynamic measurements continuously inside selected living cells dramatically increases the usefulness and reliability of information traditionally derived from cells that have been killed and broken apart.

Reference: Holman, H.-Y., et al. 2009. “Real-Time Molecular Monitoring of Chemical Environment in Obligate Anaerobes During Oxygen Adaptive Response,” Proceedings of the National Academy of Sciences (USA) 106, 12599–604.

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Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

Neutron Crystallography Reveals How Carbonic Anhydrases (CAs) Work

CAs are a family of enzymes that play an essential role in the metabolism of carbon dioxide by converting it into a carbonate ion and a proton. Because they are very stable and inexpensive, CAs could be used in significant large-scale applications such as carbon sequestration processes and biofuel production. However, little is known about the arrangement of the active site of CAs while they carry out their function, a gap that has impeded design of optimized CAs for these applications. Neutron crystallography experiments at the Los Alamos Neutron Science Center to determine the structure of human carbonic anhydrase II have revealed the orientation of amino acids around the zinc ion in the active site, as well as the unexpected presence of a water molecule bound to the metal ion. This structural information has enabled development of a mechanism to explain the proton transfer process and is being used to re-engineer the enzyme to be pH insensitive and thermally stable for carbon sequestration or biodiesel production.

Reference: Fisher, S. Z., et al. 2010. “Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer,” Biochemistry 49, 415–21.

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Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

New Insights into D-Xylose Isomerase (XI)

XI is an important enzyme because it can convert sugars that resist bioconversion to fuel into those readily fermented by, for example, yeasts. Through neutron diffraction experiments at the Los Alamos Neutron Science Center, researchers were able to map the positioning of individual hydrogen atoms as XI moves them from one carbon to another on a sugar molecule. They were able to model how specific amino acids in the XI structure are involved in proton movement. Results may enable new approaches for modifying the enzyme to improve its performance for biofuel and other applications. This research was featured on the June 9, 2010, cover of Structure.

Reference: Kovalevsky, A. Y., et al. 2010. “Metal Ion Roles and the Movement of Hydrogen During Reaction Catalyzed by D-Xylose Isomerase: A Joint X-Ray and Neutron Diffraction Study,” Structure 18, 688–99.

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Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2011

Understanding Enzymes That Process Sugars and Carbohydrates

In two separate studies at the Advanced Photon Source, researchers used high-resolution synchrotron protein crystallography to determine the crystal structures of ROK (bacterial Repressors, uncharacterized Open reading frames, and sugar Kinases) fructokinase from Bacillus subtilis and a recombinant a-glucosidase from the human gut bacterium Ruminococcus obeum. The results provided new information about how enzymes bind, recognize, and process carbohydrate substrates and how variations in enzyme structure impact enzyme function. These findings are expected to improve the conversion of biomass to fuels by using structural information to optimize enzymes for bioprocessing.

References: Nocek, B., et al. 2011. “Structural Studies of ROK Fructokinase YdhR from Bacillus subtilis: Insights into Substrate Binding and Fructose Specificity,” Journal of Molecular Biology 406, 325–42.

Tan, K., et al. 2010. “Novel a-Glucosidase from Human Gut Microbiome: Substrate Specificities and Their Switch,” The FASEB Journal 24, 3939–49.

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Division: SC-23.2 Biological Systems Science Division, BER


February 14, 2011

Learning New Tricks from Fungi to Improve Biomass Processing

Knowing how biomass is degraded in nature will advance understanding in how to process biomass for conversion to biofuels. The biodegradation of plant material generally involves removal of the resistant lignin barrier that prevents enzymes from reaching cellulose and degrading it to sugar. However, brown rot fungi, natural biomass recycler in coniferous forests, degrade biomass without removing much of the lignin. DOE researchers at the University of Wisconsin, Madison, and the Great Lakes Bioenergy Research Center (GLBRC) in Madison, Wisconsin, report that these fungi can disrupt the lignin in wood even though it remains in place. They discovered that key chemical linkages (ethers) in lignin’s complex molecular structure are broken, likely using reactive oxygen species such as hydroxyl radicals. They applied newly developed nuclear magnetic resonance (NMR) technology to look at the chemistry of wood attacked by a brown rot fungus. These results will enable development of new routes to access cellulose in biomass as part of the large-scale production of biofuels and will also improve understanding of natural carbon cycling from wood.

Reference: Yelle, D., D. Wei, J. Ralph, and K. E. Hammel. 2011. “Multidimensional NMR Analysis Reveals Truncated Lignin Structures in Wood Decayed by the Brown Rot Basidiomycete Postia placenta,” Environmental Microbiology doi:10.1111/j.1462-2920.2010.02417.x.

Contact: Arthur Katz, SC-23.2, (301) 903-4932
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Division: SC-23.2 Biological Systems Science Division, BER


February 07, 2011

Diversity Among Rice Varieties Indicates Multiple Targets for Biomass Improvement

Breeding cellulosic feedstock crops with enough biomass for sustainable liquid fuel production is a major challenge. We can exploit natural variation in bioenergy-relevant traits, but many of the most promising feedstock crops, such as perennial grasses, have large genomes and limited genetic resources, making breeding for such traits difficult. However, such tools are readily available for rice, a well-studied crop plant that shares many developmental and physiological processes as well as gene content with other grasses. These shared characteristics make rice useful as a model for modifying other newly emerging bioenergy crops. Researchers at Colorado State University, in collaboration with the International Rice Research Institute (IRRI) in the Philippines, assessed variation in traits such as biomass, height, tiller number, plant girth, cell-wall composition, and water-use efficiency among a diverse set of 20 rice varieties at different stages of development. Significant variation was found for all traits, and this variation was determined to be heritable. Additionally, high yields exhibited by different varieties were achieved through different combinations of traits, indicating the contribution of multiple genetic loci to overall biomass productivity and suggesting that multiple targets can be utilized in traditional breeding programs to develop other energy feedstocks with enhanced yield.

Reference: Jahn, C. E., J. Mckay, R. Mauleon, J. Stephens, K. L. McNally, D. R. Bush, H. Leung, and J. E. Leach. 2011. “Genetic Variation in Biomass Traits Among 20 Diverse Rice Varieties,” Plant Physiology 155, 157–68.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
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Division: SC-23.2 Biological Systems Science Division, BER


February 07, 2011

Water Flea Genome Sequenced: Sentinel of Environmental Change

The water flea Daphnia pulex is a keystone species of freshwater ecosystems, a principal grazer of algae, a primary food source for fish, a sentinel of still water inland ecosystems, and a sentinel species used to assess the ecological impact of environmental change. The genome of this species has just been sequenced by DOE’s Joint Genome Institute (JGI). They find that the Daphnia genome is only 200 megabases in size, but contains at least 30,000 genes, which is thought to be about 25% more than in the human genome. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the largest gene families are specific to the Daphnia lineage. These Daphnia-specific genes, including many additional sequenced genes that have not been assigned any functions, are the most responsive genes to ecological challenges. These results will enable better understanding of real-world environmental changes through knowledge of how a genome responds to gene-environment interactions. The study is published in the February 4, 2011, issue of Science magazine.

Reference: Colbourne, J. K., et al. 2011. “The Ecoresponsive Genome of Daphnia pulex,” Science 331, 555–61.

Contact: Dan Drell, SC-23.2, (301) 903-4742
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Division: SC-23.2 Biological Systems Science Division, BER


January 31, 2011

"Mining" Cows for New Enzymes to Degrade Biomass

Successful development of biofuels depends on being able to break down cellulose-rich feedstocks such as switchgrass. In nature enzymes called cellulases break down plant material into simple sugars that can be converted into biofuels. Cattle and other plant eating animals have microbes that carry out this breakdown in the rumen portion of their stomachs. Now scientists at the DOE’s Joint Genome Institute (JGI) report on a metagenomics study of the microbes in the cow rumen. The JGI team was able to obtain and sequence 270 billion DNA bases from the resident microbes feeding on switchgrass in the rumen of a fistulated cow. The researchers developed a candidate set of 30,000 genes that encoded biomass degrading enzymes. They tested a sample of 90 of the proteins encoded by these genes and found that more than 50% had cellulose degrading activity. The JGI researchers were also able to assemble complete genomes of 15 novel microbial species from the cow rumen sample. The research demonstrates that large scale sequencing and data analysis capabilities are enabling researchers to accurately identify genes of biological interest and to provide draft genomes of uncultured novel organisms in the environment. It also defines a powerful strategy for finding new enzymes with significance for DOE missions. The research was led by Matthias Hess of the JGI and is published in the January 28, 2011, issue of Science.

Reference: Hess, M., A. Sczybra, R. Egan, T.-W. Kim, H. Chokhawala, G. Schroth, S. Luo, D. Clark, F. Chen, T. Zhang, R. Mackie, L. Pennacchio, S. Tringe, A. Visel, T. Woyke, Z. Wang, and E. Rubin. 2011. “Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen,” Science 331, 463–67.

Contact: Dan Drell, SC-23.2, (301) 903-4742, Susan Gregurick, SC-23.2, (301) 903-7672
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Division: SC-23.2 Biological Systems Science Division, BER


January 18, 2011

Genomic Analysis Provides New Clues on the Origins of Metabolic Pathways in Earth’s Biosphere

For the first three billion years of life’s history on Earth, microbes were the original and predominant form of life, but evolution during this period remains a mystery due to the lack of significant fossil evidence. Analysis of microbial gene sequences across the tree of life has yielded clues on the development of fundamental biological processes; however, horizontal gene transfer (HGT), the exchange of genetic material across species, has confounded efforts to map out deep evolutionary processes operating over geological time periods. In new results published in the January 6th issue of Nature, researchers at the Massachusetts Institute of Technology describe a new comparative genomics approach for analyzing molecular evolution while accounting for HGT. The authors identified a period of rapid gene innovation between 3.3 and 2.8 billion years ago that gave rise to 27% of modern gene families. This evolutionary burst coincided with a period when oxygen concentrations in the atmosphere rapidly increased. The genes originating during this period include many involved in expanded energy production and metabolic reactions associated with an oxidizing environment. These results shed new light on fundamental processes that have shaped the metabolic potential of life on Earth and that continue to govern adaptation of the biosphere to changing conditions. This research was funded as part of a DOE Science Focus Area at Lawrence Berkeley Lab.

Reference: David, L. A., and E. J. Alm. 2011. “Rapid Evolutionary Innovation During an Archaean Genetic Expansion,” Nature 469, 93–96.

Contact: Joseph Graber, SC-23.2, (301) 903-1239
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Division: SC-23.2 Biological Systems Science Division, BER


January 03, 2011

Making Trees More Bioenergy Friendly

Wood is a heterogeneous compound composed of the polysaccharides cellulose and hemicellulose, from which bioethanol can be derived, and the polymer lignin, which encloses the cellulosic material, provides rigidity and durability to the plant and makes it difficult to convert the cellulosic material to bioethanol. The content and composition of lignin varies by species of tree and by tissue and organ within a tree. A tree with reduced lignin content in the stems but with higher lignin in the roots would provide for more efficient and higher yielding ethanol production while at the same time enhancing carbon sequestration in the non-harvested below-ground tissues. Researchers at the DOE BioEnergy Research Center at Oak Ridge National Lab used pyrolysis molecular beam mass spectroscopy to characterize the lignin content in stems and roots from progeny of a three-generation pedigree of poplar, a tree species widely regarded as a potential biofuel crop. Several genetic regions associated with lignin content were identified that were root- and/or stem-specific, indicating the existence of gene(s) that differentially regulate lignin biosynthesis above and below ground. These results suggest that it may be possible to decrease stem lignin content through conventional or molecular breeding methods without impacting lignin in the roots.

Reference: Yin, T., X. Zhang, L. Gunter, R. Priya, R. Sykes, M. Davis, S.D. Wullschleger, and G.A. Tuskan. 2010. "Differential Detection of Genetic Loci Underlying Stem and Root Lignin Content in Populus," PLoS ONE 5(11):e14021.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
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Division: SC-23.2 Biological Systems Science Division, BER


January 03, 2011

Systems Biology Analysis of Cellulose Degradation by Clostridium thermocellum

The bacterium Clostridium thermocellum is highly specialized to degrade cellulosic plant material through the use of cellulosomes, complex multi-component molecular machines tethered to the bacteria’s surface. The microbe can adjust the modular composition of its cellulosomes in response to various types of substrates and environmental conditions, but the mechanisms regulating this process remain poorly understand. Researchers at the DOE Great Lakes Bioenergy Research Center at the University of Wisconsin, Madison, have completed a global analysis of gene expression in C. thermocellum during controlled growth on cellulose and cellobiose (a simpler two sugar compound). Over 350 genes involved in cellulosome assembly, cellulose chain deconstruction, product uptake, and downstream synthesis of ethanol and hydrogen were observed to be differentially expressed depending on substrate and growth rate. In addition, the study provided new clues on the roles of numerous C. thermocellum genes that are currently categorized as having unknown functions. These results reveal the complex control that C. thermocellum exerts over its cellulose degrading machinery and provides new routes for development of this organism for bioenergy production.

Reference: Riederer, A., T. E. Takasuka, S. Makino, D. M. Stevenson, Y.V. Bukhman, N. L. Elsen, and B. G. Fox. 2010. “Global Gene Expression Patterns in Clostridium thermocellum from Microarray Analysis of Chemostat Culture on Cellulose or Cellobiose,” Applied and Environmental Microbiology, DOE:10.1128/AEM.02008-10

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER