BER Research Highlights

Search Date: March 23, 2017

76 Records match the search term(s):


December 06, 2010

A New Mechanism for Microbial Community Metabolism

Outside of laboratories, microbial species rarely exist in isolation. Many important environmental processes are actually mediated by complex communities of microbes. In many cases, two or more species have evolved to perform a cooperative metabolic activity that would be energetically unfavorable for either organism acting independently. Research published in the December 3 issue of Science and led by DOE scientist Derek Lovley of the University of Massachusetts, Amherst, describes a new mechanism by which the bacterium Geobacter metallireducens consumes ethanol, an important intermediate compound in oxygen free soils and sediments, in cooperation with a second organism Geobacter sulfureducens. For this reaction to yield energy for either partner, electrons produced from ethanol oxidation must be rapidly consumed. Although it was previously assumed that the first organism uses a hydrogen production mechanism to pass electrons to its partner, the authors have discovered that electrons are instead directly fed to G. sulfureducens via conductive "nanowires" called pili on the cell surface, resulting in much more efficient collaborative growth. These results provide important new clues on the fundamentals used by microbes to mediate important environmental processes such as carbon cycling and contaminant transformation and suggest intriguing new approaches to direct generation of electricity in microbial fuel cell systems.

Reference: Summers, Z.M., H. E. Fogarty, C. Leang, A. E. Franks, N. S. Malvankar, and D. R. Lovley. 2010. "Direct Electron Exchange Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria," Science 330:1413-15.

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

Division: SC-23.2 Biological Systems Science Division, BER


December 06, 2010

Genome of Methane-Oxidizing Microbe Sequenced

Methane is a more potent greenhouse gas than CO2 on a per molecule basis although far more CO2 than methane is released into the atmosphere. Methane production and oxidation (usually conversion to methanol) is a common property of many bacteria. To better understand the basis for bacterial methane processing and its potential role in the global greenhouse gas cycle, the genome sequence of a methane-oxidizing microbe, Methylosinus trichosporium, has now been published. This microbe has been used to elucidate the structure and function of several key enzymes that oxidize methane. In particular, the catalytic properties of a soluble methane monooxygenase enzyme from this bacterium have been studied extensively as it is also involved in biodegradation of recalcitrant hydrocarbons, such as trichloroethylene. The sequence of this bacterium's genome should provide insights into both methane processing and organic contaminant degradation. The sequencing was carried out by the DOE Joint Genome Institute as part of its Community Sequencing user Program.

Reference: Stein, L.Y., et.al. December 2010. "Genome Sequence of the Obligate Methanotroph Methylosinus trichosporium Strain OB3b," Journal of Bacteriology, 192, 6497-98.

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

Division: SC-23.2 Biological Systems Science Division, BER


December 06, 2010

Progress and Prospects for Metabolic Engineering of Microbes for Biofuels Production

In a review article in the December 3, 2010, issue of Science, DOE Joint Bioenergy Institute director Jay Keasling discusses advances in metabolic engineering and outlines current efforts to develop economical production of biofuel compounds by microbes. Keasling points to recent improvements in DNA sequencing, bioinformatics, and systems biology approaches as key elements enabling recent breakthroughs in microbial production of high value products such as pharmaceuticals. As petroleum prices continue to rise, engineering microbes to synthesize next generation biofuels compatible with existing engines and infrastructure has become more feasible economically. However, more work is needed to provide low cost starting materials from cellulosic biomass, improve genetic tools that allow introduction of metabolic pathways and control elements into microbial genomes, and develop a broader range of host microbes that can produce tailored biofuel compounds and withstand stresses associated with industrial fuel production. Given the rapid pace of recent progress in these areas, Keasling considers the prospects for economical microbial production of biofuels from renewable resources to be very strong.

Reference: Keasling, J.D. 2010. “Manufacturing Molecules Through Metabolic Engineering,” Science 330:1355-1358.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 29, 2010

Computational Approaches to Simulate Microbial Ecosystems

A basic challenge in microbial ecology is to understand and to predict the growth and behavior of complex microbial communities, in fact most isolated microbes cannot be readily grown in culture. These communities are important for biogeochemical processes such as nitrification, hydrogen production, and methanogensis. They also show promise for the degradation of complex oligosaccharides in biomass to fermentable sugars for biofuel production. A new method for genome-scale metabolic simulation has been developed by DOE scientists Niels Klitgord and Daniel Segrè of Boston University that will predict the optimal media for promoting the growth of microbes in a community. The method has been successfully tested on a community consisting of hydrogen producing and methane producing microbes as well as the model co-culture Escherichia coli and Saccharomyces cerevisiae. Research is now underway to extend this method to simulating microbial community growth involving more than two species. The new method has just been published in PLoS Computational Biology. This new predictive capability may expand our ability to take advantage of the vast and diverse capabilities found in the microbial world.

Reference: Klitgord, N., and D. Segrè. November 2010. "Environments that Induce Synthetic Microbial Ecosystems," PLoS Computational Biology 6.(Reference Link)

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

Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2010

DOE Scientists to Receive Franklin Institute Medals

Jillian F. Banfield, a University of California, Berkeley, biogeochemist and geomicrobiologist, will receive the Benjamin Franklin Medal in Earth and Environmental Science, “for discovering the underlying principles of mineral formation and alteration by microbes, which are critical to understanding the form, composition, and distribution of minerals in the presence of living organisms.” Using cutting-edge technology, Banfield has fully characterized this unique microbial ecosystem by sequencing the genomes of the different species of bacteria and cataloguing the proteins they produce. Banfield has been supported by DOE for the past decade. Banfield also is one of five recipients of the 2011 For Women in Science awards from the L'Oréal Foundation and United Nations Educational, Scientific and Cultural Organization (UNESCO) and will received this award on March 3, 2011, at UNESCO headquarters in Paris.

George Church of the Harvard Medical School is recipient of the Franklin Institute’s Bower Award for “innovative and creative contributions to genomic science, including the development of DNA sequencing technologies, as well as for his subsequent efforts to promote personal genomics and synthetic biology.” Church’s research has been supported by DOE since 1988. During this time he has been a leader in bringing improvements in cost and speed to bioanalytical technologies and their applications across the life sciences. Many technologies flowing from his projects have been commercialized.

Banfield and Church are two of seven recipients of the 2011 Franklin Medal, presented every year to “preeminent trailblazers in science, business and technology.”

References:

Bower Award: George Church

Banfield: News article

Contact: Dan Drell, SC-23.2, (301) 903-4742, Marvin Stodolsky, SC-23.2, (301) 903-4475
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Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2010

Interactions of Bacteria with Uranium in the Environment

Uranium in the 6+ oxidation state is quite soluble and can thus move rapidly in uranium-contaminated subsurface environments. In contrast, uranium in the 4+ state is highly insoluble, and is therefore less likely to move the subsurface environment. New research has identified important aspects of how bacteria reduce uranium 6+ to uranium 4+, showing that the latter is produced in a variety of forms, not just in the expected, simple form of uraninite (UO2). The authors of the new study used a variety of techniques at the Stanford Synchrotron Radiation Lightsource (SSRL) to characterize the products of uranium reduction in various microbial cultures, including x-ray absorption spectroscopy (XAS). The XAS experiments showed that many of the uranium 4+ products lacked the spectral peak characteristic of uraninite. Instead, a variety of complex solids involving uranium and phosphate, and in some cases also calcium were identified, as well as solids in which uranium 4+ is bound to the surface of the bacterial biomass. These results will be helpful in modeling the mobility of uranium species at contaminated DOE sites. The research was led by Rizlan Bernier-Latmani of the École Polytechnique Fédérale de Lausanne in Switzerland, and involved scientists at SSRL. It is just published online in Environmental Science & Technology.

Reference: Bernier-Latmani, R., et al. 2010. "Non-uraninite Products of Microbial U(VI) Reduction," Environmental Science & Technology, online November 11, 2010. DOI: 10.1021/es101675a

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
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Division: SC-23.1 Climate and Environmental Sciences Division, BER


November 22, 2010

Predicting Function of Unknown Genes

Recent advances in plant genomics have identified many new genes, but many are of unknown function. Experimental determination of the function of individual genes is difficult because gene duplication occurs frequently among plants so large, functionally redundant gene families are common. Researchers at the DOE Joint BioEnergy Institute have used a phylogenetic (evolutionary relatedness) approach to computationally predict the biological function of individual genes within the very large (1,508-member) rice kinase gene family by combining gene expression data from various rice tissues and different experimental conditions with protein interaction data and looking for similarities. Function could be inferred for genes showing similar patterns in diverse tissues and conditions. Certain members of the kinase gene family regulate the responses of plants to a range of stresses such as drought and pathogens, as well as being involved in other signaling cascades. Rice can be used as a model for bioenergy grass crops such as sorghum and switchgrass, thus integration of gene data from these plants could facilitate functional predictions of genes important for bioenergy-relevant traits.

Reference: Jung, K-H., P. Cao, Y-S. Seo, C. Dardick, and P.C. Ronald. 2010. "The Rice Kinase Phylogenomics Database: A Guide for Systematic Analysis of the Rice Kinase Super-family," Trends in Plant Science 15(11), 595-99.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2010

The Challenge of Redesigning Lignin for Biofuel Applications

Secondary cell walls of plants contain lignins that provide rigidity and pathogen resistance to the plant, but hinder breakdown of cell walls during biomass processing. This limits the efficient use of plants as bioenergy feedstocks. Lignins are polymers formed from several different chemical monomers and the nature of these monomers determines the properties of the lignin polymer. Modifying the lignin composition could significantly improve the ease of conversion of biomass to biofuel products, while retaining the critical functions of lignins for the plants growing in the field. Researchers at the DOE Great Lakes Bioenergy Center (GLBRC) have found that by altering two genes in Arabidopsis, a plant often used as a research model, a unique lignin is produced that contains a non-traditional monomer. The altered plant exhibits reduced lignin content, a trait desirable for increasing efficiency of deconstruction, but also shows aberrant growth and development and large metabolic shifts. The GLBRC researchers found evidence for genetic interactions between two lignin biosynthetic pathways. These results are an example of the type of unanticipated effects that will need to be taken into account when designing strategies for genetically engineering plant cell walls for bioenergy applications.

Reference: Vanholme, R., J. Ralph, T. Akiyama, F. Lu, J.R. Pazo, H. Kim, J.H. Christensen, B. Van Reusel, V. Storme, R. De Rycke, A. Rohde, K. Morreel, and W. Boerjan. 2010. "Engineering Traditional Monolignols Out of Lignin by Concomitant F5H1-up- and COMT-down-regulation in Arabidopsis," Plant Journal. doe:10.1111/j.1365-313X.2010.04353.x.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 15, 2010

Jill Banfield to Receive Franklin Medal and L'Oréal-UNESCO Award

DOE-funded scientist Jillian F. Banfield, a University of California, Berkeley, biogeochemist and geomicrobiologist, will receive two prestigious awards - the Benjamin Franklin Medal in Earth and Environmental Science and the L'Oréal-UNESCO 'For Women in Science' award – for her groundbreaking work on how microbes alter rocks and interact with the natural world. She has used cutting-edge techniques to sequence the genomes of the different species of bacteria and to catalogue the proteins they produce, fully characterizing this unique microbial ecosystem. Banfield has been at UC Berkeley since 2001, where she is a professor of earth and planetary science, of environmental science, policy and management, and of materials science and engineering, and a faculty scientist at Lawrence Berkeley National Laboratory. She is one of seven recipients of the 2011 Franklin Medal, presented every year to "preeminent trailblazers in science, business and technology." Banfield is one of five recipients of the 2011 For Women in Science awards from the L'Oréal Foundation and United Nations Educational, Scientific and Cultural Organization (UNESCO). The awards ceremony will take place on March 3, 2011, at UNESCO headquarters in Paris. Each laureate will receive $100,000 in recognition of her contributions to science.

Reference: News Article

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

Division: SC-23.2 Biological Systems Science Division, BER


November 01, 2010

Methane-Oxidizing Bacterium Sequenced at DOE-JGI

Methane is one of the most important greenhouse gases, 21 times more potent molecule-for-molecule than carbon dioxide. Methane-oxidizing bacteria (methanotrophs) that are common in terrestrial and marine environments help reduce levels of atmospheric methane. To better understand the bacteria involved in the global methane cycle, the DOE JGI sequenced and annotated the genome of Methylosinus trichosporium OB3b. This microbe has been studied extensively to identify and characterize several key enzymes involved in methane oxidation. For example, one crucial enzyme uses copper to efficiently oxidize methane. Aside from genes involved in methane oxidation, genes involved in nitrogen fixation and ammonia transport were also identified. An improved understanding of microbial methane biochemistry will help characterize the biological components of global climate models. The new results were just published online ahead of print in the Journal of Bacteriology.

Reference: Stein, L.Y., S. Yoon, J.D. Semrau, A.A. DiSpirito, J.C. Murrell, S. Vuilleumier, M.G. Kalyuzhnaya, H.J.M. Op den Camp, F. Bringel, D. Bruce, J.-F Cheng, A. Copeland, L. Goodwin, S. Han, L Hauser, M.S.M. Jetten, A. Lajus, M.L. Land, A. Lapidus, S. Lucas, C. Médigue, S. Pitluck, T. Woyke, A. Zeytun, and M.G. Klotzl. "Genome sequence of the obligate methanotroph, Methylosinus trichosporium strain OB3b," Journal of Bacteriology doi:10.1128/JB.01144-10. Published online ahead of print on 15 October 2010.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 01, 2010

New Microfluidic Chips for Large-Scale Screening of Biomass Hydrolysis

Large numbers of cellulose enzymes, the enzymes used to break down cellulosic biomass to produce fermentable sugars, need to be screened to identify the best enzymes and the most effective processing conditions for biofuel production from cellulosic biomass. Researchers at DOE's Joint BioEnergy Institute (JBEI) have developed a new microfluidic chip-based assay to rapidly and precisely characterize biomass hydrolysis products, especially glycan and xylan sugars. They solved the difficult challenge of separating and identifying these closely related sugars by modeling and optimizing the process in the microfluidic system. They describe the use of this new system, demonstrating its ability to rapidly screen for hydrolysis products on the order of one minute. These results suggest that that this new system could be adapted to large-scale, rapid characterization of cellulase enzyme cocktails. This study was featured on the November 15, 2010 cover of Analytical Chemistry.

Reference: Bharadwaj, R., Z. Chen, S. Data, B.M. Holmes, R. Sapra, B.A. Simmons, P.D. Adams, and A.K. Singh. 2010. "Microfluidic Glycosyl Hydrolase Screening for Biomass-to-Biofuel Conversion," Analytical Chemistry. Released online on October 22, 2010, DOI: 10.1021/ac102243f/

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

Division: SC-23.2 Biological Systems Science Division, BER


November 01, 2010

New Modeling Tool for Optimizing Biofuels Production

Many feedstocks and conversion options are available to produce biofuels. DOE's Joint BioEnergy Institute (JBEI) has developed a new publicly available model to evaluate the relative advantages of various biofuel production approaches. The model includes the flow of materials from feedstocks leaving the farm through finished products leaving the biorefinery. It tracks the use of heat, power, and raw materials and predicts costs as well as energy and material balances. A preliminary, traditional scenario involving corn stover as feedstock, acid pretreatment, and conversion to ethanol using yeast engineered to ferment five and six carbon sugars is the basis of comparison. The model facilitates input from the user community to provide suggestions and modify assumptions. JBEI is using the model to guide its research emphasis. For example, the model predicts that acetate produced during fermentation could limit ethanol production more than the accumulation of ethanol suggesting that feedstocks and feedstock processing should be optimized to reduce acetylation. The model is also highlighted in the October 22 issue of Science Magazine.

Reference: Klein-Marcuschamer, et al. 2010. "Technoeconomic Analysis of Biofuels: A Wiki-Based Platform for Lignocellulosic Biorefineries," Biomass and Bioenergy, doi:10:1016/j.biombioe.2010.07.033.

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

Division: SC-23.2 Biological Systems Science Division, BER


November 01, 2010

Sneak Peak at How Stressed Plants Mobilize the Resources

The ability of plants to withstand stresses depends on a coordinated chain of events from the molecular level to the whole plant. Our ability to effectively develop plants as sustainable feedstocks for biofuels requires that we understand the impacts of these stresses. DOE-funded researchers at Brookhaven National Laboratory and Tufts University have shown that plants re-allocate a significant portion of their below-ground nitrogen resources when defense mechanisms are triggered in response to herbivory (being eaten or under attack). Using a combination of short-lived PET (positron emission tomography) radioisotopes, including carbon-11 and nitrogen-13, administered to leaves of intact tomato plants, they were able to "see" the movement of sugars and amino acids away from the simulated attack sites. The results argue for strong physiological adaptive responses by plants as a tolerance defense mechanism. This research has important implications for bioenergy feedstock development since the next generation of plant feedstocks will need to withstand many environmental challenges including drought, limited nutrients and disease. Modifying plants with the right defense traits could improve the robustness of future feedstocks. The research is reported in the November issue of New Phytologist, along with a commentary on the significance of the new findings.

References:

Gómez, S., R.A. Ferrieri, M. Schueller, and C. M. Orians. 2010. "Methyl Jasmonate Elicits Rapid Changes in Carbon and Nitrogen Dynamics in Tomato" New Phytologist 188, 835-44.

Anten, N.P.R., and R. Pierik. 2010. "Moving Resources Away From the Herbivore: Regulation and Adaptive Significance," New Phytologist 188, 643-45.

Contact: Prem Srivastava, SC-23.2, (301) 903-4071
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 25, 2010

Could Biofuels Replace a Large Fraction of the U.S. Petroleum Demand?

Sustainability of large-scale biofuel domestic production is a serious concern. A new model has been developed at the DOE Great Lakes BioEnergy Research Center to assess the potential impact of existing and emerging technologies for the production of biofuels and animal feed. The model assumes that all land used for human food, forests, rangeland, and most other uses will not be affected by the production of bioenergy and animal feed. The only land considered for these technologies is currently allocated to animal feed and corn ethanol. The technologies considered in this study include separating and concentrating leaf protein, pretreating forage, and double cropping where possible. These results outlined in a recent article in Environmental Science & Technology indicate the potential for annual production of about 100 billion gallons of ethanol with no impact on domestic food production or indirect land use change, while significantly reducing U.S. greenhouse gas emissions, increasing soil fertility, and promoting biodiversity.

Reference: Dale B., Bals B., Kim S., and Eranki P., "Biofuels Done Right: Land Efficient Animal Feeds Enable Large Environmental and Energy Benefits," Environ. Sci. Technol, 10.1021/es101864b, October 7, 2010

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

Division: SC-23.2 Biological Systems Science Division, BER


October 25, 2010

Human Metabolic Disease Leads to New Understanding of Oil Accumulation in Plants

A major challenge in developing plants for biofuels production is the difficulty involved in breaking down lignocellulosic material, the main constituent of plant biomass. An alternate approach to biofuel production in plants would involve engineering plants to accumulate larger amounts of lipids (the precursors of oils normally found in seeds) in vegetative tissues such as leaves. Lipids and oils could then be directly harvested for biodiesel or converted to other biofuels. DOE researchers at the University of North Texas recently identified a gene in the model plant Arabidopsis thaliana that is surprisingly similar to a gene known to be involved in Chanarin-Dorfman syndrome, a human metabolic disorder that results in excessive production of lipids in non-fatty tissues. When this gene was disrupted in Arabidopsis, plants had a 10-fold increase in total lipid content in vegetative plant tissue although the plants appeared to grow normally. Lipid levels in seeds were unchanged. These results suggest a surprising degree of similarity of lipid metabolism between plants and animals. Although Arabidopsis is unlikely to be developed as a bioenergy feedstock, this represents a major advance in understanding of oil synthesis in plants and presents promising new targets for metabolic engineering of biomass crops.

Reference: James, C.N., P. J. Horn, C. R. Case, S. K. Gidd, D. Zhang, R. T. Mullen, J. M. Dyer, R. G. W. Anderson, and K. D. Chapman. 2010 "Disruption of the Arabidopsis CGI-58 homologue produces Chanarin–Dorfman-like lipid droplet accumulation in plants," Proc. of the Natl. Acad. Sci. 107:17833-17838.

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

Division: SC-23.2 Biological Systems Science Division, BER


October 12, 2010

New Route to Lignin Biosynthesis Offers New Opportunity to Improve Biofuels Production

The biosynthetic pathway of lignin, the compound that confers strength and rigidity to plant cell walls and makes their breakdown into biofuels so difficult, is quite complex. Early steps in the pathway are common to the production of a number of different compounds but each path eventually diverges at a specific point. The first step committed to lignin (monolignol) biosynthesis occurs with the enzyme cinnamoyl CoA reductase (CCR). DOE researchers from the Samuel Roberts Noble Foundation have discovered a second, distinct CCR enzyme in a relative of alfalfa, Medicago truncatula, that apparently provides an alternate route to monolignol. This second CCR may give the plant the flexibility to adapt to various developmental conditions. One approach to developing feedstocks with reduced lignin that are easier to deconstruct for biofuel production is to modify genes in the lignin biosynthetic pathway. This new understanding of the lignin biosynthetic pathway will facilitate identification of potential target genes for modification.

Reference: Zhou R, Jackson L, Shadle G, Nakashima J, Temple S, Chen F, and Dixon RA. 2010. "Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula," Proc Natl Acad Sci doi:10.1073/pnas.1012900107 (Early Edition, October 7 2010).

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

Division: SC-23.2 Biological Systems Science Division, BER


September 27, 2010

Ant Farmers Provide New Clues for the Breakdown of Plant Biomass

Leaf cutter ants rely on complex farms of bacteria and fungi in their underground nests to deconstruct harvested plant biomass and convert it to food. The communities of microbes responsible for rapid turnover of massive amounts of cellulosic material in tropical ecosystems are poorly understood and could serve as a source of novel microbes and enzymes for industrial biomass conversion. Researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) and the DOE Joint Genome Institute (JGI) have completed the first microbial community metagenome sequencing project for leaf cutter ant nests. The results reveal a unique community with distinct microbial subpopulations responsible for degrading material of varying degrees of recalcitrance in different parts of the nest. The metagenome library contained gene signatures for a broad range enzymes involved in deconstruction of cellulose, hemicellulose, and other plant polymers. The team has isolated two of the more dominant bacteria found in the ant nests and demonstrated cellulose degradation capabilities. These results provide a new understanding of a highly evolved natural system for biomass deconstruction that could inform development of new consolidated biomass processing approaches.

Reference: Suen, G. et al. 2010. "An Insect Herbivore Microbiome with High Plant Biomass Degrading Capacity," PLoS Genetics. 6:e1001129

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

Division: SC-23.2 Biological Systems Science Division, BER


September 20, 2010

GeoChip 3.0 Improves Analysis of Microbial Community Function

Microbial communities perform a central role in mediating ecosystem biogeochemical cycles and transforming environmental contaminants. However, examining the functional properties of these communities and how they respond to changing conditions is a challenge. The GeoChip, a chip containing an array of molecular probes, enables scientists to efficiently analyze many DNA samples from environments of interest for genes involved in key functional processes including biomass breakdown, nitrogen use, organic contaminant degradation, and metal resistance. A new version of the chip, GeoChip 3.0, is now available that features twice the number of functional gene families, improved analytical tools and software, and a greatly increased capability to trace functional properties to specific community members. This new tool provides enhanced capabilities for understanding the functional processes of environmental microbes and monitoring their response to changing variables. The GeoChip was developed by a collaborative team of investigators at the University of Oklahoma and Lawrence Berkeley National Laboratory. The original version won an R&D 100 award.

Reference: He, Z. et al. 2010. "GeoChip 3.0 as a High-Throughput Tool for Analyzing Microbial Community Composition, Structure, and Functional Activity," ISME Journal: 4: 1167-1179.

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

Division: SC-23.2 Biological Systems Science Division, BER


September 20, 2010

New Approach to Understand Microbial Gene Function

Understanding the functions of the thousands of genes found in a microbial genome is a difficult but important challenge. Derek Lovley and his team at the University of Massachusetts, Amherst, have used a new approach that combines several experiment-based predictions of gene function (called "annotations") to understand the biology of Geobacter sulfurreducens, a microbe with important roles in bioremediation of contaminant metals. The team integrated data on messenger RNA transcription, RNA translation into proteins, and biochemical data obtained under a variety of conditions to achieve a more precise and comprehensive annotation of Geobacter. Their approach resulted in the identification of previously undetected genes and other features in the Geobacter, genome such as "antisense" transcripts, that could be tentatively linked to functions and Geobacter's regulatory complexity. This new, experimental-based approach to predicting gene function reveals a much greater richness in gene expression phenomena than approaches based solely on DNA sequence or comparisons with other sequenced microbes.

Reference: Qiu Y, Cho BK, Park YS, Lovley D, Palsson Bø, Zengler K. "Structural and operational complexity of the Geobacter sulfurreducens genome," Genome Res. 2010 (Sept.); 20, 1304-11.

Contact: Dan Drell, SC-23.2, (301) 903-4742, Marvin Stodolsky, SC-23.2, (301) 903-4475
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 20, 2010

New Method Allows Genetic Manipulation of Cellulose Degrading Clostridia

To be most useful for biofuel production, microbes need to have useful biochemical properties and be manipulable genetically. The cellulose degrading bacterium Clostridium thermocellum, while a promising candidate for consolidated bioprocessing approaches to biofuel production, has significant genetic manipulation challenges that have limited understanding of its mechanisms of biomass deconstruction. Researchers at DOE's Bioenergy Science Center (BESC) now report a new method for genetic modification of C. thermocellum in the Proceedings of the National Academy of Sciences. This new method enabled the construction of a mutant lacking the gene for one of the organism's major cellulase enzymes, Cel48S. The mutant depolymerizes crystalline cellulose 80% slower than the parent strain but, given sufficient time, it is still capable of complete cellulose degradation. This finding demonstrates that although Cel48S plays a major role in cellulose degradation, other less understood enzymes also contribute to this process and require further study. This result represents an important step forward in our ability to engineer this organism for bioenergy applications.

Reference: Olson, D. G. et al. 2010. "Deletion of the Cel48S Cellulase from Clostridium thermocellum," PNAS doi/pnas.1003584107

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

Division: SC-23.2 Biological Systems Science Division, BER


September 13, 2010

Microbes Work Together to Process Dissolved Organic Carbon

Marine dissolved organic matter (DOM) contains as much carbon as the Earth’s atmosphere and represents a critical component of the global carbon cycle. While we know that microbial processes and activities drive most of Earth’s biogeochemical cycles, those associated with marine DOM cycling are poorly understood. DOE scientists at the Massachusetts Institute of Technology analyzed the responses of microbial communities to high-molecular weight DOM. Following the addition of DOM both cell numbers and a variety of gene transcripts from different microbial groups doubled over a 27 hour period. Gene transcripts that were increased included those associated with sensor systems, phosphate and nitrogen processing, chemotaxis, and motility. The data also indicated that different microbial species played different roles in the partitioning of DOM. These findings suggest that coordinated, cooperative activities of a variety of bacterial “specialists” may be critical in the cycling of marine DOM, emphasizing the importance of microbial community dynamics in the global carbon cycle. The research was led by Edward F. DeLong and has just been published on-line in the Proceedings of the National Academy of Sciences (PNAS).

Reference: McCarren, J, Becker, J.W., Repeta, D.J., Shia, Y., Young, C.R., Malmstrom, R.R., Chisholm, S.W. and DeLong, E.F. “Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea” PNAS (2010) www.pnas.org/cgi/doi/10.1073/pnas.1010732107.

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

Division: SC-23.2 Biological Systems Science Division, BER


September 07, 2010

A New Approach to Understand Complex Microbial Communities

Microorganisms control the rates of numerous processes in the environment including contaminant degradation and biogeochemical cycling of carbon and other nutrients; however, they rarely perform these functions alone or in isolation. Microorganisms exist in communities whose dynamic activities and responses to environmental influences remain poorly understood. Building on the increasing availability of microbial species whose genomes have been sequenced, researchers at Oak Ridge National Laboratory developed a model system of three microbial species to probe the details of microbial community interactions and physiology. Co-cultures containing a Clostridia, Desulfovibrio and Geobacter species were used to examine carbon and energy flow in an anaerobic microbial community. The availability of genomic information for each microbe enabled the use of powerful techniques for analysis of gene and protein expression to understand the dynamic shifts in metabolism resulting from environmental changes and/or association or competition within the microbial community. The model system is applicable to numerous environmental processes where fermentative production of simple organic acids (by Clostridia) drives microbial metabolism such as sulfate-reduction (by Desulfovibrio) or iron reduction (by Geobacter). This project will advance our predictive understanding of microbial community interactions in a manner not previously possible and will increase our understanding of environmental processes relevant to DOE such as carbon and nutrient cycling in soils and contaminant biotransformation in contaminated groundwater.

Reference: Miller, L. D., J. J. Mosher, A. Venkateswaran, Z. K. Yang, A. V. Palumbo, T. J. Phelps, M. Podar, C. W. Schadt, and M. Keller. 2010. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments. BMC Microbiology. 10:149

Contact: Robert T. Anderson, SC 23.1, (301) 903-5549, Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

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


September 07, 2010

Improving Access to Cellulose in Biomass for Biofuel Production

The conversion of cellulosic biomass to fermentable sugars usually requires a costly and time-consuming pretreatment step to increase the material's porosity, decrease its crystallinity and reduce the amount of structural lignin in the cell wall. Researchers at Oak Ridge National Laboratory have used small angle neutron scattering (SANS) to probe the morphological changes of switchgrass cell walls during dilute acid pretreatment. When the pretreatment temperature is in the vicinity of the glass transition temperature of lignin (the temperature at which lignin transforms from a liquid to a glass-like material), they find that the lignin rapidly redistributes on the surface of the cellulose as large aggregates that can be washed away with solvent. The underlying cellulose does not break down and is readily available for cellulose degradation by enzymatic hydrolysis (both desirable features) but appears to form a more crystalline structure (an undesirable feature). This work provides an alternative approach for efficient hemicellulose and lignin removal, improving the quantity and accessibility of cellulose but in a form (crystalline fibrils) that is not optimal for enzymatic hydrolysis. The research has just been published online in the journal Biomacromolecules. This work is sponsored by DOE’s Office of Biological and Environmental Research.

Reference: V. Pingali, et al., “Breakdown of Cell Wall Nanostructure in Dilute Acid Pretreated Biomass,” Biomacromolecules, (August 20, 2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 07, 2010

Two New Prochlorococcus Clades from Iron-Depleted Oceans

Prochlorococcus is one of the most abundant marine photosynthetic microbes and one of the main producers of “food” in the world’s oligotrophic (nutrient poor) oceans. DOE funded research led by the J. Craig Venter Institute has characterized two new distinct clades (branches on the tree of life) of Prochlorococcus. Both clades dominate the eastern equatorial pacific and tropical Indian oceans, known for their high temperatures and low nutrient and iron availability. Using both a phylogenetic and genomic analyses, the two clades were found to be distinct from each other and from other known lineages adapted to high-light environments, and to lack certain iron-reducing proteins which aids them in adapting to the low iron availability. These findings explain why these organisms do not respond to ocean iron-fertilization experiments and shed the light on how phytoplankton adapt to variations in nutrient availability in the oceans. This new characterization of Prochlorococcus and its role in the energy and nutrient cycling in the oceans’ ecosystems will greatly enhance our understanding of both the marine diversity and the biogeochemical cycle. The research has just been published in the Proceedings of the National Academy of Sciences (PNAS) Early Edition.

Reference: Douglas B. Rusch, Adam C. Martiny, Christopher L. Dupont, Aaron L. Halpern, and J. Craig Venter “Characterization of Prochlorococcus clades from iron-depleted oceanic regions” PNAS published ahead of print August 23, 2010, doi:10.1073/pnas.1009513107

Contact: Shireen Yousef, SC-23.2, (301) 903-6020
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 23, 2010

Metagenomics of Globally Important Eukaryotic Phytoplankton

Global CO2 fixation is divided equally among terrestrial and marine ecosystems, each accounting for ~50 billion tons of carbon per year. Tiny “pico” phytoplankton are responsible for much of the CO2 capture in marine ecosystems; however, the genomes of only six of these organisms have been sequenced. In a new study published this month in the Proceedings of the National Academy of Sciences(USA)), members of the prymnesiophyte phytoplankton lineage sequenced at the DOE Joint Genome Institute. Because most of these tiny organisms cannot be grown in culture, metagenomic approaches (the study of genetic material recovered directly from environmental samples) were used to analyze cells from subtropical North Atlantic waters. The organisms analyzed have composite genomes with strong evolutionary derivations from different sources. This lineage is thought to be responsible for 25% of the global picophytoplankton biomass whose abundance varies in different biogeographical areas. Changes in ocean temperatures associated with global climate processes could lead to changes in the abundance of these important organisms, with as yet poorly characterized consequences. This study shows the value of culture-independent metagenomic analyses for characterizing the marine microbiome with the potential for exploring its impacts on climate change processes. The research was led by Alexandra Worden at the Monterey Bay Aquarium and Research Institute.

Reference: Cuveliera, M.L. et.al., “Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton” (2010) Proc. Nat. Acad. Sci.(USA) 107, 14679–14684.

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

Division: SC-23.2 Biological Systems Science Division, BER


August 16, 2010

Looking Inside Plant Cell Walls

The recalcitrance of plant cell walls to degradation is a major hurdle for the cost effective production of biofuels from biomass. This is further complicated by our inability to characterize plant materials with sufficient spatial resolution to understand the degradation process. Researchers at the DOE Bioenergy Sciences Center (BESC) at Oak Ridge have developed a new imaging system that provides atomic-resolution, non-destructive characterization of the physical properties of biological tissues and other samples. Called Mode-Synthesizing Atomic Force Microscopy, the new system extends traditional Atomic Force Microscopy (AFM) which uses a force-sensing cantilever with a sharp tip to measure the topography and other properties of surfaces. The new technique provides subsurface information otherwise unavailable through AFM and 50nm resolution for imaging plant polymers. This new technique provides access to high resolution plant structure and chemistry within native and pretreated plant cell walls. The technology was developed as an intermediate step toward technology that will enable molecular-level, spectroscopic measurements of plant tissues, and is receiving a 2010 R&D 100 award.

Reference: Tetard L., Passian A., and Thundat T. "New modes for subsurface atomic force microscopy through nanomechanical coupling," Nature Nanotechnology volume 5, pages 105-109 (2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 16, 2010

Solving the Mystery of Metabolism in Clostridium acetobutylicum – an Important Biofuel Producer

The bacterium Clostridium acetobutylicum produces butanol, ethanol, and hydrogen as end products of biomass fermentation and is already has industrial uses. C. acetobutylicum also serves as a model for an important class of soil-based organisms mediating carbon degradation in terrestrial ecosystems. However, scientists have not been able to map this organism’s metabolic processes since the genes encoding several key enzymes necessary for basic cell physiology seem to be missing. DOE scientists at Princeton University have used an innovative approach to resolve this mystery. By following the incorporation of radiolabeled carbon into various intermediate compounds, they identified a unique series of reactions used in carbon conversion and developed the first ever quantitative model of metabolic flux for C. acetobutylicum. These results provide critical information on the pathway used by these organisms to perform important processes in the global carbon cycle and greatly enhance the prospects of being able to engineer Clostridia’s metabolism for biofuels synthesis. The research has just been published on-line in the Journal of Bacteriology.

Reference: D. Amador-Noguez, X.-J. Feng, J. Fan, N. Roquet, H. Rabitz and J. D. Rabinowitz. 2010 “Systems-level metabolic flux profiling elucidates a complete, bifurcated TCA cycle in Clostridium acetobutylicum”, J. Bacteriology, (2010) doi:10.1128/JB.00490-10

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

Division: SC-23.2 Biological Systems Science Division, BER


August 16, 2010

Using Genomic Research Tools to Reach the Next Generation of Scientists

The Integrated Microbial Genomes (IMG) platform is an informatics environment that scientists can use to annotate genes in newly sequenced genome sequences. It was developed by scientists at the DOE Joint Genome Institute (JGI). JGI scientist Cheryl Kerfeld and colleagues now report how they used the IMG platform to develop the Integrated Microbial Genomes–Annotation Collaboration Toolkit (IMG-ACT), an educational resource that provides access to genomes sequenced by the JGI and offers students virtually endless research possibilities, bioinformatics databases, instructor course management and student notebooks. Since IMG-ACT was launched in 2008, more than 100 faculty members and 1,600 students nationwide have participated in the program. An example of the impact of IMG-ACT is at the University of California, Los Angeles, where all life science majors use the IMG-ACT platform as part of an interdisciplinary laboratory curriculum to develop a community of peer experts in bioinformatics.

Reference: Jayna L. Ditty, et al., “Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum” PLoS Biol (2010) 8(8): e1000448. doi:10.1371/journal.pbio.1000448

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


August 02, 2010

New Technology for Looking Inside Plant Cell Walls

The structure of plant cell walls determines how easy or hard it will be to deconstruct plant feedstocks to produce biofuels. Plant cell walls contain the cellulose that is converted to fuels but the cellulose is surrounded by a tough lignin matrix that limits accessibility of the cellulose. Michael Thelen at the Lawrence Livermore National Laboratory, together with researchers from Lawrence Berkeley National Lab and the National Renewable Energy Laboratory have combined fluorescence microscopy, synchrotron radiation based Fourier transform infrared spectromicroscopy and atomic force microscopy to study the fine-scale organization and chemical composition of plant cell walls. Using the Zinnia as a model plant because of its ease of growth in liquid cultures, the team observed the formation of the tube-like xylem cells that carry water from roots to leaves and that also contain the bulk of the plant’s cellulose and lignin. Their results suggest that these combined imaging techniques can be used to see critical changes in cell wall structure that occur during enzymatic and microbial degradation as part of biofuel production potentially leading to the design of more efficient and cost effective deconstruction strategies.

Reference: Catherine I. Lacayo, Alexander J. Malkin, Hoi-Ying N. Holman, Liang Chen, Shi-You Ding, Mona S. Hwang, and Michael P. Thelen, "Imaging Cell Wall Architecture in Single Zinnia elegans Tracheary Elements," Plant Physiology. Published online July 6, 2010.

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

Division: SC-23.2 Biological Systems Science Division, BER


August 02, 2010

Switchgrass Genome Structure Revealed

Switchgrass is an important biofuel feedstock because it grows on marginal lands, is highly adaptable, and as a perennial does not require annual planting. The species contain a considerable amount of natural genetic diversity that can be tapped to improve traits such as biomass yield, but as a perennial breeding improved switchgrass cultivars can take several years. Breeding time can be reduced by using a technique known as marker assisted selection (MAS); however, this approach requires detailed knowledge of the species’ genome structure. Researchers at the USDA Western Regional Research Center, the Samuel Roberts Noble Foundation, and Pennsylvania State University, supported in part by DOE, have constructed the first complete genetic map of switchgrass. The map, consisting of eighteen distinct groups of genes corresponding to each chromosome, reveals a close genetic relationship between switchgrass and the potential bioenergy grasses foxtail millet and sorghum. This new genetic tool will enable development of MAS strategies to improve switchgrass and other potential bioenergy grass species.

Reference: Okada M, Lanzatella C, Saha MC, Bouton J, Wu R, and Tobias CM. 2010. “Complete switchgrass genetic maps reveal subgenome colinearity, preferential pairing, and multilocus interactions.” Genetics 185(3):745-760.

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

Division: SC-23.2 Biological Systems Science Division, BER


August 02, 2010

Understanding How Plants Make Cell Wall Lignin

Plant development is regulated by many complex processes involving both environmental and genetic factors. One of these processes, the phenylpropanoid pathway, is responsible for biosynthesis of the cell wall structural component lignin as well as flavonoids, a diverse set of compounds involved in plant pigmentation and defense. Lignin protects polysaccharides in the plant cell wall from degradation. However, this natural protection also impedes our ability to breakdown biomass for biofuel production. Plants with lower lignin content are smaller overall, i.e., have decreased biomass production, but it has not been clear whether this decrease in plant fitness is due to lignin deficiency or flavonoid accumulation. Researchers at Purdue University studying the model plant Arabidopsis thaliana present evidence linking growth reduction in mutant varieties of Arabidopsis to lignin deficiency. These studies of the phenylpropanoid pathway help define its impacts on biomass production, information of great importance in seeking improved biofuel feedstocks.

Reference: Xu L, Bonawitz ND, Weng J-K, and Chapple C. 2010. “The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids.” Plant Cell 22(5):1620-1632.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Alterations in Poplar Lignin Could Enhance Pretreatment Efficiency

Alterations in lignin content or structure in plant cell walls can have a profound effect on chemical or enzymatic degradability and the efficiency by which certain pretreatment methods remove lignin from polysaccharides. GLBRC researchers found that overexpression of a particular gene [ferulate 5-hydroxylase (F5H)] in the lignin biosynthetic pathway of a hybrid poplar created lignin with a structure and composition that can enhance lignin removal from cellulose, while still maintaining normal growth and development. When compared to wild-type poplar, the up-regulated F5H poplar has a much simpler lignin structure that is less branched and more homogeneous in its subunit composition, which makes the lignin easier to separate from cellulose during pretreatment. This and other poplar transgenic materials under investigation by GLBRC researchers have cell walls that release more sugar than wild-type poplar over a range of pretreatment methods. Ongoing work is examining the effect of ammonia fiber expansion pretreatment on these transgenic poplars.

Reference: Details on the lignin structure of F5H up-regulated poplar were reported in Stewart, J. J., et al. 2009. "The Effects on Lignin Structure of Overexpression of Ferulate 5-Hydroxylase in Hybrid Poplar," Plant Physiology 150(2), 621-35.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Chemical Process Produces Simple, Fermentable Sugars from Raw Biomass

A GLBRC research team has developed a promising new chemical method to liberate the sugar molecules trapped inside inedible plant biomass, a key step in the creation of cellulosic biofuels. The new chemical process combines ionic liquids and dilute acid to degrade cellulosic biomass without the use of cellulases. In this approach, ionic liquids make cell-wall polysaccharides accessible to chemical reactions by decrystallizing lignocellulosic biomass and dissolving cellulose. Then, dilute hydrochloric acid at 105°C is used to hydrolyze cellulose and hemicellulose into individual sugar subunits. Applying this process to pure cellulose resulted in nearly 90% yield of glucose, and applying it to raw corn stover achieved sugar yields of 70% to 80%. By adding the right balance of water to the mixture, the researchers reduced the formation of unwanted by-products and demonstrated significant improvement in fermentable sugar yields from ionic liquid treatment of lignocelluloses with yields comparable to those of enzymatic hydrolysis. Ionexclusion chromatography was used to separate sugars from the reaction mixture and recover the ionic liquids for reuse. Sugars recovered from the hydrolyzed stover were readily converted to ethanol by Escherichia coli and the yeast Pichia stipitis.

Reference: This research was reported in Binder, J. B., and R. T. Raines. 2010. "Fermentable Sugars by Chemical Hydrolysis of Biomass," Proceedings of the National Academy of Sciences 107, 4516-21.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Compost Microbes Adapted to Produce Switchgrass-Degrading Enzymes

By incubating switchgrass with a mix of microbes isolated from compost, JBEI researchers provided the selective pressure needed to grow a new microbial community enriched with enzymes that degrade cell-wall polymers specific to switchgrass. The sample was incubated in a bioreactor for 31 days under typical composting conditions. Metagenomic sequencing of the switchgrass-adapted compost (SAC) community on day 31 was carried out to investigate the sample's diverse pool of glycoside hydrolases-enzymes that break bonds between carbohydrate molecules. The sample contained a high proportion of genes encoding enzymes that attack the branches and backbone of a major hemicellulose in grass cell walls. Analysis of the small-subunit ribosomal RNA (rRNA) isolated from the microbial community revealed dramatic changes in the community profile with more than a 20-fold increase for some bacterial populations in the SAC. Although metagenomic DNA sequence is highly fragmented, making isolation of full genes from complex communities difficult, two full-length genes for cellulose-degrading enzymes were discovered, synthesized, expressed in Escherichia coli, and tested for enzyme activity.

Reference: This research was reported in Allgaier, M., et al. 2010. "Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community," PLoS One 5(1), e8812.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Heat-Tolerant Bacteria Efficiently Degrade Non-Pretreated Biomass

Presenting the possibility of eliminating the pretreatment step from cellulosic biofuel production, a hot springs bacterium known as Caldicellulosiruptor bescii has shown that it can efficiently degrade crystalline cellulose, xylan (a hemicellulose), and various types of non-pretreated biomass including hardwoods such as poplar, high-lignin grasses such as switchgrass, and low-lignin grasses such as Bermuda grass. With an optimal growth temperature of 75°C, C. bescii was able to break down 65% of switchgrass biomass without pretreatment. This bacterium is the most heat-tolerant biomass degrader known (withstanding temperatures up to 90°C), and it primarily produces hydrogen as an end product when grown on plant biomass. BESC researchers have discovered another hot springs bacterium (Caldicellulosiruptor obsidiansis), isolated from Yellowstone National Park, that thrives at 78°C and can ferment all the simple sugars in cell-wall polysaccharides into diverse products including ethanol. Combining the functional capabilities of C. bescii and C. obsidiansis theoretically could yield organisms that both deconstruct and ferment plant biomass at temperatures above the boiling point of ethanol (78.4°C). Producing ethanol in the vapor phase could greatly reduce the inhibitory effects of ethanol on cell growth.

References: C. bescii (formerly called Anaerocellum thermophilum DSM 6725) findings are from Yang, S. J., et al. 2009. “Efficient Degradation of Lignocellulosic Plant Biomass, Without Pretreatment, by the Thermophilic Anaerobe ‘Anaerocellum thermophilum’ DSM 6725,” Applied and Environmental Microbiology 75(14), 4762–69. The discovery of C. obsidiansis was reported in Hamilton-Brehm, S. D., et al. 2010. “Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park,” Applied and Environmental Microbiology 76(4), 1014–20.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Key Genes for Biosynthesis of Hydrocarbon Biofuels Identified in Bacterium Micrococcus luteus

JBEI researchers have elucidated the genes and a proposed biochemical pathway for the production of long-chain alkenes - key chemical components of petroleum-based gasoline and diesel fuels - in the bacterium Micrococcus luteus. Building on insights from microbial alkene research reported 4 decades ago, JBEI researchers hypothesized that a key mechanism for long-chain alkene biosynthesis would involve decarboxylation and condensation of fatty acids. By searching the genome of the alkene-producing bacterium M. luteus, researchers found three candidate genes with conserved sequences associated with condensing enzymes. Expression of these genes in E. coli resulted in long-chain alkene production, but additional research will be needed to reveal the specific biochemical role that each of the enzymes encoded by these genes plays in alkene synthesis. A wide range of bacteria has been found to contain genes similar to those that encode M. luteus alkene biosynthesis enzymes, so researchers will have an opportunity to learn more about these enzymes by exploring their diversity in nature.

Reference: This research was reported in Beller, H. R., E. B. Goh, and J. D. Keasling. 2010. "Genes Involved in Long-Chain Alkene BioBiosynthesis in Micrococcus luteus," Applied and Environmental Microbiology 76(4), 1212-23.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Key Targets from a Complex Family of Lignin Biosynthesis Genes Identified in Switchgrass

Although lignin content and composition have been manipulated in several plant species by targeting the monolignol biosynthesis pathway, little is known about the genes and enzymes associated with this pathway in switchgrass. Cinnamoyl CoA reductase (CCR) catalyzes the first step in this pathway dedicated to monolignol synthesis. However, switchgrass contains numerous copies of CCR-like genes, complicating the selection of the best gene targets for altering lignin to reduce cell-wall recalcitrance. By analyzing the RNA of expressed CCR genes, BESC researchers show that one of the expressed genes (PvCCR1) encodes an enzyme actively involved in lignification and thus is a prime target for down-regulation to improve the degradability and sugar yield from switchgrass. Ongoing research is investigating how reducing the expression of the PvCCR1 gene impacts lignin composition and plant structure.

Reference: This research was reported in Escamilla-Treviño, L. L., et al. 2009. “Switchgrass (Panicum virgatum) Possesses a Divergent Family of Cinnamoyl CoA Reductases with Distinct Biochemical Properties,” New Phytologist 185, 143–55.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Mass Spectrometry-Based Protein Detection Technique Speeds Optimization of Biofuel Protein Levels in Metabolically Engineered Microbes

JBEI researchers have developed a mass spectrometry-based protein detection technique called multiple-reaction monitoring (MRM) for identifying microbial proteins that can convert cellulosic sugars into biofuels. With the MRM technique, researchers can detect multiple target proteins in the complex protein mixtures of native cells and rapidly change the specific proteins to be targeted, something not possible with conventional protein detection technology. When coupled to liquid chromatography, MRM analysis offers high selectivity and sensitivity. It eliminates background signal and noise even in the most complex protein mixtures by utilizing two targeted points - a peptide mass and a specific fragment mass generated by mass spectrometry. Since the entire mass range is not scanned and only combinations of peptide and fragment masses are monitored, MRM can be used to detect and quantify up to 10 different proteins in a single liquid chromatography separation.

Reference: The MRM technique is a valuable tool for analyzing enzyme complexes in a variety of JBEI projects such as the synthetic protein scaffold work reported in Dueber, J. E., et al. 2009. "Synthetic Protein Scaffolds Provide Modular Control over Metabolic Flux," Nature Biotechnology 27(8), 753-59.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

New Approach to Visualize Biomass Solubilization During Ionic Liquid Pretreatment

JBEI researchers have developed a technique, based on the natural autofluorescence of plant cell walls, that enables the dynamic imaging of biomass solubilization during ionic liquid pretreatment. Using this technique, researchers can accurately and quickly assess the ionic liquid’s performance without the need for labor-intensive and time-consuming chemical and immunological labeling. Working with switchgrass and using the ionic liquid known as 1-n-ethyl-3-methylimidazolium acetate (EmimAc), the researchers observed a rapid swelling of secondary plant cell walls within 10 minutes of exposure at relatively mild pretreatment temperatures (120°C). This reaction indicates a disruption of hydrogen bonding within cellulose and between cellulose and lignin. The swelling was followed by complete dissolution of biomass over 3 hours. By adding water to the solubilized biomass mixture, cellulose can be precipitated out and separated from the lignin, which remains in solution. This recovered cellulose was efficiently hydrolyzed into its sugar components by a commercial cellulase cocktail over a relatively short time interval. Currently, those ionic liquids that are most effective at dissolving plant cell-wall polymers are prohibitively expensive for use on a mass scale. Understanding how ionic liquids are able to dissolve lignocellulosic biomass could pave the way for finding new and better varieties for use in biofuel production.

Reference: This research was reported in Singh, S., B. A. Simmons, and K. P. Vogel. 2009. “Visualization of Biomass Solubilization and Cellulose Regeneration During Ionic Liquid Pretreatment of Switchgrass,” Biotechnology and Bioengineering 104(1), 68–75.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

New Modeling Tool Combines Environmental and Economic Analysis of the Biorefinery in Agricultural Landscapes

GLBRC researchers have provided a direct simulation of different biorefinery configurations in realistic agricultural landscapes for diverse locations throughout the United States. Since no full-scale commercial examples of a cellulosic biorefinery yet exist, forecasting the risks and tradeoffs of the complete biofuel production chain requires the use of modeling tools. Developed at GLBRC, the Biorefinery and Farm Integration Tool (BFIT) enables a combined modeling approach, including both crop and animal production, for analyzing potential economic profitability as well as environmental impacts. Focusing on ethanol production from the two largest anticipated sources of cellulosic biomass—corn stover and switchgrass—BFIT simulated the farm-biorefinery interactions for nine different agricultural regions using county-specific data for soil, weather, and farm practice patterns. In all cases, cellulosic biofuel production was integrated into existing farmlands. Results from the simulated scenarios include projections for land area requirements, annual farm income, nitrogen loss, greenhouse gas emissions, total project investment, and minimum ethanol selling price. Based on these projections, GLBRC researchers show that introducing the cellulosic biorefinery and associated markets could improve farm economics and reduce emissions without additional clearing of lands for biofuels.

Reference: BFIT research results are reported in Sendich, E. D., and B. E. Dale. 2009. “Environmental and Economic Analysis of the Fully Integrated Biorefinery,” GCB Bioenergy 1, 331–45.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

New Strategy Enhances Microbial Resistance to Inhibitory Pretreatment Chemicals

The chemical and physical processes for pretreating biomass help unravel the complex matrix of cell-wall components and enhance enzyme accessibility to these materials, but pretreatments also generate chemicals such as acetate that inhibit sugar fermentation to biofuels. Using a combination of adaptation, genetic engineering, and systems biology tools, BESC researchers have developed acetate-resistant strains of two industrial ethanol producers (the bacterium Zymomonas mobilis and the yeast Saccharomyces cerevisiae) by changing the expression of genes encoding transport proteins that move substances across the cell membrane. These proteins (called antiporters) transport proton and sodium ions and form gradients that are adversely impacted by the presence of acetate. By resequencing a Z. mobilis strain that had been adapted to withstand high acetate concentrations, BESC researchers discovered specific mutations in antiporter genes that enable acetate resistance. The specific antiporter mutations were validated using genetically engineered Z. mobilis and yeast showing the broad impact of these changes.

Reference: This research is reported in Yang, S., et al. 2010. “Paradigm for Industrial Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccharomyces cerevisiae,” Proceedings of the National Academy of Sciences 107(23), 10395-400.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Researchers Target Expressed Genes in Vascular Tissues of Switchgrass

Using a laser-based technique for microdissecting plant tissues, BESC researchers have targeted and analyzed DNA that is actively expressed in switchgrass vascular tissues where secondary cell walls are synthesized and reinforced with lignin. A total of 2,766 unique genes were identified from 5,734 expressed DNA segments (known as expressed sequence tags or ESTs). A significant number of these expressed sequences are novel with no significant hits to existing EST data. A small subset of the identified genes was targeted with labeled probes to visualize the expression of these genes in live plant tissue, and researchers found that several genes have much higher expression in the vascular bundles. The gene list generated from this study provides an important genomic resource for narrowing the range of molecular targets that could play key roles in modifying the lignin content of switchgrass and other related bioenergy crops.

Reference: This research was reported in Srivastava, A. C., et al. 2010. “Collection and Analysis of Expressed Sequence Tags Derived from Laser Capture Microdissected Switchgrass (Panicum virgatum L. Alamo) Vascular Tissues,” BioEnergy Research, DOI: 10.1007/s12155-010-9080-8.ps.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Sequencing Characterizes Bacterial Rhizosphere Communities of Biofuel Crops on Marginal Lands

Using a new high-capacity sequencing technology, GLBRC researchers characterized the structure of bacterial communities living in the rhizosphere (microscopic zone surrounding roots) of corn, soybean, canola, sunflower, and switchgrass. Samples were taken from agricultural sites and adjacent native forest in four locations with different soil types in Michigan. Three of the locations were marginal lands unsuitable for conventional agriculture, and a fourth site served as an experimental control to evaluate crop yield and quality on nonmarginal land. Although bacterial communities from biofuel crops and forest were clearly differentiated, the communities grouped mainly by location rather than by crop species, and soil environment and land management were key factors influencing community structure. Although more limited in plant diversity, greater bacterial diversity was observed in the biofuel crop samples than in the forest samples. Species of Acidobacteria were the most abundant community members in the rhizospheres of all plants, yet no strains have been isolated for cultivation and characterization in the laboratory.

Reference: This research was reported in Jesus, E. C., et al. 2010. “Bacterial Communities in the Rhizosphere of Biofuel Crops Grown on Marginal Lands as Evaluated by 16S rRNA Gene Pyrosequences,” Bioenergy Research 3, 20–27.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Study Provides Insights on Maximizing Energy-Rich Lipid Content in Leaves

Energy-rich lipids—with two times more energy than carbohydrates or proteins—are life’s primary molecules for energy storage. Preventing the breakdown of lipids as leaves age during the process of senescence is estimated to increase the energy content of leaves by about 20%. GLBRC researchers systematically studied the age-dependent changes in the fatty acids of Arabidopsis, Brachypodium distachyon (a model grass), and switchgrass leaves during natural plant senescence. Researchers found that surface lipids were more stable during senescence than membrane lipids, thus a potential strategy for increasing the energy content of biofuel crops might be to enhance surface lipid production.

Reference: This research was reported in Yang, Z., and J. B. Ohlrogge. 2009. “Turnover of Fatty Acids During Natural Senescence of Arabidopsis, Brachypodium, and Switchgrass and in Arabidopsis ?-Oxidation Mutants,” Plant Physiology 150, 1981–89.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Thousands of Proteins from Developing Xylem Cells in Poplar Are Identified

Woody biomass in trees primarily consists of the secondary cell walls of dead xylem tissue, so developing xylem cells are useful models for investigating secondary cell-wall formation. To provide subcellular context for identified protein functions and to enhance the detection of low-abundance proteins, subcellular fractionation techniques were used to obtain crude (soluble protein), pellet (insoluble protein), and nuclear protein fractions for analysis. Applying an automated approach known as MudPIT (Multidimensional Protein Identification Technology), BESC researchers successfully isolated and identified 6,000 different proteins from developing xylem cells in the stems of poplar plants. Results from this project greatly expanded the number of proteins that had been identified in previous poplar proteome studies. The protein products of several cell-wall synthesis genes (e.g., cellulose synthase, sucrose synthase, and polygalacturonase) were found to be associated with cellular membranes, and numerous new candidate genes for cell-wall synthesis were discovered - many are promising targets for further functional genomic analysis. Measuring differences in the whole proteomes of different poplar variations will increase understanding of the fundamental properties that underlie the recalcitrance of woody biomass to degradation.

Reference: This research was reported in Kalluri, U. C., et al. 2009. "Shotgun Proteome Profile of Populus Developing Xylem," Proteomics 9, 4871-80.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 29, 2010

Unique Database Provides Functional and Phylogenomic Information for Rice Glycosyltransferases

JBEI researchers have made major advances in comprehensively identifying all rice glycosyltransferases (GT), an important class of enzymes involved in synthesizing polysaccharide sugars in plant cell walls. Because rice and other grasses such as switchgrass and Miscanthus share similar cell-wall characteristics, whole genome–scale analysis of rice has enabled the discovery of several candidate genes for more in-depth functional analysis that can help researchers understand and manipulate grass cell walls for biofuel production. This research has led to the development of JBEI’s Rice GT Database, a publicly available resource for integrating and displaying diverse sets of functional genomic information for GTs (ricephylogenomics.ucdavis.edu/cellwalls/gt/). The database contains information on 793 putative gene models for rice GTs, and the loci for these genes are distributed across all 12 rice chromosomes. In addition to defining phylogenetic relationships among groups of rice GT genes based on sequence similarity, JBEI researchers also compared the number of different GT gene models identified for rice, Arabidopsis, and poplar (Populus trichocarpa). From the hundreds of possible GT genes that have been identified, scientists revealed 33 rice-diverged GTs that are highly expressed in vegetative, aboveground tissues and that serve as prime targets for mutagenesis studies and enzyme activity screens.

Reference: This database was reported in Cao, P. J., et al. 2008. “Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases,” Molecular Plant 1(5), 858–77.

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

Division: SC-23.2 Biological Systems Science Division, BER


July 19, 2010

Engineering Endoglucanase Enzymes for Higher Thermostability

Endoglucanase enzyme complexes break down the internal structure of cellulose, disrupting its crystalline structure and leading to glucose, the desired end product needed for fermentation to ethanol. Like all enzymes, endoglucanases only function within a certain temperature range; however, high temperatures are often part of the biomass breakdown process. Research at DOE's Bioenergy Research Center (BESC) at Oak Ridge is pushing the upper boundary of the temperature range for endoglucanases from the microbe Clostridium phytofermentans. Percival Zhang and colleagues studied directed mutational evolution of mutant proteins from the endoglucanase Cel5A family. They found mutants that are actually more active at 60°C, with the exact activity dependant on the specific cellulose substrate used. These results suggest that there may be a more complex relationship between endoglucanase activity and soluble or solid cellulose substrates then was previously thought. Further research will seek additional improvements of endogluconases for potential application to biofuel production.

Reference: W. Liu, et al., "Engineering of Clostridium phytofermentans Endoglucanase Cel5A for Improved Thermostability," Appl. Environ. Microbiol. 76, 4914-4917 (2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 21, 2010

Bionformatics Helps Identify Genes Associated with Plant Cell Wall Traits

The completion of the whole genome sequence of poplar (Populus) has made possible the use of bioinformatics and evolutionary methods to identify new candidate genes associated with plant cell wall traits. Researchers at DOE's BioEnergy Science Center at the Oak Ridge National Laboratory have used information on the poplar genome structure and its duplication, quantitative trait locus mapping, and analysis of publicly available microarray data to reduce the thousands of poplar genes that could contribute to cell wall traits down to 15-20 candidate genes. These genes are now being tested experimentally to identify their functions. This research highlights how bioinformatics can help focus research in the most promising directions potentially reducing time consuming experimental methods for correlating genes with phenotype. The results will facilitate research to enhance plant biomass properties for more efficient conversion into biofuels.

Reference: P. Ranjan, et al., "Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus," Bioenergy Research, June 2010, Vol. 3 pg. 172-182.

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

Division: SC-23.2 Biological Systems Science Division, BER


June 14, 2010

Mechanisms of Industrial Stress Tolerance in Biofuel Producing Microbes

In industrial biofuels production, complex plant biomass is often initially chemically pretreated to reduce the recalcitrance of lignocellulose to degradation. These processes liberate sugars that can be converted to biofuels by fermentative microbes. However, compounds such as acetic acid that inhibit the growth and productivity of these organisms are also produced. Oak Ridge National Laboratory researchers working at the DOE Bioenergy Science Center (BESC) have used a functional genomics approach to examine acetate tolerance in the biofuel producing bacteria Zymomonas mobilis. These studies have identified a new gene in a selectively evolved Z. mobilis strain whose overexpression results in increased tolerance to acetic acid. Structural characterization of the gene's product suggests that it is membrane protein involved in protecting the interior of the cell from acidic environmental conditions. Similar genes conferring acetic acid tolerance were also identified in the biofuel-producing yeast Saccaromyces cerevisiae. These results provide new targets for continued engineering and improvement of microbes for use in industrial production of cellulosic biofuels.

Reference: S. Yang et al. (2010) "Paradigm for Industrial Strain Improvement Identifies Sodium Acetate Tolerance Loci in Zymomonas mobilis and Saccaromyces cerevisiae," Proceedings of the National Academy of Science (USA) 107 (23) 10395-10400.

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

Division: SC-23.2 Biological Systems Science Division, BER


June 07, 2010

Lower Viscosity Seed Oil has Potential as Direct-use Biodiesel

Vegetable oils are often suggested as an alternative fuel source, but their long-chain fatty acid-containing triacylglycerols cause coking and gum formation, precluding their direct use in diesel engines. However, seed tissues from the common ornamental shrub Burning Bush (Euonymus alatus) store high levels of an unusual type of triacylglycerol called acetyl glycerides (acTAGs). acTAGs have unique physical and chemical properties that render the oil 30% less viscous than conventional vegetable oils, suggesting potential for direct use as a biofuel source. Researchers at the DOE Great Lakes Bioenergy Research Center have discovered the specific gene that is responsible for synthesis of acTAGs in Euonymus. This gene was identified by a new low-cost DNA sequencing approach performed at the DOE Joint Genome Institute that greatly increases the probability of detecting rare genes. Transgenic Arabidopsis plants expressing the Euonymus acyltransferase produced acTAGs, resulting in highly modified seed oil. The expression of this gene and subsequent synthesis of these unusual oils in commercial oilseed crops offers potential for large-scale production as direct-use biodiesel.

Reference: Durrett TP, McClosky DD, Tumaney AW, Elzinga DA, Ohlrogge J, and Pollard M. 2010. "A distinct DGAT with sn-3 acetyltransferase activity that synthesizes unusual, reduced-viscosity oils in Euonymus and transgenic seeds," Proc Nat Acad Sci 107(20):9464-9469.

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

Division: SC-23.2 Biological Systems Science Division, BER


May 24, 2010

New Cellulose Degrading Bacteria and Enzymes Isolated From High Temperature Compost

Current approaches for conversion of cellulosic biomass to biofuels rely on cocktails of cellulose degrading enzymes (i.e. cellulases) that are expensive, relatively inefficient, and not well adapted to industrial conditions. Researchers at Dartmouth College and the DOE Bioenergy Science Center (BESC) are exploring a variety of high temperature, cellulose rich environments to identify new microbes and enzyme systems with improved biomass deconstruction capabilities. They now report the discovery of genes encoding 48 new cellulase enzymes from microbes collected from a compost site with temperatures ranging from 52-72°C. Many of these genes, most of which originate from members of the bacterial class Clostridia, have substantial sequence variation from known cellulases and may have substantially different properties. In addition to providing promising new targets for developments as industrial biofuels production enzymes, these genes expand the database of cellulase gene sequences and will enable improvement of probes for discovery of additional cellulases in environmental samples.

Reference: J. A. Izquierdo, M. V. Sizova, & L. R. Lynd. 2010 "Diversity of Bacteria and Glycosyl Hydrolase Family 48 Genes in Cellulolytic Consortia Enriched from Thermophilic Biocompost" Applied and Environmental Microbiology 76: 3545-3553

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

Division: SC-23.2 Biological Systems Science Division, BER


May 24, 2010

Systems Biology Research on Cellulose and Lignin Degrading Fungi

Plant biomass is made up of long, repeated sugar chains (cellulose and hemicelluloses) interwoven with a complex interlinked network of aromatic compounds (lignin). The resulting structures are remarkably resilient to degradation, but a number of microbes have evolved sophisticated enzymatic systems that allow them to deconstruct and feed on biomass. A collaborative team of researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC), the DOE Joint Genome Institute, and the USDA Forest Products Laboratory have now completed a systems biology study examining gene expression and enzyme secretion by two wood-degrading fungi. The goal of the research was to compare mechanisms of wood-decay between a relatively well characterized cellulose-degrading fungus and a poorly understood fungus capable of degrading the lignin portion of wood. Although the two fungi were shown to share some common mechanisms for biomass deconstruction, substantial differences were observed in the timing and types of enzymes expressed during wood degradation, especially in those mediating the iron catalyzed reaction that breaks apart lignin moieties. The results of this study increase our understanding of molecular mechanisms that allow degradation of complex biomass, providing new insights into a major carbon cycling process in forest ecosystems and development of novel approaches for biofuels production.

Reference: A.V. Wymelenberg et al. 2010 "Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium" Applied and Environmental Microbiology 76: 3599-3610

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

Division: SC-23.2 Biological Systems Science Division, BER


May 17, 2010

OptForce - A New Method to Enhanced Production of Valuable Metabolic Products

The holy grail of metabolic (bio)engineering is to trick an organism into overproducing one particular metabolic product, for example, the production of ethanol through a fermentation pathway in a microbe such as Bacillus subtilis. However, optimizing just one metabolic pathway is not sufficient, since metabolic pathways are interconnected in an organism's physiology through a dynamic set of processes. Researchers at Penn State University have introduced a new method, OptForce, that will identify all possible metabolic pathways in an organism that are supported by existing experimental data, and provide a collective set of genetic changes that must be imparted on the organism to achieve a target level of product. This method will not only translate predictive metabolic pathways into quantifiable levels of products produced by an organism, but will also show where inadequate experimental data limits progress in optimizing output of desired products. Results of this work are published in PLoS, Computational Biology.

Reference: S. Ranganathan, P. Suthers and C. Maranas, "OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions" PLoS, Computational Biology, volume 6, issue 4, pages 1-11 (2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 10, 2010

Joint Genome Institute (JGI) Frog Genome Featured on Cover of Science

The draft genome sequence of the Western clawed frog, Xenopus tropicalis, a sentinel species for potential impacts of environmental contamination and climate change has just been reported in Science (and featured on the cover of the journal). X. tropicalis displays rapid and easily monitored embryonic development along with tractable genetics. Uffe Hellsten of the JGI, with 48 co-authors from 24 institutions, presents a X tropicalis draft genome sequence assembly that encodes more than 20,000 protein-coding genes compared to an estimated 23,000 genes in the human genome. The frog genome exhibits substantial organizational similarity (in terms of gene order) with human and chicken genomes over major parts of large chromosomes. Amphibians such as the frog have become highly important for scientific studies on environmental pollution, as harbingers of toxins produced by industrial and other activities, and for interpreting and understanding the human genome.

Reference: U. Hellsten, et al., "Assembly, annotation, and analysis of the frog genome compares gene content and synteny with the human and chicken genomes", Science, 328, 633-636 (2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 10, 2010

Mechanism of Microbial Oxidation of Methane

Industrial processes to convert methane to other fuel molecules and chemical feedstocks are inefficient, requiring substantial energy inputs. In contrast, methantrophic bacteria efficiently convert methane to methanol, which can then be converted to other fuels and chemicals. This methane to methanol conversion is catalyzed by methane mono-oxygenase (MMO) enzymes. A team led by Timothy Stemmler of Wayne State University and Amy Rosenzweig of Northwestern University used an x-ray spectroscopy station at the Stanford Synchrotron Radiation Lightsource to demonstrate that the active site of MMOs in the methanotroph Methylococcus capsulatus contains two copper atoms. They also showed that the active site is in a soluble domain of the enzyme not the membrane bound component. This resolves long-standing uncertainties about whether the active site contains an iron or a copper atom, and how many metal atoms are in the active site. These results will enable the design of enzyme-based systems for large-scale conversion of methane to other molecules.

Reference: R. Balasubramanian, et al., "Oxidation of methane by a biological dicopper centre", Nature, 465, 115-119 (2010).

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

Division: SC-23.2 Biological Systems Science Division, BER


May 03, 2010

Stressful Living in Contaminated Groundwater

Microorganisms are the primary drivers of key subsurface geochemical processes but we only have limited understanding of the composition and function of the microbial communities involved. "Metagenomic" sequencing is providing insights into the metabolic capabilities of these microbial communities and microbial adaptations to environmental changes. A multi-institutional team from the University of Oklahoma, Oak Ridge and Lawrence Berkeley National Laboratories, and the DOE Joint Genome Institute has now sequenced microbial community DNA isolated from groundwater at a site with low pH and high levels of uranium, technetium, nitrate, and organic solvents. The analysis reveals a significant reduction in microbial diversity from background and an overabundance of genes that confer tolerance for nitrate, heavy metals, and organic solvents. In addition, the overabundance of genes for DNA recombination and repair suggests the presence of lateral gene transfer induced by exposure to extreme environmental conditions. These results expand our understanding of how microbial communities adapt to and influence the fate of environmental contaminants.

Reference: Hemme, C.L., Y. Deng, T.J. Gentry, M.W. Fields, L. Wu, S. Barua, K. Barry, S.G. Tringe, D.B. Watson, Z. He, T.C. Hazen, J.M. Tiedje, E.M. Rubin, and J. Zhou. 2010. "Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community." ISME Journal 4: 660-672.

Contact: Joseph Graber, SC-23.2, (301) 903-1239, Paul E. Bayer, SC-23.1, (301) 903-5324
Topic Areas:

Division: SC-23 BER


May 03, 2010

Versatile Waste-degrading Microbe Sequenced by JGI

In spite of the large number and diversity of microbial genomes sequenced by the DOE-Joint Genome Institute (JGI), unusual biology and metabolisms continue to be discovered. In the March 22, 2010, issue of PLoS ONE, scientists working with the JGI report the sequence of the proteobacterium Cupriavidus necator JMP134 that possesses 11 of the 12 main metabolic pathways used to break down chloroaromatic compounds, including chlorophenols, halobenzoates and nitrophenols. These organic contaminants are found at DOE and other waste sites, some contaminated by spilled fuels or solvents commonly identified as BTEX carcinogens (benzene, toluene, ethylbenzene and xylene). This microbe is able to derive energy from these toxic compounds. C. necator was also shown to have genes commonly found in microbes that associate with plant roots and could play a role in the rhizobial communities critical to nutrient incorporation by plants, including Bioenergy relevant plants. The genome sequence will be useful to understand the basis for this microbe's "versatile degradative abilities," as well as providing insights into the evolution of multicomponent genomes.

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

Division: SC-23.2 Biological Systems Science Division, BER


April 19, 2010

Computational Simulations Provide New Insights for the Interaction of Cellulose With Ionic Liquids

Developing effective pre-treatment methods for lignocellulosic biomass for production of biofuels is an active area of research. Room temperature ionic liquids are highly effective solvents for cellulosic biomass, but the dissolution mechanism is not well understood. Seema Singh and Hanbin Liu and co-workers at DOE's Joint BioEnergy Institute (JBEI) have used high performance computational simulations to investigate the mechanism of action of imidazolium acetate ionic liquids on cellulose. They found that the anionic component of the ionic liquids forms hydrogen bonds with cellulose that are three times stronger than those found in water. Furthermore the cationic species in the ionic liquids also play a pivotal role in the dissolution process through hydrophobic interactions with the polysaccharide chains of cellulose. This research opens new possibilities for rapid computational screening of a wide range of ionic liquids for pre-treatment processes. The research made use of leadership computing capabilities at the National Energy Research Scientific Computing Center (NERSC) and has just been published in the Journal of Physical Chemistry Section B.

Reference: Hanbin Liu, Kenneth L. Sale, Bradley M. Holmes, Blake A. Simmons and Seema Singh, "Understanding the Interactions of Cellulose with Ionic Liquids: A Molecular Dynamics Study," J. Phys. Chem. B, volume 114, pages 4293-4301 (April 1, 2010)

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

Division: SC-23.2 Biological Systems Science Division, BER


April 12, 2010

New Tools for Understanding the Breakdown of Lignocellulosic Biomass

Biomass is resistant to enzymatic breakdown into sugars needed for fermentation into renewable biofuels, requiring extensive pretreatment to make the biomass more amenable to bio-processing. Understanding this degradation process will enable design of more efficient approaches for converting plant material into biofuels. DOE research at the Universities of Notre Dame and of Illinois, Urbana-Champaign, has used confocal Raman imaging and mass spectrometry imaging to monitor structural and chemical changes in the of pretreatment of Miscanthus x giganteus, a potential energy crop. Raman images of samples treated with sodium hydroxide shows that lignin is completely removed at long processing time while the cellulose is largely undisturbed. Lignin is also removed preferentially from the interior surface of the cell wall. These results illustrate how even simple pretreatments can lead to spatially complex biological profiles due to differential rates of attack on the major components of the cell wall. The researchers also showed that laser desorption/ionization mass spectrometry and secondary ion mass spectrometry can be used to visualize and understand pretreatment induced chemical changes that affect the spatial distribution of several saccharides.

References: Chu, L., R. Masyuko, J. V. Sweedler, and P. W. Bohn. 2010. "Base-Induced Delignification of Miscanthus x Giganteus Studied by Three-Dimensional Confocal Raman Imaging," Bioresource Technology 101(13), 4919-4925. DOI: http://dx.doi.org/10.1016/j.biortech.2009.10.096. (Reference link)

Li, Z., P. W. Bohn, and J. V. Sweedler. 2010. "Comparison of Sample Pre-Treatments for Laser Desorption Ionization and Secondary Ion Mass Spectrometry Imaging of Miscanthus x giganteus," Bioresource Technology 101(14), 5578–5585. DOI: http://dx.doi.org/10.1016/j.biortech.2010.01.136. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


April 05, 2010

DOE Joint Genome Institute (JGI) Receives Second National Ergonomics Award

Preventing ergonomic injuries is a major concern for DOE laboratories, especially at the JGI, where its sequencing procedures involve highly repetitive tasks both in the laboratory and in the office. The JGI management has developed ergonomic solutions suited to each worker and his/her surrounding work environment to reduce injuries caused by these tasks. The JGI now has a matched pair of Ergo Cups after winning its second award at the 13th Annual Applied Ergonomics Conference held March 22-25, 2010 in San Antonio, Texas. The Ergo Cup recognizes innovations that utilize better equipment and practices to reduce musculoskeletal disorders in the workplace. The JGI's 2010 award-winning entry, in the Ergonomic Program Improvement Initiatives category, focused on employee-driven elements of its program that help promote awareness of ergonomics and safety and encourage employee involvement in both safety and ergonomics. In 2007, the JGI won the Ergo Cup for its Shake 'N Plate instrument that eases upper body fatigue for employees working on the DNA sequencing production line.

Reference: "Congratulations to the 2010 Ergo Cup winners!" link to article

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

Division: SC-23.2 Biological Systems Science Division, BER


March 22, 2010

New Approaches for Visualizing Biomass Degradation

Biomass recalcitrance is the resistance of inedible plant fiber materials, mainly comprised of lignin and cellulose, to enzymatic breakdown into fermentable sugars for conversion into renewable biofuels. Researchers at the DOE BioEnergy Science Center (BESC) have applied novel imaging tools to achieve a deeper understanding of the chemical and structural architectures of plant cell walls, an important step towards overcoming recalcitrance. Coherent Anti-Stokes Raman Scattering (CARS) microscopy was used to measure the vibration patterns of individual plant cell wall molecules; these patterns were then translated into high spatial resolution chemical images of lignin within the cell wall material. Key advantages of this imaging method include the ability to study plant cell walls without chemical pretreatment to remove interfering background signals from fluorescent pigments (e.g. chlorophyll), thus minimizing damage to the native structure of the cell walls, and the ability to monitor almost simultaneously different cell wall locations. CARS was able to distinguish significant differences in lignin from normal plants versus plants engineered for low-lignin content, demonstrating its potential as a promising tool to monitor increased efficiency of chemical pretreatment and enzymatic breakdown during the biomass conversion process. The research was carried out by a team of BESC scientists at the National Renewable Energy Laboratory, Oak Ridge National Laboratory and the Samuel Roberts Noble Foundation in collaboration with Harvard University.

Reference: Yining Zeng & Brian G. Saar & Marcel G. Friedrich & Fang Chen & Yu-San Liu & Richard A. Dixon & Michael E. Himmel & X. Sunney Xie & Shi-You Ding, "Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy" Bioenerg. Res. DOI 10.1007/s12155-010-9079-1

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

Division: SC-23.2 Biological Systems Science Division, BER


March 22, 2010

New Ionic Liquids Treatment for Converting Biomass to Sugars

Digestion of cellulosic biomass to release fermentable sugars remains a major challenge: current biomass treatment approaches typically involve large volumes of hazardous concentrated acids, expensive secondary enzymatic digestion, and energy intensive heating. Researchers at the DOE Great Lakes Bioenergy Research Center have developed an improved chemical treatment method to liberate sugars from biomass. This approach uses a combination of ionic liquids, water, and dilute acid, resulting in the release of over 75% of the sugar molecules locked in corn stover. This approach produces fewer toxic byproducts that inhibit growth of the fermentative microbes used to convert released sugars to ethanol and other biofuels. Although the current experiments were performed at laboratory scale, potential avenues have been identified for scaling the approach for commercial development. The new results are published in the March 9th issue of the Proceedings of the National Academy of Sciences.

Reference: Binder, J. B. and R. T. Raines. 2010. "Fermentable Sugars by Chemical Hydrolysis of Biomass" Proceedings of the Natl. Academy of Sciences 107:4516-4521

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

Division: SC-23.2 Biological Systems Science Division, BER


March 22, 2010

Watt Webb to receive Hollaender Award in Biophysics from National Academy of Sciences

Watt W. Webb, Samuel B. Eckert Professor in Engineering at Cornell University, will receive the 2010 Alexander Hollaender Award in Biophysics from the National Academy of Sciences. The award recognizes his research "pioneering the applications of rigorous physical principles to the development of optical tools that have broadly impacted our ability to examine biological systems." DOE supported Webb's research for new DNA sequencing technologies as part of the Human Genome Program that is now ready for commercialization. This research led to a new approach that rapidly produces sequences of 1000 or more base pairs. The longer "reads" make it easier and faster to assemble complete sequences of long strands of DNA. Pacific Biosciences will be shipping the first instruments based on this technology this spring to ten research institutions, including the DOE Joint Genome Institute.

References: "Academy honors 17 for major contributions to science" link to article

"PacBio Names First 10 Customers for $695,000 Single-Molecule Sequencer" Genome Web, link to article

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

Division: SC-23.2 Biological Systems Science Division, BER


March 15, 2010

Understanding Microbial Tolerance to Next Generation Biofuels

Short chain alcohols such as n-butanol are promising candidates as next generation biofuels because of their high energy density and compatibility with existing fuel supply infrastructure. Although several types of microbes can synthesize these compounds from biomass-derived sugars, their toxicity to the microbes limits the total quantities that can be produced. Scientists at the DOE Joint Bioenergy Institute (JBEI) have reported how exposure to n-butanol causes global changes in gene and protein expression in the model bacterium E. coli. Their studies provide clues on how the microbe regulates its response to this form of stress. These results identify new targets for reengineering microbes to improve their tolerance to n-butanol and other next generation biofuels. The research is published in the March 15th issue of Applied & Environmental Microbiology.

Reference: Rutherford, B. J., R. H. Dahl, R. E. Price, H. L. Szmidt, P. I. Benke, A. Muchopadhyay, and J. D. Keasling. 2010. "Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli," Appl. & Environ. Microbiol. 76:1935-1945.

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

Division: SC-23.2 Biological Systems Science Division, BER


March 08, 2010

Great Lakes Bioenergy Research Center (GLBRC) Featured in Special Issue of BioEnergy Research

The March issue of BioEnergy Research features research results from the DOE GLBRC. Eleven journal articles highlight four broad research themes: sustainable biofuels landscapes, improved biofuels feedstocks, improved conversion into advanced biofuels, and improved cellulosic biomass processing. The topics include the analysis of ecosystem services, soil microbial communities, the use of natural genetic mutations to create more suitable feedstocks for deconstruction into liquid fuels, bacterial pathways from nutrients to hydrogen, and enzyme and plant trait assays to improve conversion efficiencies. This is the second of three special issues of the journal to be devoted to the DOE Bioenergy Centers.

Reference: BioEnergy Research, Volume 3, Number 1, March 2010, link to article

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

Division: SC-23.2 Biological Systems Science Division, BER


February 16, 2010

Finding Rice Stress Response Genes to Improve Bioenergy Crops

Production of fuels from dedicated perennial grass crops has the potential to decrease dependence on oil imports and release of climate-changing, greenhouse gasses. However, dedicated biofuel crops will need to be grown on large scales on marginal land over many years. Thus it will be necessary to utilize genetically improved varieties that can withstand diverse environmental stresses, such as salinity, flooding and drought, which are major constraints to crop production in many areas of the world. Researchers at the DOE Joint BioEnergy Institute (JBEI) have now developed a gene expression profiling approach to identify novel genes that confer tolerance to flooding stress in rice. Rice is used as a model for studies of perennial grasses such as switchgrass, one of the most promising of the grasses for large-scale production of biofuels. A set of 12 genes was identified that are regulated by a single gene that has an effect on several flooding response pathways. These genes can be classified into three functional groups each involved in a different metabolic response to stress. The research is published in the current issue of Plant Physiology.

Reference: Jung K-H, Seo Y-S, Walia H, Cao P, Fukao T, Canlas PE, Amonpant F, Bailey-Serres J, and Ronald PC. 2010. "The Submergence Tolerance Regulator Sub1A Mediates Stress-responsive Expression of AP2/ERF Transcription Factors," Plant Physiol January 27, 2010; 10.1104/pp.109.152157.

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

Division: SC-23.2 Biological Systems Science Division, BER


February 01, 2010

Advances in On-Line Resources for Microbial Research

Substantial bioinformatics capabilities are required for systems biology approaches to solve DOE mission-related research problems in bioenergy and the environment. This is particularly true when microbiology is involved, as new technologies are generating vast amounts of data. DOE efforts to meet the scientific need for database systems are highlighted in the latest issue of Nucleic Acids Research. These include:

MicrobesOnLine (A. Arkin, Joint Bioenergy Institute and LBNL), a resource to integrate experimental data with genomic sequence data to understand microbial evolution and compare microbial functions under varied experimental conditions;

MiST2 (I. Zhulin, BioEnergy Science Center), which catalogs signalling proteins;

RegPrecise (D. Rodionov, LBNL), which catalogs transcription factor genes and will assist our understanding of cellular activity; and

IMG (N. Kyrpides, Joint Genome Institute), the Integrated Microbial Genomes resource provides new tools such as phylogenetic tools for comparative genomic analysis.

Taken together, these bioinformatics resources are leading to a more complete systems biological framework for microbial studies.

Reference: Nucleic Acids Research. January 2010, Vol. 38.

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

Division: SC-23.2 Biological Systems Science Division, BER


February 01, 2010

MIT Microbiologist Wins National Academy of Sciences Agassiz Medal

The National Academy of Sciences (NAS) has just announced that Sallie Chisholm is the 2010 recipient of the Alexander Agassiz medal, which recognizes original contributions in the science of oceanography. Professor Chisholm is being honored for pioneering studies of the dominant photosynthetic microbes in the sea and for integrating her results into a new understanding of the global ocean. Chisholm is currently supported by DOE for her genomic and environmental studies on Prochlorococcus, a marine microbe that is the dominant agent of carbon fixation in the oceans and the most abundant photosynthetic cell on Earth. She is the Lee and Geraldine Martin Professor of Environmental Studies at the Massachusetts Institute of Technology. The medal is awarded every three years and will be presented to Chisholm at the Annual Meeting of the NAS on April 25, 2010.

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

Division: SC-23.2 Biological Systems Science Division, BER


February 01, 2010

New Insights on Gene Function and Regulation in Archaea

The archaea occupy a unique position in the tree of life, appearing similar to bacteria but having some properties related to those found in plants, animals, and fungi. Many archaea possess novel metabolic capabilities enabling them to withstand extreme conditions of temperature and acidity that could be useful in addressing DOE missions. However, the archaea remain poorly characterized, which limits their current utility. Collaborating researchers at the DOE Joint Bioenergy Institute, the DOE Joint Genome Institute, and Israel's Weizmann Institute of Science have now generated the first in depth gene expression map for Sulfolobus solfataricus, an archaeon that grows optimally under highly acidic conditions at 80°C. This study provides valuable new information on gene function and regulation in S. solfataricus and enables further development of this organism as a sturdy new platform or source of biological parts for biofuel production.

Reference: Wurtzel, O., R. Sapra, F. Chen, Y. Zhu, B. A. Simmons, R. Sorek. 2010. "A Single-Base Resolution Map of an Archaeal Transcriptome," Genome Research 20:133-141.

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


January 25, 2010

Breaking Down the Steps of Plant Cell Wall Lignin Degradation

We need to understand the biological mechanisms for cleaving the plant wall component lignin to develop new strategies for producing biofuels from lignocellulosic biomass. Researchers from the Forest Products Laboratory at the University of Wisconsin have shown how different unsaturated fatty acids assist a peroxidase enzyme in lignin breakdown. Some peroxidases from wood-decay fungi can cleave the major recalcitrant structures in lignin, but these reactions require the participation of low molecular weight mediators that apparently act as diffusible free radical oxidants. The new results show that the major unsaturated fatty acid produced by the fungi, linoleic acid, is also the most effective mediator for breakdown of lignin. Future experiments will examine the effectiveness of lignocellulosic degradation using peroxidases by including linoleic acid or linoleate esters in the formulations.

Reference: Kapich, A. N. et al., Oxidizability of unsaturated fatty acids and of a non-phenolic lignin structure in the manganese peroxidase-dependent lipid peroxidation system. Enzyme & Microbial Technology 46 (2010) 136-140.

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


January 25, 2010

Mining Compost for New Microbial Enzymes to Degrade Switchgrass

Enzymatic breakdown of plant biomass is one of the most expensive steps in the production of cellulosic biofuels, mostly due to the low efficiencies of current commercially available enzymes. Deconstruction of grass feedstocks such as switchgrass and corn stover presents a particular challenge. Grass material is effectively broken down by microbial communities in compost piles, but the involved enzymes have remained largely unexplored because it is difficult to isolate the responsible organisms. Now researchers at the DOE Joint Bioenergy Institute (JBEI) have identified biomass degrading enzymes produced by compost microbes during growth on switchgrass. Led by Phil Hugenholtz of Lawrence Berkeley National Laboratory, the team characterized genes thought to be involved in biomass breakdown and synthesized two reconstructed hemicellulose-degrading enzymes. These enzymes are promising candidates for further study and improvement by genetic engineering andsuggest potential pathways to new enzymatic treatment strategies tailored to specific biomass feedstocks.

Reference: Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P. 2010. "Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community," PLoS ONE 5(1): e8812.

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


January 19, 2010

New Technique for Studying Biogeochemical Transformation on Uranium

Understanding the fate and transport of uranium in subsurface environments is a major concern for planning remediation of contamination at the DOE cleanup sites. Yet it is very difficult to study the biogeochemical processes that impact uranium mobility in these environments. Research at the Argonne National Laboratory has now led to a realistic laboratory-based approach that uses sediments from field contaminated locations in microcosms prepared and maintained under conditions that closely match those in the field. Tests of the new technique were carried out using sediment samples from the Oak Ridge National Laboratory Integrated Field-Research Challenge site. The microcosms were maintained under anaerobic (no oxygen) conditions to ensure that microbial activity would match that in the sampled subsurface field site. Changes in chemical characteristics of the uranium in each microcosm were determined periodically over an eleven month period using x-ray absorption spectroscopy beamlines at the Advanced Photon Source. Analysis of the results of these experiments, along with biochemical and geochemical data, indicates that at least two distinct processes are taking place that gradually transform the highly mobile uranium (VI) to highly immobile uranium (IV). The research has just been published in Environmental Science & Technology.

Reference: S.D. Kelly, et al., "Uranium transformations in static microcosms", Environ. Sci. Technol. 2010 44(1), 236-242.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
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Division: SC-23.2 Biological Systems Science Division, BER


January 19, 2010

Understanding How Microbes Sequester Potentially Deadly Metabolites

Living cells use precise control processes to regulate critical metabolic processes. Sometimes cells produce volatile or potentially damaging byproducts that need to be sequestered to protect the cells. Scientists at the University of California, Los Angeles-DOE Institute for Genomics and Proteomics have discovered the structure of an important type of microcompartment in microbial cells that enables ethanolamine to be metabolized without releasing the volatile intermediate, acetaldehyde. They determined the structures of the four proteins that make up the walls of the microcompartment and used this information to discover how the combined structures enable selective transport across the walls to protect the microbe from toxic damage. The understanding gained in the research could enable design of nanoparticles using proteins modified to enhance production of molecules for biofuels and other applications. The research has just been published in Science.

Reference: S. Tanaka, M.R. Sawaya and T.O. Yeates "Structure and mechanisms of a protein-based organelle in Escherichia coli" Science 2010 327(1) 81-84.

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
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Division: SC-23.2 Biological Systems Science Division, BER


January 11, 2010

Genome Sequence of Soybean Released

Soybean is one of the most important agricultural crops in the world, providing substantial amounts of both protein and oil for foods, and also serving as a significant resource for producing biodiesel fuel. In the January 14, 2010, issue of Nature, researchers at the Joint Genome Institute (JGI) report the complete genome sequence of soybean. Over 46,000 protein-coding genes were identified in the billion base pair genome, with nearly 75% of these genes present in multiple copies. Research that will be enabled using the soybean genome is expect to have a significant impact not only on agriculture but also on efforts to improve yields of soybean oil for conversion into diesel fuels. The newly published genomic information will serve as the reference with which to study all beans and other legumes, offering insights into important traits such as nitrogen fixation.

Reference: Schmutz J, Cannon SB, Schlueter J, Ma J, Hyten D, Song Q, Mitros T, Nelson W, May GD, Gill N, Peto M, Goodstein D, Thelen JJ, Cheng J, Sakurai T, Umezawa T, Du J, Bhattacharyya M, Sandhu D, Grant D, Joshi T, Libault M, Zhang X-C, Xu D, Futrell-Griggs M, Abernathy B, Hellsten U, Berry K, Grimwood J, Wing RA, Cregan P, Stacey G, Specht J, Rokhsar D, Shoemaker RC, and Jackson SA. 2010. Genome sequence of the paleopolyploid soybean (Glycine max, (L.) Merr.). Nature.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549, Dan Drell, SC-23.2, (301) 903-4742
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Division: SC-23.2 Biological Systems Science Division, BER


January 04, 2010

DOE Joint Genome Institute Genomic Encyclopedia Sheds Light on Microbial Dark Matter

The Genomic Encyclopedia of the Bacteria and Archaea (GEBA) was highlighted in the December 29 Science Times section of the New York Times, following its inaugural publication in the December 24 issue of Nature magazine. These articles focus on efforts to unlock the diversity of microbial communities to benefit DOE mission needs in biofuel production, global carbon storage, and bioremediation. GEBA now includes 56 microbial species whose complete genomes were sequenced by the Joint Genome Institute in Walnut Creek, CA. These microbes were selected to NOT be in the well-sampled branches of known microbial life and will thus provide insights into microbial "dark matter," areas of the vast microbial world where large amounts of unknown biology await exploration. Already, one discovery, a salt-tolerant cellulase enzyme, may have promise for bioenergy applications. Additional value expected from the ongoing GEBA initiative includes better tools for understanding what happens to microbial communities in soils and at waste sites associated with DOE activities. The GEBA project represents a collaborative, international project led by expert scientists but also enlisting assistance from interested undergraduate biologists to help analyze these diverse genomes.

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

Division: SC-23.2 Biological Systems Science Division, BER


January 04, 2010

Identification of a Lignocellulosic Biosynthesis Gene in Switchgrass

Biofuels produced from plant lignocellulosic biomass offer a promising alternative to starch-based (e.g., corn) biofuels. However, the lignin component of plant cell walls makes plants difficult to breakdown and convert to biofuels. Researchers at the Oak Ridge BioEnergy Research Center (BESC) have identified a gene putatively encoding an enzyme involved in lignin biosynthesis in switchgrass, a major perennial feedstock for lignocellulosic ethanol production. Their results provide a potential target for modification in the development of switchgrass as a bioenergy crop. Modifying plant lignin content may adversely affect plant growth; however, since this newly discovered gene catalyzes a step late in the lignin biosynthetic pathway its modification may have less of an effect on overall plant structure. Reduced expression of this gene has been shown to reduce lignin levels in several non-grass plant species but until now little was known about its effects in bioenergy-relevant grasses. This research was carried out by BESC scientists at Oak Ridge National Laboratory and their collaborators at the Samuel Roberts Noble Foundation and the University of Georgia.

Reference: Escamilla-Trevino, L. L., et al. 2009. "Switchgrass (Panicum virgatum) Possesses a Divergent Family of Cinnamoyl CoA Reductases with Distinct Biochemical Properties," New Phytologist 185(1), 143-155.

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

Division: SC-23.2 Biological Systems Science Division, BER