BER Research Highlights

Search Date: August 16, 2017

38 Records match the search term(s):


December 29, 2014

Statistics to Help Optimize Engineered Heterologous Pathways

For metabolic engineering to reach its full potential, systematic pathway optimization approaches are needed for biofuel production. In previous work, Department of Energy Joint Bioenergy Institute (JBEI) researchers assembled a set of nine heterologous genes in Escherichia coli to produce from glucose the monoterpene limonene, a potential biofuel. While they were able to achieve 435 mg/L of limonene production, they believed further optimization was possible. In a new research article, the JBEI scientists present and demonstrate a computational tool (principal component analysis of proteomics; PCAP) that uses quantitative targeted proteomics data to guide metabolic engineering and achieve higher production of target molecules from heterologous pathways. Counterintuitively, PCAP suggested that an overexpression of the terpene synthase combined with a balanced expression of the remaining enzymes was key to improving limonene production. The PCAP-guided engineering resulted in a more than 40% improvement in the production of limonene and a second valuable terpene. Thus, PCAP could be broadly applied to heterologous pathways for optimized biofuel production.

Reference: Alonso-Gutierrez, J., E.-M. Kim, T. S. Batth, N. Cho, Q. Hu, L. J. G. Chan, C. J. Petzold, N. J. Hillson, P. D. Adams, J. D. Keasling, H. G. Martin, and T. S. Lee. 2015. “Principal Component Analysis of Proteomics (PCAP) as a Tool to Direct Metabolic Engineering,” Metabolic Engineering 28, 123–33. DOI: 10.1016/j.ymben.2014.11.011. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 24, 2014

Elucidating Control of Secondary Cell Wall Synthesis

The plant cell wall plays an important role in cell function and environmental response by providing both mechanical support and a barrier against invading pathogens. Furthermore, the highly-abundant secondary cell walls, which are composed of cellulose, hemicelluloses and lignin, are an important source of dietary fiber, raw material for paper and pulp, and feedstock for biofuel production. Despite the importance of the plant secondary cell wall for renewable resources, knowledge of the precise mechanisms that regulate these critical functions is limited. New research results published in the journal Nature report the identification of a gene network in the model plant Arabidopsis thaliana that controls synthesis of the biopolymers that comprise the secondary cell wall. Instead of using a gene-by-gene approach, the scientists undertook a comprehensive, large-scale analysis, which revealed a highly integrated network involving hundreds of genes and protein-DNA interactions. Furthermore, they found that the extremely large number of combinatorial possibilities provided by this arrangement allows for subtle adaptation to specific abiotic stresses such as salt stress and iron deprivation. These findings provide a framework for future work to dissect and refine specific gene functions, enabling targeted manipulation of the network to produce high-yielding plant feedstocks for bioenergy production. The Nature paper is accompanied by a commentary by two prominent plant scientists. This research was supported by the U.S. Department of Agriculture-Department of Energy Plant Feedstocks Genomics for Bioenergy program.

References: Taylor-Teeples, M., L. Lin, M. de Lucas, G. Turco, T. W. Toal, A. Gaudinier, N. F. Young, G. M. Trabucco, M. T. Veling, R. Lamothe, P. P. Handakumbura, G. Xiong , C. Wang, J. Corwin, A. Tsoukalas, L. Zhang, D. Ware, M. Pauly, D. J. Kliebenstein, K. Dehesh, I. Tagkopoulos, G. Breton, J. L. Pruneda-Paz, S. E. Ahnert, S. A. Kay, S. P. Hazen, and M. Brady.   2014. “An Arabidopsis Gene Regulatory Network for Secondary Cell Wall Synthesis,” Nature 517, 571–75. DOI: 10.1038/nature14099.   (Reference link)

Bishopp, A., and M. J. Bennett. 2015. “Seeing the Wood and the Trees,” Nature 517, 558–59. DOI:10.1038/nature14085. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


December 19, 2014

Field Production of Novel Plant Oils in Camelina

Some plants synthesize acetyl-triacylglycerols (acetyl-TAGs), some of which are suitable as ‘drop-in’ biodiesel. A diacylglycerol acetyltransferase from Euonymus alatus, EaDAcT, synthesizes such acetyl-TAGs when expressed in Arabidopsis, Camelina, and soybean. Compared to most vegetable oils, acetyl-TAGs have reduced viscosity and improved cold temperature properties that confer advantages in applications as biodegradable lubricants, food emulsifiers, plasticizers, and ‘drop-in’ fuels for some diesel engines. Previously, researchers in the Department of Energy’s Great Lakes Bioenergy Research Center (GLBRC) engineered a Camelina line producing high levels of oleic to express the EaDAcT gene to produce acetyl-TAG oils with fatty acid compositions and physiochemical properties complementary to wild-type acetyl-TAG. In field-grown engineered Camelina, the acetyl-TAGs accumulated to 70 mol% of seed TAG and had minor or no effect on seed weight, oil content, harvest index, and seed yield. The total moles of TAG increased up to 27%, reflecting the ability to synthesize more acetyl-TAG from the same supply of long-chain fatty acid. The crystallization temperature of high-oleic acetyl-TAG was reduced by 30? C compared to control TAG. The viscosity of high-oleic acetyl-TAG was 27% lower than TAG from the high-oleic control, and the caloric content was reduced by 5%. Field production of T4 and T5 transgenic plants yielded over 250 kg seeds for oil extraction and analysis. These results demonstrate that high-oleic Camelina lines can be engineered to produce desirable oils for ‘drop-in’ biodiesel and that establishing crop production of Camelina acetyl-TAG will enable sufficient quantities of acetyl-TAG to be produced for further agronomic and commercial development.

Reference: Liu, J., H. Tjellstrom, K. McGlew, V. Shaw, A. Rice, J. Simpson, D. Kosma, W. Ma, W. Yang, M. Strawsine, E. Cahoon, T. P. Durrett, and J. Ohlrogge. 2015 “Field Production, Purification, and Analysis of High-Oleic Acetyl-Triacylglyceros from Transgenic Camelina sativa,” Industrial Crops and Products 65, 259-68. DOI: 10.1016/j.indcrop.2014.11.019. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 16, 2014

Key Transcription Factor in Plant Senescence Regulates Chlorophyll Degradation and Abscisic Acid Biosynthesis

The timing of plant senescence can have a significant impact on the yield and quality of bioenergy feedstocks. Therefore, more knowledge is welcome on the regulation of and genes involved in plant senescence. Department of Energy BioEnergy Science Center researchers have gained new understanding of senescence in the experimentally tractable plant Arabidopsis thaliana. Chlorophyll degradation is an important part of leaf senescence, but the underlying regulatory mechanisms are largely unknown. The researchers found that the dark, excised leaves of an Arabidopsis thaliana transcription factor mutant (nap) exhibit a stay-green phenotype. This finding is correlated with lower transcript levels of several known chlorophyll degradation genes, and higher chlorophyll retention than the wild type during dark-induced senescence. Several plant hormones play a role in senescence; one of them, abscisic acid (ABA), is known to induce leaf senescence. Transcriptome coexpression analysis revealed that ABA metabolism/signaling genes were disproportionately represented among those positively correlated with expression of the NAP transcription factor. To further investigate ABA’s role in senescence and the stay-green phenotype, ABA was applied exogenously to excised NAP mutant leaves. Transcript levels of several chlorophyll degradation enzymes increased and the stay-green phenotype was suppressed. Collectively, the results show that the NAP transcription factor promotes chlorophyll degradation by enhancing transcription of the ABA biosynthesis gene, AAO3, which leads to increased levels of the senescence-inducing hormone ABA. This new understanding will be helpful in improving yields of bioenergy feedstocks by controlling senescence.

Reference: Yang, J., E. Worley, and M. Udvard. 2014. “A NAP-AA03 Regulatory Module Promotes Chlorophyll Degradation via ABA Biosynthesis in Arabidopsis leaves,” The Plant Cell 26, 4862–74. DOI: 10.1105/tpc.114.133769. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 18, 2014

A Fungal Garden’s Microbial Makeup

Leafcutter ants (Atta cephalotes) are of interest to bioenergy researchers because they farm gardens made up of communities of bacteria and fungi that break down plant biomass. Beetles and termites have similar symbiotic relationships with microbial communities in the gardens they cultivate for food, suggesting that different insect hosts have exploited microbes more than once as a strategy for breaking down biomass. In a recent collaboration, scientists from the Department of Energy’s (DOE) Great Lakes Bioenergy Research Center and DOE Joint Genome Institute used genomic techniques to analyze the composition of microbial communities in these fungal gardens. They found that regardless of their geographic location, these gardens have a similar microbial makeup. The high whole-genome similarity across distantly related insect hosts that reside thousands of miles apart shows that these bacteria are an important and underappreciated feature of diverse, fungus-growing insects. Because of the similarities in the agricultural lifestyles of these insects, this is an example of convergence between both the life histories of the host insects and their symbiotic microbiota. These results may point the way to both bacteria and fungi that are predisposed to having genes for enzymes and pathways useful for breaking down biomass to potential bioenergy feedstock sources.

Reference: Aylward, F. O., G. Suen, P. H. W. Biedermann, A. S. Adams, J. J. Scott, S. A. Malfatti, T. Glavina del Rio, S. G. Tringe, M. Poulsen, K. F. Raffa, K. D. Klepzig, and C. R. Curriea. 2014. “Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects,” mBio 5(6), e02077-14. DOI: 10.1128/mBio.02077-14. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 12, 2014

Genomic Selection to Accelerate Switchgrass Breeding

The perennial grass switchgrass (Panicum virgatum L.) shows great promise as a biofuel feedstock due to its ability to produce high biomass yields with relatively few inputs, and on lands not typically used for agricultural crops. The high genetic variability among different switchgrass accessions indicates that varieties with improved biomass quality traits could be developed through traditional breeding programs. However, this potential has been largely unattained due to the lengthy breeding cycle as well as a need for accurate measurement of biomass yield. A new approach known as genomic selection, which uses whole-genome, high-density molecular markers developed with high-throughput genotyping, has been used successfully with livestock and forest trees. Taking advantage of available genomic resources for switchgrass, including a reference genome, researchers have evaluated the accuracy of three genomic selection models in predicting phenotypic values of seven morphological and 13 biomass quality traits in a switchgrass association panel. Most traits were predicted with high accuracy, suggesting that the application of genomic selection to switchgrass breeding would be highly beneficial. Rather than waiting until the plant reaches adulthood, accurate prediction of biomass yield will allow DNA marker-based selection of seedlings, thus greatly accelerating breeding and potentially transforming switchgrass improvement efforts. The research was funded in part by the U.S. Department of Agriculture-Department of Energy Plant Feedstock Genomics for Bioenergy program.

Reference: Lipka, A. E., F. Lu, J. H. Cherney, E. S. Buckler, M. D. Casler, and D. E. Costich.  2014. “Accelerating the Switchgrass (Panicum virgatum L.) Breeding Cycle Using Genomic Selection Approaches,” PLoS ONE 9(11), e112227. DOI: 10.1371/journal.pone.0112227. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


November 03, 2014

High-Temperature Microbe Metabolically Engineered to Produce Biofuel Alcohols

The U.S. bioethanol industry depends largely on glucose conversion by yeast wherein pyruvate is decarboxylated to acetaldehyde and then reduced to the 2-carbon biofuel, ethanol. Interest is growing, however, in microorganisms that produce longer-chain alcohols with superior characteristics as fuel molecules compared to ethanol. Examples include microbial strains engineered to produce a specific alcohol such as isopropanol, n-butanol, or isopentanol. Much of the research to date focuses on engineered organisms that operate at ambient temperatures (e.g, 37°C), but the ability to produce bioalcohols at temperatures above 70°C has several advantages over ambient-temperature processes, including lower risk of microbial contamination, higher diffusion rates, and lower cooling and distillation costs. Researchers at the Department of Energy’s BioEnergy Science Center describe the metabolic engineering of a hyperthermophilic archaeon, Pyrococcus furiosus, to produce not only ethanol but a range of alcohols at 70-80°C via a synthetic pathway not known in nature and fundamentally different from those previously described. Specifically, the researchers engineered P. furiosus to produce various alcohols from their corresponding organic acids by constructing a novel synthetic route termed the aldehyde ferredoxin oxidoreductase (AOR)/alcohol dehydrogenase (AdhA) pathway. For example, in addition to converting acetate to ethanol, the synthetic pathway was shown to convert longer chain acids such as propionate to propanol, isobutyrate to isobutanol, and phenylacetate to phenylalcohol. This study is the first example of significant alcohol formation in an archaeon, emphasizing the biotechnological potential of novel microorganisms for biofuel production.

Reference: Basen, M., G. J. Schut, D. M. Nguyen, G. L. Lipscomb, R. A. Benn, C. J. Prybol, B. J. Vaccaro, F. L. Poole, R. M. Kelly, and M. W. W. Adams. 2014. “Single Gene Insertion Drives Bioalcohol Production by a Thermophilic Archaeon,” Proceedings of the National Academy of Sciences (USA) 111(49), 17,618-623. DOI: 10.1073/pnas.1413789111. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 02, 2014

Improved Lignin Depolymerization for Higher-Value Products

Lignin is a heterogeneous aromatic biopolymer that accounts for nearly 30% of the organic carbon on Earth and is one of the few renewable sources of aromatic chemicals. As the most recalcitrant of the three components of lignocellulosic biomass (cellulose, hemicellulose, and lignin), lignin has been treated as a waste product in the pulp and bioenergy industries, where it is sometimes burned to provide energy. Creation of higher-value bioproducts from lignin will increase the economic viability of integrated biorefineries. Depolymerization is an important starting point for many lignin valorization strategies, because it can generate valuable aromatic chemicals and provide a source of low-molecular-mass feedstocks suitable for downstream processing. Commercial precedents show that certain types of lignin (lignosulphonates) may be converted into vanillin and other marketable products, but new technologies are needed to enhance the lignin value chain. Lignin’s complex, irregular structure complicates chemical conversion efforts, and known depolymerization methods typically afford ill-defined products in low yields (that is, less than 10-20 wt%). Researchers of the Department of Energy’s Great Lakes Bioenergy Research Center describe a method for the depolymerization of oxidized lignin under mild conditions in aqueous formic acid that results in more than 60 wt% yield of low molecular-mass aromatics. This facile C-O cleavage method was used to depolymerize aspen lignin, providing mechanistic insights into the reaction. Efficient lignin depolymerization and biomass refining have the potential to contribute to the commercial and economic viability of lignocellulosic biofuels.

Reference: Rahimi, A., A. Ulbrich, J. J. Coon, and S. S. Stahl. 2014. “Formic-Acid-Induced Depolymerization of Oxidized Lignin to Aromatics,” Nature 515, 249-52. DOI: 10.1038/nature13867. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 31, 2014

Unraveling Nitrogen Cycling by Soil Microbes

Large amounts of nitrogen enter soil ecosystems as nitrate (NO3-) fertilizers. In addition to being available as a nitrogen source, a variety of soil microbes can generate energy from NO3- either by (1) denitrification, the conversion of NO3 to ammonia (NH4+), or (2) respiratory ammonification, which results in a mixture of nitrous oxide and dinitrogen gas (N2O and N2). NH4+ remains in soil while N2O and N2 are lost to the atmosphere, where N2O acts as a potent greenhouse gas. Understanding the microorganisms that perform these competing pathways is important for both agriculture and global climate change. Researchers at the University of Tennessee and Oak Ridge National Laboratory examined the systems biology properties of an unusual microbe able to perform both of these processes. While the majority of microbes utilizing NO3- as an energy source perform either denitrification or ammonification, the bacterium Shewanella loihica was shown to possess both pathways and thus offers a unique opportunity to examine the specific environmental factors that result in production of NH4+ versus N2O and N2. Using a series of careful physiological studies coupled to measurements of gene expression, the team determined that S. loihica activates the most energetically favorable pathway depending on its growth conditions, with the ratio of available carbon substrates to nitrogen availability (C/N ratio) playing the most influential role in the organism opting for either ammonification or denitrification. Recent studies have shown that organisms like S. loihica that are capable of both denitrification and ammonification are far more common in soil ecosystems than previously suspected. As such, this study’s findings have major implications for predicting climate change impacts on terrestrial biogeochemical cycles and designing more sustainable bioenergy agriculture practices.

Reference: Yoon, S., C. Cruz-Garcia, R. Sanford, K. M. Ritalahti, and F. E. Loffler. 2014. “Denitrification Versus Respiratory Ammonification: Environmental Controls of Two Competing Dissimilatory NO3-/NO2- Reduction Pathways in Shewanella loihica Strain PV-4,” The ISME Journal, DOI: 10.1038/ismej.2014.201. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 23, 2014

Microbial Community Dynamics Dominate Greenhouse Gas Production in Thawing Permafrost

Northern permafrost ecosystems are changing rapidly, with rising temperatures causing the transition of many previously frozen environments to wetlands. As permafrost thaws, the trapped organic carbon is accessible to decomposition by microbes and can be released to the atmosphere as greenhouse gases (GHGs). Understanding of these communities is limited, especially the specific nature of processes that impact rates of carbon decomposition and the balance of the carbon dioxide (CO2) versus methane (CH4) released to the atmosphere. Although both gases are GHGs, CH4 is much more potent in the short term, so understanding the microbial mechanisms driving these large-scale processes would significantly improve predictions of possible climate change impacts.

An interdisciplinary team of researchers led by the University of Arizona has examined microbial community dynamics at a site in northern Sweden that occupies a natural temperature gradient. Northern portions of this site are frozen permafrost while southern areas are thawed fens. Over several years, the team measured CO2 and CH4 production along the gradient, examined isotopic signatures of gases characteristic of distinct microbial processes, and correlated the data with measured shifts in microbial community composition and abundance. Only small amounts of GHGs were released from frozen permafrost, but in progressively more thawed sites, CH4 was the dominant product released. The team was able to link these observations with extensive shifts in microbial community composition, revealing a reproducible succession pattern of different types of CH4-producing microbes (methanogens) across the thaw gradient. Surprisingly, a single methanogen species, Candidatus Methanoflorens stordalenmirensis, was dominant in recently thawed sites and its relative abundance strongly correlated with the magnitude and specific type of CH4 produced at any given site.

The striking dominance of a single microbial species in mediating a large-scale carbon cycle process is highly unusual and provides an opportunity to more effectively track and predict the impacts of climate change across an entire region. The team has begun to incorporate integrated datasets on biogeochemical process measurements and microbial community patterns into ecosystem-scale models of carbon cycle processes. This effort represents a significant advance in understanding and more accurately representing critical biogeochemical processes in permafrost that are performed by microbes, improving predictions of climate change impacts on these delicate ecosystems and their potential atmospheric consequences.

Reference: McCalley, C. K., B. J. Woodcroft, S. B. Hodgkins, R. A. Wehr, E.-H. Kim, R. Mondav, P. M. Crill, J. P. Chanton, V. I. Rich, G. W. Tyson, and S. R. Saleska. 2014. “Methane Dynamics Regulated by Microbial Community Response to Permafrost Thaw,” Nature 514, 478-81. DOI: 10.1038/nature13798. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 21, 2014

Microbial Community Dynamics Impacting Methane Consumption in Freshwater Lakes

Decay of plant material in oxygen-limited sediments of lakes and wetlands results in the production of massive amounts of methane (CH4), a potent greenhouse gas. However, only a fraction of the CH4 produced in these environments enters the atmosphere due to the metabolic activities of microbial methanotrophs. Methanotrophs are a class of bacteria capable of consuming CH4 and using it as both a source of carbon and energy to fuel their growth. Understanding even the basic physiology of methanotrophs remains limited, as evidenced by the recent discovery of a new fermentative mode of methanotrophic metabolism in organisms that were previously thought to strictly require oxygen for growth. In a new study by researchers at the University of Washington, experimental microcosms established with lake sediments were used to examine methanotrophic communities and their response to varying levels of oxygen. By tracking community composition through DNA pyrosequencing, the team determined that the methanotroph community features a nonrandom assemblage of organisms, with specific types adapted to either high or low oxygen levels. When the methanotroph community shifted in response to oxygen availability, an array of nonmethanotrophic microbes also changed. Preliminary evidence suggests that these organisms are metabolically partnered with methanotrophs, exchanging nutrients and facilitating methanotrophic processes. These results represent the first detailed examination of microbial community dynamics in a methanotrophic ecosystem and suggest a high degree of complexity in their response to shifting environmental variables. Gain­ing a more sophisticated understanding of microbial community dynamics influencing methano­trophs in natural settings will help to facilitate more accurate predictions of environmental CH4 production and consumption.

Reference: Oshkin, I. Y., D. A. C Beck, A. E. Lamb, V. Tchesnokova, G. Benuska, T. L. McTaggart, M. G. Kalyuzhnaya, S. N. Dedysh, M. E. Lidstrom, and L. Chistoserdova. 2014. “Methane-Fed Microbial Microcosms Show Differential Community Dynamics and Pinpoint Taxa Involved in Communal Response,” The ISME Journal, DOI: 10.1038/ismej.2014.203. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 17, 2014

Enhancing Microbial Pathways for Biofuel Production

Produced in microbes and plants, terpenes are high-energy compounds that could be used for producing biofuels. For example, U.S. Department of Energy (DOE) researchers at the Joint BioEnergy Institute (JBEI) had reported that bisabolane, a biofuel derived from the sesquiterpene precursor bisabolene, could serve as an alternative to diesel fuel. Enhancing terpene yields in suitable microbes and plants is thus an important step toward commercial-scale production of these biofuels. Terpene synthesis in the majority of bacterial species, as well as in plant plastids, takes place via a pathway in which one-sixth of the carbon in the starting metabolites is lost as carbon dioxide (CO2). JBEI researchers wanted to improve terpene production in Escherichia coli by developing a pathway that would not result in any carbon loss as CO2. To do this, they focused on using a novel route that would form terpenes from 5-carbon (C5) sugars such as xylose, which is a breakdown product of hemicellulose. The researchers created a mutant in the metabolism of C5 sugars and then selected for complementary mutants that could grow on the C5 sugar xylose. E. coli colonies that were able to grow under this selective pressure were sequenced at DOE’s Joint Genome Institute and all were found to have mutations in the ribB gene. The researchers then inserted the pathway for bisabolene production into the strains able to grow on xylose, and they found bisabolene production in these strains. Further manipulation of the pathways by gene fusion and varying the gene order enhanced bisabolene yields several fold. These results demonstrate that biosynthetic pathways that are not found in nature may be constructed by selection and targeted engineering. This pathway is can now be further optimized for terpene yield in preparation for commercial-scale production.

Reference: Kirby, J., M. Nishimoto, R. W. N. Chow, E. E. K. Baidoo, G. Wang, J. Martin, W. Schackwitz, R. Chan, J. L. Fortman, and J. D. Keasling. 2015. “Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate,” Applied and Environmental Microbiology 81,130–8. DOI: 10.1128/AEM.02920-14. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 14, 2014

New Target for Engineering Lignin for Biofuel Production

Plant cell walls contain polysaccharides that can be hydrolyzed into fermentable sugars, but this process is inhibited by lignin. Altering lignin composition or structure can reduce the amount of effort needed to release glucose from cellulose, thus improving the economics of cellulosic biofuels production. Department of Energy Great Lakes Bioenergy Research Center (GLBRC) researchers John Ralph and Hoon Kim and their colleagues at Ghent University and Flanders Institute of Biology have a goal of understanding the control points in the lignin biosynthetic pathway and how to use them to improve biomass properties. They identified a new target for engineering lignin for biofuel production by using transcriptomics and microarray studies to identify genes that co-express with other known lignin biosynthesis genes. In the model plant Arabidopsis, there are three cytochrome P450 reductase genes, and one of these three genes controls an enzyme (ATR2) that is co-expressed with lignin biosynthetic genes. By studying mutant plants in which the atr2 gene was down-regulated via T-DNA insertion, researchers found that the atr2 mutants had increased glucose release from cellulose relative to the wild type following base pretreatment. This increase in saccharification appeared to result from both altered lignin structure and altered lignin content. The results support the contention that ATR2 is involved in the lignin pathway and is thus a target for engineering plant cell walls that are better suited for biofuels applications. The study also suggests additional candidates in the lignin pathway for future study.

Reference: Sundin, L., R. Vanholme, J. Geerinck, G. Goeminne, R. Höfer, H. Kim, J. Ralph, and W. Boerjan. 2014. “Mutation of the Inducible ARABIDOPSIS THALIANA CYTOCHROME P450 REDUCTASE2 Alters Lignin Composition and Improves Saccharification,”Plant Physiology 166, 1956–71. DOI: 10.1104/pp.114.245548. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 10, 2014

Investigating Nitrogen Fixation in a Photosynthetic Microbial Community

Photosynthetic microbial mats dominated by cyanobacteria achieve high rates of productivity using little more than sunlight, atmospheric gases (CO2 and N2), and trace nutrients. These complex, stratified ecosystems thus can provide experimentally tractable models to investigate functional properties of microbial communities and serve as valuable analogues for bioenergy production systems. The high rates of photosynthetic productivity observed in microbial mats are made possible by microbial nitrogen fixation, the process of converting N2 gas into biologically useful forms of nitrogen. Identifying which community members perform this process would provide a key to understanding overall community function. A team of investigators led by Lawrence Livermore National Laboratory scientists have reported new findings on nitrogen fixation in photosynthetic microbial mats using a combination of community gene expression analysis (metatranscriptomics), high-resolution microscopy, and nanoscale mass spectrometry (nanoSIMS). Metatranscriptomic analysis provided an overview of metabolically active community members capable of N2 fixation, thus providing an initial roster of target species worthy of further examination. Microscopically enabled nanoSIMS then provided the capability to narrow the search, tracking isotopically labeled nitrogen through the community at the scale of single cells. By coupling these two technologies, the team was able to identify specific members of the cyanobacterial portion of the community as the dominant N2 fixers and examine their spatial relationships within the overall community structure. These findings highlight the importance of pairing omics-driven techniques with complementary approaches that provide validation of functional predictions. By coupling cutting-edge experimental capabilities, researchers are developing a more sophisticated understanding of the biological rules that govern community structure and function, potentially enabling construction of analogous systems devoted to high-efficiency bioenergy production.

Reference: Woebken, D., L. C. Burow, F. Behnam, X. Mayali, A. Schintlmeister, E. D. Fleming, L. Prufert-Bebout, S. W. Singer, A. Lopez Cortes, T. M. Hoehler, J. Pett-Ridge, A. M. Spormann, M. Wagner, P. K. Weber, and B. M. Bebout. 2015. “Revisiting N2 Fixation in Guerrero Negro Intertidal Microbial Mats with a Functional Single-Cell Approach,” The ISME Journal 9, 485–96. DOI: 10.1038/ismej.2014.144. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 29, 2014

Tracking the Evolution of a Methane-Producing Symbiosis in Real Time

Just below the surface of soils and sediments, large portions of Earth’s biosphere exist in the absence of oxygen. The microbial inhabitants of these anoxic environments drive planetary biogeochemical cycles, and their metabolic activities impact the bioavailability of nutrients, metals, and environmental contaminants. To survive in these energy-limited habitats, many microbial species have evolved collaborative symbiotic lifestyles that allow two organisms to perform metabolic processes that neither would be capable of independently (i.e., “mutualistic syntrophy”). In a new study by Lawrence Berkeley National Laboratory scientists, an experimental evolutionary system was constructed that pairs a common sulfate-reducing bacterium, Desulfovibrio vulgaris, with a methane-producing archaea, Methanococcus maripaludis, neither of which is known to grow via mutualistic syntrophy in nature. Experimental conditions were manipulated so that neither organism would have access to an energy source it could use independently. In 21 independent experiments over 1,000 generations, mutualistic syntrophies that closely resembled associations observed in nature evolved between the two organisms 13 times. In these syntrophies, consumption of lactate (a common product of fermentation in anoxic environments) by D. vulgaris provided hydrogen and carbon dioxide to M. maripaludis, which, in turn, produced methane and maintained an energetic environment favorable to continued consumption of lactate by D. vulgaris. The partners quickly improved their performance efficiency for coupled syntrophic growth, but in many cases, D. vulgaris lost its ability to grow in the absence of M. maripaludis even under normal growth conditions. By sequencing the genomes of the evolved strains from the various experimental replicates, it was determined that D. vulgaris quickly accumulated loss of function mutations, particularly in three key sulfate reduction genes needed for independent growth. The team currently is examining the relationship between the loss of capacity for independent growth and improved symbiotic performance. These results provide a fascinating glimpse at the molecular underpinnings of a natural selection process and demonstrate the importance of tradeoffs between growth efficiency and metabolic flexibility during the evolution of a symbiotic partnership. In the broader sense, understanding the molecular factors governing the formation of these associations and their performance under changing environmental conditions could provide valuable new insights into the way that carbon and energy flow through anoxic environments.

Reference: Hillesland, K. L., S. Lim, J. Flowers, S. Turkarslan, N. Pinel, G. Zane, N. Elliott, Y. Qin, L. Wu, N. Baliga, J. Zhou, J. Wall, and D. Stahl. 2014. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism,” Proceedings of the National Academy of Sciences (USA) 111(41), 14822-827. DOI: 10.1073/pnas.1407986111. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 22, 2014

Integration of Carbon, Sulfur, and Iron Cycling in Anaerobic Methane Oxidation

Coastal wetlands and ocean sediments are significant sites of methane (CH4) production, either through decomposition of organic material or via natural seepage from deeper geological reservoirs. These environments are home to unique microbial communities capable of converting CH4 to carbon dioxide (CO2) even in the absence of oxygen, which does not penetrate below the top few centimeters of sediment. No individual microbe or microbial species can generate enough energy to survive using this mode of metabolism. However, symbiotic partnerships between methane-consuming archaea and sulfate-reducing bacteria thrive using a collaborative metabolism called anaerobic oxidation of methane (AOM). In this mode of growth, electrons freed during CH4 oxidation by archaea are transferred to sulfate (SO4) by the bacterial partner, generating energy for both organisms. Since this process results in the conversion of up to 90% of available CH4 to CO2 (a much less potent greenhouse gas) in some environments, studying its mechanistic basis and the organisms performing it could have major implications for understanding the global carbon cycle and potential climate change impacts. Researchers at the California Institute of Technology and partner institutions in the United Kingdom and Israel have uncovered new evidence of a significant role for iron minerals in accelerating the rates of AOM processes. Sediments with higher levels of iron oxides had decreased rates of methane release and increases in AOM processes. By using a series of microcosm experiments and carefully tracking conversion of isotopically labeled CH4 and SO4 in the presence of varying concentrations of the iron mineral hematite, the team determined that the presence of iron oxides stimulated bacterial sulfate reduction, facilitating recycling of reduced sulfur compounds back to SO4, and driving increased rates of methane consumption by archaea. These findings reveal new biological linkages in the biogeochemical cycling of carbon, sulfur, and iron and will have important implications in predicting the contribution of AOM processes to the global carbon cycle.

Reference: Sivan, O., G. Antler, A. V. Turchyn, J. J. Marlow, and V. J. Orphan. 2014. “Iron Oxides Stimulate Sulfate-Driven Anaerobic Methane Oxidation in Seeps,” Proceedings of the National Academy of Sciences (USA), DOI:10.1073/pnas.1412269111. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 20, 2014

Identification of Two Key Enzymes in Xylan Synthesis and Acetylation in Plant Cell Walls

Only a few dozen of the thousands of genes involved plant cell wall biosynthesis have been identified and confirmed. Xylan, a part of hemicellulose, is a major component of plant cell walls and the third most abundant polysaccharide on Earth. The key enzymes responsible for elongation of the xylan backbone and addition of acetyl groups had not been identified, but researchers from the BioEnergy Science Center of Oak Ridge National Laboratory recently identified two key enzymes for the synthesis of this polysaccharide and confirmed their function biochemically. Mutations that impair synthesis of the xylan backbone give rise to plants with collapsed xylem cells and poor growth. Phenotypic analysis of these mutants has implicated many possible proteins in xylan biosynthesis. To further investigate the role of the mutant genes in xylan biosynthesis, recombinant tagged proteins encoded by the Arabidopsis thaliana genes, IRX10-L and ESK1/TBL29, were expressed in vitro and purified. Enzymatic activity of these proteins was inferred from the similarity of their primary amino acid sequence to enzymes of known function. Their enzyme activity was analyzed in vitro by mass spectroscopy and nuclear magnetic resonance. This direct biochemical evidence confirmed the A. thaliana protein IRX10-L enzyme as the xylan synthase and ESK1/TBL29 as the archetypal plant polysaccharide O-acetyltransferase. Thus, two key enzymes for two critical process in xylan (and secondary plant cell wall) synthesis now have been identified, purified, and confirmed. These findings will accelerate understanding of and the ability to manipulate plant cell wall structures for advanced renewable feedstocks for conversion into sugars and fuels or into valuable products such as biomaterials.

Reference: Urbanowicz, B. R., M. J. Peña, H. A. Moniz, K. W. Moremen, and W. S. York. 2014. “Two Arabidopsis Proteins Synthesize Acetylated Xylan In Vitro,” The Plant Journal 80(2), 197-206. DOI:10.1111/tpj.12643. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 24, 2014

Identifying Representative Corn Rotation Patterns in the U.S. Western Corn Belt

To accurately assess the impacts of biofuel crop production on regional ecosystem services such as crop yields, carbon and nutrient cycling, soil erosion, water quality, and pest and disease control, it is necessary to have an accurate picture of which crop rotation systems are utilized by growers. Despite the availability of databases such as the Cropland Data Layer (CDL), which provide remotely sensed data on U.S. crop types on a yearly basis, crop rotation patterns remain poorly mapped due to the lack of tools that allow for efficient and consistent analysis of multiyear CDLs. Researchers at the Department of Energy’s Great Lakes Bioenergy Research Center created an algorithm that can select representative crop rotation systems by combining and analyzing multiyear CDLs. Among the findings using this algorithm is that only 82 representative crop rotations accounted for over 90% of the spatiotemporal variability of the more than 13,000 rotations in the Western Corn Belt; it also can detect pronounced shifts from grassland to monoculture corn and soybean cultivation. Furthermore, the area estimates of the rotation systems are comparable to those obtained from agricultural census data. Given this algorithm’s novel capability to flexibly and efficiently derive representative crop rotation patterns in a spatially and temporally explicit manner, it is expected to be a useful tool for providing input data to drive agro-ecosystem models and for detecting shifts in cropping patterns in response to environmental and socio-economic changes.

Reference: Sahajpal, R., X. Zhang, R. C. Izaurralde, I. Gelfand, and G. C. Hurtt. 2014.   “Identifying Representative Crop Rotation Patterns and Grassland Loss in the U.S. Western Corn Belt,” Computers and Electronics in Agriculture 108, 173–82. DOI: 10.1016/j.compag.2014.08.005. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 21, 2014

New Technologies Facilitate Investigation of Wood Formation

Woody plants are an important source of renewable biomass for bioenergy feedstocks. Wood formation is a complex, highly regulated process generating key sources of material for bioenergy and bioproducts. Understanding the gene regulatory networks underlying wood formation would facilitate efforts to develop higher biomass yielding, sustainable trees as bioenergy feedstocks. However, the nature of woody material makes it recalcitrant to genetic manipulation, presenting a significant challenge. Researchers funded by the Department of Energy’s Genomic Science program report the development of two new methods optimized for woody material and expediting molecular genetic approaches for investigating wood formation in Populus trichocarpa, a model woody plant and bioenergy feedstock. They detail systematic and extensive modification of the chromatin immunoprecipitation (ChIP) procedure, widely used to identify chromatin-associated DNA-protein interactions in nonwoody plants and animals, making it usable for the first time with wood-forming tissues. Using this new protocol, the researchers identified genome-wide specific transcription factor-DNA interactions associated with the regulation of wood formation. They also describe a new higher-yielding and faster method for the isolation and transfection of high-quality protoplasts from P. trichocarpa wood-forming tissue. Protoplasts are useful for transient transgene expression-based studies, particularly for woody plants that are difficult to genetically transform and for which mutants are unavailable. Both methods should be broadly applicable to other woody species, enabling comparative analyses of the evolution of the genetic regulation and epigenetic modifications of wood formation. These advances will facilitate essential genome-wide studies of wood formation and biomass productivity in woody feedstocks.

References: Li, W., Y.-C. Lin, Q. Li, R. Shi, C.-Y. Lin, H. Chen, L. Chuang, G.-Z. Qu, R. R. Sederoff, and V. L. Chiang. 2014. “A Robust Chromatin Immunoprecipitation Protocol for Studying Transcription Factor-DNA Interactions and Histone Modifications in Wood-Forming Tissue,” Nature Protocols 9(9), 2180-93. DOI:10.1038/nprot.2014.146. (Reference link)

Lin, Y.-C., W. Li, H. Chen, Q. Li, Y.-H. Sun, R. Shi, C.-Y. Lin, J. P. Wang, H.-C. Chen, L. Chuang, G.-Z. Qu, R. R. Sederoff, and V. L. Chiang. 2014. “A Simple Improved-Throughput Xylem Protoplast System for Studying Wood Formation,” Nature Protocols 9(9), 2194-2205. DOI:10.1038/nprot.2014.147. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 18, 2014

Ionic Liquids Provide Effective Biomass Pretreatment

Ionic liquids (ILs) have been shown to be an excellent pretreatment solvent for biomass in preparation for hydrolysis into its component sugars. However, IL availability and high cost remain an issue. Researchers from the Department of Energy’s Joint BioEnergy Institute sought to decrease the cost of ILs by synthesizing new ILs directly from lignin monomers and hemicellulose, which are found in the biomass. Tertiary amine-based ILs were synthesized from aromatic aldehydes derived from lignin and hemicellulose. Molecular modeling was used to compare IL solvent parameters with experimentally obtained compositional analysis data.

Effective pretreatment using these new ILs of switchgrass was investigated by powder X-ray diffraction showing structural changes in cellulose and glycome profiling showing changes in the extractability of hemicellulose epitopes. Deriving ILs from lignocellulosic biomass shows significant potential for the realization of a “closed-loop” process for future lignocellulosic biorefineries and has far-reaching economic impacts for other IL-based conversion technology currently using ILs synthesized from petroleum sources. IL synthesis by reductive animation of aromatic aldehydes, followed by treatment with phosphoric acid, provided three biomass-derived ILs in excellent yields without the need for chromatographic purification. When these renewable biomass-derived ILs were used in pretreatment of switchgrass biomass, comparable high yields of sugar were generated and saccharification was comparable to current imidazolium-based ILs. Cost projections of renewable ILs are $4/kg, much lower than top performing conventional ILs, improving the economic viability of lignocellulosic-derived sugars.

Reference: Socha, A. M., R. Parthasarathia, J. Shia, S. Pattathil, D. Whyte, M. Bergeron, A. George, K. Tran, V. Stavila, S. Venkatachalam, M. G. Hahn, B. A. Simmons, and S. Singh. 2014. “Efficient Biomass Pretreatment Using Ionic Liquids Derived from Lignin and Hemicellulose,” Proceedings of the National Academy of Sciences (USA) 111(35), E3587-95. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 06, 2014

Evolution of Substrate Specificity in Bacterial Lytic Polysaccharide Monooxygenases

Cellulose is one of the most abundant polysaccharides in nature and one of the primary components of plant cell walls. The biofuels industry has devoted significant efforts to establish processes to convert these energy-rich molecules into sugars that can be fermented into biofuels or other bioproducts. However, the hydrolysis of these polysaccharides, a key step in converting them to biofuels, is difficult due to their crystalline structure, the stability of some bonds within their structure, and how closely they are associated with structure-modifying molecules such as hemicellulose and lignin. Efficient hydrolysis requires a cocktail of different enzymes. Enzymes capable of hydrolyzing these polymers have been identified in various organisms, especially bacteria and fungi, but the pathways for deconstruction of certain polysaccharides, such as cellulose and chitin, are only partially understood. Researchers at the Department of Energy’s Great Lakes Bioenergy Research Center analyzed the sequences, structures, and evolution of two families of enzymes, fungal AA9 and bacterial AA10, both lytic polysaccharide monooxygenases (LPMOs), to understand the factors that influence substrate specificity in these families and to characterize the selective pressures that may have led to their functional diversification. Their sequence similarity suggests that both families share a distant common ancestor and that certain clades within the AA10 family are specialized for different substrates, while others went through a diversifying selection at surface-exposed regions of the protein. Understanding the diversity of these lignocellulosic-degrading enzymes in nature provides information that can help improve enzymatic cocktails used in the biofuels industry.

Reference: Book, A. J., R. M. Yennamalli, T. E. Takasuka, C. R. Currie, G. N. Phillips, and B. G. Fox. 2014. “Evolution of Substrate Specificity in Bacterial AA10 Lytic Polysaccharide Monooxygenases,” Biotechnology for Biofuels 7,109. DOI: 10.1186/1754-6834-7-109. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 25, 2014

Role of Post-Translational Protein Modification in Community-Scale Processes

Although biological processes are often modulated by the direct regulation of gene expression, post-translational modifications (PTM) of expressed proteins frequently play an equally important regulatory role. PTM occurs when protein function is altered by the addition of a phosphate, acetate, or other small molecule in response to a sensed environmental cue. These alterations create rippling signal cascades, often leading to pervasive changes in cellular metabolism and functional properties. PTM-based regulation has been extensively studied in individual organisms, but the role of this regulatory mechanism at the scale of complex communities remains poorly understood. In a new study, a collaborative team of researchers at the University of California, Berkeley, and Oak Ridge National Laboratory developed a novel technique that allows PTM analysis in proteins collected from an intact microbial community (i.e., the metaproteome) using high-resolution mass spectrometry coupled to high-performance computing. The investigators examined PTM in a model biofilm community found in a highly acidic environment and were able to link this regulatory mechanism to several community-scale phenotypes that could not be explained by observed changes in gene expression. Community-level attributes associated with PTM in this study included alterations in community structure, nutrient acquisition strategies, and resistance to viral invasion. This finding represents a considerable advance in the application of systems biology approaches to community-level analysis. The team now is working to scale up this technique to enable investigations of more complex communities and environments.
Reference: Li, Z., Y. Wang, Q. Yao, N. B. Justice, T.-H. Ahn, D. Xu, R. L. Hettich, J. F. Banfield, and C. Pan. 2014. “Diverse and Divergent Protein Post Translational Modifications in Two Growth Stages of a Natural Microbial Community,” Nature Communications 5, 4405. DOI: 10.1038/ncomms5405. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 20, 2014

Characterization of Poplar Budbreak Gene Enhances Understanding of Spring Regrowth

Trees in temperate climates undergo annual cycles of growth and dormancy corresponding to summer and winter seasons, a critical strategy that allows perennial plants to survive cold and dehydration during the winter months. These important transitions are controlled by photoperiod and temperature, but the exact mechanisms by which key physiological processes are initiated are still poorly understood. Researchers at Michigan Technological University and Oregon State University have identified and functionally characterized a gene in the bioenergy feedstock tree Populus called Early Bud-Break 1 (EBB1). EBB1 serves as a “master regulator” in the timing of spring growth reactivation, or budbreak. In addition, the protein encoded by EBB1 was found to function in many other processes critical to poplar survival, including nutrient cycling and root growth. These results enhance understanding of dormancy release in woody perennial plants and will enable new approaches for breeding trees better adapted to changing environments such as a warmer climate. The research was supported by the U.S. Department of Agriculture-Department of Energy Plant Feedstock Genomics for Bioenergy Program. (Reference link)

Reference: Yordanov, Y. S., C. Ma, S. H. Strauss, and V. G. Busov. 2014. “Early Bud-Break 1 (EBB1) is a Regulator of Release from Seasonal Dormancy in Poplar Trees,” Proceedings of the National Academy of Sciences (USA) 111(27), 10,001-10,006. DOI: 10.1073/pnas.1405621111. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 02, 2014

Ethanol Produced from Switchgrass Biomass Without Pretreatment

One strategy for reducing costs associated with biomass deconstruction and fermentation of sugars to biomass into advanced biofuels is consolidated bioprocessing (CBP). In CBP, non-pretreated biomass is converted to a biofuel in a single process by a cellulolytic microbe that breaks down the biomass and ferments the sugars. U.S. Department of Energy BioEnergy Research Center (BESC) scientists have been working toward CBP by looking at a variety of thermophilic cellulolytic bacteria. A candidate CBP microbe is Caldicellulosiruptor bescii, a natural thermophilic cellulolytic bacterium for which BESC researchers have developed genetic tools for gene insertion and deletion. In this study, BESC researchers demonstrate the successful CBP of switchgrass cellulosic biomass using an engineered strain of C. bescii.

C. bescii had been shown to ferment untreated switchgrass biomass, but it lacked the genes to make ethanol. As C. bescii is a thermophile and CBP is carried out at elevated temperatures, a gene for a heat-stable enzyme for ethanol synthesis was needed. A candidate gene was identified in Clostridium thermocellum and cloned into C. bescii. The engineered C. bescii strain now produced ethanol from cellobiose, Avicel, and switchgrass. To optimize the fermentation of ethanol, two genes were deleted that would otherwise divert fermentation products. In this new C. bescii strain, roughly 30% of biomass was fermented and 1.7 moles of ethanol was produced for each mole of glucose, close to the theoretical 2.0 moles of ethanol per mole of glucose. While there are opportunities to further improve efficiencies, this is an important step in actualizing the CBP’s potential and provides a platform for engineering the production of advanced biofuels and other bioproducts directly from cellulosic biomass without harsh and expensive pretreatment.

Reference: Chung, D., M. Cha, A. M. Guss, and J. Westpheling. 2014. “Direct Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii,” Proceedings of the National Academy of Sciences (USA) 111, 8931–36. DOI:10.1073/pnas.1402210111. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 01, 2014

Evolution of Potential Energy Grass Genome Structure

The Saccharinae group of grasses contains two members that are potentially important sources of sugar and lignocellulosic biomass for bioenergy, due at least in part to highly efficient C4 photosynthesis. These grasses are the warm temperate-tropical sugarcane (Saccharum officinarum) and Miscanthus spp., which can yield high levels of biomass at temperate latitudes. A close relative is sorghum (Sorghum bicolor), also grown as a bioenergy feedstock in addition to its use as food and feed. In contrast to sorghum, the Saccharinae grasses are known for polyploidy and possess high chromosome numbers, offering an opportunity to investigate the evolutionary processes of genome duplication, genome structure, and the implications for crop improvement strategies. Researchers funded by the joint U.S. Department of Agriculture-Department of Energy Plant Feedstock Genomics for Bioenergy program have applied genome sequencing and global comparative analyses of Miscanthus, Saccharum, and sorghum to gain insight into the different evolutionary fates of Miscanthus and Saccharum after they diverged from sorghum. The researchers report evidence for the existence of a genome duplication shared between Saccharum and Miscanthus as well as an additional Saccharum-specific duplication event. Understanding the genome structure of these two complex grasses in relation to the closely related and fully sequenced sorghum genome will facilitate breeding efforts to improve bioenergy-relevant traits such as biomass yield and adaptation to changing environments.

Reference: Kim, C., X. Wang, T.-H. Lee, K. Jakob, G.-J. Lee, and A. H. Paterson. 2014. “Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates,” Plant Cell 26, 2420-29. DOI:10.1105/tpc.114.125583. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 01, 2014

Poplar Tree Root Response to Symbiotic Fungus Determines Success of Fungal Colonization

Microbial communities sharing the soil environment with plant roots can have a pro­found influence on the overall health and vitality of the plant. One well-known example of a beneficial relationship is that formed between forest trees and shrubs and a type of mutualistic fungi known as ectomycorrhizal fungi (ECM). In a compatible reaction, ECM facilitate the plant’s access to nutrients and increase its tolerance to biotic and abiotic stress through formation of an “organ” between fungal hyphae and plant roots called the ECM root tip. However, little is known about the metabolic reprogramming that leads to the development of this hybrid tissue. Researchers at Oak Ridge National Laboratory, funded through the Department of Energy’s Plant-Microbe Interfaces Science Focus Area, characterized the metabolic changes taking place during the interaction between the ECM fungus Laccaria bicolor and two different species of the bioenergy feedstock tree Populus. They found that when P. trichocarpa is colonized by the fungus shifts occurred in aromatic acid, organic acid, and fatty acid metabolism. On the contrary, this metabolic reprogramming was repressed in the incompatible P. deltoides interaction, which was instead characterized by the production of more defense-related secondary metabolites. The results highlight distinct differences in mechanisms control­ling compatibility between beneficial and nonbeneficial inter­actions, and increase under­standing of how plant roots respond to the presence of L. bicolor, which determines the out­come of the fungal-host interaction.

Reference: Tschaplinski, T. J., J. M. Plett, N. L. Engle, A. Deveau, K. C. Cushman, M. Z. Martin, M. J. Doktycz, G. A. Tuskan, A. Brun, A. Kohler, and M. Martin. 2014. “Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic Fungus Laccaria bicolor,” Molecular Plant-Microbe Interactions 27(6), 546-56. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 23, 2014

Microbes Disprove Long-Held Assumption that All Organisms Share a Common Vocabulary

Four letters—A, C, G, and T—make up the DNA bases in all organisms on Earth. The particular order, or sequence, of these same four letters genetically defines an organism and is a main reason that determining the genome sequence is now a foundational starting point for many biological investigations. Within this sequence are shorter, three-letter groups called codons that represent amino acids, the building blocks of proteins that carry out the myriad functions critical to life and biology. There are 64 of these codons and, routinely, 61 of them code for the 20 known amino acids. Three of these triplets function as stop signals and are used to mark the end of protein generation. Given that all organisms have genomes built on the same four letters, scientists had long assumed that they also all shared the same vocabulary and the 64 codons would be interpreted the same way across the board. However, a recent study from the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) shows that for some organisms the instructions for these three codons mean anything but stop. The researchers focused on uncultivated microbes, whose genomes had been described through single-cell genomics and metagenomics, and on a collection of viral sequences. Nearly six trillion bases of sequence data were analyzed from 1,776 samples collected from the human body and several sites around the world. The study found that these stop codons often were reassigned to code for amino acids. This work builds on a previous study in which DOE JGI researchers successfully employed single-cell genomics to shed insight on a plethora of microbes representing 29 “mostly uncharted” branches on the tree of life.

Reference: Ivanova, N., et al. 2014. “Stop Codon Reassignments in the Wild,” Science 344, 909–13. DOI:10.1126/science.1250691. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 20, 2014

Developing Synthetic Microbial Communities to Improve Predictions of Their Behavior

Microbial communities populate every natural environment, playing critical roles in fundamen­tal biological and environmental processes such as food webs and carbon cycling. Members of microbial communities interact with each other both as competitors and collabora­tors. Understanding the complex interactions within these communities is necessary to predict and eventually manipulate their behavior for biotechnol­ogy applica­tions. Studying natural microbial consortia is extremely challenging, so simple microbial cocultures are often used to gain insights on microbial crossfeeding and communication. However, such studies rarely represent natural systems, and, therefore, more complex synthetic microbial communities are needed to model the development and evolution of microbial populations. Researchers at Harvard and Columbia universities report the development of a system of synthetic microbial communities composed of up to 14 Escherichia coli mutants, each one incapable of synthesizing a different amino acid. Using this system, the investigators could experimentally determine the behavior of the different members of the consortium, identifying mutants that act as keystone species or that promote positive or negative interactions. After several generations, these bacterial populations tend to become enriched in mutants that cannot produce metabolically costly amino acids (those that require more energy to synthesize). The authors hypothesize that such mutants persist in the population by crossfeeding from less abundant microbes that provide needed amino acids. This hypothesis was supported by the observation that the majority of the microorganisms whose genomes have been sequenced do not have the metabolic capacity to produce costly amino acids. These results will enable develop­ment of more accurate predictive models of microbial communities and their iterative improve­ment by experimentation, advancing toward a more comprehensive understanding of microbial communities such as those involved in carbon cycling.   

Reference: Meea, M. T., J. J. Collins, G. M. Church, and H. H. Wang. 2014. “Syntrophic Exchange in Synthetic Microbial Communities,” Proceedings of the National Academy of Sciences (USA) 111(20), E2149-56. DOI:10.1073/pnas.1405641111. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 20, 2014

Fungal Protein Allows Beneficial Colonization in Populus

The soil environment surrounding plant roots is filled with bacteria and fungi, both harmful and beneficial, many of which attempt to colonize root tissues to gain access to and use plant nutrients. In response, plant hormones such as jasmonic acid (JA) mediate the plant’s defense signaling system. By altering this pathway, some microorganisms can gain entry into the plant root cells and promote colonization. Investigating the symbiotic relationship between the bioenergy feedstock tree Populus trichocarpa and the beneficial fungus Laccaria bicolor, researchers at Oak Ridge National Laboratory found that a fungal protein essential for root establishment (called MiSSP7; Mycorrhiza-induced Small Secreted Protein 7) interacts with a plant-produced protein within the host plant nuclei to promote symbiosis. While both pathogenic and mutualistic fungi use fungal “effector” proteins to facilitate colonization, the results suggest how the mechanisms used to overcome the plant’s defenses differ between these two types of organisms, furthering understanding of how L. bicolor alters the plant’s response to JA and allows formation of symbiotic relationships.

Reference: Plett, J. M., Y. Daguerre, S. Wittulsky, A. Vayssières, A. Deveau, S. J. Melton, A. Kohler, J. L. Morrell-Falvey, A. Brun, C. Veneault-Fourrey, and F. Martin. 2014. “Effector MiSSP7 of the Mutualistic Fungus Laccaria bicolor Stabilizes the Populus JAZ6 Protein and Represses Jasmonic Acid (JA) Responsive Genes,” Proceedings of the National Academy of Sciences (USA) 111(22), 8299-304. DOI: 10.1073/pnas.1322671111. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


April 21, 2014

Engineered Switchgrass Shows Increased Ethanol Production During 2-Year Field Trial

A major assumption in much plant-focused bioenergy research is that key plant cell wall traits can be genetically manipulated to reduce recalcitrance and increase biofuel yields per unit of biomass. A number of greenhouse experiments have shown promise, but few field studies have been completed to assess this assumption. Researchers at the BioEnergy Science Center (BESC) are the first to report a field study evaluating the biofuel potential of genetically engineered switchgrass (Panicum virgatum L.). BESC researchers previously had used RNAi (inhibitory RNA) to down-regulate caffeic acid O-methyltransferase (COMT), a key enzyme in the synthesis of lignin precursors. Switchgrass plants engineered in this way and grown in the greenhouse had less lignin and a shift in the quality of lignin to a more hydrolysable form. These plants showed less recalcitrance and a greater percentage of cell wall sugars being converted to ethanol than control plants. However, greenhouse results do not always replicate in the field, so researchers were anxious to learn if COMT-engineered switchgrass would show reduced recalcitrance and increased ethanol production when grown in the field.      

The 2-year field trial in large part recapitulated the greenhouse results. Namely, the transgenic switchgrass plants had a reduction in the quantity of lignin and a shift in the quality of lignin. A greater percentage of the cell wall sugars were released with pretreatment, and ethanol yield increased by as much as 28% in the transgenic lines relative to controls. These results were with senescent tissues, whereas the greenhouse studies had only looked at green tissues. Importantly for agronomic applications, the transgenic plants were not more susceptible to rust (Puccinia emaculata) or other plant pests. This important 2-year field study affirms genetic engineering of the plant cell wall as a viable strategy to improve plant biomass for the production of high-energy biofuels.  

Reference: Baxter, H. L.; M. Mazarei; N. Labbe; L. M. Kline; Q. Cheng; M. T. Windham; D. G. J. Mann; C. Fu; A.  Ziebell; R. W. Sykes; M. Rodriguez, Jr.; M. F. Davis; J. R. Mielenz; R. A. Dixon; Z. W. Wang; and C. N. Stewart, Jr. 2014. “Two-Year Field Analysis of Reduced Recalcitrance Transgenic Switchgrass,” Plant Biotechnology Journal 1–11. DOI:10.1111/pbi.12195. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 04, 2014

Engineered Poplar Lignin Improves Wood Degradability

Lignin is an irregular phenolic plant cell wall polymer that is integral to plant strength and function. It is important in bioprocessing of plant biomass because it inhibits deconstruction of plant cell wall sugar polymers, such as cellulose and hemicellulose, into sugar monomers, a key step in biofuel production. The irregular structure and types of linkages among the phenolic monolignol precursors contribute to lignin’s recalcitrance to cleavage and hydrolysis. Interestingly, the enzymes that polymerize lignin are known to be promiscuous and can incorporate nonstandard monolignols if alternate precursors are supplied. Exploiting this promiscuity to construct a lignin more amenable to hydrolysis, Great Lakes Bioenergy Research Center (GLBRC) researchers genetically engineered poplar—an attractive biofuels feedstock—to biosynthesize ferulate conjugated monolignols in the developing cell wall of plant tissues that contain significant amounts of lignin. The ferulate monolignols are of particular interest because they form ester bonds in lignin that are more hydrolysable than the typical ether bonds that normally connect lignin monolignols. The modified lignin altered the amount of sugars released from the poplar cell walls, and the researchers found that mild alkaline pretreatment released as much as double the glucose compared to the unmodified poplar lignin. These studies demonstrate the usefulness of modifying plant lignin as a means to simplify and improve processing of plant biomass and increasing sugar yields from plant biomass for biofuel production. These improvements are important advances in overcoming the technical barriers to an economically viable and sustainable biofuels industry.

Reference: Wilkerson, C. G., S. D. Mansfield, F. Lu, S. Withers, J.-Y. Park, S. D. Karlen, E. Gonzales-Vigil, D. Padmakshan, F. Unda, J. Rencoret, and J. Ralph. 2014. “Monolignol Ferulate Transferase Introduces Chemically Labile Linkages into the Lignin Backbone,” Science 344, 90–93. DOI:10.1126/science.1250161. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 26, 2014

Engineering Escherichia coli to Tolerate Ionic Liquids for Biofuel Production

Ionic liquids (IL) are a class of environmentally friendly solvents that are effective at loosening cellulose from lignin in plant biomass. This is an important step in the production of biofuels as it makes cellulose available for breakdown into its component sugars. The sugars are fermented into biofuels by microbes such as Escherichia coli. While most of the IL is recovered from the processed biomass, some remains and can inhibit the growth of E. coli and the enzymes that convert cellulose into biofuel, greatly reducing yields of biofuel product. To address this inhibition, scientists at the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI) looked for genes that might confer tolerance on the E. coli to the ILs. They looked to Enterobacter lignolyticus, a bacterium known to grow in the presence of ILs. First, they moved large parts of the E. lignolyticus genome into E. coli and asked the E. coli to grow in the presence of the IL. Several colonies were found to now tolerate the IL; each colony had two E. lignolyticus genes in common, an efflux pump gene and its regulator. Efflux pumps confer tolerances by transporting toxic compounds out of the cell into the medium. To determine if the tolerance conferring efflux pump could improve biofuel synthesis in the presence of IL, the efflux pump genes were placed together in a strain of E. coli engineered to produce a biofuel precursor, bisabolene. The resulting strain was able to produce more bisabolene in the presence of much greater amounts of IL than the E. coli strain without the efflux pump. An E. coli strain that tolerates ILs and synthesizes bisabolene means that ILs can be used to treat biomass to free cellulose from lignin without negatively impacting subsequent biofuel production. This can reduce biofuel production costs because extra expense is not needed to remove the last amounts of IL from the processed biomass. As cellulosic biofuel production plants come online, such adaption of technological advances like these that will improve their economic viability.

Reference: Rüegg, T. L., E.-M. Kim, B. A. Simmons, J. D. Keasling, S. W. Singer, T. S. Lee, and M. P. Thelen. 2014. “An Auto-Inducible Mechanism for Ionic Liquid Resistance in Microbial Biofuel Production,” Nature Communications 5. DOI:10.1038/ncomms4490. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
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Division: SC-23.2 Biological Systems Science Division, BER


February 20, 2014

Microbes in Antarctic Lake Divvy Up the Waters

Four microbes, recently sequenced at the U.S. Department of Energy’s Joint Genome Institute, dominate in Antarctica’s Deep Lake, making up 70% of the microbial community. They belong to a group called haloarchaea, which require high salt concentrations to grow and are naturally adapted to extreme conditions that would prove lethally cold to other organisms. In a recent study, researchers found that three of the four haloarchaea are adapted to niche environments within the lake. The most abundant of the four, strain tADL (44% of the lake community), has genes for light harvesting and gas vesicles that help it float near the light-rich surface. The second most abundant haloarchaea, strain DL31 (18% of the community), appears to be adept at metabolizing proteins and peptides. H. lacusprofundi (10% of the lake community)appears to be a more versatile generalist that can feed on a variety of nutrients. The least abundant, strain DL1 (0.3% of the lake community), shows a taste for amino acids and is the only one without genes for using glycerol as a nutrient. The next step is to use metaproteomics (study of proteins in an environmental sample) to investigate whether protein abundance in Deep Lake supports the research team’s hypothesis about niche specialization. Understanding how haloarchaea thrive in extreme polar niches could be used to improve the role of microbes in contaminated site cleanup in permanently or seasonally cold regions. Also, the genes that allow them to adapt to select conditions can be re-tooled for use in industrial or environmental remediation settings.

Reference: Williams, T. J., et al. 2014. “Microbial Ecology of an Antarctic Hypersaline Lake: Genomic Assessment of Ecophysiology Among Dominant Haloarchaea,” The ISME Journal 8, 1645-58. DOI:10.1038/ismej.2014.18. (Reference link)

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


February 19, 2014

Floating Water Weed Could Be Used as Biofuels Feedstock

Duckweed is one of the world’s smallest and fastest-growing flowering plants and can be a hard-to-control weed in ponds and small lakes. It shows great promise as a biofuel feedstock, however, and private companies are already exploring its use in fuel production. Researchers at Rutgers University, the Department of Energy’s Joint Genome Institute, and several other facilities recently sequenced the complete genome of Greater Duckweed (Spirodela polyrhiza) and analyzed it in comparison with several other plants, including rice and tomato. S. polyrhiza’s very small genome is missing many genes for plant maturation and production of cellulose and lignin but has more genes than comparable plants for starch production. Determining which genes produce desirable traits will allow researchers to create new varieties of duckweed with enhanced biofuel traits.

Reference: Wang, W., et al. 2014. “The Spirodela polyrhiza Genome Reveals Insights into Its Neotenous Reduction Fast Growth and Aquatic Lifestyle,” Nature Communications 5, 3311. DOI: 10.1038/ncomms4311. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742, John Houghton, SC-23.2, (301) 903-8288
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Division: SC-23.2 Biological Systems Science Division, BER



Comparison of Fronds and Turions. Duckweed is a relatively simple plant with fronds that float on the surface and roots that extend into the water (right). In the flask on the left, dormant phase turions have dropped to the bottom. [Image credit: Rutgers University]



February 18, 2014

Understanding Ecological Forces Governing Assembly and Function of Microbial Communities

A complex, dynamic, and interactive set of ecological forces governs the assembly of a microbial community in any given environment. The composition and structure of the resulting community in turn controls functional biological processes performed at the site, influencing biogeochemical cycling of nutrients, transport of contaminants, and interactions with other organisms. As such, understanding the rules that govern assembly and successional change of microbial communities in different types of environments is critical to predicting changes in ecosystem-scale processes under changing environmental conditions. In a new study by Lawrence Berkeley National Laboratory’s ENIGMA Science Focus Area, researchers examined mechanisms driving microbial community assembly and succession in an experimentally manipulated groundwater ecosystem. The team tested a set of theoretical models to compare the relative importance of stochastic (i.e., random) and deterministic processes in shaping community structure after an environmental change (in this case, the addition of nutrients). Community assembly and succession were found to be driven by a dynamic, time-dependent interaction of stochastic and deterministic processes, with stochastic forces dominating. By identifying the mechanisms controlling microbial community assembly and succession, this study makes an important contribution to the mechanistic understanding essential for a predictive microbial ecology of natural and managed ecosystems.

Reference: Zhou, J., Y. Deng, P. Zhang, K. Xue, Y. Liang, J. D. Van Nostrand, Y. Yang, Z. He, L. Wu, D. A. Stahl, T. C. Hazen, J. M. Tiedje, and A. P. Arkin. 2014. “Stochasticity, Succession, and Environmental Perturbations in a Fluidic Ecosystem,” Proceedings of the National Academy of Sciences (USA), DOI: 10.1073/pnas.1324044111. (Reference link)

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


February 14, 2014

Novel Methanogenic Microbe Discovered in Thawing Permafrost

Northern high-latitude ecosystems are undergoing rapid changes with rising temperatures catalyzing the transition of many permafrost sites to wetlands. As the organic carbon locked in permafrost thaws, it becomes accessible to decomposition by microbial communities. Understanding of these communities is limited, especially regarding functional processes that impact rates of carbon degradation and the balance of carbon dioxide (CO2) versus methane (CH4) released to the atmosphere. In a new U.S. Department of Energy Genomic Science Program study led by researchers at the University of Arizona, a combination of metagenomics, metaproteomics, and geochemical flux measurements were used to characterize microbial community structure and function at a thawing permafrost site in northern Sweden. A new species of archaea, Candidatus Methanoflorens stordalenmirensis, was found to dominate methanogen populations in the thawing active layer of permafrost. Using deep metagenomic sequencing, the team was able to assemble a nearly complete genome from this organism and identify the metabolic pathway for methanogenesis—consumption of hydrogen and CO2 and production of CH4. Measurements of CH4 flux at the thawing permafrost site and quantitative in situ detection of M. stordalenmirensis methanogensis proteins suggest that this organism may perform the majority of methane production at these sites, especially during thawing. The team also searched published metagenomic libraries collected from permafrost sites across the northern hemisphere and detected closely related methanogens at high numbers in the majority of sites. The dominance of a single organism in methane production is a surprising finding. Given evidence for the global distribution of this type methanogen in thawing permafrost sites, these results may have wide-ranging implications for understanding of climate change impacts.

Reference: Mondav, R., B. J. Woodcroft, E.-H. Kim, C. K. McCalley, S. B. Hodgkins, P. M. Crill, J. Chanton, G. B. Hurst, N. C. VerBerkmoes, S. R. Saleska, P. Hugenholtz, V. I. Rich, and G. W. Tyson. 2014. “Discovery of a Novel Methanogen Prevalent in Thawing Permafrost,” Nature Communications 5, DOI: 10.1038/ncomms4212. (Reference link)

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


January 16, 2014

Genome Watch Highlights DOE JGI Explorations of Microbial “Dark Matter.”

Adam Walker of the Wellcome Trust’s Sanger Institute has published an analysis of the Department of Energy’s Joint Genome Institute’s (DOE JGI) explorations of “microbial dark matter” metagenomics and single cell genomics. Four recent publications are highlighted, two directly from DOE JGI and two involving past and present collaborators. All used novel technologies to characterize microbes and microbial communities refractory to standard culture in the lab and involved in mission-relevant activities such as bioenergy and bioremediation. Most microbes cannot be readily grown in culture, so they are difficult to study with molecular and genetic approaches that require large amounts of starting genomic material. With the advent of single cell techniques, it is now possible to derive information about the genome of single isolated cells without a cultivation step. Furthermore, with the massive sequencing throughput available at DOE JGI, the DNA from bulk environmental samples can be characterized and a “fingerprint” of the sampled environment can be studied and compared, for example, both before and after perturbations. Even some whole microbial genomes can be assembled from the sequence fragments. These genomes, as noted by Walker, can provide new opportunities for biochemistries relevant to bioenergy, environmental remediation, and carbon and nutrient processing.

Reference: Walker, A. 2014. “Adding Genomic ‘Foilage’ to the Tree of Life,” Nature Reviews Microbiology 12, 78. DOI:10.1038/nrmicro3203. (Reference link)

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


January 02, 2014

Understanding Mineral Transport in Switchgrass for Enhanced Sustainability

A viable bioenergy industry will depend on the development of sustainably grown feedstocks, which are bioenergy crops that yield high amounts of biomass with minimal inputs of water, fertilizer, and other chemicals. The efficient acquisition and mobilization of mineral nutrients by feedstocks are key to their sustainability. Additionally, the platform used to produce biofuel from plant feedstocks (e.g., pyrolysis and thermochemical) is affected by biomass minerals (e.g., high levels of silicon in ash decreases conversion efficiency). In perennial bioenergy plants such switchgrass, certain minerals are recycled—mobilized from senescing tissues in the autumn to perennial crowns, rhizomes, and roots for winter storage, and remobilized and translocated to growing stem and leaf tissues in the spring. This seasonal storage and recycling of minerals depends on specific transporters for movement into and out of cells, a poorly understood process. With funding from the joint U.S. Department of Agriculture-Department of Energy Plant Feedstocks Genomics for Bioenergy activity, researchers combined bioinformatics and real-time qRT-PCR approaches to classify mineral transporter genes and gene families in switchgrass and to discern differential expression of these genes during the growing season. In this first molecular study of mineral transporter genes in switchgrass, 520 genes in 40 different families were identified and both tissue and temporal specificity of expression was observed. These results provide the foundation for correlating expression of specific genes with mineral translocation. This will facilitate functional characterization of genes critical for efficient nutrient transport and use and will lead to the development of sustainable, high-yielding switchgrass cultivars.

Reference: Palmer, N. A., A. J. Saathoff, B. M. Waters, T. Donze, T. M. Heng-Moss, P. Twigg, C. M. Tobias, and G. Sarath. 2014. “Global Changes in Mineral Transporters in Tetraploid Switchgrasses (Panicum virgatum L.),” Frontiers in Plant Science 4, DOI: 10.3389/fpls.2013.00549. (Reference link)

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