BER Research Highlights

Search Date: June 28, 2017

40 Records match the search term(s):


December 24, 2013

Discovery of Key Brachypodium Regulators May Help Improve Bioenergy Feedstocks

The wild grass Brachypodium distachyon is a model system for temperate grasses, including biofuel plants such as switchgrass and Miscanthus. Because of its relatively small, sequenced genome and a large and growing number of genetic and genomic resources, Brachypodium is useful for studying bioenergy-relevant traits such as grass cell wall characteristics and regulation of plant processes. One key type of regulator is microRNAs (miRNAs), short RNA moleculas involved in many processes such as development and stress response. miRNAs regulate expression of specific genes by pairing with target mRNAs. While many miRNAs have been identified in plants, little is known about these critical regulators in temperate grasses. With funding from the joint U.S. Department of Agriculture-Department of Energy Plant Feedstocks Genomics for Bioenergy program, researchers sequenced small RNAs from different tissues and environmental stress-treated Brachypodium plants and identified miRNAs using a computational approach. Both conserved, newly discovered miRNAs and nonconserved miRNAs not found in other plants were detected. Newly identified regulation of a flowering time gene was found, as well as miRNAs differentially expressed in various tissues. The results improve understanding of the role of miRNAs and their target-specific regulation in Brachypodium and related grasses, and may suggest strategies for bioenergy crop improvement.

Reference: Jeong, D.-H., S. A. Schmidt, L. A. Rymarquis, S. Park, M. Ganssmann, M. A. German, M. Accerbi, J. Zhai, N. Fahlgren, S. E. Fox, D. F. Garvin, T. C. Mockler, J. C. Carrington, B. C. Meyers, and P. J. Green. 2013. “Parallel Analysis of RNA Ends Enhances Global Investigation of microRNAs and Target RNAs of Brachypodium distachyon,” Genome Biology 14, R145. DOI: 10.1186/gb-2013-14-12-r145. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


December 03, 2013

New Metabolic Pathway Discovered in Methane-Consuming Bacteria

Methane is an essential component of the global carbon cycle and one of the most powerful greenhouse gases. Major uncertainties remain as to how global climate change will impact the release of carbon stored in ecosystems, particularly in terms of the balance between CO2 and methane entering the atmosphere. Recent technological advances in natural gas extraction from the deep subsurface also have vastly increased the supply of methane for energy production and potentially as an alternate carbon source for synthesis of fuels and other value-added chemicals. These developments have focused increased attention on biological processes that involve methane. For example, aerobic methane-consuming bacteria (methanotrophs) perform key ecosystem processes that affect methane release and represent a potential biological platform for methane-based industrial biocatalysis. In a new study, U.S. Department of Energy investigators at the University of Washington used a multifaceted systems biology approach to examine methane utilization by the methanotrophic bacterium Methylomicrobium alcaliphilum. Their results reveal a previously unknown metabolic pathway in which methane uptake is tightly coupled with glycolytic carbon metabolism, resulting in a novel form of fermentation-based methanotrophy. Under oxygen-limited conditions, this pathway produces acetate and other organic compounds as endproducts rather than CO2, which had been thought to be the sole product of methanotrophic metabolism. This discovery significantly alters our understanding of the role of methanotrophs in environmental carbon cycle processes and presents new opportunities for metabolic engineering of these organisms as platforms for biological conversion of methane to advanced biofuels and other products.

Reference: Kalyuzhnaya, M. G., S. Yang, O. N. Rozova, N. E. Smalley, J. Clubb, A. Lamb, G. A. Nagana Gowda, D. Raftery, Y. Fu, F. Bringel, S. Vuilleumier, D. A. C. Beck, Y. A. Trotsenko, V. N. Khmelenina,  and M. E. Lidstrom. 2013. “Highly Efficient Methane Biocatalysis Revealed in a Methanotrophic Bacterium,” Nature Communications 4, 2785. DOI: 10.1038/ncomms3785. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


November 26, 2013

New Method for Identifying Genetic Regulatory Networks in Poplar

Wood is an important renewable material for bioenergy and other industrial products, but its formation, a complex process regulated at many levels, is poorly understood. Such processes often involve interactions between regulatory genes known as transcription factors (TFs) and their direct DNA targets. These TF-DNA interactions constitute a regulatory hierarchy. To begin to understand these systems in poplar trees, researchers at North Carolina State University funded by the Department of Energy’s Genomic Science Program developed a robust, high-throughput pipeline to study the hierarchy of genetic regulation of wood formation using tissue-specific single cells known as protoplasts. A new method for isolating protoplasts from the wood-forming stem differentiating xylem (SDX) tissues of Populus trichocarpa was developed and used to study the expression of a specific poplar TF affecting wood formation. By integrating this novel system with computational approaches, a hierarchical layer of genes was inferred that was then functionally validated in SDX. This approach will be particularly useful in studying complex processes in plant species that lack mutants and a stable transformation system. It also can be used to improve forest tree productivity with more precise genetic approaches.

Reference: Lin, Y.-C., W. Li, Y.-H. Sun, S. Kumari, H. Wei, Q. Li, S. Tunlaya-Anukit, R. R. Sederoff, and V. L. Chiang VL. 2013. “SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa,” Plant Cell 25, 4324-41. DOI: 10.1105/tpc.113.117697. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2013

Predictive Modeling of Microbial Partnerships

Many biogeochemical processes involved in the global carbon cycle are not performed by individual organisms, but rather by collaborative partnerships between two or more microbes. Referred to as “syntrophy,” these partnerships often involve consumption of carbon compounds that cannot be used by any individual organism, but yield sufficient energy for growth when paired organisms couple their metabolic capabilities. These associations are critical to carbon decomposition processes and are particularly important in oxygen-limited environments such as wetlands, sediments, and subsurface aquifers. In a new study funded by the Department of Energy’s Genomic Science Program, a team of researchers has developed a novel genome-scale, multi-omics based modeling approach to investigate the systems biology of syntrophic microbial partnerships. The team focused on Geobacter metallireducens and Geobacter sulfurreducens, two microbes that are capable of syntrophically consuming ethanol and formate (two major products of carbon decomposition). By examining the flow of metabolites within and between the partners, and coupling this information to genome-wide analysis of shifts in gene expression, a new model was developed that enabled the team to test the hypothesis that direct transfer of electrons between the two species permits this mode of metabolism. The study’s results shed new light on a poorly understood aspect of carbon cycle processes. They also represent a significant advance in our ability to extend genome scale systems biology modeling approaches to multispecies microbial consortia. This publication was selected as a research highlight in the January 2014 issue of the journal Nature Reviews Microbiology.

Reference: Nagarajan, H., M. Embree, A.-E. Rotaru, P. M. Shrestha, A. M. Feist, B. Ø. Palsson, D. R. Lovley, and K. Zengler. 2013. “Characterization and Modelling of Interspecies Electron Transfer Mechanisms and Microbial Community Dynamics of a Syntrophic Association,” Nature Communications 4, 2809. DOI:10.1038/ncomms3809. (Reference link)

Research Highlight: Molloy, S. 2013. “Disentangling Syntrophy,” Nature Reviews Microbiology 12, 7. DOI:10.1038/nrmicro3194. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 29, 2013

Understanding Thermal Pretreatment of Lignocellulosic Biomass

Plants contain substantial amounts of cellulose, hemicellulose, and lignins. Much research is being devoted to developing ways to convert these materials (commonly called ‘lignocellulose’) into fuels. The first step, breaking down the biomass into these three constituents, is particularly difficult to study due to the complexity of ways in which they are entangled in biomass. A new approach has been developed that combines x-ray and neutron beam studies with advanced computational modeling to visualize the breakdown of biomass in wood chips from aspen trees. The research, led by scientists at Oak Ridge National Laboratory, studied the wood chips as they were exposed to a variety of treatments, including steam explosion pretreatment, dilute acid pretreatment, and ammonia fiber expansion. The experiments visualized the structural changes in the biomass during the processing, showing for example how porosity of the cell walls and extent of hydration of the different biomass components changes as treatments proceed. The key mechanisms responsible for structural changes are the dehydration of cellulose fibers and lignin-hemicellulose phase separation. These fundamental insights will guide the development of more efficient pretreatments. The research was featured on the January 2014 cover of Green Chemistry.

Reference: Langan, P., L. Petridis, H. M. O'Neill, S. Venkatesh Pingali, M. Foston, Y. Nishiyama, R. Schulz, B. Lindner, B. L. Hanson, S. Harton, W. T. Heller, V. Urban, B. R. Evans, S. Gnanakaran, A. J. Ragauskas, J. C. Smith, and B. H. Davison. 2014. Common Processes Drive the Thermochemical Pretreatment of Lignocellulosic Biomass,Green Chemistry 16, 63–68. DOI:10.1039/C3GC41962B. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 27, 2013

Faster, Bigger, Stronger: Genome Database Improvements

The Department of Energy’s Joint Genome Institute (DOE JGI) maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of partially assembled genome reads from microbial communities (metagenomes). Both have recently been upgraded to address the increase in genome sequences and provide more options for users. IMG was introduced in 2005. Since the last published report in 2012, both systems have grown and improved. The improvements for both systems are described in a pair of reports in the Jan. 1, 2014, issue of Nucleic Acids Research.

The late 2013 version of IMG contains more than 16,000 genome datasets with more than 42 million protein-coding genes. Most (nearly 12,000) are bacterial, archaeal, and eukaryotic genomes. The number of genomes is more than three times the number two years ago. IMG also includes thousands of viral genomes, plasmids that did not come from a specific microbial genome sequencing project, and hundreds of genome fragments. Also in late 2013, IMG/M contained 3,328 metagenome datasets from 460 metagenome studies, with more than 19.5 billion protein coding genes.

Both systems have enhanced analysis tools for publicly available datasets. The latest version of IMG includes tools for recording and analyzing single cell genomes, RNA sequencing data, and gene clusters coding for synthesis of complex organic molecules (biosynthetic clusters).
Both systems are continually being improved to keep up with recent advances in genomics. Future advances will include incorporating pangenomic data (genes that make up the core genes common to all individuals in a species as well as variant genes to enable some individuals to adapt to different environments) and analysis tools for IMG and metaproteomics datasets (protein samples collected from environmental sources) in IMG/M.

References: Markowitz, V. M., et al. 2013. “IMG 4 Version of the Integrated Microbial Genomes Comparative Analysis System,” Nucleic Acids Research 42(D1), D560–67. DOI:10.1093/nar/gkt963. (Reference link)

Markowitz, V. M., et al. 2013. “IMG/M 4 Version of the Integrated Metagenome Comparative Analysis System,” Nucleic Acids Research 42 (D1), D568–73. DOI:10.1093/nar/gkt919. (Reference link)

Related Links:
IMG website: https://img.jgi.doe.gov/
IMG/M website: https://img.jgi.doe.gov/cgi-bin/m/main.cgi

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

Division: SC-23.2 Biological Systems Science Division, BER


October 18, 2013

Recoding a Bacterial Genome Allows Biosynthesis of Proteins with New Functions

Engineered bacteria are used in biotechnology for producing enzymes and other proteins as well as the biological molecules they synthesize. However, the spectrum of possible proteins that can be biotechnologically produced is limited by the 20 amino acids in the genetic code. One way to expand the possibilities of potential engineered protein functions is to add more amino acids to the repertoire that can be incorporated into proteins. In a recent article published in Science, researchers at Yale and Harvard Universities altered the genome of the model bacterium Escherichia coli so that one of the three stop codons (three-letter words that constitute the genetic code) is no longer used. In this recoded E. coli strain, the freed stop codon (UAG) could now be used to incorporate new amino acids by providing the necessary machinery (a modified tRNA that recognizes UAG and a special aminoacyl–tRNA synthetase, the enzyme that loads amino acids onto the tRNA). With these tools, the researchers showed that they can incorporate novel amino acids into a selected protein without affecting the rest of the bacterial proteins, while maintaining a normal cellular physiology. In addition, the recoded cells are less susceptible to viral infection, and the risk of transferring altered DNA to other organisms is minimized because the normal protein synthesis machinery will not work properly with the recoded genes from the recoded strain. This work has tremendous implications for engineering new organisms that can be used for producing novel proteins that perform new functions needed in DOE-relevant processes such as biofuels production.    

Reference: Lajoie, M. J., A. J. Rovner, D. B. Goodman, H.-R. Aerni, A. D. Haimovich, G. Kuznetsov, J. A. Mercer, H. H. Wang, P. A. Carr, J. A. Mosberg, N. Rohland, P. G. Schultz, J. M. Jacobson, J. Rinehart, G. M. Church, and F. J. Isaacs. 2013. “Genomically Recoded Organisms Expand Biological Functions,” Science 342, 357-60. DOI:10.1126/science.1241459. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


October 16, 2013

Root Microbial Populations May Enhance Tree Productivity

Bacterial and fungal communities inhabiting the soil around a plant’s roots (the rhizosphere) as well as within the roots (the endosphere) can signifi­cantly benefit the plant’s overall health and productivity, especially in long-lived perennials such as trees. However, the molecular mechanisms that regulate these very complex interactions between plants and microbes are difficult to study and poorly understood. To gain insight into these interactions, researchers at Oak Ridge National Laboratory conducted a detailed study of the rhizosphere and endosphere “microbiomes” of the Eastern Cottonwood tree (Populus deltoides), a promising bioenergy feedstock candidate, from two natural settings in North Carolina and Tennessee and over two seasons. While much of the observed variation is still to be explained, the group did find significant differences in microbial communities between the two locations and between the fall and spring seasons. Additionally, they found that microbes within roots were very different from those just outside the roots, indicating that selection for specific, rather than random, microbes to colonize plant roots may occur. The results suggest that these beneficial microbes might be manipulated to enhance plant growth and productivity as well as increase resistance and adaptability to environmental stresses.

Reference: Shakya, M., N. Gottel, H. Castro, Z. K. Yang, L. Gunter, J. Labbé, W. Muchero, G. Bonito, R. Vilgalys, G. Tuskan, M. Podar, and C. W. Schadt. 2013 “A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees,” PLoS ONE 8(10), e76382. DOI:10.1371/journal.pone.0076382. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 26, 2013

Discovery of a New Way that Bacteria Regulate Their Genes

The amino acid composition of proteins is encoded in DNA in the form of three-letter words (codons). Each amino acid can be coded for by more than one codon and, for a given amino acid, different organisms use one codon more frequently than the alternatives. This codon usage preference, particularly near the start of genes, has a strong influence in gene expression, but the causes and precise effects of such codon preference are unclear. Scientists at Harvard University analyzed thousands of synthetic gene constructs containing either frequent or infrequent codons toward their start. Using next-generation sequencing to determine gene expression and fluorescent cell sorting to assess protein abundance, the investigators concluded that the presence of infrequent codons near the start of genes dramatically increases protein expression. Furthermore, using computational methods to predict RNA structure, the authors demonstrated that the three-letter sequence of infrequent codons reduces the formation of secondary structures in the messenger RNA (mRNA) molecule involved in the protein synthesis process, facilitating the translation of the DNA sequence of genes into proteins. This mRNA structural modification is in large part responsible for the observed increase in expression of genes with infrequent codons. These results have important implications for the design of synthetic genes that can be more efficiently expressed in engineered organisms for the production of new biomolecules such as biofuels.      

Reference: Goodman, D. B., G. M. Church, and S. Kosuri. 2013. “Causes and Effects of N-Terminal Codon Bias in Bacterial Genes,” Science 342(6157), 475 €"79. DOI:10.1126/science.1241934. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 19, 2013

Diverse Microbial Community Found on Sea Squirt Coat

The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology. Ciona is the closest invertebrate relative to the chordate (backboned) lineage to which humans and other primates belong. Little is known about its associated bacterial community in spite of growing evidence that microbes play key roles in organisms from plants to humans. New research supported by the Department of Energy’s Joint Genome Institute (DOE JGI) combined several technologies to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The Ciona tunic is a complex cellulose and mucopolysaccharide envelope; the sequencing data demonstrates that the bacterial community structure on Ciona’s tunic differs from that of bacteria in the surrounding seawater. The observed tunic bacterial consortium contains a shared community of less than 10 abundant bacterial phylotypes across three individuals. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and bacterial enzymes that could digest or alter celluloses. Leveraging the original sequencing work of the C. intestinalis by DOE JGI, this work was supported by an interagency program, the International Collaborative Biodiversity Group program administered by the National Institutes of Health’s Fogarty International Center, in which multiple agencies participated.

Reference: Blasiak, L. C., S. H. Zinder, D. H. Buckley, and R. T. Hill. 2014. “Bacterial Diversity Associated with the Tunic of the Model Chordate Ciona intestinalis,” The ISME Journal 8, 309–20. DOI:10.1038/ismej.2013.156. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


September 09, 2013

Tropical Soil Bacterium Frees Plant Sugars for Biofuels

The lignocellulose component of plants could be a sustainable alternative fuel if it could be easily degraded and transformed for use in biofuels. In a recent study, a team of scientists—from the University of Massachusetts, Amherst; U.S. Department of Energy (DOE) Joint BioEnergy Institute; and DOE Environmental Molecular Sciences Laboratory (EMSL)—used proteomic, transcriptomic, and metabolomic approaches at EMSL to examine the ability of Enterobacter lignolyticus SCF1 to degrade lignocellulose. SCF1 is found in tropical forest soils and is known to rapidly decompose leaf litter. This study demonstrated that this bacterium can degrade the lignin portion of plant cellulosic biomass by both assimilatory and dissimilatory pathways. By breaking down the lignin, SCF1 is able to free the cellulosic sugars found in plant cells, thereby making those sugars available for use in biofuels. These research findings are the first to demonstrate that an anaerobic soil bacterium can use both assimilatory and dissimilatory pathways to reduce lignocellulose, as well as demonstrating the importance of a multi-omics, holistic approach to studying biochemical processes in microbes.

Reference: DeAngelis, K. M., D. Sharma, R. Varney, B. Simmons, N. G. Isern, L. M. Markillie, C. Nicora, A. D. Norbeck, R. C. Taylor, J. T. Aldrich, and E. W. Robinson. 2013. “Evidence Supporting Dissimilatory and Assimilatory Lignin Degradation in Enterobacter lignolyticus SCF1,” Frontiers in Microbiology 10.3389/fmicb.2013.00280. (Reference link)
Related link

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

Division: SC-23.1 Climate and Environmental Sciences Division, BER,SC-23.2 Biological Systems Science Division, BER


September 04, 2013

Candidate Genes Involved in Lignin Degradation Found in Wood-Boring Beetle’s Mid Gut

The Asian longhorned beetle (Anoplophora glabripennis ) is an invasive species first discovered in the United States in 1996. It attacks both healthy and stressed hardwood trees, including the bioenergy candidate feedstocks poplar and willow, and has no natural enemies in this environment. The microbial community in the beetle’s midgut is capable of breaking down the lignin, cellulose, and hemicellulose in the trees to acquire needed nutrients, but little is known about the processes involved. To learn more about how microbial communities in the guts of such wood-boring insects break down these woody tissues, a team including researchers from the Department of Energy’s (DOE) Joint Genome Institute (JGI) sequenced, assembled, and analyzed the Asian longhorned beetle’s midgut metagenome.

In the study published in Plos ONE , the team compared the metagenome assembly from the wood beetles to annotated assemblies in DOE JGI’s IMG/M database. These datasets came from microbial communities associated with herbivores that feed to plant tissues, insects that feed on specific plant tissues, and insects (e.g., termites) that feed on woody tissues. The findings revealed that the beetle’s midgut contained a community dominated by aerobes, which research­ers expected, noting that large-scale lignin-degrading reactions require oxygen and have only been demonstrated in aerobic environments. They identified several genera of fungi and bacteria in the assembly; many of the microbes have been associated with break down of lignocellulose, hemicellulose, and other similar compounds. The metagenome assembly also led to the identifi­ca­tion of candidate genes for a variety of functions, including lignin-degrading enzymes, cellu­lases, xylose utilization, and fermentation as well as for nitrogen and nutrient acquisition.

This study is the first large-scale functional metagenomic analysis of the midgut micro­bial community of a beetle with known lignin-degrading capabilities. Lignin is one of the most recalcitrant components of plant biomass. The candidate genes identified from by the functional profile could lead to novel enzymes that might either be useful for industrial biofuels applications or else be used to control this invasive insect.

Reference: Scully, E. D., et al. 2013. “Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle,” PLoS ONE 8(9), e73827. DOI: 10.1371/journal.pone.0073827. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742, John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



The Asian longhorn beetle is an invasive pest that can break down lignin in host deciduous trees. (Wikimedia Commons)



September 02, 2013

POPSEQ for Plant Genome Assembly: New Approach Allows Researchers to Work on Many Species Regardless of Sequence Resources

One of the challenges in assembling plant genome “contigs,” fragments of the entire genome that are identified by the assembly algorithms, is that they are not easily linked together or even placed in their proper order. In an effort to mitigate this problem, researchers with the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) teamed with other researchers to develop another approach for assembling contigs.

In a study published in The Plant Journal, the team reports on the results of testing the approach they call POPSEQ with the barley genome. The plant was selected for DOE JGI’s 2011 Community Sequencing Program portfolio in part for its potential as a bioenergy feedstock crop. Grown on four million acres in the United States, the crop could be used to produce cellulosic ethanol from the straw. More than 80 percent of the 5.1 billion-base genome is composed of repeats, adding to its complexity.

Using POPSEQ, researchers assembled the barley genome while testing a number of variables. For example, they used datasets obtained from different mapping populations, or, in another case, assembled the genome based solely on short reads. The team reported that the results from these tests were comparable with the assembly previously produced by the International Barley Sequencing Consortium. “By comparison,” they wrote, “POPSEQ is inexpensive, rapid, and conceptually simple, the most time-consuming step being the construction of a mapping population…The method is independent of the need for any prior sequence resources,” and this proof of principle demonstrates that POPSEQ can be effectively applied to many species.

Reference: Mascher, M., et al. 2013. “Anchoring and Ordering NGS Contig Assemblies by Population Sequencing (POPSEQ),” The Plant Journal, DOI: 10.1111/tpj.12319. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742, John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Image: Cultivated barley is the fourth most abundant crop in the world and a model for plant genetics research.
(Image courtesy of freefotouk, Flickr CC BY 2.0)



August 15, 2013

New Gene Discovery Clarifies Lignin Biosynthetic Pathway

Lignin is integral to plant cell wall strength and function. It is also 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 the production of biofuels. Lignin’s irregular polymeric structure has made it difficult to establish a clear biosynthetic pathway for its formation, making it a challenging target for genetic engineering of plants for enhanced bioprocessing of plant biomass. Recently, scientists at the U.S. Department of Energy’s Great Lakes Bioenergy Research Center (GLBRC) identified a new enzyme in the biosynthetic pathway of lignin monomers. The enzyme caffeoyl shikimate esterase (CSE) was found to catalyze a previously unidentified step in the biosynthesis of lignin monomers. Analysis of plant lines with a mutation in CSE demonstrated altered accumulation of lignin precursors consistent with its hypothesized activity and position in the lignin biosynthetic pathway. This enzymatic step is important, leading to a lignin that is less inhibitory to deconstruction than wild type lignin. In fact, one CSE mutant showed significantly more saccharification (78%) than wild type (18%), though plant growth was stunted. The discovery of this previously unknown enzymatic step highlights the success of genomics, global gene expression studies, data sharing, and bioinformatics, because the gene was found by searching publicly available gene expression databases for genes of unknown function that are co-expressed with other known lignin biosynthesis genes. This more complete knowledge of the lignin biosynthesis pathway will enable more intelligent engineering of lignin biosynthesis that may lead to more efficient bioprocessing without negatively impacting plant growth and viability. The GLBRC research was carried out in collaboration with an international team of scientists from Belgium and the United Kingdom.

Reference: Vanholme, R., I. Cesarino, K. Rataj, Y. Xiao, L. Sundin, G. Goeminne, H. Kim, J. Cross, K. Morreel, P. Araujo, L. Welsh, J. Haustraete, C. McClellan, B. Vanholme, J. Ralph, G. G. Simpson, C. Halpin, and W. Boerjan. 2013. “Caffeoyl Shikimate Esterase (CSE) is an Enzyme in the Lignin Biosynthetic Pathway,” Science 341, 1103–06. DOI: 10.1126/science.1241602. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 07, 2013

Novel Bioengineering Technique for Genome-Scale Tuning of Gene Expression

Introduction of new genes encoding desired functional attributes has long been a central tool for metabolic engineering and synthetic biodesign of microorganisms. However, difficulties in accurately predicting the expression levels of these genes in their new hosts significantly slow the design cycle and hinder progress. This is particularly problematic in synthetic biology, where large genetic constructs containing multiple genes are often introduced. Now researchers present a novel technique to more accurately predict gene expression levels in engineered biosystems by combining recent advances in DNA synthesis with novel, multiplexed methods for measuring DNA, RNA, and protein levels simultaneously using next-generation sequencing. This new technique allowed the team to simultaneously measure transcription and translation rates of thousands of synthetic regulatory elements introduced into the model microbe Escherichia coli . The resulting dataset was then used to model gene and protein expression levels under various sets of regulatory elements and “compose” a designed regulatory strategy that enables accurate prediction of expression levels of introduced genetic elements. This new technique has the potential to allow much more sophisticated forward design of genetic engineering strategies to improve production of biofuels and other bioproducts.

Reference: Kosuri, S. D. B. Goodman, G. Cambray, V. K. Mutalik, Y. Gao, A. P. Arkin, D. Endy, and G. M. Church. 2013. “Composability of Regulatory Sequences Controlling Transcription and Translation in Escherichia coli ,” Proceedings of the National Academy of Sciences USA 110 , 14024–29. DOI: 10.1073/pnas.1301301110. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 05, 2013

Microbes from Phyla Chloroflexi Provide Clues to Carbon Cycling, Respiration in Sediments

Through metagenomics, researchers sequenced 86 organisms from the phylum Chloroflexi, representing 15 distinct lineages, to discover the secrets of microbial life within terrestrial aquifer sediment deposits.

These Chloroflexi microbes were found to have metabolic processes involved in plant biomass degradation, which could be useful for biofuels production, as well as a better understanding of the subsurface nitrogen and carbon cycles. Microorganisms in aquifer sediments are responsible for subterranean carbon turnover and the degradation of organic contaminants. Consequently, these microorganisms can heavily impact the quality of underground drinking water. In earlier studies, it was determined that Chloroflexi represent a significant amount of the microbial population in sediments. However, these microbes are poorly understood, as only six of about 30 Chloroflexi classes have been sequenced. For this reason, a team of researchers including scientists from the Department of Energy’s Joint Genome Institute (DOE JGI) conducted a study on the microbial composition of these aquifer sediments to gain a broader knowledge of the metabolic characteristics of Chloroflexi microbes.

The researchers were able to reconstruct three near-complete Chloroflexi genomes from the metagenomic data collected at the Integrated Field-Scale Subsurface Research Challenge Site in Colorado as part of a DOE JGI Community Sequencing Program project led by Jill Banfield of the University of California, Berkeley. Metabolic analyses revealed that Chloroflexi can break down plant mass, influence subsurface carbon and nitrogen cycles, and adapt to changing oxygen levels. These traits, the researchers noted, were likely to apply to Chloroflexi in other sediment environments, making these microbes good candidates for mining useful enzymes and pathways for DOE missions of bioenergy and carbon processing as well as for biodegradation.

Reference: Hug, L. A., et al. 2013. “Community Genomic Analyses Constrain the Distribution of Metabolic Traits Across the Chloroflexi Phylum and Indicate Roles in Sediment Carbon Cycling,” Microbiome 1(22), DOI:10.1186/2049-2618-1-22. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 05, 2013

Using Mass Spectrometry to Localize Lipid Metabolites in Camelina Seeds

Camelina sativa is a nonfood oilseed crop that, because of relatively low production costs and potential for use in a number of industrial applications, shows promise as a bioenergy feedstock. Additionally, the relative ease with which the plant can be genetically modified offers potential for altering the seed oil composition through engineering of the lipid and fatty acid metabolic pathways. To do this, however, it is important to understand how these pathways are regulated in different seed tissues. With funding from the Department of Energy’s Office of Science Genomic Science Program, researchers from the University of North Texas used mass spectrometry imaging techniques to show that the distribution of various lipid-related metabolites and precursors are specific to certain distinct tissues within the seed embryo. This high-resolution metabolite mapping in Camelina seeds can be used to reveal new insights into tissue-based variation and illustrates the importance of considering spatial heterogeneity when designing metabolic engineering strategies for manipulating seed lipid composition. This work will facilitate more refined and accurate targeting when engineering plants for optimal seed oil composition.
 
Reference: Horn, P. J., J. E. Silva, D. Anderson, J. Fuchs, L. Borisjuk, T. J. Nazarenus, V. Shulaev, E. B. Cahoon, and K. D. Chapman. 2013. “Imaging Heterogeneity of Membrane and Storage Lipids in Transgenic Camelina Sativa Seeds with Altered Fatty Acid Profiles,” The Plant Journal 76(1), 138 €"50. DOI:10.1111/tpj.12278. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


August 01, 2013

Hope for Reestablishing Microbial Populations in the Gulf of Mexico

Researchers used metatranscriptomic analyses to compare the microbial populations in the Gulf of Mexico before and after the Deepwater Horizon oil spill to learn more about the impact of   petroleum being spilled into the waters. Though the oil spill reduced the diversity of the microbial communities in the Gulf of Mexico, some microbial populations remain unchanged suggesting that they may be important in reestablishing the original microbial community.
One of the first studies published in the aftermath of the Deepwater Horizon oil spill involved the Department of Energy’s Joint Genome Institute (DOE JGI) researchers and confirmed that microbial communities did play a role in dispersing the hydrocarbons from the waters. A second study released in 2012 tracked the populations of several microbial species in the Gulf of Mexico as they dominated in the waters at various time points to remove different fractions of the oil.

DOE JGI associated researchers recently carried out a new study of the microbial populations in the Gulf of Mexico, this time focusing on the expressed genetic information of an ecosystem, its metatranscriptomes. They examined species in the bathypelagic zone at depths of 1,000 to 4,000 meters underwater where no sunlight penetrates. The analysis of roughly 66 million transcripts sequenced for the study attributes 40% of the reads to just six genomes from Gammaproteobacteria known to be capable of breaking down methane and petroleum. The findings confirm that the diversity of microbes and their functional roles in the waters have decreased since the oil spill. However, the team also found that some microbial populations did not appear to be affected by the events that took place three years ago, as their numbers remain similar both before and after 2010.

“Despite the enormous bloom of hydrocarbon-degrading Gammaproteobacteria that increased bacterial cell counts by two orders of magnitude, members of the natural microbial community persisted at their pre-bloom activity levels and may be important in reestablishing the original microbial community,” the researchers concluded.

Reference: Rivers A.R., et al. 2013. “Transcriptional Response of Bathypelagic Marine Bacterioplankton to the Deepwater Horizon Oil Spill,” The ISME Journal 7, 2315-29. DOI:10.1038/ismej.2013.129. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER



Comparing the expressed genetic information from microbial communities before and after the 2010 Deepwater Horizon spill indicated that while the overall population diversity has changed, some microbes were unaffected. (Image courtesy of Green Fire Productions, Flickr CC BY 2.0)



July 28, 2013

New Understanding of Microbial Community Processes Improves Carbon Cycle Models

Current Earth system models (ESMs) draw on soil carbon cycle models that use relatively simple representations of the biogeochemical processes performed by microbial communities. Now, investigators at the University of California, Irvine, have developed a new module for the Community Land Model (CLM) that attempts to more accurately represent the distribution of soil microbial communities and their functional processes related to carbon degradation. Projections of climate change impacts on soil carbon stocks using this module showed improved agreement with results observed during experimental studies. Developing improved models of microbial processes will generate more accurate projections of soil carbon feedbacks on climate change and reduce a source of uncertainty in current ESMs.

Reference: W. R.Wieder, G. B. Bonan, and S. D. Allison. 2013. “Global Soil Carbon Projections Are Improved by Modeling Microbial Processes,” Nature Climate Change. DOI: 10.1038/NCLIMATE1951. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 27, 2013

Higher Yields of Advanced Biofuels from Genetically Engineered Yeast

The development of renewable substitutes for fuels and chemicals supplied by petroleum is an important aspect of achieving energy security. Currently, the United States annually produces more than 10 billion gallons of the biofuel ethanol from microbial fermentation of corn sugars using yeast. As this industry has matured, it has become clear that ethanol is not an ideal gasoline replacement due to its low-energy density, handling challenges, and limited compatibility with the current transportation fleet. Focus therefore has shifted to the production of advanced biofuels, designed to be “drop-in” fuels, having the same properties as gasoline, diesel, or jet fuel. Researchers at the Joint BioEnergy Institute (JBEI) recently achieved the highest ever reported yields of drop-in fuel precursors in yeast. Diesel fuels are composed mainly of long-chain hydrocarbon esters, similar to the fatty acids produced by yeast and other microorganisms for construction of their cell membranes. Overproduction of fatty acids in yeast is no easy task as elaborate regulatory and feedback systems exist to prevent excessive accumulation of these building blocks. To overcome this hurdle, the JBEI researchers replaced the highly-regulated native promoters for fatty acid production machinery with new high-intensity promoters. These promoters are effectively always “on,” directing the cell to make more fatty acid assembly machinery. The researchers also engineered cellular machinery to reroute fatty acids from cell membrane manufacture to free fatty acids that can be transformed through industrial processes to drop-in biofuels. These engineering changes led to an over 500-fold increase in production of free fatty acids when compared to the native strain. Strains also were engineered to produce drop-in biofuels directly, rerouting fatty acids into fatty alcohols and fatty acid ethyl esters that can be used in diesel engines. With these increased yields of fatty alcohols and fatty acid ethyl esters, this work represents a major advance toward production of next generation drop-in biofuels.

Reference: Runguphan, W., and J. D. Keasling. 2013. “Metabolic Engineering of Sacchromyces cerevisiae for Production of Fatty Acid-Derived Biofuels and Chemicals,” Metabolic Engineering 21, 103 €"13. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 23, 2013

Physcomitrella Moss Genome Expected to Help In Understanding Potential Climate Change

An international team of scientists has re-annotated the genome of Physcomitrella patens, a moss sequenced by the Department of Energy’s Joint Genome Institute (DOE JGI) that contains about 10,000 more genes than humans. It is widely believed that the information contained in the P. patens genome can help researchers improve crop yields, disease and insect resistance, drought tolerance, and more efficient biofuel production. Researchers were able to provide a functional analysis of many of its previously unknown genes, adding to its value as a model plant and for interpreting other sequenced plant genomes.

P. patens has long been the experimental moss of choice for researchers around the world and was first sequenced by DOE JGI in 2007. P. patens can be more efficiently studied than other plants, mainly due to its accelerated lifecycle, hence short generation time. An international team of researchers from Germany, Belgium, and Japan has worked with the genes of what DOE JGI refers to as a “flagship genome,” a term meaning that sustained and significant computational and experimental resources are directed to this organism. By using the sequencing information from DOE JGI, the team was able to suggest potential functions for 58% of all the genes identified, a large increase over the 41% in the earlier publication.

“One of our intriguing findings is that 13% of the Physcomitrella genes have no clear relatives in any other sequenced organism so far. Analyzing these orphan genes more deeply will reveal the hidden treasures of the moss genome,” said University of Freiburg Chair of Plant Biotechnology Ralf Reski, a senior coordinator on the study. The study’s findings were made available at www.cosmoss.org, as well as further information regarding moss genomes through DOE JGI’s Phytozome.

Reference: Zimmer, A. D., et al. 2013. “Reannotation and Extended Community Resources for the Genome of the Non-Seed Plant Physcomitrella patens Provide Insights into the Evolution of Plant Gene Structures and Functions,”BMC Genomics 14, DOI:10.1186/1471-2164-14-498. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 14, 2013

Illuminating Biology’s Dark Matter

In cosmology, dark matter is said to account for the majority of mass in the universe. Its presence, however, is inferred by indirect effects rather than detected through telescopes. The biological equivalent is “microbial dark matter,” a largely unexplored realm of microbial life on Earth that can profoundly influence key environmental processes such as plant growth, nutrient cycles, the global carbon cycle, and climate processes. An international collaboration, led by the U.S. Department of Energy’s Joint Genome Institute (DOE JGI) where the sequencing of genomes isolated from single cells was carried out, targeted uncultivated microbial cells from nine diverse habitats, derived from 28 major, but previously uncharted branches of the tree of life. The results fall into three main areas: 1) metabolic features previously only seen in bacteria are also found in Archaea, such as an enzyme used by bacteria to “thin out” their protective cell wall so that the cell can expand during cell division ; 2) the ability to correctly assign d ata from 340 million DNA fragments from other habitats to the proper lineage, linking these fragments to organisms and particular ecosystems, as well as providing insights into possible functional roles; and 3) the ability to more accurately resolve microbial taxonomical relationships within and between microbial phyla, which is critical to predict ecological niches and capabilities. The new results will enable scientists to better predict metabolic properties and other useful traits of different microbial groups. The Nature publication builds upon a DOE JGI pilot project, the Genomic Encyclopedia of Bacteria and Archaea (GEBA: http://www.jgi.doe.gov/programs/GEBA/).

Reference: Rinke, C., P. Schwientek, A. Sczyrba, N. N. Ivanova, I. J. Anderson, J.-F. Cheng, A. Darling, S. Malfatti, B. K. Swan, E. A. Gies, J. A. Dodsworth, B. P. Hedlund, G. Tsiamis, S. M. Sievert, W.-T. Liu, J. A. Eisen, S. Hallam, N. C. Kyrpides, R. Stepanauskas, E. M. Rubin, P. Hugenholtz, and T. Woyke. 2013. “Insights into the Phylogeny and Coding Potential of Microbial Dark Matter,” Nature 499 , 431–37. DOI: 10.1038/nature12352. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 12, 2013

Unraveling Plant-Microbe Communication

The soil environment contains a complex of microbial communities living in close association with plants, both outside the root (rhizosphere) and within (endosphere). These interactions between plants and microbes can significantly influence plant growth and development and, in the case of beneficial microorganisms, increase plant health and yield. These complex interactions involve cell-to-cell communication, but very little is known about how these signals are triggered and regulated. To better understand the dynamics of these systems, scientists at Oak Ridge National Laboratory have undertaken an extensive survey of the “microbiome” of the woody perennial Populus , a tree that has intimate associations with many types of beneficial fungi and bacteria and is a potential biofuel feedstock for cellulosic ethanol production. Focusing on a specific type of sensing molecule known as acyl-homoserine lactone (AHL), the researchers screened 129 bacterial isolates from P. deltoides (Eastern cottonwood) and found that 40% were AHL positive. Furthermore, they found a subgroup of AHL-controlled regulators that respond to unknown plant-derived signals rather than bacterial AHLs. The results indicate that the microbiota that comprises the Populus root zone has substantial capacity for cell-to-cell communication, furthering our understanding of the role these microbial signaling molecules play in the plant’s biology.

Reference: Schaefer, A. L., C. R. Lappala, R. P. Morlen, D. A. Pelletier, T.-Y. S. Lu, P. K. Lankford, C. S. Harwood, and E. P. Greenberg. 2013. “LuxR- and LuxI-type Quorum Sensing Circuits Are Prevalent in Members of the Populus deltoides Microbiome,” Applied and Environmental Microbiology 79 , 5745–52. DOI: 10.1128/AEM.01417-13. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


July 02, 2013

Lipid Droplet-Associated Proteins in Plant Tissues

Lipid droplets (“oil bodies”) are found within the cells of all multicellular organisms, and they provide storage of high-energy carbon reserves. These subcellular organelles are well characterized in seeds, but they also occur in nearly all plant cells, although little is known about the proteins associated with nonseed lipid droplets. To elucidate the mechanisms involved in lipid droplet metabolism in nonseed plant tissues, researchers at the University of North Texas in collaboration with the U.S. Department of Energy’s Great Lakes Bioenergy Research Center used a multi-pronged approach to investigate lipid-associated proteins in the oil-rich tissues of avocado, a fruit widely used as a model system to study lipid synthesis. They identified a new class of lipid droplet-associated proteins (LDAPs) in nonseed tissues very similar to small rubber particle proteins found in rubber-producing plants; these LDAPs may be important to lipid particle binding and stabilization. The results further understanding of the subcellular processes involved with lipid metabolism and will be useful for endeavors to increase concentrations of energy-dense lipids in plants that may serve as bioenergy crops.

Reference: Horn, P. J., C. N. James, S. K. Gidda, A. Kilaru, J. M. Dyer, R. T. Mullen, J. B. Ohlrogge, and K. D. Chapman. 2013. “Identification of a New Class of Lipid Droplet-Associated Proteins in Plants,” Plant Physiology 162 , 1926–36. DOI: 10.1104/pp.113.222455. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 22, 2013

How Amines Penetrate Cellulose Fibers and Make Cellulose Accessible for Bioconversion

Cellulose is a major component of biomass and the primary biomass component being studied for biofuel production. However, cellulose fibers are extremely resistant to solvents, preventing enzymes, which are needed for conversion to products, from entering the fibers. Ammonia and simple organic amine molecules are well-known exceptions to this rule, but the mechanism by which they make cellulose fibers accessible is not understood. New research by an international team led by scientists at Oak Ridge National Laboratory (ORNL) combines neutron fiber diffraction and computational simulation to show how ethylene diamine (EDA, a representative amine solvent) binds to cellulose fibers. Experimental neutron diffraction data for EDA-cellulose complexes were the starting point for quantum chemical construction of optimized atomic-level structures that were then studied using computational molecular dynamics simulations. The results show how EDA disrupts normal hydrogen bonding in cellulose fibers, and the MD simulations explain the dynamic nature of EDA action. These results will help optimize techniques for breakdown of cellulose fibers to convert them on a large scale to biofuels and other renewable products. The research is featured on the cover of the August 2013 issue of the journal Cellulose and was carried out at ORNL; French National Center for Scientific Research (CNRS) and Institut Laue Langevin in Grenoble, France; Los Alamos National Laboratory; Keele University; University of Tokyo; and Kyung Hee University in the Republic of Korea.

Reference: Sawada, D., Y. Nishiyama, L. Petridis, R. Parthasarathi, S. Gnanakaran, V. T. Forsyth, M. Wada, and P. Langan. 2013. “Structure and Dynamics of a Complex of Cellulose with EDA: Insights into the Action of Amines on Cellulose,” Cellulose 20 , 1563–71. DOI: 10.1007/s10570-013-9974-7. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 12, 2013

Algal Pan-Genome Fills Gap in Tree of Life

To World War II soldiers, “The White Cliffs of Dover” was a morale-boosting song that lifted spirits in dark times. To scientists, the white cliffs are towering structures made of the chalky, white calcium carbonate exoskeleton that envelop the single-celled photosynthetic alga known as Emiliania huxleyi or “Ehux.” In some marine ecosystems, Ehux can trap as much as 20 percent of organic carbon derived from CO2 , making it a critical player in the marine carbon cycle . The Department of Energy’s Joint Genome Institute (DOE JGI) has sequenced the Ehux genome and compared it with sequences from other algal isolates. The Ehux genome turned out to be large and complex. Also, Ehux does not exist as a clearly defined species with a uniform genome, but as a more diffuse community—a “pan-genome”—with different individuals possessing a shared core of genes, supplemented by different gene sets to cope with the particular challenges of a local environment. DOE JGI and its collaborators compared 13 Ehux strains, revealing the first ever algal pan-genome. Ehux ’s genomic variability helps explain its ability to thrive in oceans from the equator to the subarctic. The researchers found that the core gene sets include genes that enable Ehux to survive in low levels of phosphorus and to assimilate and break down nitrogen-rich compounds. Additionally, the algal genome offers hints that Ehux may be involved in the global sulfur cycle, as it is able to produce a compound that can influence cloud formation and the climate.

Reference: Read, B. A., J. Kegel, M. J. Klute, A. Kuo, S. C. Lefebvre, F. Maumus, C. Mayer, J. Miller, A. Monier, A. Salamov, J. Young, M. Aguilar, J.-M. Claverie, S. Frickenhaus, K. Gonzalez, E. K. Herman, Y.-C. Lin, J. Napier, H. Ogata, A. F. Sarno, J. Shmutz, D. Schroeder, C. de Vargas, F. Verret, P. von Dassow, and et al. 2013. “Pan Genome of the Phytoplankton Emiliania Underpins Its Global Distribution,” Nature 499 , 209–13. DOI DOI: 10.1038/nature12221. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 07, 2013

Emerging Discipline of Structural Systems Biology Reveals E. coli Heat Tolerance

Microbial sensitivity to heat, or thermosensitivity, depends on the stability of cellular proteins and their ability to remain in an active, folded state. Research to improve microbial survival and function at higher temperatures has mainly focused on strategies for increasing the structural stability of individual proteins. A new approach called structural systems biology directly assesses the genome-scale metabolic potential of a model organism, E. coli, for thermostability. Using this approach, metabolic reactions of E. coli were integrated with three-dimensional structures of each catalytic enzyme. To simulate E. coli growth at various temperatures, protein (structural) activity functions were defined to impose temperature constraints on the metabolic models. This combined metabolic-structural method allows researchers to integrate temperature-dependent information about enzyme function with simulations of microbial metabolic growth. This approach enabled simulation of E. coli growth under various temperature conditions that was in good agreement with experimental growth data. It also provided mechanistic interpretations of mutations that conferred greater thermostability in E. coli. This new approach has important implications for developing industrial microbes as biocatalysts.

Reference: Chang, R. L., K. Andrews, D. Kim, Z. Li, A. Godzik, and B. O. Palsson. 2013. “Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli,” Science 340, 1220–23. DOI: 10.1126/science/1234012. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


June 03, 2013

Engineering Thermophilic Bacteria for Efficient Fermentation of Plant Biomass

Higher temperatures make plant biomass more accessible for processing, so thermophilic bacteria, which are active at higher temperatures than other bacteria, are promising candidates for biofuel production systems. To take full advantage of their potential in consolidated bioprocessing, efficient genetic tools are needed to metabolically engineer the thermophile. Researchers at the U.S. Department of Energy’s BioEnergy Science Center have been developing a series of genetic tools to manipulate Caldicellulosiruptor bescii. C. bescii is one of the most promising thermophiles for deconstructing and fermenting lignocellulose from nonfood plants. New research demonstrates a gene replacement strategy used to delete the lactate dehydrogenase gene from C. bescii. Because the plasmid contains a gene for which there is both positive and negative selection, it is possible to select first for recombination of the deleted ldh gene and then for loss of the plasmid sequences. This method allows clean genetic insertions and deletions, leaving no residual genetic material so that the method can be used repeatedly for adding and subtracting genes for metabolic engineering. The C. bescii strain containing the ldh gene deletion exhibited the expected metabolism changes, namely the engineered strain no longer produced lactate and had increased acetate and H2 production. This gene replacement demonstration paves the way for further genetic manipulation of C. bescii to produce desired biofuel fermentation products directly from plant biomass.

Reference: Cha, M., D. Chung, J. G. Elkins, A. M. Guss, and J. Westpheling. 2013. “Metabolic Engineering of Caldicellulosiruptor bescii Yields Increased Hydrogen Production from Lignocellulosic Biomass,” Biotechnology for Biofuels 6, 85. DOI: 10.1186/1754-6834-6-85. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 18, 2013

Bioinformatics Web Tool Aids Functional Annotation of Plant and Microbial Genomes

Gene sequencing has become very fast and inexpensive, yet the bottleneck of producing reliable functional annotations of gene sequences remains a challenge. Functional annotations commonly use a protocol based on pairwise sequence comparison algorithms such as the Basic Local Alignment Search Tool (BLAST). However, these methods can miss important phylogenetic relationships such as orthology. Phylogenetic methods that explicitly reconstruct evolutionary relationships in multigene families have a higher precision for whole genome functional annotation. A new phylogenetic web server and analysis platform, PhyloFacts, integrates experimental and annotation data from different resources including SwissProt, Gene Ontology, Pfam, BioCyc, Enzyme Commission, and third-party orthology databases. These data are then used to provide functional annotations for user-inputted protein sequences. PhyloFacts also allows users to drill down and view provenance and supporting data for functional annotations. PhyloFacts makes use of Hidden Markov Model (HMM) algorithms to place user-submitted sequences into precalculated phylogenetic relationships, or trees. As a result, its functional subclassifications have greater precision when compared with other orthology web services. Funding for PhyloFacts was provided as part of the Department of Energy’s Systems Biology Knowledgebase (KBase) enabling tools program and will be a component of future KBase services.

Reference: Afrasiabi, C., B. Samad, D. Dineen, C. Meacham, and K. Sjölander. 2013. “The PhyloFacts FAT-CAT Web Server: Ortholog Identification and Function Prediction Using Fast Approximate Tree Classification,” Nucleic Acids Research, 1–7. DOI: 10.1093/nar/gkt399. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 17, 2013

Thermophilic Bacterium Efficiently Deconstructs All Major Plant Biomass Components

Conversion of plant biomass to biofuels holds great promise for developing renewable and secure energy sources. However, the presence of lignin in plant biomass creates problems because of its recalcitrance to solubilization and because it limits access to energy-rich polysaccharides, cellulose, and hemicellulose. New research has iden­tified a thermophilic bacterium, Caldicellulosiruptor bascii, that can solubilize the lignin under the same conditions used for degradation of cellulose and hemicellulose, allowing efficient use of plant biomass for microbial growth and biosynthesis of fermentation products. This finding could enable the development of more economical and environ­mental­ly sustainable biomass conversion processes. This research was carried out by a team of scientists at the University of Georgia as part of the U.S. Department of Energy’s BioEnergy Science Center.

Reference: Kataevaa, I., M. B. Foston, S.-J. Yang, S. Pattathil, A. K. Biswal, F. L. Poole II, M. Basen, A. M. Rhaesa, T. P. Thomas, P. Azadi, V. Olman, T. D. Saffold, K. E. Mohler, D. L. Lewis, C. Doeppke, Y. Zeng, T. J. Tschaplinsk, W. S. York, M. Davis, D. Mohnen, Y. Xu, A. J. Ragauskas, S.-Y. Ding, R. M. Kelly, M. G. Hahn, and M. W. W. Adams. 2013. “Carbohydrate and Lignin Are Simultaneously Solubilized from Unpretreated Switchgrass by Microbial Action at High Temperature,” Energy and Environmental Science 6, 2186–95. DOI: 10.1039/C3EE40932E. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


May 05, 2013

New Technique for Improved Microbial Genome Assembly

In addition to sequencing the genomes of microbes, plants, fungi, and metagenomes, the U.S. Department of Energy’s (DOE) Joint Genome Institute (JGI) develops tools to improve the assembly and analysis of the DNA sequences that it generates. One tool, HGAP (Hierarchical Genome Assembly Process), provides a fully automated workflow for users of the Pacific Biosciences’ single molecule, real-time DNA sequencing machine. The “PacBio” sequencer generates initial DNA sequences up to 10 or more times longer than those provided by other technologies, which is a great assistance in the assembly of sequences into more complete genomes, but at a higher cost and lower accuracy. Competing sequencing technologies involve creating multiple DNA libraries, conducting multiple runs, and combining the data. I n contrast, HGAP requires just a single, long-insert, shotgun DNA library, enabling the resolution of long regions of repeated DNA sequence that often complicate other assembly methods. This new assembly method was tested using three microbes previously sequenced by DOE JGI. The HGAP produced final assemblies with >99.999% accuracy when compared to the reference sequences for these microbes. Next steps in the project will focus on extending HGAP’s utility beyond microbes to the larger genomes of more complex organisms. By improving sequence assemblies in this way, sequencing information can more readily be developed into understanding the role of biological processes and genes in DOE bioenergy and environmental missions.

Reference: Chin, C.-S., D. H. Alexander, P. Marks, A. K. Klammer, J. Drake, C. Heiner, A. Clum, A. Copeland, J. Huddleston, E. E. Eichler, S. W. Turner, and J. Korlach. 2013. “Nonhybrid, Finished Microbial Genome Assemblies from Long-Read SMRT Sequencing Data,” Nature Methods 10, 563–69. DOI: 10.1038/nmeth.2474. (Reference link)

For more information, see: http://bit.ly/JGI-Assembly.

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

Division: SC-23.2 Biological Systems Science Division, BER


April 25, 2013

Carbon-11 Azelaic Acid as a Signaling Molecule for Mechanistic Studies in Plants

When a pathogen attacks a plant, the plant mounts an immune response that alerts the rest of the plant, a response called systemic acquired resistance (SAR). The chemical compound(s) responsible for inducing the immunity is a topic of intense interest for agriculture, including for bioenergy crops. For example, the application of a 9-carbon-atom-chain (C-9) dicarboxylic acid, azaleic acid, induces immunity, but the similar C-8 and C-10 diacids do not. One hypothesis is that the azaleic acid, but not the related acids, moves to distant parts of the plant. New radiochemistry imaging research at Brookhaven National Laboratory has developed a rapid method to label these three acids with Carbon-11 (11C, half-life of 20.4 min) for short-term (minutes to hours) tracking of their movement within the plant, and with Carbon-14 (14C, half-life of 5730 years) for long-term (hours to days) studies. When applied to a leaf, [11C]-azaleic acid shows substantial movement within an hour. When [14C]-azaleic acid is applied to the roots, it distributes throughout the whole plant within a day. These studies demonstrate that azaleic acid has the potential to be a mobile signaling molecule. The radioactive-carbon labeled diacids will have utility as scientific tools to unravel SAR mechanisms and other phenomena that impact production of robust bioenergy crops.

References: Yu, K., J. M. Soares, M. K. Mandal, C. Wang, B. Chanda, A. N. Gifford, J. S. Fowler, D. Navarre, A. Kachroo, and P. Kachroo. 2013. “A Feedback Regulatory Loop Between G3P and Lipid Transfer Proteins DIR1 and AZI1 Mediates Azelaic-Acid-Induced Systemic Immunity,” Cell Reports 3, 1266–78. DOI: 10.1016/j.celrep.2013.03.030. (Reference link)

Best, M., A. N. Gifford, S. W. Kim, B. Babst, M. Piel, F. Roesch, J. S. Fowler. 2012. “Rapid Radiosynthesis of [11C] and [14C]Azaleic, Suberic, and Sebacic Acids for in vivo Mechanistic Studies of Systemic Acquired Resistance in Plants,” Journal of Labelled Compounds and Radiopharmaceuticals 55, 39-43. DOI: 10.1002/jlcr.1951. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


April 16, 2013

Challenging Traditional Understanding of Microbial Gene Regulation

The traditional view of adaptive gene regulation is that bacteria adapt to sense their environment and then selectively tune the expression of their genes for optimal growth efficiency and survival (i.e., fitness) under those conditions. Numerous observations of seemingly nonoptimal gene expression in various microbes suggest, however, that reality is more complex. Researchers at Lawrence Berkeley National Laboratory’s ENIGMA Science Focus Area are gaining a more sophisticated understanding of bacterial gene regulation by examining over a thousand different combinations of gene expression patterns and growth conditions to determine their relation to overall fitness. Four genetically tractable bacterial species representing a broad diversity of microbial lifestyles have been studied: the aquatic metal-reducing environmental microbe Shewanella oneidensis, common intestinal bacterium Escherichia coli, ethanol-producing bacterium Zymomonas mobilis, and anaerobic sulfate-reducing bacterium Desulfovibrio alaskensis. In all four organisms, evidence of adaptive gene regulation was observed for only a small minority of genes; most gene expression was determined to be neutral or even detrimental to growth efficiency and fitness under experimental conditions. While these observations need testing in more realistic environmental settings and in microbial communities, the team concludes that under laboratory conditions, most gene expression is nonadaptive and reflects some form of indirect control unrelated to functional properties of specific genes. These study results add a new layer of complexity to our knowledge of the forces governing gene expression in microorganisms. They have important implications in understanding fundamental systems biology of microbes and attempts to engineer organisms with modified functional capabilities. This publication was selected as a research highlight in the June 2013 issue of Nature Reviews Microbiology.

Reference: Price, M. N., A. M. Deutschbauer, J. M. Skerker, K. M. Wetmore, T. Ruths, J. S. Mar, J. V Kuehl, W. Shao, and A. P. Arkin. 2013. “Indirect and Suboptimal Control of Gene Expression Is Widespread in Bacteria,” Molecular Systems Biology 9(660), DOI: 10.1038/msb.2013.16. (Reference link)

Research Highlight: Hofer, U. 2013. “Unfit Expression,” Nature Reviews Microbiology 11, 362–63. DOI: 10.1038/nrmicro3035. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


February 14, 2013

Understanding Genome Evolution with the Help of Plasmid Gene Pools

Understanding how genomes of organisms change over time underlies much of biology and its practical applications. Plasmids are DNA molecules that can replicate independently of chromosomal DNA in a cell. This enables organisms to "collect" and move genes to other organisms through lateral gene transfer (like “genomic email”) and contributes to prokaryotic genome evolution. To understand the depth and breadth of the prokaryote plasmid gene pool, scientists have isolated, sequenced, and compared plasmids from two wastewater sludge communities. The authors studied the “mobilome,” a name for the mobile elements in a community genome, by specifically targeting, separating, and purifying closed circular supercoiled DNAs (CCSD) originating from the plasmids. They found that the plasmids isolated from the sludge wastewater microbial communities turned out to contain primarily uncharacterized coding sequences. Besides lending credence to the idea that plasmids are crucial to genome innovation, evolution, and community structure and functioning, this study generated a large library of new genes involved in wastewater sludge degradation and processing that could enable new approaches to microbial wastewater cleanup. The study was enabled by the DOE Joint Genome Institute.

Reference: Sentchilo, V., A. P. Mayer, L. Guy, R. Miyazaki, S. G. Tringe, K. Barry, S. Malfatti, A. Goessmann, M. Robinson-Rechavi, and J. R. van der Meer. 2013. “Community-Wide Plasmid Gene Mobilization and Selection,” The ISME Journal, DOI: 10.1038/ismej.2013.13. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


February 06, 2013

New Method Reveals Bacterial Diversity in Subsurface Sediments

A fundamental question in microbial ecology is how do community diversity and composition change in response to perturbations. Most ecological studies have a limited ability to deeply sample community structure or a limited taxonomic resolution to track changing microbial diversity. To address this issue, researchers at the University of California, Berkeley, developed a method to assemble full length 16S rRNA sequences from short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. This approach, termed EMIRGE and optimized for large sequencing data size, allows researchers to differentiate the community composition among samples acquired before and after an environmental perturbation. Briefly, EMIRGE relies on a database of candidate 16S sequences for a template-guided assembly. An iterative method, sequencing reads are first aligned and probabilistically attributed to candidate 16S genes. Subsequently, candidate gene abundances and consensus sequences are adjusted based on the calculated probabilistic read attribution. The results were highly reproducible across very high alpha microbial diversity and abundant organisms from phyla that do not have cultivated representatives. This method allows for sensitive, accurate profiling of the “long tail” of low-abundance organisms that exist in many microbial communities and can resolve population dynamics in response to environmental change.

Reference: Miller, C. S., K. M. Handley, K. C. Wrighton, K. R. Frischkorn, B. C. Thomas, and J. F. Banfield. 2013. “Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments,” PLoS ONE 8(2), e56018. DOI: 10.1371/journal.pone.0056018. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


February 06, 2013

Understanding Enzymes that Help Convert Biomass to Biofuels

A key step in the production of biofuels from biomass is hydrolytic breakdown of cellulose, a major component of all plants, into simple, fermentable sugars. Many natural systems carry out this breakdown, and much research is devoted to find systems that are highly efficient and thus candidates for inclusion in a biofuel production system. A new study of a subfamily of glucosidase enzymes (6-P-β-glucosidases), critical to efficient hydrolysis of cellulose, uses x-ray crystallography to determine their structures and how they bind to cellulose molecules. The researchers isolated these enzymes from two bacteria commonly found in the digestive tracts of many mammals, including humans: Lactobacillus plantarum and Streptococcus mutans. They obtained structures of the enzymes alone and bound to key cellulose breakdown molecules, using the Structural Biology Center’s stations at Argonne National Laboratory’s Advanced Photon Source. Different bacteria show different P-β-glucosidase and P-β-galactosidase activities. The structures and functional studies enabled the scientists to define structural features shared by glucosidases and galactosidases and those that are unique to the 6-P-β-glucosidases subfamily. Both enzymes show hydrolytic activity against 6’-P-β-glucosides but exhibit surprisingly different kinetic properties and affinities for substrates. Considering the conservation of the overall structures and active sites of various 6-P-β-glucosidases, the differences at their ligand binding subsites and the entrance to the active site are likely the determinants of their substrate specificities. These new findings will help scientists studying the design of efficient enzyme systems for biofuel production and will also have implications for human health.

Reference: Michalska, K., K. Tan, H. Li, C. Hatzos-Skintges, J. Bearden, G. Babnigg, and A. Joachimiak. 2013. “GH1-Family 6-P-ß-Glucosidases from Human Microbiome Lactic Acid Bacteria,” Acta Crystallographica Section D: Biological Crystallography 69, 451–63. DOI: 10.1107/S0907444912049608. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


February 01, 2013

Improving Cyanobacterial Synthesis of Alkanes

Cyanobacteria are important photoautotrophic organisms that can capture carbon dioxide and convert it into a suite of organic compounds such as high-density liquid fuels. Using synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy as a high-throughput imaging method, researchers tracked metabolic phenotypes of Synechocystis 6803, which was engineered for enhanced production of alkanes and free fatty acids. Multivariate SR-FTIR data analysis revealed biochemical shifts in the engineered cells. These results demonstrate the applicability of SR-FTIR spectromicroscopy for rapid metabolic screening and phenotyping of live individual cells. The research was conducted using resources at the Advanced Light Source at Lawrence Berkeley National Laboratory.

Reference: Hu, P., et al. 2013. “Metabolic Phenotyping of the Cyanobacterium Synechocystis 6803 Engineered for Production of Alkanes and Free Fatty Acids,” Applied Energy 102, 850–59. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER



Alkane Biosynthesis. Comparison of visible and infrared images shows localized production of alkanes adhering to a cyanobacterium’s outer cell surface (represented by rainbow-colored speckles; red = maximum). more...

Image Credit: Lawrence Berkeley National Laboratory



January 30, 2013

Plants, Fungi, and Microbes: Symbiosis in Carbon and Nitrogen Cycling

Arbuscular mycorrhizal (AM) fungi form intimate affiliations with the roots of many plant types. This classic example of symbiosis is commonly understood to involve AM fungi helping the plants take up soil nutrients. In exchange, the fungi receive some of the sugars generated by the plants from photosynthesis. Although AM fungi play a large role in carbon and nitrogen cycling in terrestrial environments, details of how they actually function remain poorly understood. In particular, the impact of AM fungi on soil microbe communities has not been examined in detail due to the difficulty of tracking nanoscale processes in complex soil habitats. U.S. Department of Energy researchers at the University of California Berkeley and Lawrence Livermore National Laboratory used a combination of "omics" tools and nanoscale tracking of isotopically labeled compounds to dissect interactions of AM fungi and soil microbial communities in carefully constructed soil microcosms. Plant-affiliated AM fungi were allowed to colonize small chambers containing soil samples and radiolabelled dead plant material ("litter"). The team found that the AM fungi have a significant impact on surrounding microbial community composition, increasing the abundance of microbes involved in plant litter degradation. During degradation of litter in soil, microbes play an important role in liberating nitrogen compounds bound in dead plant matter. The team observed significant uptake of microbially released nitrogen (but not carbon) by the AM fungi. These findings reveal another layer of complexity in this symbiotic system and yield another important puzzle piece towards understanding the complex routes by which carbon and nitrogen flow through ecosystems.

Reference: Nuccio, E. E., A. Hodge, J. Pett-Ridge, D. J. Herman, P. K. Weber, and M. K. Firestone. 2013. "An Arbuscular Mycorrhizal Fungus Significantly Modifies the Soil Bacterial Community and Nitrogen Cycling During Litter Decomposition," Environmental Microbiology, DOI: 10.1111/1462-2920.12081. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


January 17, 2013

New Analytical Tool Enables Switchgrass Improvement

Switchgrass (Panicum virgatum L.) is a prime bioenergy feedstock candidate due to its high biomass yields, minimal input requirements, broad adaptability, and perenniality. However, its large genome size, complicated genetics, and lack of a reference genome make efforts to improve switchgrass extremely challenging. Some of these difficulties can be overcome with genotyping-by-sequencing (GBS), a relatively low-cost method that targets a fraction of the genome for sequencing. GBS has already been used in many plant species to find molecular markers called single nucleotide polymorphisms (SNPs). To be both accurate and economical, however, this strategy requires a fully sequenced and assembled reference genome. To respond to this challenge, researchers funded in part by the joint U.S. Department of Agriculture-U.S. Department of Energy Plant Feedstocks Genomics for Bioenergy Program used GBS to develop a SNP discovery platform that does not require a reference genome and that can be applied to any complex plant species. This pipeline, called the Universal Network-Enabled Analysis Kit (UNEAK), was validated with maize and then successfully tested on switchgrass. Over one million SNPs were discovered in the switchgrass collection and used to construct high-density linkage maps, providing insight into the genetic diversity, population structure, phylogeny, and evolution of this species. UNEAK is providing an invaluable resource for switchgrass improvement programs.

Reference: Lu, F., A. E. Lipka, J. Glaubitz, R. Elshire, J. H. Cherney, M. D. Casler, E. S. Buckler, and D. E. Costich. 2013. "Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol," PLoS Genetics 9(1), e1003215. DOI: 10.1371/journal.pgen.1003215. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER


January 16, 2013

Marginal Lands: A Valuable Resource for Sustainable Bioenergy Production

Growing plants on marginal lands, or lands unsuitable for conventional agricultural crops, is a promising route towards attaining sufficient cellulosic biomass for the production of biofuels without compromising food crops. However, both the availability of such lands as well as the potential environmental impacts (e.g., greenhouse gas emissions) resulting from widespread biofuel crop production remain uncertain. Researchers at the U.S. Department of Energy's Great Lakes Bioenergy Research Center (GLBRC) report results from the first assessment of the total biomass potential of these lands, including an estimate of greenhouse gas benefits and the productivity potential of unmanaged lands. Using 20 years of data from 10 Midwest states, the researchers compared both productivity and greenhouse gas impacts of several potential biofuel feedstocks, including corn, poplar, alfalfa, and old field vegetation, and then used supercomputers to model the biomass production required to support local biorefineries. The assessment shows that if properly managed, marginal lands could provide sufficient biomass to support a viable cellulosic biofuel production industry while benefiting conservation efforts and the environment.

Reference: Gelfand, I., R. Sahajpal, X. Zhang, R. C. Izaurralde, K. L. Gross, and G. P. Robertson. 2013. "Sustainable Bioenergy Production from Marginal Lands in the U. S. Midwest," Nature, DOI: 10.1038/nature11811. (Reference link)

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

Division: SC-23.2 Biological Systems Science Division, BER