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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Program
February 2013

The Genomic Science program within DOE’s Office of Biological and Environmental Research supports fundamental research to achieve a predictive, systems-level understanding of plants, microbes, and biological communities through the integration of fundamental science and technology development.

Major research areas include the DOE Systems Biology Knowledgebase, Bioenergy Research Centers, USDA-DOE Plant Feedstocks Genomics for Bioenergy program, microbial and plant Biofuels studies, Biosystems Design projects to enable next-generation biofuels, characterization and genomic-based analyses of Microbes and Microbial Communities, and Biological Systems Research on the Role of Microbial Communities in Carbon Cycling. The Genomic Science program also supports Small Business Innovation Research relevant to DOE energy and environmental missions.

Listed below for each of these areas are ongoing research projects in or associated with the program in 2013.

Section Sub-Section Abstract Title Principal Investigator Institute
DOE Systems Biology Knowledgebase (KBase)KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research Adam Arkin Argonne National Laboratory
DOE Systems Biology Knowledgebase (KBase)The DOE Systems Biology Knowledgebase: Microbial Communities Science Domain Adam Arkin Argonne National Laboratory
DOE Systems Biology Knowledgebase (KBase)The DOE Systems Biology Knowledgebase: Microbial Science Domain Adam Arkin Lawrence Berkeley National Laboratory
DOE Systems Biology Knowledgebase (KBase)The DOE Systems Biology Knowledgebase: Plants Science Domain Adam Arkin Cold Spring Harbor Laboratory
DOE Systems Biology Knowledgebase (KBase)The KBase Architecture and Infrastructure Design Adam Arkin Argonne National Laboratory
DOE Systems Biology Knowledgebase (KBase)Development of a Regulated Model for Clostridia acetybutilicum Costas Maranas Pennsylvania State University
DOE Systems Biology Knowledgebase (KBase)Defining Complex Worlds in COMETS: Multiple Species and Dynamic Environments Daniel Segre Boston University
DOE Systems Biology Knowledgebase (KBase)The Ribosomal Database Project: Data and Tools for Microbial Analysis James Cole Michigan State University
DOE Systems Biology Knowledgebase (KBase)PhyloFacts FAT-CAT: A New DOE Webserver for Genome Functional Annotation Kimmen Sjolander University of California, Berkeley
DOE Systems Biology Knowledgebase (KBase)Comparison of Soil Microbial Communities Under Different Bioenergy Crops Suggests Sustainable Options Kirsten Hofmockel, Folker Meyer Iowa State University
DOE Systems Biology Knowledgebase (KBase)Bioenergy-Related Curation of the MetaCyc Database of Metabolic Pathways Peter D. Karp SRI International
DOE Systems Biology Knowledgebase (KBase)Computation of Atom Mappings and Novel Synthetic Pathways Peter Karp SRI International
DOE Systems Biology Knowledgebase (KBase)The Pathway Tools Software and BioCyc Database Collection Peter Karp SRI International
DOE Systems Biology Knowledgebase (KBase)Network Portal: An Integrated Framework for Storing, Analyzing, and Visualizing Biological Networks Serdar Turkarslan Institute for Systems Biology
DOE Systems Biology Knowledgebase (KBase)Kinetic Model of Methanogenesis in Methanosarcina acetivorans Zaida Luthey-Schulten University of Illinois, Urbana-Champaign
DOE Systems Biology Knowledgebase (KBase)Using MetRxn in Metabolic Model Development and Strain Design Costas Maranas Pennsylvania State University, University Park
DOE Systems Biology Knowledgebase (KBase)Extension of the Ensemble Modeling of Metabolic Networks to Genome-Scale Descriptions James Liao, Costas Maranas, and Gregory Stephanopoulos University of California, Los Angeles; Pennsylvania State University; and Massachusetts Institute of Technology
DOE Systems Biology Knowledgebase (KBase)RegPrecise 2.1: Toward Systems Biology Knowledgebase on Transcriptional Regulation in Bacteria Dmitry Rodionov Lawrence Berkeley National Laboratory
Bioenergy Research CentersBioEnergy Science Center (BESC)Advances in High-Throughput Screening of Biomass Recalcitrance Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)An Arabidopsis Cell Wall Proteoglycan Consists of Pectin and Arabinoxylan Covalently Linked to an Arabinogalactan Protein Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Application of Chemical Imaging by TOF-SOMS to Understand Recalcitrance Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Characterization of GXMT1 Reveals a New Family of Co2+-Dependent Enzymes that Catalyze the Methylation of Glucuronoxylan Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Chemical Control in Lignin Bioynthesis: Molecular Orbital Analyses of H and G Lignans Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Clostridium thermocellum Transcriptomic Profiles After Exposure to Ethanol, Furfural, or Heat Stress Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Comparative Glycomics of Plant Cell Walls/Biomass: Insights into Composition, Diversity, Formation and Recalcitrance Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)High Solubilization of Grassy Feedstocks Via Consolidated Bioproccessing (CBP) Without Pretreatment Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Implications of the Improved Dedicated Feedstock, Populus Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Improving Clostridium thermocellum and Caldicellulosiruptor bescii to Enhance Cellulose Digestion Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Integration of Metabolomics with Association Genetics for Large-Scale Gene Discovery in Populus trichocarpa Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Metabolic Engineering of Clostridium thermocellum for Biofuel Production from Cellulosic Substrates Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Methylation by Cognate Methyltransferases is Essential for DNA Transformation of Caldicellulosiruptor Species: Extending Genetic Methods to Members of this Genus Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Molecular Breeding of Switchgrass for Enhanced Biomass Yield and Quality Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Population Genomics and Association Mapping in Populus trichocarpa Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Protease-Optimized Spectral Indexing (POSI) Increases Confidence in Label-Free Quantification of Shotgun Proteomics Datasets Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)PvMYB4-Overexpression Switchgrass Yields Very High Cellulosic Ethanol Levels Without Pretreatment Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Real-Time Nanoscale Imaging Provides New Insights into Improvement of Biomass Pretreatment and Enzyme Hydrolysis Paul Gilna BioEnergy Science Center
Bioenergy Research CentersBioEnergy Science Center (BESC)Extracellular, Cell-Associated Proteins Play a Role in Plant Biomass Degradation by Extremely Thermophilic Caldicellulosiruptor Species Robert M. Kelly North Carolina State University
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Impact of Mixed Feedstocks and Feedstock Densification on Ionic Liquid Pretreatment Efficiency Blake A. Simmons Joint BioEnergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Design and Optimization of Novel Ionic Liquids for Biomass Pretreatment Blake Simmons Joint BioEnergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Recent Developments in Fatty Acid-Derived Fuels at JBEI Harry Beller Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Identification of Glycosyltransferases Involved in Galactan Biosynthesis Henrik V. Scheller Joint Bioenergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Quantitative Metabolic Modeling in JBEI's Fuel Synthesis Division Jay Keasling Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Isolation of Golgi Proteomes from Grasses Joshua Heazlewood Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Engineering Bacterial Tolerance to an Ionic Liquid Used in Advanced Biofuel Production Michael Thelen Joint Bioenergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)PR-PR Programming a Robot — Laboratory Automation Platform Nathan J. Hillson Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Inactivation of Xylosyl Arabinosyl Substitution of Xylan 1 (XAX1) in Rice Leads to Decreased Ferulic Acid and Increased Saccharification Pamela Ronald Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Structure-Based Engineering of Sulfolobus acidocaldarius Geranylgeranyl Reductase Paul Adams Joint BioEnergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)A Multiplexed, High-Throughput Screening Pipeline for Lignocellulosic Enzyme Discovery and Evolution Richard Heins Joint BioEnergy Institute
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Thermoascus aurantiacus is a Promising Thermophilic Fungal Platform for Enzymatic Biomass Deconstruction Steven Singer Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)High-Titer Production of Isopentenol Through Rational Pathway Engineering Taek Soon Lee Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Large-Scale Characterization of Glycoside Hydrolase Enzymes for Biofuel Development Trent R. Northen Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
Bioenergy Research CentersJoint BioEnergy Institute (JBEI)Studies of Biomass Enzymatic Hydrolysis by Tagged Glycans Trent R. Northen Joint BioEnergy Institute
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)A Phylogenetic-Based, Systems-Analysis of Biomass Deconstruction in the Genus Streptomyces Cameron Currie University of Wisconsin, Madison
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Mixed-Linkage Glucan Stored in Stem Parenchyma Tissue as a Path to Better Plants for Biofuel Feedstocks Curtis G. Wilkerson Great Lakes Bioenergy Research Center
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Transcriptome and Genome Diversity in Switchgrass Kevin Childs Great Lake Bioenergy Research Center and Michigan State University
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Productivity of Biomass Cropping Systems in the Upper Midwest Kurt Thelen Michigan State University
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Phenolic Inhibitors Derived from Ammonia-Pretreated Lignocellulose Activate Specific Regulatory Circuits and Inhibit Bacterial Conversion of Xylose to Ethanol Robert Landick Great Lakes Bioenergy Research Center and University of Wisconsin, Madison
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Catalysis with Cu(bpy) Improves AHP Pretreatment of Woody Biomass Timothy Donohue Great Lakes Bioenergy Research Center
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Characterization of Xylose Fermentation from AFEX™-Pretreated Corn Stover Hydrolysate by Evolved, Stress-Tolerant Yeast Strains Trey K. Sato Great Lakes Bioenergy Research Center and University of Wisconsin, Madison
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Production of a "Drop-in" Diesel Fuel in Crops John Ohlrogge Michigan State University
Bioenergy Research CentersGreat Lakes Bioenergy Research Center (GLBRC)Phenotypic and Genetic Dissection of Maize Internode Length Natalia De Leon Great Lakes Bioenergy Research Center and Michigan State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Burkholderia phytofirmans Strain PsJN Enhances the Growth of Switchgrass Chuansheng Mei Institute for Advanced Learning and Research and Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Effect of the Endophytic Bacterium Burkholderia phytofirmans Strain PsJN on Drought-Stessed Switchgrass Chuansheng Mei Virginia Polytechnic Institute and State University and the Institute for Advanced Learning and Research
USDA-DOE Plant Feedstock Genomics for Bioenergy Genetic Responses of Switchgrass to the Endophytic Bacterium Burkholderia phytofirmans Strain PsJN Chuansheng Mei Institute for Advanced Learning and Research
USDA-DOE Plant Feedstock Genomics for Bioenergy Tubulins as New Targets for Bioenergy Trait Improvement CJ Tsai University of Georgia
USDA-DOE Plant Feedstock Genomics for Bioenergy Functional Genomics of Sugar Content in Sweet Sorghum Stems David Braun University of Missouri
USDA-DOE Plant Feedstock Genomics for Bioenergy The Ability of XylemM NAC Domain 1 to Block Xylem Differentiation Depends on its Retinoblastoma Related Interaction Domain Eric Beers Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy The Interactions of Poplar and Arabidopsis ROP GTPases with CSN5A: Negative Regulation of CSN5A by ROP11 Eric Beers Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy The Interactome Network of a Novel Endomembrane Protein in Populus trichocarpa Eric Beers Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy The Poplar RWI Protein Binds to Myb Domain and Homeodomain Proteins Through Its Distinct Myb-Like N-Terminal and DUF3755 C-Terminal Domains Eric Beers Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Genetic Structure of Miscanthus sinensis from Asia and the United States Erik Sacks University of Illinois
USDA-DOE Plant Feedstock Genomics for Bioenergy An Integrated Approach to Improving Plant Biomass Production Jan Leach Colorado State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Exploring Genetic Diversity in the World Collection of Sugarcane and Related Grasses Jianping Wang University of Florida
USDA-DOE Plant Feedstock Genomics for Bioenergy Insertional Mutagenesis of Brachypodium distachyon John Vogel U.S. Department of Agriculture, Agricultural Research Service
USDA-DOE Plant Feedstock Genomics for Bioenergy Phenomic Analysis of Natural and Induced Variation in Brachypodium distachyon John Vogel U.S. Department of Agriculture, Agricultural Research Service
USDA-DOE Plant Feedstock Genomics for Bioenergy Identifying Differences in Abiotic Stress Gene Networks Between Lowland and Upland Ecotypes of Switchgrass Kevin L. Childs Michigan State University and Virginia Polytechnic Institute and State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Development of Genomic Resources and Novel Species Hybrids for the Genetic Improvement of Shrub Willow Feedstock Crops Larry Smart Cornell University
USDA-DOE Plant Feedstock Genomics for Bioenergy Association Genetics and Functional Genomics of Switchgrass Cell Wall Quality Regulation Laura Bartley University of Oklahoma
USDA-DOE Plant Feedstock Genomics for Bioenergy Identification of Putative Secondary Cell Wall Regulators Through a Comparative Analysis of the R2R3 MYB Family Across Arabidopsis, Poplar, Rice, Maize, and Switchgrass Laura E. Bartley University of Oklahoma
USDA-DOE Plant Feedstock Genomics for Bioenergy Expression of Putative Arabinoxylan Feruloyl Transferase Genes in Brachypodium distachyon Marcia M. De Oliveira Buanafina Pennsylvania State University
USDA-DOE Plant Feedstock Genomics for Bioenergy Maize Candy-Leaf (Cal) Mutants as Feedstocks with Improved Biorefinery Characteristics Markus Pauly University of California, Berkeley
USDA-DOE Plant Feedstock Genomics for Bioenergy Co-Ordinate Regulation of Growth and Development Genes by MiRNA in Perennial Miscanthus Matthew Hudson University of Illinois
USDA-DOE Plant Feedstock Genomics for Bioenergy Genome-Wide Analysis of MiRNA Targets in Brachypodium and Biomass Energy Crops Pamela Green University of Delaware
USDA-DOE Plant Feedstock Genomics for Bioenergy Altered Salicin Partitioning in SUT4-RNAi Poplars Scott Harding University of Georgia
USDA-DOE Plant Feedstock Genomics for Bioenergy Genomic and Breeding Foundations for Bioenergy Sorghum Hybrids Stephen Kresovich University of South Carolina
USDA-DOE Plant Feedstock Genomics for Bioenergy Associating Genetic Variation in the Shoot Maturation Pathway with Bioenergy Traits in Sorghum Stephen Moose University of Illinois
USDA-DOE Plant Feedstock Genomics for Bioenergy The Genetics of Biofuel Traits in Panicum Grasses: Developing a Model System with Panicum haliii Thomas Juenger University of Texas, Austin
USDA-DOE Plant Feedstock Genomics for Bioenergy Regulation of Root Development in Populus in Response to Nitrogen Deficiency Victor Busov Michigan Technological University
USDA-DOE Plant Feedstock Genomics for Bioenergy Construction of a Gene Interaction Network for Poplar Pankaj Jaiswal Oregon State University
Biofuels ResearchMicrobes, Archaea, and FungiEngineering Biofuel Tolerance in Microbes* Mary Dunlop University of Vermont
Biofuels ResearchMicrobes, Archaea, and FungiConstruction of Metabolic Models for a Family of Cyanobacteria Himadri Pakrasi Washington University
Biofuels ResearchMicrobes, Archaea, and FungiPathways and Regulatory Network of Hydrogen Production from Cellulose by Clostridium thermocellum JH David Wu University of Rochester
Biofuels ResearchMicrobes, Archaea, and FungiMetabolomics of Sugar Catabolism in C. cellulolyticum Josh D. Rabinowitz Princeton University
Biofuels ResearchMicrobes, Archaea, and FungiFunctional and Evolutionary Genomics of Nanoarchaeota Systems Mircea Podar University of Tennessee
Biofuels ResearchMicrobes, Archaea, and Fungi13C Metabolic Flux Analysis of Clostridial Cell Growth Eleftherios T. Papoutsakis University of Delaware
Biofuels ResearchMicrobes, Archaea, and FungiMimicking Fungal Biomass Decomposition, Assuming a Biphasic Mechanism Jonathan P. Schilling University of Minnesota
Biofuels ResearchMicrobes, Archaea, and FungiAnalysis of the Butanol Stress Response Regulatory Network in Clostridium acetobutylicum Eleftherios T. Papoutsakis University of Delaware
Biofuels ResearchMicrobes, Archaea, and FungiSystems Analysis of the Clostridium Metabolite Stress Response for Bioenergy Applications Eleftherios T. Papoutsakis University of Delaware
Biofuels ResearchMicrobes, Archaea, and FungiThe Small RNome of Clostridium acetobutylicum with and Without Metabolite Stress Eleftherios T. Papoutsakis University of Delaware
Biofuels ResearchMicrobes, Archaea, and FungiSensitive Staining Method for Detection and Localization of Acid Groups Formed on Lignocellulose During Deconstruction Kenneth Hammel University of Wisconsin, Madison
National Renewable Energy Laboratory Science Focus AreaDesign Principles Controlling Hydrogen Metabolism in Phototrophic Organisms Maria Ghirardi National Renewable Energy Laboratory
Oak Ridge National Laboratory Science Focus AreaInsights Into Cel7A Structure During Cellulose Digestion Brian H. Davison Oak Ridge National Laboratory
Oak Ridge National Laboratory Science Focus AreaThe Physical Processes Driving Biomass Pretreatment for Bioproducts Brian H. Davison Oak Ridge National Laboratory
PlantsNext-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstock Joseph Ecker Howard Hughes Medical Institute and Salk Institute
PlantsTemperature Cycles Primarily Drive Diurnal Growth Rhythms in the Model Grass, Brachypodium distachyon Steve Kay University of Southern California
PlantsUncovering Genetic Mechanisms for Biological Conversion Efficiency in Brachypodium distachyon* Samuel Hazen University of Massachusetts
PlantsWhole-Genome Association Analysis of the Molecular Regulation of Biomass Growth and Composition in Populus deltoides* Matias Kirst University of Florida
PlantsRegulation of Neutral Lipid Accumulation in Plant Leaves Kent Chapman University of North Texas
PlantsA Splice Variant of the SND1 Transcription Factor is a Dominant Negative of the SND1 Family Members and the SND1-Regulated Network in Populus trichocarpa Vincent L. Chiang Forest Biotechnology Group, North Carolina State University
PlantsDefining Determinants and Dynamics of Cellulose Microfibril Biosynthesis, Assembly, and Degradation Jocelyn Rose Cornell University
PlantsDevelopment of Quantum Dot Probes for Studies of Synergy Between the Components of Wood-Degrading Fungal Enzymes Haw Yang Princeton University
PlantsStudy of Plant Cell Wall Polymers Affected by Metal Accumulation Using Stimulated Raman Scattering Microscopy Sunney Xie Harvard University
Biosystems DesignMicrobesStoichiometric and Dynamic Models of Oleaginous Yeasts Gregory Stephanopoulos Massachusetts Institute of Technology
Biosystems DesignMicrobesA Platform for Genome-Scale Design, Redesign, and Optimization of Bacterial Systems Ryan Gill University of Colorado, Boulder
Biosystems DesignMicrobesComparing the Transcriptomes of Fibrobacter succinogenes S85 Associated with Growth on Cellulose or Glucose* Garret Suen University of Wisconsin, Madison
Biosystems DesignMicrobesRepurposing the Saccharomyces cerevisiae Peroxisome for Compartmentalizing Multi-Enzyme Pathways* John Dueber University of California, Berkeley
Biosystems DesignPlantsModeling and Manipulating Phenylpropanoid Pathway Flux for Bioenergy Clint Chapple Purdue University
Biosystems DesignPlantsExpanding the Breeder's Toolbox for Perennial Grasses Eduardo Blumwald University of California, Davis
Biosystems DesignPlantsEngineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments John C. Cushman University of Nevada
Biosystems DesignPlantsGetting to the Root of Drought Stress in the Model C4 Grass Setaria viridis Jose R. Dinneny Carnegie Institution for Science
Biosystems DesignPlantsA Systems-Level Analysis of Drought and Density Response in the Model C4 Grass Setaria viridis Thomas P. Brutnell Donald Danforth Plant Science Center
Microbes and Microbial CommunitiesSystems Biology of Marine Green Algae: Insights from the Dual Micromonas Model Alexandra Worden Monterey Bay Aquarium Research Institute
Microbes and Microbial CommunitiesHeterogeneity in Protein Expression Induces Metabolic Variability in a Modeled E. coli Population Zaida Luthey-Schulten University of Utah
Microbes and Microbial CommunitiesMethanobactin and MmoD Work in Concert to Act as the “Copper-Switch” in Methanotrophs Jeremy Semrau Iowa State University
Microbes and Microbial CommunitiesMicrobial CommunitiesTracking Dynamics of Alleles, Genotypes, or Species in Synthetic Microbial Consortia Christopher Marx Harvard University
Microbes and Microbial CommunitiesMicrobial CommunitiesToward Validation of a Genome-Scale Model of Nitrosomonas europaea and N. winogradskyi Using Absolute Gene Expression Daniel J. Arp Oregon State University
Microbes and Microbial CommunitiesMicrobial CommunitiesDiscovery of Geobacter sulfurreducens Proteins Essential for Electron Transfer and Biofilm Conductivity Via Massively Parallel Mutant Analysis Daniel R. Bond University of Minnesota
Microbes and Microbial CommunitiesMicrobial CommunitiesPhylogenetic Diversity and Abundance Patterns of Thaumarchaeal and Bacterial AmoA Genes in Soils Influenced by Cultivars of Potential Biofuels Crops David Stahl University of Washington
Microbes and Microbial CommunitiesMicrobial CommunitiesDetecting Nitrous Oxide Reductase (nosZ) Genes in Metagenomes: Method Development and Application to Midwestern Soils Frank Löeffler Georgia Institute of Technology
Microbes and Microbial CommunitiesMicrobial CommunitiesPUNCS: Towards Predictive Understanding of Nitrogen Cycling in Soils —> the Role of Ammonia-Forming Nitrite Reductase (NrfA) Frank Löffler University of Illinois, Urbana-Champaign
Microbes and Microbial CommunitiesMicrobial CommunitiesIn Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities Paul W. Bohn University of Notre Dame
Microbes and Microbial CommunitiesMicrobial CommunitiesIn Situ Spectroscopy on Intact Leptospirillum ferriphilum Reveals That Cytochrome 579 Behaves Differently in Situ Than It Does in Vitro Robert Blake II Xavier University of Louisiana
Microbes and Microbial CommunitiesMicrobial CommunitiesImproved Understanding of Microbial Iron and Sulfate Reduction Through a Combination of Bottom-Up and Top-Down Functional Proteomics Assays Ruth E. Richardson Cornell University
Microbes and Microbial CommunitiesMicrobial CommunitiesMetagenomic Approaches to the Study of Microbial Communities at Subsurface Sites Undergoing Natural Attenuation of Uranium Barbara Methe J. Craig Venter Institute
Microbes and Microbial CommunitiesMicrobial CommunitiesPan-Genome-Scale Reconstruction of the Geobacteraceae Metabolic Network Based on Metagenome from Subsurface Samples Barbara Methe and Radhakrishnan Mahadevan University of Toronto
Microbes and Microbial CommunitiesMicrobial CommunitiesAdvances in Proteomic and Biochemical Analysis During Poplar – Laccaria Mycorrhizal Interactions Leland Cseke University of Alabama, Huntsville
Pacific Northwest National Laboratory Plant-Microbe Science Focus AreaLive Cell Characterization of Dynamic Cyclical Redox Regulation by Chemical Profiling in the Photoautotroph Synechococcus Alexander Beliaev Pacific Northwest National Laboratory
Pacific Northwest National Laboratory Plant-Microbe Science Focus AreaMaintenance of Fast Growth Under High Irradiances in Synechococcus sp. PCC 7002 Alexander Beliaev Pacific Northwest National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Factors Associated with Microbial Community Association Patterns in the Populus Rhizosphere Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Organizing and Mining Diverse Information Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Comparative Genomics of Pseudomonas Isolates from the Populus Microbiome Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Dissecting Populus-Fungal-Bacterial Systems Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Intra- and Inter-Specific Variations in INDEL Polymorphisms Co-Segregating with QTLs for Populus-Laccaria Interaction Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: Proteomes of Bacteria, Fungi, and Plants Mitchel Doktycz Oak Ridge National Laboratory
Oak Ridge National Laboratory Plant-Microbe Science Focus AreaPlant-Microbe Interfaces: The Role of Constructed Microbial Communities on the Extended Plant Phenotype Mitchel Doktycz Oak Ridge National Laboratory
Argonne National Laboratory Plant-Microbe Science Focus AreaMolecular Mechanisms that Mediate Environment Sensing and Response Frank Collart Argonne National Laboratory
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMetagenomics of Microbial Communities from the Leaf Litter — Insights Into the Plant-Polymers Degradation Adam C. Martiny University of California, Irvine
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingiTEP: An Integrated Toolkit for the Exploration of Pan-Genomes Bill Metcalf University of Illinois
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingRelating Microbial Physiological Performance to Genome Content Chris Blackwood Kent State University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingUnderstanding Gene Expression and Physiology in Response to Switching Carbon Substrate Chris Blackwood Kent State University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingDetection of Latent Biotic Covariation Embedded in Environmental Gradient Responses Chris Blackwood and Gail Rosen Drexel University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingNavigating the Soil Microbial Food Web: Using 13C-Stable Isotope Probing to Track Carbon Cycling in Complex Microbial Communities Daniel H. Buckley Cornell University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingA Custom Database for Functional Annotation of Soil Omics Datasets Using Hidden Markov Models David Myrold Oregon State University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMulti-Omics Assessment of Active Microbial Communities and their C Cycling Function in Native Prairie Soil David Myrold Oregon State University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMulti-Omics of RaMPs Field Study Reveals Impacts of Altered Rainfall Patterns on Carbon Cycling in Native Prairie Soils David Myrold Oregon State University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMeta-Omics Analysis of the Mechanisms for Direct Interspecies Electron Transfer (DIET) in Natural Methanogenic Communities and Defined Co-Cultures Derek Lovley University of Massachusetts
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMicrobial Mechanisms Mediating Increased Soil C Storage Under Elevated N Deposition Donald R. Zak University of Michigan
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingSuppression of N Cycle Functional Genes in Response to Chronic Atmospheric N Deposition Donald R. Zak University of Michigan
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingTemperature Sensitivity of Soil Organic Matter Decomposition from Alaskan Tundra Edward A.G. Schuur University of California
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingFunctional Fizzy: a Feature Selection Tool Over Varying Sample Phenotypes Gail Rosen Drexel University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingApproaches to Characterize Community Structure, Nutrient Flow, and Response to Perturbation in a Model Microbial Community Using "Omics" and Stable Isotope Probing Jill Banfield University of California, Berkeley
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingAssessment of Soil Fungal Diversity in Permafrost and Tallgrass Prairie Artificial Warming Soils by 28S LSU Pyrosequencing Jizhong Zhou University of Oklahoma
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingIntegrating Functional Groups of Genes into Carbon Decomposition Model Jizhong Zhou University of Oklahoma
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMicrobial Communities and Networks Along a Long-Term Permafrost Thaw Gradient in Alaska Jizhong Zhou University of Oklahoma
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMicrobial Community Responses to Warming in Temperate and Permafrost Soils as Revealed by Comparative Metagenomics Jizhong Zhou Georgia Institute of Technology
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingSoil Microbial Community Determines Vulnerability of Soil Carbon Exposed to Warming in Northern Permafrost Jizhong Zhou University of Oklahoma
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingA Metagenomic Insight into Freshwater Methane-Utilizing Communities and Evidence for Cooperation Between the Methylococcaceae and the Methylophilaceae Ludmila Chistoserdova University of Washington
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingChallenging the Plate Count Anomaly in Grassland Rhizosphere Mary Firestone University of California, Berkeley
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMicrobial Compositional and Functional Succession in the Rhizosphere Soil — Under Elevated and Ambient CO2 Mary Firestone University of California, Berkeley
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingMulti-Domain Stable Isotope Probing of Carbon Cycling in the Rhizosphere Mary Firestone University of California, Berkeley
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingExamining the Controls on CH4 Dynamics Along a Permafrost Thaw Gradient: C Isotopes and Organic Matter Structure Scott Saleska University of Arizona
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingSeason Drives Precipitation and N Deposition Impacts on Soil Nitrous Oxide, Methane and Carbon Dioxide Emissions, and Microbial Composition in a CA Grassland Steve Allison University of California, Irvine
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingCoupled High-Throughput Functional Metagenomics and Next Generation Sequencing for Reconciling Phylogeny and Function During Plant Litter Decomposition Steven Allison Lawrence Berkeley National Laboratory
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingResolving Cellular Metabolisms of Diverse Anaerobic Methane Oxidizing Consortia at the Single-Cell Level Victoria Orphan California Institute of Technology
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingExamining the Controls on CH4 Dynamics Along a Permafrost Thaw Gradient: Microbial Community Composition and Expression Virginia Rich University of Arizona
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingA Systems Biology View of the Methanosarcinales William W. Metcalf University of Illinois
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingCarbon Cycling by Microbial Communities in High Arctic Active Layer and Permafrost: A Combined Geochemical, Genomic, and Proteomic Approach Tullis Onstott Princeton University
Biological Systems Research on the Role of Microbial Communities in Carbon CyclingPatterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Biogeochemical Gradients and Methane Emissions* Susannah Tringe DOE Joint Genome Institute
Small Business Innovation Research (SBIR)Development of a Descriptive Phenotypic Ontology and Associated Online Resources George Garrity NamesforLife, LLC and Michigan State University

*Early Career Program