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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Contractors–
Grantees Meeting
USDA-DOE Plant Feedstock Genomics for
Bioenergy Meeting
February 2017

Abstract Book PDF

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, 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.

Genomic Science Contractors– Grantees Meeting and USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, February 6-8, 2017, Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Agenda PDF

Meeting Introduction
Todd Anderson, Director, Biological Systems Science Division, DOE BER

Individual Abstract PDFs

Principal Investigator Abstract Title
Adams, Paul High-quality protein production for structural studies: From plant cell wall synthesis to microbial production of bioproducts.
Adams, Paul Exposure History Dependence of Microbial Mediated Substrate Transformation Rates in Groundwater
Adams, Paul High-throughput testing of carbon source on microbial community assembly and antibiotic production
Adams, Paul Identification of Novel Biosynthetic and Catabolic Pathways in Diverse Bacteria Using Highthroughput Genetics
Adams, Paul Mechanism for Microbial Population Collapse in a Fluctuating Resource Environment
Adams, Paul Mechanisms of Uranium Reduction in Sulfate-Reducing Bacteria
Adams, Paul Microbes at the blurred boundary of natural and built environments
Adams, Paul Microbial Interactions with Natural Organic Matter Extracted from the Oak Ridge FRC
Adams, Paul Multiplex characterization of microbial traits using dual barcoded genome fragment expression library in diverse bacteria
Adams, Paul Stress mediates relative importance of deterministic and stochastic assembly in groundwater microbial communities
Adams, Paul Systems Biology Guided by Global Isotope Metabolomics
Adams, Paul Temporal Variability and Microbial Activity in Groundwater Ecosystems
Adams, Paul The role of adaptive evolution in shaping the structure and function of model microbial consortia
Adams, Paul Understanding the thermodynamic Foundations of microbial Growth Efficiencies in the Lab and Field
Allison, Steven Trait-based approaches for linking metagenomic data with microbial carbon cycling under drought conditions
Alonso, Ana Paula Development of Resources and Tools to Improve Oil Content and Quality in Pennycress
Amador-Noguez, Daniel Limited thermodynamic driving force in glycolysis of cellulolytic clostridia
Amador-Noguez, Daniel Development of metabolomic methods for investigating metabolic regulation of the MEP pathway in Zymomonas mobilis and Escherichia coli
Arkin, Adam Pooled Assembly, Genotyping and Scoring of Complex Synthetic Genomic Libraries
Baker, Scott Nitrogen limitation and lipid production in Yarrowia lipolytica
Balint-Kurti, Peter Physiological and Molecular-Genetic Characterization of Basal Resistance in Sorghum
Banfield, Jillian Microbial community proteogenomic analyses indicate extensive depth-dependent CO oxidation and C1 metabolism in soil and increased capacity for N2O reduction with increased rainfall
Beller, Harry Discovery of a Novel Bacterial Enzyme Enabling First-Time Biochemical Production of Toluene
Betenbaugh, Michael Constraint-Based Community Modeling Reveals Condition-Dependent Interactions
Blumwald, Eduardo Biocontainment in Perennial Grasses: Transgenic Pollen Ablation in Brachypodium sylvaticum and Panicum virgatum
Blumwald, Eduardo Genome Editing of CENH3 in Switchgrass and Brachypodium: A Histone Variant Essential for Centromere Specification
Brandizzi, Federica Optimizing MLG Production for Improved Biofuel Crop
Brem, Rachel Functional Genomics of Lipid Accumulation in Rhodosporidium toruloides
Brodie, Eoin A Trait Based Dynamic Energy Budget Approach to Explore Emergent Microalgal-Bacterial Dynamics and Productivity
Brown, Patrick A Sorghum NAC Gene Affects Vascular Development and Biomass Properties
Brown, Jack Developing Non-food Grade Brassica Biofuel Feedstock Cultivars with High Yield, Oil Content, and Oil Quality that are Suitable for Low Input Production Dryland Systems.
Brunner, Amy Spatiotemporal Transcriptomics of Populus Growth in Response to Daylength and Nutrient Availability
Bruns, Thomas D A Simple Pyrocosm for Controlled, Replicated Studies of Post-Fire Soil Microbial Communities
Bruns, Thomas Determination of the Roles of Pyrophilous Microbes in the Breakdown and Sequestration of Pyrolyzed Forms of SOM
Brutnell, Thomas High throughput phenotyping and quantitative genetics to understand productivity and drought traits in the model C4 grass Setaria
Brutnell, Thomas Utilizing Setaria viridis as a Model for Molecular Characterization of Jasmonate- Mediated Growth and Defense Responses
Brutnell, Thomas Quantitative Trait Loci for Leaf Carbon Isotopic Signature and Transpiration Efficiency in the C4 grass Setaria
Brutnell, Thomas Seteria viridis as a Model System to Accelerate Gene Discovery in Panicoid Grasses
Brutnell, Thomas Grasses Suppress Shoot-Borne Roots to Conserve Water During Drought
Brutnell, Thomas Development and application of novel phenotyping techniques to understand the genetic control of productivity and drought traits in the model C4 grass Setaria
Buckley, Daniel High Resolution DNA Stable Isotope Probing of Soil Indicates Changes in Microbial Community Metabolism Associated in Disturbance Due to Tillage
Buckley, Daniel Mapping microbial food web dynamics in soil with high resolution stable isotope probing
Buell, C. Robin Exploiting Natural Diversity to Identify Alleles and Mechanisms of Cold Adaptation in Switchgrass
Cannon, William Multi-scale Modeling of Circadian Rhythms: From Metabolism to Regulation and Back
Chapple, Clint Model-Guided Metabolic Engineering of Increased 2-Phenylethanol Production in Plants
Chapple, Clint Measurement and modeling of phenylpropanoid metabolic flux in Arabidopsis
Chen, Jay Plant-Microbe Interfaces: Populus genomics, genetics and molecular biology
Church, George Design, Synthesis, and Testing Toward a 57-Codon Genome
Church, George Exploring Species Specificity of Lambda Red Recombination
Church, George Non-Standard Amino Acid Incorporation in the New Era of Recoded Genomes
Church, George Retron Library Recombineering: Construction and Functional Interrogation of Trackable Genomic Edits
Clubb, Robert Quantitative Measurements of Cellulase Display in the Model Gram+ Microbe Bacillus subtilis Define Determinants Required for Enzyme Display and Activity
Cole, James RDP: Data and Tools for Microbial Community Analysis
Coleman, Heather Expression of a Hyperthermophilic Endoglucanase in Poplar to Improve Ethanol Production
Coleman, Heather Extreme Inducible Expression of Cellulases in Poplar
Coleman, Heather Modified Cell Wall Composition through Expression of an Expansin-Like Protein in Poplar
Comai, Luca A population of copy number variants for poplar functional genomics
Coon, Joshua GLBRC Targeted Metabolomics
Coruzzi, Gloria EvoNet: A Phylogenomic and Systems Biology approach to identify genes underlying plant survival in marginal, low-Nitrogen soils
Cuevas, Hugo Genomic dissection of anthracnose resistant response in sorghum [Sorghum bicolor (L.)]
Currie, Cameron Extracellular Products Mediate Bacterial Synergism in Cellulose Degradation
Cushman, John Leveraging Agave and Kalanchoe Genomics Resources to Transfer Crassulacean Acid Metabolism (CAM) Modules into C3 Species Using Synthetic Biology Approaches
Cushman, John Engineering Crassulacean Acid Metabolism (CAM) to Improve Water-use Efficiency of Bioenergy Feedstocks
Dantas, Gautam Aromatic tolerance and utilization in adapted Rhodococcus opacus strains for lignin bioconversion
Davison, Brian Combining Deuterium-Labeling and Neutron Scattering to GAin Molecular-Level Insights Relevant to Biomass Deconstruction
Davison, Brian Conformation of Low-Molecular Weight Lignin in Water: Insights on the Chemical Character of Lignin
Davison, Brian Deuteration Effects on Switchgrass Structure and Mechanism: Lignin Deposition Changes in Cell Walls of Deuterated Switchgrass
Davison, Brian Real-Time Elucidation of Structure and Morphology of Native and Mutant Poplar During Dilute Acid and Alkali Pretreatments Using Neutron Scattering
DeAngelis, Kristen Get Your Model Out of the Clouds! Ground-Truthing Assumptions About how the Earthfs Tiniest Engines Drive the Carbon Cycle
Ding, Shi-You Quantification of monolignol ferulate conjugate in Zip-lignin poplar by stimulated Raman scattering microscopy
Donohue, Timothy Using Genetic and Bioreactor Engineering to Produce Oleaginous Bacteria
Dueber, John Repurposing the Yeast Peroxisome for Compartmentalizing Multi-enzyme Pathways
Dunbar, John Ecological Factors Affecting Carbon Flow from Surface Litter
Dunbar, John Microbial Community Traits Linked to Carbon Flux Patterns in Soil
Dyer, John Genomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop
Edme, Serge Genetics and Genomics of Pathogen Resistance in Switchgrass
Eng, Thomas Genome Wide Identification of Bacterial Membrane Capacity Determinants
Evans, Sarah Is there a direct link between free-living nitrogen fixation rates and nitrogen mineralization rates?
Evans, Sarah The Effects of Growth Promoting Rhizobacteria and Endophytes on Switchgrass Growth and Root Architecture
Evans, Sarah Switchgrass Growth and Transcriptomic Responses to Nitrogen Availability and the Rhizosphere Microbiome
Evans, Sarah The Contribution of Alternative Nitrogenases to Nitrogen Fixation in Switchgrass Rhizospheres on Marginal Lands
Firestone, Mary Bacterial Traits Linking Avena Exudate Chemistry and Rhizosphere Bacterial Community Structure During Root Development
Firestone, Mary Monitoring fluxes of atmospherically-reactive gases (CO2, CH4 and N2O) during the conversion of grasslands into a biofuel crop (Panicum virgatum)
Firestone, Mary Plant-microbe and microbe-microbe interactions mediate switchgrass sustainability: following rhizosphere microbial communities during switchgrass establishment
Firestone, Mary Dissecting the Chemistry of Switchgrass-Microbe Interactions Using Cultivation, Exometabolomics and Mass Spectrometry Imaging
Firestone, Mary Faunal Population Dynamics Throughout Switchgrass Developmental Stages
Firestone, Mary Directing traffic in the rhizosphere: how phage and fauna shape the flow and fate of root carbon through microbial pathways
Firestone, Mary Mapping the pathways of root carbon flow into and through soil microbial food webs
Firestone, Mary Roots stimulate expression of decomposition transcripts in the soil microbiome
Fleming, Ronan Automatic generation of genome-scale metabolism and expression models for bacteria
Fleming, Ronan CHRR: Coordinate hit-and-run with rounding for uniform sampling of metabolic networks
Fleming, Ronan Comparative evaluation of atom mapping algorithms for metabolic reactions
Fleming, Ronan DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia
Fleming, Ronan Software development of The Constraint-Based Reconstruction and Analysis Toolbox
Fleming, Ronan Thermodynamically constraining a genome-scale metabolic model with von Bertalanffy .0
Fleming, Ronan Cardinality optimisation in constraint-based modelling of metabolism
Fox, Brian A Cellulase Family Reunion: Observing and Predicting the Structural Changes Accompanying the Evolution of GH5 Enzyme Specificity
Frey, Serita Fungal Responses To Elevated Temperature And Soil Nitrogen Availability
Frey, Serita Microbial Growth and Metabolism in Soil . Refining the Interpretation of Carbon Use Efficiency
Funnell-Harris, Deanna Resistance to Stalk Pathogens for Bioenergy Sorghum
Martin, Hector Garcia Quantitative metabolic modeling at the Joint BioEnergy Institute (JBEI)
Gardner, Jeffrey Systems analysis in Cellvibrio japonicus resolves predicted redundancy of Β- glucosidases and determines essential physiological functions
Ghirardi, Maria The Algal Ferredixin Interactome
Gill, Ryan A novel design strategy for industrially relevant, unnatural modular megasynthases
Gill, Ryan T. Combinatorial engineering of 3-hydroxypropionate production from hemicellulose hydrolysate
Gill, Ryan Developing a predictive method for tunable control over gene expression based on CRISPR interference technology
Gill, Ryan Enhanced CRISPR-based trackable protein engineering using modeling
Gill, Ryan Extending functional genome annotations using high-throughput CRISPRi
Gill, Ryan Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli
Gill, Ryan Genome-scale design and engineering approach towards optimizing ethylene production in E. coli
Gilna, Paul Characterization of Populus Transgenic Plants Overexpressing PtDUF266A (OXPtDUF266A) and Biofuel Production
Gilna, Paul Defined Tetra-Allelic Gene Disruption of the 4-Coumarate:Coenzyme A ligase 1 Gene by CRISPR/Cas9 in Switchgrass Results in Lignin Reduction and S/G Ratio Alteration
Gilna, Paul Evaluation of Multiple Levers for Overcoming the Recalcitrance of Cellulosic Biomass
Gilna, Paul Explaining and Predicting Biomass Recalcitrance with Rigidity Percolation Theory
Gilna, Paul Field Experiments of Nine Switchgrass TOP Lines
Gilna, Paul From Gene to Network: Switchgrass TOP Line RNA-seq Data Analysis Pipeline at BESC
Gilna, Paul Gene Expression Differences between Clostridium thermocellum Biofilm and Planktonic Cells Lead to Specialized Activities and Growth
Gilna, Paul Investigating the Role of Polysaccharide Methylation in the Plant Cell Wall
Gilna, Paul Lignin Valorization through Biologial Funneling
Gilna, Paul Metabolic Network Modeling of Clostridium thermocellum for Systems Biology and Metabolic Engineering
Gilna, Paul Modification of Pectin Biosynthesis Leads to Higher Biomass Yield and Saccharification in Bioenergy Feedstock
Gilna, Paul Modifying Carbon, Nitrogen, and Electron Metabolism in Clostridium thermocellum to Enhance Cellulosic Biofuel Yield and Titer
Gilna, Paul New Insights on the Lignin Pathway in Grasses
Gilna, Paul Pleiotropy Decomposition of 609 Populus trichocarpa Genotypes
Gilna, Paul Pyruvate Decarboxylase: Rationally Evolving Thermostable Enzymes for Metabolic Engineering
Gilna, Paul Rational Methyltransferase Expression in Escherichia coli for Transformation of New Organisms
Gilna, Paul Signaling Between Switchgrass and Fungal
Gilna, Paul Switchgrass Fermentation by Thermophilic Microbiomes
Gilna, Paul The Effect of Lignin and Hemicellulose Removal on Switchgrass Deconstruction by Clostridium thermocellum
Gilna, Paul The Unique Mechanism of the Dominant Multi-Component Cellulase from Caldicellulosiruptor bescii
Harrison, Maria Genetic dissection of AM symbiosis to improve the sustainability of feedstock production
Harwood, Caroline Plant-Microbe Interfaces: Probing the molecular mechanisms of plant-bacterial interactions
Hegg, Eric Using N and O Isotopes to Determine the Source of Microbial N2O Production
Hildebrand, Mark A Systems Biology and Pond Culture-Based Understanding and Improvement of Metabolic Processes Related to Productivity in Diverse Microalgal Classes for Viable Biofuel Production.
Hildebrand, Mark The Effect of Carbon Flux Topology and Synchronized Culture Growth on Microalgal Productivity
Hillson, Nathan j5 Software Through the Years: Insights from Aggregate Public Usage Metrics
Hofmockel, Kirsten Molecular interactions of the plant-soil-microbe continuum of bioenergy ecosystems
Hungate, Bruce Quantitative stable isotope probing with 15N in soil microbial communities
Hungate, Bruce Studying Microbial Stress Responses in Soil Ecosystems
Jacobson, Daniel Plant-Microbe Interfaces: Plant-based genome-wide association viriome/microbiome analysis (GWAVA)
Jiao, Yongqin Identification of a U/Zn/Cu responsive global regulatory two-component system in Caulobacter crescentus
Juenger, Thomas Climate adaption and sustainability in switchgrass: Exploring plant-microbe-soil interactions across continental scale environmental gradients
Kaeppler, Shawn Transcriptional Analysis of Flowering Time in Switchgrass
Keasling, Jay Engineering Polyketide Synthases to Generate Lightly Branched Biofuels
Kuske, Cheryl Comparative Analyses of the Genomes and Secretomes of Ascomycota Fungi Reveal Diverse Functions in Plant Biomass Decomposition
Kuske, Cheryl Meta-omic, Enzymatic and Soil Chemical Measures Identify Surface Soil Decomposition Processes as Influenced by N Amendment in a Temperate Pine Forest
Landick, Robert Optimization of Isobutanol Production by Zymomonas mobilis
Lee, Taek Soon Isopentenyl diphosphate (IPP)-bypass mevalonate pathways for C5 alcohol production
Lemaux, Peggy EPICON: Epigenetic Control of Drought Response in Sorghum
Liao, James Robust non-Oxidative Glycolysis in Escherichia coli
Liao, James Predicting multiple gene targets for optimal oil production in acetic acid metabolism of Yarrowia lipolytica by ensemble modeling
Lidstrom, Mary Communal Metabolism of Methane and the Rare Earth Element Switch
Loffler, Frank Multiomic Insights into the Activity and Dynamics of Soil Nitrifier Communities in Midwestern Agricultural Soils
Loque, Dominique Development of Novel Approaches to Optimize Energy Crops
Loque, Dominique Expression of S-adenosylmethionine Hydrolase in Tissues Synthesizing Secondary Cell Walls Alters Specific Methylated Cell Wall Fractions and Improves Biomass Digestibility
Loque, Dominique Transcript switches for fine-tuning of transgene expression
Lu, Chaofu Systems Biology to Improve Camelina Seed and Oil Quality Traits
Magnuson, Jon Rhodosporidium toruloides for conversion of depolymerized cellulose, hemicellulose, and lignin into bioproducts
Maravelias, Christos T Process Systems Engineering for Biofuels and Bio-based Chemicals
Maranas, Costas 13C-assisted flux elucidation using genome-scale carbon mapping models
Maranas, Costas Application of the MetRxn database to highlight multi-tissue/organisms and expansion to include algorithms for predicting novel reactions and pathways
Maranas, Costas Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production
Maranas, Costas k-ecoli457: A genome-scale Escherichia coli kinetic metabolic model satisfying flux data for multiple mutant strains
Marks, M. David Advancing Field Pennycress as a New Oilseed Biofuels Feedstock that does not Require New Land Commitments
Martiny, Jennifer Analysis of an Abundant Bacterial Genus in a Leaf Litter Community
Mayali, Xavier Isotope tracing and phylogenetic composition of simplified bacterial communities conferring growth and biomass enhancements to biofuel-producing microalgae
McCue, Lee Ann Chemical Analysis of Carbon and Nitrogen Cycling Through the Extracellular Matrix Produced During the Formation of a Multi-Species Community
McCue, Lee Ann High-Resolution Spatial Analysis Reveals How Nitrogen Source Governs Carbon Partitioning Between Members in a Phototrophic Consortium
McCue, Lee Ann Metabolite Characterization in Complex Microbial Communities
McCue, Lee Ann Modeling Approaches for Understanding Metabolic Coupling in Microbial Communities
McCue, Lee Ann Newly Identified Regulatory Roles for Vitamin B12 Suggest Coordination of Community Metabolism
McKay, John Germplasm Development for Sustainable Production of Camelina sativa Oil
McKinlay, James Factors Governing Mutualism Dynamics in a Hydrogen-Producing Coculture
Meile, Christof Potential Mechanisms of Anaerobic Methane Oxidation and Challenges to Slow-Growing Microbial Communities
Merchant, Sabeeha Functional analysis of copper and silver storage sites and their role in metal homeostasis in Chlamydomonas
Merchant, Sabeeha An O-Glycosylated Archaeal Flagellin
Ming, Ray Pyramiding genes and alleles for improving energy cane biomass yield
Moran, James Spatially Resolved Rhizosphere Function for Elucidating Key Controls on Below-ground Nutrient Interactions
Morgan, John Kinetic modeling of the phenylpropanoid pathway in Arabidopsis
Morrell-Falvey, Jennifer Plant-Microbe Interfaces: Comparative genomics and functional characterization of Populus-associated endophytes
Mortimer, Jenny Characterization of Plant Golgi-Localized Nucleotide Sugar Transporters
Muchero, Wellington Species-specific evolution of membrane.bound receptors mediating hostsymbiont specificity in the genus Salix
Mullet, John Utility of a Sorghum bicolor RNA atlas for improving energy sorghum stem composition
Mullet, John Genomics of Energy Sorghum's Water Use Efficiency/Drought Resilience
Navid, Ali System-level analysis of metabolic trade-offs and changes during diurnal cycle of Chlamydomonas reinhardtii
Newcombe, George Characterizing the Defense Hierarchy of Populus trichocarpa
Nielsen, Jens Leucine Biosynthesis is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica
Nielsen, Jens Lipid Accumulation and its Impact on Amino Acid Metabolism in Saccharomyces cerevisiae
Nikolau, Basil Integrated and Dynamic Multispectroscopic In Situ Imaging of Plant Metabolism at the Level of Subcellular Compartments
Noirot, Philippe Multi-Omics Analysis of a Mycorrhizal System
Noirot, Philippe Functional assignment of ligand specificities for Pseudomonas transport proteins
Noirot, Philippe Strain-Specific Transportomic Capacity of Pseudomonas fluorescens Linked to Plant Growth Promotion in Aspen Seedlings under Nutrient Stress
Noirot, Philippe Genetic Systems to Enable Biosystems Design in Rhizosphere Pseudomonas
Northen, Trent Linking Soil Biology and Chemistry Using Knowledge of Exometabolite Substrate Preferences
Northen, Trent Self-Assembled Gold Nanoparticle Film For Nanostructure-Initiator Mass Spectrometry With Passive On-Line Salt Fractionation
O'Malley, Michelle Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown
Orphan, Victoria Anabolic activity in Geobacter biofilms as a function of distance to insoluble electron acceptor
Orphan, Victoria Comparative genomics and functional characterization of assimilatory sulfate reduction in methanogenic and methanotrophic archaea
Pakrasi, Himadri Systems Level Study of a Novel Fast-Growing Cyanobacterial Strain for Next Generation Biofuel Production
Payne, Samuel Enabling Metaproteomics Research
Peay, Kabir Does mycorrhizal symbiosis determine the climate niche for Populus as a bioenergy feedstock?
Pelletier, Dale Plant-Microbe Interfaces: Understanding the Populus microbiome structure in response to host stress
Pett-Ridge, Jennifer Hyper-accumulated Mn, co-localized in Chlamydomonas reinhardtii acidocalcisomes with Ca and P, can be mobilized in Mn-deficient situations and protects against oxidative stress
Pett-Ridge, Jennifer How Redox Fluctuation Shapes Microbial Community Structure and Mineral- Organic Matter Relationships in a Humid Tropical Forest Soil
Petzold, Christopher High-throughput quantitative proteomic profiling of Escherichia coli central carbon metabolism
Pfleger, Brian RNase III as a Tool to Manipulate Transcript Stability: Identifying in vivo Targets in Escherichia coli
Polz, Martin Identifying the most efficient algal degrading communities: Diversity, composition and mechanisms
Polz, Martin The Ecology of Macroalgal Polysaccharide Utilization: Verrucomicrobia Isolates Initiate Fucoidan and Carrageenan Degradation Cascades
Rabinowitz, Joshua Glycolysis Balances Enzyme Efficiency and Metabolic Adaptivity
Rabinowitz, Joshua Systems-Level Analysis of Mechanisms Regulating Yeast Metabolic Flux
Ralph, John Suppression of CINNAMOYL-CoA REDUCTASE increases the level of monolignol-ferulates in maize lignins
Raman, Srivatsan Designing highly specific protein-based small molecule biosensors
Rao, Christopher Characterization of the Alginate Lyases and Laminarinases from Vibrio sp.
Rao, Chris Protein Acylomes in Fuel-Producing E. coli. Changes in Posttranslational Modifications with Different Carbon Sources
Rao, Christopher Amino Acids Are Preferred Over Glucose and Other Sugars in Escherichia coli by a Novel Mechanism of Carbon Catabolite Repression
Rao, Christopher Increasing growth yield and decreasing acetylation in Escherichia coli by optimizing the carbon-to-magnesium ratio in peptide-based media
Reed, Jennifer Approaches for Evaluating the Production Potential of High Volume Products in Microbial Systems
Reed, Jennifer Application of machine learning and active learning to enhance chemical yields in microbes
Rich, Virginia Linking Arctic Lake Sediment Microbial Ecology to Carbon Biogeochemistry
Rich, Virginia The IsoGenieDB: An Integrated Solution to Cross-Disciplinary Data Management
Robertson, Phil Methods for high-throughput massively parallel soil ecofunctional gene analysis
Robertson, G. Philip Associative Nitrogen Fixation across a Nitrogen Input Gradient
Robertson, G Philip Partitioning Nitrous Oxide (N2O) Emissions from Ammonia Oxidizing Bacteria (AOB) and Ammonia Oxidizing Archaea (AOA) in Corn and Switchgrass Ecosystems
Ronald, Pamela Functional analysis of cell wall related genes in Sorghum bicolor
Sale, Kenneth Formation of a phenyl-choline ether structure in lignin reduces inhibition of cellulase activity by lignin
Schachtman, Daniel Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome
Schachtman, Daniel Harvesting the Root Microbiome of Grasses toward Sustainable Increases in Crop Production
Schachtman, Daniel Metabolomics as a Molecular Tool to Understand the Mechanism of Nitrogen Use Efficiency and Interactions with the Soil Microbiome in Energy Sorghum.
Schadt, Christopher Plant-Microbe Interfaces: Dissecting the microbiome of Populus tree species from the soil to the canopy using amplicon sequencing and shotgun metagenomic analyses
Schadt, Christopher Plant-Microbe Interfaces: Linking host genotype fitness and soil conditions to microbiome community assembly in the Populus root-soil interface
Scheller, Henrik At the Interface: Glycoproteins, Glycolipids, and WAK-mediated Signaling are Required for Plant-Microbial Symbiosis in Medicago truncatula
Schilling, Jonathan Spatial Connectomics to Identify Agents Relevant to Lignocellulose Deconstruction in Fungi
Schilling, Jonathan Distinct growth patterns and time-dependent secretome alterations by two taxonomically divergent brown rot fungi
Scown, Corinne Life Cycle Assessment of Ionic Liquid-based Biofuel Production
Segre, Daniel Synthetic microbial ecology for biofuel production from lignocellulose
Shade, Ashley A New Synthetic Community System for Studying Microbial Interactions Driven by Exometabolites
Singer, Steven A Bacterial Pioneer Leaves a Complex Legacy
Singh, Anup Droplet-Based Analog and Digital Microfluidic Platforms for High-Throughput Screening and Synthetic Biology Applications
Singh, Seema Ionic Liquid Pretreatment Technology: Challenges and Opportunities
Siuzdak, Gary Systems Biology Guided by Global Isotope Metabolomics
Smart, Lawrence Genomics-Assisted Breeding for Leaf Rust (Melampsora) Resistance in Shrub Willow (Salix) Bioenergy Crops
Smart, Lawrence Differential Expression, Regulatory Divergence, and Sex Dimorphism Pervade the Shrub Willow (Salix spp.) Transcriptome
Stahl, David Factors Affecting Nitrous Oxide Production from Ammonia Oxidizers and Possible Mitigation Options
Stephanopoulos, Gregory Optimal feed control for maximization of lipid production from dilute acetic acid by an engineered oleaginous yeast Yarrowia lipolytica
Stephanopoulos, Gregory rewiring metabolism for maximum lipid production in oleaginous yeast Yarrowia lipolytica
Stuart, Rhona Exploring the functional aspects of microalgal interactions with associated microbes, predators and pathogens
Suen, Garret Evaluating the Cellulolytic Properties of Novel Fibrobacteres isolates from Mammalian Herbivores
Sullivan, Matthew Soil viral ecology along a permafrost thaw gradient
Thompson, Janelle Systems biology towards a continuous platform for biofuels production: Engineering an environmentally-isolated Bacillus strain for biofuel production and recovery under supercritical CO2.
Thompson, Janelle Systems biology towards a continuous platform for biofuels production: Heterologous gene expression and isobutanol synthesis in B. megaterium SR7 and biofuel extraction under supercritical CO2.
Tschaplinski, Timothy Plant-Microbe Interfaces: Metabolic consequences of the introduction of a Populus trichocarpa lectin receptor-like kinase into Arabidopsis thaliana, a non-ectomycorrhizal host species
Vilgalys, Rytas Plant-Microbe Interfaces: Characterizing the diversity and function of the ectomycorrhizome of Populus trichocarpa
Weber, Peter Quantifying the contribution of viruses and phage to nutrient cycling with NanoSIMS
Weston, David Plant-Microbe Interfaces: Model communities of Populus bacterial isolates to study mechanisms of microbiome function
Wilkerson, Curtis Exploring RNA-Seq Expression Data With GxSeq
Yang, Xiaohan Plant-Microbe Interfaces: Small-RNA (sRNA) and open reading from (sORF) response to endo- and eco-mycorrhizal symbioses in Populous
Yeates, Todd Design, Characterization, and Emerging Applications of Highly Symmetric Protein Nanostructures
Young, Jamey Mapping photoautotrophic metabolism of engineered cyanobacteria to identify reactions that limit production of renewable chemicals
Zengler, Karsten Omics-Driven Analysis of Clostridium ljundhalii Disentangles the Complexity of Energy Conservation in Autotrophic and Heterotrophic Growth Conditions
Zengler, Karsten Using a Metabolic and Gene-Expression Model to Predict and Analyze the Phenotypic Response of Acetogen Clostridium ljungdahlii
Zhang, Yaoping Comparative Studies of Diverse Feedstocks and Identification of High Levels of Hemicellulose and Degradation Inhibitors That Impact Microbial Biofuel Synthesis
Zhao, Huimin Optimization of Alginate Utilization in Engineered Bacteria for Biofuels Production
Zhou, Jizhong Long-term priming-induced changes in permafrost soil organic matter decomposition
Zhou, Jizhong Time-series metagenomics of experimentally warmed Alaskan tundra and Oklahoma temperate soils enables fine-resolution assessment of belowground C cycling feedbacks to climate change
Zhou, Jizhong Successional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping



Interagency Strategic Plan for Microbiome Research, FY 2018-2022 [04/18]

2018 Research Summaries [02/18]

GSP Overview Brochure [01/18]

Grand Challenges for Biological and Environmental Research: Progress and Future Vision [11/17]

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment [9/17]



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