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Genomic Science Program

Early Career Awards

Genomic Science Program
Early Career Research Program Awardee Abstracts

The Early Career Research Program is managed by DOE’s Office of Science and awards research grants to young scientists and engineers at U.S. universities and national laboratories. The grants are designed to bolster the nation’s scientific workforce by providing support to exceptional researchers during the crucial early years of their careers.

Opportunities exist in the following program areas: Advanced Scientific Computing Research, Biological and Environmental Research (BER), Basic Energy Sciences, Fusion Energy Sciences, High Energy Physics, and Nuclear Physics. For more information, see the DOE Office of Science Early Career Research Program website.

Early Career Awards funded by BER’s Genomic Science program are described below.

Fiscal Year 2017

Microbial Environmental Feedbacks and the Evolution of Soil Organic Matter
Nicholas J. Bouskill, Lawrence Berkeley National Laboratory
The vast majority of Earth’s organic matter is stored in soil. The products of microbial metabolism as well as dead microbes (necromass), along with residues from plants and other organisms at different stages of decomposition, constitute a large fraction of that soil organic matter (SOM). The ability of microbes to modify and degrade SOM depends on physicochemical characteristics of the soil, affecting SOM stability and persistence. While the contributions of microbes to the decomposition and loss of SOM have been intensively studied, their role in maintaining the terrestrial SOM is poorly understood. Specifically, how fungi, bacteria, and archaea participate in the production of SOM, the interaction between SOM and minerals, and the formation of soil aggregates remain significant gaps in the understanding of the terrestrial nutrient cycle. The chemical composition of SOM is largely determined by soil bacterial metabolism, which is impacted by changes in rainfall patterns. This research will conduct field and laboratory experiments and computational modeling to understand the role of microbial communities in stabilizing SOM under different water availability conditions in tropical soils. The results of this project will increase understanding of the effects that microbes have on the global geochemical and nutrient cycles, addressing DOE’s mission in energy and the environment.

Awakening the Sleeping Giant: Multi-Omics Enabled Quantification of Microbial Controls on Biogeochemical Cycles in Permafrost Ecosystems
Neslihan Taş Baas, Lawrence Berkeley National Laboratory
Large expanses of permanently frozen soils, called permafrost, are found in the Earth’s polar regions. Arctic soils store large amounts of biomass and water from warmer periods in the history of Earth that became preserved in permafrost during cooling and glaciation events. Permafrost soils contain a broad diversity of cold-adapted microbes, whose metabolic activity depends on environmental factors such as temperature changes that cause cycles of freezing and thawing in the soil. Microbial metabolism leads to decomposition of soil organic matter, substantially impacting the cycling of nutrients and significantly affecting the Arctic landscape. However, the relationship between permafrost microbial properties and biogeochemical cycles is poorly understood. This project will use field experiments, laboratory manipulations, and multi-omics approaches to examine how microbial processes, biogeochemical transformations, and hydrology interact during permafrost thaw in different sites in Alaska to determine how these factors drive biogeochemical cycles in different Arctic soils. This project will lead to an in-depth understanding of the underlying microbial processes governing biogeochemical cycles in an environment relevant to DOE’s mission.

Determining the Genetic and Environmental Factors Underlying Mutualism within a Plant-Microbiome System Driving Nutrient Acquisition and Exchange
David J. Weston, Oak Ridge National Laboratory
The importance of symbiosis is highlighted in plant-microbe interactions where a microbe can acquire nitrogen from the air (nitrogen fixation) and provide it to the plant in exchange for sugars necessary for growth and metabolism. However, such beneficial interactions can shift to commensal (neutral) or even antagonistic, depending on genetic and environmental factors that are poorly understood. This project will provide a fundamental quantitative understanding on the role of plant host and microbial genetics on maintaining beneficial symbiosis during environmental perturbations. With that fundamental understanding, it will be possible to select host and microbes with the appropriate genetic makeup to manipulate symbiotic relationships adapted to different environmental conditions. The study systems will be a community composed of the moss Sphagnum and nitrogen-fixing cyanobacteria because of the genomic resources available for these organisms and their suitability for advanced genomic and imaging technologies. This effort will identify the genes and metabolic functions involved in nutrient exchange between the interacting plants and microbes and determine how symbiotic systems respond to environmental perturbations in laboratory and field settings. Ultimately, fundamental knowledge of the genetic and environmental factors driving plant and microbial nutrient exchange will enhance the understanding of nutrient cycling in natural systems and provide the foundation to improve bioenergy crop productivity in more complex biological communities.

Genomes to Ecosystem Function: Targeting Critical Knowledge Gaps in Methanogenesis and Translation to Updated Global Biogeochemical Models
Kelly C. Wrighton, The Ohio State University
Natural freshwater temperate wetland systems currently represent the largest natural source of atmospheric methane but are relatively understudied using systems biology tools (e.g., meta-omics) compared to other high-producing methane systems (e.g. peat, tropical, or reconstructed wetlands). Using field investigations at the NOAA-operated sentinel site on Lake Erie, methane-producing activities and responses to geochemical conditions will be determined along seasonal and spatial gradients (Objective 1). Here, a combination of high-throughput activity and gas measurements, combined with high-resolution systems biology and analytical methods, will provide in-depth knowledge of the microbiological, chemical, and physical constraints on methane production in wetlands. Using laboratory microcosms, the formation of anoxic microsites and their capacity to facilitate methane production in wetland soils will be simulated (Objective 2). This objective will validate the findings from the field investigations, offering a more controlled environment for teasing out the role of different, yet interrelated, variables. Lastly, these field and laboratory data will be used for multiscale, process-level evaluation of an ecosystem biogeochemical model that accommodates these newly identified processes and parameterizes representation of these processes along relevant environmental gradients (Objective 3). This research will identify multiple interacting geochemical, ecological, and metabolic constraints that are poorly understood, oversimplified, or missing in global biogeochemical methane models. This proposal targets the role of oxygen limitation on methane processes in soil domains to improve reactive transport models of microbial carbon cycling across terrestrial-aquatic soils and generate data on nutrient cycling activities in Great Lake wetlands. This information could provide new insights into the microbial controllers of Lake Erie eutrophication.

Fiscal Year 2016

Molecular Interactions of the Plant-Soil-Microbe Continuum of Bioenergy Ecosystems
Kirsten S. Hofmockel, Pacific Northwest National Laboratory
The accumulation and stabilization of organic matter in soil are important for the global carbon cycle because organic matter contributes to soil fertility and helps reduce the release of the greenhouse gas carbon dioxide into the atmosphere. A better understanding of the processes related to soil carbon accumulation is critical for designing strategies to increase soil carbon storage. Emerging experimental and theoretical evidence suggests that the residues of dead soil microbes play an important role in increasing the stabilization and long-term storage of carbon in soil. This project will study the deposition of dead microbial cells on different mineral surfaces and its effects on long-term carbon stabilization in soils used for both annual and perennial bioenergy crops. This research will identify the metabolic pathways and chemical components of microbes that contribute to soil carbon accumulation under controlled laboratory conditions. Field experiments will also be conducted to characterize the accumulation of microbial cells in response to crop selection and soil characteristics. The experimental data will be used to develop models of carbon cycling in bioenergy cropping systems under different soil conditions. These models will generate new knowledge on beneficial plant-microbe-soil interactions that increase carbon storage in biofuel agroecosystems. As new marginal lands are cleared and greater quantities of biomass are harvested, this project will provide the basic science needed to develop sustainable biofuel feedstocks to ensure healthy soils and promote a low carbon-economy outcome.

Spatially Resolved Rhizosphere Function: Elucidating Key Controls on Nutrient Interactions
James J. Moran, Pacific Northwest National Laboratory
Microbes play a key role in providing nutrients to plants. A better understanding of plant-microbe interactions is thus important for ensuring sustainable biofuel production from plant feedstocks in the face of a changing climate. Plants acquire their nutrients from the soil around their roots (the rhizosphere) through a process controlled by a dynamic suite of biogeochemical cycles. These cycles facilitate nutrient exchange among the soil, microbes, and plant roots through the rhizosphere interface. There is spatial heterogeneity in both microbial activity and nutrient accessibility throughout this interface. This project will improve the understanding of the spatial controls on rhizosphere nutrient exchange, identify key microbial functions involved in nutrient exchange, and test whether nutrient amendments to the soil can be used to stimulate plant-microbe interactions in spots of high activity (i.e., hotspots) within the rhizosphere to increase plant biomass productivity. Central to this study is the use of a series of spatially resolved techniques to pinpoint specific locations within the rhizosphere where enhanced nutrient exchange between roots and soil organisms occurs. How these nutrient exchange hotspots are generated will be characterized through elemental and functional analyses of the rhizosphere. Fundamental understanding of these crossroads of nutrient exchange at the spatial scale of the rhizosphere will form a knowledge framework for directed manipulations of these complex, yet vitally important, nutrient conduits. Ultimately, effective management of rhizosphere processes will enable enhanced plant nutrient acquisition from marginal lands, thereby contributing to improved biofuel feedstock productivity with lower chemical inputs.

Host-Microbial Genetic Features Mediating Symbiotic Interactions in the Bioenergy Crop Salix
Wellington Muchero, Oak Ridge National Laboratory
Many microbes present in the soil surrounding plant roots (the rhizosphere) can be beneficial for the plant, promoting growth and the incorporation of carbon dioxide into the plant biomass. Yet, only 10% of the microbes in the rhizosphere are able to establish a beneficial interaction with plant hosts due to defense mechanisms that evolved in plants to protect them from microbial infections. Those defense mechanisms pose a fundamental challenge in the utilization of symbiotic microbes to enhance sequestration of carbon dioxide, a potent greenhouse gas, and its fixation into economically valuable plant feedstocks. In compatible plant-microbe interactions, biomass increases of up to 200% have been achieved in perennial feedstocks inoculated with growth-promoting symbiotic microbes. However, compatible interactions are largely host specific, thereby limiting application across diverse plant species. Using Salix (i.e., willow), a widely used biofuel feedstock and pioneer species with increasing presence in the warming arctic region, this project will identify and characterize unique host-derived genetic factors that allow select microbes to successfully evade defense mechanisms and establish a functional presence inside the plant with no adverse effects. The plant cell surface contains proteins called membrane-bound pattern recognition receptors (PRRs) whose function is to recognize microbes with high fidelity through their microbe-associated molecular patterns (MAMPs). Upon recognition of MAMPs, PRRs trigger a signaling cascade that results in the suppression of host defense mechanisms and facilitates plant colonization by the microbe. Understanding these molecular dynamics presents a unique opportunity to couple new growth-promoting microbes with willow to increase carbon sequestration in the vulnerable arctic region. This project will advance DOE’s missions in energy and the environment by increasing plant biomass yields for the sustainable production of cellulosic biofuels.

Does Mycorrhizal Symbiosis Determine the Climate Niche for Populus as a Bioenergy Feedstock?
Kabir G. Peay, Stanford University
Microbes are found in virtually every environment on Earth, and many of them play beneficial roles, maintaining the health of plants and animals. Perhaps the most ubiquitous form of beneficial interaction in terrestrial ecosystems occurs between fungi and plant roots. In these fungus-root (or “mycorrhizal”) symbioses, the plant provides sugars that feed the fungus that in turn supplies the plant with critical nutrients such as nitrogen and phosphorous. Most plants are associated with a diverse variety of mycorrhizal fungi. However, the ecological factors that control the distribution and abundance of mycorrhizal symbioses are still poorly understood. To advance toward understanding the role of climate, soil environment, and mycorrhizal interactions in determining growth and competition in plant communities, this project will focus on Populus, a native North American tree and a potential biofuel feedstock, and the mycorrhizal fungi associated with it. Using a global forest database, the distribution of different Populus-mycorrhizal associations will be mapped and modeled across different regions and climates. Based on those models, laboratory experiments will be conducted to measure the precise ways in which beneficial plant-mycorrhizal interactions determine the distribution of Populus in its natural habitat and how these interactions affect competition with other tree species. Finally, the flow of carbon from Populus to mycorrhizal fungi and other soil microbes will be studied in different environmental conditions using stable isotope labeling. These experiments will not only provide fundamental insights into the way beneficial interactions shape the natural world, they will also allow the prediction of how carbon flow is affected by climate change. The knowledge gained in this project will have a direct impact on predicting the suitability of different environments for bioenergy crops.

Fiscal Year 2015

Functional Characterization and Regulatory Modeling of Lignocellulose Deconstruction in the Saprophytic Bacterium Cellvibrio japonicus
Jeffrey G. Gardner, University of Maryland–Baltimore County
The degradation of plant biomass (lignocellulose) is a critical component of global carbon cycling and renewable energy production. Every year, microorganisms in the environment degrade 100 billion tons of plant biomass. These microorganisms have found effective ways to completely break down plant biomass and use it for energy. This process is very efficient because the microorganisms in the environment produce large numbers of enzymes that can degrade lignocellulose. While some of the mechanisms of lignocellulose breakdown are understood, less is known about which enzymes are essential to plant biomass degradation and how their production is regulated. There is little understanding of how plant biomass degradation is regulated in bacteria because it is not known how these microorganisms are able to detect plant biomass as a nutrient source. This project will use the plant biomass-degrading bacterium Cellvibrio japonicus to address these questions. Using next-generation DNA sequencing technologies, this research will determine which enzymes are highly produced when C. japonicus is degrading lignocellulose. This information will direct additional experiments to identify the essential enzymes for plant biomass degradation and will compare the enzymes that C. japonicus produces to those currently used for biofuel production. Finally, by understanding how C. japonicus effectively degrades plant biomass, this project will create a model of how microorganisms in the environment are able to detect lignocellulose as a nutrient. The knowledge obtained from this research will help develop biotechnology strategies to enhance the economical production of biofuels.

Defining the Minimal Set of Microbial Genes Required for Valorization of Lignin Biomass
Elizabeth S. Sattely, Stanford University
As the world population surpasses 7 billion, science and engineering are faced with the pressing challenge of creating technology to shift reliance on petroleum resources to renewable feedstocks for the production of liquid fuels and platform chemicals. A primary candidate feedstock is plant biomass, where most current efforts have focused on converting cellulosic sugars to biofuels, replacement petrochemicals, and novel renewable materials. However, the other major fraction of plant biomass is lignin, a hydrocarbon-rich biopolymer left over after cellulose is used to make ethanol and other liquid biofuels. Lignin is the second most abundant biopolymer on Earth and represents a critically underutilized renewable resource that could be a major feedstock for future biorefineries. Unfortunately, without sufficient tools to convert lignin into its simple aromatic components, valuable compounds from this abundant biopolymer cannot be generated; instead, lignin is typically burned for thermal energy. This project will use a novel approach to identify the minimal set of microbial enzymes necessary for the synthesis of valuable chemicals from lignin as a byproduct of biofuel production from biomass. This research will examine two separate stages of lignin breakdown carried out by the microbes that do it best: (1) early breakdown of lignin into soluble fragments by wood-rotting fungi and (2) further conversion of those lignin fragments into useful chemicals performed by specific soil microbes. The initial goal of the project is the discovery and biochemical characterization of the enzymes required for lignin metabolism. The fungal and bacterial genes that code for those enzymes then will be used to engineer a microbial host that will efficiently convert lignin waste streams directly into valuable platform chemicals. This effort will leverage DOE investments in microbial genome analysis and secure a critical channel for lignin biomass utilization that will also help to render lignocellulosic biomass a viable feedstock for the production of renewable liquid biofuels.

Fiscal Year 2014

Understanding Microbial Carbon Cycling in Soils Using Novel Metabolomics Approaches
Trent R. Northen, Lawrence Berkeley National Laboratory
To predict and mitigate the adverse effects of climate change, improved understanding of carbon cycling in soils is urgently needed. Carbon is accumulated in soils as decayed plant matter and chemically transformed by the metabolism of microorganisms that live in the ground. The products (metabolites) of these transformations carried out by microbes make up a large fraction of the soil carbon. While very little is known about the metabolite composition of soils, much is known about the types of microorganisms found in soils. This is a result of significant efforts to study soil microbes using DNA sequencing technologies. Unfortunately lacking, however, are the vital data needed to enable scientists to link this sequence information to the microbial metabolic transformations that govern carbon cycling in soils. The project will help bridge this gap by resolving the current “black box” of soil metabolites and develop approaches to understand how specific microorganisms produce and transform the soil metabolite pools. This will be achieved by pioneering analytical technologies to identify and quantify soil metabolites. These technologies will be used to characterize the cascades of microbial activities that follow wetting of dry soils to correlate soil metabolite composition and microorganisms’ activities. Detailed methods will then be developed to determine the uptake and release of specific soil metabolites by key soil bacteria to make and test predictions of carbon cycling based on DNA sequence data. This program will provide an urgently needed complement to DNA sequencing that will enable the understanding and mathematical modeling of soil carbon cycling, ultimately improving the ability to predict and mitigate the effects of climate change.

Microbial Carbon Transformations in Wet Tropical Soils: The Importance of Redox Fluctuations
Jennifer Pett-Ridge, Lawrence Livermore National Laboratory
Tropical forest soils store more carbon—in the form of plant litter and decomposed organic matter—than any other terrestrial ecosystem and play a critical role in the production of greenhouse gases (e.g., methane, nitrous oxide, carbon dioxide) that affect both atmospheric chemistry and climate. Humid tropical forests also exchange vast amounts of carbon, water, and energy with the atmosphere and can lose large amounts of dissolved carbon via runoff and leaching. The rapid carbon cycling characteristic of wet tropical ecosystems is driven in part by high rainfall and warm temperatures. This combination of environmental conditions causes tropical soils to alternate between oxygenated and anaerobic conditions and affects the behavior of tropical soil microorganisms that regulate many aspects of the belowground carbon cycle. In the coming half century, tropical forests are predicted to see a 2 to 5 degree Celsius temperature increase and substantial differences in the amount and timing of rainfall. Although the importance of tropical soils to the global carbon cycle is clear, the current understanding of how soil carbon cycling in wet tropical forests will respond to climate change is surprisingly poor. This makes predicting future climate impacts extremely difficult. The ability to forecast how new moisture and temperature patterns will shape tropical microbial activity is also a gap in knowledge because so little is known about the fundamental abilities and chemical preferences of tropical soil microorganisms. If wet tropical forests experience shifts in rainfall patterns, becoming generally drier and more aerated, microbially mediated processes that produce greenhouse gases or help store soil carbon will likely be affected. Only a few studies of microbial diversity have been conducted in wet tropical soils, and only a handful of them have evaluated microbial function with modern DNA sequencing technologies. This project will examine the genomic content and potential of tropical soil microorganisms as they experience shifts in soil temperature, moisture, and oxygen availability. By also tracking the degradation and fate of organic carbon compounds, this work will increase the accuracy of predictions about how microbial processes affect whether organic carbon is retained or lost from tropical systems. The mechanistic understanding produced by this research will directly benefit attempts to improve the predictive capacity of mathematical models that forecast future tropical soil carbon balance.

Fiscal Year 2013

Extreme Expression of Cellulases in Poplar
Heather D. Coleman, Syracuse University
Cellulose, the major component of plant cell walls, is composed of long chains of sugars linked together. Plant cellulosic biomass (stalks, trunks, stems, and leaves) provides a vast untapped source of sugars that can be fermented to produce biofuels. Sugars are extracted from biomass using enzymes (cellulases) that break down cellulose. However, a major roadblock to developing an economically viable cellulosic biofuel production process is the cost of those enzymes, typically produced and purified using bacteria or fungi. An alternative and potentially more economic approach is to produce the enzymes within the plant itself. The goal of this research is to implement a new genetic engineering technology to produce large amounts of exogenous cellulases into poplar cells. This technology allows the researcher to control the production of the enzymes within the plant using an inducer substance that triggers the rapid accumulation of the cellulases. The transformation of poplar trees using this approach will increase the efficiency of converting cellulose to fermentable sugars and will increase the understanding of plant cell walls. Furthermore, the cellulases produced by these transformed trees could be purified in a cost-effective way, paving the way for developing a sustainable alternative for the production of biofuels from woody feedstocks.

Developing Synthetic Biology Tools to Engineer Plant Root Systems and Improve Biomass Yield and Carbon Sequestration
Dominique Loque, Lawrence Berkeley National Laboratory
Dedicated crops for bioenergy production must be grown in marginal environments to avoid competition with food crops that are cultivated in high-quality arable land. However, nutrient and water availability is very low in these marginal environments. Therefore, energy crops must be engineered to improve their ability to extract those vital elements from poor soils so that they can reach their full yield potential without the cost and environmental impact of chemical fertilization. The root system not only anchors a plant to the ground but is responsible for acquiring essential mineral nutrients and water and for maintaining interactions with the soil environment, all critical for plant growth. Despite their importance for biomass accumulation, plant roots are relatively understudied and few engineering tools area available to better understand and improve root function. This project will address this need by developing “universal” root expression tools that are functional across a broad range of plant species. These tools will be used to engineer metabolic pathways that will be designed to optimize nutrient acquisition by energy crops such as switchgrass and Camelina. This research will deliver a diversity of building blocks for plant root engineering that will be instrumental in advancing DOE goals for sustainable production of bioenergy.

Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown
Michelle A. O’Malley, University of California, Santa Barbara
Renewable biofuels derived from plant biomass (stems, stocks, and leaves, mainly composed of cellulose and lignin) are attractive alternatives to petroleum-based fuels. To produce biofuels, enzymes are used to break down cellulose into simple sugars, which are then fermented into fuels such as ethanol and butanol. However, because the structure of cellulose is a tightly bound network of crystalline cellulosic fibers and lignin, existing biomass-degrading enzymes are not very efficient. New technologies to break down plant material into sugar can be developed by studying how microbes digest lignocellulose in biomass-rich environments, such as the digestive tract of large herbivores. Anaerobic fungi that live in the absence of oxygen and are native to the gut and rumen of these animals have evolved powerful enzymes to degrade plant biomass. This project will develop new experimental tools to engineer anaerobic fungi for lignocellulose breakdown and biofuel production. To accomplish this goal, a panel of anaerobic fungi will be isolated from different herbivores and screened for their ability to degrade several types of lignin-rich grasses and agricultural waste. Focusing on a model anaerobic fungus, the basic metabolic processes that control enzyme production will be determined. This information will be used to develop new genetic engineering strategies to manipulate gut fungi at the molecular level. Understanding the biology of these anaerobic organisms will result in the development novel platforms for biofuel production.

Application of Next-Generation Sequencing to Engineering mRNA Turnover in Cyanobacteria
Brian F. Pfleger, University of Wisconsin–Madison
The ability to control gene expression in microorganisms is essential for biotechnology applications such as renewable fuel production and carbon dioxide fixation. To carry out their function, genes coded in the DNA must be transcribed into a messenger RNA (mRNA), which is translated into a protein with biological activity. While the processes of transcription and translation are well understood in many organisms, much less is known about the stability of the mRNA and how its lifespan affects gene expression. Thus, genetic engineering tools used to express foreign genes in microbes rarely consider key factors that influence mRNA stability. The goal of this project is to fill this gap in knowledge for a model photosynthetic bacterium, a cyanobacterium. Using the latest DNA sequencing technologies, this research will identify mRNA sequence features that affect the rate of mRNA turnover. Those features will be used to design strategies for altering mRNA stability and to improve oil production in cyanobacteria. The planned experiments will leverage the DOE Joint Genome Institute’s DNA and RNA sequencing capabilities and will contribute data for the computational infrastructure provided by the DOE Knowledgebase. The knowledge gained from this project will help the development of more accurate gene expression models and will facilitate metabolic engineering projects needed to advance toward the sustainable production of biofuels.

Fiscal Year 2012

Repurposing the Saccharomyces Cerevisiae Peroxisome for Compartmentalizing Multi-Enzyme Pathways
John Dueber, University of California–Berkeley
To replace fossil fuels and other chemicals with biofuels and biomaterials from renewable sources, microbes can be engineered to alter their metabolism to maximize production of the desired chemicals. To do this, biosynthetic pathways from other species are added to a host organism, often resulting in the accumulation of new chemical compounds that are detrimental to the engineered microbe. Thus, a major challenge in microbial engineering is to enable high-yielding biofuel production without affecting the microorganism’s health. One solution to this problem is to spatially separate engineered metabolic pathways from the rest of the metabolic machinery within the microbial cell. In fact, many organisms already use subcellular compartments, called organelles, to isolate cellular functions by encapsulating components within impermeable membranes. The goal of this research is to repurpose one of these organelles, specifically the peroxisome, for use in engineered yeasts. The peroxisome is unique in that it is not necessary for healthy cellular growth in most environmental conditions. Therefore, this organelle can serve as a minimal compartment where unnecessary components are replaced by desired ones. This research will determine how the peroxisome can be specialized for encapsulating synthetic metabolic processes that can facilitate the production of biofuels to address DOE’s mission of advancing the development of renewable energy sources.

Metabolism and Evolution of a Biofuel-Producing Microbial Coculture
James McKinlay, Indiana University
Some microbes can convert renewable resources such as carbohydrates and sunlight into biofuels. Therefore, they offer an urgently needed alternative to nonrenewable fuels. Most research efforts in this area have focused on genetically engineering individual microbial species to improve biofuel production. However, a lesson can be taken from nature, where multiple microbial species help each other to thrive on food sources such as plant residues that the individual species cannot use on their own. Furthermore, mixtures of specialized microbes can sometimes outperform a single engineered strain for producing chemicals of value to society. This research will make use of a mixture of two microbial species (i.e., a coculture) that work together using sugar and energy from sunlight to produce more hydrogen gas than either microbe could by itself. A major challenge in using cocultures is ensuring that the different species maintain a long-term cooperative relationship. This research will stabilize such cooperation by forcing each microbe to provide a nutrient that the other requires to survive. This approach enables experiments that will decipher how the metabolisms of the two species interact and thereby how they can be optimized for biofuel production. Studying the evolution of the microbes in the coculture will also lead to the discovery of traits that enhance biofuel production. This information will ultimately lead to the design and engineering of tailor-made microbial mixtures for the economical production of hydrogen gas and other biofuels from renewable resources.

Improved Sensitivity and Utility of Metaproteomics Analyses
Samuel Payne, Pacific Northwest National Laboratory
Microbial communities are found in virtually any environment. Understanding the relationship between microbes and their environment is key to the U.S. Department of Energy’s goal of manipulating microorganisms for biofuel production. Microorganisms use proteins to interact with their natural environments and digest their food for growth and survival. Analyzing proteins from microbial communities thus facilitates understanding the relationship between microbes and their environment. Mass spectrometry is a powerful technique to identify proteins in complex biological samples such as the microbes that constitute an environmental community. The objective of this project is to develop novel computational methods to dramatically improve the ability to detect and identify new proteins in these complex samples. Current protein identification methods require the use of protein databases to infer the function of the proteins present in the sample under study. The methods that will be developed in this project take advantage of the similarity among proteins that perform comparable functions in different organisms, circumventing the need for protein databases. These studies will focus on the cow rumen environment, where the microbial community degrades a variety of renewable resources such as plant residue. A final goal of the project is to improve the ability to identify the species of origin for newly discovered proteins within the cow rumen bacterial community. In a natural environment with thousands of different organisms, this complex process is crucial for understanding the specialized roles that individual microbes play within the community and how they convert plant material into biofuels.

Systems Approach to Engineering Cyanobacteria for Biofuel Production
Jennifer Reed, University of Wisconsin–Madison
Most of the energy consumed in the United States is derived from nonrenewable fuels (e.g., petroleum and natural gas), with a significant fraction of this energy being used for transportation. To reduce the amount of oil used to satisfy U.S. transportation energy needs and to alleviate dependence on foreign sources of oil, renewable sources of transportation fuels are needed. Cyanobacteria offer a promising route for directly converting solar energy and carbon dioxide into biofuels. Certain cyanobacterial strains can be engineered to produce butanol, a biofuel that is compatible with the existing infrastructure for fuel transportation and use. The objective of this research is to integrate computational modeling and experimental approaches to guide the engineering of cyanobacteria with improved butanol production. New computational approaches will be developed to facilitate the design of experiments, predict their outcomes, and evaluate the results. In this way, this project will identify genetic engineering strategies for improving butanol production in cyanobacteria. Experiments will subsequently be performed to construct and evaluate new engineered cyanobacterial strains. The developed approaches will be systematically applied to identify engineering strategies for improving production of a variety of biofuels in five other microorganisms, supporting the U.S. Department of Energy’s mission for developing renewable ways of producing advanced biofuels.

Deciphering the Genetic and Molecular Underpinnings of Carbohydrate-Degrading Systems in Ruminal
Garrett Suen, University of Wisconsin–Madison
Biofuels like ethanol can be obtained from cellulose present in plant cell walls. A challenge in the production of biofuels is the efficient breakdown of cellulose into simple sugars. Current industrial approaches rely on cocktails of cellulose-degrading enzymes. These strategies can be improved by identifying and characterizing more active enzymes. Arguably the most optimized natural cellulose degrading system is found in the rumen of domesticated cows. The rumen contains a diverse group of bacteria with highly active enzymes that digest cellulose in feed and convert this energy source into nutrients usable by the cow. This research will characterize the mechanism through which three bacteria from the rumen degrade cellulose. Each of these bacteria employs different strategies for cellulose degradation and will provide contrasting models that can increase the understanding of this fundamental process. This work will leverage existing genomic sequences for these bacteria to identify the genes and enzymes relevant for cellulose degradation. Importantly, these enzymes will be purified and biochemically tested for their capacity to degrade cellulose. Novel enzymes characterized in this way will not only expand the current set of cellulose-degrading enzymes but will also provide insights into how these specialized microbes accomplish cellulose degradation in natural systems. The results of this research will advance the DOE mission of supporting the development of advanced biofuels.

Enhancing Metabolic Flux to Photosynthetic Biofuels
Jamey Young, Vanderbilt University
Developing liquid transportation fuels that are both renewable and compatible with existing fuel infrastructure is a major research challenge of the next decade. Corn ethanol provides nearly all the renewable fuel currently used in the United States. However, attention is shifting to “advanced” biofuels that more closely resemble gasoline. Several recent studies have demonstrated the feasibility of producing advanced biofuels in engineered strains of photosynthetic cyanobacteria. These organisms could be used to produce liquid fuels directly from sunlight and carbon dioxide (CO2) on land unsuitable for agriculture, thereby minimizing energy-intensive harvesting, transporting, and degrading of plant-derived feedstocks. However, cyanobacterial fuel productivity is currently too low for industrial feasibility. Therefore, this project will test new metabolic engineering approaches for maximizing carbon flux from CO2 to biofuels in cyanobacterial hosts. Tools will be developed for analyzing carbon flux and engineering the metabolic pathways that result in biofuel production. This will be further optimized by reprogramming the “biological clock” that controls daily metabolic rhythms that may affect those metabolic pathways. This work will have an important positive impact on the development of bioprocesses that rely upon photosynthetic microorganisms. In addition, it will provide fundamental insights into the role of biological clock genes in regulating photosynthesis and carbon fixation in engineered cyanobacteria. This research will directly contribute to DOE’s mission by advancing toward production of renewable fuels that do not compete with agriculture.

Fiscal Year 2011

Engineering Robust Hosts for Microbial Biofuel Production
Mary Dunlop, University of Vermont
Microbes contain a vast diversity of metabolic pathways that can be subtly tweaked and redesigned for the conversion of biomass to biofuels compounds. Next-generation biofuels such as short-chain hydrocarbons are particularly attractive target molecules since they would be compatible with existing engines and infrastructure. However, high levels of these compounds are often toxic to the microbes synthesizing them, limiting the potential rate and yield of industrial biofuel production. The objective of this research is to understand hydrocarbon tolerance mechanisms used by microbes inhabiting natural hydrocarbon seeps or oil-contaminated sites, searching genome sequences of these organisms for efflux pumps and other molecular machines that microbes use to separate toxic hydrocarbons from their delicate biological systems. Promising candidates will be introduced into biofuel synthesizing strains of E. coli and tuned for optimal gene expression to determine if it is possible to engineer strains with enhanced tolerance to hydrocarbons and improved efficiency of overall synthesis.

Plant-Microbe Genomic Systems Optimization for Energy
Samuel Hazen, University of Massachusetts–Amherst
To evolve from promise to practice, essential optimization of each step of an advanced biofuel industry based on cellulosic biomass is already underway. In this research, a bioassay will be used to measure rates of ethanol production in various accessions of the energy crop model Brachypodium distachyon and then assess genetic diversity for this trait in this species. In doing so, the research will seek to resolve the mechanisms underlying plant feedstock quality through genetic analysis with a focus on energy crop improvement. As a second phase, to determine the plausibility of specific positive interactions between plant and microbial genotypes, pairwise comparisons will be made, varying both plant and microbial genotypes. Similar to adapting crop varieties to different environments, these experiments will link the need for specific feedstock properties to biomass conversion processes. Importantly, the development and optimization of unified plant-microbe genomic systems will advance the concept of “plant-microbe co-development” within the industry, thus improving the efficiency of cellulosic biofuels production from ecologically and economically sustainable resources without affecting the food supply.

Systems-Level Investigation of Uranium Resistance and Regulation by Caulobacter crescentus
Yongqin Jiao, Lawrence Livermore National Laboratory
Microbes are known to play a major role in influencing the movement of uranium and other environmental contaminants. In addition to simply surviving exposure to radionuclides, some microbes are capable of using these compounds to promote their growth, altering their chemical state to restrict their movement in the environment. However, understanding of the basic mechanisms that microbes use to perform these metabolic reactions is limited, especially in environments exposed to oxygen. This research project will examine the biological systems of the bacterium Caulobacter crescentus that allow it to detect uranium in the environment, accumulate the metal at the cell’s surface, and use it to generate energy via respiratory metabolism (essentially “breathing” uranium). The long-term goal of the project is to develop a conceptual model of uranium cycling that could be used to understand processes occurring at contaminated sites and inform potential bioremediation strategies.

Microbial Communities in Biological Carbon Sequestration
Susannah Tringe, Lawrence Berkeley National Laboratory
Wetland ecosystems are known to cycle and potentially store massive amounts of carbon on an annual basis. Carbon dioxide captured from the atmosphere by plants moves, through the action of roots or the death of biomass, below the water or soil surface where it is subject to the processing by complex communities of microorganisms. This can result in the degradation of organic carbon back to carbon dioxide or methane or to more stable forms that may be stored for long periods of time. Relatively little is known about the organisms performing these processes or what conditions influence the storage or release of carbon. The current research will use cutting-edge genomic techniques to examine microbial community structure and functional properties in a restored wetland habitat in San Francisco bay, with an emphasis on characterizing processes that result in increased biosequestration of organic carbon over time. The study will leverage resources at the U.S. Department of Energy Joint Genome Institute to link activities of dominant environmental microbes to major carbon cycle processes to enhance the understanding of critical biogeochemical cycles and ecosystem sustainability.

Fiscal Year 2010

A Systems Biology, Whole-Genome Association Analysis of the Molecular Regulation of Biomass Growth and Composition in Populus deltoides
Matias Kirst, University of Florida
The goal of this research is to identify the genes that are the basis for the variation in biomass and biofuel productivity–related traits in the genus Populus (the poplar tree). Poplars are the principal woody crop species used for clean, renewable, and sustainable fuels in North America because of their fast, perennial growth habit and wide natural distribution in a broad range of environments. This project will identify genes underlying bioenergy-associated traits in poplar using an innovative approach to map genome-wide changes related to lignocellulosic biomass formation. This novel method—that will use data from previously sequenced poplar cultivars to capture biomass-related genes in a poplar population—promises to reveal a much larger fraction of the poplar genetic diversity than previously possible. The results will help answer the very important question of which genes regulate biomass productivity and its composition.

Integrative Molecular and Microanalytical Studies of Syntrophic Partnerships Linking C, S, and N Cycles in Anoxic Environments
Victoria Orphan, California Institute of Technology
The objective of this research is to improve understanding of anaerobic oxidation of methane by microbes, a globally significant biogeochemical process. Anaerobic methane oxidation results in the consumption of methane, a potent greenhouse gas, in numerous anoxic environments and is thought to have potentially global climate significance as a biogeochemical carbon cycle pathway. This research will focus on a metabolic partnership between sulfate-reducing bacteria and methane-oxidizing archaea that allows metabolism of methane for energy under anoxic conditions. The work emphasizes the optimization of new technologies for visualization of interactions between the partner organisms at the level of single microbial cells and the tracking of joint metabolic processes.

Spatial and Temporal Proteomics for Characterizing Protein Dynamics and Post-Translational Modifications
Wei-Jun Qian, Pacific Northwest National Laboratory
This project aims to develop a suite of quantitative proteomics technologies that enable spatially resolved measurements of subcellular protein abundance changes and the dynamics of post-translational modifications in environmental eukaryotes to gain understanding of the regulation of cellular function. The research will integrate subcellular fractionation, post-translational modifications, and quantitative proteomics technologies to establish a general approach for enabling spatial and temporal proteomics. The effectiveness and utility of these technologies for biological applications will be demonstrated using the filamentous fungus Aspergillus niger, an organism that plays an important role in biofuel production and global carbon cycling, to attain a better understanding of how its morphology is regulated. The unique suite of technologies will have broad application in diverse studies of microbial and plant organisms and in systems biology studies aimed at better understanding of cellular machineries. Such capabilities not only provide core value for current systems biology efforts, but they also add unique datasets for refining gene models, genome annotation, and future predictive modeling.

Consolidating Biomass Pretreatment with Saccharification by Resolving the Spatial Control Mechanisms of Fungi
Jonathan Schilling, University of Minnesota
The aim of this project is to characterize enzymatic mechanisms used by brown rot fungi to degrade woody biomass. The research will examine the enzymatic mechanisms used by Postia placenta, a brown rot fungus, to degrade woody biomass, since this fungus has already “developed” its own solution to the efficient use of lignocellulose for energy production. In particular, the work will address potential spatial partitioning of delignification reactions used by fungi to prepare the wood for digestion from final enzymatic deconstruction of cellulose, a natural analogue to the separate steps used in industrial biomass treatment processes. A combination of physical characterization of partially digested wood samples, microscopic examination of the wood-fungus interface, and analysis of gene expression will be used to address the study questions. The aim of the work is to provide new mechanistic understanding of fungal processes that could be used to develop new approaches to consolidated industrial bioprocessing for biofuels production.



Bioenergy Research Centers 10-Year Retrospective: Breakthroughs and Impacts 2007-2017 [09/18]

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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