The U.S. Department of Energy’s (DOE) Genomic Science program, managed within the Office of Biological and Environmental Research (BER), supports basic research aimed at identifying the foundational principles that drive biological systems.GSP aims to solve critical challenges in energy security and environmental stewardship. As part of its mission, BER invests in crosscutting technologies and programs to enable multiscale, systems-level research to achieve a predictive understanding of systems biology, biological community function, and environmental behavior. BER aims to provide the necessary fundamental science to understand, predict, manipulate, and design biological processes that underpin innovations for bioenergy and bioproduct research and to enhance the understanding of natural environmental processes relevant to DOE. BER supports fundamental research to understand the systems biology of plants and microbes through the GSP. The GSP’s portfolio includes research that builds on a foundation of genomic data and combines experimental physiology studies with “omics”-driven tools of modern systems biology and computational approaches to harness the power of microorganisms and microbial communities as cellular factories. Through this portfolio of highly interdisciplinary and integrated research projects, the GSP aims to meet the challenges associated with microbial production of advanced biofuels and bioproducts from plant-derived biomass.
The ability to manipulate microbial biosynthetic pathways and metabolism using synthetic biology provides unprecedented opportunities to address a wide range of topics related to DOE’s mission in sustainable bioenergy development. This includes research that enhances the production of advanced biofuels and bioproducts, as well as the conversion and upcycling of synthetic polymers. To enable a future where biological systems can be designed and modified for desired specific outcomes and deliver positive impacts for the environment and the bioeconomy, the GSP solicited applications in two subtopic areas for this Funding Opportunity Announcement (FOA): sustainable bioenergy and polymer upcycling.
The immense diversity and versatility of microbial metabolism offers the potential to sustainably produce bioenergy and bioproducts that are not dependent on fossil fuels. Realizing this potential requires a fundamental understanding of how biological systems behave. It is thus necessary to develop ways to design and control the functional capabilities within living systems to harness the biosynthetic processing power of the microbial world. The past decade has seen tremendous technological advances in the development of multiomics tools, high-throughput phenotypic screening approaches, and computational modeling methods to analyze, modify, and select specific functional properties of biological systems. Enhanced genomic biology capabilities allow for the development of pathways, strains, and microbial consortia to achieve novel chemistries, reduce barriers, and develop innovative solutions for biomass conversion. These advances, combined with new synthetic biology tools, provide an opportunity to help achieve DOE’s mission.
With the immense physiological and genetic diversity across the microbial world, there is potential to develop and engineer novel and model microorganisms with unique capabilities and biosynthetic pathways beyond what is currently used in industry. However, to engineer microorganisms to produce sustainable biofuels and bioproducts derived from lignocellulosic plant biomass or using carbon produced as a byproduct of photosynthesis, it is necessary to improve our understanding of microbial physiology and metabolism. It is also imperative to determine how to efficiently shunt precursors and intermediates from central metabolism into complex products while rebalancing organismal carbon allocations. Systems biology-driven approaches will build on the understanding of these processes to design new pathways and tools for biofuels and bioproducts.
This subtopic specifically targeted systems biology-driven basic research for the production of advanced biofuels (i.e., biologically synthesized compounds with the potential to serve as energy dense transportation fuels such as gasoline, diesel, and aviation fuel) compatible with existing engines and fuel distribution infrastructure, and for the production of useful bioproducts. In this context, the following areas were of interest:
Globally, more than 350 million metric tons of plastic polymers are produced annually, and their production is anticipated to quadruple by 2050. As much as three quarters of this material is single use, and only a small proportion is currently recycled. Key difficulties, such as separating mixed waste streams and the need for high temperatures or specialized catalysts for their conversion to usable chemical forms, present important economic disincentives for recycling. Discarding plastics into landfills wastes the energy equivalent of tens of billions of dollars annually and creates a long-term, unsustainable waste legacy. Biological solutions for polymer upcycling may offer unique advantages over traditional thermal cracking and catalyst-based approaches by allowing processing at ambient temperatures, eliminating the need for specialized metal catalysts, and potentially reducing capital investment. However, biological solutions for the breakdown of most synthetic polymers are currently unavailable, representing an important knowledge gap and basic research opportunity.
BER intends to build on rapid advances in genomic science, biosystems design, and computational biology to develop enhanced capabilities for biologically based polymer recycling. BER seeks to apply principles of genome engineering and microbiome science to deconstruct polymers and/or to convert polymer waste streams to usable monomers for new materials. Though synthetic polymers are typically considered to be highly recalcitrant to biological depolymerization, evidence indicates that some plastics, such as polyethylene terephthalate (PET) and ester-based polyurethanes, can be enzymatically deconstructed. However, enzymatic pathways for the depolymerization of many other polymers, such as polystyrene, polyamides, or ether-based substrates, remain unknown. Leveraging the tools of synthetic and computational biology may provide opportunities to redesign metabolic pathways in established or emerging model organisms and/or within complex communities to depolymerize difficult synthetic substrates. Both known and novel biochemical pathways and methods for deconstruction and conversion to new products were of interest.
This subtopic specifically targeted synthetic biology and omics-driven basic research on the bioconversion and reuse of synthetic polymers in the following areas:
In conjunction with research addressing the two subtopics outlined above, applicants could propose use-inspired basic research to develop analytical technologies to better understand how to evaluate and characterize relevant functional processes or how high-throughput phenotyping capabilities can be used to evaluate modified biofuel producing strains to enhance the design, build, test, and learn cycle, as long as the applications were tightly integrated with the stipulated subtopics.
Energy and Carbon Optimized Conversion of Lignocellulose to Biobased Chemicals by Extreme Thermophiles
Converting Methoxy Groups on Lignin-Derived Aromatics from a Toxic Hurdle to a Useful Resource: A Systems-Driven Approach
Cell-Free Systems Biology of an Atypical Glycolytic Pathway
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood Decomposer
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-Fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform Chemicals
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene Synthesis
Quantitative Analysis of Metabolic Segregation of Lignin Deconstruction and Catabolism in Outer Membrane Vesicles of Soil Pseudomonas species
Optogenetic Control of Microbial Consortia for Biofuel and Chemical Production
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in Cyanobacteria
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic Pathways
Synthetic Metabolic Pathways and Biosensors to Expand Lignin-Based Bioconversion
The Whole is Greater than the Sum of Its Parts: Multi-Scale Modeling and Engineering of Microbial Communities for Next-Generation Bioproduction
Harnessing the Robust Metabolism of Bacillus coagulans for Efficient Conversion of Lignocellulosic Biomass Hydrolysates to Designer Bioesters
Improving Bioprocess Robustness by Cellular Noise Engineering
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic Rubber
Optimizing Enzymes for Plastic Upcycling Using Machine Learning Design and High Throughput Experiments
Novel Enzymes and Synthetic Metabolic Pathways for Complete Degradation and Upcycling of Recalcitrant Polyamides
Discovery of Distributed Pathways for Plastic Conversion in the Yellow Mealworm Microbiome
Developing a Consolidated Biological Process to Upcycle Plastics
SynThetic BiolOgy Driven Approach to Repurpose PolyaMides (STORM)
U.S. Department of Energy
Office of Biological and Environmental Research
Dr. Boris Wawrik
U.S. Department of Energy
Office of Biological and Environmental Research