BER’s Grant for Biosystems Design in Next-Generation Biofuels, Bioproducts, and Biomaterials Production

BER supports fundamental, interdisciplinary research to achieve a predictive systems-level understanding of Earth, environmental and biological systems. The overarching goals of the BER Program are to support transformative science 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. BSSD within 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 our understanding of natural environmental processes relevant to DOE. BSSD supports fundamental research to understand the systems biology of plants and microbes through the GSP. The GSP’s portfolio includes systems biology research that builds on a foundation of multi-omics data and integrates multidisciplinary experimental and computational approaches. Within this framework, one of the objectives of the GSP is to develop the next generation of genome engineering technologies to unlock the potential of plants and microorganisms for the safe and efficient conversion of renewable biomass, captured CO2 from the atmosphere, and/or petroleum-derived polymers into fuels, valuable chemicals, and materials with novel properties, advancing towards a sustainable and secure bioeconomy. The iterative application and testing of those engineering technologies to design living organisms with new functional properties also leads to a deeper understanding of the fundamental principles governing those organisms. Therefore, this “design, build, test, learn” (DBTL) cycle not only results in improved biosystems design, but also leads to a more comprehensive knowledge of relevant biological systems.

During the last decade, the fields of systems and synthetic biology and artificial intelligence have seen momentous advances that have dramatically accelerated the DBTL cycle for engineering biology. More efficient approaches for genome-wide editing, analysis, and phenotyping become available, and new computational tools and modeling algorithms can handle increasingly large datasets while continuously improving their prediction accuracy. To bring these advances to the next level, integrative multidisciplinary applications are solicited for highly innovative, fundamental multi-omics and systems biology research and technology development for biosystems design. Applications should respond to one of the following two research topics:

1. Microbial biosystems design for the production of biofuels, bioproducts, and biomaterials: Applications should pursue multidisciplinary approaches to develop genome-wide design and editing, and in vivo or cell-free engineering technologies for eukaryotic or prokaryotic microbes to produce biofuels, bioproducts, or biomaterials from lignocellulosic biomass, petroleum-derived synthetic polymers, or as a byproduct of photosynthesis. Applications are expected to propose the development of highly innovative, high-throughput platforms for biological design and testing, supported by advanced modeling and computational tools. A focus on new or emerging model systems to expand the breadth of platform microorganism for engineering is encouraged. Genome engineering strategies to develop organisms that efficiently produce chemicals or materials while sequestering atmospheric CO2 are also encouraged. Research areas of interest include but are not limited to: i) in vivo, cell-free, or intercellular systems to confer new functionalities such as biosensors, tunable genetic circuits, and subcellular compartmentalization that enable the synthesis of desirable products; ii) orthogonal metabolic, macromolecular synthesis, and signaling pathways that equip cells to biologically carry out processes not found in nature; iii) design of recoded, minimal, and/or synthetic genomes with novel properties; iv) engineering microorganisms that can break down petroleum-derived synthetic polymers and/or convert them into valuable products; and v) design and engineering microorganisms for the production of biominerals, inorganic-organic composites, and composites of inorganic materials and living cells (living materials) with wholly new properties not found in known organisms.
2.  Plant biosystems design for bioenergy, bioproducts, and biomaterials: Applications should focus on integrative studies to engineer plant systems to achieve sustainable production of biofuels, bioproducts, and biomaterials; substantially improve bioenergy crop performance in marginal environments; and/or increase biomass yield while making it more amenable to deconstruction and conversion into desirable chemicals. Relevant goals for crop design and engineering include but are not limited to: i) increasing abiotic stress tolerance, ii) achieving higher water and/or nutrient use efficiency, iii) improving photosynthetic capacity, iv) facilitating cell wall deconstruction and subsequent conversion to advanced biofuels and bioproducts, and v) engineering the production of bioproducts or biomaterials. Proposed research should include innovative technologies for the introduction and expression of large, stable, multigene DNA constructs, genome-wide editing and recombineering, and high-throughput phenotyping, supported by computational approaches for modeling and design. Epigenetic engineering approaches to attain programable and tunable gene expression across the genome are encouraged. Research on model plants should be kept to a minimum and the main focus of the applications should be on potential or emerging bioenergy crops, including but not limited to switchgrass, poplar, Miscanthus, eucalyptus, sorghum, energy cane, and non-food oilseed crops.

BER supports fundamental, interdisciplinary research to achieve a predictive systems-level understanding of Earth, environmental and biological systems. The overarching goals of the BER Program are to support transformative science 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. BSSD within 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 our understanding of natural environmental processes relevant to DOE. BSSD supports fundamental research to understand the systems biology of plants and microbes through the GSP. The GSP’s portfolio includes systems biology research that builds on a foundation of multi-omics data and integrates multidisciplinary experimental and computational approaches. Within this framework, one of the objectives of the GSP is to develop the next generation of genome engineering technologies to unlock the potential of plants and microorganisms for the safe and efficient conversion of renewable biomass, captured CO2 from the atmosphere, and/or petroleum-derived polymers into fuels, valuable chemicals, and materials with novel properties, advancing towards a sustainable and secure bioeconomy. The iterative application and testing of those engineering technologies to design living organisms with new functional properties also leads to a deeper understanding of the fundamental principles governing those organisms. Therefore, this “design, build, test, learn” (DBTL) cycle not only results in improved biosystems design, but also leads to a more comprehensive knowledge of relevant biological systems.

During the last decade, the fields of systems and synthetic biology and artificial intelligence have seen momentous advances that have dramatically accelerated the DBTL cycle for engineering biology. More efficient approaches for genome-wide editing, analysis, and phenotyping become available, and new computational tools and modeling algorithms can handle increasingly large datasets while continuously improving their prediction accuracy. To bring these advances to the next level, integrative multidisciplinary applications are solicited for highly innovative, fundamental multi-omics and systems biology research and technology development for biosystems design. Applications should respond to one of the following two research topics:

1. Microbial biosystems design for the production of biofuels, bioproducts, and biomaterials: Applications should pursue multidisciplinary approaches to develop genome-wide design and editing, and in vivo or cell-free engineering technologies for eukaryotic or prokaryotic microbes to produce biofuels, bioproducts, or biomaterials from lignocellulosic biomass, petroleum-derived synthetic polymers, or as a byproduct of photosynthesis. Applications are expected to propose the development of highly innovative, high-throughput platforms for biological design and testing, supported by advanced modeling and computational tools. A focus on new or emerging model systems to expand the breadth of platform microorganism for engineering is encouraged. Genome engineering strategies to develop organisms that efficiently produce chemicals or materials while sequestering atmospheric CO2 are also encouraged. Research areas of interest include but are not limited to: i) in vivo, cell-free, or intercellular systems to confer new functionalities such as biosensors, tunable genetic circuits, and subcellular compartmentalization that enable the synthesis of desirable products; ii) orthogonal metabolic, macromolecular synthesis, and signaling pathways that equip cells to biologically carry out processes not found in nature; iii) design of recoded, minimal, and/or synthetic genomes with novel properties; iv) engineering microorganisms that can break down petroleum-derived synthetic polymers and/or convert them into valuable products; and v) design and engineering microorganisms for the production of biominerals, inorganic-organic composites, and composites of inorganic materials and living cells (living materials) with wholly new properties not found in known organisms.
2.  Plant biosystems design for bioenergy, bioproducts, and biomaterials: Applications should focus on integrative studies to engineer plant systems to achieve sustainable production of biofuels, bioproducts, and biomaterials; substantially improve bioenergy crop performance in marginal environments; and/or increase biomass yield while making it more amenable to deconstruction and conversion into desirable chemicals. Relevant goals for crop design and engineering include but are not limited to: i) increasing abiotic stress tolerance, ii) achieving higher water and/or nutrient use efficiency, iii) improving photosynthetic capacity, iv) facilitating cell wall deconstruction and subsequent conversion to advanced biofuels and bioproducts, and v) engineering the production of bioproducts or biomaterials. Proposed research should include innovative technologies for the introduction and expression of large, stable, multigene DNA constructs, genome-wide editing and recombineering, and high-throughput phenotyping, supported by computational approaches for modeling and design. Epigenetic engineering approaches to attain programable and tunable gene expression across the genome are encouraged. Research on model plants should be kept to a minimum and the main focus of the applications should be on potential or emerging bioenergy crops, including but not limited to switchgrass, poplar, Miscanthus, eucalyptus, sorghum, energy cane, and non-food oilseed crops.