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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Data for Bioprocessing, Recovery, and Mass Balance of Vegetative Lipids from Metabolically Engineered ‘Oilcane’ Demonstrates Its Potential as an Alternative Feedstock for Drop-In Fuel Production

Plant oils are increasingly in demand as renewable feedstocks for biodiesel and biochemicals. Currently, oilseeds are the primary source of plant oils. Although the vegetative tissues of plants express lipid metabolism pathways, they do not hyper-accumulate lipids. Elevated synthesis, storage, and accumulation of lipids in vegetative tissues have been achieved by metabolic engineering of sugarcane to produce “oilcane.” This study evaluates the potential of oilcane as a renewable feedstock for the co-production of lipids and fermentable sugars. Oilcane was grown under favorable climatic and field conditions in Florida (FLOC) as well as during an abbreviated growing season, outside its typical growing region, in Illinois (ILOC). The potential lipid yield of 0.35 tons/ha was projected from the hyperaccumulation of fatty acids in the stored vegetative biomass of FLOC, which is approaching the lipid yield of soybean (0.44 tons/ha). Processing of the vegetative tissues of oilcane recovered 0.20 tons/ha, which represents the recovery of 55% of the total lipids from FLOC. Chemical-free hydrothermal bioprocessing of ILOC and FLOC bagasse and leaves at 180 °C for 10 min prevented the degeneration of in situ plant lipids. This allowed the recovery of lipids at the end of the bioprocess with a major fraction of lipids remaining in the biomass residues after pretreatment and saccharification. Improvements through refined biomass processing, crop management, and metabolic engineering are expected to boost lipid yields and make oilcane a prime feedstock for the production of biodiesel.

Conversion↗
DOE OSTI2022

Bioprocessing, Recovery, and Mass Balance of Vegetative Lipids from Metabolically Engineered “Oilcane” Demonstrates Its Potential as an Alternative Feedstock for Drop-In Fuel Production

Plant oils are increasingly in demand as renewable feedstocks for biodiesel and biochemicals. Currently, oilseeds are the primary source of plant oils. Although the vegetative tissues of plants express lipid metabolism pathways, they do not hyper- accumulate lipids. Elevated synthesis, storage, and accumulation of lipids in vegetative tissues have been achieved by metabolic engineering of sugarcane to produce “oilcane”. This study evaluates the potential of oilcane as a renewable feedstock for the co- production of lipids and fermentable sugars. Oilcane was grown under favorable climatic and field conditions in Florida (FLOC) as well as during an abbreviated growing season, outside its typical growing region, in Illinois (ILOC). The potential lipid yield of 0.35 tons/ha was projected from the hyperaccumulation of fatty acids in the stored vegetative biomass of FLOC, which is approaching the lipid yield of soybean (0.44 tons/ha). Processing of the vegetative tissues of oilcane recovered 0.20 tons/ha, which represents the recovery of 55% of the total lipids from FLOC. Chemical-free hydrothermal bioprocessing of ILOC and FLOC bagasse and leaves at 180 °C for 10 min prevented the degeneration of in situ plant lipids. Here, this allowed the recovery of lipids at the end of the bioprocess with a major fraction of lipids remaining in the biomass residues after pretreatment and saccharification. Improvements through refined biomass processing, crop management, and metabolic engineering are expected to boost lipid yields and make oilcane a prime feedstock for the production of biodiesel.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Bioelectrocatalytic conversion of CO₂ to PHA bioplastics using engineered methylotrophs

The sustainable generation of biodegradable plastics represents an opportunity to capture atmospheric CO 2 while reducing plastic waste accumulation in the environment. This study implements an integrated platform for bioelectrocatalytic CO 2 conversion to medium-chain-length polyhydroxyalkanoates (mcl-PHAs). Immobilizing cobalt phthalocyanine electrocatalysts on a covalent-organic framework in a gas recirculation electrolyzer enabled CO 2 -to-methanol conversion with a carbon conversion efficiency of 98%. Integration of polymer biosynthesis pathways enabled Methylotuvimicrobium alcaliphilum 20Z R to produce ~20% mcl-PHA of the dry cell weight with a CO 2 -to-bioproducts carbon conversion efficiency of 50%. This cell line was adapted to high sodium bicarbonate media, eliminating costly intermediate separation steps while improving economic potential. Transcriptomic analysis revealed sulfate transporters and peptidoglycan biosynthesis as key pathways involved in sodium bicarbonate halotolerance. Altogether, this research presents a foundation for integrating divergent chemical and biological processes into a transformative electrobiomanufacturing platform, addressing the need for alternative pipelines for generating valuable plastics and chemicals.

CO2 utilization↗
DOE OSTI2023

ABF Industry Engagement Lab Call with Danimer Scientific

This Agile BioFoundry Directed Funding Opportunity project with Danimer Scientific focuses on the development of a strain and a corresponding bioprocess to convert bio-based feedstocks to mixed composition polyhydroxyalkanoates (PHAs). Danimer Scientific produces PHAs today at industrial scale in proprietary strains and for many applications where bio-based, biodegradable materials are advantaged. The project team consists of NREL to lead the strain engineering efforts, PNNL to conduct systems biology experiments that will inform further strain engineering, and Danimer to conduct bioprocess development and materials development. To date, we have on-boarded Danimer strains and demonstrated successful engineering thereof. We anticipate conducting systems biology studies in Spring 2023. Overall, the impact of this DFO project could be improved material properties accessed through the Design-Build-Test-Learn cycle for designer PHA production.

bio-based feedstocks↗
DOE OSTI2024

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Abstract Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Transgenic Sugarcane–Oilcane: An Alternative Feedstock for the Production of Drop-in Fuel and Value-Added Bioproducts

The utilization of plants and other agricultural produce can partly offset petroleum dependency for energy requirements and can potentially provide sustainable solutions to global environmental problems. To this end, synthetic biology has shown great potential in developing transgenic bioenergy grasses such as sugarcane, sorghum, miscanthus, and energy cane that hyperaccumulate energy-rich lipid molecules in their vegetative tissues, such as leaves, stems, and roots. These perennial high-biomass transgenic C4 grasses are not targeted to grow on prime agricultural land and can be dedicatedly used to produce biofuels and other value-added bioproducts. Recently, sugarcane has been metabolically engineered to sequestrate carbon from juice towards biosynthesis of lipid molecules in the vegetative tissues. Transgenic sugarcane is referred to as “oilcane.” Transgenic sugarcane–oilcane has improved energy density due to an elevated lipid content in the vegetative tissues. Transgenic bioenergy crops cater to both cellulosic sugars and vegetative lipids, hence resulting in higher biofuel yield (biodiesel/renewable diesel and bioethanol) per unit area of cultivable land. In this book chapter, the genetic engineering of sugarcane and its bioprocessing are discussed to illustrate its development and use as an alternative feedstock for the production of biofuels (bio-jet fuel, biodiesel, and bioethanol) and value-added bioproducts.

Maitra, Shraddha↗
DOE OSTI2023

Characterization and Amelioration of Filtration Difficulties Encountered in Metabolomic Studies of Clostridium thermocellum at Elevated Sugar Concentrations

Clostridium thermocellum , a promising candidate for consolidated bioprocessing, has been subjected to numerous engineering strategies for enhanced bioethanol production. Measurements of intracellular metabolites at substrate concentrations high enough (>50 g/L) to allow the production of industrially relevant titers of ethanol would inform efforts toward this end but have been difficult due to the production of a viscous substance that interferes with the filtration and quenching steps during metabolite extraction. To determine whether this problem is unique to C. thermocellum , we performed filtration experiments with other organisms that have been engineered for high-titer ethanol production, including Escherichia coli and Thermoanaerobacterium saccharolyticum . Here, we addressed the problem through a series of improvements, including active pH control (to reduce problems with viscosity), investigation of different filter materials and pore sizes (to increase the filtration capacity), and correction for extracellular metabolite concentrations, and we developed a technique for more accurate intracellular metabolite measurements at elevated substrate concentrations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Engineering Yeast for the Production of Acids and Esters (CRADA Final Report)

NREL and Lygos have a mutual interest in engineering yeast for the production of acids and esters as intermediates towards fuels or bioproducts. In particular, the yeast Pichia kudriavzevii is a fantastic candidate for the production of acid and ester based products including butyric acid and ethyl butyrate. However, the strain is relatively uncommon in the biotechnological space and as such there are not an abundant amount of genetic tools that are publically available. However, Lygos has been working with this species in particular for several years and has developed genetic tools and physiological characteristics and are well versed in engineering this strain for acid based products. While currently focusing on malonic acid-derived products, Lygos is not currently targeting butyric acid and ethyl butyrate but have a long term interest in these molecules and derivatives therein. This CRADA proposal seeks to leverage NREL’s immediate focus on butyric acid and ethyl butyrate, and general bioprocess expertise with Lygos’ specific knowledge on engineering P. kudriavzevii for the production of acid-based products.

09 BIOMASS FUELS↗
DOE OSTI2026

Data for Creating Yellow Seed Camelina sativa with Enhanced Oil Accumulation by CRISPR-Mediated Disruption of Transparent Testa 8

Camelina ( Camelina sativa L.), a hexaploid member of the Brassicaceae family, is an emerging oilseed crop being developed to meet the increasing demand for plant oils as biofuel feedstocks. In other Brassicas, high oil content can be associated with a yellow seed phenotype, which is unknown for camelina. We sought to create yellow seed camelina using CRISPR/Cas9 technology to disrupt its Transparent Testa 8 (TT8) transcription factor genes and to evaluate the resulting seed phenotype. We identified three TT8 genes, one in each of the three camelina subgenomes, and obtained independent CsTT8 lines containing frameshift edits. Disruption of TT8 caused seed coat colour to change from brown to yellow reflecting their reduced flavonoid accumulation of up to 44%, and the loss of a well-organized seed coat mucilage layer. Transcriptomic analysis of CsTT8-edited seeds revealed significantly increased expression of the lipid-related transcription factors LEC1, LEC2, FUS3, and WRI1 and their downstream fatty acid synthesis-related targets. These changes caused metabolic remodelling with increased fatty acid synthesis rates and corresponding increases in total fatty acid (TFA) accumulation from 32.4% to as high as 38.0% of seed weight, and TAG yield by more than 21% without significant changes in starch or protein levels compared to parental line. These data highlight the effectiveness of CRISPR in creating novel enhanced-oil germplasm in camelina. The resulting lines may directly contribute to future net-zero carbon energy production or be combined with other traits to produce desired lipid-derived bioproducts at high yields.

Biofuels↗
DOE OSTI2025

Engineered Membrane Vesicle Production via oprF or oprI Deletion Has Distinct Phenotypic Effects in Pseudomonas putida

Membrane vesicle (MV) production is a natural phenomenon in Gram-negative bacteria and represents an emerging synthetic biology tool for the secretion of biomolecules or bioproducts. Manipulation of membrane components has proven successful in enhancing MV production. However, the impact of membrane disruptions on strain fitness and protein composition warrants further investigation for the use of MVs in industrial bioprocesses. Here, we identify and characterize two genetic engineering strategies for inducing hypervesiculation-deletion of genes for the outer membrane porin OprF or the lipoprotein OprI-in the commonly used platform Pseudomonas putida KT2440. Deletion of oprI generated up to a 1.5-fold increase in MVs, larger MVs with a greater proportion of outer membrane proteins, and no significant impact on strain fitness compared to wild type. In contrast, deletion of oprF, relative to wild type, generated up to a 4-fold increase in MVs but diminished growth, permeabilized membranes, and increased cytosolic protein packaging. Both hypervesiculation phenotypes increased nontargeted and MV-targeted mNeonGreen extracellular signal by up to 6-fold, demonstrating vesiculation as a mechanism for protein secretion. Despite increased blebbing of MVs from gene deletions, proteins involved in membrane biosynthesis were not elevated relative to wild type. Overexpression of gpsA, which initiates glycerophospholipid biosynthesis, in the ΔoprF background improved the membrane integrity by 37% and maintained MV formation, highlighting the importance of membrane biosynthesis in restoring the membrane in hypervesiculating strains. Together, this study provides genetic engineering strategies with corresponding phenotypic outcomes toward providing a synthetic biology toolset for MV deployment in P. putida.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Final Technical Report for DE-SC0022206

This project developed foundational genetic, genomic, and epigenetic tools for anaerobic fungi (Neocallimastigomycota), a group of microorganisms with exceptional natural abilities to deconstruct lignocellulosic biomass. Efficient biomass deconstruction remains a major barrier to economical production of renewable fuels, chemicals, and materials from agricultural and forestry residues. The project sought to enable mechanistic studies and future engineering of anaerobic fungi by improving genomic resources, establishing methods for gene expression, and investigating epigenetic regulation of biomass-degrading pathways. Major accomplishments included generation of the first chromosome-scale genome assemblies for multiple anaerobic fungal species, providing publicly available genomic resources that support both engineering and fundamental biological research. The project established the first reproducible system for heterologous gene expression in anaerobic fungi and identified genomic features and mobile genetic elements that may support future development of stable transformation technologies. In parallel, the project demonstrated direct conversion of untreated lignocellulosic biomass into fuels and specialty chemicals through a fungal-yeast bioprocess and identified anaerobic fungal enzymes with utility for metabolic engineering. The research also revealed that epigenetic regulation plays an important role in controlling fungal gene expression and enzyme production, identifying potential strategies for enhancing biomass degradation. Collectively, this work established anaerobic fungi as a tractable emerging platform for bioenergy and biomanufacturing research, generated valuable public resources, trained the next generation of researchers, and advanced DOE-BER goals related to predictive biology, sustainable bioprocessing, and the circular bioeconomy.

Solomon, Kevin [University of Delaware] (ORCID:000↗
DOE OSTI2025

Engineering Clostridium thermocellum for production of 2,3-butanediol from cellulose

Clostridium thermocellum is a promising host for consolidated bioprocessing due to its ability to directly ferment cellulose into fuels and chemicals. However, natural product formation in this organism is limited. Here, we report engineering C. thermocellum for the production of 2,3-butanediol (23BD), a valuable industrial chemical. We functionally expressed a thermophilic 23BD pathway in this organism resulting in a 23BD titer of 19.7 mM from cellulose, representing a metabolic yield of 24%. We used a cell-free systems biology approach to identify limiting steps in the 23BD pathway, revealing that exogenous 23BD dehydrogenase (BDH) activity was essential for production, while native acetolactate synthase (ALS) and acetolactate decarboxylase (ALDC) activities were present but limiting in the parent strain. This approach also revealed redox balance limitations. We demonstrated that this improved understanding of redox balance limitations could be used to increase 23BD titer in vivo, showing that adding acetate could be used to increase 23BD yield. This work establishes a foundation for developing C. thermocellum into a robust platform for 23BD production directly from cellulose and highlights the utility of cell-free systems for guiding metabolic engineering in non-model organisms.

09 BIOMASS FUELS↗
DOE OSTI2023

Systematic approaches to C-lignin engineering in Medicago truncatula

Abstract Background C-lignin is a homopolymer of caffeyl alcohol present in the seed coats of a variety of plant species including vanilla orchid, various cacti, and the ornamental plant Cleome hassleriana . Because of its unique chemical and physical properties, there is considerable interest in engineering C-lignin into the cell walls of bioenergy crops as a high-value co-product of bioprocessing. We have used information from a transcriptomic analysis of developing C. hassleriana seed coats to suggest strategies for engineering C-lignin in a heterologous system, using hairy roots of the model legume Medicago truncatula . Results We systematically tested strategies for C-lignin engineering using a combination of gene overexpression and RNAi-mediated knockdown in the caffeic acid/5-hydroxy coniferaldehyde 3/5-O-methyltransferase ( comt ) mutant background, monitoring the outcomes by analysis of lignin composition and profiling of monolignol pathway metabolites. In all cases, C-lignin accumulation required strong down-regulation of caffeoyl CoA 3- O -methyltransferase (CCoAOMT) paired with loss of function of COMT. Overexpression of the Selaginella moellendorffii ferulate 5-hydroxylase ( SmF5H ) gene in comt mutant hairy roots resulted in lines that unexpectedly accumulated high levels of S-lignin. Conclusion C-Lignin accumulation of up to 15% of total lignin in lines with the greatest reduction in CCoAOMT expression required the strong down-regulation of both COMT and CCoAOMT, but did not require expression of a heterologous laccase, cinnamyl alcohol dehydrogenase (CAD) or cinnamoyl CoA reductase (CCR) with preference for 3,4-dihydroxy-substituted substrates in M. truncatula hairy roots. Cell wall fractionation studies suggested that the engineered C-units are not present in a heteropolymer with the bulk of the G-lignin.

09 BIOMASS FUELS↗
DOE OSTI2025

An argument for using anaerobes as microbial cell factories to advance synthetic biology and biomanufacturing

Anaerobes thrive in the absence of oxygen and are an untapped reservoir of biotechnological potential. Therefore, bioprospecting efforts focused on anaerobic microbial diversity could rapidly uncover new enzymes, pathways, and chassis organisms to drive biotechnology innovation. Despite their potential utility, anaerobic fermenters are viewed as inefficient from a biochemical perspective because their metabolisms produce fewer ATP (~2) per molecule of glucose processed than heterotrophic respirers (~32–38 ATP). While aerobes excel at ATP generation, they are often less efficient than anaerobes at processes that compete with ATP generation for cellular resources. This perspective highlights how anaerobic adaptations are advantageous for synthetic biology and biomanufacturing applications through the engineering of microbial cell factories. We further highlight emerging applications of anaerobic bioprocessing, including the use of anaerobic metabolisms for lignocellulosic bioprocessing, human and environmental health, and value-added bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Xylose metabolic engineering of Issatchenkia orientalis for 3-hydroxypropionic acid production from cellulosic hydrolysate without nutrient supplementation

Bioconversion of lignocellulosic biomass offers a promising alternative to petroleum-based chemical production. However, inefficient xylose utilization and toxic compounds in cellulosic hydrolysate limit microbial fermentation, as the hydrolysate contains substantial amounts of xylose in addition to glucose. To address these challenges, we engineered Issatchenkia orientalis to produce 3-hydroxypropionic acid (3-HP) directly from sorghum hydrolysate under low-pH conditions. A heterologous xylose utilization pathway consisting of XYL1, XYL2, and XYL3 from Scheffersomyces stipitis was introduced into an engineered 3-HP producing strain, enabling efficient conversion of xylose to 3-HP. The engineered strain produced 46.8 g/L 3-HP from sorghum hydrolysate without nutrient supplementation. To eliminate the lag phase under low-pH conditions, fermentation was conducted at pH 6.0 for the first three days, after which pH control was discontinued and in situ 3-HP accumulation buffered the culture. This partial pH control strategy increased 3-HP productivity by 55% from 0.20 to 0.31 g/L∙h, while maintaining low-pH conditions. Introducing an additional copy of XYL2 further increased 3-HP titer to 53.5 g/L and the yield by 33%, from 0.30 to 0.40 g/g sugars, with pH reaching 4.5 at the end of fermentation. This represents one of the highest reported 3-HP titers and yields from cellulosic hydrolysate without additional nutrient supplementation. This work demonstrates a nutrient-independent and low-pH bioprocess for upgrading lignocellulosic hydrolysate into 3-HP, highlighting the industrial potential of engineered xylose-utilizing I. orientalis for sustainable production of platform chemicals from renewable feedstocks.

3-Hydroxypropionic acid↗
DOE OSTI2025

From the bench to the reactor: engineered filamentous fungi for biochemical and biomaterial production

Filamentous fungi can convert a wide variety of naturally occurring chemical compounds, including organic biomass and waste streams, into a range of products. They have long been used for industrial organic acid production and food preparation. In this review, we will discuss production of products such as organic acids, lipids, small molecules, enzymes, materials, and foods, and highlight advances in metabolic and protein engineering, including CRISPR-Cas9-mediated strain improvements. We discuss to what extent these products are already being made on a commercial scale, as well as what is still required to make certain promising concepts industrially and commercially relevant. Despite significant progress, the systematic application of synthetic biology to filamentous fungi remains in its infancy, with many opportunities for discovery and innovation as new strains and genetic tools are developed. The integration of fungal biotechnology into circular and bio-based economies promises to address critical challenges in waste management, resource sustainability, and the development of new materials for terrestrial and extraterrestrial applications, but requires further developments in genetic engineering and process design.

09 BIOMASS FUELS↗
DOE OSTI2025

Alpha ketoacid decarboxylases: Diversity, structures, reaction mechanisms, and applications for biomanufacturing of platform chemicals and fuels

In living cells, alpha-ketoacid decarboxylases (KDCs, EC 4.1.1.-) are a class of enzymes that convert alpha-ketoacids into aldehydes through decarboxylation. These aldehydes serve as either drop-in chemicals or precursors for the biosynthesis of alcohols, carboxylic acids, esters, and alkanes. These compounds play crucial roles in cellular metabolism and fitness and the bioeconomy, facilitating the sustainable and renewable biomanufacturing of platform chemicals and fuels. This review explores the diversity and classification of KDCs, detailing their structures, mechanisms, and functions. We highlight recent advancements in repurposing KDCs to enhance their efficiency and robustness for biomanufacturing. Additionally, we present modular KDC-dependent metabolic pathways for the microbial biosynthesis of aldehydes, alcohols, carboxylic acids, esters, and alkanes. Lastly, we discuss recent developments in the modular cell engineering technology that can potentially be applied to harness the diversity of KDC-dependent pathways for biomanufacturing platform chemicals and fuels.

09 BIOMASS FUELS↗