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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Advanced Algal Biofoundries for the Production of Polyurethane Precursors (CRADA Final Report)

The primary goal of the BEEPs project was to develop a process that could accelerate the development of algae as bioproduction platforms, from initial chemical product concept to an economically viable market supply. Under this program we elected to develop strains of algae that could generate polyurethane precursors, while simultaneously developing basic genetic tools to enable improved algal production systems. This program was specifically designed to incorporate National Laboratories as a means to utilize the expertise and facilities for new bioproduction platforms.

09 BIOMASS FUELS↗
DOE OSTI2023

Carbon optimized production of 3-hydroxypropionic acid in the Agile BioFoundry organism Rhodosporidium toruloides

The modern global economy relies heavily on carbon-based products that are derived from petroleum, which presents sustainability, resource management, and greenhouse gas exacerbated climate change challenges. Due to these challenges, there is the need for a global industrial transition towards green and sustainable production. Microbial production of valuable chemicals from renewable biomass represents one promising route. However, high-volume low-value products such as commodity chemicals are still difficult to make profitable. One fundamental bottleneck is a waste of more than 1/3 of the feedstock carbon as CO 2 in the fermentation process. Here the project focuses on fundamentally reconfiguring the metabolism to reduce CO 2 loss in central metabolic pathways thereby also improving bioproduct yields. Here we present technologies to prevent CO 2 loss and balance reducing equivalents within the cell to enable complete conversion of glucose from renewable feedstocks into bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Enabling Capabilities and Resources: 2024 Principal Investigator Meeting Proceedings

As a major supporter of basic genome-enabled research, BER’s Biological Systems Science Division (BSSD) fosters scientific discovery by funding - fundamental biological research across disciplines in conjunction with enabling investigational tools and computational capabilities that include world-class user facilities. The overarching goal of BSSD is to provide the necessary fundamental science to understand, predict, manipulate, and design biological systems that underpin innovations for bioenergy and bioproduct production and enhance understanding of natural, DOE-relevant environmental processes (Biological Systems Science Division Strategic Plan, 2021). To accelerate the U.S. bioeconomy, BSSD pursues innovative science underpinning advances in sustainable biofuels and bioproducts and the development of next-generation technologies and computational resources for systems biology research. The 2024 BSSD Enabling Capabilities and Resources (ECR) Principal Investigator (PI) meeting brought together PIs across the BSSD ECR portfolio to confer on shared interests and opportunities. The meeting was held concurrently with the Genomic Science program (GSP) PI meeting to optimize collaboration on research to advance bioenergy and the bioeconomy. Rick Stevens of Argonne National Laboratory gave a keynote on How Generative Artificial Intelligence Can Impact Biological Research (see Keynote: How Generative Artificial Intelligence Can Impact Biological Research, this page). Plenary presentations included several joint sessions that illuminated the integration and understanding of the larger BSSD mission. GSP’s objective is to provide systems-level understanding of plants, microbes, and their communities through its Bioenergy Research, Biosystems Design, and Environmental Microbiome Research portfolios. The objective of the ECR portfolio is to support development of computational and instrumental platforms to advance fundamental GSP research—and BER more broadly— toward the overall goal of understanding the functional principles of living systems and their response to environmental challenges.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Creating multifunctional synthetic lichen platforms for sustainable biosynthesis of biofuel precursors

In this project, we were creating a sustainable platform for biofuel production, utilizing carbon-fixing autotrophs to supply oxygen and organic substrates to heterotrophic partners, which in turn produce carbon dioxide to feed the autotrophs. This symbiotic lichen community could lower the input cost, optimize metabolic exchanges and improve the generation of biofuel precursors through multi-omics driven genetic engineering. The cyanobacteria Synechococcus elongatus (S. elongatus) was used as the primary autotroph to provide oxygen and organic substrates, especially sucrose, to a co-culture system. The strain with overexpression of sucrose transporter cscB demonstrated a significant increase in sucrose production under salt stress as what we expected. We also implemented 13C metabolic flux analysis on the sucrose secreting strain S. elongatus cscB-NaCl. Next, transporters proteins like glutamate exporter mscCG from Corynebacterium glutamicum was overexpressed in S. elongatus to improve metabolite exchange. We provided sucrose and glutamate to filamentous fungi to enable their growth and production of biochemicals using substrates from the cyanobacterium. Two fungi ( Aspergillus nidulans and Aspergillus niger ) and two yeast strains ( Rhodotorula toruloides and Lipomyces starkeyi ) served as heterotrophs in this system. They were co-cultured with S.elongatus under different pH condition, and growth on different carbon source to understand the symbiotic system and optimize the parameters for production. The two fungi strained grew much better at pH 7, 8 and 9 with Yeast Nitrogen Base (YNB ) supplementation. Two yeast strains grew well on pH 7 and 8 with YNB supplementation. All four species achieved the highest biomass level when utilizing sucrose as the main carbon sources, which demonstrates a great pairing with S.elongatus . In addition to investigate the metabolite exchange and growth condition of the co-culture system, we incorporated an Aspergillus strain expressing three genes (PAND, BAPAT and HPDH). Expression of these three genes enabled production of 3-hydroxypropionic acid (3HP) with a titer of 3-6 g/L regardless of pH and other nutrient conditions. Moreover, we developed a computational model with different heterotrophic fungi symbiosing with S.elongatus to evaluate the exchange of hundreds of metabolites. The accuracy and sensitivity had been optimized by high-throughput phenotyping assays. This project demonstrated ways to enhance a synthetic lichen platform’s efficiency and scalability to create a robust system for sustainable bioproduct synthesis. The project has enabled us to explore the technological and commercial potential of sustainable lichen co-culture. The project has also trained the next generation of scientists to address sustainability, carbon fixation, and design solutions to contemporary global challenges. The lichen platform represented a novel approach to sustainably producing bioproducts with a reduced carbon footprint and lower costs.

09 BIOMASS FUELS↗
DOE OSTI2026

Resilient Crop Production for the Bioeconomy: Frontier Science for the Bioeconomy Workshop Series

A bioeconomy based on energy, chemicals, and bioproducts derived from nonfood crops promotes U.S. prosperity, energy independence, and national security. Crop productivity (i.e., yield) affects profitability for farmers, whereas biomass and seed oil quality affects profitability for biorefineries through the conversion efficiency of feedstock crops into energy, chemicals, and bioproducts. Scientific breakthroughs in plant genetics and genomics, ecological processes, bioprocessing, microbial engineering and design, and conversion technologies have improved the potential market viability of products derived from nonfood crops specifically cultivated as biomass and seed oil feedstocks. Improving understanding of a plant’s complex responses to withstand or recover from stress is crucial to maintaining feedstock yield and quality, particularly in challenging production zones. Stress may be related to biotic or abiotic (i.e., nonliving) environmental conditions that negatively affect plant growth, development, and productivity. Research and development to enhance the environmental resilience of feedstock crops will enable improved production by minimizing losses during stress and improving production on currently economically nonviable marginal lands.

09 BIOMASS FUELS↗
DOE OSTI2026

A multiomics mass spectrometry workflow for fast and comprehensive strain optimization (Abstract CRADA 726 )

The Agile Biofoundry (ABF) is a multi-national lab consortium funded by the DOE Bioenergy Technologies Office that has developed a biofoundry that enables the rapid deployment of bioproducts into the market. The ABF is a flexible platform that can adjust to the needs of numerous government, academic and industrial partners, thus enabling them to rapidly develop and optimize the production of a wide range of bioproducts. To enhance this capability, PNNL and Agilent Technologies are collaborating to expand and demonstrate a prototype system that processes hundreds of samples per day by liquid chromatography-mass spectrometry-based untargeted and targeted methods, and artificial intelligence software for multiomics applications, including metabolomics, lipidomics and proteomics.

Bilbao, Aivett (ORCID:0000000329858249)↗
DOE OSTI2021

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides

An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides . High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.

09 BIOMASS FUELS↗
DOE OSTI2021

Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4× after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Pomraning, Kyle R.↗
DOE OSTI2021

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on “omics” driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in “omics” technologies, compare the pros and cons of the different “omics” technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of “omics” technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of “omics” technologies to agricultural and food biotechnology, and review the impact of “omics” on current COVID-19 research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress

Corynebacterium glutamicum is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50 mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an C. glutamicum strain engineered to produce IP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Corynebacterium glutamicum as an Efficient Omnivorous Microbial Host for the Bioconversion of Lignocellulosic Biomass

Corynebacterium glutamicum has been successfully employed for the industrial production of amino acids and other bioproducts, partially due to its native ability to utilize a wide range of carbon substrates. We demonstrated C. glutamicum as an efficient microbial host for utilizing diverse carbon substrates present in biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its natural ability to assimilate lignin-derived aromatics. As a case study to demonstrate its bioproduction capabilities, L-lactate was chosen as the primary fermentation end product along with acetate and succinate. C. glutamicum was found to grow well in different aromatics (benzoic acid, cinnamic acid, vanillic acid, and p-coumaric acid) up to a concentration of 40 mM. Besides, 13 C-fingerprinting confirmed that carbon from aromatics enter the primary metabolism via TCA cycle confirming the presence of β-ketoadipate pathway in C. glutamicum . 13 C-fingerprinting in the presence of both glucose and aromatics also revealed coumarate to be the most preferred aromatic by C. glutamicum contributing 74 and 59% of its carbon for the synthesis of glutamate and aspartate respectively. 13 C-fingerprinting also confirmed the activity of ortho-cleavage pathway, anaplerotic pathway, and cataplerotic pathways. Finally, the engineered C. glutamicum strain grew well in biomass hydrolysate containing pentose and hexose sugars and produced L-lactate at a concentration of 47.9 g/L and a yield of 0.639 g/g from sugars with simultaneous utilization of aromatics. Succinate and acetate co-products were produced at concentrations of 8.9 g/L and 3.2 g/L, respectively. Our findings open the door to valorize all the major carbon components of biomass hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.

13C-fingerprinting↗
DOE OSTI2022

Biological funneling of phenolics from transgenic plants engineered to express the bacterial 3-dehydroshikimate dehydratase (qsuB) gene

The economic and environmental sustainability of lignocellulosic biomass biorefineries is predicated on generating biofuels and bioproducts from cell-wall polysaccharide and lignin polymers. Historical efforts in plant genetic engineering have focused on the development of strategies that facilitate biomass deconstruction, with more recently efforts including the synthesis of high-value chemicals in planta . One such genetic modification is the expression of the bacterial quinate and shikimate utilization B ( qsuB ) gene that increases the accumulation of protocatechuic acid in lignocellulosic biomass. Herein, we evaluated the effectiveness of an alkaline pretreatment process to extract phenolics directly from wild-type and QsuB-transgenic lines of Arabidopsis, poplar, and sorghum, and then upgrade them to the polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC) with an engineered strain of Novosphingobium aromaticivorans . Protocatechuic acid extracted from all QsuB transgenic lines was found to be mostly in the glycosylated form. Glycosylated protocatechuic acid and other plant-derived phenolics were effectively metabolized by N. aromaticivorans, and PDC production was greatest using extracts from an Arabidopsis QsuB transgenic line (∼5% w/w), followed by QsuB sorghum (∼1.1% w/w), and QsuB poplar (∼0.4% w/w) lines. The comparison of PDC production from wild-type and QsuB transgenic lines of Arabidopsis, poplar, and sorghum demonstrates the utility of a mild alkaline pretreatment to liberate phenolics from plant biomass that are either naturally present or that accumulate as a consequence of genetic engineering strategies. All QsuB transgenic lines outperformed their wild-type counterparts with respect to observed PDC yields. In addition, microbial funneling to PDC was effective even when most of the protocatechuic acid extracted was in glycosylated form, clearly demonstrating that this bacterium can metabolize these aromatic conjugates. These findings illustrate the benefits of combining plant and microbial engineering for bioproduct formation from phenolics in lignocellulosic biorefineries.

Umana, German E.↗
DOE OSTI2023

Factors that influence the activity of biomass-degrading enzymes in the presence of ionic liquids—a review

Ionic liquids (ILs) are seen as a more sustainable alternative to volatile organic solvents that are accelerating innovations in many industries such as energy storage, separations, and bioprocessing. The ability to effectively deconstruct lignocellulosic biomass is a significant hurdle in the biorefining/bioprocessing industry and presents limitations towards the commercial production of bioproducts (such as biofuels, biomaterials, etc. ). Certain ILs have been shown to promote effective lignin removal, cellulose recovery, and sugar yields from various biomass feedstocks such as corn stover, wheat straw, sugarcane bagasse, sorghum, switchgrass, miscanthus, poplar, pine, eucalyptus, and certain mixtures of municipal solid waste. However, these improvements are often counteracted by the limited biocompatibility of ILs, which results in an IL-induced reduction in enzyme activity and stability—an important downstream step in the conversion of biomass to biofuels/bioproducts. As a result, significant efforts have been made to discover and engineer compatible enzyme-IL systems and to improve our understanding on the effect that these ILs have on these systems. This review seeks to examine the impact of ionic liquids on enzymes involved in lignocellulosic biomass deconstruction, with a specific focus on their relevance in the context of pretreatment. Beyond presenting an overview of the ionic liquid pretreatment landscape, we outline the main factors that influence enzyme activity and stability in the presence of ILs This data is consolidated and analyzed to apply this body of knowledge towards new innovations that could lead to improvements in the processing of biomass to biofuels and bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae

Introduction: Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. Methods: The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. Results: The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. Discussion: This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

09 BIOMASS FUELS↗
DOE OSTI2022

Solid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall Polymers

Efficient separation of the plant cell wall polymers during lignocellulose processing has been historically challenging due to insolubility of the polymers and their propensity for recalcitrant reassembly. Methods, such as “lignin first” extraction techniques, have advanced efficient biomass use, but the molecular mechanisms for recalcitrance remain enigmatic. Here, we discuss how solid-state Nuclear Magnetic Resonance (NMR) approaches report on the 3D organization of cellulose, xylan, and lignin in the plant cell wall. Recent results illustrate that the organization of these polymers varies across biomass sources and sample preparation methods, with even minimal physical processing causing significant effects. These structural differences contribute to variable extraction efficiencies for bioproducts after downstream processing. We propose that solid-state NMR methods can be applied to follow biomass processing, providing an understanding of the polymer rearrangements that can lead to poor yields for the desired bioproducts. The utility of the technique is illustrated for mechanical processing using lab-scale vibratory ball milling of Sorghum bicolor .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integrated Biorefinery Research Facility: Partnering with Industry to Advance the Bioeconomy

NREL's National Bioenergy Center has entered into more than 130 collaborations in recent years with companies ranging in size from start-ups to those that appear on Fortune magazine's Fortune 100 list. The Integrated Biorefinery Research Facility (IBRF) showcases NREL's commitment to collaboration and to meeting the nation's biofuels and bioproducts development and deployment goals. Designed to speed the growth of the biofuels and bioproducts industries, the IBRF is a unique $33.5-million pilot facility capable of supporting a variety of projects.

bioenergy↗
DOE OSTI2022

Biological Lignin Valorization

Given lignin's heterogeneity, catalytic depolymerization results in aromatic compound mixtures, and conversion of this complex substrate to a single product is challenging. To that end, the Biological Lignin Valorization (BLV) project is pursuing biological funneling, wherein aromatic catabolic microbes are engineered to convert a mixture of lignin-derived compounds to a single product. Namely, we employ Pseudomonas putida and pursue atom-efficient products, such as muconic acid, which can be further converted to direct replacements or used in performance-advantaged bioproducts. Overall, biological lignin conversion can make major contributions to reduce the minimum fuel selling price of the integrated biorefinery. Early industrial efforts in this area are also leading to value-added products, including in collaboration with the BLV project. Primary challenges associated with BLV efforts include accessing bio-available monomers from lignin (with the Lignin Utilization project), enabling commercial titers, rates, and yields of bioproducts from lignin-derived compounds, and overcoming substrate and product toxicity. To date, we have 1) demonstrated 49 g/L of muconate from aromatic compounds and 4 g/L of muconate from lignin, 2) improved the toxicity tolerance of P. putida to key aromatic substrates, 3) debottlenecked biological funneling for higher rates, and 4) engineered P. putida to convert S, G, and H-type lignin-derived compounds to a single product.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗
DOE OSTI2025

Data for Redefining the Product Portfolio of Oilcane Bagasse Biorefinery: Recovering Natural Colorants, Vegetative Lipids and Sugars

:Bioenergy crops have been known for their ability to produce biofuels and bioproducts. In this study, the product portfolio of recently developed transgenic sugarcane (oilcane) bagasse has been redefined for recovering natural pigments (anthocyanins), sugars, and vegetative lipids. The total anthocyanin content in oilcane bagasse has been estimated as 92.9 ± 18.9 µg/g of dried bagasse with cyanidin-3-glucoside (13.5 ± 18.9 µg per g of dried bagasse) as the most prominent anthocyanin present. More than 85 % (w/w) of the total anthocyanins were recovered from oilcane bagasse at a pretreatment temperature of 150 °C for 15 min. These conditions for the hydrothermal pretreatment also led to a 2-fold increase in the glucose yield upon the enzymatic saccharification of the pretreated bagasse. Further, a 1.5-fold enrichment of the vegetative lipids was demonstrated in the pretreated residue. Re-defining green biorefineries with multiple high-value products in a zero-waste approach is the need of the hour for attaining sustainability.

Biomass Analytics↗