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At least 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Continuous culture of anaerobic fungi enables growth and metabolic flux tuning without use of genetic tools

Anaerobic gut fungi (AGF) have potential to valorize lignocellulosic biomass owing to their diverse repertoire of carbohydrate-active enzymes (CAZymes). However, AGF metabolism is poorly understood, and no stable genetic tools are available to manipulate growth and metabolic flux to enhance production of specific targets, e.g., cells, CAZymes, or metabolites. Herein, a cost-effective, Arduino-based, continuous-flow anaerobic bioreactor with online optical density control is presented to probe metabolism and predictably tune fluxes in Caecomyces churrovis. Varying the C. churrovis turbidostat setpoint titer reliably controlled growth rate (from 0.04 to 0.20 h −1 ), metabolic flux, and production rates of acetate, formate, lactate, and ethanol. Bioreactor setpoints to maximize production of each product were identified, and all continuous production rates significantly exceed batch rates. Formate spike-ins increased lactate flux and decreased acetate, ethanol, and formate fluxes. The bioreactor and turbidostat culture schemes demonstrated here offer tools to tailor AGF fermentations to application-specific hydrolysate product profiles.

Agriculture↗
DOE OSTI2023

Atomistic origins of biomass recalcitrance in organosolv pretreatment

Separation of lignocellulosic biomass components for use in sustainable energy and biomaterials applications remains challenging, since biopolymers such as cellulose and hemicellulose carbohydrates and polyaromatic lignin are found in close proximity within the plant secondary cell wall. Organic solvents have been used to pretreat recalcitrant biomass and separate the interacting polymers, solubilizing the lignin fraction for lignin-first valorization approaches. However, no single organosolv pretreatment approach has proven superior for heterogeneous biomass samples. Here we present a complementary atomic view of interactions between biomass components using molecular simulations, specific to lignin and cellulose, resolving mechanistic hypotheses for how lignin-cellulose composition influences separation processes. Further, using lignin-cellulose binding free energy calculated using molecular simulations, we find polar protic solvents such as methanol and ethanol separate lignin from cellulose, irrespective of the charge on the lignin monomer. Aprotic organic solvents (DMSO, THF, 1,4-dioxane) separate uncharged lignin (phenols and monolignols) from cellulose, while charged lignin (cinnamates) prefer binding to cellulose.

09 BIOMASS FUELS↗
DOE OSTI2023

Bioleaching to produce clean loblolly pine for thermochemical conversion

Lignocellulosic biomass contains inorganic elements that could induce slagging, ash fouling, and emission of both corrosive and harmful gases during thermochemical conversion. Water leaching pretreatment can remove most of the water-soluble elements, while it has limited industrial applicability due to its ineffectiveness in removing water-insoluble elements. Bioleaching is an alternative pretreatment method which has not been fully studied. In this work, bioleaching by Aspergillus niger strains NRRL 2001, NRRL 3122, and NRRL 567 was conducted to pretreat loblolly pine biomass with added water. Further, the removal of inorganic elements (K, Ca, Mg, and S) by bioleaching with A. niger NRRL 2001 was compared with chemical leaching with citric acid, HCl, and NaOH. It was shown that the pH reduction during bioleaching greatly improved K and Mg leaching to the point comparable to acid leaching, whereas Ca was precipitated by oxalic acid produced by the fungus. Bioleaching was also conducted in manually separated needles and chips components of loblolly pine. Glucose was added at different levels to assist bioleaching. At higher glucose levels, gluconic acid and citric acid were produced during bioleaching, leading to the increase of K, Ca, and Mg removal rates by more than 35%, 180%, and 390%, respectively, from the feedstock as compared with water leaching. Overall, bioleaching greatly improved removal of K, Ca, Mg, but not S from loblolly pine feedstocks as compared with water leaching.

09 BIOMASS FUELS↗
DOE OSTI2024

Investigation of the alkaline hydrogen peroxide pretreatment: From cellulose saccharification to lignin isolation

Alkaline hydrogen peroxide (AHP) pretreatment, a green and effective technology for biomass fractionation, was studied to overcome the recalcitrance of bamboo for lignin isolation and facilitating enzymatic saccharification. In order to explore the impact of AHP pretreatment on the cellulose saccharification of bamboo, the glucan/xylan recovery, lignin removal, and structural properties of solid substrate were investigated in this research. AHP pretreatment at 90 °C for 60 min with 3.0 % H 2 O 2 resulted in the maximum glucan/xylan hydrolysis yield reaching 90.62 % and 88.30 %, respectively. Specially, for the first time, the recovered lignin from the AHP liquid possesses up to 59.84/100Ar of β-O-4 linkages, abundant ferulic acid (FA), and p-coumarate (pCE) structures, as well as a homogeneous molecular structure with high purity (84.04%-96.20%) and preferable antioxidant activities (IC50: 0.015–0.018 mg/mL). Finally, these results provided theoretical support for the comprehensive valorization of lignocellulose, which is favorable for achieving viable biorefineries.

09 BIOMASS FUELS↗
DOE OSTI2026

Evaluating CO 2 mitigation strategies in SAF biorefineries: Techno-economic and life cycle analysis

The aviation sector requires scalable decarbonization strategies, and lignocellulosic sustainable aviation fuel (SAF) represents a promising pathway. This study comparatively evaluates the techno-economic analysis and life cycle assessment (LCA) of three CO 2 management strategies integrated within a U.S.-based gasification–Fischer–Tropsch SAF biorefinery: (i) catalytic hydrogenation of captured CO 2 to methanol, (ii) geological CO 2 sequestration, and (iii) mineralization to sodium bicarbonate (NaHCO 3 ). Techno-economic analysis indicates that methanol synthesis requires approximately 26% higher capital investment and 33% higher operating costs than mineralization. Although methanol co-production generates the highest gross revenue, NaHCO 3 production reduces the SAF minimum selling price by approximately 38% relative to both methanol synthesis and geological sequestration pathways, reflecting a more balanced cost allocation through mineral co-product valorization. Geological sequestration lowers operating costs by nearly 50% compared with methanol synthesis but remains highly dependent on carbon credit mechanisms. LCA reveals substantial divergence in climate performance. Relative to methanol synthesis, sequestration improves net greenhouse gas performance by approximately 163%, transitioning the system from net-positive to net-negative emissions. Mineralization further enhances carbon mitigation, achieving roughly 85% greater carbon reduction than sequestration and over sixfold improvement relative to methanol synthesis within the defined system boundary. Sensitivity analysis identified hydrogen price, co-product market value, and process emissions as dominant drivers. Under baseline assumptions, CO 2 mineralization is found to offer the most balanced pathway.

Carbon capture and storage↗
DOE OSTI2025

Emergence of deep eutectic solvents (DES): chemistry, preparation, properties, and applications in biorefineries and critical materials

The emergence of renewable deep eutectic solvents (DES) as clean and efficient catalysts and solvents has created new opportunities for lignocellulosic biorefineries and critical material sectors, including chemical, energy, pharmaceutical, textile, and hydrometallurgical industries. This review provides an in-depth overview of DES, covering their chemistry, classifications, preparation methods, processing characteristics, and recyclability, while highlighting their unique attributes and industry relevant applications. Emphasis is placed on the integration of DES into advanced biorefinery systems, focusing on their tunable physicochemical and thermodynamic properties for biomass pretreatment and the production of value-added products. The review explores how DES can be tuned for selective dissolution of biomass components and evaluates production and valorization of DES-derived biochemicals, with attention to lignin extraction mechanisms and conversion of biomass into bioproducts and biofuels. Beyond biorefineries, the scope extends to DES applications in electrochemical energy devices, where they serve as electrolytes, synthesis media for electrode materials, and leaching agents in battery recycling. The multifunctional roles of DES in pharmaceutical, hydrometallurgical, and textile sectors are also explored for contributions to sustainable processing. Finally, the review identifies future research directions, outlining benefits, challenges, and knowledge gaps, for continued industrial development.

09 BIOMASS FUELS↗
DOE OSTI2025

CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing

Valorization of lignocellulosic biomass for sustainable production of high-value chemicals is challenged by the complexity of lignin, a phenolic biopolymer. Beyond the classical lignin monomers derived from p-coumaryl, coniferyl, and sinapyl alcohol, grass lignins incorporate substantial amounts of monolignol p-coumarates that are produced by p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE (PMT). Here, the CRISPR/Cas9-mediated mutation of ZmPMT1 in maize enabled the design of biomass depleted in p-coumaroylated lignin and enriched in guaiacyl lignin. Lignin-first biorefining of stem biomass from zmpmt1 mutants by reductive catalytic fractionation (RCF) generated a lignin oil depleted in carboxylates and enriched in guaiacyl-derived alcohols, which are desirable substrates for bio-based polyurethane synthesis. Furthermore, the reported lignin engineering in maize is a promising strategy for designing a dual-purpose crop, providing both food and feed, along with a renewable feedstock for the production of plant-based chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Selective One-Dimensional 13 C– 13 C Spin-Diffusion Solid-State Nuclear Magnetic Resonance Methods to Probe Spatial Arrangements in Biopolymers Including Plant Cell Walls, Peptides, and Spider Silk

Two-dimensional (2D) and 3D through-space 13 C– 13 C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13 C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13 C– 13 C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13 C– 13 C spin-diffusion methods described here apply in select cases in which the 1D 13 C solid-state NMR spectrum displays chemical shift-resolved moieties. Furthermore, this is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13 C– 13 C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13 C– 13 C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13 C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ~0.45–0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Bioconversion of Agave Bagasse Lignin to Medium-Chain-Length Polyhydroxyalkanoates by Pseudomonas putida

Inadequate disposal of Agave tequilana bagasse (ATB) brings environmental and economic issues to tequila producing regions. Recent works have proposed technologies for valorization of the polysaccharide’s fractions of ATB. However, lignin bioconversion has not been investigated due to its recalcitrant nature. In this work, a systematic pretreatment is proposed to release the lignocellulosic fractions and produce medium-chain-length polyhydroxyalkanoates (PHA) from the lignin fraction of ATB. Nuclear magnetic resonance (NMR) analyses revealed that ATB lignin contained 63% of β-O-4 interunit linkages, making this lignin more suitable for pretreatment and biodegradation compared to other lignins. Exploratory experiments revealed that two-stage fermentation is suitable for PHA production from ATB lignin using wild type and engineered Pseudomonas putida strains. PHA increased from 0.09 to 0.39 g/L compared to single batch fermentation. Further improvement to 0.76 g/L was possible by using a central composite design to optimize the inoculum, substrate, and nitrogen concentrations. Finally, PHA depolymerase gene phaZ was knocked out from P. putida and tested at optimal conditions, enabling a PHA titer of 0.97 g/L. Analyses by NMR and GC-MS confirmed lignin derivatives consumption and decrease of β-O-4 linkages. This study lays the foundations to enable agave lignin bioprocessing and opens new avenues for ATB biorefineries.

PHA↗
DOE OSTI2025

Lignin-Derived Phenolic Compounds and Water Are Effective Cosolvents for Reductive Catalytic Fractionation

Reductive catalytic fractionation (RCF) is an effective lignin-first biorefining method to extract lignin as a stabilized oil from lignocellulosic biomass. To realize RCF at scale, process modeling has shown that minimizing the use of exogenous organic solvents is critical. To this end, here we investigate the ability of lignin-derived monomers to act as either solvents or cosolvents for RCF. We begin by examining the influence of lignin-derived aromatic compounds (4-propylguaiacol, 4-propylphenol, and propylbenzene) on RCF monomer yields and subsequently extend our analysis to mixtures of 4-propylguaiacol and either methanol or water. Here, we demonstrate that 4-propylguaiacol is an effective solvent for lignin extraction and depolymerization during RCF, especially when used in combination with water as a cosolvent. Cosolvent mixtures of 4-propylguaiacol and water enable up to 81% lignin extraction, monomer yields up to 25 wt %, and postreaction phase separation. However, unlike methanol, water as a cosolvent fails to inhibit aromatic ring hydrogenation when conducted over Ru/C as a catalyst, potentially leading to excess hydrogen consumption in a process utilizing this approach. Nonetheless, these results suggest a promising strategy for eliminating external organic solvents from RCF by utilizing mixtures of lignin-derived compounds and water as alternative extraction solvents.

09 BIOMASS FUELS↗
DOE OSTI2024

Toward a Circular Bioeconomy: Designing Microbes and Polymers for Biodegradation

Polymer production is rapidly increasing, but there are no large-scale technologies available to effectively mitigate the massive accumulation of these recalcitrant materials. One potential solution is the development of a carbon-neutral polymer life cycle, where microorganisms convert plant biomass to chemicals, which are used to synthesize biodegradable materials that ultimately contribute to the growth of new plants. Realizing a circular carbon life cycle requires the integration of knowledge across microbiology, bioengineering, materials science, and organic chemistry, which itself has hindered large-scale industrial advances. This review addresses the biodegradation status of common synthetic polymers, identifying novel microbes and enzymes capable of metabolizing these recalcitrant materials and engineering approaches to enhance their biodegradation pathways. Design considerations for the next generation of biodegradable polymers are also reviewed, and finally, opportunities to apply findings from lignocellulosic biodegradation to the design and biodegradation of similarly recalcitrant synthetic polymers are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multiscale investigation of the mechanism of biomass deconstruction in the dimethyl isosorbide/water Co-solvent pretreatment system

In the context of promoting a circular bioeconomy, the development of green and efficient lignocellulosic biomass pretreatment technologies so as to realize high value-added biomass utilization is of intense interest. We demonstrated the potential of the bio-based green solvent dimethyl isosorbide (DMI) for the fractionation of Eucalyptus biomass with excellent performance. Here, to investigate the mechanisms involved in biomass fractionation, microimaging and microspectroscopic techniques were employed together with molecular dynamics (MD) simulation and COSMO-RS quantum chemical calculations to derive multiscale information. Both the microstructure and regional chemistry of the cell wall vary significantly with the volume ratio of DMI/H 2 O. The strongest effects were found at DMI/H 2 O = 9:1 and showed visible cell wall tearing cracks and cell wall deformation and collapse as well as the lowest values of cell wall thickness and circularity. From the MD simulations, lignin exhibits collapsed-like structure in pure H 2 O with low solvent accessibility surface area (SASA) and radius of gyration (R g ). In contrast, lignin in DMI/H 2 O shows extended structure with high SASA and solvent interactions dominated by van der Waals forces, with maximal contact in the 9:1 (v/v) system. Further, the COSMO-RS calculated sigma (σ-) potential suggests the intermolecular interactions in DMI and DMI/H 2 O co-solvent are weak, leading to stronger interaction with lignin and correspondingly higher lignin dissolution. The radial distribution functions and σ-potential all show that again DMI/H 2 O at 9:1 is an optimal volume ratio for high lignin dissolution. Finally, this study provides a solvent-ratio dependent mechanism for the action of polar aprotic solvents in the deconstruction of biomass.

09 BIOMASS FUELS↗
DOE OSTI2024

Single-molecule tracking reveals dual front door/back door inhibition of Cel7A cellulase by its product cellobiose

Degrading cellulose is a key step in the processing of lignocellulosic biomass into bioethanol. Cellobiose, the disaccharide product of cellulose degradation, has been shown to inhibit cellulase activity, but the mechanisms underlying product inhibition are not clear. We combined single-molecule imaging and biochemical investigations with the goal of revealing the mechanism by which cellobiose inhibits the activity of Trichoderma reesei Cel7A, a well-characterized exo-cellulase. We find that cellobiose slows the processive velocity of Cel7A and shortens the distance moved per encounter; effects that can be explained by cellobiose binding to the product release site of the enzyme. Cellobiose also strongly inhibits the binding of Cel7A to immobilized cellulose, with a K i of 2.1 mM. The isolated catalytic domain (CD) of Cel7A was also inhibited to a similar degree by cellobiose, and binding of an isolated carbohydrate-binding module to cellulose was not inhibited by cellobiose, suggesting that cellobiose acts on the CD alone. Finally, cellopentaose inhibited Cel7A binding at micromolar concentrations without affecting the enzyme’s velocity of movement along cellulose. Together, these results suggest that cellobiose inhibits Cel7A activity both by binding to the “back door” product release site to slow activity and to the “front door” substrate-binding tunnel to inhibit interaction with cellulose. These findings point to strategies for engineering cellulases to reduce product inhibition and enhance cellulose degradation, supporting the growth of a sustainable bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Engineering robust microorganisms for organic acid production

Abstract Organic acids are an important class of compounds that can be produced by microbial conversion of renewable feedstocks and have huge demands and broad applications in food, chemical, and pharmaceutical industries. An economically viable fermentation process for production of organic acids requires robust microbial cell factories with excellent tolerance to low pH conditions, high concentrations of organic acids, and lignocellulosic inhibitors. In this review, we summarize various strategies to engineer robust microorganisms for organic acid production and highlight their applications in a few recent examples.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Developmentally-specific physiological and metabolic responses support drought resilience in switchgrass and constrains biofuel yield

Switchgrass (Panicum virgatum) is a promising bioenergy crop due in part to its resilience to drought stress. However, the significance of drought timing remains poorly understood, both from a plant biology perspective and its impact on downstream biofuel production. This study determines the developmental stage-specific physiological and metabolic responses of switchgrass to drought stress and its implications for biofuel production using a custom-built programmable irrigation system. Vegetative, flowering, and senescence-stage drought significantly reduced carbon dioxide assimilation, and stomatal conductance without affecting biomass yield. Metabolic profiling revealed significant accumulation of glucose, fructose, quinic acid, shikimate and GABA during vegetative-stage drought, while flowering and senescence stages exhibited limited metabolic changes. Similarly, specialized metabolites also displayed distinct developmental patterns, with vegetative-stage drought driving the most pronounced metabolic alterations. Thermochemically-treated and hydrolyzed switchgrass biomass from vegetative-stage drought showed elevated lignocellulose-derived compounds and saponins with the latter most positively correlating with fermentation lag times. Conversely, senescence-stage drought enhanced ethanol yields while lowering saponin levels in the hydrolysates. While vegetative-stage drought enhanced physiological resilience, it compromises downstream biofuel production by introducing fermentation inhibitors, particularly saponins.

biofuel↗
DOE OSTI2023

Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus

Abstract Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08 T , Bs12 T and Bsc2 T , are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter. The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12 T , purple; others beige to brown), marine salt requirement (Bs12 T , Bsc2 T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08 T and T. turnerae strains) and the ability to respire nitrate (Bs08 T ). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08 T =ATCC TSD-121 T =KCTC 62964 T ), Teredinibacter purpureus sp. nov. (type strain Bs12 T =ATCC TSD-122 T =KCTC 62965 T ) and Teredinibacter franksiae sp. nov. (type strain Bsc2 T =ATCC TSD-123 T =KCTC 62966 T ).

59 BASIC BIOLOGICAL SCIENCES↗