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All sourcesNASA NTRSDOE OSTI
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 OSTI2021

WEST Diversity Panel GBS information (Ferguson et al., 2020)

Genotyping by sequencing information (5,512,653 SNPs on 850 individuals [842 unique]) used in the manuscript "Machine learning enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions" (Ferguson et al., 2020) DOI:10.1101/2020.11.02.365213.

09 BIOMASS FUELS↗
DOE OSTI2020

Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass

There is strong interest in the valorization of lignin to produce valuable products; however, its structural complexity has been a conversion bottleneck. Chemical pretreatment liberates lignin-derived soluble fractions that may be upgraded by bioconversion. Here, cholinium ionic liquid pretreatment of sorghum produced soluble, aromatic-rich fractions that were converted by Pseudomonas putida (P. putida), a promising host for aromatic bioconversion. Growth studies and mutational analysis demonstrated that P. putida growth on these fractions was dependent on aromatic monomers but unknown factors also contributed. Proteomic and metabolomic analyses indicated that these unknown factors were amino acids and residual ionic liquid; the oligomeric aromatic fraction derived from lignin was not converted. A cholinium catabolic pathway was identified, and the deletion of the pathway stopped the ability of P. putida to grow on cholinium ionic liquid. This work demonstrates that aromatic-rich fractions obtained through pretreatment contain multiple substrates; conversion strategies should account for this complexity.

09 BIOMASS FUELS↗
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 OSTI2025

Comparison of the efficacy of a biocompatible and a distillable solvent for pretreatment of mixed bioenergy feedstocks

Biomass deconstruction is a crucial step in the production of lignocellulosic biofuels and bioproducts. However, identifying and selecting an optimal pretreatment solvent that enhances enzymatic saccharification while being cost-efficient and ensuring sustainability remains a challenge. In this study, we compare the effectiveness of the biocompatible ionic liquid cholinium lysinate ([Ch][Lys]) against the distillable solvent ethanolamine, when used for the pretreatment of mixed bioenergy feedstocks, including poplar, switchgrass, and sorghum. [Ch][Lys] was used at a concentration of 10 % wt. in a one-pot configuration without biomass washing and ethanolamine was used in a concentrated form and removed with a vacuum oven, before performing enzymatic hydrolysis and microbial conversion. Our results show that ethanolamine pretreatment consistently enhances the glucose yield across various biomass types compared to [Ch][Lys], with improvements ranging from 22.0 % to 52.7 %. The highest combined sugar release was observed when the three feedstocks were combined in equal amounts and pretreated with ethanolamine, achieving a glucose yield of 84.6 % and a xylose yield of 76.6 %. Additionally, ethanolamine exhibited exceptional solvent recovery efficiency, with removal efficiencies exceeding 99.8 % at 120 °C across all feedstocks, highlighting its advantage over non-distillable solvents. While both solvents produced biocompatible hydrolysates, the hydrolysates prepared using ethanolamine resulted in higher bioproduct formation. These findings highlight the industrial relevance of selecting recyclable and biocompatible solvents for scalable, sustainable, and cost-effective bioenergy production. This study contributes to the development of economically viable and scalable pretreatment technologies for bioenergy applications using different feedstocks and process configurations.

Rahman, Maksudur↗
DOE OSTI2024

Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates

Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Microbial valorization of lignin to malic acid by Aspergillus niger

Lignin is the largest renewable source of aromatic carbon, yet its heterogeneity and recalcitrance limit its use in higher-value bioconversion processes. In this study, Aspergillus niger was engineered to enable the bioconversion of lignin-derived aromatics and base-catalyzed depolymerized (BCD) lignin streams into malic acid, a value-added C4 dicarboxylic acid with broad industrial relevance. Overexpression of the C4 dicarboxylate transporter C4T318 from Aspergillus oryzae enhanced malic acid secretion, while medium optimization under buffered conditions further improved the production. The engineered strain efficiently assimilated representative lignin-derived aromatics, including 4-hydroxybenzoic acid and p-coumaric acid, producing up to 3.9 g/L malic acid. Conversion of BCD lignin liquors from poplar and sorghum demonstrated effective utilization of heterogeneous aromatic mixtures, generating up to 0.82 g/L malic acid. This work demonstrates direct fungal conversion of real lignin streams into malic acid and establishes A. niger as a promising platform for sustainable lignin valorization.

Aromatic bioconversion↗
DOE OSTI2025

A network-enabled pipeline for gene discovery and validation in non-model plant species

Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 ( CSLF6 ), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum. Our analyses uncover regulators of CSLF6 and also shed light on the evolutionary conservation or divergence of gene regulatory elements among grass species. These results highlight NEEDLE’s capability to provide biologically relevant TF predictions and demonstrate its value for non-model plant species with dynamic transcriptome datasets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Bioenergy crops as alternative feedstocks for recovery of anthocyanins: A review

Anthocyanins are plant-based pigments known for their wide range of industrial applications. Berries, grapes, purple yam, purple corn, and black rice are among the chief dietary sources of anthocyanins. However, these sources have a well-established market in the food sector and cannot be diverted completely for the extraction of anthocyanins. Hence, there is a need to identify alternative sources of these natural colorants. In this review, color-bearing bioenergy crops with high productivity such as miscanthus, sorghum, and sugarcane have been proposed as potential feedstocks for the recovery of anthocyanins as co-products. The role of genetic modification in the biosynthesis of anthocyanins in these crops has been discussed. A consolidated bioprocessing approach has been proposed for the recovery of anthocyanins from bioenergy crops along with the production of bioethanol and lignin-based chemicals. Such an integrated process could make the overall process for the production of biofuels cost-effective.

09 BIOMASS FUELS↗
DOE OSTI2025

In planta production of the nylon precursor beta-ketoadipate

Beta-ketoadipate (βKA) is an intermediate of the βKA pathway involved in the degradation of aromatic compounds in several bacteria and fungi. Beta-ketoadipate also represents a promising chemical for the manufacturing of performance-advantaged nylons. We established a strategy for the in planta synthesis of βKA via manipulation of the shikimate pathway and the expression of bacterial enzymes from the βKA pathway. Using Nicotiana benthamiana as a transient expression system, we demonstrated the efficient conversion of protocatechuate (PCA) to βKA when plastid-targeted bacterial-derived PCA 3,4-dioxygenase (PcaHG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaB) were co-expressed with 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (AroG) and 3-dehydroshikimate dehydratase (QsuB). This metabolic pathway was reconstituted in Arabidopsis by introducing a construct (pAtβKA) with stacked pcaG, pcaH, and pcaB genes into a PCA-overproducing genetic background that expresses AroG and QsuB (referred as QsuB-2). The resulting QsuB-2 x pAtβKA stable lines displayed βKA titers as high as 0.25 % on a dry weight basis in stems, along with a drastic reduction in lignin content and improvement of biomass saccharification efficiency compared to wild-type controls, and without any significant reduction in biomass yields. Using biomass sorghum as a potential crop for large-scale βKA production, techno-economic analysis indicated that βKA accumulated at titers of 0.25 % and 4 % on a dry weight basis could be competitively priced in the range of $2.04-34.49/kg and $0.47-2.12/kg, respectively, depending on the selling price of the residual biomass recovered after βKA extraction. This study lays the foundation for a more environmentally-friendly synthesis of βKA using plants as production hosts.

Kazaz, Sami↗
DOE OSTI2025

A “Sweet” Biorefinery: Sugar-derived ionic liquids for the pretreatment of lignocellulosic biomass

Sugar-based ionic liquids (ILs) derived from biomass-based cations (choline, betaine) and sugar-derived anions were developed as sustainable pretreatment solvents to advance the concept of self-reliant biorefinery. Cholinium gluconate ([Ch][GlcA]) enabled streamlined one-pot sorghum pretreatment without the need for pH adjustment or washing, while betainium gluconate ([Bet][GlcA]) achieved higher sugar yields, improving overall process efficiency and economics. Both ILs produced hydrolysates fully compatible with microbial fermentation, demonstrating their potential for efficient, simplified biomass conversion. This work positions sugar-based ILs as powerful platforms that unite sustainable chemistry with integrated bioprocessing, marking a pivotal step toward realizing the self-reliant biorefinery.

Biomass-based ions↗
DOE OSTI2026

NMR of Fully and Partially 13 C-Enriched Biomass Enhances Pendent Group Structural Characterization

Traditional solution-state NMR experiments may either fail or yield unsatisfactory results when employing fully- 13 C-labeled biomass due to complications arising from 13 C– 13 C coupling. Constant-time analogs of HSQC experiments mitigate such issues and deliver enhanced sensitivity. A rarely reported CT-HSQC-TOCSY experiment allows the proton coupling network to deliver much of the same value as the parent experiment on unlabeled or 10–15%- 13 C-labeled biomass polymers but with enhanced sensitivity. In the absence of a viable HMBC analog for long-range correlations, a relayed C–C experiment, i.e., via directly bonded 13 C-labeled networks, enables the reliable assignment of coupled carbons, with the added advantage of correlating the more elusive quaternaries. A C–C-FLOPSY experiment takes advantage of fully- 13 C-labeled materials for mapping extensive carbon networks in the complex polymer mixtures inherent in biomass. Various pendent groups (tricin units, cis- and trans-p-coumarates, and p -hydroxybenzoates) that adorn lignins, and the cis- and trans-ferulates on arabinoxylan polysaccharides, are exquisitely revealed in spectra from isolated lignins or whole-cell-wall materials from maize, sorghum, and poplar.

biopolymers↗
DOE OSTI2020

Cost and Life-Cycle Greenhouse Gas Implications of Integrating Biogas Upgrading and Carbon Capture Technologies in Cellulosic Biorefineries

We discuss gaseous streams in biorefineries that have been undervalued and underutilized. In cellulosic biorefineries, coproduced biogas is assumed to be combusted alongside lignin to generate process heat and electricity. Biogas can instead be upgraded to compressed biomethane and used as a transportation fuel. Capturing CO 2 -rich streams generated in biorefineries can also contribute to greenhouse gas (GHG) mitigation goals. We explore the economic and life-cycle GHG impacts of biogas upgrading and CO 2 capture and storage (CCS) at ionic liquid-based cellulosic ethanol biorefineries using biomass sorghum. Without policy incentives, biorefineries with biogas upgrading systems can achieve a comparable minimum ethanol selling price (MESP) and reduced GHG footprint ($1.38/liter gasoline equivalent (LGE) and 12.9 gCO 2e /MJ) relative to facilities that combust biogas onsite ($1.34/LGE and 24.3 gCO 2e /MJ). Incorporating renewable identification number (RIN) values advantages facilities that upgrade biogas relative to other options (MESP of $0.72/LGE). Incorporating CCS increases the MESP but dramatically decreases the GHG footprint (-21.3 gCO 2e /MJ for partial, -110.7 gCO 2e /MJ for full CCS). The addition of CCS also decreases the cost of carbon mitigation to as low as $52-$78/t CO 2 , depending on the assumed fuel selling price, and is the lowest-cost option if both RIN and California's Low Carbon Fuel Standard credits are incorporated.

09 BIOMASS FUELS↗
DOE OSTI2026

Rapid Evaluation of Amine-Functionalized Solvents for Biomass Deconstruction Using High-Throughput Screening and One-Pot Enzymatic Saccharification

Efficient and sustainable pretreatment of lignocellulosic biomass is critical for biofuel and biochemical production, yet its optimization is often hindered by slow, labor-intensive experimental methods. Here, we report the first demonstration of a custom-built, miniaturized, high-throughput screening platform integrated with one-pot enzymatic saccharification, enabling parallel evaluation of solvent type, feedstock, and temperature with minimal material use and high reproducibility. As a proof-of-concept, the HTX platform was used to screen five amine-functionalized solvents, including isopropanolamine, butylamine, N-methylbutylamine, ethanolamine, and ethanolamine acetate across three bioenergy crops (sorghum, poplar, and switchgrass) and pretreatment temperatures ranging from 80 to 140 °C. Vacuum drying successfully removed more than 99% of the solvents from the pretreated biomass, eliminating the need for water washing prior to saccharification. Isopropanolamine and N-methylbutylamine yielded the highest glucose (70–80%) and xylose (58–67%) release, with trends reflecting feedstock recalcitrance. The produced hydrolysates supported robust growth of an engineered strain of the yeast Rhodosporidium toruloides, confirming biocompatibility. This high-throughput platform provides a scalable, feedstock-agnostic framework for rapid pretreatment screening, accelerating solvent–feedstock pairing and process optimization. Its ability to integrate pretreatment, solvent removal, saccharification, and microbial conversion in a miniaturized format offers significant advantages for cost-competitive biorefinery development.

Biomass↗
DOE OSTI2023

Evolution of the Cellulose Microfibril through Gamma-Valerolactone-Assisted Co-Solvent and Enzymatic Hydrolysis

Biomass recalcitrance during deconstruction remains a key bottleneck to affordable biomass processing technologies. A clear connection between the cell wall structure and biomass deconstruction is necessary to understand how lignocellulosic material is broken down to valuable monomeric components. Here, we monitor changes in the cellulose microfibril domains of poplar, sorghum, and switchgrass throughout gamma-valerolactone (GVL)–water co-solvent pretreatment and enzymatic hydrolysis using solid-state 13 C cross-polarization magic angle spinning nuclear magnetic resonance spectroscopy (CP/MAS 13 C-NMR) and wide-angle X-ray scattering (WAXS). Spectral fitting of NMR peaks corresponding to different cellulose microenvironments at the C 4 carbon center suggests that a mildly acidic GVL–water co-solvent pretreatment of poplar leads to nearly full removal of xylan–cellulose linkages, which primes the cellulose for enzymatic attack. The spectral fitting also suggests that the pretreatment causes significant depletion of the inaccessible fibril surface domains with an increase in more thermally stable crystalline resonances (I β ). WAXS confirmed a decrease in the lattice spacing between (200) crystalline planes with increasing co-solvent pretreatment severity. These results are interpreted as an opening of bound microfibril surfaces previously inaccessible to the co-solvent system, which leaves behind a more thermally stable, crystalline domain that is potentially prone to relaxation and recrystallization. Full conversion of residual GVL-pretreated biomass was achieved after the GVL co-solvent pretreatment at 140 °C using a commercial enzyme cocktail, CTec2, which contains different cellulases and other enzymes. Spectral fitting of enzymatically hydrolyzed samples by a single engineered cellulase, CelR, suggests that the residual cellulose recalcitrance is mainly due to the inability of CelR to digest the I β crystalline domain present in pretreated samples. This work helps to provide new information regarding the structure of the cell wall and recalcitrance throughout GVL–water mild acidolysis and CelR enzymatic biomass deconstruction by tracking the evolution of structural domains within the cellulose microfibril. This work further directs recommendations for improving the conversion and sugar yields in future studies. Finally, our findings inform inquiry into larger questions of cellulose recalcitrance through GVL pretreatment and CelR enzymatic hydrolysis and give insight into subsequent required steps for full cellulose conversion with attention to the most recalcitrant cellulose structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

Abstract Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus . Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Expression profiling of MADS-box gene family revealed its role in vegetative development and stem ripening in S. spontaneum

Sugarcane is the most important sugar and biofuel crop. MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in plants. Systematic analyses of MADS-box genes have been reported in many plant species, but its identification and characterization were not possible until a reference genome of autotetraploid wild type sugarcane specie, Saccharum spontaneum is available recently. We identified 182 MADS-box sequences in the S. spontaneum genome, which were annotated into 63 genes, including 6 (9.5%) genes with four alleles, 21 (33.3%) with three, 29 (46%) with two, 7 (11.1%) with one allele. Paralogs (tandem duplication and disperse duplicated) were also identified and characterized. These MADS-box genes were divided into two groups; Type-I (21 Mα, 4 Mβ, 4 Mγ) and Type-II (32 MIKCc, 2 MIKC*) through phylogenetic analysis with orthologs in Arabidopsis and sorghum. Structural diversity and distribution of motifs were studied in detail. Chromosomal localizations revealed that S. spontaneum MADS-box genes were randomly distributed across eight homologous chromosome groups. The expression profiles of these MADS-box genes were analyzed in leaves, roots, stem sections and after hormones treatment. Important alleles based on promoter analysis and expression variations were dissected. qRT-PCR analysis was performed to verify the expression pattern of pivotal S. spontaneum MADS-box genes and suggested that flower timing genes ( SOC1 and SVP ) may regulate vegetative development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome-wide discovery of G-quadruplexes in barley

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5' untranslated region (5' UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

54 ENVIRONMENTAL SCIENCES↗