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DOE OSTI2023

Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose

Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the end goal of accelerating the adoption of R. opacus in biofuel production, during the grant period we have expanded the phenotypic characterization of R. opacus grown in single aromatic (model lignocellulosic) compounds or their mixtures, modeling the growth conditions in lignocellulosic biomass. Harnessing the power of adaptive evolution, we produced evolved R. opacus isolates with superior lignin valorization capabilities and identified differentially expressed genes and pathways after adaptation. We used next generation multi-omic techniques such as genomic, transcriptomic, and metabolomic analyses, to identify the catabolic pathways used by R. opacus to degrade aromatic compounds and funnel these degradation products into central metabolism, as well as the aromatic transport genes required for increased tolerance and utilization. Taking this information one step further, we identified endogenous transcription factors and regulatory mechanisms important for degradation of five model aromatic compounds. To accurately estimate R. opacus growth and consumption on model lignin compounds we pioneered the use of novel extraction procedures prior to GC-MS analysis. Alongside 13 C-metabolic flux analysis, we have elucidated the metabolic routes preferred by Rhodococcus opacus during aromatic compound degradation. Finally, we used in tandem lipidomics and high-resolution mass spectrometry to identify the modulation of mycolic acids and phospholipid membrane composition modification as a strategy for aromatic tolerance in R. opacus. Being a non-model organism, R. opacus lacks the breadth of tools and technical foundation which drive biofuel research in more well-understood microbes such as Escherichia coli. To reduce this burden for use, we designed and produced new tools for genomic manipulation and engineering in R. opacus. These engineering breakthroughs support efficient genomic editing, enabling gene overexpression, repression, and genetic alteration. Using these tools, we have generated synthetically engineered strains with increased lipogenesis and growth, both positive traits required for increased lignin valorization. Optimizing engineered strains for biofuel production from lignocellulose requires extremely sophisticated synthetic rewiring of metabolism. To facilitate systems-level reorganization of metabolism in R. opacus, we created a genome-scale model that accurately predicts metabolic flux and growth rates on the aromatic compound phenol. Lignin requires extensive pre-treatment before biological degradation by R. opacus. Towards an eventual goal of degrading real-world lignin, we developed new depolymerization processes to generate lignin breakdown products (LBP). We optimized LBP storage and composition analysis techniques, enabling accurate prediction of specific LBP compound integration into cell wall components. Overall, through the work funded by this grant we generated 20 manuscripts (17 published, 3 in review/preparation), methods for increased accuracy in metabolomics of aromatic compounds, multiple genetic tools for altering the R. opacus genome, genome scale models for predicting flux through metabolic pathways, as well as multi-omic data for community use. The work funded by this grant has increased the knowledge of aromatic degradation in bacteria and advanced our efforts to optimize R. opacus for lignin valorization.

09 BIOMASS FUELS↗

DOE OSTI2023

Disposition of Solids from Hydrothermal Liquefaction of Biomass: Current Understanding, Research Gaps, and Opportunities

Characteristics of solid residuals generated during hydrothermal liquefaction (HTL) of biomass are reported to establish disposition options for these residuals to reduce liability or barriers to commercialization of HTL. HTL solids from pilot scale are reported and compared to existing HTL solids literature for a variety of biomass feedstocks and HTL configurations, noting differences among literature HTL solids due to solids collection methods. Reported analyses include CHNOS, moisture, ash, inorganics by Inductively Coupled Plasma (ICP), and High Heating Value (HHV). HTL solids are determined to be substantially compatible with U.S. Environmental Protection Agency (EPA) disposal regulations within existing data. Disposition and valorization routes are identified, yet combustion as valorization is determined to be not economically beneficial. Further, research gaps are identified, which include the need for future research to be performed on HTL solids that are representative of a continuous, commercializable flowsheet; verification that specific HTL solids meet EPA disposal requirements; exploration of valorization options; and the need for invention of continuous HTL solids separations/management.

09 BIOMASS FUELS↗

DOE OSTI2025

Engineered Methylobacterium extorquens grows well on methoxylated aromatics due to its formaldehyde metabolism and stress response

ABSTRACT Lignin is a vast yet underutilized source of renewable energy. The microbial valorization of lignin is challenging due to the toxicity of its degradation intermediates, particularly formaldehyde. In this study, we engineeredMethylobacterium extorquensPA1 to metabolize lignin-derived methoxylated aromatics, vanillate (VA) and protocatechuate (PCA), by introducing thevanandpcagene clusters. Compared toPseudomonas putida,M. extorquensPA1 exhibited better formaldehyde detoxification, enabling robust growth on VA without accumulation of formaldehyde. Genetic analyses confirmed that formaldehyde oxidation and stress response systems, rather than C 1 assimilation, were important for VA metabolism. Additionally, VA and PCA were found to disrupt membrane potential, contributing to their inherent toxicity. Our findings establishM. extorquensPA1 as a promising chassis for lignin valorization and provide a framework for engineering formaldehyde-resistant microbial platforms. IMPORTANCE In developing biotechnological solutions for a circular economy, it is critical to valorize all parts of renewable resources, such as lignocellulose from vegetative components of agricultural crops and from bioenergy feedstocks. After chemical breakdown, the aromatics arising from lignin present significant challenges for use due to their toxicity. Here, we address one component of this challenge—the methoxy groups that get released as formaldehyde—and show that existing biotechnological platform organisms with strong formaldehyde metabolism, such asMethylobacterium extorquens, can be transformed into highly capable utilizers of methoxylated aromatics.

Microbiology↗

DOE OSTI2022

Effect of ash in paper sludge on enzymatic hydrolysis

The valorization of paper sludge is a high-potential process to develop renewable fuels and chemicals, which can be integrated with pulp and paper mills. Calcium carbonate is the main ash component in sludge, which plays a role in buffering pH and potentially lowering the conversion during enzymatic hydrolysis. Therefore, it is important to investigate the effect of ash on sugar yields and examine pH change to introduce efficient and economical enzymatic hydrolysis of sludge. Carbohydrate conversion was enhanced when the ash was removed by fractionation. On the other hand, the highest sugar recovery was obtained when the sludge contained 20% ash content. The pH change during enzymatic hydrolysis was influenced by ash and explained why sludge-derived hydrolysate showed lower carbohydrate conversion. Therefore, a high shear process with the increased acid amount is suggested to prohibit the negative effect of ash and enhance the accessibility of cellulase to fibers. Finally, this study highlights the feasibility of using wet waste streams generated by the paper industry.

09 BIOMASS FUELS↗

DOE OSTI2024

Perspective on Lignin Conversion Strategies That Enable Next Generation Biorefineries

The valorization of lignin, a currently underutilized component of lignocellulosic biomass, has attracted attention to promote a stable and circular bioeconomy. Successful approaches including thermochemical, biological, and catalytic lignin depolymerization have been demonstrated, enabling opportunities for lignino-refineries and lignocellulosic biorefineries. Although significant progress in lignin valorization has been made, this review describes unexplored opportunities in chemical and biological routes for lignin depolymerization and thereby contributes to economically and environmentally sustainable lignin-utilizing biorefineries. This review also highlights the integration of chemical and biological lignin depolymerization and identifies research gaps while also recommending future directions for scaling processes to establish a lignino-chemical industry.

09 BIOMASS FUELS↗

DOE OSTI2025

Utilization of Hemp Processing Waste for 3D Printing of Biocomposites

Unlike stem biomass, the residues after the extraction of cannabidiol (CBD) oil from hemp flower are challenging to utilize because of their high extractive content (~ 40%, mainly lipids) and are typically considered waste and landfilled. This study presented a novel approach to effectively valorize this underutilized hemp processing waste via chemical processing for three-dimensional (3D) printing applications. Hemp processing waste was processed with sodium hydroxide (NaOH) to control extractives for solving nozzle clogging and then applied as a biofiller in polylactic acid (PLA) composites to improve the mechanical strength. The novelty of this work lies in demonstrating that controlled extractive removal via NaOH treatment not only improves processability but also enhances mechanical performance in 3D-printed biocomposites. We systematically investigated the effect of the processed biofiller content (2.5–10 wt%) on the mechanical and thermal properties of the biocomposites. The decrease in the content of extractives reduced the non-structural components and improved the surface compatibility of the hemp waste with the PLA matrix, thereby enhancing the polymer-biofiller interactions. The best performance was achieved at 2.5 wt% loading, where Young’s modulus increased from 2.3 GPa to 2.6 GPa and tensile strength from 42.7 MPa to 48.8 MPa. Interestingly, the complete removal of extractives also reduced the mechanical strength of their biocomposites, indicating the interfacial adhesion effects of extractives. Furthermore, this study provides new insights into balancing extractive content for optimal mechanical properties, offering a sustainable solution for waste valorization in additive manufacturing.

Additive manufacturing↗

DOE OSTI2020

The critical role of lignin in lignocellulosic biomass conversion and recent pretreatment strategies: A comprehensive review

Heterogeneity and rigidity of lignocellulose causing resistance to its deconstruction have provided technical and economic challenges in the current biomass conversion processes. Lignin has been considered as a crucial recalcitrance component in biomass utilization. An in-depth understanding of lignin properties and their influences on biomass conversion can provide clues to improve biomass utilization. Also, utilization of lignin can significantly increase the economic viability of biorefinery. Recent lignin-targeting pretreatments have aimed not only to overcome recalcitrance for biomass conversion but also to selectively fractionate lignin for lignin valorization. Numerous studies have been conducted in biomass characteristics and conversion technologies, and the role of lignin is critical for lignin valorization and biomass pretreatment development. In this review, we provide a comprehensive review of lignin-related biomass characteristics, the impact of lignin on the biological conversion of biomass, and recent lignin-targeting pretreatment strategies. The desired lignin properties in biorefinery and future pretreatment directions are also discussed.

09 BIOMASS FUELS↗

DOE OSTI2022

Effective biomass fractionation and lignin stabilization using a diol DES system

A sustainable and renewable biorefinery will increase the economic viability of lignocellulose-derived products. In this study, a diol-based deep eutectic solvent (DES) was developed to reduce the recalcitrance of bamboo, facilitate saccharification and valorize the lignin fraction. The DES pretreatment dramatically enhanced glucan digestibility by the effective removal of lignin (as high as 85.45%) and xylan (91.12%). Notably, the recovered lignin from DES pretreatment was protected during the fractionation, showing well-preserved β-O-4 structures (31.82%–59.06%). The mechanism of lignin protection was analyzed to be accomplished by incorporating the diol hydroxyl functional groups into the α position of the lignin β-O-4 structure via etherification. This work highlighted that diol DES is a promising pretreatment solvent to valorize both cellulose and lignin fractions with high enzymatic hydrolysis yield and high-quality lignin co-product.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

RB-TnSeq identifies genetic targets for improved tolerance of Pseudomonas putida towards compounds relevant to lignin conversion

We report lignin-derived mixtures intended for bioconversion commonly contain high concentrations of aromatic acids, aliphatic acids, and salts. The inherent toxicity of these chemicals places a significant bottleneck upon the effective use of microbial systems for the valorization of these mixtures. Pseudomonas putida KT2440 can tolerate stressful quantities of several lignin-related compounds, making this bacterium a promising host for converting these chemicals to valuable bioproducts. Nonetheless, further increasing P. putida tolerance to chemicals in lignin-rich substrates has the potential to improve bioprocess performance. Accordingly, we employed random barcoded transposon insertion sequencing (RB-TnSeq) to reveal genetic determinants in P. putida KT2440 that influence stress outcomes during exposure to representative constituents found in lignin-rich process streams. The fitness information obtained from the RB-TnSeq experiments informed engineering of strains via deletion or constitutive expression of several genes. Namely, ΔgacAS, ΔfleQ, ΔlapAB, ΔttgR::P tac :ttgABC, Ptac:PP_1150:PP_1152, ..delta..relA, and ΔPP_1430 mutants showed growth improvement in the presence of single compounds, and some also exhibited greater tolerance when grown using a complex chemical mixture representative of a lignin-rich chemical stream. Overall, this work demonstrates the successful implementation of a genome-scale screening tool for the identification of genes influencing stress tolerance against notable compounds within lignin-enriched chemical streams, and the genetic targets identified herein offer promising engineering targets for improving feedstock tolerance in lignin valorization strains of P. putida KT2440.

09 BIOMASS FUELS↗

DOE OSTI2022

Critical Enzyme Reactions in Aromatic Catabolism for Microbial Lignin Conversion

The application of microbes to valorize aromatic compounds derived from the abundant plant biopolymer lignin is a rapidly developing area of research that may ultimately enable viable conversion of this recalcitrant and heterogeneous resource to valuable bio-based chemical products. Starting from the three canonical lignin building blocks, which differ in the extent of aromatic ring methoxylation, several common classes of enzymatic reaction occur in the upper pathways of aromatic catabolism to prepare aromatic compounds for assimilation into central carbon metabolism, including aromatic O-demethylation, hydroxylation and decarboxylation. These critical enzymatic steps can often be rate-limiting for efficient biological funnelling of aromatic compounds. Here we review the known enzymatic mechanisms for these reactions that are relevant for aerobic aromatic catabolism of lignin-related monomers, highlighting opportunities at the intersection of biochemistry, enzyme engineering and metabolic engineering for applications in the expanding field of microbial lignin valorization.

aromatic catabolism↗

DOE OSTI2024

The Catabolism of Lignin-Derived p-Methoxylated Aromatic Compounds by Rhodococcus jostii RHA1

Emergent strategies to valorize lignin, an abundant but underutilized aromatic biopolymer, include tandem processes that integrate chemical depolymerization and biological catalysis. To date, aromatic monomers from C-O bond cleavage of lignin have been converted to bioproducts, but the presence of recalcitrant C-C bonds in lignin limits the product yield. A promising chemocatalytic strategy that overcomes this limitation involves phenol methyl protection and autoxidation. Incorporating this into a tandem process requires microbial cell factories able to transform the p-methoxylated products in the resulting methylated lignin stream. In this study, we assessed the ability of Rhodococcus jostii RHA1 to catabolize the major aromatic products in a methylated lignin stream and elucidated the pathways responsible for this catabolism. RHA1 grew on a methylated pine lignin stream, catabolizing the major aromatic monomers: p-methoxybenzoate (p-MBA), veratrate, and veratraldehyde. Bioinformatic analyses suggested that a cytochrome P450, PbdA, and its cognate reductase, PbdB, are involved in p-MBA catabolism. Gene deletion studies established that both pbdA and pbdB are essential for growth on p-MBA and several derivatives. Furthermore, a deletion mutant of a candidate p-hydroxybenzoate (p-HBA) hydroxylase, ..delta..pobA, did not grow on p-HBA. Veratraldehyde and veratrate catabolism required both vanillin dehydrogenase (Vdh) and vanillate O-demethylase (VanAB), revealing previously unknown roles of these enzymes. Finally, a ..delta..pcaL strain grew on neither p-MBA nor veratrate, indicating they are catabolized through the ..beta..-ketoadipate pathway. This study expands our understanding of the bacterial catabolism of aromatic compounds and facilitates the development of biocatalysts for lignin valorization.

aromatic biopolymers↗

DOE OSTI2021

Lignin-Derived Chemicals from Pulping Liquors: Cooperative Research and Development CRADA Number CRD-17-00714 (Final Report)

National Renewable Energy Laboratory (NREL) has developed a robust portfolio for lignin valorization using a “biological funneling” approach, which adopts a microbial process to convert the inherent heterogeneity of lignin-rich streams into single high-value products. In parallel, Sustainable Fiber Technologies (SFT) has developed a proprietary, high-pH process to convert non-woody biomass into valuable pulp for myriad biomaterial applications. Therefore, by combining the expertise of both SFT and NREL, this project aimed to valorize co-products from an industrial pulping process of non-woody feedstocks. A detailed analytical characterization of an SFT pulping stream was used to aid the development of a bench-scale separations strategy to isolate a mixture of low molecular weight compounds, and ultimately to aid in bioreactor cultivations used to produce polyhydroxyalkanoate (PHA) biopolymers at titers, rates, and yields necessary for moving towards commercialization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Lignin Utilization

Valorization of lignin has massive potential economic and sustainability benefits for the lignocellulosic biorefinery. However, challenges remain to realize lignin conversion to coproducts, especially related to selective, high yield depolymerization to monomers and quantitative analytics on lignin, the latter of which is critical for accurate process modeling. Towards these goals, the Lignin Utilization project focuses on catalytic lignin deconstruction chemistries for C-O and C-C bond cleavage, development of analytical chemistry techniques to quantitatively characterize lignin, and syntheses of requisite model compounds for understanding lignin transformations. This work is done with and supports multiple BETO projects, including the Biological Lignin Valorization (BLV) project, the Separations Consortium, and others. Outcomes of Lignin Utilization for analytics and synthesis include 1) development of new mass spectrometry (MS) methods to characterize lignin dimers/oligomers in process streams, 2) deployment of a computational-experimental tool (with Biochemical Process Modeling and Simulation) to identify lignin-derived compounds with high fidelity from MS, and 3) delivery of >40 unique compounds. From a catalysis perspective, we have developed new oxidative approaches to cleave C-O and C-C bonds and produce >50% bio-available aromatic monomers for biological funneling for the BLV project and have developed recoverable bases for base-catalyzed deconstruction of lignin.

BIOMASS FUELS↗

DOE OSTI2026

Understanding Depolymerization and Repolymerization Toward Repurposing Polymer Waste Into Valuable Chemicals & Materials

The versatility of synthetic polymers has led to their continual and escalating production that has accompanied mismanagement at their end-of-life. Exploring and understanding complementary avenues to repurpose plastic waste beyond traditional mechanical recycling can unlock new opportunities in providing feedstock flexibility, securing supply chains, recovering valuable materials, and enabling new valorization paths. Chemical recycling allows for the return to monomers, tailored oligomers, and polymers, even from mixed states of post-consumer waste plastics. This review article summarizes our research team's efforts on elucidating key insights surrounding plastic depolymerization and repolymerization into valorized products. We revealed organocatalyst design rules lead to highly effective and selective deconstruction of condensation polymers. The intricacies of tailoring the reaction environment to produce products of specific lengths and desired functionalities transform low-value waste feedstocks into high-performance materials with embedded circularity. Other types of polymers, including polyolefins and polyakenamers, have also been designed and converted into valuable products. There remain opportunities for further developments such as low-energy and precision depolymerization, adoption of cutting-edge small molecule transformation to access functionalized polymer scaffolds typically inaccessible otherwise, as well as precision design and understanding through the aid of advanced tools.

Galan, Nick [ORNL]↗

DOE OSTI2022

Mechanistic Differences between Electrochemical Hydrogenation and Hydrogenolysis of 5‐Hydroxymethylfurfural and Their pH Dependence

Abstract Hydrogenation and hydrogenolysis are two important reactions for electrochemical reductive valorization of biomass‐derived oxygenates such as 5‐hydroxymethylfurfural (HMF). In general, hydrogenolysis (which combines hydrogenation and deoxygenation) is more challenging than hydrogenation (which does not involve the cleavage of carbon–oxygen bonds). Thus, identifying factors and conditions that can promote hydrogenolysis is of great interest for reductive valorization of biomass‐derived oxygenates. For the electrochemical reduction of HMF and its derivatives, it is known that aldehyde hydrogenation is not a part of aldehyde hydrogenolysis but rather a competing reaction; however, no atomic‐level understanding is currently available to explain their electrochemical mechanistic differences. In this study, combined experimental and computational investigations were performed using Cu electrodes to elucidate the key mechanistic differences between electrochemical hydrogenation and hydrogenolysis of HMF. The results revealed that hydrogenation and hydrogenolysis of HMF involve the formation of different surface‐adsorbed intermediates via different reduction mechanisms and that lowering the pH promoted the formation of the intermediates required for aldehyde and alcohol hydrogenolysis. This study for the first time explains the origins of the experimentally observed pH‐dependent selectivities for hydrogenation and hydrogenolysis and offers a new mechanistic foundation upon which rational strategies to control electrochemical hydrogenation and hydrogenolysis can be developed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Isolation, Characterization, and Depolymerization of L -Cysteine Substituted Eucalyptus Lignin

Lignin condensation reactions are hard to avoid or control during separation, which is a deterrent to lignin isolation and post-conversation, especially for the full utilization of lignocelluloses. Selective protection of β-aryl ether linkages in the isolation process is crucial to lignin valorization. Herein, a two-step acid/alkali separation method assisted with l-cysteine for eucalyptus lignin separation is developed, and the isolated L -cysteine lignins (LCLs) are comprehensively characterized by 2D NMR, 31 P NMR, thioacidolysis, etc. Compared to the two-step control treatment, a much higher β-O-4 content is preserved without reducing the separation efficiency assisted by L -cysteine, which is also significantly higher than alkali lignin and kraft lignin. The results of hydrogenolysis show that LCLs generate a much higher monomer yield than that of control sample. Structural analysis of LCLs suggests that lignin condensation reaction, to some extent, is suppressed by adding L -cysteine during the two-step acid/alkali separation. Further, mechanistic studies using dimeric model compound reveals that L -cysteine may be the α-carbon protective agent in the two-step separation. The role of L -cysteine in the two-step lignin isolation method provides novel insights to the selective fractionation of lignin from biomass, especially for the full valorization of lignocellulosic biomass.

09 BIOMASS FUELS↗

DOE OSTI2022

Enzymatic synthesis of kraft lignin-acrylate copolymers using an alkaline tolerant laccase

Abstract Softwood kraft lignin is a major bioresource relevant to the production of sustainable bio-based products. Continued challenges to lignin valorization, however, include poor solubility in organic solvents and in aqueous solutions at neutral pH. Herein, an alkaline tolerant laccase was used to graft acrylate functionalities onto softwood kraft lignin, which is expected to enhance the reactivity of lignin with isocyanate when producing bio-based polyurethanes. Proton nuclear magnetic resonance, Fourier-transform infrared spectroscopy, and high-performance liquid chromatography were used to confirm successful grafting of the acrylate monomer onto lignin and verify the importance of including tert-butyl hydroperoxide as an initiator in the grafting reaction. Laccase-mediated grafting of softwood kraft lignin under alkaline conditions produced lignin products with approximately 30% higher hydroxyl value and higher reactivity toward isocyanate. The reported enzymatic and aqueous process presents an opportunity for the sustainable valorization of softwood kraft lignin. Key points • Softwood kraft lignin displayed high phenolic hydroxyl content, polydispersity index and average molecular weight • Grafting hydroxyethyl acrylate (HEA) monomer onto kraft lignin by laccase was successful at 60 °C and alkaline conditions • Lignin-HEA grafted copolymer showed an increase in total OH value and an increase in average molecular weight

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Electrochemical Reduction Selectivity of Crotonaldehyde on Copper

Lignocellulosic waste is a potential feedstock for the generation of fuels and commodity chemicals, but existing conversion methods are too cost-intensive to be viable long-term solutions. Electrochemical reductions are promising for decentralized biomass valorization due to their modular scaling and capacity to run intermittently and without high temperatures or pressures. Using crotonaldehyde as a multi-functional model compound for the many partially unsaturated oxygenates found in processed biomass, we here demonstrate the production of butanal, butanol, butene, and butane (variously useful as commodity chemicals and major components of liquified petroleum gas) under ambient conditions by reductive bulk electrolysis with a copper mesh working electrode. We identify an optimum potential for reduced organic production under the reaction conditions and compare product distributions from reductions of intermediate species to further propose branching reaction pathways. Though butanal is typically the most abundant product from crotonaldehyde reduction, most of the butene and butane appear to result from a pathway involving initial reduction of the aldehyde group. We discuss evidence that selectivity is driven by interplay between crotonaldehyde reduction, local pH shifts due to the hydrogen evolution reaction, and changes in site reactivity and availability due to electrode fouling. This demonstration of model electrochemical biomass valorization also serves to inform further exploration into reduction of multi-functional molecules and electrochemical biomass processing in general.

biomass↗