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DOE OSTI2026

Evaluating the Transport Mechanism for Lignocellulosic Inhibitors in Zymomonas mobilis

The conversion of lignocellulosic biomass to biofuels and bioproducts is limited by small inhibitory molecules generated during the pretreatment process. The diverse compounds within the cell wall hydrolysate including aldehydes, carboxylic acids, phenolics, and alcohols inhibit microbial growth by disrupting microbial membranes. Although Zymomonas mobilis combines high ethanol productivity with hopanoid-rich membranes that confer solvent tolerance, hydrolysate compounds still inhibit microbial growth. One proposed mitigation strategy is to pump these molecules out through active transport processes, reducing direct toxicity. However, if passive permeation rates are high, active transport would create a futile cycle where the exported molecules diffuse back in, creating a net drag on fitness. To investigate this hypothesis, we measure the passive permeation for thirty-three lignocellulose derived compounds using atomistic molecular dynamics simulations with enhanced sampling. Permeability coefficients determined spanned more than eight orders of magnitude driven largely by the balance between hydrophobicity and polarity. Hydrophobic inhibitors such as aromatic acids, aldehydes, and short chain alcohols readily partitioned into the membrane and showed high permeability consistent with rapid passive influx and strong toxicity. Most polar molecules have lower but still appreciable permeation rates, with only the most polar sugars having low permeabilities. By integrating these predictions together with hydrolysate composition information, we find that most of these molecules are so permeable that futile cycles where passive permeation overwhelms efflux is highly likely. These findings provide a predictive framework for strain engineering, highlighting that, for highly permeable inhibitors, reducing extracellular inhibitor concentrations through hydrolysate detoxification, pretreatment optimization, or dilution may be necessary to mitigate futile cycling and improve microbial productivity in industrial biorefineries.

Zymomonas mobilis↗

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 OSTI2023

Chapter 4 - Pretreatment Technologies for Lignocellulosic Biomass Refineries

Pretreatment is a critical step in processing lignocellulosic biomass into biofuel and bioproducts and is considered the energy and cost center of the biomass conversion process. Although a large number of pretreatment technologies have been developed, not all the techniques are viable on a commercial scale at this stage. Moreover, the technology choice and process conditions depend highly on the type of biomass and the overall biorefinery scheme. This chapter provides an overview of different pretreatment methods, including their mechanism, important process parameters, current status, and challenges. The opportunities associated with new technologies and approaches are presented. Emphasis is placed on low-severity thermal pretreatment technologies. The chapter also provides a brief discussion of the challenges to achieving the economic viability of the technologies on a commercial scale.

BIOMASS FUELS↗

DOE OSTI2022

Utilization of lignocellulosic biofuel conversion residue by diverse microorganisms

Lignocellulosic conversion residue (LCR) is the material remaining after deconstructed lignocellulosic biomass is subjected to microbial fermentation and treated to remove the biofuel. Technoeconomic analyses of biofuel refineries have shown that further microbial processing of this LCR into other bioproducts may help offset the costs of biofuel generation. Identifying organisms able to metabolize LCR is an important first step for harnessing the full chemical and economic potential of this material. In this study, we investigated the aerobic LCR utilization capabilities of 71 Streptomyces and 163 yeast species that could be engineered to produce valuable bioproducts. The LCR utilization by these individual microbes was compared to that of an aerobic mixed microbial consortium derived from a wastewater treatment plant as representative of a consortium with the highest potential for degrading the LCR components and a source of genetic material for future engineering efforts. We analyzed several batches of a model LCR by chemical oxygen demand (COD) and chromatography-based assays and determined that the major components of LCR were oligomeric and monomeric sugars and other organic compounds. Many of the Streptomyces and yeast species tested were able to grow in LCR, with some individual microbes capable of utilizing over 40% of the soluble COD. For comparison, the maximum total soluble COD utilized by the mixed microbial consortium was about 70%. This represents an upper limit on how much of the LCR could be valorized by engineered Streptomyces or yeasts into bioproducts. To investigate the utilization of specific components in LCR and have a defined media for future experiments, we developed a synthetic conversion residue (SynCR) to mimic our model LCR and used it to show lignocellulose-derived inhibitors (LDIs) had little effect on the ability of the Streptomyces species to metabolize SynCR. We found that LCR is rich in carbon sources for microbial utilization and has vitamins, minerals, amino acids and other trace metabolites necessary to support growth. Testing diverse collections of Streptomyces and yeast species confirmed that these microorganisms were capable of growth on LCR and revealed a phylogenetic correlation between those able to best utilize LCR. Identification and quantification of the components of LCR enabled us to develop a synthetic LCR (SynCR) that will be a useful tool for examining how individual components of LCR contribute to microbial growth and as a substrate for future engineering efforts to use these microorganisms to generate valuable bioproducts.

09 BIOMASS FUELS↗

DOE OSTI2025

pH adjustment increases biofuel production from inhibitory switchgrass hydrolysates

Biofuels derived from renewable and sustainable lignocellulosic biomass, such as switchgrass, offer a promising means to limit greenhouse gas emissions. However, switchgrass grown under drought conditions contains high levels of chemical compounds that inhibit microbial conversion to biofuels. Fermentation of drought switchgrass hydrolysates by engineered Saccharomyces cerevisiae and Zymomonas mobilis results in lower ethanol production than does fermentation of hydrolyzed switchgrass from a typical rainfall year. Here, it is demonstrated that this inhibitory effect can be alleviated by altering the pH of drought switchgrass hydrolysates produced by two different pretreatment methods: Ammonia Fiber Expansion (AFEX) and Soaking in Aqueous Ammonia (SAA). Fermentation rates and biofuel production by Saccharomyces cerevisiae and Zymomonas mobilis were higher at pH 5.8 than at pH 5.0 from all feedstock years and following both pretreatment methods. SAA pretreatment of drought switchgrass furthermore enabled increased fermentation rates and biofuel titers compared to AFEX pretreatment. A synthetic mimic of switchgrass hydrolysate was developed and identified relief from pH-dependent inhibition by lignocellulose-derived inhibitors as the cause of increased biofuel production above a pH of 5.0. These results demonstrate that SAA pretreatment and pH adjustment can significantly improve fermentation and biofuel production from inhibitory feedstocks by industrial microorganisms.

09 BIOMASS FUELS↗

DOE OSTI2022

Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions

Abstract The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.

09 BIOMASS FUELS↗

DOE OSTI2023

Mechanism of furfural toxicity and metabolic strategies to engineer tolerance in microbial strains

Abstract Lignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans—furfural and 5-hydroxymethyl furfural—and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.

5-hydroxymethyl furfural↗

DOE OSTI2026

Data for Resourceful and Economical Designing of Fermentation Medium for Lab and Commercial Strains of Yeast from Alternative Feedstock: Transgenic Oilcane

Sugarcane plant engineered to accumulate lipids in its vegetative tissue is being developed as a new bioenergy crop. The new crop would be a source of juice, oil, and cellulosic sugars. However, limited tolerance of industrially recognized yeasts towards inhibitors generated during the processing of lignocellulosic biomass to produce fermentable sugars is a major challenge in developing scalable processes for second-generation drop-in fuel production. To this end, hydrolysates generated from engineered sugarcane—‘oilcane’ bagasse contain added phenolics and fatty acids that further restrict the growth of fermenting microorganisms and necessitate nutrient supplementation and/or detoxification of hydrolysate which makes the fermentation process expensive. Herein, we propose a resourceful and economical approach for growing lab and commercial strains of S. cerevisiae on unrefined cellulosic sugars aerobically and fermentatively. An equal ratio of hydrolysate and juice was found optimum for growth and fermentation by lab and commercial strains of Saccharomyces cerevisiae engineered for xylose fermentation. The industrial strain grew and fermented efficiently under low aeration conditions having an ethanol titer, yield, specific and volumetric productivities of 46.96 ± 0.19 g/l, 0.51 ± 0.00 g/g, 0.27 ± 0.02 g/g.h and 1.95 ± 0.01 g/l.h, respectively, while the lab strain grew better under higher aeration conditions having the ethanol titer, yield, specific and volumetric productivities of 24.93 ± 0.09, 0.27 ± 0.00 g/g, 0.17 ± 0.00 g/g.h and 1.04 ± 0.00 g/l.h, respectively. Acclimation of cultures in a blended medium significantly improved the performance of the yeast strains. The addition of transgenic oilcane juice, which is inedible and rich in amino acids, to the hydrolysate averted the need for expensive nutrient supplementation and detoxification steps of hydrolysate. The approach provides an economical solution to reduce the cost of fermentation at an industrial scale for second-generation drop-in fuel production.

Biomass Analytics↗

DOE OSTI2021

Complete and efficient conversion of plant cell wall hemicellulose into high-value bioproducts by engineered yeast

Abstract Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae . The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an enginered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Data for Complete and Efficient Conversion of Plant Cell Wall Hemicellulose into High-Value Bioproducts by Engineered Yeast

Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae . The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an engineered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass.

Conversion↗

DOE OSTI2023

Comparative feedstock analysis in Setaria viridis L. as a model for C 4 bioenergy grasses and panicoid crop species

Second generation feedstocks for bioethanol will likely include a sizable proportion of perennial C4 grasses, principally in the Panicoideae clade. The Panicoideae contain agronomically important annual grasses including Zea mays L. (maize), Sorghum bicolor (L.) Moench (sorghum), and Saccharum officinarum L. (sugar cane) as well as promising second generation perennial feedstocks including Miscanthus × giganteus and Panicum virgatum L. (switchgrass). The underlying complexity of these polyploid grass genomes is a major limitation for their direct manipulation and thus driving a need for rapidly cycling comparative model. Setaria viridis (green millet) is a rapid cycling C4 panicoid grass with a relatively small and sequenced diploid genome and abundant seed production. Stable, transient, and protoplast transformation technologies have also been developed for Setaria viridis making it a potentially excellent model for other C4 bioenergy grasses. Here, the lignocellulosic feedstock composition, cellulose biosynthesis inhibitor response and saccharification dynamics of Setaria viridis are compared with the annual sorghum and maize and the perennial switchgrass bioenergy crops as a baseline study into the applicability for translational research. A genome-wide systematic investigation of the cellulose synthase-A genes was performed identifying eight candidate sequences. Two developmental stages; (a) metabolically active young tissue and (b) metabolically plateaued (mature) material are examined to compare biomass performance metrics.

09 BIOMASS FUELS↗

DOE OSTI2021

Improving tolerance of yeast to lignocellulosic-derived feedstocks and products

Combined substrate-product toxicity remains one of the main obstacles hampering the scale-up and cost-effectiveness of bioprocesses harnessing lignocellulosic feedstocks, the most abundant, renewable terrestrial resource. Hydrolytic pretreatments release numerous inhibitors impinging on cell viability: the three most acute to yeast S. cerevisiae (the industry dominant biocatalyst) — and universal to all plant sources — are furfural, hydroxymethylfurfural (HMF), and acetic acid. Likewise, desired fermentation products, such as fuel ethanol or commodity organic acids, are toxic to microbes, typically via unknown biological mechanisms. Here, we have engineered both hydrolysate and end-product tolerance in yeast by combining previously-shown alcohol protective modifications with evolved genetic activities targeting the major pretreatment inhibitors. When tested on a wide sampling of genuine lignocellulosic feedstocks, ethanol production increased by >30% on average to titers >100 g/L, achieving parity with clean-sugar equivalents where conditions permit. Furthermore, we designed the tolerance capability to be fully transferable to pre-existing metabolic chassis strains. As such, we “drop-in” hydrolysate competence into one producing lactic acid, demonstrating the first-ever production of a cellulosic plastic at industrial titers. Our advances thus renew the potential of cellulosic biomass utilization for sustainable fuel and non-fuel products at scale.

09 BIOMASS FUELS↗

DOE OSTI2025

Resourceful and economical designing of fermentation medium for lab and commercial strains of yeast from alternative feedstock: ‘transgenic oilcane’

09 BIOMASS FUELS↗

DOE OSTI2023

Liquefaction of different corn stover fractions assisted by enzyme-biomass deconstruction

Recalcitrant properties of different sources of lignocellulosic biomass represent challenges in materials processing within a biorefinery, as well as enzyme efficient deconstruction to fermentable sugars. Limitations include lignin derived enzyme inhibitors, enzyme inhibition by hydrolysis products, and resistance to mixing due to rheological properties of lignocellulosic particulates at high solids loadings. Consequently, we examined conditions that might be used to achieve liquid slurries (i.e., liquefaction) at solids loadings of 300 g/L before the material enters the biorefinery through a pretreatment step. This work explores enzyme-assisted liquefaction in a fed-batch process using the commercial enzymes Celluclast 1.5L or Ctec-2 at 1FPU/g or 3 FPU/g of dry solids, basis. Corn stover pellets were fed into a 1 L stirred bioreactor containing enzyme solution over a 5-hour period until reaching 30% solids loading (dry wgt / vol basis). After 6, 24 and 96 hours from the start of the run, samples were taken and characterized with respect to their sugar composition, rheology, water absorption and enzyme activity. Slurries with dramatically reduced yield stresses were achieved for corn stover. Yield stresses of 178±7 Pa (3 FPU, Celluclast 1.5L) and 79±6 Pa (3FPU, Ctec-2) were measured for corn stover at 24 hours, compared to 6,000 Pa for samples without enzyme.Yield stress was 155± 29 Pa (3FPU, Ctec-2) and 257 ± 72 Pa (1 FPU, Celluclast 1.5L) for corn cobs at 24 hours.A profile based on 6, 24 and 96h of yield stress measurements and sugar conversion is presented. Enzyme activity is measured and the impact of liquefaction on an integrated processing in a biorefinery operation is discussed.

Gutierrez, Diana↗

DOE OSTI2024

Sustainable strategies to achieve industrial ethanol titers from different bioenergy feedstocks: scale-up approach for better ethanol yield

Hydrothermal pretreatment is a promising approach to lignocellulosic biomass processing for enzymatic hydrolysis and high-yield bioethanol fermentation, as it reduces downstream inhibitor content and the amount of toxic byproducts generated. In this paper, the ethanol yield and productivity of an engineered xylose-fermenting strain of Saccharomyces cerevisiae were tested on lignocellulosic hydrolysates produced with varying citrate buffer concentration, solid loading, supplemental nitrogen source, and feedstock of origin, and a semi-integrated bioprocess which integrates enzymatic hydrolysis and bioethanol fermentation was developed. The greatest ethanol yields (g p /g s ) of 0.490 ± 0.008, 0.460 ± 0.001, 0.420 ± 0.002 and 0.410 ± 0.002 were obtained from bioenergy sorghum (BES), Miscanthus × giganteus (MG), energy cane (EC), and oilcane (OC), respectively. In addition, an equivalent of 291 L, 253.54 L, 257.8 L, and 260.3 L of bioethanol were produced per ton of BES, MG, EC, and OC, respectively, by using urea as a nitrogen source in a bioreactor.

09 BIOMASS FUELS↗

DOE OSTI2022

Declining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic tests

Abstract Background For economically viable 2nd generation biofuels, processing of high solid lignocellulosic substrate concentrations is a necessity. The cellulolytic thermophilic anaerobe Clostridium thermocellum is one of the most effective biocatalysts for solubilization of carbohydrate harbored in lignocellulose. This study aims to document the solubilization performance of Clostridium thermocellum at increasing solids concentrations for two lignocellulosic feedstocks, corn stover and switchgrass, and explore potential effectors of solubilization performance. Results Monocultures of Clostridium thermocellum demonstrated high levels of carbohydrate solubilization for both unpretreated corn stover and switchgrass. However, fractional carbohydrate solubilization decreases with increasing solid loadings. Fermentation of model insoluble substrate (cellulose) in the presence of high solids lignocellulosic spent broth is temporarily affected but not model soluble substrate (cellobiose) fermentations. Mid-fermentation addition of cells ( C. thermocellum ) or model substrates did not significantly enhance overall corn stover solubilization loaded at 80 g/L, however cultures utilized the model substrates in the presence of high concentrations of corn stover. An increase in corn stover solubilization was observed when water was added, effectively diluting the solids concentration mid-fermentation. Introduction of a hemicellulose-utilizing coculture partner, Thermoanaerobacterium thermosaccharolyticum, increased the fractional carbohydrate solubilization at both high and low solid loadings. Residual solubilized carbohydrates diminished significantly in the presence of T. thermosaccharolyticum compared to monocultures of C. thermocellum, yet a small fraction of solubilized oligosaccharides of both C 5 and C 6 sugars remained unutilized. Conclusion Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum -mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum , which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture.

09 BIOMASS FUELS↗

DOE OSTI2022

Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids

Economically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.

09 BIOMASS FUELS↗

DOE OSTI2021

A multiplexed nanostructure-initiator mass spectrometry (NIMS) assay for simultaneously detecting glycosyl hydrolase and lignin modifying enzyme activities

Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Analytical tools capable of quickly detecting both glycan and lignin deconstruction are needed to support the development and characterization of efficient enzymes/enzyme cocktails. Previously we have described nanostructure-initiator mass spectrometry-based assays for the analysis of glycosyl hydrolase and most recently an assay for lignin modifying enzymes. Here we integrate these two assays into a single multiplexed assay against both classes of enzymes and use it to characterize crude commercial enzyme mixtures. Application of our multiplexed platform based on nanostructure-initiator mass spectrometry enabled us to characterize crude mixtures of laccase enzymes from fungi Agaricus bisporus (Ab) and Myceliopthora thermophila (Mt) revealing activity on both carbohydrate and aromatic substrates. Using time-series analysis we determined that crude laccase from Ab has the higher GH activity and that laccase from Mt has the higher activity against our lignin model compound. Inhibitor studies showed a significant reduction in Mt GH activity under low oxygen conditions and increased activities in the presence of vanillin (common GH inhibitor). Ultimately, this assay can help to discover mixtures of enzymes that could be incorporated into biomass pretreatments to deconstruct diverse components of lignocellulosic biomass.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗