Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass

Pre-treatment of a sugarcane bagasse-based substrate prior to saccharification: Effect of coffee pulp and urea on laccase and cellulase activities of Pycnoporus sanguineus

Production of second-generation bioethanol uses lignocellulose from agricultural by-products such as sugarcane bagasse (SCB). A lignocellulose pre-treatment is required to degrade lignin, ensuring further efficient saccharification. Two experimental designs were set up to define culture conditions of Pycnoporus sanguineus in mesocosms to increase laccase activities and thus delignification. The first experimental design tested the effect of phenolic complementation (via coffee pulp) and the use of urea as a simple nitrogen source and the second defined more precisely the percentages of coffee pulp and urea to enhance delignification. The responses measured were: lignocellulolytic activities, laccase isoform profiles by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the chemical transformation of the substrate using solid-state NMR of 13C. Adding 10% of coffee pulp increased laccase activities and fungal biomass (32.5% and 16% respectively), enhanced two constitutive isoforms (R_f 0.23 and 0.27), induced a new isoform (R_f 0.19) and led to a decrease in total aromatics. However, higher concentrations of coffee pulp (25%) decreased laccase and cellulase activities but no decrease in aromaticity was observed, potentially due to the toxic effect of phenols from coffee pulp. Moreover, laccase production was still inhibited even for lower concentrations of urea (0-5%). Our findings revealed that an agricultural by-product like coffee pulp can enhance laccase activity -though to a threshold- and that urea limited this process, indicating that other N-sources should be tested for the biological delignification of SCB.

Protein expression analysis revealed a fine-tuned mechanism of in situ detoxification pathway for the tolerant industrial yeast Saccharomyces cerevisiae

Inhibitory compounds liberated from lignocellulose pretreatment are representative toxic chemicals that repress microbial growth and metabolism. A tolerant strain of the industrial yeast Saccharomyces cerevisiae is able to detoxify a major class of toxic compounds while producing ethanol. Knowledge on the yeast tolerance was mostly obtained by gene expression analysis and limited protein expression evidence is yet available underlying the yeast adaptation. Here we report a comparative protein expression profiling study on Y-50049, a tolerant strain compared with its parental industrial type strain Y-12632. We found a distinctive protein expression of glucose-6-phosphate dehydrogenase (Zwf1) in Y-50049 but not in Y-12632, in the relatively conserved glycolysis and pentose phosphate pathway (PPP) in response to a combinational challenge of 2-furaldehyde (furfural) and 5-hydroxymethyl-2-furaldehyde (HMF). A group of proteins with aldehyde reduction activity was uniquely induced expressed in Y-50049 but not in Y-12632. Such evidence allowed fine-tuning a mechanism of the renovated in situ detoxification by Y-50049. As the key protein, Zwf1 drove the glucose metabolism in favor of the oxidative branch of the PPP facilitating in situ detoxification of the toxic chemicals by Y-50049. The activated expression of Zwf1 generated the essential cofactor nicotinamide adenine dinucleotide phosphate (NADPH) enabling reduction of furfural and HMF through a group of aldehyde reduction enzymes. In return, the activate aldehyde reductions released desirable feedbacks of NADP⁺ stimulating continued oxidative activity of Zwf1. Thus, a well-maintained cofactor regeneration cycle was established to restore the cofactor imbalance caused by furfural-HMF. Challenges and perspectives on adaptation of significantly differential expressions of ribosomal proteins and other unique proteins are also discussed.

The Influence of Vinification Methods and Cultivars on the Volatile and Phenolic Profiles of Fermented Alcoholic Beverages from Cranberry

This study investigated the effects of vinification techniques and cultivars (Stevens, Pilgrim and Bergman) on cranberry wine quality. Three winemaking technologies were conducted to prepare cranberry musts before fermentation, including traditional red and white vinifications (Red and White), and thermovinification (Thermo). In wine products, proanthocyanins (PACs) and anthocyanins (ANCs) are dominant in phenolics, while esters and alcohols are prevalent in volatiles, with phenylethyl alcohol, β-damascenone, benzyl alcohol, etc. as the main contributors to the aroma. The phenolic compositions of wines were in the same pattern with cultivars: the Stevens and Bergman wines contained the highest amount of ANCs and PACs, respectively, while the Pilgrim wines had the lowest total phenolic contents (TPC), and antioxidant capacities (AOC). Nevertheless, products from Pilgrim cultivar had a distinctive pattern of volatiles compared to Stevens and Bergman, especially for aromatic compounds. Considering vinification methods, Thermo demonstrated advantages on correlations with both phenolic and volatile (polymeric and monomeric) compositions.

PKA and HOG signaling contribute separable roles to anaerobic xylose fermentation in yeast engineered for biofuel production

Lignocellulosic biomass offers a sustainable source for biofuel production that does not compete with food-based cropping systems. Importantly, two critical bottlenecks prevent economic adoption: many industrially relevant microorganisms cannot ferment pentose sugars prevalent in lignocellulosic medium, leaving a significant amount of carbon unutilized. Furthermore, chemical biomass pretreatment required to release fermentable sugars generates a variety of toxins, which inhibit microbial growth and metabolism, specifically limiting pentose utilization in engineered strains. Here we dissected genetic determinants of anaerobic xylose fermentation and stress tolerance in chemically pretreated corn stover biomass, called hydrolysate. We previously revealed that loss-of-function mutations in the stress-responsive MAP kinase HOG1 and negative regulator of the RAS/Protein Kinase A (PKA) pathway, IRA2, enhances anaerobic xylose fermentation. However, these mutations likely reduce cells' ability to tolerate the toxins present in lignocellulosic hydrolysate, making the strain especially vulnerable to it. We tested the contributions of Hog1 and PKA signaling via IRA2 or PKA negative regulatory subunit BCY1 to metabolism, growth, and stress tolerance in corn stover hydrolysate and laboratory medium with mixed sugars. We found mutations causing upregulated PKA activity increase growth rate and glucose consumption in various media but do not have a specific impact on xylose fermentation. In contrast, mutation of HOG1 specifically increased xylose usage. We hypothesized improving stress tolerance would enhance the rate of xylose consumption in hydrolysate. Surprisingly, increasing stress tolerance did not augment xylose fermentation in lignocellulosic medium in this strain background, suggesting other mechanisms besides cellular stress limit this strain's ability for anaerobic xylose fermentation in hydrolysate.

Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stover

BACKGROUND

Fast, complete, and ultimate removal of inhibitory compounds derived from lignocellulose pretreatment is the prerequisite for efficient production of cellulosic ethanol and biochemicals. Biodetoxification is the most promising method for inhibitor removal by its unique advantages. The biodetoxification mechanisms of a unique diploid fungus responsible for highly efficient biodetoxification in solid-state culture was extensively investigated in the aspects of cellular structure, genome sequencing, transcriptome analysis, and practical biodetoxification.

RESULTS

The inborn heterozygous diploid structure of A. resinae ZN1 uniquely contributed to the enhancement of inhibitor tolerance and conversion. The co-expression of gene pairs contributed to the enhancement of the degradation of lignocellulose-derived model inhibitors. The ultimate inhibitors degradation pathways and sugar conservation were elucidated by microbial degradation experimentation as well as the genomic and transcriptomic sequencing analysis.

CONCLUSIONS

The finding of the heterozygous diploid structure in A. resinae ZN1 on biodetoxification took the first insight into the global overview of biodetoxification mechanism of lignocellulose-derived inhibitors. This study provided a unique and practical biodetoxification biocatalyst of inhibitor compounds for lignocellulose biorefinery processing, as well as the synthetic biology tools on biodetoxification of biorefinery fermenting strains.

Tolerance and transcriptional analysis of Corynebacterium glutamicum on biotransformation of toxic furaldehyde and benzaldehyde inhibitory compounds

Furaldehydes and benzaldehydes are among the most toxic inhibitors from lignocellulose pretreatment on microbial growth and metabolism. The bioconversion of aldehyde inhibitors into less toxic alcohols or acids (biotransformation) is the prerequisite condition for efficient biorefinery fermentations. This study found that Corynebacterium glutamicum S9114 demonstrated excellent tolerance and biotransformation capacity to five typical aldehyde inhibitors including two furaldehydes: 2-furaldehyde (furfural), 5-(hydroxymethyl)-2-furaldehyde, and three benzaldehydes: 4-hydroxybenzaldehyde, 4-hydroxy-3-methoxybenzaldehyde (vanillin), and 4-hydroxy-3,5-dimethoxybenzaldehyde (syringaldehyde). Transcription levels of 93 genes hypothesized to be responsible for five aldehydes biotransformation were examined by qRT-PCR. Multiple genes showed significantly up-regulated expression against furaldehydes or benzaldehydes. Overexpression of CGS9114_RS01115 in C. glutamicum resulted in the increased conversion of all five aldehyde inhibitors. The significant oxidoreductase genes responsible for each or multiple inhibitors biotransformation identified in this study will serve as a component of key gene device library for robust biorefinery fermentation strains development in the future biorefinery applications.

Bio-detoxification Bacteria Isolated from Dye-Polluted Soils Promote Lactic Acid Production from Ammonia Pretreated Corn Stover

Agro-stovers are the most abundant substrates for producing lactic acid, which has great potential application in the production of biodegradable and biocompatible polylactic acid polymers. However, chemical pretreatments on agro-stovers generate inhibitors that repress the subsequent lactic acid fermentation. In this study, three bacterial strains (Enterococcus faecalis B101, Acinetobacter calcoaceticus C1, and Pseudomonas aeruginosa CS) isolated from dye-polluted soils could utilize phenolic inhibitor mimics (vanillin, 4- hydroxybenzaldehyde, or syringaldehyde) from alkaline pretreated corn stovers as a sole carbon source. Lactic acid titer increased from 27.42 g/L (Bacillus coagulans LA204 alone) to 44.76 g/L (CS and LA204) using 50 g/L glucose with 1 g/L 4-hydroxybenzaldehyde added. Lactic acid production from 50 g/L ammonia pretreated corn stover was increased nearly twofold by inoculating phenolic degradation bacteria and lactic acid bacteria (C1& Lactobacillus pentosus FL0421). In the control (FL0421 alone), only 16.98 g/L of lactic acid was produced. The isolated and identified strains degraded the phenolic compounds and increased the lactic acid production from glucose and ammonia pretreated corn stover. These characteristics of the strains support industrial application with efficient in situ detoxification of phenolic compounds during lactic acid production from agro-stovers using simultaneous saccharification and fermentation (SSF).

Genomic and transcriptomic analysis of a coniferyl aldehyde-resistant Saccharomyces cerevisiae strain obtained by evolutionary engineering

Phenolic inhibitors in lignocellulosic hydrolysates interfere with the performance of fermenting microorganisms. Among these, coniferyl aldehyde is one of the most toxic inhibitors. In this study, genetically stable Saccharomyces cerevisiae mutants with high coniferyl aldehyde resistance were successfully obtained for the first time by using an evolutionary engineering strategy, based on the systematic application of increasing coniferyl aldehyde stress in batch cultures. Among the selected coniferyl aldehyde-resistant mutants, the highly resistant strain called BH13 was also cross-resistant to other phenolic inhibitors, vanillin, ferulic acid and 4-hydroxybenzaldehyde. In the presence of 1.2 mM coniferyl aldehyde stress, BH13 had a significantly reduced lag phase, which was less than 3 h and only about 25% of that of the reference strain and converted coniferyl aldehyde faster. Additionally, there was no reduction in its growth rate, either. Comparative transcriptomic analysis of a highly coniferyl aldehyde-resistant mutant revealed upregulation of the genes involved in energy pathways, response to oxidative stress and oxidoreductase activity in the mutant strain BH13, already under non-stress conditions. Transcripts associated with pleiotropic drug resistance were also identified as upregulated. Genome re-sequencing data generally supported transcriptomic results and identified gene targets that may have a potential role in coniferyl aldehyde resistance.

Twenty-first-century chemical odyssey: fuels versus commodities and cell factories versus chemical plants

The harmful effects of pollution from the massive and widespread use of fossil fuels have led various organizations and governments to search for alternative energy sources. To address this, a new energy bioprocess is being developed that utilizes non-edible lignocellulose - the only sustainable source of organic carbon in nature. In this mini-review, we consider the potential use of synthetic biology to develop new-to-nature pathways for the biosynthesis of chemicals that are currently synthesized using classical industrial approaches. The number of industrial processes based on starch or lignocellulose is still very modest. Advances in the area require the development of more efficient approaches to deconstruct plant materials, better exploitation of the catalytic potential of prokaryotes and lower eukaryotes and the identification of new and useful genes for product synthesis. Further research and progress is urgently needed in order for government and industry to achieve the major milestone of transitioning 30% of the total industry to renewable sources by 2050.

Detoxification of Hydrolysates of the Red Seaweed Gelidium amansii for Improved Bioethanol Production

In this study, bioethanol was produced from the seaweed Gelidium amansii as biomass through separate hydrolysis and fermentation (SHF) processes. The SHF processes examined in this study include thermal acid hydrolysis pretreatment, enzymatic saccharification, detoxification, and fermentation. Thermal acid hydrolysis pretreatment was conducted using H₂SO₄, with a slurry content of 8-16% and treatment time of 15-75 min. The optimal conditions for thermal acid hydrolysis pretreatment were 12% (w/v) seaweed slurry content and 180 mM H₂SO₄ at 121 °C for 45 min, at which 26.1 g/L galactose and 6.8 g/L glucose were produced. A monosaccharide (mainly glucose) was also obtained from the enzymatic saccharification of thermal acid hydrolysate using 16 U/mL Celluclast 1.5 L enzyme at 45 °C for 36 h. Detoxification was performed using the adsorption method with activated carbon, the overliming method with Ca (OH)₂, and the ion exchange method with polyethyleneimine. Among those detoxification methods, activated carbon showed the best performance for hydroxymethylfurfural removal. Ethanol fermentation was performed using 12% (w/v) seaweed hydrolysate with Saccharomyces cerevisiae adapted to galactose as well as various detoxification treatments.

Microbial electrolysis using aqueous fractions derived from Tail-Gas Recycle Pyrolysis of willow and guayule

This study investigated microbial electrolysis of two aqueous phase waste products derived from guayule and willow generated from Tail Gas Recycle Pyrolysis (TGRP). The highest average current density achieved was 5.0 ± 0.7 A/m² and 1.8 ± 0.2 A/m² for willow and guayule respectively. Average hydrogen productivity was 5.0 ± 1.0 L/L-day from willow and 1.5 ± 0.2 L/L-day for guayule. Willow also generated higher coulombic efficiency, anode conversion efficiency, and hydrogen recovery than guayule at most organic loading conditions. Compounds investigated exceeded 80% degradation, which included organic acids, sugar derivatives, and phenolics. Mass spectrometric analysis demonstrated the accumulation of a long chain amine not present in either substrate before treatment, and the persistence of several peptide residues resulting from the TGRP process. New biorefineries may one day capitalize on this otherwise discarded byproduct of TGRP, further improving the potential applications and value of microbial electrolysis towards energy production.

Overexpression of RCK1 improves acetic acid tolerance in Saccharomyces cerevisiae

Mixed sugars derived from lignocellulosic biomass can be converted into biofuels and chemicals by engineered microorganisms, but toxic fermentation inhibitors produced from harsh depolymerization processes of lignocellulosic biomass pose a critical challenge for economic production of biofuels and chemicals. Unlike other fermentation inhibitors generated from sugar degradation, acetic acid is inevitably produced from acetylated hemicellulose, and its concentrations in cellulosic hydrolysates are substantially higher than other fermentation inhibitors. The aim of this study was to identify novel genetic perturbations for improved acetic acid tolerance in Saccharomyces cerevisiae. Through a genomic library-based approach, we identified an overexpression gene target RCK1 coding for a protein kinase involved in oxidative stress. Overexpression of RCK1 significantly improved glucose and xylose fermentation under acetic acid stress conditions. Specifically, the RCK1-overexpressing strain exhibited a two-fold higher specific ethanol productivity than the control strain in glucose fermentation under the presence of acetic acid. Interestingly, the engineered S. cerevisiae overexpressing RCK1 showed 40% lower intracellular reactive oxygen species (ROS) levels as compared to the parental strain when the strains were exposed to acetic acid, suggesting that RCK1 overexpression might play a role in reducing the oxidative stress caused by acetic acid.

Effect of salts formed by neutralization for the enzymatic hydrolysis of cellulose and acetone–butanol–ethanol fermentation

Neutralization is essential to maintain the pH for enzymatic hydrolysis of cellulose followed by fermentation of biofuels. This study investigated the effect of salts formed during the neutralization on the enzymatic hydrolysis of cellulosic materials and acetone–butanol–ethanol (ABE) fermentation. The results showed that the formed Ca-citrate salt considerably decreased the glucose release by 26.9% and 26.1% from Avicel and sulfuric acid-pretreated hybrid Pennisetum, respectively, which was probably due to the unproductive adsorption of cellulases by Ca-citrate solids. On the other hand, the formed soluble Na and Ca salts severely inhibited ABE fermentation, thereby decreasing the ABE concentration from 12.8 g L⁻¹ to 0–10.7 g L⁻¹ in different degrees, but no or slight inhibition was observed when the Ca salts formed as precipitates. In particular, Ca-sulfate did not show apparent inhibition of both hydrolysis and fermentation. Therefore, the selection of suitable pretreatment and neutralizing reagents is an alternative way to avoid process inhibition in biofuel production from lignocellulosic materials.

The salts formed by neutralization after sulfuric, acetic, and citric acid pretreatments affected enzymatic hydrolysis of lignocellulosic materials and acetone–butanol–ethanol (ABE) fermentation to various degrees.

Physiological mechanism of improved tolerance of Saccharomyces cerevisiae to lignin-derived phenolic acids in lignocellulosic ethanol fermentation by short-term adaptation

BACKGROUND

Phenolic acids are lignin-derived fermentation inhibitors formed during many pretreatment processes of lignocellulosic biomass. In this study, vanillic, p-hydroxybenzoic, and syringic acids were selected as the model compounds of phenolic acids, and the effect of short-term adaptation strategies on the tolerance of S. cerevisiae to phenolic acids was investigated. The mechanism of phenolic acids tolerance in the adapted yeast strains was studied at the morphological and physiological levels.

RESULTS

The multiple phenolic acids exerted the synergistic inhibitory effect on the yeast cell growth. In particular, a significant interaction between vanillic and hydroxybenzoic acids was found. The optimal short-term adaptation strategies could efficiently improve the growth and fermentation performance of the yeast strain not only in the synthetic media with phenolic acids, but also in the simultaneous saccharification and ethanol fermentation of corncob residue. Morphological analysis showed that phenolic acids caused the parental strain to generate many cytoplasmic membrane invaginations with crack at the top of these sites and some mitochondria gathered around. The adapted strain presented the thicker cell wall and membrane and smaller cell size than those of the parental strain. In particular, the cytoplasmic membrane generated many little protrusions with regular shape. The cytoplasmic membrane integrity was analyzed by testing the relative electrical conductivity, leakage of intracellular substance, and permeation of fluorescent probe. The results indicated that the short-term adaptation improved the membrane integrity of yeast cell.

CONCLUSION

The inhibition mechanism of phenolic acid might be attributed to the combined effect of the cytoplasmic membrane damage and the intracellular acidification. The short-term adaptation strategy with varied stressors levels and adaptive processes accelerated the stress response of yeast cell structure to tolerate phenolic acids. This strategy will contribute to the development of robust microbials for biofuel production from lignocellulosic biomass.

Novel Approach in the Construction of Bioethanol-Producing Saccharomyces cerevisiae Hybrids§

Bioethanol production from lignocellulosic hydrolysates requires a producer strain that tolerates both the presence of growth and fermentation inhibitors and high ethanol concentrations. Therefore, we constructed heterozygous intraspecies hybrid diploids of Saccharomyces cerevisiae by crossing two natural S. cerevisiae isolates, YIIc17_E5 and UWOPS87-2421, a good ethanol producer found in wine and a strain from the flower of the cactus Opuntia megacantha resistant to inhibitors found in lignocellulosic hydrolysates, respectively. Hybrids grew faster than parental strains in the absence and in the presence of acetic and levulinic acids and 2-furaldehyde, inhibitors frequently found in lignocellulosic hydrolysates, and the overexpression of YAP1 gene increased their survival. Furthermore, although originating from the same parental strains, hybrids displayed different fermentative potential in a CO₂ production test, suggesting genetic variability that could be used for further selection of desirable traits. Therefore, our results suggest that the construction of intraspecies hybrids coupled with the use of genetic engineering techniques is a promising approach for improvement or development of new biotechnologically relevant strains of S. cerevisiae. Moreover, it was found that the success of gene targeting (gene targeting fidelity) in natural S. cerevisiae isolates (YIIc17_E5α and UWOPS87-2421α) was strikingly lower than in laboratory strains and the most frequent off-targeting event was targeted chromosome duplication.

Ensiled Wet Storage Accelerates Pretreatment for Bioconversion of Corn Stover

Organic acids produced during ensiled wet storage are beneficial during the storage process, both for biomass preservation, and to aid in mild in-situ pretreatment. However, there is concern these acids could later have negative impacts on downstream processes, especially microbial fermentation. Organic acids can inhibit microbial metabolism or growth, which in turn could affect biofuel productivity or yield. This study investigated the interaction of organic acids produced during ensiled storage with subsequent pretreatment of the resulting corn stover silage, as well as the potential for interference with downstream ethanol fermentation. Interaction with pretreatment was observed by measuring xylan and glucan removal and the formation of inhibitors. The results indicated that organic acids generally do not impede downstream processes and in fact can be beneficial. The levels of organic acids produced during 220 days of storage jar tests at 23°C or 37°C, and their transformation during pretreatment, remained below inhibitory levels. Concentrations of individual acids did not exceed 6 g per liter of the pretreated volume, and < 5% on a dry matter basis. Whereas, unensiled corn stover required 15 min of 190°C pretreatment to optimize sugar release, ensiled corn stover could be treated equally effectively at a lower pretreatment duration of 10 min. Furthermore, the different organic acid profiles that accumulate at various storage moisture levels (35-65%) do not differ significantly in their impact on downstream ethanol fermentation. These results indicate biorefineries using ensiled corn stover feedstock at 35-65% moisture levels can expect as good or better biofuel yields as with unensiled stover, while reducing pretreatment costs.

Increasing ethanol yield through fiber conversion in corn dry grind process

Conversion of corn fiber to ethanol in the dry grind process could increase ethanol yields, reduce downstream processing costs and improve overall process profitability. This work investigates the in-situ conversion of corn fiber into ethanol (cellulase addition during simultaneous saccharification and fermentation) during dry grind process. Addition of 30 FPU/g fiber cellulase resulted in 4.6% increase in ethanol yield compared to the conventional process. Use of excess cellulase (120 FPU/g fiber) resulted in incomplete fermentation and lower ethanol yield compared to the conventional process. Multiple factors including high concentrations of ethanol and phenolic compounds were responsible for yeast stress and incomplete fermentation in excess cellulase experiments.

Selective Sequestration of Aromatics from Aqueous Mixtures with Sugars by Hydrophobic Molecular Calixarene Cavities Grafted on Silica

The separation of aromatic contaminants from sugar-aromatic aqueous mixtures is required in second-generation biorefineries because aromatic compounds deactivate (bio)catalysts typically involved in upgrading lignocellulosic biomass to fuels and chemicals. This separation remains challenging, however, because of the degree of molecular recognition needed to sequester dilute aromatic impurities from concentrated sugar streams. Herein, we demonstrate that hydrophobic cavities of p- tert-butylcalix[4]arene macrocycles grafted on amorphous silica (calix/SiO₂) perform this separation selectively and efficiently by acting as selective molecular hosts that adsorb aromatic compounds (5-hydroxymethylfurfural, vanillin, and vanillic acid) while excluding monomeric sugar (glucose chosen as a prototypical model) in aqueous mixtures. By comparing calix/SiO₂ to a range of organically modified SiO₂ surfaces and other porous adsorbents, we demonstrate that the organization of hydrophobic functional groups within discrete nests consisting of calixarene cavities is crucial for facilitating the adsorption of aromatics. Density functional theory calculations of the host-guest complex indicate that adsorption is brought about by weak dispersive (van der Waals) interactions between tert-butyl upper-rim substituents in calixarene hosts and aromatic guests. Calix/SiO₂ can be repeatedly reused, demonstrating its viability as an adsorbent within a continuous biorefining process. These calix/SiO₂ adsorbents expand the palette of materials available for selective sugar-aromatic separations, which until now have been limited to pyrene-based sites of metal-organic framework NU-1000, and demonstrate that sites consisting of relatively simple hydrophobic tert-butyl substituents organized around a hemispherical molecular cavity provide a sufficient degree of molecular recognition for performing this separation selectively.

Characterization of a New Glyoxal Oxidase from the Thermophilic Fungus Myceliophthora thermophila M77: Hydrogen Peroxide Production Retained in 5-Hydroxymethylfurfural Oxidation

Myceliophthora thermophyla is a thermophilic industrially relevant fungus that secretes an assortment of hydrolytic and oxidative enzymes for lignocellulose degradation. Among them is glyoxal oxidase (MtGLOx), an extracellular oxidoreductase that oxidizes several aldehydes and α-hydroxy carbonyl substrates coupled to the reduction of O2 to H2O2. This copper metalloprotein belongs to a class of enzymes called radical copper oxidases (CRO) and to the “auxiliary activities” subfamily AA5_1 that is based on the Carbohydrate-Active enZYmes (CAZy) database. Only a few members of this family have been characterized to date. Here, we report the recombinant production, characterization, and structure-function analysis of MtGLOx. Electron Paramagnetic Resonance (EPR) spectroscopy confirmed MtGLOx to be a radical-coupled copper complex and small angle X-ray scattering (SAXS) revealed an extended spatial arrangement of the catalytic and four N-terminal WSC domains. Furthermore, we demonstrate that methylglyoxal and 5-hydroxymethylfurfural (HMF), a fermentation inhibitor, are substrates for the enzyme.

Sodium Acetate Responses in Saccharomyces cerevisiae and the Ubiquitin Ligase Rsp5

Recent studies have revealed the feasibility of sodium acetate as a potentially novel inhibitor/stressor relevant to the fermentation from neutralized lignocellulosic hydrolysates. This mini-review focuses on the toxicity of sodium acetate, which is composed of both sodium and acetate ions, and on the involved cellular responses that it elicits, particularly via the high-osmolarity glycerol (HOG) pathway, the Rim101 pathway, the P-type ATPase sodium pumps Ena1/2/5, and the ubiquitin ligase Rsp5 with its adaptors. Increased understanding of cellular responses to sodium acetate would improve our understanding of how cells respond not only to different stimuli but also to composite stresses induced by multiple components (e.g., sodium and acetate) simultaneously. Moreover, unraveling the characteristics of specific stresses under industrially related conditions and the cellular responses evoked by these stresses would be a key factor in the industrial yeast strain engineering toward the increased productivity of not only bioethanol but also advanced biofuels and valuable chemicals that will be in demand in the coming era of bio-based industry.

Corn stover pretreatment by metal oxides for improving lignin removal and reducing sugar degradation and water usage

Five metal oxides, Fe₂O₃, CuO, NiO, ZnO, and MgO, were investigated as catalysts to improve lignin removal and reduce sugar degradation during corn stover pretreatment. Liquid hot water (LHW) pretreatment was used as control. Among the five metal oxides, MgO was the most suitable for biomass pretreatmen. The optimal pretreatment condition was the solid/liquid ratio of 1/10 with 0.10 mol/L MgO at 190 °C for 40 min. The fermentable xylose (85%) and glucose (97%) from MgO pretreatment were equivalent to those (89 and 95%) from LHW pretreatment, and lignin removal was 1.5-fold more than that from LHW pretreatment. The pH of the resulting biomass slurry was close to 7.0 and without furfural and 5-hydroxymethylfurfural formation. Thus, the water-washing step for inhibitor removal can be omitted. The biomass liquor can be used directly for downstream hydrolysis and fermentation. Acid-resistant equipment is not required due to the absence of acids.

Utilization of Lignocellulosic Biomass via Novel Sustainable Process

In this review, we show novel methods for utilizing lignocellulosic biomass, polysaccharides, and lignin. Firstly, the simultaneous enzymatic saccharification and comminution (SESC) of plant materials is described as an extraction method for lignocellulosic biomass that does not require toxic reagents or organic solvents. Secondly, we demonstrate the material utilization of non-deteriorated lignocellulosic biomass extracted by SESC, such as for sugar and ethanol synthesis, and as a heatproof filler. Finally, we exhibit the use of a functional monomer (e.g., in disinfection chemicals, cesium chelation, and building blocks for polymers), 2-pyrone-4,6-dicarboxylic acid, derived from lignin via metabolic degradation.

Mathematical model to appraise the inhibitory effect of phenolic compounds derived from lignin for biobutanol production

This study aimed to establish a mathematical modeling to evaluate the inhibitory effect of phenolic derivatives on acetone-butanol-ethanol (ABE) fermentation by Clostridium saccharoperbutylacetonicum N1-4. Vanillin, 4-hydroxybenzoic acid, and syringaldehyde were selected to represent guaiacyl, hydroxyphenyl, and syringyl phenols, respectively, to be examined in a series of fed-batch experiments. Results show the presence of phenolic derivatives blocked the pathway of the assimilation of organic acids and reduced cell growth and glucose utilization. The inhibition model projected that the levels of 0.13, 0.14, and 0.04 g L^-1 for vanillin, 4-hydroxybenzoic acid, and syringaldehyde, respectively, resulted in 25% inhibition of butanol production, whereas 100% inhibition was predicted at the levels of 4.94, 4.37, and 4.20 g L^-1 for vanillin, 4-hydroxybenzoic acid, and syringaldehyde, respectively. Syringaldehyde was more toxic than the other two compounds. The established model described that the phenolic compounds derived from different phenyl propane monomers of lignin severely obstructed biobutanol production.

Inactivation of the transcription factor mig1 (YGL035C) in Saccharomyces cerevisiae improves tolerance towards monocarboxylic weak acids: acetic, formic and levulinic acid

Toxic concentrations of monocarboxylic weak acids present in lignocellulosic hydrolyzates affect cell integrity and fermentative performance of Saccharomyces cerevisiae. In this work, we report the deletion of the general catabolite repressor Mig1p as a strategy to improve the tolerance of S. cerevisiae towards inhibitory concentrations of acetic, formic or levulinic acid. In contrast with the wt yeast, where the growth and ethanol production were ceased in presence of acetic acid 5 g/L or formic acid 1.75 g/L (initial pH not adjusted), the m9 strain (Δmig1::kan) produced 4.06 ± 0.14 and 3.87 ± 0.06 g/L of ethanol, respectively. Also, m9 strain tolerated a higher concentration of 12.5 g/L acetic acid (initial pH adjusted to 4.5) without affecting its fermentative performance. Moreover, m9 strain produced 33% less acetic acid and 50–70% less glycerol in presence of weak acids, and consumed acetate and formate as carbon sources under aerobic conditions. Our results show that the deletion of Mig1p provides a single gene deletion target for improving the acid tolerance of yeast strains significantly.

Engineered global regulator H-NS improves the acid tolerance of E. coli

Background

Acid stress is often encountered during industrial fermentation as a result of the accumulation of acidic metabolites. Acid stress increases the intracellular acidity and can cause DNA damage and denaturation of essential enzymes, thus leading to a decrease of growth and fermentation yields. Although acid stress can be relieved by addition of a base to the medium, fermentations with acid-tolerant strains are generally considered much more efficient and cost-effective.

Results

In this study, the global regulator H-NS was found to have significant influence on the acid tolerance of E. coli. The final OD₆₀₀ of strains overexpressing H-NS increased by 24% compared to control, when cultured for 24 h at pH 4.5 using HCl as an acid agent. To further improve the acid tolerance, a library of H-NS was constructed by error-prone PCR and subjected to selection. Five mutants that conferred a significant growth advantage compared to the control strain were obtained. The final OD₆₀₀ of strains harboring the five H-NS mutants was enhanced by 26–53%, and their survival rate was increased by 10- to 100-fold at pH 2.5. Further investigation showed that the improved acid tolerance of H-NS mutants coincides with the activation of multiple acid resistance mechanisms, in particular the glutamate- and glutamine-dependent acid resistance system (AR2). The improved acid tolerance of H-NS mutants was also demonstrated in media acidified by acetic acid and succinic acid, which are common acidic fermentation by-products or products.

Conclusions

The results obtained in this work demonstrate that the engineering of H-NS can enhance the acid tolerance of E. coli. More in general, this study shows the potential of the engineering of global regulators acting as repressors, such as H-NS, as a promising method to obtain phenotypes of interest. This approach could expand the spectrum of application of global transcription machinery engineering.

Electronic supplementary material

The online version of this article (10.1186/s12934-018-0966-z) contains supplementary material, which is available to authorized users.

Model-Based Complete Enzymatic Production of 3,6-Anhydro-l-galactose from Red Algal Biomass

3,6-Anhydro-l-galactose (l-AHG) is a bioactive constituent of agar polysaccharides. To be used as a cosmetic or pharmaceutical ingredient, l-AHG is more favorably prepared by enzymatic saccharification of agar using a combination of agarolytic enzymes. Determining the optimum enzyme combination from the natural repertoire is a bottleneck for designing an efficient enzymatic-hydrolysis process. We consider all theoretical enzymatic-saccharification routes in the natural agarolytic pathway of a marine bacterium, Saccharophagus degradans 2-40. Among these routes, three representative routes were determined by removing redundant enzymatic reactions. We simulated each l-AHG production route with simple kinetic models and validated the reaction feasibility with an experimental procedure. The optimal enzyme mixture (with 67.3% maximum saccharification yield) was composed of endotype β-agarase, exotype β-agarase, agarooligosaccharolytic β-galactosidase, and α-neoagarobiose hydrolase. This approach will reduce the time and effort needed for developing a coherent enzymatic process to produce l-AHG on a mass scale.

Novel micronized woody biomass process for production of cost-effective clean fermentable sugars

Thermo-chemical pretreatments of biomass typically result in environmental impacts from water use and emission. The degradation byproducts in the resulting sugars can be inhibitory to the activities of enzymes and yeasts. The results of this study showed that combining existing commercial comminution technology can reduce total energy consumption with improved saccharification yield while eliminating chemical use. Impact mill was found to be the most efficient milling for size reduction of forest residual chips from ca. 2 mm to a specific value below 100 µm. The further micronization effectively disrupted the recalcitrance of the woody biomass and produced the highly saccharifiable substrates for downstream processing. In addition, extrusion can be integrated into a clean cellulosic sugar process for further fibrillation in place of the conventional mixing processing. The highest energy efficiency was observed on the impact-milled samples with 0.515 kg sugars kWh^-1.

A review on microbial lipids as a potential biofuel

Energy security, environmental concerns, and unstable oil prices have been the driving trifecta of demand for alternative fuels in the United States. The United States' dependence on energy resources, often from unstable oil-producing countries has created political insecurities and concerns. As we try to gain energy security, unconventional oil becomes more common, flooding the market, and causing the major downshift of the usual unstable oil prices. Meanwhile, consumption of fossil fuels and the consequent CO₂ emissions have driven disruptions in the Earth's atmosphere and are recognized to be responsible for global climate change. While the significance of each of these three factors may fluctuate with global politics or new technologies, transportation energy will remain the prominent focus of multi-disciplined research. Bioenergy future depends on the price of oil. Current energy policy of the United States heavily favors petroleum industry. In this review, the current trend in microbial lipids as a potential biofuel is discussed.

Effect of overliming and activated carbon detoxification on inhibitors removal and butanol fermentation of poplar prehydrolysates

BACKGROUND

Biomass prehydrolysates from dilute acid pretreatment contain a considerable amount of fermentable sugars for biofuels production. However, carbonyl degradation compounds present severe toxicity to fermentation microbes. Furans (such as furfural and hydroxymethylfurfural), aliphatic acids (such as acetic acid, formic acid and levulinic acid) and phenolic compounds (such as vanillin and syringaldehyde) have been suggested to be the main inhibitors in biomass prehydrolysates. However, no single compound has been determined as the dominant toxic inhibitor. The effects of various detoxification methods on inhibitors removal have not been fully understood.

RESULTS

The effects of overliming and activated carbon (AC) detoxification on the removal of inhibitors and butanol fermentation of the poplar prehydrolysates were investigated. Gas chromatography-mass spectrometry (GC/MS) was used to identify and quantify 46 carbonyl compounds as potential inhibitors. It was observed that overliming and AC treatment alone did not make the prehydrolysates fermentable with Clostridium saccharobutylicum. The sequential overliming and AC resulted in a remarkable fermentability and a high butanol yield at 0.22 g g-1 sugar. The inhibitor removal in the prehydrolysates treated by overliming and AC was also examined by GC/MS. Overliming removed 75.6% of furan derivatives and 68.1% of aromatic monomers. In comparison, AC (5.0% w/v) removed 77.9% of furan derivatives and 98.6% of aromatic monomers. In addition, overliming removed much more 2,5-furandicarboxyaldehyde, 5-ethylfuran-2-carbaldehyde and 2,5-hexanedione than AC did. On the contrary, AC could remove considerably more phenolic acids than overliming. In the sequential detoxification, both dialdehydes/diketones and phenolic acids were extensively removed. This could be the main reason why the sequential detoxification enabled a remarkable ABE fermentation for the prehydrolysates.

CONCLUSIONS

This study indicated that the effect of overliming and AC treatment on inhibitors removal was related to their chemical structures. Overliming removed more dialdehydes and diketones than AC treatment, while AC removed more phenolic acids than overliming. Sequential overliming and AC treatment were required to make the prehydrolysates fermentable with C. saccharobutylicum. The study also suggested different detoxification method was needed for ABE fermentation of the prehydrolysate as compared to ethanol fermentation.

Rapid Determination of Acetic Acid, Furfural, and 5-Hydroxymethylfurfural in Biomass Hydrolysates Using Near-Infrared Spectroscopy

Near-infrared spectroscopy (NIRS) is a rapid detection technique that has been used to characterize biomass. The objective of this study was to develop suitable NIRS models to predict the acetic acid, furfural, and 5-hydroxymethylfurfural (HMF) contents in biomass hydrolysates. Using a uniform distribution of pretreatment conditions, 60 representative biomass hydrolysates were prepared. Partial least-squares regression was used to develop models capable of predicting acetic acid, furfural, and HMF contents. Optimal models were built using the wavenumber range of 9000-8000 and 7000-5000 cm^-1 with high R ² for calibration and validation models, small root-mean-square error of calibration (<0.21) and root-mean-square error of prediction (RMSEP, <0.42), and a ratio of the standard deviation of the reference values to the RMSEP of >2.7. The NIRS method largely reduced the analytical time from ∼55 to <1 min and has no cost for reagents.

Batch bioethanol production via the biological and chemical saccharification of some Egyptian marine macroalgae

AIMS

Marine seaweeds (macroalgae) cause an eutrophication problem and affects the touristic activities. The success of the production of the third-generation bioethanol from marine macroalgae depends mainly on the development of an ecofriendly and eco-feasible pretreatment (i.e. hydrolysis) technique, a highly effective saccharification step and finally an efficient bioethanol fermentation step. Therefore, this study aimed to investigate the potentiality of different marine macroalgal strains, collected from Egyptian coasts, for bioethanol production via different saccharification processes.

METHODS AND RESULTS

Different marine macroalgal strains, red Jania rubens, green Ulva lactuca and brown Sargassum latifolium, have been collected from Egyptian Mediterranean and Red Sea shores. Different hydrolysis processes were evaluated to maximize the extraction of fermentable sugars; thermochemical hydrolysis with diluted acids (HCl and H₂ SO₄ ) and base (NaOH), hydrothermal hydrolysis followed by saccharification with different fungal strains and finally, thermochemical hydrolysis with diluted HCl, followed by fungal saccharification. The hydrothermal hydrolysis of S. latifolium followed by biological saccharification using Trichoderma asperellum RM1 produced maximum total sugars of 510 mg g^-1 macroalgal biomass. The integration of the hydrothermal and fungal hydrolyses of the macroalgal biomass with a separate batch fermentation of the produced sugars using two Saccharomyces cerevisiae strains, produced approximately 0·29 g bioethanol g^-1 total reducing sugars. A simulated regression modelling for the batch bioethanol fermentation was also performed.

CONCLUSIONS

This study supported the possibility of using seaweeds as a renewable source of bioethanol throughout a suggested integration of macroalgal biomass hydrothermal and fungal hydrolyses with a separate batch bioethanol fermentation process of the produced sugars.

SIGNIFICANCE AND IMPACT OF THE STUDY

The usage of marine macroalgae (i.e. seaweeds) as feedstock for bioethanol; an alternative and/or complimentary to petro-fuel, would act as triple fact solution; bioremediation process for ecosystem, renewable energy source and economy savings.

Understanding the tolerance of the industrial yeast Saccharomyces cerevisiae against a major class of toxic aldehyde compounds

Development of the next-generation biocatalyst is vital for fermentation-based industrial applications and a sustainable bio-based economy. Overcoming the major class of toxic compounds associated with lignocellulose-to-biofuels conversion is one of the significant challenges for new strain development. A significant number of investigations have been made to understand mechanisms of the tolerance for industrial yeast. It is humbling to learn how complicated the cell's response to the toxic chemicals is and how little we have known about yeast tolerance in the universe of the living cell. This study updates our current knowledge on the tolerance of industrial yeast against aldehyde inhibitory compounds at cellular, molecular and the genomic levels. It is comprehensive yet specific based on reproducible evidence and cross confirmed findings from different investigations using varied experimental approaches. This research approaches a rational foundation toward a more comprehensive understanding on the yeast tolerance. Discussions and perspectives are also proposed for continued exploring the puzzle of the yeast tolerance to aid the next-generation biocatalyst development.

Improving methane production from anaerobic digestion of Pennisetum Hybrid by alkaline pretreatment

Alkaline pretreatment with NaOH was used to improve methane yield from Pennisetum Hybrid. The pretreatments were carried out with different NaOH solutions (2-8% w/w) at three temperatures (35, 55 and 121 °C) for different periods of time (24, 24 and 1 h). All treated and untreated Pennisetum Hybrid were digested under mesophilic conditions (37 °C) to biogas, significant effects of the pretreatments on the yield of methane were observed. Results showed the modified Gompertz equation was reliable (determination coefficients (R²) greater than 0.96) to describe the kinetic behavior of anaerobic digestion of Pennisetum Hybrid. The best result, obtained by the treatment at 35 °C 2% NaOH for 24 h, resulted in the methane yield of 301.7 mL/g VS, corresponding to 21.0% improvement in the methane yield. Compositional, SEM, XRD and FTIR analysis confirmed that lignin removal, structural modification and cellulose crystalline variation were responsible for the improvement.

Fractionation of lignocellulosic biopolymers from sugarcane bagasse using formic acid-catalyzed organosolv process

A one-step formic acid-catalyzed organosolv process using a low-boiling point acid-solvent system was studied for fractionation of sugarcane bagasse. Compared to H₂SO₄, the use of formic acid as a promoter resulted in higher efficiency and selectivity on removals of hemicellulose and lignin with increased enzymatic digestibility of the cellulose-enriched solid fraction. The optimal condition from central composite design analysis was determined as 40 min residence time at 159 °C using water/ethanol/ethyl acetate/formic acid in the respective ratios of 43:20:16:21%v/v. Under this condition, a 94.6% recovery of cellulose was obtained in the solid with 80.2% cellulose content while 91.4 and 80.4% of hemicellulose and lignin were removed to the aqueous-alcohol-acid and ethyl acetate phases, respectively. Enzymatic hydrolysis of the solid yielded 84.5% glucose recovery compared to available glucan in the raw material. Physicochemical analysis revealed intact cellulose fibers with decreased crystallinity while the hemicellulose was partially recovered as mono- and oligomeric sugars. High-purity organosolv lignin with < 1% sugar cross-contamination was obtained with no major structural modification according to Fourier-transform infrared spectroscopy. The work represents an alternative process for efficient fractionation of lignocellulosic biomass in biorefineries.