Repeated-batch fermentation of lignocellulosic hydrolysate to ethanol using a hybrid Saccharomyces cerevisiae strain metabolically engineered for tolerance to acetic and formic acids

How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses

The yeast Saccharomyces cerevisiae is an excellent candidate for establishing cell factories to convert lignocellulosic biomass into chemicals and fuels. To enable this technology, yeast robustness must be improved to withstand the fermentation inhibitors (e.g., weak organic acids, phenols, and furan aldehydes) resulting from biomass pretreatment and hydrolysis. Here, we discuss how evolution experiments performed in the lab, a method commonly known as adaptive laboratory evolution (ALE), may contribute to lifting yeast tolerance against the inhibitors of lignocellulosic hydrolysates (LCHs). The key is that, through the combination of whole-genome sequencing and reverse engineering, ALE provides a robust platform for discovering and testing adaptive alleles, allowing to explore the genetic underpinnings of yeast responses to LCHs. We review the insights gained from past evolution experiments with S. cerevisiae in LCH inhibitors and propose experimental designs to optimise the discovery of genetic variants adaptive to biomass toxicity. The knowledge gathered through ALE projects is envisaged as a roadmap to engineer superior yeast strains for biomass-based bioprocesses.

Formate Dehydrogenase Improves the Resistance to Formic Acid and Acetic Acid Simultaneously in Saccharomyces cerevisiae

Bioethanol from lignocellulosic biomass is a promising and sustainable strategy to meet the energy demand and to be carbon neutral. Nevertheless, the damage of lignocellulose-derived inhibitors to microorganisms is still the main bottleneck. Developing robust strains is critical for lignocellulosic ethanol production. An evolved strain with a stronger tolerance to formate and acetate was obtained after adaptive laboratory evolution (ALE) in the formate. Transcriptional analysis was conducted to reveal the possible resistance mechanisms to weak acids, and fdh coding for formate dehydrogenase was selected as the target to verify whether it was related to resistance enhancement in Saccharomyces cerevisiae F3. Engineered S. cerevisiae FA with fdh overexpression exhibited boosted tolerance to both formate and acetate, but the resistance mechanism to formate and acetate was different. When formate exists, it breaks down by formate dehydrogenase into carbon dioxide (CO₂) to relieve its inhibition. When there was acetate without formate, FDH1 converted CO₂ from glucose fermentation to formate and ATP and enhanced cell viability. Together, fdh overexpression alone can improve the tolerance to both formate and acetate with a higher cell viability and ATP, which provides a novel strategy for robustness strain construction to produce lignocellulosic ethanol.

A review on enzymes and pathways for manufacturing polyhydroxybutyrate from lignocellulosic materials

Currently, major focus in the biopolymer field is being drawn on the exploitation of plant-based resources grounded on holistic sustainability trends to produce novel, affordable, biocompatible and environmentally safe polyhydroxyalkanoate biopolymers. The global PHA market, estimated at USD 62 Million in 2020, is predicted to grow by 11.2 and 14.2% between 2020-2024 and 2020-2025 correspondingly based on market research reports. The market is primarily driven by the growing demand for PHA products by the food packaging, biomedical, pharmaceutical, biofuel and agricultural sectors. One of the key limitations in the growth of the PHA market is the significantly higher production costs associated with pure carbon raw materials as compared to traditional polymers. Nonetheless, considerations such as consumer awareness on the toxicity of petroleum-based plastics and strict government regulations towards the prohibition of the use and trade of synthetic plastics are expected to boost the market growth rate. This study throws light on the production of polyhydroxybutyrate from lignocellulosic biomass using environmentally benign techniques via enzyme and microbial activities to assess its feasibility as a green substitute to conventional plastics. The novelty of the present study is to highlight the recent advances, pretreatment techniques to reduce the recalcitrance of lignocellulosic biomass such as dilute and concentrated acidic pretreatment, alkaline pretreatment, steam explosion, ammonia fibre explosion (AFEX), ball milling, biological pretreatment as well as novel emerging pretreatment techniques notably, high-pressure homogenizer, electron beam, high hydrostatic pressure, co-solvent enhanced lignocellulosic fractionation (CELF) pulsed-electric field, low temperature steep delignification (LTSD), microwave and ultrasound technologies. Additionally, inhibitory compounds and detoxification routes, fermentation downstream processes, life cycle and environmental impacts of recovered natural biopolymers, review green procurement policies in various countries, PHA strategies in line with the United Nations Sustainable Development Goals (SDGs) along with the fate of the spent polyhydroxybutyrate are outlined.

Rational engineering of Saccharomyces cerevisiae towards improved tolerance to multiple inhibitors in lignocellulose fermentations

BACKGROUND

The fermentation of lignocellulose hydrolysates to ethanol requires robust xylose-capable Saccharomyces cerevisiae strains able to operate in the presence of microbial inhibitory stresses. This study aimed at developing industrial S. cerevisiae strains with enhanced tolerance towards pretreatment-derived microbial inhibitors, by identifying novel gene combinations that confer resistance to multiple inhibitors (thus cumulative inhibitor resistance phenotype) with minimum impact on the xylose fermentation ability. The strategy consisted of multiple sequential delta-integrations of double-gene cassettes containing one gene conferring broad inhibitor tolerance (ARI1, PAD1 or TAL1) coupled with an inhibitor-specific gene (ADH6, FDH1 or ICT1). The performances of the transformants were compared with the parental strain in terms of biomass growth, ethanol yields and productivity, as well as detoxification capacities in a synthetic inhibitor cocktail, sugarcane bagasse hydrolysate as well as hardwood spent sulphite liquor.

RESULTS

The first and second round of delta-integrated transformants exhibited a trade-off between biomass and ethanol yield. Transformants showed increased inhibitor resistance phenotypes relative to parental controls specifically in fermentations with concentrated spent sulphite liquors at 40% and 80% v/v concentrations in 2% SC media. Unexpectedly, the xylose fermentation capacity of the transformants was reduced compared to the parental control, but certain combinations of genes had a minor impact (e.g. TAL1 + FDH1). The TAL1 + ICT1 combination negatively impacted on both biomass growth and ethanol yield, which could be linked to the ICT1 protein increasing transformant susceptibility to weak acids and temperature due to cell membrane changes.

CONCLUSIONS

The integration of the selected genes was proven to increase tolerance to pretreatment inhibitors in synthetic or industrial hydrolysates, but they were limited to the fermentation of glucose. However, some gene combination sequences had a reduced impact on xylose conversion.

Lipid Accumulation by Xylose Metabolism Engineered Mucor circinelloides Strains on Corn Straw Hydrolysate

Previously, we presented a novel approach for increasing the consumption of xylose and the lipid yield by overexpressing the genes coding for xylose isomerase (XI) and xylulokinase (XK) in Mucor circinelloides. In the present study, an in-depth analysis of lipid accumulation by xylose metabolism engineered M. circinelloides strains (namely Mc-XI and Mc-XK) using corn straw hydrolysate was to be explored. The results showed that the fatty acid contents of the engineered M. circinelloides strains were, respectively, increased by 19.8% (in Mc-XI) and 22.3% (in Mc-XK) when compared with the control strain, even though a slightly decreased biomass in these engineered strains was detected. Moreover, the xylose uptake rates of engineered strains in the corn straw hydrolysate were improved significantly by 71.5% (in Mc-XI) and 68.8% (in Mc-XK), respectively, when compared with the control strain. Maybe the increased utilization of xylose led to an increase in lipid synthesis. When the recombinant M. circinelloides strains were cultured in corn straw hydrolysate medium with the carbon-to-nitrogen ratio (C/N ratio) of 50 and initial pH of 6.0, at 30 °C and 500 rpm for 144 h, a total biomass of 12.6-12.9 g/L with a lipid content of 17.2-17.7% (corresponding to a lipid yield of 2.17-2.28 g/L) was achieved. Our study provides a foundation for the further application of the engineered M. circinelloides strains to produce lipid from lignocelluloses.

Origin, Impact and Control of Lignocellulosic Inhibitors in Bioethanol Production—A Review

Bioethanol production from lignocellulosic biomass is still struggling with many obstacles. One of them is lignocellulosic inhibitors. The aim of this review is to discuss the most known inhibitors. Additionally, the review addresses different detoxification methods to degrade or to remove inhibitors from lignocellulosic hydrolysates. Inhibitors are formed during the pretreatment of biomass. They derive from the structural polymers-cellulose, hemicellulose and lignin. The formation of inhibitors depends on the pretreatment conditions. Inhibitors can have a negative influence on both the enzymatic hydrolysis and fermentation of lignocellulosic hydrolysates. The inhibition mechanisms can be, for example, deactivation of enzymes or impairment of vital cell structures. The toxicity of each inhibitor depends on its chemical and physical properties. To decrease the negative effects of inhibitors, different detoxification methods have been researched. Those methods focus on the chemical modification of inhibitors into less toxic forms or on the separation of inhibitors from lignocellulosic hydrolysates. Each detoxification method has its limitations on the removal of certain inhibitors. To choose a suitable detoxification method, a deep molecular understanding of the inhibition mechanism and the inhibitor formation is necessary.

Repeated batches as a strategy for high 2G ethanol production from undetoxified hemicellulose hydrolysate using immobilized cells of recombinant Saccharomyces cerevisiae in a fixed-bed reactor

BACKGROUND

The search for sustainable energy sources has become a worldwide issue, making the development of efficient biofuel production processes a priority. Immobilization of second-generation (2G) xylose-fermenting Saccharomyces cerevisiae strains is a promising approach to achieve economic viability of 2G bioethanol production from undetoxified hydrolysates through operation at high cell load and mitigation of inhibitor toxicity. In addition, the use of a fixed-bed reactor can contribute to establish an efficient process because of its distinct advantages, such as high conversion rate per weight of biocatalyst and reuse of biocatalyst.

RESULTS

This work assessed the influence of alginate entrapment on the tolerance of recombinant S. cerevisiae to acetic acid. Encapsulated GSE16-T18SI.1 (T18) yeast showed an outstanding performance in repeated batch fermentations with cell recycling in YPX medium supplemented with 8 g/L acetic acid (pH 5.2), achieving 10 cycles without significant loss of productivity. In the fixed-bed bioreactor, a high xylose fermentation rate with ethanol yield and productivity values of 0.38 gethanol/gsugars and 5.7 g/L/h, respectively were achieved in fermentations using undetoxified sugarcane bagasse hemicellulose hydrolysate, with and without medium recirculation.

CONCLUSIONS

The performance of recombinant strains developed for 2G ethanol production can be boosted strongly by cell immobilization in alginate gels. Yeast encapsulation allows conducting fermentations in repeated batch mode in fixed-bed bioreactors with high xylose assimilation rate and high ethanol productivity using undetoxified hemicellulose hydrolysate.

Zymomonas mobilis Biofilm Reactor for Ethanol Production Using Rice Straw Hydrolysate Under Continuous and Repeated Batch Processes

Plastic composited corn silk was developed as a biotic/abiotic carrier for Zymomonas mobilis biofilm formation for the purpose of ethanol production. Furthermore, we explored the use of rice straw hydrolysate as substrate in both multistage continuous culture and repeated batch processes and compared the ethanol production efficiency by two strains of Z. mobilis. Biofilm formed by bacterial strains Z. mobilis ZM4 and TISTR551 were detected, and its proficiencies were compared under various conditions by scanning electron microscopy (SEM) and crystal violet assays. The greatest biofilm formed by both strains was found on day five after the inoculation. Z. mobilis strain ZM4 grown in repeated batch biofilm reactors produced higher yields of ethanol than TISTR551 grown under the same conditions, while TISTR551 produced higher yields of ethanol in the multistage continuous process. The yields were highly maintained, with no significant differences (p < 0.05) among the three consecutive repeated batches. These experiments highlight exciting uses for agricultural byproducts in the production of ethanol using Z. mobilis biofilm reactors.

Production of 1,3-Propanediol from Pure and Crude Glycerol Using Immobilized Clostridium butyricum

The present study describes the production of the value-added chemical 1,3-propanediol (1,3-PD) from crude glycerol, a waste by-product formed during biodiesel production. The efficiency, robustness, and stability of the process were improved by immobilization of the anaerobic bacterium Clostridium butyricum into a polyvinyl alcohol (PVA) hydrogel. The highest average productivity, 6.8 ± 0.2 g/(L·h), was achieved in 10 consecutive, repeated batch fermentations, with an initial concentration of pure glycerol 45.5 ± 0.7 g/L, after 2.5 hours. The highest final concentration and yield of 1,3-PD, 28.3 ± 0.6 g/L, and 0.42 ± 0.01 g/g, respectively, were achieved in eleven repeated batch fermentations, after increasing the initial pure glycerol concentration to 70.4 ± 1.9 g/L. Two different types of crude glycerol, produced from used cooking oil (UCO) and rapeseed oil (RO), were tested in repeated batch fermentations, with an average productivity achieved of 2.3 ± 0.1 and 3.5 ± 0.3 g/(L·h), respectively. The highest final concentration and yield of 1,3-PD, 12.6 ± 0.9 g/L, and 0.35 ± 0.02 g/g, respectively, were observed in fifteen repeated batch fermentations with RO crude glycerol. An excellent stability of the immobilized anaerobic bacteria and increase of productivity in fermentation of crude glycerol was demonstrated.

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.

Effective usage of sorghum bagasse: Optimization of organosolv pretreatment using 25% 1-butanol and subsequent nanofiltration membrane separation

We investigated the use of low concentrations of butanol (<40%, all v/v) as an organosolv pretreatment to fractionate lignocellulosic biomass into cellulose, hemicellulose, and lignin. The pretreatment conditions were optimized for sorghum bagasse by focusing on four parameters: butanol concentration, sulfuric acid concentration, pretreatment temperature, and pretreatment time. A butanol concentration of 25% or higher together with 0.5% or higher acid was effective for removing lignin while retaining most of the cellulose in the solid fraction. The highest cellulose (84.9%) and low lignin (15.3%) content were obtained after pretreatment at 200 °C for 60 min. Thus, pretreatment comprising 25% butanol, 0.5% acid, 200 °C, and 60 min process time was considered optimal. Enzymatic saccharification and fermentation by Saccharomyces cerevisiae produced 61.9 g/L ethanol from 200 g/L solid fraction obtained following pretreatment, and 10.2 g/L ethanol was obtained from the liquid fraction by xylose-utilizing S. cerevisiae following membrane nanofiltration to remove butanol.

A spent coffee grounds based biorefinery for the production of biofuels, biopolymers, antioxidants and biocomposites

Spent coffee grounds are composed of lipid, carbohydrates, carbonaceous, and nitrogen containing compounds among others. Using n-hexane and n-hexane/isopropanol mixture highest oil yield was achived during soxhlet extraction of oil from spent coffee grounds. Alternatively, supercritical carbon dioxide can be employed as a green solvent for the extraction of oil. Using advanced chemical and biotechnological methods, spent coffee grounds are converted to various biofuels such as, biodiesel, renewable diesel, bioethanol, bioethers, bio-oil, biochar, and biogas. The in-situ transesterification of spent coffee grounds was carried out in a large scale (4 kg), which led to 80-83% biodiesel yield. In addition, a large number of value added and diversified products viz. polyhydroxyalkanoates, biosorbent, activated carbon, polyol, polyurethane foam, carotenoid, phenolic antioxidants, and green composite are obtained from spent coffee grounds. The principles of circular economy are applied to develop a sustanaible biorefinery based on valorisation of spent coffee grounds.

Physico-Chemical Conversion of Lignocellulose: Inhibitor Effects and Detoxification Strategies: A Mini Review

A pretreatment of lignocellulosic biomass to produce biofuels, polymers, and other chemicals plays a vital role in the biochemical conversion process toward disrupting the closely associated structures of the cellulose-hemicellulose-lignin molecules. Various pretreatment steps alter the chemical/physical structure of lignocellulosic materials by solubilizing hemicellulose and/or lignin, decreasing the particle sizes of substrate and the crystalline portions of cellulose, and increasing the surface area of biomass. These modifications enhance the hydrolysis of cellulose by increasing accessibilities of acids or enzymes onto the surface of cellulose. However, lignocellulose-derived byproducts, which can inhibit and/or deactivate enzyme and microbial biocatalysts, are formed, including furan derivatives, lignin-derived phenolics, and carboxylic acids. These generation of compounds during pretreatment with inhibitory effects can lead to negative effects on subsequent steps in sugar flat-form processes. A number of physico-chemical pretreatment methods such as steam explosion, ammonia fiber explosion (AFEX), and liquid hot water (LHW) have been suggested and developed for minimizing formation of inhibitory compounds and alleviating their effects on ethanol production processes. This work reviews the physico-chemical pretreatment methods used for various biomass sources, formation of lignocellulose-derived inhibitors, and their contributions to enzymatic hydrolysis and microbial activities. Furthermore, we provide an overview of the current strategies to alleviate inhibitory compounds present in the hydrolysates or slurries.

Development of combined nanofiltration and forward osmosis process for production of ethanol from pretreated rice straw

A membrane process combining nanofiltraion (NF) and forward osmosis (FO) was developed for the sugar concentration with the aim of high bio-ethanol production from the liquid fraction of rice straw. The commercial NF membrane, ESNA3, was more adequate for removal of fermentation inhibitors (such as acetic acid) than the FO membrane, whereas the commercial FO membrane, TFC-ES, was more adequate for concentration of the sugars than the NF membrane. The liquid fraction was subjected to the following process: NF concentration with water addition (NF_(+H2O))→enzymatic hydrolysis→FO concentration. This NF_(+H2O)-FO hybrid process generated a total sugar content of 107g·L^-1. Xylose-assimilating S. cerevisiae produced 24g·L^-1 ethanol from the liquid fraction that was diluted 1.5-fold and then concentrated by the NF_(+H2O)-FO hybrid process. The NF_(+H2O)-FO hybrid process has the potential for optimized ethanol production from pretreated lignocellulosic biomass.

Mathematical modeling of continuous ethanol fermentation in a membrane bioreactor by pervaporation compared to conventional system: Genetic algorithm

In this paper, genetic algorithm was used to investigate mathematical modeling of ethanol fermentation in a continuous conventional bioreactor (CCBR) and a continuous membrane bioreactor (CMBR) by ethanol permselective polydimethylsiloxane (PDMS) membrane. A lab scale CMBR with medium glucose concentration of 100gL(-1) and Saccharomyces cerevisiae microorganism was designed and fabricated. At dilution rate of 0.14h(-1), maximum specific cell growth rate and productivity of 0.27h(-1) and 6.49gL(-1)h(-1) were respectively found in CMBR. However, at very high dilution rate, the performance of CMBR was quite similar to conventional fermentation on account of insufficient incubation time. In both systems, genetic algorithm modeling of cell growth, ethanol production and glucose concentration were conducted based on Monod and Moser kinetic models during each retention time at unsteady condition. The results showed that Moser kinetic model was more satisfactory and desirable than Monod model.

Improving ethanol yield in acetate-reducing Saccharomyces cerevisiae by cofactor engineering of 6-phosphogluconate dehydrogenase and deletion of ALD6

BACKGROUND

Acetic acid, an inhibitor of sugar fermentation by yeast, is invariably present in lignocellulosic hydrolysates which are used or considered as feedstocks for yeast-based bioethanol production. Saccharomyces cerevisiae strains have been constructed, in which anaerobic reduction of acetic acid to ethanol replaces glycerol formation as a mechanism for reoxidizing NADH formed in biosynthesis. An increase in the amount of acetate that can be reduced to ethanol should further decrease acetic acid concentrations and enable higher ethanol yields in industrial processes based on lignocellulosic feedstocks. The stoichiometric requirement of acetate reduction for NADH implies that increased generation of NADH in cytosolic biosynthetic reactions should enhance acetate consumption.

RESULTS

Replacement of the native NADP(+)-dependent 6-phosphogluconate dehydrogenase in S. cerevisiae by a prokaryotic NAD(+)-dependent enzyme resulted in increased cytosolic NADH formation, as demonstrated by a ca. 15% increase in the glycerol yield on glucose in anaerobic cultures. Additional deletion of ALD6, which encodes an NADP(+)-dependent acetaldehyde dehydrogenase, led to a 39% increase in the glycerol yield compared to a non-engineered strain. Subsequent replacement of glycerol formation by an acetate reduction pathway resulted in a 44% increase of acetate consumption per amount of biomass formed, as compared to an engineered, acetate-reducing strain that expressed the native 6-phosphogluconate dehydrogenase and ALD6. Compared to a non-acetate reducing reference strain under the same conditions, this resulted in a ca. 13% increase in the ethanol yield on glucose.

CONCLUSIONS

The combination of NAD(+)-dependent 6-phosphogluconate dehydrogenase expression and deletion of ALD6 resulted in a marked increase in the amount of acetate that was consumed in these proof-of-principle experiments, and this concept is ready for further testing in industrial strains as well as in hydrolysates. Altering the cofactor specificity of the oxidative branch of the pentose-phosphate pathway in S. cerevisiae can also be used to increase glycerol production in wine fermentation and to improve NADH generation and/or generation of precursors derived from the pentose-phosphate pathway in other industrial applications of this yeast.

Phenotypic characterization and comparative transcriptomics of evolved Saccharomyces cerevisiae strains with improved tolerance to lignocellulosic derived inhibitors

BACKGROUND

Lignocellulosic biomass continues to be investigated as a viable source for bioethanol production. However, the pretreatment process generates inhibitory compounds that impair the growth and fermentation performance of microorganisms such as Saccharomyces cerevisiae. Pinewood specifically has been shown to be challenging in obtaining industrially relevant ethanol titers. An industrial S. cerevisiae strain was subjected to directed evolution and adaptation in pretreated pine biomass and resultant strains, GHP1 and GHP4, exhibited improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. A comparative transcriptomic approach was applied to identify and characterize differences in phenotypic stability of evolved strains.

RESULTS

Evolved strains displayed different fermentative capabilities with pretreated pine that appear to be influenced by the addition or absence of 13 inhibitory compounds during pre-culturing. GHP4 performance was consistent independent of culturing conditions, while GHP1 performance was dependent on culturing with inhibitors. Comparative transcriptomics revealed 52 genes potentially associated with stress responses to multiple inhibitors simultaneously. Fluorescence microscopy revealed improved cellular integrity of both strains with mitochondria exhibiting resistance to the damaging effects of inhibitors in contrast to the parent.

CONCLUSIONS

Multiple potentially novel genetic targets have been discovered for understanding stress tolerance through the characterization of our evolved strains. This study specifically examines the synergistic effects of multiple inhibitors and identified targets will guide future studies in remediating effects of inhibitors and further development of robust yeast strains for multiple industrial applications.

Inverse metabolic engineering based on transient acclimation of yeast improves acid-containing xylose fermentation and tolerance to formic and acetic acids

Improving the production of ethanol from xylose is an important goal in metabolic engineering of Saccharomyces cerevisiae. Furthermore, S. cerevisiae must produce ethanol in the presence of weak acids (formate and acetate) generated during pre-treatment of lignocellulosic biomass. In this study, weak acid-containing xylose fermentation was significantly improved using cells that were acclimated to the weak acids during pre-cultivation. Transcriptome analyses showed that levels of transcripts for transcriptional/translational machinery-related genes (RTC3 and ANB1) were enhanced by formate and acetate acclimation. Recombinant yeast strains overexpressing RTC3 and ANB1 demonstrated improved ethanol production from xylose in the presence of the weak acids, along with improved tolerance to the acids. Novel metabolic engineering strategy based on the combination of short-term acclimation and system-wide analysis was developed, which can develop stress-tolerant strains in a short period of time, although conventional evolutionary engineering approach has required long periods of time to isolate inhibitor-adapted strains.

Pretreatment of lignocellulose: Formation of inhibitory by-products and strategies for minimizing their effects

Biochemical conversion of lignocellulosic feedstocks to advanced biofuels and other commodities through a sugar-platform process involves a pretreatment step enhancing the susceptibility of the cellulose to enzymatic hydrolysis. A side effect of pretreatment is formation of lignocellulose-derived by-products that inhibit microbial and enzymatic biocatalysts. This review provides an overview of the formation of inhibitory by-products from lignocellulosic feedstocks as a consequence of using different pretreatment methods and feedstocks as well as an overview of different strategies used to alleviate problems with inhibitors. As technologies for biorefining of lignocellulose become mature and are transferred from laboratory environments to industrial contexts, the importance of management of inhibition problems is envisaged to increase as issues that become increasingly relevant will include the possibility to use recalcitrant feedstocks, obtaining high product yields and high productivity, minimizing the charges of enzymes and microorganisms, and using high solids loadings to obtain high product titers.

Assessment of holocellulose for the production of bioethanol by conserving Pinus radiata cones as renewable feedstock

Renewable and green energy sources are much sought. Bioethanol is an environmentally friendly transportation fuel. Pine cones from Pinus radiata were shown to be a potential feedstock for the production of bioethanol. Alkaline (NaOH) pretreatment was carried out to delignify the lignocellulosic material and generate holocellulose (72 wt. % yield). The pretreated biomass was hydrolysed using HCl as catalyst under microwave irradiation and hydrothermal conditions. Microwave irradiation was found to be better than the hydrothermal process. Microwave irradiation accelerated the hydrolysis of biomass (42 wt. % conversion) with the reaction conditions being 3 M HCl and 5 min of irradiation time. Interestingly, even the xylose, which is the major component of the hydrolyzate was found to be metabolized to ethanol using Baker's yeast (Saccharomyces cerevisiae) under the experimental conditions. 5.7 g of ethanol could be produced from 100 g of raw pine cones.

Nanofiltration concentration of extracellular glutathione produced by engineered Saccharomyces cerevisiae

This study aimed to optimize extracellular glutathione production by a Saccharomyces cerevisiae engineered strain and to concentrate the extracellular glutathione by membrane separation processes, including ultrafiltration (UF) and nanofiltration (NF). Synthetic defined (SD) medium containing 20 g L(-1) glucose was fermented for 48 h; the fermentation liquid was passed through an UF membrane to remove macromolecules. Glutathione in this permeate was concentrated for 48 h to 545.1 ± 33.6 mg L(-1) using the NF membrane; this was a significantly higher concentration than that obtained with yeast extract peptone dextrose (YPD) medium following 96 h NF concentration (217.9 ± 57.4 mg L(-1)). This higher glutathione concentration results from lower cellular growth in SD medium (final OD600 = 6.9 ± 0.1) than in YPD medium (final OD600 = 11.0 ± 0.6) and thus higher production of extracellular glutathione (16.0 ± 1.3 compared to 9.2 ± 2.1 mg L(-1) in YPD medium, respectively). Similar fermentation and membrane processing of sweet sorghum juice containing 20 g L(-1) total sugars provided 240.3 ± 60.6 mg L(-1) glutathione. Increased extracellular production of glutathione by this engineered strain in SD medium and subsequent UF permeation and NF concentration in shortend time may help realize industrial recovery of extracellular glutathione.

Mechanical milling and membrane separation for increased ethanol production during simultaneous saccharification and co-fermentation of rice straw by xylose-fermenting Saccharomyces cerevisiae

Mechanical milling and membrane separation were applied to simultaneous saccharification and co-fermentation from hydrothermally pretreated rice straw. Mechanical milling with minimized 4 cycles enabled 37.5±3.4gL(-1) and 45.3±4.4gL(-1) of ethanol production after 48h by xylose-fermenting Saccharomyces cerevisiae from solid fractions (200 and 250gL(-1)) of pretreated rice straw with 5 filter paper unitg-biomass(-1) cellulase (respectively, 77.3±7.1% and 74.7±7.3% of theoretical ethanol yield). Use of a membrane-based process including nanofiltration and ultrafiltration increased the sugar concentrations in the liquid fraction of pretreated rice straw and addition of this liquid fraction to 250gL(-1) solid fraction increased ethanol production to 52.0±0.4gL(-1) (73.8±0.6% of theoretical ethanol yield). Mechanical milling was effective in increasing enzymatic hydrolysis of the solid fraction and membrane separation steps increased the ethanol titer during co-fermentation, leading to a proposal for combining these processes for ethanol production from whole rice straw.

Repeated ethanol production from sweet sorghum juice concentrated by membrane separation

Sequential batch fermentation from sweet sorghum juice concentrated by membrane separation (ultrafiltration permeation and nanofiltration concentration) to increase sugar contents, was investigated. Ethanol production at 5th batch fermentation by Saccharomyces cerevisiae BY4741 attained 113.7±3.1 g L(-1) (89.1±2.2% of the theoretical ethanol yield) from 270.0±22.6 g L(-1) sugars, corresponding to 98.7% of ethanol titer attained at the 1st batch fermentation. This titer was comparable to ethanol production of 115.8±0.6 g L(-1) (87.1±2.7% of the theoretical ethanol yield) obtained at 5th batch fermentation with 3 g L(-1) yeast extract and 6 g L(-1) polypeptone. Increase of cell density in the concentrated sweet sorghum juice was observed during sequential batch fermentation, as indicated by increased OD600. Utilization of sweet sorghum juice as the sole source, membrane separation, and S. cerevisiae was a cost-effective process for high ethanol production.

Simultaneous utilization of glucose and mannose from woody hydrolysate for free fatty acid production by metabolically engineered Escherichia coli

In this study, the Escherichia coli strain MG1655 with fadD mutant (named as ML103), and MG1655 with fadD and ptsG double mutant (named as ML190) carrying the plasmid with the acyl-ACP thioesterase (TE) from Ricinus communis (pXZ18) or the plasmid with the combination of the TE and the native (3R)-hydroxyacyl-ACP dehydrase (fabZ) (pXZ18Z), produced free fatty acids (FFAs) efficiently using mannose as the sole carbon source. Due to the carbon catabolite repression (CCR) regulation, ML103(pXZ18) utilized glucose and mannose sequentially in the mixed sugar culture, while ML190(pXZ18) and ML190(pXZ18Z), with ptsG mutation, used glucose and mannose simultaneously. The highest total FFA concentration from the mixed sugar culture reached 2.96g/L by ML190(pXZ18Z). Furthermore, the strain ML190(pXZ18Z) can produce 2.86g/L FFAs with a high yield of 0.23g/g using hydrolysate mainly contained glucose and mannose from a commercial plant.

Enhanced tolerance of Saccharomyces cerevisiae to multiple lignocellulose-derived inhibitors through modulation of spermidine contents

Fermentation inhibitors present in lignocellulose hydrolysates are inevitable obstacles for achieving economic production of biofuels and biochemicals by industrial microorganisms. Here we show that spermidine (SPD) functions as a chemical elicitor for enhanced tolerance of Saccharomyces cerevisiae against major fermentation inhibitors. In addition, the feasibility of constructing an engineered S. cerevisiae strain capable of tolerating toxic levels of the major inhibitors without exogenous addition of SPD was explored. Specifically, we altered expression levels of the genes in the SPD biosynthetic pathway. Also, OAZ1 coding for ornithine decarboxylase (ODC) antizyme and TPO1 coding for the polyamine transport protein were disrupted to increase intracellular SPD levels through alleviation of feedback inhibition on ODC and prevention of SPD excretion, respectively. Especially, the strain with combination of OAZ1 and TPO1 double disruption and overexpression of SPE3 not only contained spermidine content of 1.1mg SPD/g cell, which was 171% higher than that of the control strain, but also exhibited 60% and 33% shorter lag-phase period than that of the control strain under the medium containing furan derivatives and acetic acid, respectively. While we observed a positive correlation between intracellular SPD contents and tolerance phenotypes among the engineered strains accumulating different amounts of intracellular SPD, too much SPD accumulation is likely to cause metabolic burden. Therefore, genetic perturbations for intracellular SPD levels should be optimized in terms of metabolic burden and SPD contents to construct inhibitor tolerant yeast strains. We also found that the genes involved in purine biosynthesis and cell wall and chromatin stability were related to the enhanced tolerance phenotypes to furfural. The robust strains constructed in this study can be applied for producing chemicals and advanced biofuels from cellulosic hydrolysates.

Combined cell-surface display- and secretion-based strategies for production of cellulosic ethanol with Saccharomyces cerevisiae

BACKGROUND

Engineering Saccharomyces cerevisiae to produce heterologous cellulases is considered as a promising strategy for production of bioethanol from lignocellulose. The production of cellulase is usually pursued by one of the two strategies: displaying enzyme on the cell surface or secreting enzyme into the medium. However, to our knowledge, the combination of the two strategies in a yeast strain has not been employed.

RESULTS

In this study, heterologous endoglucanase (EG) and cellobiohydrolase I (CBHI) were produced in a β-glucosidase displaying S. cerevisiae strain using cell-surface display, secretion, or a combined strategy. Strains EG-D-CBHI-D and EG-S-CBHI-S (with both enzymes displayed on the cell surface or with both enzymes secreted to the surrounding medium) showed higher ethanol production (2.9 and 2.6 g/L from 10 g/L phosphoric acid swollen cellulose, respectively), than strains EG-D-CBHI-S and EG-S-CBHI-D (with EG displayed on cell surface and CBHI secreted, or vice versa). After 3-cycle repeated-batch fermentation, the cellulose degradation ability of strain EG-D-CBHI-D remained 60 % of the 1st batch, at a level that was 1.7-fold higher than that of strain EG-S-CBHI-S.

CONCLUSIONS

This work demonstrated that placing EG and CBHI in the same space (on the cell surface or in the medium) was favorable for amorphous cellulose-based ethanol fermentation. In addition, the cellulolytic yeast strain that produced enzymes by the cell-surface display strategy performed better in cell-recycle batch fermentation compared to strains producing enzymes via the secretion strategy.

Development of a GIN11/FRT-based multiple-gene integration technique affording inhibitor-tolerant, hemicellulolytic, xylose-utilizing abilities to industrial Saccharomyces cerevisiae strains for ethanol production from undetoxified lignocellulosic hemicelluloses

Background

Bioethanol produced by the yeast Saccharomyces cerevisiae is currently one of the most promising alternatives to conventional transport fuels. Lignocellulosic hemicelluloses obtained after hydrothermal pretreatment are important feedstock for bioethanol production. However, hemicellulosic materials cannot be directly fermented by yeast: xylan backbone of hemicelluloses must first be hydrolyzed by heterologous hemicellulases to release xylose, and the yeast must then ferment xylose in the presence of fermentation inhibitors generated during the pretreatment.

Results

A GIN11/FRT-based multiple-gene integration system was developed for introducing multiple functions into the recombinant S. cerevisiae strains engineered with the xylose metabolic pathway. Antibiotic markers were efficiently recycled by a novel counter selection strategy using galactose-induced expression of both FLP recombinase gene and GIN11 flanked by FLP recombinase recognition target (FRT) sequences. Nine genes were functionally expressed in an industrial diploid strain of S. cerevisiae: endoxylanase gene from Trichoderma reesei, xylosidase gene from Aspergillus oryzae, β-glucosidase gene from Aspergillus aculeatus, xylose reductase and xylitol dehydrogenase genes from Scheffersomyces stipitis, and XKS1, TAL1, FDH1 and ADH1 variant from S. cerevisiae. The genes were introduced using the homozygous integration system and afforded hemicellulolytic, xylose-assimilating and inhibitor-tolerant abilities to the strain. The engineered yeast strain demonstrated 2.7-fold higher ethanol titer from hemicellulosic material than a xylose-assimilating yeast strain. Furthermore, hemicellulolytic enzymes displayed on the yeast cell surface hydrolyzed hemicelluloses that were not hydrolyzed by a commercial enzyme, leading to increased sugar utilization for improved ethanol production.

Conclusions

The multifunctional yeast strain, developed using a GIN11/FRT-based marker recycling system, achieved direct conversion of hemicellulosic biomass to ethanol without the addition of exogenous hemicellulolytic enzymes. No detoxification processes were required. The multiple-gene integration technique is a powerful approach for introducing and improving the biomass fermentation ability of industrial diploid S. cerevisiae strains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-014-0145-9) contains supplementary material, which is available to authorized users.

Increased ethanol production from sweet sorghum juice concentrated by a membrane separation process

The aim of this investigation was to attain high ethanol concentration by concentrating sweet sorghum juice using a two-step membrane separation process. Ultrafiltration permeation of the juice was used to remove residues, followed by nanofiltration concentration to increase the sugar concentration. The concentrated juice containing 180.0 g L(-1) sucrose, 59.3 g L(-1) glucose and 49.3 g L(-1) fructose supplemented with nitrogen sources (10 and 20 g L(-1) of yeast extract and polypeptone, respectively) was fermented by Saccharomyces cerevisiae BY4741 to produce 133.5 g L(-1) of ethanol (87.6% of theoretical yield) after 48 h fermentation. Importantly, the addition of lower concentrations of exogenous nitrogen sources (3 and 6 g L(-1) of yeast extract and polypeptone, respectively) or no exogenous nitrogen sources resulted in the production of 131.4 and 132.8 g L(-1) of ethanol (84.8% and 86.0% of theoretical yield), respectively, after 48 h fermentation.

Optimized membrane process to increase hemicellulosic ethanol production from pretreated rice straw by recombinant xylose-fermenting Saccharomyces cerevisiae

Oligomeric sugars in the liquid fraction of hot water-pretreated rice straw are more amenable to membrane process than monomeric sugars, as lower pressure is required. Following membrane process was employed: nanofiltration (NF) concentration → (dilution → NF concentration) × 2 times → enzymatic hydrolysis (EH) → ultrafiltration (UF) permeation [

IMPLICATION

NF for recovery of oligomeric sugars, dilution and NF for removal of low molecular weight fermentation inhibitors, UF for removal of high molecular weight fermentation inhibitors and recovery of monomeric sugars after EH]. This process provided the liquid fraction containing 111.4 g L(-1) of sugars, corresponding to 681.0mM as monomeric sugars, from the original liquid fraction (181.1mM monomeric sugars). Concentrations of low molecular weight fermentation inhibitors, acetic and formic acids, were decreased to 24% and 48%, respectively. Xylose-fermenting recombinant Saccharomyces cerevisiae produced 34.5 ± 2.2 g L(-1) ethanol from the 0.8 times liquid fraction (76% of theoretical yield).

Pretreatment of Japanese cedar by ionic liquid solutions in combination with acid and metal ion and its application to high solid loading

BACKGROUND

Lignocellulosic biomass from plant biomass, especially softwoods, are well-known to present difficulties during attempts at hydrolysis due to their rigid structure. Pretreatment of lignocellulosic biomass with ionic liquids (ILs) is attractive as this requires to a low input of energy. However, IL pretreatment has the disadvantage of the presence of large amounts of water. Recently, it was reported that a small amount of acid has a positive effect on the degradation of biomass in IL with water. In this study the pretreatment of Japanese cedar, the most abundant softwood in Japan, was investigated using a combination of IL, acid and metal ions.

RESULTS

First, the novel ionic liquid pretreatment was investigated by changing the pretreatment solvent and the anti-solvent. A mixture of IL, acid and ferric oxide (Fe(3+)) ion was most effective for pretreatment, and an acetone-water mixture was also most effective on the precipitation of biomass. These optimized pretreatment combinations attained a higher degree of glucose release from the pretreated biomass. The amount of cellulose was concentrated from to a level of 36 to 84% of the insoluble fraction by the optimized pretreatment. Based on this result, it was assumed that the extraction of the lignin fraction from the biomass into an anti-solvent solution was attained. Finally, this optimized pretreatment was applied to the enzymatic hydrolysis of Japanese cedar at high-solid biomass loading, and 110 g/L of glucose production was attained. In addition, the ethanol fermentation with this hydrolyzed solution by Saccharomyces cerevisiae achieved 50 g/L ethanol production, and this yield reached 90% of the theoretical yield.

CONCLUSIONS

We developed an effective pretreatment protocol by changing to a pretreatment solvent containing IL, acid, metal ion and anti-solvent. The optimized pretreatment has an effect on softwood and separately retrieved lignin as a by-product. The saccharified solution at high-solid biomass loading was converted to ethanol in a high yield. This proposed methodology would boost the performance of the bioconversion of low-cost materials to other chemicals, and would not be limited to only ethanol but also would include other target chemicals.

Investigation of fatty acid accumulation in the engineered Saccharomyces cerevisiae under nitrogen limited culture condition

In this study, the Saccharomyces cerevisiae wild type strain and engineered strain with an overexpressed heterologous ATP-citrate lyase (acl) were cultured in medium with different carbon and nitrogen concentrations, and their fatty acid production levels were investigated. The results showed that when the S. cerevisiae engineered strain was cultivated under nitrogen limited culture condition, the yield of mono-unsaturated fatty acids showed higher than that under non-nitrogen limited condition; with the carbon concentration increased, the accumulation become more apparent, whereas in the wild type strain, no such correlation was found. Besides, the citrate level in the S. cerevisiae under nitrogen limited condition was found to be much higher than that under non-nitrogen limited condition, which indicated a relationship between the diminution of nitrogen and accumulation of citrate in the S. cerevisiae. The accumulated citrate could be further cleaved by acl to provide substrate for fatty acid synthesis.

Bio-ethanol Production from Green Onion by Yeast in Repeated Batch

Considered to be the cleanest liquid fuel, bio-ethanol can be a reliable alternative to fossil fuels. It is produced by fermentation of sugar components of plant materials. The common onions are considered to be a favorable source of fermentation products as they have high sugar contents as well as contain various nutrients. This study focused on the effective production of ethanol from Green onion (Allium fistulosum L.) by the yeast "Saccharomyces cerevisiae" in repeated batch. The results showed that the total sugar concentration of onion juice was 68.4 g/l. The maximum rate of productivity, ethanol yield and final bio-ethanol percentage was 7 g/l/h (g ethanol per liter of onion juice per hour), 35 g/l (g ethanol per liter of onion juice) and 90 %, respectively.

Harnessing genetic diversity in Saccharomyces cerevisiae for fermentation of xylose in hydrolysates of alkaline hydrogen peroxide-pretreated biomass

The fermentation of lignocellulose-derived sugars, particularly xylose, into ethanol by the yeast Saccharomyces cerevisiae is known to be inhibited by compounds produced during feedstock pretreatment. We devised a strategy that combined chemical profiling of pretreated feedstocks, high-throughput phenotyping of genetically diverse S. cerevisiae strains isolated from a range of ecological niches, and directed engineering and evolution against identified inhibitors to produce strains with improved fermentation properties. We identified and quantified for the first time the major inhibitory compounds in alkaline hydrogen peroxide (AHP)-pretreated lignocellulosic hydrolysates, including Na(+), acetate, and p-coumaric (pCA) and ferulic (FA) acids. By phenotyping these yeast strains for their abilities to grow in the presence of these AHP inhibitors, one heterozygous diploid strain tolerant to all four inhibitors was selected, engineered for xylose metabolism, and then allowed to evolve on xylose with increasing amounts of pCA and FA. After only 149 generations, one evolved isolate, GLBRCY87, exhibited faster xylose uptake rates in both laboratory media and AHP switchgrass hydrolysate than its ancestral GLBRCY73 strain and completely converted 115 g/liter of total sugars in undetoxified AHP hydrolysate into more than 40 g/liter ethanol. Strikingly, genome sequencing revealed that during the evolution from GLBRCY73, the GLBRCY87 strain acquired the conversion of heterozygous to homozygous alleles in chromosome VII and amplification of chromosome XIV. Our approach highlights that simultaneous selection on xylose and pCA or FA with a wild S. cerevisiae strain containing inherent tolerance to AHP pretreatment inhibitors has potential for rapid evolution of robust properties in lignocellulosic biofuel production.

Ethanol fermentation by xylose-assimilating Saccharomyces cerevisiae using sugars in a rice straw liquid hydrolysate concentrated by nanofiltration

Concentrating sugars using membrane separation, followed by ethanol fermentation by recombinant xylose-assimilating Saccharomyces cerevisiae, is an attractive technology. Three nanofiltration membranes (NTR-729HF, NTR-7250, and ESNA3) were effective in concentrating glucose, fructose, and sucrose from dilute molasses solution and no permeation of sucrose. The separation factors of acetate, formate, furfural, and 5-hydroxymethyl furfural, which were produced by dilute acid pretreatment of rice straw, over glucose after passage through these three membranes were 3.37-11.22, 4.71-20.27, 4.32-16.45, and 4.05-16.84, respectively, at pH 5.0, an applied pressure of 1.5 or 2.0 MPa, and 25 °C. The separation factors of these fermentation inhibitors over xylose were infinite, as there was no permeation of xylose. Ethanol production from approximately two-times concentrated liquid hydrolysate using recombinant S. cerevisiae was double (5.34-6.44 g L(-1)) that compared with fermentation of liquid hydrolysate before membrane separation (2.75 g L(-1)).

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

Complex chemical stress arises during the production of biofuels. Large-scale mutant fitness profiling was used to identify bacterial and yeast tolerance genes and to model fitness in a complex hydrolysate mixture. The resulting model can be used to engineer more tolerant strains.

Genome-wide fitness profiling was used to identify plant hydrolysate tolerance genes in Zymomonas mobilis and Saccharomyces cerevisiae.

We modeled fitness in hydrolysate as a mixture of fitness in its components.

Outliers in our model led to the identification of a previously unknown component of hydrolysate.

Overexpression of a Z. mobilis tolerance gene of unknown function improved ethanol productivity in plant hydrolysate.

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.

Metabolic engineering of industrial platform microorganisms for biorefinery applications--optimization of substrate spectrum and process robustness by rational and evolutive strategies

Bio-based production promises a sustainable route to myriads of chemicals, materials and fuels. With regard to eco-efficiency, its future success strongly depends on a next level of bio-processes using raw materials beyond glucose. Such renewables, i.e., polymers, complex substrate mixtures and diluted waste streams, often cannot be metabolized naturally by the producing organisms. This particularly holds for well-known microorganisms from the traditional sugar-based biotechnology, including Escherichia coli, Corynebacterium glutamicum and Saccharomyces cerevisiae which have been engineered successfully to produce a broad range of products from glucose. In order to make full use of their production potential within the bio-refinery value chain, they have to be adapted to various feed-stocks of interest. This review focuses on the strategies to be applied for this purpose which combine rational and evolutive approaches. Hereby, the three industrial platform microorganisms, E. coli, C. glutamicum and S. cerevisiae are highlighted due to their particular importance.

Kinetics of ethanol production from sugarcane bagasse enzymatic hydrolysate concentrated with molasses under cell recycle

In this work, a kinetic model for ethanol fermentation from sugarcane bagasse enzymatic hydrolysate concentrated with molasses was developed. A model previously developed for fermentation of pure molasses was modified by the inclusion of a new term for acetic acid inhibition on microorganism growth rate and the kinetic parameters were estimated as functions of temperature. The influence of the hydrolysate on the kinetic parameters is analyzed by comparing with the parameters from fermentation of pure molasses. The impact of cells recycling in the kinetic parameters is also evaluated, as well as on the ethanol yield and productivity. The model developed described accurately most of the fermentations performed in several successive batches for temperatures from 30 to 38°C.