Bioethanol production by recycled Scheffersomyces stipitis in sequential batch fermentations with high cell density using xylose and glucose mixture

Advancing cellulose utilization and engineering consolidated bioprocessing yeasts: current state and perspectives

Despite the lack of implementation of consolidated bioprocessing (CBP) at an industrial scale, this bioconversion strategy still holds significant potential as an economically viable solution for converting lignocellulosic biomass (LCB) into biofuels and green chemicals, provided an appropriate organism can be isolated or engineered. The use of Saccharomyces cerevisiae for this purpose requires, among other things, the development of a cellulase expression system within the yeast. Over the past three decades, numerous studies have reported the expression of cellulase-encoding genes, both individually and in combination, in S. cerevisiae. Various strategies have emerged to produce a core set of cellulases, with differing degrees of success. While one-step conversion of cellulosic substrates to ethanol has been reported, the resulting titers and productivities fall well below industrial requirements. In this review, we examine the strategies employed for cellulase expression in yeast, highlighting the successes in developing basic cellulolytic CBP-enabled yeasts. We also summarize recent advancements in rational strain design and engineering, exploring how these approaches can be further enhanced through modern synthetic biology tools to optimize CBP-enabled yeast strains for potential industrial applications. KEY POINTS: • S. cerevisiae's lack of cellulolytic ability warrants its engineering for industry. • Advancements in the expression of core sets of cellulases have been reported. • Rational engineering is needed to enhance cellulase secretion and strain robustness. • Insights gained from omics strategies will direct the future development of CBP strains.

Hydroxycinnamic Acid Extraction from Multiple Lignocellulosic Sources: Correlations with Substrate Composition and Taxonomy for Flavoring and Antioxidant Applications

The extraction of hydroxycinnamic acids (HCADs) is a strategy for lignocellulosic biomass valorization due to their high value-added nature and the possibility of application as flavoring and antioxidants. This study proposes correlations between the composition and taxonomy of 28 globally available agro-industrial feedstocks with the production of HCADs using chemometric tools. Principal component analysis indicated strong correlations between ferulic acid release and hemicellulose type and content, especially in grass biomasses. Conversely, p-coumaric acid release was mainly correlated with cellulose content across diverse taxonomic origins. Among the evaluated agro-industrial feedstocks, corn-based biomasses were identified as prime sources of ferulic acid after mild alkaline treatment, releasing up to 10.5 g kg-1 and producing hydrolysates with an antioxidant capacity up to 3.3 mmol Trolox equivalents g-1. Notably, sugar cane bagasse was the best source of p-coumaric acid, yielding 4.8 g kg-1. Corn hydrolysates were successfully converted into 4-vinylguaiacol using a genetically modified Saccharomyces cerevisiae strain, achieving high yields of 0.75 g L-1. This work enhances our understanding of HCAD sources and biomass valorization strategies, demonstrating potential applications in the food and cosmetics sectors.

First- and second-generation integrated process for bioethanol production: Fermentation of molasses diluted with hemicellulose hydrolysate by recombinant Saccharomyces cerevisiae

The integration of first- (1G) and second-generation (2G) ethanol production by adding sugarcane juice or molasses to lignocellulosic hydrolysates offers the possibility to overcome the problem of inhibitors (acetic acid, furfural, hydroxymethylfurfural and phenolic compounds), and add nutrients (such as salts, sugars and nitrogen sources) to the fermentation medium, allowing the production of higher ethanol titers. In this work, an 1G2G production process was developed with hemicellulosic hydrolysate (HH) from a diluted sulfuric acid pretreatment of sugarcane bagasse and sugarcane molasses. The industrial Saccharomyces cerevisiae CAT-1 was genetically modified for xylose consumption and used for co-fermentation of sucrose, fructose, glucose, and xylose. The fed-batch fermentation with high cell density that mimics an industrial fermentation was performed at bench scale fermenter, achieved high volumetric ethanol productivity of 1.59 g L-1 h-1, 0.39 g g-1 of ethanol yield, and 44.5 g L-1 ethanol titer, and shown that the yeast was able to consume all the sugars present in must simultaneously. With the results, it was possible to establish a mass balance for the global process: from pretreatment to the co-fermentation of molasses and HH, and it was possible to establish an effective integrated process (1G2G) with sugarcane molasses and HH co-fermentation employing a recombinant yeast.

Sugar Beet Pulp as a Biorefinery Substrate for Designing Feed

An example of the implementation of the principles of the circular economy is the use of sugar beet pulp as animal feed. Here, we investigate the possible use of yeast strains to enrich waste biomass in single-cell protein (SCP). The strains were evaluated for yeast growth (pour plate method), protein increment (Kjeldahl method), assimilation of free amino nitrogen (FAN), and reduction of crude fiber content. All the tested strains were able to grow on hydrolyzed sugar beet pulp-based medium. The greatest increases in protein content were observed for Candida utilis LOCK0021 and Saccharomyces cerevisiae Ethanol Red (ΔN = 2.33%) on fresh sugar beet pulp, and for Scheffersomyces stipitis NCYC1541 (ΔN = 3.04%) on dried sugar beet pulp. All the strains assimilated FAN from the culture medium. The largest reductions in the crude fiber content of the biomass were recorded for Saccharomyces cerevisiae Ethanol Red (Δ = 10.89%) on fresh sugar beet pulp and Candida utilis LOCK0021 (Δ = 15.05%) on dried sugar beet pulp. The results show that sugar beet pulp provides an excellent matrix for SCP and feed production.

Metabolomic profiling of Spathaspora passalidarum fermentations reveals mechanisms that overcome hemicellulose hydrolysate inhibitors

Understanding the mechanisms involved in tolerance to inhibitors is the first step in developing robust yeasts for industrial second-generation ethanol (E2G) production. Here, we used ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) and MetaboAnalyst 4.0 for analysis of MS data to examine the changes in the metabolic profile of the yeast Spathaspora passalidarum during early fermentation of hemicellulosic hydrolysates containing high or low levels of inhibitors (referred to as control hydrolysate or CH and strategy hydrolysate or SH, respectively). During fermentation of SH, the maximum ethanol production was 16 g L^-1 with a yield of 0.28 g g^-1 and productivity of 0.22 g L^-1 h^-1, whereas maximum ethanol production in CH fermentation was 1.74 g L^-1 with a yield of 0.11 g g^-1 and productivity of 0.01 g L^-1 h^-1. The high level of inhibitors in CH induced complex physiological and biochemical responses related to stress tolerance in S. passalidarum. This yeast converted compounds with aldehyde groups (hydroxymethylfurfural, furfural, 4-hydroxybenzaldehyde, syringaldehyde, and vanillin) into less toxic compounds, and inhibitors were found to reduce cell viability and ethanol production. Intracellularly, high levels of inhibitors altered the energy homeostasis and redox balance, resulting in lower levels of ATP and NADPH, while that of glycolytic, pentose phosphate, and tricarboxylic acid (TCA) cycle pathways were the most affected, being the catabolism of glucogenic amino acids, the main cellular response to inhibitor-induced stress. This metabolomic investigation reveals interesting targets for metabolic engineering of ethanologenic yeast strains tolerant against multiple inhibitors for E2G production. KEY POINTS: • Inhibitors in the hydrolysates affected the yeast's redox balance and energy status. • Inhibitors altered the glycolytic, pentose phosphate, TCA cycle and amino acid pathways. • S. passalidarum converted aldehyde groups into less toxic compounds.

Comparison of Spathaspora passalidarum and recombinant Saccharomyces cerevisiae for integration of first- and second-generation ethanol production

First-generation ethanol (E1G) is based on the fermentation of sugars released from saccharine or starch sources, while second-generation ethanol (E2G) is focused on the fermentation of sugars released from lignocellulosic feedstocks. During the fractionation process to release sugars from hemicelluloses (mainly xylose), some inhibitor compounds are released hindering fermentation. Thus, the biggest challenge of using hemicellulosic hydrolysate is selecting strains and processes able to efficiently ferment xylose and tolerate inhibitors. With the aim of diluting inhibitors, sugarcane molasses (80% of sucrose content) can be mixed to hemicellulosic hydrolysate in an integrated E1G-E2G process. Cofermentations of xylose and sucrose were evaluated for the native xylose consumer Spathaspora passalidarum and a recombinant Saccharomyces cerevisiae strain. The industrial S. cerevisiae strain CAT-1 was modified to overexpress the XYL1, XYL2 and XKS1 genes and a mutant ([4-59Δ]HXT1) version of the low-affinity HXT1 permease, generating strain MP-C5H1. Although S. passalidarum showed better results for xylose fermentation, this yeast showed intracellular sucrose hydrolysis and low sucrose consumption in microaerobic conditions. Recombinant S. cerevisiae showed the best performance for cofermentation, and a batch strategy at high cell density in bioreactor achieved unprecedented results of ethanol yield, titer and volumetric productivity in E1G-E2G production process.

Secretome analysis as a tool to elucidate bacterial contamination influence during second-generation ethanol production in a Melle-Boinot process

Melle-boinot fermentation process can be used to increase the ethanol productivity in second-generation ethanol process (2G). However, bacterial contamination can result in decreased ethanol production and sugars consumption. The available literature on microbial contamination in the 2G at the secretome level, microbial interactions and their impacts on ethanol production are scarce. In this context, the cultivation of Spathaspora passalidarum was studied in pure and co-culture with Lactobacillus fermentum under conditions that mimic the Melle-boinot process. Glucose consumption and ethanol production by S. passalidarum were not affected by bacterial contamination. Xylose consumption was higher in pure culture (11.54 ± 2.62, 16.23 ± 1.76 and 6.50 ± 1.68 g) than in co-culture fermentation (11.89 ± 0.38, 7.29 ± 0.49 and 5.54 ± 2.63 g) in cycle 2. The protein profile of the fermented broth was similar in pure and co-culture fermentation. The low effect of L. fermentum on fermentation and protein profile may be associated with the inhibition of the bacteria by the low nutrient fermentation broth, with centrifugation and/or with sulfuric acid washing. Thereby, considering that research on microbial contamination in the 2G fermentation process is very limited, particularly at the omics level, these findings may contribute to the lignocellulosic biomass fermentation industry.

Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts

Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using ¹³C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.

The dairy biorefinery: Integrating treatment processes for cheese whey valorisation

With an estimated worldwide production of 190 billion kg per year, and due to its high organic load, cheese whey represents a huge opportunity for bioenergy and biochemicals production. Several physical, chemical and biological processes have been proposed to valorise cheese whey by producing biofuels (methane, hydrogen, and ethanol), electric energy, and/or chemical commodities (carboxylic acids, proteins, and biopolymers). A biorefinery concept, in which several value-added products are obtained from cheese whey through a cascade of biotechnological processes, is an opportunity for increasing the product spectrum of dairy industries while allowing for sustainable management of the residual streams and reducing disposal costs for the final residues. This review critically analyses the different treatment options available for energy and materials recovery from cheese whey, their combinations and perspectives for implementation. Thus, instead of focusing on a specific valorisation platform, in the present review the most relevant aspects of each strategy are analysed to support the integration of different routes, in order to identify the most appropriate treatment train.

Designing a cocktail containing redox enzymes to improve hemicellulosic hydrolysate fermentability by microorganisms

Bioproducts production using monomeric sugars derived from lignocellulosic biomass presents several challenges, such as to require a physicochemical pretreatment to improve its conversion yields. Hydrothermal lignocellulose pretreatment has several advantages and results in solid and liquid streams. The former is called hemicellulosic hydrolysate (HH), which contains inhibitory phenolic compounds and sugar degradation products that hinder microbial fermentation products from pentose sugars. Here, we developed and applied a novel enzyme process to detoxify HH. Initially, the design of experiments with different redox activities enzymes was carried out. The enzyme mixture containing the peroxidase (from Armoracia rusticana) together with superoxide dismutase (from Coptotermes gestroi) are the most effective to detoxify HH derived from sugarcane bagasse. Butanol fermentation by the bacteria Clostridium saccharoperbutylacetonicum and ethanol production by the yeast Scheffersomyces stipitis increased by 24.0× and 2.4×, respectively, relative to the untreated hemicellulosic hydrolysates. Detoxified HH was analyzed by chromatographic and spectrometric methods elucidating the mechanisms of phenolic compound modifications by enzymatic treatment. The enzyme mixture degraded and reduced the hydroxyphenyl- and feruloyl-derived units and polymerized the lignin fragments. This strategy uses biocatalysts under environmentally friendly conditions and could be applied in the fuel, food, and chemical industries.

Boosting Ethanol Productivity of Zymomonas mobilis 8b in Enzymatic Hydrolysate of Dilute Acid and Ammonia Pretreated Corn Stover Through Medium Optimization, High Cell Density Fermentation and Cell Recycling

The presence of toxic degradation products in lignocellulosic hydrolysate typically reduced fermentation rates and xylose consumption rate, resulting in a decreased ethanol productivity. In the present study, Zymomonas mobilis 8b was investigated for high cell density fermentation with cell recycling to improve the ethanol productivity in lignocellulosic hydrolysate. The fermentation performances of Z. mobilis 8b at various conditions were first studied in yeast extract-tryptone medium. It was found that nutrient level was essential for glucose and xylose co-fermentation by Z. mobilis 8b and high cell density fermentation with cell recycling worked well in yeast extract-tryptone medium for 6 rounds fermentation. Z. mobilis 8b was then studied in enzymatic hydrolysates derived from dilute acid (DA) pretreated corn stover (CS) and ammonia pretreated CS for high cell density fermentation with cell recycling. Ethanol productivity obtained was around three times higher compared to traditional fermentation. Ethanol titer and metabolic yield were also enhanced with high cell density fermentation. Z. mobilis 8b cells showed high recyclability in ammonia pretreated CS hydrolysate.

Sugarcane must fed-batch fermentation by Saccharomyces cerevisiae: impact of sterilized and non-sterilized sugarcane must

The presence of microbial contaminants is common in the sugarcane ethanol industry and can decrease process yield, reduce yeast cell viability and induce yeast cell flocculation. To evaluate the effect of microbial contamination on the fermentation process, we compared the use of sterilized and non-sterilized sugarcane must in the performance of Saccharomyces cerevisiae with similar fermentation conditions to those used in Brazilian mills. Non-sterilized sugarcane must had values of 10³ and 10⁸ CFU mL^-1 of wild yeast and bacterial contamination, respectively; decreased total reducing sugar (TRS); and increased lactic and acetic acids, glycerol and ethanol concentrations during storage. During fermentation cycles with sterilized and non-sterilized sugarcane must, S. cerevisiae viability did not change, whereas ethanol yield varied from 74.1 to 80.2%, but it did not seem to be related to must microbial contamination. Ethanol productivity decreased throughout the fermentation cycles and was more pronounced in the last two fermentation cycles with non-sterilized must, but that may be related to the decrease in must TRS. High values of the ratio of total acid production per ethanol were reported at the end of the last two fermentation cycles conducted with non-sterilized must. Additionally, the values of wild yeast contamination increased from 10² to 10³ CFU mL^-1 and bacterial contamination increased from 10⁴ to 10⁶ CFU mL^-1 when comparing the first and last fermentation cycles with non-sterilized must. In addition to the increase in microbial contamination and acid concentration, ethanol yield and yeast viability rates were not directly affected by the microbial contamination present in the non-sterilized sugarcane must.

Scheffersomyces stambukii f.a., sp. nov., a d-xylose-fermenting species isolated from rotting wood

Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade. The novel species, Scheffersomyces stambukii f.a., sp. nov., is proposed to accommodate these isolates. The type strain of Scheffersomyces stambukii sp. nov. is UFMG-CM-Y427^T (=CBS 14217^T). The MycoBank number is MB 824093. In addition, we studied the xylose metabolism of this new species.

The Coptotermes gestroi aldo-keto reductase: a multipurpose enzyme for biorefinery applications

BACKGROUND

In nature, termites can be considered as a model biological system for biofuel research based on their remarkable efficiency for lignocellulosic biomass conversion. Redox enzymes are of interest in second-generation ethanol production because they promote synergic enzymatic activity with classical hydrolases for lignocellulose saccharification and inactivate fermentation inhibitory compounds produced after lignocellulose pretreatment steps.

RESULTS

In the present study, the biochemical and structural characteristics of the Coptotermes gestroi aldo-keto reductase (CgAKR-1) were comprehensively investigated. CgAKR-1 displayed major structural differences compared with others AKRs, including the differences in the amino acid composition of the substrate-binding site, providing basis for classification as a founding member of a new AKR subfamily (family AKR1 I). Immunolocalization assays with anti-CgAKR-1 antibodies resulted in strong fluorescence in the salivary gland, proventriculus, and foregut. CgAKR-1 supplementation caused a 32% reduction in phenolic aldehydes, such as furfural, which act as fermentation inhibitors of hemicellulosic hydrolysates, and improved ethanol fermentation by the xylose-fermenting yeast Scheffersomyces stipitis by 45%. We observed synergistic enzymatic interactions between CgAKR-1 and commercial cellulosic cocktail for sugarcane bagasse saccharification, with a maximum synergism degree of 2.17 for sugar release. Our data indicated that additive enzymatic activity could be mediated by reactive oxygen species because CgAKR-1 could produce hydrogen peroxide.

CONCLUSION

In summary, we identified the founding member of an AKRI subfamily with a potential role in the termite digestome. CgAKR-1 was found to be a multipurpose enzyme with potential biotechnological applications. The present work provided a basis for the development and application of integrative and multipurpose enzymes in the bioethanol production chain.

Enhanced fuel ethanol production from rice straw hydrolysate by an inhibitor-tolerant mutant strain of Scheffersomyces stipitis

A novel process for bioethanol production from lignocellulosic biomass using an inhibitor-tolerant mutant strain of Scheffersomyces stipitis and cell-recycling continuous fermentation.