Improvement of Brazilian bioethanol production – Challenges and perspectives on the identification and genetic modification of new strains of Saccharomyces cerevisiae yeasts isolated during ethanol process

Enhancing the Antibiotic Production by Thermophilic Bacteria Isolated from Hot Spring Waters via Ethyl Methanesulfonate Mutagenesis

Antibiotic-resistant bacteria represent a serious public health threat. For that reason, the development of new and effective antibiotics to control pathogens has become necessary. The current study aims to search for new microorganisms expressing antibiotic production capacity. Fifteen sites covering a wide range of harsh environmental conditions in Egypt were investigated. Two hundred and eighty bacterial isolates were obtained and then tested against pathogenic bacteria using the agar disk diffusion technique. Fifty-two (18.6% of the total) of the isolates exhibited antagonistic properties, which affected one or more of the tested pathogens. The isolate 113 was identified as Bacillus licheniformis and isolate 10 was identified as Brevibacillus borstelensis using the 16S rRNA technique. The B. licheniformis strain was stronger in antibiotic production against S. typhi, M. luteus, and P. ariginosa, whereas the strain Br. borstelensis was more efficient against B. cereus, E. coli, and Klebs. sp. The sensitivity of the strains to commercial antibiotics showed that B. licheniformis was highly sensitive to seven commercial antibiotics, whereas Br. borstelensis was sensitive to nine antibiotics. The two strains were subjected to ethyl methanesulfonate (EMS) mutagenesis to obtain mutants with a higher antibiotic production. The total bacterial count was measured after treatment with EMS mutagen and showed a significant gradual increase in the antimicrobial activity, which was achieved via shaking in the presence of EMS for 60 min. High antimicrobial activities were noted with 17 and 14 mutants from the B. licheniformis and Br. borstelensis strains, respectively. The mutant B. licheniformis (M15/Amo) was more active than the parent strain against S. aureus (212.5%), while the mutant Br. borstelensis (B7/Neo) was more effective against S. typhi (83.3%). The present study demonstrates the possibility of obtaining potent antibiotic-producing bacteria in hot spring waters and further improving the indigenous bacterial capacity to produce antibiotics by using EMS mutagenesis.

Isolation and characterization of bioethanol producing wild yeasts from bio-wastes and co-products of sugar factories

Purpose

Yeasts are widely used for the production of bioethanol from biomasses rich in sugar. The present study was aimed at isolating, screening, and characterizing fermentative wild yeast recovered from bio-waste and co-products of Ethiopian sugar factories for bioethanol production using sugarcane molasses as a substrate.

Method

The wild yeasts were identified according to their cellular morphology and D1/D2 and ITS1-5.8S-ITS2 rDNA sequencing. Analysis of ethanol and by-product concentration was done by HPLC equipped with a UV detector. Higher alcohols, acetaldehyde, and methanol were analyzed using GC-MS equipped with a flame ionization detector (FID).

Result

Seven strains (Meyerozyma caribbica MJTm3, Meyerozyma caribbica MJTPm4, Meyerozyma caribbica SHJF, Saccharomyces cerevisiae TA2, Wickerhamomyces anomalus MJTPm2, Wickerhamomyces anomalus 4m10, and Wickerhamomyces anomalus HCJ2F) were found tolerant to 18% (v/v) ethanol, whereas one strain Meyerozyma caribbica MJTm3 tolerated 20%. These strains also showed tolerance to 45°C, 50% of sugar, and pH 2–10. Meyerozyma caribbica MJTm3 produced 12.7% (v/v) of alcohol with an actual ethanol concentration of 26 g L−1, an ethanol yield of 47%, 78% of theoretical yield, and a productivity of 0.54 g L−1 h−1 from 30 °Brix of molasses at 48 h incubation under laboratory scale. Based on the one variable at a time optimization (OVAT), the optimal parameters for maximum bioethanol production were at initial pH 5.5, 35 °Brix, 30°C, 15% inoculum size, 150 rpm, 4 g L−1 di-ammonium phosphate supplement, and 48 h incubation. Under these optimum conditions, 14% (v/v) alcohol, 42 g L−1 actual ethanol concentration, 69% ethanol yield, 89% of theoretical yield, and productivity of 0.88 g L−1 h−1 were obtained.

Conclusion

These results indicated that M. caribbica MJTm3 should further be evaluated, optimized, and improved for industrial bioethanol production due to its fermentation potential.

Integrated biorefinery approaches for the industrialization of cellulosic ethanol fuel

Lignocellulosic biomass is an abundant and sustainable raw material, but its conversion into ethanol fuel has not yet achieved large-scale industrialization and economic benefits. Integrated biorefineries have been widely identified as the key to achieving this goal. Here, four promising routes were summarized to assemble the new industrial plants for cellulose-based fuels and chemicals, including 1) integration of cellulase production systems into current cellulosic ethanol processes; 2) combination of processes and facilities between cellulosic ethanol and first-generation ethanol; 3) application of enzyme-free saccharification processes and computational approaches to increase the bioethanol yield and optimize the integration process; 4) production of multiple products to maximize the value derived from the lignocellulosic biomass. Finally, the remaining challenges and perspectives of this field are also discussed.

Production of Bioethanol—A Review of Factors Affecting Ethanol Yield

Fossil fuels are a major contributor to climate change, and as the demand for energy production increases, alternative sources (e.g., renewables) are becoming more attractive. Biofuels such as bioethanol reduce reliance on fossil fuels and can be compatible with the existing fleet of internal combustion engines. Incorporation of biofuels can reduce internal combustion engine (ICE) fleet carbon dioxide emissions. Bioethanol is typically produced via microbial fermentation of fermentable sugars, such as glucose, to ethanol. Traditional feedstocks (e.g., first-generation feedstock) include cereal grains, sugar cane, and sugar beets. However, due to concerns regarding food sustainability, lignocellulosic (second-generation) and algal biomass (third-generation) feedstocks have been investigated. Ethanol yield from fermentation is dependent on a multitude of factors. This review compares bioethanol production from a range of feedstocks, and elaborates on available technologies, including fermentation practices. The importance of maintaining nutrient homeostasis of yeast is also examined. The purpose of this review is to provide industrial producers and policy makers insight into available technologies, yields of bioethanol achieved by current manufacturing practices, and goals for future innovation.

Biomass Waste as Sustainable Raw Material for Energy and Fuels

Sustainable development is the common goal of the current concepts of bioeconomy and circular economy. In this sense, the biorefineries platforms are a strategic factor to increase the bioeconomy in the economic balance. The incorporation of renewable sources to produce fuels, chemicals, and energy, includes sustainability, reduction of greenhouse gases (GHG), and creating more manufacturing jobs fostering the advancement of regional and social systems by implementing the comprehensive use of available biomass, due to its low costs and high availability. This paper describes the emerging biorefinery strategies to produce fuels (bio-ethanol and γ-valerolactone) and energy (pellets and steam), compared with the currently established biorefineries designed for fuels, pellets, and steam. The focus is on the state of the art of biofuels and energy production and environmental factors, as well as a discussion about the main conversion technologies, production strategies, and barriers. Through the implementation of biorefineries platforms and the evaluation of low environmental impact technologies and processes, new sustainable production strategies for biofuels and energy can be established, making these biobased industries into more competitive alternatives, and improving the economy of the current value chains.

Yeast Cellular Stress: Impacts on Bioethanol Production

Bioethanol is the largest biotechnology product and the most dominant biofuel globally. Saccharomyces cerevisiae is the most favored microorganism employed for its industrial production. However, obtaining maximum yields from an ethanol fermentation remains a technical challenge, since cellular stresses detrimentally impact on the efficiency of yeast cell growth and metabolism. Ethanol fermentation stresses potentially include osmotic, chaotropic, oxidative, and heat stress, as well as shifts in pH. Well-developed stress responses and tolerance mechanisms make S. cerevisiae industrious, with bioprocessing techniques also being deployed at industrial scale for the optimization of fermentation parameters and the effective management of inhibition issues. Overlap exists between yeast responses to different forms of stress. This review outlines yeast fermentation stresses and known mechanisms conferring stress tolerance, with their further elucidation and improvement possessing the potential to improve fermentation efficiency.

Physiological characterization of a new thermotolerant yeast strain isolated during Brazilian ethanol production, and its application in high-temperature fermentation

BACKGROUND

The use of thermotolerant yeast strains can improve the efficiency of ethanol fermentation, allowing fermentation to occur at temperatures higher than 40 °C. This characteristic could benefit traditional bio-ethanol production and allow simultaneous saccharification and fermentation (SSF) of starch or lignocellulosic biomass.

RESULTS

We identified and characterized the physiology of a new thermotolerant strain (LBGA-01) able to ferment at 40 °C, which is more resistant to stressors as sucrose, furfural and ethanol than CAT-1 industrial strain. Furthermore, this strain showed similar CAT-1 resistance to acetic acid and lactic acid, and it was also able to change the pattern of genes involved in sucrose assimilation (SUC2 and AGT1). Genes related to the production of proteins involved in secondary products of fermentation were also differentially regulated at 40 °C, with reduced expression of genes involved in the formation of glycerol (GPD2), acetate (ALD6 and ALD4), and acetyl-coenzyme A synthetase 2 (ACS2). Fermentation tests using chemostats showed that LBGA-01 had an excellent performance in ethanol production in high temperature.

CONCLUSION

The thermotolerant LBGA-01 strain modulates the production of key genes, changing metabolic pathways during high-temperature fermentation, and increasing its resistance to high concentration of ethanol, sugar, lactic acid, acetic acid, and furfural. Results indicate that this strain can be used to improve first- and second-generation ethanol production in Brazil.

Destressing Yeast for Higher Biofuel Yields: Can Excess Chaotropicity Be Mitigated?

Biofuels have the capacity to contribute to carbon dioxide emission reduction and to energy security as oil reserves diminish and/or become concentrated in politically unstable regions. However, challenges exist in obtaining the maximum yield from industrial fermentations. One challenge arises from the nature of alcohols. These compounds are chaotropic (i.e. causes disorder in the system) which causes stress in the microbes producing the biofuel. Brewer's yeast (Saccharomyces cerevisiae) typically cannot grow at ethanol concentration much above 17% (v/v). Mitigation of these properties has the potential to increase yield. Previously, we have explored the effects of chaotropes on model enzyme systems and attempted (largely unsuccessfully) to offset these effects by kosmotropes (compounds which increase the order of the system, i.e. the "opposite" of chaotropes). Here we present some theoretical results which suggest that high molecular mass polyethylene glycols may be the most effective kosmotropic additives in terms of both efficacy and cost. The assumptions and limitations of these calculations are also presented. A deeper understanding of the effects of chaotropes on biofuel-producing microbes is likely to inform improvements in bioethanol yields and enable more rational approaches to the "neutralisation" of chaotropicity.

Functional Biodiversity of Yeasts Isolated from Colombian Fermented and Dry Cocoa Beans

Yeasts play an important role in the cocoa fermentation process. Although the most relevant function is the degradation of sugars and the production of ethanol, there is little understanding of the enzyme activities and attributes that allow them to survive even after drying. The present study explored the functional biodiversity of yeasts associated with Criollo Colombian cocoa fermented beans, able to survive after drying. Twelve species belonging to 10 genera of osmo-, acid-, thermo-, and desiccation-tolerant yeasts were isolated and identified from fermented and dry cocoa beans, with Pichia kudriavzevii and Saccharomyces cerevisiae standing out as the most frequent. For the first time, we reported the presence of Zygosaccharomyces bisporus in cocoa fermented beans. It was found that resistance to desiccation is related to the different degradation capacities of fermentation substrates, which suggests that associative relationships may exist between the different yeast species and their degradation products. Besides, the increased thermotolerance of some species was related to the presence of polyphenols in the medium, which might play a fundamental role in shaping the microbial community composition.

The roles and applications of chaotropes and kosmotropes in industrial fermentation processes

Chaotropicity has long been recognised as a property of some compounds. Chaotropes tend to disrupt non-covalent interactions in biological macromolecules (e.g. proteins and nucleic acids) and supramolecular assemblies (e.g. phospholipid membranes). This results in the destabilisation and unfolding of these macromolecules and assemblies. Unsurprisingly, these compounds are typically harmful to living cells since they act against multiple targets, comprising cellular integrity and function. Kosmotropes are the opposite of chaotropes and these compounds promote the ordering and rigidification of biological macromolecules and assemblies. Since many biological macromolecules have optimum levels of flexibility, kosmotropes can also inhibit their activity and can be harmful to cells. Some products of industrial fermentations, most notably alcohols, are chaotropic. This property can be a limiting factor on rates of production and yields. It has been hypothesised that the addition of kosmotropes may mitigate the chaotropicity of some fermentation products. Some microbes naturally adapt to chaotropic environments by producing kosmotropic compatible solutes. Exploitation of this in industrial fermentations has been hampered by scientific and economic issues. The cost of the kosmotropes and their removal during purification needs to be considered. We lack a complete understanding of the chemistry of chaotropicity and a robust, quantitative framework for estimating overall chaotropicities of mixtures. This makes it difficult to predict the amount of kosmotrope required to neutralise the chaotropicity. This review considers examples of industrial fermentations where chaotropicity is an issue and suggests possible mitigations.

Neither 1G nor 2G fuel ethanol: setting the ground for a sugarcane-based biorefinery using an iSUCCELL yeast platform

First-generation (1G) fuel ethanol production in sugarcane-based biorefineries is an established economic enterprise in Brazil. Second-generation (2G) fuel ethanol from lignocellulosic materials, though extensively investigated, is currently facing severe difficulties to become economically viable. Some of the challenges inherent to these processes could be resolved by efficiently separating and partially hydrolysing the cellulosic fraction of the lignocellulosic materials into the disaccharide cellobiose. Here, we propose an alternative biorefinery, where the sucrose-rich stream from the 1G process is mixed with a cellobiose-rich stream in the fermentation step. The advantages of mixing are 3-fold: (i) decreased concentrations of metabolic inhibitors that are typically produced during pretreatment and hydrolysis of lignocellulosic materials; (ii) decreased cooling times after enzymatic hydrolysis prior to fermentation; and (iii) decreased availability of free glucose for contaminating microorganisms and undesired glucose repression effects. The iSUCCELL platform will be built upon the robust Saccharomyces cerevisiae strains currently present in 1G biorefineries, which offer competitive advantage in non-aseptic environments, and into which intracellular hydrolyses of sucrose and cellobiose will be engineered. It is expected that high yields of ethanol can be achieved in a process with cell recycling, lower contamination levels and decreased antibiotic use, when compared to current 2G technologies.

History of the International Symposium on Fungal Stress - ISFUS, a dream come true!

The International Symposium on Fungal Stress (ISFUS) was born in a dream that Drauzio Eduardo Naretto Rangel had in 2013. This article reviews the first three ISFUSs and prospects for the future meetings. Although ISFUS was born as a small family organized meeting, since the first meeting, ISFUS has achieved great success, receiving very important research grants from FAPESP, FAPEG, and CAPES to bring international scientists to Brazil. Moreover, three special issues in leading journals have been published with articles relating to the talks presented at each ISFUS. For the first meeting, most speakers published in a special issue in Current Genetics. From the second and third meeting, articles from the speakers were published in special issues of the top mycology journal, Fungal Biology, published by Elsevier on behalf of the British Mycological Society. Here we show that following the dreams with a full heart and adding lots of love, passion, and hard work can achieve success.

Enhanced ethanol production from sugarcane molasses by industrially engineered Saccharomyces cerevisiae via replacement of the PHO4 gene

Replacement of a novel candidate ethanol fermentation-associated regulatory gene, PHO4, from a fast-growing strain MC15, as determined through comparative genomics analysis among three yeast strains with significant differences in ethanol yield, is hypothesised to shorten the fermentation time and enhance ethanol production from sugarcane molasses. This study sought to test this hypothesis through a novel strategy involving the transfer of the PHO4 gene from a low ethanol-producing, yet fast-growing strain MC15 to a high ethanol-producing industrial strain MF01 through homologous recombination. The results indicated that PHO4 in the industrially engineered strain MF01-PHO4 displayed genomic stability with a mean maximum ethanol yield that rose to 114.71 g L⁻¹, accounting for a 5.30% increase in ethanol yield and 12.5% decrease in fermentation time in comparison with that in the original strain MF01, which was the current highest ethanol-producing strain in SCM fermentation in the reported literature. These results serve to advance our current understanding of the association between improving ethanol yield and replacement of PHO4, while providing a feasible strategy for industrially engineered yeast strains to improve ethanol production efficiently.

Replacement of a novel candidate ethanol fermentation-associated regulatory gene, PHO4, from a fast-growing strain through a novel strategy (SHPERM-bCGHR), is hypothesised to shorten fermentation time and enhance ethanol yield from sugarcane molasses.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.

Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica

Ionic liquids show promise for deconstruction of lignocellulosic biomass prior to fermentation. Yet, imidazolium ionic liquids (IILs) can be toxic to microbes even at concentrations present after recovery. Here, we show that dominant overexpression of an Ilt1p homolog (encoded by YlILT1/YALI0C04884) from the IIL-tolerant yeast Yarrowia lipolytica confers an improvement in 1-ethyl-3-methylimidazolium acetate tolerance in Saccharomyces cerevisiae compared to the endogenous Ilt1p (ScILT1/YDR090C). We subsequently enhance tolerance in S. cerevisiae through directed evolution of YlILT1 using growth-based selection, leading to identification of mutants that grow in up to 3.5% v/v ionic liquid. Lastly, we demonstrate that strains expressing YlILT1 variants demonstrate improved growth rate and ethanol production in the presence of residual IIL. This shows that dominant overexpression of a heterologous protein (wild type or evolved) from an IIL-tolerant yeast can increase tolerance in S. cerevisiae at concentrations relevant to bioethanol production from IIL-treated biomass.

Mitigating stress in industrial yeasts

The yeast, Saccharomyces cerevisiae, is the premier fungal cell factory exploited in industrial biotechnology. In particular, ethanol production by yeast fermentation represents the world's foremost biotechnological process, with beverage and fuel ethanol contributing significantly to many countries economic and energy sustainability. During industrial fermentation processes, yeast cells are subjected to several physical, chemical and biological stress factors that can detrimentally affect ethanol yields and overall production efficiency. These stresses include ethanol toxicity, osmostress, nutrient starvation, pH and temperature shock, as well as biotic stress due to contaminating microorganisms. Several cell physiological and genetic approaches to mitigate yeast stress during industrial fermentations can be undertaken, and such approaches will be discussed with reference to stress mitigation in yeasts employed in Brazilian bioethanol processes. This article will highlight the importance of furthering our understanding of key aspects of yeast stress physiology and the beneficial impact this can have more generally on enhancing industrial fungal bioprocesses.

Selected Aspects of Biofuels Market and the Electromobility Development in Poland: Current Trends and Forecasting Changes

This work presents basic information associated with markets of selected alternative fuels used in transport, such as methyl esters, conventional bioethanol and lignocellulosic bioethanol, and the market of electrical vehicles. Legal conditions, which stimulate development and regulate the mode of functioning of the liquid biofuel market until 2020 are discussed, based on provisions of EU directives. Data on biofuel production in Poland are presented, as well as biofuel consumption in the EU, the USA and Brazil in 2017. The most important conclusions of the proposal for a directive on the promotion of renewable energy sources in transport in EU member states in years 2021–2030 are discussed. The authors have also indicated the key legal and territorial conditions associated with the development of electromobility and present basic information on electric vehicles in Poland and Europe. The results of the research on the attractiveness of these sectors in 2018 are presented and compared with the results obtained in years 2007–2017. A score-based sector attractiveness method was used in the research.

A Case Study of Genomic Instability in an Industrial Strain of Saccharomyces cerevisiae

The Saccharomyces cerevisiae strain JAY270/PE2 is a highly efficient biocatalyst used in the production of bioethanol from sugarcane feedstock. This strain is heterothallic and diploid, and its genome is characterized by abundant structural and nucleotide polymorphisms between homologous chromosomes. One of the reasons it is favored by many distilleries is that its cells do not normally aggregate, a trait that facilitates cell recycling during batch-fed fermentations. However, long-term propagation makes the yeast population vulnerable to the effects of genomic instability, which may trigger the appearance of undesirable phenotypes such as cellular aggregation. In pure cultures of JAY270, we identified the recurrent appearance of mutants displaying a mother-daughter cell separation defect resulting in rough colonies in agar media and fast sedimentation in liquid culture. We investigated the genetic basis of the colony morphology phenotype and found that JAY270 is heterozygous for a frameshift mutation in the ACE2 gene (ACE2/ace2-A7), which encodes a transcriptional regulator of mother-daughter cell separation. All spontaneous rough colony JAY270-derived isolates analyzed carried copy-neutral loss-of-heterozygosity (LOH) at the region of chromosome XII where ACE2 is located (ace2-A7/ace2-A7). We specifically measured LOH rates at the ACE2 locus, and at three additional chromosomal regions in JAY270 and in a conventional homozygous diploid laboratory strain. This direct comparison showed that LOH rates at all sites were quite similar between the two strain backgrounds. In this case study of genomic instability in an industrial strain, we showed that the JAY270 genome is dynamic and that structural changes to its chromosomes can lead to new phenotypes. However, our analysis also indicated that the inherent level of genomic instability in this industrial strain is normal relative to a laboratory strain. Our work provides an important frame of reference to contextualize the interpretation of instability processes observed in the complex genomes of industrial yeast strains.

The second International Symposium on Fungal Stress: ISFUS

The topic of 'fungal stress' is central to many important disciplines, including medical mycology, chronobiology, plant and insect pathology, industrial microbiology, material sciences, and astrobiology. The International Symposium on Fungal Stress (ISFUS) brought together researchers, who study fungal stress in a variety of fields. The second ISFUS was held in May 8-11 2017 in Goiania, Goiás, Brazil and hosted by the Instituto de Patologia Tropical e Saúde Pública at the Universidade Federal de Goiás. It was supported by grants from CAPES and FAPEG. Twenty-seven speakers from 15 countries presented their research related to fungal stress biology. The Symposium was divided into seven topics: 1. Fungal biology in extreme environments; 2. Stress mechanisms and responses in fungi: molecular biology, biochemistry, biophysics, and cellular biology; 3. Fungal photobiology in the context of stress; 4. Role of stress in fungal pathogenesis; 5. Fungal stress and bioremediation; 6. Fungal stress in agriculture and forestry; and 7. Fungal stress in industrial applications. This article provides an overview of the science presented and discussed at ISFUS-2017.