Special Issue "Yeast Biotechnology"

A special issue of Fermentation (ISSN 2311-5637).

Deadline for manuscript submissions: closed (20 May 2016).

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Prof. Dr. Ronnie G. Willaert
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Guest Editor
Structural Biology Brussels Lab, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan , Brussels, Belgium
Interests: yeast biotechnology; cell immobilization; beer brewing biochemistry and fermentation; mini- and microbioreactors; Saccharomyces cerevisiae; Candida; yeast space biology (bioreactors for microgravity research); yeast adhesins; yeast systems biology; glycobiology; nanobiotechnology; Atomic Force Microscopy; protein crystallization; yeast protein structural biology
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Special Issue Information

Dear Colleagues,

Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels and biopharmaceuticals. Saccharomyces cerevisiae (bakers’ yeast) is the yeast species that is surely the most exploited by man. Saccharomyces is a top choice organism for industrial applications, although its use for producing beer dates back to at least the 6th millennium BC. Bakers’ yeast has been a cornerstone of modern biotechnology, enabling the development of efficient production processes for antibiotics, biopharmaceuticals, technical enzymes, and ethanol and biofuels. Today, diverse yeast species are explored for industrial applications, such as e.g. Saccharomyces species, Pichia pastoris and other Pichia species, Kluyveromyces marxianus, Hansenula polymorpha, Yarrowia lipolytica, Candida species, Phaffia rhodozyma, wild yeasts for beer brewing, etc.

This Special Issue is focused on recent developments of yeast biotechnology with topics including recent techniques for characterizing yeast and their physiology (including omics and nanobiotechnology techniques), methods to adapt industrial strains (including metabolic, synthetic and evolutionary engineering) and the use of yeasts as microbial cell factories to produce biopharmaceuticals, enzymes, alcohols, organic acids, flavours and fine chemicals, and advances in yeast fermentation technology and industrial fermentation processes.

Topics including but not limited to:

Yeast characterization and analysis
Brewing yeasts (including wild yeasts), wine yeasts, baker’s yeasts.
Evolution and variation of genomes of industrial yeasts.
Yeast systems biology: genomics, proteomics, fluxomics, metabolomics, omics integration.
Yeast nanobiotechnology (nanoanalysis techniques, construction of nanostructures, etc.).

Yeast strain engineering
Yeast metabolic engineering: production of biofuels, secondary metabolites, commodity chemicals, proteins, biopharmaceuticals, material precursors.
Yeast synthetic biology: yeasts as cell factories, tools for controlling enzyme expression levels, strategies for regulating spatial localization of enzymes in yeast, regulatory networks, biomolecular logic gates.
Strain improvement via evolutionary engineering.

Fermentation technology
Industrial bioreactors.
Mini- and microbioreactors: single-cell analysis, high-throughput screening, microfluidic bioreactors.
Process intensification: high-density fermentations, high-gravity fermentation.
Fermentative stress adaptation.

Industrial fermentation processes
Production of food (bread, etc.) and beverages (beer, wine, cider, etc.).
Production of baker’s yeast.
Production of biofuels (bioethanol, 1-butanol, biodiesel, jetfuels), commodity chemicals, pharmaceuticals, material precursors, secondary metabolites.

Prof. Dr. Ronnie G. Willaert
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • systems biology
  • genomics
  • proteomics
  • fluxomics
  • metabolomics
  • synthetic yeast biology
  • metabolic engineering
  • evolutionary engineering
  • industrial yeast products
  • beer
  • wine
  • bread
  • biofuels
  • commodity chemical
  • biopharmaceuticals
  • material precursors
  • yeast fermentation technology
  • industrial bioreactors
  • mini- and microbioreactors
  • high-density fermentations
  • yeast stress adaptation

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Published Papers (11 papers)

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Editorial

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Open AccessEditorial
Yeast Biotechnology
Fermentation 2017, 3(1), 6; https://doi.org/10.3390/fermentation3010006 - 26 Jan 2017
Cited by 1
Abstract
Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels, and biopharmaceuticals. Saccharomyces cerevisiae (brewers’ or bakers’ yeast) is the yeast species that [...] Read more.
Yeasts are truly fascinating microorganisms. Due to their diverse and dynamic activities, they have been used for the production of many interesting products, such as beer, wine, bread, biofuels, and biopharmaceuticals. Saccharomyces cerevisiae (brewers’ or bakers’ yeast) is the yeast species that is surely the most exploited by man.[...] Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available

Research

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Open AccessFeature PaperArticle
Gravity-Driven Adaptive Evolution of an Industrial Brewer’s Yeast Strain towards a Snowflake Phenotype in a 3D-Printed Mini Tower Fermentor
Fermentation 2017, 3(1), 4; https://doi.org/10.3390/fermentation3010004 - 05 Jan 2017
Cited by 2
Abstract
We designed a mini tower fermentor that is suitable to perform adaptive laboratory evolution (ALE) with gravity imposed as selective pressure, and suitable to evolve a weak flocculating industrial brewers’ strain towards a strain with a more extended aggregation phenotype. This phenotype is [...] Read more.
We designed a mini tower fermentor that is suitable to perform adaptive laboratory evolution (ALE) with gravity imposed as selective pressure, and suitable to evolve a weak flocculating industrial brewers’ strain towards a strain with a more extended aggregation phenotype. This phenotype is of particular interest in the brewing industry, since it simplifies yeast removal at the end of the fermentation, and many industrial strains are still not sufficiently flocculent. The flow of particles (yeast cells and flocs) was simulated, and the theoretical retainment advantage of aggregating cells over single cells in the tower fermentor was demonstrated. A desktop stereolithography (SLA) printer was used to construct the mini reactor from transparent methacrylic acid esters resin. The printed structures were biocompatible for yeast growth, and could be sterilised by autoclaving. The flexibility of 3D printing allowed the design to be optimized quickly. During the ALE experiment, yeast flocs were observed within two weeks after the start of the continuous cultivation. The flocs showed a “snowflake” morphology, and were not the result of flocculin interactions, but probably the result of (a) mutation(s) in gene(s) that are involved in the mother/daughter separation process. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessArticle
Purification and Properties of Yeast Proteases Secreted by Wickerhamomyces anomalus 227 and Metschnikovia pulcherrima 446 during Growth in a White Grape Juice
Fermentation 2017, 3(1), 2; https://doi.org/10.3390/fermentation3010002 - 26 Dec 2016
Cited by 8
Abstract
Aspartic proteases are of significant importance for medicine and biotechnology. In spite of sufficient evidence that many non-Saccharomyces yeasts produce extracellular proteases, previous research has focused on the enzymes of Candida species because of their role as virulence factors. Nowadays, there [...] Read more.
Aspartic proteases are of significant importance for medicine and biotechnology. In spite of sufficient evidence that many non-Saccharomyces yeasts produce extracellular proteases, previous research has focused on the enzymes of Candida species because of their role as virulence factors. Nowadays, there is also increasing interest for their applications in industrial processes, mainly because of their activities at low pH values. Here, we report the features of new acid proteases isolated from wine-relevant yeasts Metschnikovia pulcherrima and Wickerhamomyces anomalus. To our knowledge, this is the first detailed description of such an enzyme derived from strains of W. anomalus. Deviating to most former studies, we could demonstrate that the yeasts produce these enzymes in a natural substrate (grape juice) during the active growth phase. The enzymes were purified from concentrated grape juice by preparative isoelectric focusing. Biochemical data (maximum activity at ≈ pH 3.0, inhibition by pepstatin A) classify them as aspartic proteases. For W. anomalus 227, this assumption was confirmed by the protein sequence of WaAPR1 determined by LC-MS/MS. The sequence revealed a signal peptide for secretion, as well as a peptidase A1 domain with two aspartate residues in the active site. The enzyme has a calculated molecular mass of 47 kDa and an isolelectric point of 4.11. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessFeature PaperArticle
Batch Fermentation Options for High Titer Bioethanol Production from a SPORL Pretreated Douglas-Fir Forest Residue without Detoxification
Fermentation 2016, 2(3), 16; https://doi.org/10.3390/fermentation2030016 - 11 Aug 2016
Cited by 1
Abstract
This study evaluated batch fermentation modes, namely, separate hydrolysis and fermentation (SHF), quasi-simultaneous saccharification and fermentation (Q-SSF), and simultaneous saccharification and fermentation (SSF), and fermentation conditions, i.e., enzyme and yeast loadings, nutrient supplementation and sterilization, on high titer bioethanol production from SPORL-pretreated Douglas-fir [...] Read more.
This study evaluated batch fermentation modes, namely, separate hydrolysis and fermentation (SHF), quasi-simultaneous saccharification and fermentation (Q-SSF), and simultaneous saccharification and fermentation (SSF), and fermentation conditions, i.e., enzyme and yeast loadings, nutrient supplementation and sterilization, on high titer bioethanol production from SPORL-pretreated Douglas-fir forest residue without detoxification. The results indicated that Q-SSF and SSF were obviously superior to SHF operation in terms of ethanol yield. Enzyme loading had a strong positive correlation with ethanol yield in the range studied. Nutrient supplementation and sterility were not necessary for ethanol production from SPORL-pretreated Douglas-fir. Yeast loading had no substantial influence on ethanol yield for typical SSF conditions. After 96 h fermentation at 38 °C on shake flask at 150 rpm, terminal ethanol titer of 43.2 g/L, or 75.1% theoretical based on untreated feedstock glucan, mannan, and xylan content was achieved, when SSF was conducted at whole slurry solids loading of 15% with enzyme and yeast loading of 20 FPU/g glucan and 1.8 g/kg (wet), respectively, without nutrition supplementation and sterilization. It is believed that with mechanical mixing, enzyme loading can be reduced without reducing ethanol yield with extended fermentation duration. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessArticle
A Bacterial Laccase for Enhancing Saccharification and Ethanol Fermentation of Steam-Pretreated Biomass
Fermentation 2016, 2(2), 11; https://doi.org/10.3390/fermentation2020011 - 04 May 2016
Cited by 19
Abstract
Different biological approaches, highlighting the use of laccases, have been developed as environmentally friendly alternatives for improving the saccharification and fermentation stages of steam-pretreated lignocellulosic biomass. This work evaluates the use of a novel bacterial laccase (MetZyme) for enhancing the hydrolysability and fermentability [...] Read more.
Different biological approaches, highlighting the use of laccases, have been developed as environmentally friendly alternatives for improving the saccharification and fermentation stages of steam-pretreated lignocellulosic biomass. This work evaluates the use of a novel bacterial laccase (MetZyme) for enhancing the hydrolysability and fermentability of steam-exploded wheat straw. When the water insoluble solids (WIS) fraction was treated with laccase or alkali alone, a modest increase of about 5% in the sugar recovery yield (glucose and xylose) was observed in both treatments. Interestingly, the combination of alkali extraction and laccase treatment boosted enzymatic hydrolysis, increasing the glucose and xylose concentration in the hydrolysate by 21% and 30%, respectively. With regards to the fermentation stage, the whole pretreated slurry was subjected to laccase treatment, lowering the phenol content by up to 21%. This reduction allowed us to improve the fermentation performance of the thermotolerant yeast Kluyveromyces marxianus CECT 10875 during a simultaneous saccharification and fermentation (SSF) process. Hence, a shorter adaptation period and an increase in the cell viability—measured in terms of colony forming units (CFU/mL)—could be observed in laccase-treated slurries. These differences were even more evident when a presaccharification step was performed prior to SSF. Novel biocatalysts such as the bacterial laccase presented in this work could play a key role in the implementation of a cost-effective technology in future biorefineries. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessArticle
The Interaction of Two Saccharomyces cerevisiae Strains Affects Fermentation-Derived Compounds in Wine
Fermentation 2016, 2(2), 9; https://doi.org/10.3390/fermentation2020009 - 30 Mar 2016
Cited by 3
Abstract
Previous winery-based studies showed the strains Lalvin® RC212 (RC212) and Lalvin® ICV-D254 (D254), when present together during fermentation, contributed to >80% relative abundance of the Saccharomyces cerevisiae population in inoculated and spontaneous fermentations. In these studies, D254 appeared to out-compete RC212, [...] Read more.
Previous winery-based studies showed the strains Lalvin® RC212 (RC212) and Lalvin® ICV-D254 (D254), when present together during fermentation, contributed to >80% relative abundance of the Saccharomyces cerevisiae population in inoculated and spontaneous fermentations. In these studies, D254 appeared to out-compete RC212, even when RC212 was used as the inoculant. In the present study, under controlled conditions, we tested the hypotheses that D254 would out-compete RC212 during fermentation and have a greater impact on key fermentation-derived chemicals. The experiment consisted of four fermentation treatments, each conducted in triplicate: a pure culture control of RC212; a pure culture control of D254; a 1:1 co-inoculation ratio of RC212:D254; and a 4:1 co-inoculation ratio of RC212:D254. Strain abundance was monitored at four stages. Inoculation ratios remained the same throughout fermentation, indicating an absence of competitive exclusion by either strain. The chemical profile of the 1:1 treatment closely resembled pure D254 fermentations, suggesting D254, under laboratory conditions, had a greater influence on the selected sensory compounds than did RC212. Nevertheless, the chemical profile of the 4:1 treatment, in which RC212 dominated, resembled that of pure RC212 fermentations. Our results support the idea that co-inoculation of strains creates a new chemical profile not seen in the pure cultures. These findings may have implications for winemakers looking to control wine aroma and flavor profiles through strain selection. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessFeature PaperArticle
Improvement of Malvar Wine Quality by Use of Locally-Selected Saccharomyces cerevisiae Strains
Fermentation 2016, 2(1), 7; https://doi.org/10.3390/fermentation2010007 - 14 Mar 2016
Cited by 8
Abstract
Malvar grape juice offers relatively little in the way of a sensory experience. Our interest lies in the use of locally-selected yeast strains in experimental fermentations to improve the sensory characteristics of Malvar wines. Two locally-selected strains of Saccharomyces cerevisiae were used as [...] Read more.
Malvar grape juice offers relatively little in the way of a sensory experience. Our interest lies in the use of locally-selected yeast strains in experimental fermentations to improve the sensory characteristics of Malvar wines. Two locally-selected strains of Saccharomyces cerevisiae were used as starter cultures in vinifications and compared with spontaneous fermentations of the same cultivar musts. Wine quality was investigated by their principal oenological parameters, analysis of the volatile aroma components, and corroborated by an experienced taster panel. The most salient chemical attributes were its high concentrations of isoamyl acetate and hexyl acetate and the high acidity, which have been detected to be key constituents in setting the fruity and fresh character of Malvar wines. Winemakers of winegrowing areas where this grape variety is cultivated will have improved options to elaborate new white wines styles, using selected yeast strains that enhance its aromatic properties. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessArticle
Development of Novel Textile Bioreactor for Anaerobic Utilization of Flocculating Yeast for Ethanol Production
Fermentation 2015, 1(1), 98-112; https://doi.org/10.3390/fermentation1010098 - 23 Nov 2015
Cited by 3
Abstract
Process development, cheaper bioreactor cost, and faster fermentation rate can aid in reducing the cost of fermentation. In this article, these ideas were combined in developing a previously introduced textile bioreactor for ethanol production. The bioreactor was developed to utilize flocculating yeast for [...] Read more.
Process development, cheaper bioreactor cost, and faster fermentation rate can aid in reducing the cost of fermentation. In this article, these ideas were combined in developing a previously introduced textile bioreactor for ethanol production. The bioreactor was developed to utilize flocculating yeast for ethanol production under anaerobic conditions. A mixing system, which works without aerators, spargers, or impellers, but utilizes the liquid content in the bioreactor for suspending the flocculating yeast to form a fluidized bed, was developed and examined. It could be used with dilution rates greater than 1.0 h1 with less possibility of washout. The flow conditions required to begin and maintain a fluidized bed were determined. Fermentation experiments with flow rate and utilization of the mixing system as process variables were carried out. The results showed enhanced mass transfer as evidenced by faster fermentation rates on experiments with complete sucrose utilization after 36 h, even at 30 times lesser flow rate. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Review

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Open AccessReview
Starter Cultures for Sparkling Wine
Fermentation 2016, 2(4), 21; https://doi.org/10.3390/fermentation2040021 - 14 Dec 2016
Cited by 10
Abstract
The sparkling wine market has expanded in recent years, boosted by the increasing demand of the global market. As for other fermented beverages, technological yeasts and bacteria selected to design commercial starter cultures represent key levers to maximize product quality and safety. The [...] Read more.
The sparkling wine market has expanded in recent years, boosted by the increasing demand of the global market. As for other fermented beverages, technological yeasts and bacteria selected to design commercial starter cultures represent key levers to maximize product quality and safety. The increasing economic interest in the sector of sparkling wine has also implied a renewed interest in microbial resource management. In this review, after a brief introduction, we report an overview of the main characterization criteria in order to select Saccharomyces cerevisiae strains suitable for use as starter cultures for the production of base wines and to drive re-fermentation of base wines to obtain sparkling wines. Particular attention has been reserved to the technological characterization aspects of re-fermenting phenotypes. We also analysed the possible uses of selected non-Saccharomyces and malolactic strains in order to differentiate specific productions. Finally, we highlighted the main safety aspects related to microbes of enological interest and underlined some microbial-based biotechnological applications helpful to pursue product and process innovations. Overall, the sparkling wine industry may find a relevant benefit from the exploitation of the wide resources associated with vineyard/wine microbial diversity. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessFeature PaperReview
Yeast Nanobiotechnology
Fermentation 2016, 2(4), 18; https://doi.org/10.3390/fermentation2040018 - 21 Oct 2016
Cited by 5
Abstract
Yeast nanobiotechnology is a recent field where nanotechniques are used to manipulate and analyse yeast cells and cell constituents at the nanoscale. The aim of this review is to give an overview and discuss nanobiotechnological analysis and manipulation techniques that have been particularly [...] Read more.
Yeast nanobiotechnology is a recent field where nanotechniques are used to manipulate and analyse yeast cells and cell constituents at the nanoscale. The aim of this review is to give an overview and discuss nanobiotechnological analysis and manipulation techniques that have been particularly applied to yeast cells. These techniques have mostly been applied to the model yeasts Saccharomyces cerevisiae and Schizosaccaromyces pombe, and the pathogenic model yeast Candida albicans. Nanoscale imaging techniques, such as Atomic Force Microscopy (AFM), super-resolution fluorescence microscopy, and electron microscopy (scanning electron microscopy (SEM), transmission electron microscopy (TEM), including electron tomography) are reviewed and discussed. Other nano-analysis methods include single-molecule and single-cell force spectroscopy and the AFM-cantilever-based nanomotion analysis of living cells. Next, an overview is given on nano/microtechniques to pattern and manipulate yeast cells. Finally, direct contact cell manipulation methods, such as AFM-based single cell manipulation and micropipette manipulation of yeast cells, as well as non-contact cell manipulation techniques, such as optical, electrical, and magnetic cells manipulation methods are reviewed. Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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Open AccessReview
Application of Non-Saccharomyces Yeasts to Wine-Making Process
Fermentation 2016, 2(3), 14; https://doi.org/10.3390/fermentation2030014 - 23 Jun 2016
Cited by 12
Abstract
Winemaking is a complex process involving the interaction of different microbes. The two main groups of microorganisms involved are yeasts and bacteria. Non-Saccharomyces yeasts are present on the grape surface and also on the cellar. Although these yeasts can produce spoilage, these [...] Read more.
Winemaking is a complex process involving the interaction of different microbes. The two main groups of microorganisms involved are yeasts and bacteria. Non-Saccharomyces yeasts are present on the grape surface and also on the cellar. Although these yeasts can produce spoilage, these microorganisms could also possess many interesting technological properties which could be exploited in food processing. It has been shown that some of the metabolites that these yeasts produce may be beneficial and contribute to the complexity of the wine and secrete enzymes providing interesting wine organoleptic characteristics. On the other hand, non-Saccharomyces yeasts are the key to obtain wines with reduced ethanol content. Among secreted enzymes, β-glucosidase activity is involved in the release of terpenes to wine, thus contributing to varietal aroma while β-xylosidase enzyme is also interesting in industry due to its involvement in the degradation of hemicellulose by hydrolyzing its main heteroglycan (xylan). Full article
(This article belongs to the Special Issue Yeast Biotechnology) Printed Edition available
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