Submit to Microorganisms Review for Microorganisms Propose a Special Issue

Journal Menu

Journal Browser

Non-conventional Yeasts: Genomics and Biotechnology

Special Issue Editors
Special Issue Information
Published Papers

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 50608

Share This Special Issue

Special Issue Editor

Prof. Dr. Jürgen Wendland

E-Mail Website
Guest Editor

Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
Interests: molecular yeast breeding; fungal genetics; genomics and synthetic microbiology; wine microbiology; non-conventional yeasts

Special Issue Information

Dear Colleagues,

Beyond the well-known model organisms of Saccharomyces cerevisiae and Candida albicans, there is a fascinating world of other yeasts. These non-conventional yeasts are already contributing enormously to all aspects of microbiology, genetics, biotechnology and fermentation, bioengineering, synthetic biology, and medical biology. This is because of their novel and often unique features, vastly untapped resources, and capabilities (e.g., based on their metabolism, fermentation capacities, substrate utilization, enzyme production, secondary metabolite/volatile aroma compound/flavor production, cell biology, or as biocontrol organisms to be used in modern sustainable agriculture).

Modern technologies allow for the characterization of non-conventional yeasts at an unprecedented level. With powerful omics tools and genome editing capabilities, non-conventional yeasts are amenable to genetic engineering and have a lot to contribute in diverse sectors.

This Special Issue, “Non-conventional Yeasts: Genomics and Biotechnology”, serves to highlight the biodiversity and different the facets of non-conventional yeasts.

It will support publication of contributions on the following topics:

The general biology of non-conventional yeasts: biodiversity/taxonomy, evolution, ecology, physiology and metabolism, cell biology, signaling, or stress responses;
The genetics, genomics, transcriptomics, proteomics of non-conventional yeasts (e.g., covering whole genome sequencing and assemblies, gene expression or analyses of plasmids, mating types, centromeres, telomere gene organization, or gene family evolution);
The role of non-conventional yeasts in agriculture (e.g., as biocontrol strains, biofertilizers, and growth-promoting microbes);
Basic and applied studies on biotechnology/bioengineering or fermentations for food and beverage, chemicals, and protein production;
Systems biology and synthetic biology; and
Genome editing including cool tools and analytics for working with non-conventional yeasts

Prof. Dr. Jürgen Wendland
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 submissions that pass pre-check are 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. Microorganisms is an international peer-reviewed open access monthly 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 2700 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.

Published Papers (11 papers)

Download All Papers

Editorial

Jump to: Research, Review

2 pages, 167 KiB

Open AccessEditorial

Special Issue: Non-Conventional Yeasts: Genomics and Biotechnology

by Jürgen Wendland

Microorganisms 2020, 8(1), 21; https://doi.org/10.3390/microorganisms8010021 - 20 Dec 2019

Cited by 7 | Viewed by 2193

Abstract

Non-conventional yeasts, i.e., the vast biodiversity beyond already well-established model systems such as Saccharomyces cerevisiae, Candida albicans and Schizosaccharomyces pombe and a few others, are a huge and untapped resource of organisms. [...] Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

Research

Jump to: Editorial, Review

16 pages, 1130 KiB

Open AccessArticle

Integrated Process for Bioenergy Production and Water Recycling in the Dairy Industry: Selection of Kluyveromyces Strains for Direct Conversion of Concentrated Lactose-Rich Streams into Bioethanol

by Maria José Leandro, Susana Marques, Belina Ribeiro, Helena Santos and César Fonseca

Microorganisms 2019, 7(11), 545; https://doi.org/10.3390/microorganisms7110545 - 9 Nov 2019

Cited by 11 | Viewed by 3341

Abstract

Dairy industries have a high environmental impact, with very high energy and water consumption and polluting effluents. To increase the sustainability of these industries it is urgent to implement technologies for wastewater treatment allowing water recycling and energy savings. In this study, dairy wastewater was processed by ultrafiltration and nanofiltration or ultrafiltration and reverse osmosis (UF/RO) and retentates from the second membrane separation processes were assessed for bioenergy production. Lactose-fermenting yeasts were tested in direct conversion of the retentates (lactose-rich streams) into bioethanol. Two Kluyveromyces strains efficiently fermented all the lactose, with ethanol yields higher than 90% (>0.47 g/g yield). Under severe oxygen-limiting conditions, the K. marxianus PYCC 3286 strain reached 70 g/L of ethanol, which is compatible with energy-efficient distillation processes. In turn, the RO permeate is suitable for recycling into the cleaning process. The proposed integrated process, using UF/RO membrane technology, could allow water recycling (RO permeate) and bioenergy production (from RO retentate) for a more sustainable dairy industry. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Graphical abstract

14 pages, 836 KiB

Open AccessArticle

Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540

by Ievgeniia A. Tiukova, Huifeng Jiang, Jacques Dainat, Marc P. Hoeppner, Henrik Lantz, Jure Piskur, Mats Sandgren, Jens Nielsen, Zhenglong Gu and Volkmar Passoth

Microorganisms 2019, 7(11), 489; https://doi.org/10.3390/microorganisms7110489 - 26 Oct 2019

Cited by 7 | Viewed by 3537

Abstract

Brettanomyces naardenensis is a spoilage yeast with potential for biotechnological applications for production of innovative beverages with low alcohol content and high attenuation degree. Here, we present the first annotated genome of B. naardenensis CBS 7540. The genome of B. naardenensis CBS 7540 was assembled into 76 contigs, totaling 11,283,072 nucleotides. In total, 5168 protein-coding sequences were annotated. The study provides functional genome annotation, phylogenetic analysis, and discusses genetic determinants behind notable stress tolerance and biotechnological potential of B. naardenensis. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

15 pages, 2745 KiB

Open AccessArticle

Xylitol Production: Identification and Comparison of New Producing Yeasts

by Clara Vida G. C. Carneiro, Flávia Cristina de Paula e Silva and João R. M. Almeida

Microorganisms 2019, 7(11), 484; https://doi.org/10.3390/microorganisms7110484 - 23 Oct 2019

Cited by 36 | Viewed by 5739

Abstract

Xylitol is a sugar alcohol with five carbons that can be used in the pharmaceutical and food industries. It is industrially produced by chemical route; however, a more economical and environmentally friendly production process is of interest. In this context, this study aimed to select wild yeasts able to produce xylitol and compare their performance in sugarcane bagasse hydrolysate. For this, 960 yeast strains, isolated from soil, wood, and insects have been prospected and selected for the ability to grow on defined medium containing xylose as the sole carbon source. A total of 42 yeasts was selected and their profile of sugar consumption and metabolite production were analyzed in microscale fermentation. The six best xylose-consuming strains were molecularly identified as Meyerozyma spp. The fermentative kinetics comparisons on defined medium and on sugarcane bagasse hydrolysate showed physiological differences among these strains. Production yields vary from Y_P/S = 0.25 g/g to Y_P/S = 0.34 g/g in defined medium and from Y_P/S = 0.41 g/g to Y_P/S = 0.60 g/g in the hydrolysate. Then, the xylitol production performance of the best xylose-consuming strain obtained in the screening, which was named M. guilliermondii B12, was compared with the previously reported xylitol producing yeasts M. guilliermondii A3, Spathaspora sp. JA1, and Wickerhamomyces anomalus 740 in sugarcane bagasse hydrolysate under oxygen-limited conditions. All the yeasts were able to metabolize xylose, but W. anomalus 740 showed the highest xylitol production yield, reaching a maximum of 0.83 g xylitol/g of xylose in hydrolysate. The screening strategy allowed identification of a new M. guilliermondii strain that efficiently grows in xylose even in hydrolysate with a high content of acetic acid (~6 g/L). In addition, this study reports, for the first time, a high-efficient xylitol producing strain of W. anomalus, which achieved, to the best of our knowledge, one of the highest xylitol production yields in hydrolysate reported in the literature. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

17 pages, 5800 KiB

Open AccessArticle

Enhancement of Astaxanthin Biosynthesis in Oleaginous Yeast Yarrowia lipolytica via Microalgal Pathway

by Larissa Ribeiro Ramos Tramontin, Kanchana Rueksomtawin Kildegaard, Suresh Sudarsan and Irina Borodina

Microorganisms 2019, 7(10), 472; https://doi.org/10.3390/microorganisms7100472 - 19 Oct 2019

Cited by 67 | Viewed by 6747

Abstract

Astaxanthin is a high-value red pigment and antioxidant used by pharmaceutical, cosmetics, and food industries. The astaxanthin produced chemically is costly and is not approved for human consumption due to the presence of by-products. The astaxanthin production by natural microalgae requires large open areas and specialized equipment, the process takes a long time, and results in low titers. Recombinant microbial cell factories can be engineered to produce astaxanthin by fermentation in standard equipment. In this work, an oleaginous yeast Yarrowia lipolytica was engineered to produce astaxanthin at high titers in submerged fermentation. First, a platform strain was created with an optimised pathway towards β-carotene. The platform strain produced 331 ± 66 mg/L of β-carotene in small-scale cultivation, with the cellular content of 2.25% of dry cell weight. Next, the genes encoding β-ketolase and β-hydroxylase of bacterial (Paracoccus sp. and Pantoea ananatis) and algal (Haematococcus pluvialis) origins were introduced into the platform strain in different copy numbers. The resulting strains were screened for astaxanthin production, and the best strain, containing algal β-ketolase and β-hydroxylase, resulted in astaxanthin titer of 44 ± 1 mg/L. The same strain was cultivated in controlled bioreactors, and a titer of 285 ± 19 mg/L of astaxanthin was obtained after seven days of fermentation on complex medium with glucose. Our study shows the potential of Y. lipolytica as the cell factory for astaxanthin production. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

18 pages, 4630 KiB

Open AccessArticle

Biocontrol of Aspergillus flavus in Ensiled Sorghum by Water Kefir Microorganisms

by Mariana Gonda, Gabriela Garmendia, Caterina Rufo, Ángela León Peláez, Michael Wisniewski, Samir Droby and Silvana Vero

Microorganisms 2019, 7(8), 253; https://doi.org/10.3390/microorganisms7080253 - 10 Aug 2019

Cited by 22 | Viewed by 3976

Abstract

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incubation. Mold growth was inhibited in the presence of water kefir while no inhibition was observed when filter-sterilized water kefir was applied, demonstrating the relevant role of the microorganisms in the kefir water in the biocontrol process. Fungal and bacterial diversity in treated sorghum mini-silos was analyzed by high-throughput sequencing. Firmicutes was the predominant bacterial phyla and Lactobacillus represented the most abundant genus, while Ascomycota was the predominant fungal phyla with Saccharomyces and Pichia as the major genera. Bacterial and yeast counts before and after incubation indicated that the microbial community obtained from WK was able to grow in the sorghum mini-silos in the presence of A. flavus. Results of the present work indicate that the use of a mixed inoculum of microorganisms present in WK may represent an alternative management practice to avoid the growth of A. flavus in ensiled sorghum grains and the concomitant contamination with aflatoxins. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

20 pages, 6408 KiB

Open AccessArticle

Taxonomic Distribution of Cytochrome P450 Monooxygenases (CYPs) among the Budding Yeasts (Sub-Phylum Saccharomycotina)

by Tomas Linder

Microorganisms 2019, 7(8), 247; https://doi.org/10.3390/microorganisms7080247 - 8 Aug 2019

Cited by 8 | Viewed by 5907

Abstract

Cytochrome P450 monooxygenases (CYPs) are ubiquitous throughout the tree of life and play diverse roles in metabolism including the synthesis of secondary metabolites as well as the degradation of recalcitrant organic substrates. The genomes of budding yeasts (phylum Ascomycota, sub-phylum Saccharomycotina) typically contain fewer families of CYPs than filamentous fungi. There are currently five CYP families among budding yeasts with known function while at least another six CYP families with unknown function (“orphan CYPs”) have been described. The current study surveyed the genomes of 372 species of budding yeasts for CYP-encoding genes in order to determine the taxonomic distribution of individual CYP families across the sub-phylum as well as to identify novel CYP families. Families CYP51 and CYP61 (represented by the ergosterol biosynthetic genes ERG11 and ERG5, respectively) were essentially ubiquitous among the budding yeasts while families CYP52 (alkane/fatty acid hydroxylases), CYP56 (N-formyl-l-tyrosine oxidase) displayed several instances of gene loss at the genus or family level. Phylogenetic analysis suggested that the three orphan families CYP5217, CYP5223 and CYP5252 diverged from a common ancestor gene following the origin of the budding yeast sub-phylum. The genomic survey also identified eight CYP families that had not previously been reported in budding yeasts. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

12 pages, 2147 KiB

Open AccessArticle

Overexpression of RAD51 Enables PCR-Based Gene Targeting in Lager Yeast

by Beatrice Bernardi, Yeseren Kayacan, Madina Akan and Jürgen Wendland

Microorganisms 2019, 7(7), 192; https://doi.org/10.3390/microorganisms7070192 - 5 Jul 2019

Cited by 8 | Viewed by 4231

Abstract

Lager beer fermentations rely on specific polyploid hybrids between Saccharomyces cerevisiae and Saccharomyces eubayanus falling into the two groups of S. carlsbergensis/Saaz-type and S. pastorianus/Frohberg-type. These strains provide a terroir to lager beer as they have long traditional associations and local selection histories with specific breweries. Lager yeasts share, based on their common origin, several phenotypes. One of them is low transformability, hampering the gene function analyses required for proof-of-concept strain improvements. PCR-based gene targeting is a standard tool for manipulating S. cerevisiae and other ascomycetes. However, low transformability paired with the low efficiency of homologous recombination practically disable targeted gene function analyses in lager yeast strains. For genetic manipulations in lager yeasts, we employed a yeast transformation protocol based on lithium-acetate/PEG incubation combined with electroporation. We first introduced freely replicating CEN/ARS plasmids carrying ScRAD51 driven by a strong heterologous promoter into lager yeast. RAD51 overexpression in the Weihenstephan 34/70 lager yeast was necessary and sufficient in our hands for gene targeting using short-flanking homology regions of 50 bp added to a selection marker by PCR. We successfully targeted two independent loci, ScADE2/YOR128C and ScHSP104/YLL026W, and confirmed correct integration by diagnostic PCR. With these modifications, genetic alterations of lager yeasts can be achieved efficiently and the RAD51-containing episomal plasmid can be removed after successful strain construction. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

23 pages, 3375 KiB

Open AccessArticle

Modulating Fermentative, Varietal and Aging Aromas of Wine Using non-Saccharomyces Yeasts in a Sequential Inoculation Approach

by Inês Oliveira and Vicente Ferreira

Microorganisms 2019, 7(6), 164; https://doi.org/10.3390/microorganisms7060164 - 6 Jun 2019

Cited by 36 | Viewed by 3924

Abstract

The goal of this study is to assess to what extent non-Saccharomyces yeasts can introduce aromatic changes of industrial interest in fermentative, varietal and aged aromas of wine. Aroma precursors from Riesling and Garnacha grapes were extracted and used in two independent sequential experiments. Synthetic musts were inoculated, either with Saccharomyces cerevisiae (Sc) or with Pichia kluyveri (Pk), Torulaspora delbrueckii (Td) or Lachancea thermotolerans (Lt), followed by Sc. The fermented samples were subjected to anoxic aging at 50 °C for 0, 1, 2 or 5 weeks before an aroma analysis. The fermentative aroma profiles were consistently changed by non-Saccharomyces: all strains induced smaller levels of isoamyl alcohol; Pk produced huge levels of aromatic acetates and can induce high levels of fatty acids (FA) and their ethyl esters (EE); Td produced large levels of branched acids and of their EE after aging, and induced smaller levels of FA and their EE; Lt produced reduced levels of FA and their EE. The varietal aroma was also deeply affected: TDN (1,1,6-trimethyl-1,2- dihydronaphthalene) levels in aged wines were reduced by Pk and enhanced by Lt in Garnacha; the levels of vinylphenols can be much reduced, particularly by Lt and Pk. TD and Lt can increase linalool and geraniol in young, but not in aged wines. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Graphical abstract

14 pages, 4783 KiB

Open AccessArticle

Exploitation of Three Non-Conventional Yeast Species in the Brewing Process

by Laura Canonico, Edoardo Galli, Enrico Ciani, Francesca Comitini and Maurizio Ciani

Microorganisms 2019, 7(1), 11; https://doi.org/10.3390/microorganisms7010011 - 8 Jan 2019

Cited by 51 | Viewed by 5462

Abstract

Consumers require high-quality beers with specific enhanced flavor profiles and non-conventional yeasts could represent a large source of bioflavoring diversity to obtain new beer styles. In this work, we investigated the use of three different non-conventional yeasts belonging to Lachancea thermotolerans, Wickerhamomyces anomalus, and Zygotorulaspora florentina species in pure and mixed fermentation with the Saccharomyces cerevisiae commercial starter US-05. All three non-conventional yeasts were competitive in co-cultures with the S. cerevisiae, and they dominated fermentations with 1:20 ratio (S. cerevisiae/non-conventional yeasts ratios). Pure non-conventional yeasts and co-cultures affected significantly the beer aroma. A general reduction in acetaldehyde content in all mixed fermentations was found. L. thermotolerans and Z. florentina in mixed and W. anomalus in pure cultures increased higher alcohols. L. thermotolerans led to a large reduction in pH value, producing, in pure culture, a large amount of lactic acid (1.83 g/L) while showing an enhancement of ethyl butyrate and ethyl acetate in all pure and mixed fermentations. W. anomalus decreased the main aroma compounds in comparison with the S. cerevisiae but showed a significant increase in ethyl butyrate and ethyl acetate. Beers produced with Z. florentina were characterized by an increase in the isoamyl acetate and α-terpineol content. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research

22 pages, 567 KiB

Open AccessReview

Organic Wastes as Feedstocks for Non-Conventional Yeast-Based Bioprocesses

by Diem T. Hoang Do, Chrispian W. Theron and Patrick Fickers

Microorganisms 2019, 7(8), 229; https://doi.org/10.3390/microorganisms7080229 - 31 Jul 2019

Cited by 31 | Viewed by 4276

Abstract

Non-conventional yeasts are efficient cell factories for the synthesis of value-added compounds such as recombinant proteins, intracellular metabolites, and/or metabolic by-products. Most bioprocess, however, are still designed to use pure, ideal sugars, especially glucose. In the quest for the development of more sustainable processes amid concerns over the future availability of resources for the ever-growing global population, the utilization of organic wastes or industrial by-products as feedstocks to support cell growth is a crucial approach. Indeed, vast amounts of industrial and commercial waste simultaneously represent an environmental burden and an important reservoir for recyclable or reusable material. These alternative feedstocks can provide microbial cell factories with the required metabolic building blocks and energy to synthesize value-added compounds, further representing a potential means of reduction of process costs as well. This review highlights recent strategies in this regard, encompassing knowledge on catabolic pathways and metabolic engineering solutions developed to endow cells with the required metabolic capabilities, and the connection of these to the synthesis of value-added compounds. This review focuses primarily, but not exclusively, on Yarrowia lipolytica as a yeast cell factory, owing to its broad range of naturally metabolizable carbon sources, together with its popularity as a non-conventional yeast. Full article

(This article belongs to the Special Issue Non-conventional Yeasts: Genomics and Biotechnology)

► Show Figures