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Microorganisms
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Non-Conventional Yeasts
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Non-Conventional Yeasts

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 28650

Special Issue Editors

Dr. Benedetta Turchetti

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Guest Editor
Dipartimento Scienze Agrarie, Alimentari e Ambientali and Industrial Yeasts Collection DBVPG, Università degli Studi di Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
Interests: yeast; yeast biotechnology; yeast ecology; yeast taxonomy; yeasts collection and preservation
Dr. Neža Čadež

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Guest Editor
Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 101, 1000 Ljubljana, Slovenia
Interests: yeast ecology; taxonomy; genomics; microbial communities; fermented foods and beverages

Special Issue Information

Dear Colleagues,

To most people, yeasts are exemplified by the species Saccharomyces cerevisiae, whose genus Saccharomyces frequently appears as the dominant agent in biotechnological fermentations and represents the eukaryotic cellular model for genetic and medical studies.

This is in spite of the fact that these domesticated microorganisms represent only a little fragment of the vast biodiversity and biotechnological potential offered by yeast species array.

In recent decades, studies focused on yeast diversity of both technological and natural habitats have generated a growing number of new species descriptions and demonstrated the large diffusion of non-Saccharomyces species, most of them also labeled as nonconventional yeasts (NCYs).

The studies on genomic and metabolic diversity of NCYs have revealed innumerable peculiar and promising properties in fundamental and applied research, many of which still await exploration.

This Special Issue will cover the most recent progresses in the field of diversity, taxonomy, ecology, and physiology of NCYs, including their possible application for biotechnological purposes.  

Dr. Benedetta Turchetti
Dr. Neža Čadež
Guest Editors

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.

Keywords

  • nonconventional yeasts (NCYs)
  • non-Saccharomyces yeasts
  • NCY diversity
  • NCY biology
  • NCY biotechnology

Published Papers (7 papers)

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Research

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18 pages, 712 KiB  
Article
D-Fructose Assimilation and Fermentation by Yeasts Belonging to Saccharomycetes: Rediscovery of Universal Phenotypes and Elucidation of Fructophilic Behaviors in Ambrosiozyma platypodis and Cyberlindnera americana
by Rikiya Endoh, Maiko Horiyama and Moriya Ohkuma
Microorganisms 2021, 9(4), 758; https://doi.org/10.3390/microorganisms9040758 - 05 Apr 2021
Cited by 12 | Viewed by 3643
Abstract
The purpose of this study was to investigate the ability of ascomycetous yeasts to assimilate/ferment d-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the [...] Read more.
The purpose of this study was to investigate the ability of ascomycetous yeasts to assimilate/ferment d-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the standard set of physiological properties for characterizing yeast species, despite the ubiquitous presence of fructose in the natural environment. In this study, we examined 388 strains of yeast, mainly belonging to the Saccharomycetes (Saccharomycotina, Ascomycota), to determine whether they can assimilate/ferment d-fructose. Conventional methods, using liquid medium containing yeast nitrogen base +0.5% (w/v) of d-fructose solution for assimilation and yeast extract-peptone +2% (w/v) fructose solution with an inverted Durham tube for fermentation, were used. All strains examined (n = 388, 100%) assimilated d-fructose, whereas 302 (77.8%) of them fermented d-fructose. In addition, almost all strains capable of fermenting d-glucose could also ferment d-fructose. These results strongly suggest that the ability to assimilate/ferment d-fructose is a universal phenotype among yeasts in the Saccharomycetes. Furthermore, the fructophilic behavior of Ambrosiozyma platypodis JCM 1843 and Cyberlindnera americana JCM 3592 was characterized by sugar consumption profiles during fermentation. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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14 pages, 12624 KiB  
Article
Evaluation of Ogataea (Hansenula) polymorpha for Hyaluronic Acid Production
by João Heitor Colombelli Manfrão-Netto, Enzo Bento Queiroz, Kelly Assis Rodrigues, Cintia M. Coelho, Hugo Costa Paes, Elibio Leopoldo Rech and Nádia Skorupa Parachin
Microorganisms 2021, 9(2), 312; https://doi.org/10.3390/microorganisms9020312 - 03 Feb 2021
Cited by 4 | Viewed by 3810
Abstract
Hyaluronic acid (HA) is a biopolymer formed by UDP-glucuronic acid and UDP-N-acetyl-glucosamine disaccharide units linked by β-1,4 and β-1,3 glycosidic bonds. It is widely employed in medical and cosmetic procedures. HA is synthesized by hyaluronan synthase (HAS), which catalyzes the precursors’ ligation in [...] Read more.
Hyaluronic acid (HA) is a biopolymer formed by UDP-glucuronic acid and UDP-N-acetyl-glucosamine disaccharide units linked by β-1,4 and β-1,3 glycosidic bonds. It is widely employed in medical and cosmetic procedures. HA is synthesized by hyaluronan synthase (HAS), which catalyzes the precursors’ ligation in the cytosol, elongates the polymer chain, and exports it to the extracellular space. Here, we engineer Ogataea (Hansenula) polymorpha for HA production by inserting the genes encoding UDP-glucose 6-dehydrogenase, for UDP-glucuronic acid production, and HAS. Two microbial HAS, from Streptococcus zooepidemicus (hasAs) and Pasteurella multocida (hasAp), were evaluated separately. Additionally, we assessed a genetic switch using integrases in O. polymorpha to uncouple HA production from growth. Four strains were constructed containing both has genes under the control of different promoters. In the strain containing the genetic switch, HA production was verified by a capsule-like layer around the cells by scanning electron microscopy in the first 24 h of cultivation. For the other strains, the HA was quantified only after 48 h and in an optimized medium, indicating that HA production in O. polymorpha is limited by cultivation conditions. Nevertheless, these results provide a proof-of-principle that O. polymorpha is a suitable host for HA production. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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19 pages, 28059 KiB  
Article
Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage
by Neža Čadež, Dénes Dlauchy, Miha Tome and Gábor Péter
Microorganisms 2021, 9(2), 301; https://doi.org/10.3390/microorganisms9020301 - 02 Feb 2021
Cited by 6 | Viewed by 4219
Abstract
Taphrinomycotina is the smallest subphylum of the phylum Ascomycota. It is an assemblage of distantly related early diverging lineages of the phylum, comprising organisms with divergent morphology and ecology; however, phylogenomic analyses support its monophyly. In this study, we report the isolation of [...] Read more.
Taphrinomycotina is the smallest subphylum of the phylum Ascomycota. It is an assemblage of distantly related early diverging lineages of the phylum, comprising organisms with divergent morphology and ecology; however, phylogenomic analyses support its monophyly. In this study, we report the isolation of a yeast strain, which could not be assigned to any of the currently recognised five classes of Taphrinomycotina. The strain of the novel budding species was recovered from extra virgin olive oil and characterised phenotypically by standard methods. The ultrastructure of the cell wall was investigated by transmission electron microscopy. Comparisons of barcoding DNA sequences indicated that the investigated strain is not closely related to any known organism. Tentative phylogenetic placement was achieved by maximum-likelihood analysis of the D1/D2 domain of the nuclear LSU rRNA gene. The genome of the investigated strain was sequenced, assembled, and annotated. Phylogenomic analyses placed it next to the fission Schizosaccharomyces species. To accommodate the novel species, Novakomyces olei, a novel genus Novakomyces, a novel family Novakomycetaceae, a novel order Novakomycetales, and a novel class Novakomycetes is proposed as well. Functional analysis of genes missing in N. olei in comparison to Schizosaccharomyces pombe revealed that they are biased towards biosynthesis of complex organic molecules, regulation of mRNA, and the electron transport chain. Correlating the genome content and physiology among species of Taphrinomycotina revealed some discordance between pheno- and genotype. N. olei produced ascospores in axenic culture preceded by conjugation between two cells. We confirmed that N. olei is a primary homothallic species lacking genes for different mating types. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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11 pages, 1168 KiB  
Article
Variation among Metschnikowia pulcherrima Isolates for Genetic Modification and Homologous Recombination
by Mauro Moreno-Beltrán, Deborah Gore-Lloyd, Christopher Chuck and Daniel Henk
Microorganisms 2021, 9(2), 290; https://doi.org/10.3390/microorganisms9020290 - 31 Jan 2021
Cited by 7 | Viewed by 2117
Abstract
Metschnikowia pulcherrima is a non-conventional yeast with the potential to be used in biotechnological processes, especially involving low-cost feedstock exploitation. However, there are a lack of tools for researching it at a molecular level and for producing genetically modified strains. We tested the [...] Read more.
Metschnikowia pulcherrima is a non-conventional yeast with the potential to be used in biotechnological processes, especially involving low-cost feedstock exploitation. However, there are a lack of tools for researching it at a molecular level and for producing genetically modified strains. We tested the amenability to genetic modification of ten different strains, establishing a transformation protocol based on LiAc/PEG that allows us to introduce heterologous DNA. Non-homologous integration was broadly successful and homologous recombination was successful in two strains. Chemical inhibition of non-homologous end joining recombination had a modest effect on the improvement of homologous recombination rates. Removal of selective markers via flippase recombinase was successful across integrated loci except for those targeted to the native URA3 locus, suggesting that the genome sequence or structure alters the efficacy of this system. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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14 pages, 1937 KiB  
Article
Specialisation of Yeast Genera in Different Phases of Bee Bread Maturation
by Roxane Detry, Noa Simon-Delso, Etienne Bruneau and Heide-Marie Daniel
Microorganisms 2020, 8(11), 1789; https://doi.org/10.3390/microorganisms8111789 - 14 Nov 2020
Cited by 29 | Viewed by 5125
Abstract
Pollen stored by bees undergoes a fermentation marked by the presence of lactic acid bacteria and yeasts. It results in bee bread. Past studies have singled out Starmerella (Candida) magnoliae as the most common yeast species in honey bee-stored bee bread. [...] Read more.
Pollen stored by bees undergoes a fermentation marked by the presence of lactic acid bacteria and yeasts. It results in bee bread. Past studies have singled out Starmerella (Candida) magnoliae as the most common yeast species in honey bee-stored bee bread. Starmerella species are ecological specialists with potential biotechnological value. The rarity of recent studies on yeasts in honey bees prompted us to generate new information on yeast diversity during the conversion of bee-collected pollen to bee bread. Bees and stored pollen from two apiaries in Belgium were sampled, a yeast isolation protocol was developed, yeast isolates were grouped according to their macro- and micromorphology, and representative isolates were identified using DNA sequences. Most of the 252 identified isolates belonged to the genera Starmerella, Metschnikowia, and Zygosaccharomyces. The high abundance of yeasts in fresh bee bread decreased rapidly with the storage duration. Starmerella species dominated fresh bee bread, while mostly Zygosaccharomyces members were isolated from aged bee bread. Starmerella (Candida) apis, a rarely isolated species, was the most frequent and abundant species in fresh bee bread. Yeasts from the bee’s honey stomach and from pollen pellets obtained from bees hind legs were dominated by Metschnikowia species. The distinctive communities from pollen pellets over fresh bee bread to aged bee bread indicate a non-random distribution of these yeasts. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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16 pages, 2178 KiB  
Article
DNA Methylation Changes Induced by Cold in Psychrophilic and Psychrotolerant Naganishia Yeast Species
by Benedetta Turchetti, Gianpiero Marconi, Ciro Sannino, Pietro Buzzini and Emidio Albertini
Microorganisms 2020, 8(2), 296; https://doi.org/10.3390/microorganisms8020296 - 20 Feb 2020
Cited by 10 | Viewed by 3332
Abstract
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold [...] Read more.
The involvement of DNA methylation in the response to cold stress of two different yeast species (Naganishia antarctica, psychrophilic, and Naganishia albida, psychrotolerant), exhibiting different temperature aptitudes, has been studied. Consecutive incubations at respective optimum temperatures, at 4 °C (cold stress) and at optimum temperatures again, were performed. After Methylation Sensitive Amplified Polymorphism (MSAP) fingerprints a total of 550 and 423 clear and reproducible fragments were amplified from N. antarctica and N. albida strains, respectively. The two Naganishia strains showed a different response in terms of level of DNA methylation during cold stress and recovery from cold stress. The percentage of total methylated fragments in psychrophilic N. antarctica did not show any significant change. On the contrary, the methylation of psychrotolerant N. albida exhibited a nonsignificant increase during the incubation at 4 °C and continued during the recovery step, showing a significant difference if compared with control condition, resembling an uncontrolled response to cold stress. A total of 12 polymorphic fragments were selected, cloned, and sequenced. Four fragments were associated to genes encoding for elongation factor G and for chitin synthase export chaperon. To the best of our knowledge, this is the first study on DNA methylation in the response to cold stress carried out by comparing a psychrophilic and a psychrotolerant yeast species. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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19 pages, 2096 KiB  
Review
Metschnikowia pulcherrima and Related Pulcherrimin-Producing Yeasts: Fuzzy Species Boundaries and Complex Antimicrobial Antagonism
by Matthias Sipiczki
Microorganisms 2020, 8(7), 1029; https://doi.org/10.3390/microorganisms8071029 - 12 Jul 2020
Cited by 74 | Viewed by 5546
Abstract
Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the [...] Read more.
Yeasts affiliated with the Metschnikowia pulcherrima clade (subclade) of the large ascomycetous genus Metschnikowia frequently turn out to produce the characteristic maroon-red pulcherrimin when tested for pigment production and prove to exert antagonistic effects on many types of microorganisms. The determination of the exact taxonomic position of the strains is hampered by the shortage of distinctive morphological and physiological properties of the species of the clade and the lack of rDNA barcode gaps. The rDNA repeats of the type strains of the species are not homogenized and are assumed to evolve by a birth-and-death mechanism combined with reticulation. The taxonomic division is further hampered by the incomplete biological (reproductive) isolation of the species: certain type strains can be hybridized and genome sequencing revealed chimeric genome structures in certain strains that might have evolved from interspecies hybrids (alloploid genome duplication). Various mechanisms have been proposed for the antimicrobial antagonism. One is related to pulcherrimin production. The diffusible precursor of pulcherrimin, the pulcherriminic acid is secreted by the cells into the environment where it forms the insoluble pulcherrimin with the ferric ions. The lack of free iron caused by the immobilization of ferric ions inhibits the growth of many microorganisms. Recent results of research into the complexity of the taxonomic division of the pulcherrimin-producing Metschnikowia yeasts and the mechanism(s) underlying their antimicrobial antagonism are discussed in this review. Full article
(This article belongs to the Special Issue Non-Conventional Yeasts)
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