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Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces...
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Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 11156

Special Issue Editors

Prof. Dr. Jose Ramos

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Guest Editor
Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, E-14071 Córdoba, Spain
Interests: salt tolerance; ion homeostasis; food and D. hansenii interactions
Dr. José Luis Martinez

E-Mail Website
Guest Editor
Technical University of Denmark, Department of Biotechnology and Biomedicine, Søltofts Plads Building 223, 2800 Kgs. Lyngby, Denmark
Interests: fermentation technology; yeast cell factories; metabolic engineering; protein production; stress responses; HTS and automation
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Special Issue Information

Dear Colleagues,

Debaryomyces hansenii is a hemiascomycetous yeast of undoubted scientific relevance. Many peculiarities around this yeast are so attractive that basic and applied research is gaining momentum: it is a heterogeneous yeast species whose performance is improved in the presence of high salt, allowing it to survive extreme conditions such as low pH, higher temperatures, nutrient scarcity, and the presence of certain fermentation inhibitors derived from lignocellulosic biomass degradation.

D. hansenii has the highest coding capacity among yeast, with 6906 detected coding sequences, and the molecular characterization of this yeast is still far from being fully known. In fact, the number of well-characterized genes/proteins from D. hansenii is still very low and limited to a few families. D. hansenii belongs to the ambiguous CUG decoding group of yeasts, in which CUG codon can be ambiguously translated, mainly as serine but also as leucine, although in a small percentage. The difficulties when trying to advance in the study of D. hansenii’s metabolism have been mainly related to the limitations in the availability of highly efficient molecular tools. Additionally, several reports have described the misidentification of D. hansenii, which sets an additional level of difficulty in understanding the metabolic insights of this yeast’s peculiar behavior.

Although its biotechnological potential is still difficult to assess, due to the impossibility (to date) of implementing recombinant biosynthetic pathways allowing production of non-native products of interest at industrial scale, this yeast is currently very attractive in the food industry, where it is used in the ripening process of sausages and dry meat products. The use of D. hansenii as a biocontrol agent and to manufacture new meat products by decreasing the use of preservatives are examples of exploring research lines that will complement current knowledge and contribute to prepare new and more ecological products.

This aim of this Special Issue is to provide an interdisciplinary tool for sharing the most recent advances both in fundamental and applied research in relation to this particular yeast. As guest editors of this Special Issue, we invite you to submit original research articles, review articles, and short communications related to the isolation and screening of new D. hansenii strains, physiological characterization, -omics studies, the design of novel genome engineering methodologies, and/or bioprocess development related to the potential use of Debaryomyces for industrial  applications. 

Prof. Dr. Jose Ramos
Dr. José Luis Martinez
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. Journal of Fungi 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 2600 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

  • Debaryomyces hansenii
  • non-conventional yeast
  • stress responses
  • industrial biotechnology
  • yeast physiology

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Published Papers (4 papers)

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Research

21 pages, 4000 KiB  
Article
DhDIT2 Encodes a Debaryomyces hansenii Cytochrome P450 Involved in Benzo(a)pyrene Degradation—A Proposal for Mycoremediation
by Francisco Padilla-Garfias, Norma Silvia Sánchez, Martha Calahorra and Antonio Peña
J. Fungi 2022, 8(11), 1150; https://doi.org/10.3390/jof8111150 - 30 Oct 2022
Cited by 2 | Viewed by 2459
Abstract
Pollutants, such as polycyclic aromatic hydrocarbons (PAHs), e.g., benzo(a)pyrene (BaP), are common components of contaminating mixtures. Such compounds are ubiquitous, extremely toxic, and they pollute soils and aquatic niches. The need for new microorganism-based remediation strategies prompted researchers to identify the most suitable [...] Read more.
Pollutants, such as polycyclic aromatic hydrocarbons (PAHs), e.g., benzo(a)pyrene (BaP), are common components of contaminating mixtures. Such compounds are ubiquitous, extremely toxic, and they pollute soils and aquatic niches. The need for new microorganism-based remediation strategies prompted researchers to identify the most suitable organisms to eliminate pollutants without interfering with the ecosystem. We analyzed the effect caused by BaP on the growth properties of Candida albicans, Debaryomyces hansenii, Rhodotorula mucilaginosa, and Saccharomyces cerevisiae. Their ability to metabolize BaP was also evaluated. The aim was to identify an optimal candidate to be used as the central component of a mycoremediation strategy. The results show that all four yeast species metabolized BaP by more than 70%, whereas their viability was not affected. The best results were observed for D. hansenii. When an incubation was performed in the presence of a cytochrome P450 (CYP) inhibitor, no BaP degradation was observed. Thus, the initial oxidation step is mediated by a CYP enzyme. Additionally, this study identified the D. hansenii DhDIT2 gene as essential to perform the initial degradation of BaP. Hence, we propose that D. hansenii and a S. cerevisiae expressing the DhDIT2 gene are suitable candidates to degrade BaP in contaminated environments. Full article
(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)
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17 pages, 4218 KiB  
Article
Alternative CUG Codon Usage in the Halotolerant Yeast Debaryomyces hansenii: Gene Expression Profiles Provide New Insights into Ambiguous Translation
by Daniel Ochoa-Gutiérrez, Anya M. Reyes-Torres, Ileana de la Fuente-Colmenares, Viviana Escobar-Sánchez, James González, Rosario Ortiz-Hernández, Nayeli Torres-Ramírez and Claudia Segal-Kischinevzky
J. Fungi 2022, 8(9), 970; https://doi.org/10.3390/jof8090970 - 16 Sep 2022
Cited by 1 | Viewed by 2967
Abstract
The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the [...] Read more.
The halotolerant yeast Debaryomyces hansenii belongs to the CTG-Ser1 clade of fungal species that use the CUG codon to translate as leucine or serine. The ambiguous decoding of the CUG codon is relevant for expanding protein diversity, but little is known about the role of leucine–serine ambiguity in cellular adaptations to extreme environments. Here, we examine sequences and structures of tRNACAG from the CTG-Ser1 clade yeasts, finding that D. hansenii conserves the elements to translate ambiguously. Then, we show that D. hansenii has tolerance to conditions of salinity, acidity, alkalinity, and oxidative stress associated with phenotypic and ultrastructural changes. In these conditions, we found differential expression in both the logarithmic and stationary growth phases of tRNASer, tRNALeu, tRNACAG, LeuRS, and SerRS genes that could be involved in the adaptive process of this yeast. Finally, we compare the proteomic isoelectric points and hydropathy profiles, detecting that the most important variations among the physicochemical characteristics of D. hansenii proteins are in their hydrophobic and hydrophilic interactions with the medium. We propose that the ambiguous translation, i.e., leucylation or serynation, on translation of the CUG-encoded residues, could be linked to adaptation processes in extreme environments. Full article
(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)
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12 pages, 1331 KiB  
Article
Exploring Biocontrol of Unwanted Fungi by Autochthonous Debaryomyces hansenii Strains Isolated from Dry Meat Products
by Helena Chacón-Navarrete, Francisco Ruiz-Pérez, Francisco J. Ruiz-Castilla and José Ramos
J. Fungi 2022, 8(8), 873; https://doi.org/10.3390/jof8080873 - 19 Aug 2022
Cited by 5 | Viewed by 2608
Abstract
The exploration of alternatives to the use of chemical preservatives in food is a topic that has attracted great attention. The implementation of regulations associated with the reduction of these elements directly affects the production of cured meat products, with the premise of [...] Read more.
The exploration of alternatives to the use of chemical preservatives in food is a topic that has attracted great attention. The implementation of regulations associated with the reduction of these elements directly affects the production of cured meat products, with the premise of looking for more “natural” alternatives. From a previously identified collection of 24 strains of Debaryomyces hansenii, isolated from dry meat products of the “Valle de los Pedroches” (Córdoba), a screening was carried out to determine which strains had inhibitory potential against a battery of fungi belonging to the genera Aspergillus, Penicillium, and Candida. After a series of general trials, four strains showing the greatest potential were selected by a streak inhibition assay performed at several concentrations of NaCl. The inhibitory activity of the selected D. hansenii strains was later evaluated by measuring their fungal antagonistic diffusible and volatile compound production following radial inhibition and mouth-to-mouth approaches, respectively. Growth aspects, sporulation, and morphology changes were also considered during these assays. The results support ideas already raised in previous studies, such as the presence of D. hanseniii could imply a reduction of pathogenic fungi in food. Autochthonous yeast strains inhibited not only the mycelial growth, but also sporulation, which strengthens the biocontrol activity of this yeast. Our results show that, under certain conditions, all tested D. hansenii strains were able to alter the growth/development of fungi, being especially evident in the cases of Penicillium expansum and Aspergillus niger. Finally, our research can facilitate the future comparison of results in this area, since we contributed to standardize the methodology described to date, we quantified the number of yeast cells and spores used during the experiments, we homogenized growth conditions for both, yeasts, and molds, and applied an image analyzer software to quantify the growth of the studied microorganisms in solid media. Full article
(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)
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12 pages, 1814 KiB  
Article
Bioprocesses with Reduced Ecological Footprint by Marine Debaryomyces hansenii Strain for Potential Applications in Circular Economy
by Silvia Donzella, Claudia Capusoni, Luisa Pellegrino and Concetta Compagno
J. Fungi 2021, 7(12), 1028; https://doi.org/10.3390/jof7121028 - 30 Nov 2021
Cited by 3 | Viewed by 2171
Abstract
The possibility to perform bioprocesses with reduced ecological footprint to produce natural compounds and catalyzers of industrial interest is pushing the research for salt tolerant microorganisms able to grow on seawater-based media and able to use a wide range of nutrients coming from [...] Read more.
The possibility to perform bioprocesses with reduced ecological footprint to produce natural compounds and catalyzers of industrial interest is pushing the research for salt tolerant microorganisms able to grow on seawater-based media and able to use a wide range of nutrients coming from waste. In this study we focused our attention on a Debaryomyces hansenii marine strain (Mo40). We optimized cultivation in a bioreactor at low pH on seawater-based media containing a mixture of sugars (glucose and xylose) and urea. Under these conditions the strain exhibited high growth rate and biomass yield. In addition, we characterized potential applications of this yeast biomass in food/feed industry. We show that Mo40 can produce a biomass containing 45% proteins and 20% lipids. This strain is also able to degrade phytic acid by a cell-bound phytase activity. These features represent an appealing starting point for obtaining D. hansenii biomass in a cheap and environmentally friendly way, and for potential use as an additive or to replace unsustainable ingredients in the feed or food industries, as this species is included in the QPS EFSA list (Quality Presumption as Safe—European Food Safety Authority). Full article
(This article belongs to the Special Issue Recent Advances in Fundamental Research and Biotechnological Applications in Debaryomyces hansenii)
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