1
|
Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
Collapse
Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
| |
Collapse
|
2
|
Liu Z, Wang MM, Wang GS, Li AH, Wangmu, Wang QM. Hanseniaspora terricola sp. nov., an ascomycetous yeast isolated from Tibet. Int J Syst Evol Microbiol 2021; 71. [PMID: 33720007 DOI: 10.1099/ijsem.0.004741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight apiculate strains isolated from Tibet, PR China, were identified as Hanseniaspora taiwanica and a novel species of Hanseniaspora based on the sequence analysis of the ITS region, the D1/D2 domains of the LSU rRNA and the translation elongation factor 1-a (TEF1) gene. Among them, four strains with identical sequences of D1/D2 and ITS formed a separate branch from the known Hanseniaspora species in the phylogenetic trees, and differed from the known species by at least 17 (3 %) nucleotide (nt) substitutions in the D1/D2 domains and more than 6 % substitutions and inserts/deletes in the ITS region. The phylogenetic analysis indicated that those four strains represent a novel species of Hanseniaspora, for which the names Hanseniaspora terricola sp. nov. (holotype CGMCC 2.6175T; MycoBank MB 834591) is proposed. The other four strains belonging to H. taiwanica produce spherical, void or fusiform ascospores, which differ from the original description that ascospores are absent.
Collapse
Affiliation(s)
- Ze Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Man-Man Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Gui-Shuang Wang
- Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, Tibet, PR China.,School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| | - Ai-Hua Li
- China General Microbiological Culture Collection Center and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wangmu
- Tibet Agriculture & Animal Husbandry University, Nyingchi 860000, Tibet, PR China
| | - Qi-Ming Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, Hebei, PR China
| |
Collapse
|
3
|
Tavares MJ, Güldener U, Mendes-Ferreira A, Mira NP. Genome sequencing, annotation and exploration of the SO 2-tolerant non-conventional yeast Saccharomycodes ludwigii. BMC Genomics 2021; 22:131. [PMID: 33622260 PMCID: PMC7903802 DOI: 10.1186/s12864-021-07438-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharomycodes ludwigii belongs to the poorly characterized Saccharomycodeacea family and is known by its ability to spoil wines, a trait mostly attributable to its high tolerance to sulfur dioxide (SO2). To improve knowledge about Saccharomycodeacea our group determined whole-genome sequences of Hanseniaspora guilliermondii (UTAD222) and S. ludwigii (UTAD17), two members of this family. While in the case of H. guilliermondii the genomic information elucidated crucial aspects concerning the physiology of this species in the context of wine fermentation, the draft sequence obtained for S. ludwigii was distributed by more than 1000 contigs complicating extraction of biologically relevant information. In this work we describe the results obtained upon resequencing of S. ludwigii UTAD17 genome using PacBio as well as the insights gathered from the exploration of the annotation performed over the assembled genome. RESULTS Resequencing of S. ludwigii UTAD17 genome with PacBio resulted in 20 contigs totaling 13 Mb of assembled DNA and corresponding to 95% of the DNA harbored by this strain. Annotation of the assembled UTAD17 genome predicts 4644 protein-encoding genes. Comparative analysis of the predicted S. ludwigii ORFeome with those encoded by other Saccharomycodeacea led to the identification of 213 proteins only found in this species. Among these were six enzymes required for catabolism of N-acetylglucosamine, four cell wall β-mannosyltransferases, several flocculins and three acetoin reductases. Different from its sister Hanseniaspora species, neoglucogenesis, glyoxylate cycle and thiamine biosynthetic pathways are functional in S. ludwigii. Four efflux pumps similar to the Ssu1 sulfite exporter, as well as robust orthologues for 65% of the S. cerevisiae SO2-tolerance genes, were identified in S. ludwigii genome. CONCLUSIONS This work provides the first genome-wide picture of a S. ludwigii strain representing a step forward for a better understanding of the physiology and genetics of this species and of the Saccharomycodeacea family. The release of this genomic sequence and of the information extracted from it can contribute to guide the design of better wine preservation strategies to counteract spoilage prompted by S. ludwigii. It will also accelerate the exploration of this species as a cell factory, specially in production of fermented beverages where the use of Non-Saccharomyces species (including spoilage species) is booming.
Collapse
Affiliation(s)
- Maria J Tavares
- Department of Bioengineering, iBB- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Ulrich Güldener
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus von-Imhof- Forum 3, 85354, Freising, Germany
| | - Ana Mendes-Ferreira
- WM&B - Laboratory of Wine Microbiology & Biotechnology, Department of Biology and Environment, University of Trás-os-Montes and Alto Douro, 5001-801, Vila Real, Portugal. .,BioISI - Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal.
| | - Nuno P Mira
- Department of Bioengineering, iBB- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001, Lisbon, Portugal.
| |
Collapse
|
4
|
Guaragnella N, Chiara M, Capece A, Romano P, Pietrafesa R, Siesto G, Manzari C, Pesole G. Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential. Front Microbiol 2020; 10:3133. [PMID: 32038567 PMCID: PMC6986195 DOI: 10.3389/fmicb.2019.03133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/26/2019] [Indexed: 11/17/2022] Open
Abstract
A current trend in winemaking has highlighted the beneficial contribution of non-Saccharomyces yeasts to wine quality. Hanseniaspora uvarum is one of the more represented non-Saccharomyces species onto grape berries and plays a critical role in influencing the wine sensory profile, in terms of complexity and organoleptic richness. In this work, we analyzed a group of H. uvarum indigenous wine strains as for genetic as for technological traits, such as resistance to SO2 and β-glucosidase activity. Three strains were selected for genome sequencing, assembly and comparative genomic analyses at species and genus level. Hanseniaspora genomes appeared compact and contained a moderate number of genes, while rarefaction analyses suggested an open accessory genome, reflecting a rather incomplete representation of the Hanseniaspora gene pool in the currently available genomes. The analyses of patterns of functional annotation in the three indigenous H. uvarum strains showed distinct enrichment for several PFAM protein domains. In particular, for certain traits, such as flocculation related protein domains, the genetic prediction correlated well with relative flocculation phenotypes at lab-scale. This feature, together with the enrichment for oligo-peptide transport and lipid and amino acid metabolism domains, reveals a promising potential of these indigenous strains to be applied in fermentation processes and modulation of wine flavor and aroma. This study also contributes to increasing the catalog of publicly available genomes from H. uvarum strains isolated from natural grape samples and provides a good roadmap for unraveling the biodiversity and the biotechnological potential of these non-Saccharomyces yeasts.
Collapse
Affiliation(s)
- Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Angela Capece
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Patrizia Romano
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Rocchina Pietrafesa
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Gabriella Siesto
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Caterina Manzari
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| |
Collapse
|
5
|
Saubin M, Devillers H, Proust L, Brier C, Grondin C, Pradal M, Legras JL, Neuvéglise C. Investigation of Genetic Relationships Between Hanseniaspora Species Found in Grape Musts Revealed Interspecific Hybrids With Dynamic Genome Structures. Front Microbiol 2020; 10:2960. [PMID: 32010076 PMCID: PMC6974558 DOI: 10.3389/fmicb.2019.02960] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/09/2019] [Indexed: 01/11/2023] Open
Abstract
Hanseniaspora, a predominant yeast genus of grape musts, includes sister species recently reported as fast evolving. The aim of this study was to investigate the genetic relationships between the four most closely related species, at the population level. A multi-locus sequence typing strategy based on five markers was applied on 107 strains, confirming the clear delineation of species H. uvarum, H. opuntiae, H. guilliermondii, and H. pseudoguilliermondii. Huge variations were observed in the level of intraspecific nucleotide diversity, and differences in heterozygosity between species indicate different life styles. No clear population structure was detected based on geographical or substrate origins. Instead, H. guilliermondii strains clustered into two distinct groups, which may reflect a recent step toward speciation. Interspecific hybrids were detected between H. opuntiae and H. pseudoguilliermondii. Their characterization using flow cytometry, karyotypes and genome sequencing showed different genome structures in different ploidy contexts: allodiploids, allotriploids, and allotetraploids. Subculturing of an allotriploid strain revealed chromosome loss equivalent to one chromosome set, followed by an auto-diploidization event, whereas another auto-diploidized tetraploid showed a segmental duplication. Altogether, these results suggest that Hanseniaspora genomes are not only fast evolving but also highly dynamic.
Collapse
Affiliation(s)
- Méline Saubin
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Hugo Devillers
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Lucas Proust
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cathy Brier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cécile Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, Jouy-en-Josas, France
| | - Martine Pradal
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Luc Legras
- SPO, Univ Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| |
Collapse
|
6
|
The effects of apple variety, ripening stage, and yeast strain on the volatile composition of apple cider. Heliyon 2019; 5:e01953. [PMID: 31211267 PMCID: PMC6562328 DOI: 10.1016/j.heliyon.2019.e01953] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/11/2019] [Accepted: 06/07/2019] [Indexed: 11/20/2022] Open
Abstract
This work examined the degree of influence of apple variety, apple ripening stage, and yeast strain on the volatile composition of apple cider. Four apple varieties grown in Estonia were selected for the study – Antei, Melba, Kulikovskoye, and Orlovski Sinap. The must from the apples at various stages of ripening (unripe, ripe, overripe) underwent alcoholic fermentation using commercially available yeast strains. Gas chromatography - mass spectrometry was employed to assess the differences in volatile composition between the samples. Out of the variables analyzed in this work, apple variety turned out to be the primary attribute influencing the quality and aroma properties of apple cider. The effect of yeast strain and the maturity of the fruit was variety-specific where the volatile profiles of ciders made with Melba variety were the least influenced by the ripening stage of apples and yeast strains used for the fermentation.
Collapse
|
7
|
Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 2019; 14:e0210792. [PMID: 30699175 PMCID: PMC6353571 DOI: 10.1371/journal.pone.0210792] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/03/2019] [Indexed: 11/19/2022] Open
Abstract
A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).
Collapse
Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Ricardo Ulloa
- Laboratorio de Bioprocesos, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Neuquén, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| |
Collapse
|
8
|
Hand dermatitis with Hanseniaspora uvarum as a plausible causative agent. Postepy Dermatol Alergol 2018; 35:641-643. [PMID: 30618537 PMCID: PMC6320491 DOI: 10.5114/ada.2018.72854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 08/29/2017] [Indexed: 11/19/2022] Open
|
9
|
González B, Vázquez J, Cullen PJ, Mas A, Beltran G, Torija MJ. Aromatic Amino Acid-Derived Compounds Induce Morphological Changes and Modulate the Cell Growth of Wine Yeast Species. Front Microbiol 2018; 9:670. [PMID: 29696002 PMCID: PMC5904269 DOI: 10.3389/fmicb.2018.00670] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/21/2018] [Indexed: 12/13/2022] Open
Abstract
Yeasts secrete a large diversity of compounds during alcoholic fermentation, which affect growth rates and developmental processes, like filamentous growth. Several compounds are produced during aromatic amino acid metabolism, including aromatic alcohols, serotonin, melatonin, and tryptamine. We evaluated the effects of these compounds on growth parameters in 16 different wine yeasts, including non-Saccharomyces wine strains, for which the effects of these compounds have not been well-defined. Serotonin, tryptamine, and tryptophol negatively influenced yeast growth, whereas phenylethanol and tyrosol specifically affected non-Saccharomyces strains. The effects of the aromatic alcohols were observed at concentrations commonly found in wines, suggesting a possible role in microbial interaction during wine fermentation. Additionally, we demonstrated that aromatic alcohols and ethanol are able to affect invasive and pseudohyphal growth in a manner dependent on nutrient availability. Some of these compounds showed strain-specific effects. These findings add to the understanding of the fermentation process and illustrate the diversity of metabolic communication that may occur among related species during metabolic processes.
Collapse
Affiliation(s)
- Beatriz González
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Jennifer Vázquez
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Tarragona, Spain
| |
Collapse
|
10
|
Glycolytic Functions Are Conserved in the Genome of the Wine Yeast Hanseniaspora uvarum, and Pyruvate Kinase Limits Its Capacity for Alcoholic Fermentation. Appl Environ Microbiol 2017; 83:AEM.01580-17. [PMID: 28887422 DOI: 10.1128/aem.01580-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/03/2017] [Indexed: 01/11/2023] Open
Abstract
Hanseniaspora uvarum (anamorph Kloeckera apiculata) is a predominant yeast on wine grapes and other fruits and has a strong influence on wine quality, even when Saccharomyces cerevisiae starter cultures are employed. In this work, we sequenced and annotated approximately 93% of the H. uvarum genome. Southern and synteny analyses were employed to construct a map of the seven chromosomes present in a type strain. Comparative determinations of specific enzyme activities within the fermentative pathway in H. uvarum and S. cerevisiae indicated that the reduced capacity of the former yeast for ethanol production is caused primarily by an ∼10-fold-lower activity of the key glycolytic enzyme pyruvate kinase. The heterologous expression of the encoding gene, H. uvarumPYK1 (HuPYK1), and two genes encoding the phosphofructokinase subunits, HuPFK1 and HuPFK2, in the respective deletion mutants of S. cerevisiae confirmed their functional homology.IMPORTANCEHanseniaspora uvarum is a predominant yeast species on grapes and other fruits. It contributes significantly to the production of desired as well as unfavorable aroma compounds and thus determines the quality of the final product, especially wine. Despite this obvious importance, knowledge on its genetics is scarce. As a basis for targeted metabolic modifications, here we provide the results of a genomic sequencing approach, including the annotation of 3,010 protein-encoding genes, e.g., those encoding the entire sugar fermentation pathway, key components of stress response signaling pathways, and enzymes catalyzing the production of aroma compounds. Comparative analyses suggest that the low fermentative capacity of H. uvarum compared to that of Saccharomyces cerevisiae can be attributed to low pyruvate kinase activity. The data reported here are expected to aid in establishing H. uvarum as a non-Saccharomyces yeast in starter cultures for wine and cider fermentations.
Collapse
|
11
|
Guillamón JM, Barrio E. Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection. Front Microbiol 2017; 8:806. [PMID: 28522998 PMCID: PMC5415627 DOI: 10.3389/fmicb.2017.00806] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/19/2017] [Indexed: 01/09/2023] Open
Abstract
The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.
Collapse
Affiliation(s)
- José M Guillamón
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain
| | - Eladio Barrio
- Departamento de Biotecnología de los Alimentos, Instituto de Agroquímica y Tecnología de Alimentos - Consejo Superior de Investigaciones Científicas (CSIC)Valencia, Spain.,Departamento de Genética, Universidad de ValenciaValencia, Spain
| |
Collapse
|
12
|
Hilber-Bodmer M, Schmid M, Ahrens CH, Freimoser FM. Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi. BMC Microbiol 2017; 17:4. [PMID: 28056814 PMCID: PMC5216558 DOI: 10.1186/s12866-016-0908-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/06/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While recent advances in next generation sequencing technologies have enabled researchers to readily identify countless microbial species in soil, rhizosphere, and phyllosphere microbiomes, the biological functions of the majority of these species are unknown. Functional studies are therefore urgently needed in order to characterize the plethora of microorganisms that are being identified and to point out species that may be used for biotechnology or plant protection. Here, we used a dual culture assay and growth analyses to characterise yeasts (40 different isolates) and their antagonistic effect on 16 filamentous fungi; comprising plant pathogens, antagonists, and saprophytes. RESULTS Overall, this competition screen of 640 pairwise combinations revealed a broad range of outcomes, ranging from small stimulatory effects of some yeasts up to a growth inhibition of more than 80% by individual species. On average, yeasts isolated from soil suppressed filamentous fungi more strongly than phyllosphere yeasts and the antagonistic activity was a species-/isolate-specific property and not dependent on the filamentous fungus a yeast was interacting with. The isolates with the strongest antagonistic activity were Metschnikowia pulcherrima, Hanseniaspora sp., Cyberlindnera sargentensis, Aureobasidium pullulans, Candida subhashii, and Pichia kluyveri. Among these, the soil yeasts (C. sargentensis, A. pullulans, C. subhashii) assimilated and/or oxidized more di-, tri- and tetrasaccharides and organic acids than yeasts from the phyllosphere. Only the two yeasts C. subhashii and M. pulcherrima were able to grow with N-acetyl-glucosamine as carbon source. CONCLUSIONS The competition assays and physiological experiments described here identified known antagonists that have been implicated in the biological control of plant pathogenic fungi in the past, but also little characterised species such as C. subhashii. Overall, soil yeasts were more antagonistic and metabolically versatile than yeasts from the phyllosphere. Noteworthy was the strong antagonistic activity of the soil yeast C. subhashii, which had so far only been described from a clinical sample and not been studied with respect to biocontrol. Based on binary competition assays and growth analyses (e.g., on different carbon sources, growth in root exudates), C. subhashii was identified as a competitive and antagonistic soil yeast with potential as a novel biocontrol agent against plant pathogenic fungi.
Collapse
Affiliation(s)
- Maja Hilber-Bodmer
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland
| | - Michael Schmid
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.,SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.,SIB, Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Florian M Freimoser
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.B., 8820, Wädenswil, Switzerland.
| |
Collapse
|
13
|
Šuranská H, Raspor P, Uroić K, Golić N, Kos B, Mihajlović S, Begović J, Šušković J, Topisirović L, Čadež N. Characterisation of the yeast and mould biota in traditional white pickled cheeses by culture-dependent and independent molecular techniques. Folia Microbiol (Praha) 2016; 61:455-463. [PMID: 27027646 DOI: 10.1007/s12223-016-0455-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/02/2016] [Indexed: 11/28/2022]
Abstract
Artisanal white pickled cheese of Western Serbia is a product of complex microbial community which detection by culture-dependent method only is hampered by its limitations. Thus, in the present study, we used a culture-independent, semi-quantitative technique based on construction of an internal transcribed spacer (ITS)-clone library from metagenomic DNA. This approach, based on direct DNA extraction followed by amplification of fungal internal transcribed regions (ITS) cloned into plasmid and restricted by endonucleases, revealed greater species richness in analysed cheeses and their by-products (17 species in total) compared to the more commonly used techniques of the culture-dependent method (8 species) and LSU-DGGE (10 species). The most frequently occurring yeast species which are commonly associated with cheeses production were Debaryomyces hansenii, Kluyveromyces lactis and Candida zeylanoides. On the other hand, Yarrowia lipolytica and Galactomyces geotrichum were detected only in one cheese sample. Moreover, some species, mainly moulds (Filobasidium globisporum, Cladosporium sp., Aspergillus sp. or Alternaria sp.) were identified only by culture-independent methods. The discrepancies between the techniques were confirmed by low correlation factor and by different indices of general biodiversity and dominance of species. The ITS-clone library approach provides the opportunity to analyse complex fungal communities associated with food products.
Collapse
Affiliation(s)
- Hana Šuranská
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.,Institute of Food Science and Biotechnology, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Peter Raspor
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Ksenija Uroić
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Nataša Golić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Blaženka Kos
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Sanja Mihajlović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Begović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jagoda Šušković
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Ljubiša Topisirović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia.
| |
Collapse
|
14
|
Tufariello M, Durante M, Ramires FA, Grieco F, Tommasi L, Perbellini E, Falco V, Tasioula-Margari M, Logrieco AF, Mita G, Bleve G. New process for production of fermented black table olives using selected autochthonous microbial resources. Front Microbiol 2015; 6:1007. [PMID: 26441932 PMCID: PMC4585182 DOI: 10.3389/fmicb.2015.01007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/07/2015] [Indexed: 11/29/2022] Open
Abstract
Table olives represent one important fermented product in Europe and, in the world, their demand is constantly increasing. At the present time, no systems are available to control black table olives spontaneous fermentation by the Greek method. During this study, a new protocol for the production of black table olives belonging to two Italian (Cellina di Nardò and Leccino) and two Greek (Kalamàta and Conservolea) cultivars has been developed: for each table olive cultivar, starter-driven fermentations were performed inoculating, firstly, one selected autochthonous yeast starter and, subsequently, one selected autochthonous LAB starter. All starters formulation were able to dominate fermentation process. The olive fermentation was monitored using specific chemical descriptors able to identify a first stage (30 days) mainly characterized by aldehydes; a second period (60 days) mainly characterized by higher alcohols, styrene and terpenes; a third fermentation stage represented by acetate esters, esters and acids. A significant decrease of fermentation time (from 8 to 12 months to a maximum of 3 months) and an significant improvement in organoleptic characteristics of the final product were obtained. This study, for the first time, describes the employment of selected autochthonous microbial resources optimized to mimic the microbial evolution already recorded during spontaneous fermentations.
Collapse
Affiliation(s)
- Maria Tufariello
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Miriana Durante
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Francesca A Ramires
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Francesco Grieco
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Luca Tommasi
- Associazione "Olivicoltori di Puglia," Lecce, Italy
| | | | - Vittorio Falco
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Maria Tasioula-Margari
- Section of Food Chemistry, Department of Chemistry, University of Ioannina Ioannina, Greece
| | - Antonio F Logrieco
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari Bari, Italy
| | - Giovanni Mita
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| | - Gianluca Bleve
- Consiglio Nazionale delle Ricerche-Istituto di Scienze delle Produzioni Alimentari, Unità Operativa di Lecce Lecce, Italy
| |
Collapse
|
15
|
Genetic diversity of Clavispora lusitaniae isolated from Agave fourcroydes Lem, as revealed by DNA fingerprinting. J Microbiol 2015; 53:14-20. [PMID: 25557477 DOI: 10.1007/s12275-015-4373-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/24/2014] [Accepted: 11/01/2014] [Indexed: 10/24/2022]
Abstract
This study characterized Clavispora lusitaniae strains isolated from different stages of the processing and early fermentation of a henequen (Agave fourcroydes) spirit produced in Yucatan, Mexico using a molecular technique. Sixteen strains identified based on morphological features, obtained from different substrates, were typed molecularly. Nine different versions of the divergent D1/D2 domain of the large-subunit ribosomal DNA sequence were identified among the C. lusitaniae strains. The greatest degree of polymorphism was found in the 90-bp structural motif of the D2 domain. The MSP-PCR technique was able to differentiate 100% of the isolates. This study provides significant insight into the genetic diversity of the mycobiota present during the henequen fermentation process, especially that of C. lusitaniae, for which only a few studies in plants have been published. The applied MSP-PCR markers were very efficient in revealing olymorphisms between isolates of this species.
Collapse
|
16
|
Polyphasic re-examination of Debaryomyces hansenii strains and reinstatement of D. hansenii, D. fabryi and D. subglobosus. Persoonia - Molecular Phylogeny and Evolution of Fungi 2008; 21:17-27. [PMID: 20396575 PMCID: PMC2846122 DOI: 10.3767/003158508x336576] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 06/24/2008] [Indexed: 11/28/2022]
Abstract
The type species of the genus Debaryomyces, Debaryomyces hansenii, is a highly heterogeneous species. It has been isolated from a large diversity of natural sources including fruit, air, water, soil, but most frequently from processed food products. The species delineation of this yeast species urgently needs clarification. The heterogeneity in taxonomic characteristics has resulted in the description of varieties linked to D. hansenii. The aim of this study was to re-examine and classify D. hansenii using a polyphasic approach. A total of 65 D.hansenii isolates were examined, 57 representing the variety hansenii and nine the variety fabryi. The selection of strains for DNA reassociation and phylogenetic analysis was based on polymerase chain reaction mediated fingerprints using four mini- and microsatellite-specific primers. The discriminating power of growth at 35 °C and 37 °C was re-examined and ascospore production was observed. DNA reassociations and phylogenetic analyses were performed on selected isolates from each of the clusters obtained from the DNA fingerprint analyses. The data indicated the presence of three distinct species within the D. hansenii group, which were represented by type strains of former species and that are proposed to be reinstated: D. hansenii (CBS 767T = MUCL 49680T), D. fabryi (CBS 789T = MUCL 49731T) and D. subglobosus (CBS 792T = MUCL 49732T).
Collapse
|
17
|
Pérez-Brito D, Tapia-Tussell R, Quijano-Ramayo A, Larqué-Saavedra A, Lappe P. Molecular characterization of Kluyveromyces marxianus strains isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico. Mol Biotechnol 2007; 37:181-6. [PMID: 17952662 DOI: 10.1007/s12033-007-0036-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 05/02/2007] [Indexed: 11/30/2022]
Abstract
The molecular characterization of 14 strains of Kluyveromyces marxianus isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico, was performed by AP-PCR analysis, PCR-RFLP of 5.8S-ITS, and complete NTS regions. A sequence analysis of the D1/D2 domain of the 26S rDNA was also carried out in six selected strains. The AP-PCR approach had the highest discrimination power for the molecular characterization of new henequen K. marxianus strains. PCR-RFLP of 5.8S-ITS regions did not reveal polymorphisms in this group of strains. The restriction enzyme digestion analysis of NTS region enables the separation among strains which coincides with ascospore shape groups. The molecular tools used in this article may be useful to confirm a preliminary screen of yeasts isolated from henequen without the use of growth characteristics or morpho-physiological tests.
Collapse
Affiliation(s)
- Daisy Pérez-Brito
- Laboratorio GeMBio, Centro de Investigación Científica de Yucatán, Calle 43 # 130, Col. Chuburná de Hidalgo, Merida, Yucatan, Mexico,
| | | | | | | | | |
Collapse
|