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Harrouard J, Eberlein C, Ballestra P, Dols-Lafargue M, Masneuf-Pomarede I, Miot-Sertier C, Schacherer J, Albertin W. Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast. Mol Ecol 2022; 32:2374-2395. [PMID: 35318747 DOI: 10.1111/mec.16439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 12/24/2022]
Abstract
Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.
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Affiliation(s)
- Jules Harrouard
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Chris Eberlein
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France
| | - Patricia Ballestra
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Isabelle Masneuf-Pomarede
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,BSA, 33170, Gradignan
| | - Cécile Miot-Sertier
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM, UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
| | - Warren Albertin
- UMR 1366 OENOLOGIE, Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, 33140, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, 33600, Pessac, France
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2
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Lebleux M, Denimal E, De Oliveira D, Marin A, Desroche N, Alexandre H, Weidmann S, Rousseaux S. Prediction of Genetic Groups within Brettanomyces bruxellensis through Cell Morphology Using a Deep Learning Tool. J Fungi (Basel) 2021; 7:jof7080581. [PMID: 34436120 PMCID: PMC8396822 DOI: 10.3390/jof7080581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
Abstract
Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly strain-dependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict their stress resistance capacities. Few predictive tools are available to reveal intraspecific diversity within B. bruxellensis species; also, they require expertise and can be expensive. In this study, a Random Amplified Polymorphic DNA (RAPD) adapted PCR method was used with three different primers to discriminate 74 different B. bruxellensis isolates. High correlation between the results of this method using the primer OPA-09 and those of a previous microsatellite analysis was obtained, allowing us to cluster the isolates among four genetic groups more quickly and cheaply than microsatellite analysis. To make analysis even faster, we further investigated the correlation suggested in a previous study between genetic groups and cell polymorphism using the analysis of optical microscopy images via deep learning. A Convolutional Neural Network (CNN) was trained to predict the genetic group of B. bruxellensis isolates with 96.6% accuracy. These methods make intraspecific discrimination among B. bruxellensis species faster, simpler and less costly. These results open up very promising new perspectives in oenology for the study of microbial ecosystems.
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Affiliation(s)
- Manon Lebleux
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
- Correspondence:
| | - Emmanuel Denimal
- AgroSup Dijon, Direction Scientifique, Appui à la Recherche, 26 Boulevard Docteur Petitjean, F-21000 Dijon, France;
| | - Déborah De Oliveira
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Ambroise Marin
- Plateau D’imagerie DimaCell, Esplanade Erasme, Agrosup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France;
| | | | - Hervé Alexandre
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Stéphanie Weidmann
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
| | - Sandrine Rousseaux
- Laboratoire VAlMiS-IUVV, AgroSup Dijon, UMR PAM A 02.102, University Bourgogne Franche-Comté, F-21000 Dijon, France; (D.D.O.); (H.A.); (S.W.); (S.R.)
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3
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G-Poblete C, Peña-Moreno IC, de Morais MA, Moreira S, Ganga MA. Biodiversity among Brettanomyces bruxellensis Strains Isolated from Different Wine Regions of Chile: Key Factors Revealed about its Tolerance to Sulphite. Microorganisms 2020; 8:E557. [PMID: 32295086 PMCID: PMC7232158 DOI: 10.3390/microorganisms8040557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
Brettanomyces bruxellensis is regarded as the main spoilage microorganism in the wine industry, owing to its production of off-flavours. It is difficult to eradicate owing to its high tolerance of adverse environmental conditions, such as low nutrient availability, low pH, and high levels of ethanol and SO2. In this study, the production of volatile phenols and the growth kinetics of isolates from various regions of Chile were evaluated under stressful conditions. Through randomly amplified polymorphic DNA (RAPD) analysis, 15 strains were identified. These were grown in the presence of p-coumaric acid, a natural antimicrobial and the main precursor of off-flavours, and molecular sulfur dioxide (mSO2), an antimicrobial synthetic used in the wine industry. When both compounds were used simultaneously, there were clear signs of an improvement in the fitness of most of the isolates, which showed an antagonistic interaction in which p-coumaric acid mitigates the effects of SO2. Fourteen strains were able to produce 4-vinylphenol, which showed signs of phenylacrylic acid decarboxylase activity, and most of them produced 4-ethylphenol as a result of active vinylphenol reductase. These results demonstrate for the first time the serious implications of using p-coumaric acid, not only for the production of off-flavours, but also for its protective action against the toxic effects of SO2.
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Affiliation(s)
- Camila G-Poblete
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
| | - Irina Charlot Peña-Moreno
- Department of Genetics, Biosciences Center, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (I.C.P.-M.); (M.A.d.M.J.)
| | - Marcos Antonio de Morais
- Department of Genetics, Biosciences Center, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (I.C.P.-M.); (M.A.d.M.J.)
| | - Sandra Moreira
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
| | - María Angélica Ganga
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
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Cibrario A, Avramova M, Dimopoulou M, Magani M, Miot-Sertier C, Mas A, Portillo MC, Ballestra P, Albertin W, Masneuf-Pomarede I, Dols-Lafargue M. Brettanomyces bruxellensis wine isolates show high geographical dispersal and long persistence in cellars. PLoS One 2019; 14:e0222749. [PMID: 31851678 PMCID: PMC6919574 DOI: 10.1371/journal.pone.0222749] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023] Open
Abstract
Brettanomyces bruxellensis is the main wine spoiler yeast all over the world, yet the structure of the populations associated with winemaking remains elusive. In this work, we considered 1411 wine isolates from 21 countries that were genotyped using twelve microsatellite markers. We confirmed that B. bruxellensis isolates from wine environments show high genetic diversity, with 58 and 42% of putative triploid and diploid individuals respectively distributed in 5 main genetic groups. The distribution in the genetic groups varied greatly depending on the country and/or the wine-producing region. However, the two possible triploid wine groups showing sulfite resistance/tolerance were identified in almost all regions/countries. Genetically identical isolates were also identified. The analysis of these clone groups revealed that a given genotype could be isolated repeatedly in the same winery over decades, demonstrating unsuspected persistence ability. Besides cellar residency, a great geographic dispersal was also evidenced, with some genotypes isolated in wines from different continents. Finally, the study of old isolates and/or isolates from old vintages revealed that only the diploid groups were identified prior 1990 vintages. The putative triploid groups were identified in subsequent vintages, and their proportion has increased steadily these last decades, suggesting adaptation to winemaking practices such as sulfite use. A possible evolutionary scenario explaining these results is discussed.
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Affiliation(s)
- Alice Cibrario
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
| | - Marta Avramova
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
| | - Maria Dimopoulou
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
- Department of Food Science and Technology, Faculty of Agriculture, Forestry and Natural Environments, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maura Magani
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
| | - Cécile Miot-Sertier
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
| | - Albert Mas
- Biotecnología Enológica. Dept. Bioquímica i Biotecnologia, Facultat d‘Enologia. Universitat Rovira i Virgili. C/ Marcel·lí Domingo, Tarragona, Spain
| | - Maria C. Portillo
- Biotecnología Enológica. Dept. Bioquímica i Biotecnologia, Facultat d‘Enologia. Universitat Rovira i Virgili. C/ Marcel·lí Domingo, Tarragona, Spain
| | - Patricia Ballestra
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
| | - Warren Albertin
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
- ENSCBP, Bordeaux INP, Pessac, France
| | - Isabelle Masneuf-Pomarede
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
- Bordeaux Sciences Agro, Gradignan, France
| | - Marguerite Dols-Lafargue
- Univ. Bordeaux, ISVV, Unité de recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d’Ornon, France
- ENSCBP, Bordeaux INP, Pessac, France
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5
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Sulfur dioxide response of Brettanomyces bruxellensis strains isolated from Greek wine. Food Microbiol 2018; 78:155-163. [PMID: 30497597 DOI: 10.1016/j.fm.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/27/2018] [Accepted: 10/23/2018] [Indexed: 12/17/2022]
Abstract
Brettanomyces bruxellensis is the most common spoilage wine yeast which can provoke great economic damage to the wine industry due to the production of undesirable odors. The capacity of the species to adapt in various environmental conditions offers a selective advantage that is reflected by intraspecific variability at genotypic and phenotypic level. In this study, microsatellite analysis of 22 strains isolated from Greek wine revealed the existence of distinct genetic subgroups that are correlated with their geographical origin. The response of these strains to increasing levels of sulfur dioxide confirmed the presence of both sensitive and tolerant strains, which belong to distinguished genetic clusters. The genetic categorization of B. bruxellensis strains could be used by the winemakers as a diagnostic tool regarding sulfur dioxide sensitivity.
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6
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Thanh VN, Duc Hien D, Yaguchi T, Sampaio JP, Lachance MA. Moniliella sojae sp. nov., a species of black yeasts isolated from Vietnamese soy paste (tuong), and reassignment of Moniliella suaveolens strains to Moniliella pyrgileucina sp. nov., Moniliella casei sp. nov. and Moniliella macrospora emend. comb. nov. Int J Syst Evol Microbiol 2018; 68:1806-1814. [PMID: 29521614 DOI: 10.1099/ijsem.0.002690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The presence of yeasts at different steps of Vietnamese soy paste production was studied. Yeast growth occurred during primary soybean fermentation, with the cell density reaching 4.106 c.f.u. ml-1, and terminated during brine fermentation. The dominant species were Pichia kudriavzevii and Millerozyma farinosa. Over the span of 14 years, nine strains of Moniliella were isolated. The strains had identical PCR fingerprints generated with primer (GAC)5 and identical D1/D2 and internal transcribed spacer (ITS) sequences. A D1/D2-based phylogeny indicated that the strains were closest to a group of four previously assigned as Moniliella suaveolens strains. Together they form a new lineage that is well separated from all known species, including M. suaveolens (over 12.7 % divergence). ITS sequences indicated the presence of four species differing from each other by 9-57 nt. The name Moniliella sojae sp. nov. is proposed to accommodate the strains isolated from Vietnamese soy paste, Moniliella pyrgileucina sp. nov. is proposed for PYCC 6800 and Moniliella casei sp. nov. is proposed for CBS 157.58. An emended combination Moniliella macrospora is proposed for CBS 221.32 and CBS 223.32. The type strains and MycoBank numbers are: M. sojae sp. nov., SS 4.2T=CBS 126448T=NRRL Y-48680T and MB 822871; M. pyrgileucina sp. nov., PYCC 6800T=CBS 15203T and MB 823030; M. casei sp. nov., CBS 157.58T=IFM 60348T and MB 822872; M. macrospora emend. comb. nov., CBS 221.32T (=MUCL 11527T) and MB 822874.
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Affiliation(s)
- Vu Nguyen Thanh
- Center for Industrial Microbiology, Food Industries Research Institute, 301-Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Dinh Duc Hien
- Center for Industrial Microbiology, Food Industries Research Institute, 301-Nguyen Trai, Thanh Xuan, Hanoi, Vietnam
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Jose Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
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7
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Guzzon R, Larcher R, Guarcello R, Francesca N, Settanni L, Moschetti G. Spoilage potential of brettanomyces bruxellensis strains isolated from Italian wines. Food Res Int 2018; 105:668-677. [DOI: 10.1016/j.foodres.2017.11.078] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
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8
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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.
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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
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9
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Crauwels S, Van Opstaele F, Jaskula-Goiris B, Steensels J, Verreth C, Bosmans L, Paulussen C, Herrera-Malaver B, de Jonge R, De Clippeleer J, Marchal K, De Samblanx G, Willems KA, Verstrepen KJ, Aerts G, Lievens B. Fermentation assays reveal differences in sugar and (off-) flavor metabolism across different Brettanomyces bruxellensis strains. FEMS Yeast Res 2016; 17:fow105. [PMID: 27956491 DOI: 10.1093/femsyr/fow105] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/08/2016] [Indexed: 11/14/2022] Open
Abstract
Brettanomyces (Dekkera) bruxellensis is an ascomycetous yeast of major importance in the food, beverage and biofuel industry. It has been isolated from various man-made ecological niches that are typically characterized by harsh environmental conditions such as wine, beer, soft drink, etc. Recent comparative genomics studies revealed an immense intraspecific diversity, but it is still unclear whether this genetic diversity also leads to systematic differences in fermentation performance and (off-)flavor production, and to what extent strains have evolved to match their ecological niche. Here, we present an evaluation of the fermentation properties of eight genetically diverse B. bruxellensis strains originating from beer, wine and soft drinks. We show that sugar consumption and aroma production during fermentation are determined by both the yeast strain and composition of the medium. Furthermore, our results indicate a strong niche adaptation of B. bruxellensis, most clearly for wine strains. For example, only strains originally isolated from wine were able to thrive well and produce the typical Brettanomyces-related phenolic off-flavors 4-ethylguaiacol and 4-ethylphenol when inoculated in red wine. Sulfite tolerance was found as a key factor explaining the observed differences in fermentation performance and off-flavor production. Sequence analysis of genes related to phenolic off-flavor production, however, revealed only marginal differences between the isolates tested, especially at the amino acid level. Altogether, our study provides novel insights in the Brettanomyces metabolism of flavor production, and is highly relevant for both the wine and beer industry.
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Affiliation(s)
- Sam Crauwels
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Filip Van Opstaele
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Barbara Jaskula-Goiris
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Jan Steensels
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Christel Verreth
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Lien Bosmans
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Caroline Paulussen
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Beatriz Herrera-Malaver
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Ronnie de Jonge
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Jessika De Clippeleer
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics and Department of Information Technology, IMinds, Ghent University, B-9000 Ghent, Belgium
| | - Gorik De Samblanx
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Kris A Willems
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
| | - Kevin J Verstrepen
- VIB Lab for Systems Biology and Centre of Microbial and Plant Genetics Lab for Genetics and Genomics, MS, KU Leuven, B-3001 Heverlee, Belgium
| | - Guido Aerts
- Laboratory for Enzyme, Fermentation and Brewing Technology, MS, KU Leuven, Technology Campus Ghent, B-9000 Ghent, Belgium
| | - Bart Lievens
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems (MS), KU Leuven, Campus De Nayer, B-2860 Sint-Katelijne-Waver, Belgium
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Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. Appl Microbiol Biotechnol 2015; 99:9123-34. [PMID: 26135985 DOI: 10.1007/s00253-015-6769-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/04/2015] [Accepted: 06/09/2015] [Indexed: 12/16/2022]
Abstract
Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.
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Di Toro MR, Capozzi V, Beneduce L, Alexandre H, Tristezza M, Durante M, Tufariello M, Grieco F, Spano G. Intraspecific biodiversity and ‘spoilage potential’ of Brettanomyces bruxellensis in Apulian wines. Lebensm Wiss Technol 2015. [DOI: 10.1016/j.lwt.2014.06.059] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Albertin W, Panfili A, Miot-Sertier C, Goulielmakis A, Delcamp A, Salin F, Lonvaud-Funel A, Curtin C, Masneuf-Pomarede I. Development of microsatellite markers for the rapid and reliable genotyping of Brettanomyces bruxellensis at strain level. Food Microbiol 2014; 42:188-95. [DOI: 10.1016/j.fm.2014.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 02/24/2014] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
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Schifferdecker AJ, Dashko S, Ishchuk OP, Piškur J. The wine and beer yeast Dekkera bruxellensis. Yeast 2014; 31:323-32. [PMID: 24932634 PMCID: PMC4257070 DOI: 10.1002/yea.3023] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/19/2014] [Accepted: 06/02/2014] [Indexed: 11/26/2022] Open
Abstract
Recently, the non-conventional yeast Dekkera bruxellensis has been gaining more and more attention in the food industry and academic research. This yeast species is a distant relative of Saccharomyces cerevisiae and is especially known for two important characteristics: on the one hand, it is considered to be one of the main spoilage organisms in the wine and bioethanol industry; on the other hand, it is 'indispensable' as a contributor to the flavour profile of Belgium lambic and gueuze beers. Additionally, it adds to the characteristic aromatic properties of some red wines. Recently this yeast has also become a model for the study of yeast evolution. In this review we focus on the recently developed molecular and genetic tools, such as complete genome sequencing and transformation, to study and manipulate this yeast. We also focus on the areas that are particularly well explored in this yeast, such as the synthesis of off-flavours, yeast detection methods, carbon metabolism and evolutionary history. © 2014 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Assessing genetic diversity among Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing. Appl Environ Microbiol 2014; 80:4398-413. [PMID: 24814796 DOI: 10.1128/aem.00601-14] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brettanomyces yeasts, with the species Brettanomyces (Dekkera) bruxellensis being the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However, B. bruxellensis is also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance, Brettanomyces yeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50 Brettanomyces strains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between the B. bruxellensis fingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate of B. bruxellensis (VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminate Brettanomyces strains and provides a first glimpse at the genetic diversity and genome plasticity of B. bruxellensis.
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Barquet M, Martín V, Medina K, Pérez G, Carrau F, Gaggero C. Tandem repeat-tRNA (TRtRNA) PCR method for the molecular typing of non-Saccharomyces subspecies. Appl Microbiol Biotechnol 2011; 93:807-14. [PMID: 22113560 DOI: 10.1007/s00253-011-3714-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 10/20/2011] [Accepted: 11/06/2011] [Indexed: 11/29/2022]
Abstract
There is a worldwide trend to understand the impact of non-Saccharomyces yeast species on the process of winemaking. Although the predominant species at the end of the fermentation is Saccharomyces cerevisiae, several non-Saccharomyces species present during the first days of the process can produce and/or release aromas that improve the bouquet and complexity of the final wine. Since no genomic sequences are available for the predominant non-Saccharomyces species selected from grapes or musts (Hanseniaspora uvarum, Hanseniaspora vineae, Hanseniaspora opuntiae, Metschnikowia pulcherrima, Candida zemplinina), a reproducible PCR method was devised to discriminate strains at the subspecies level. The method combines different oligonucleotides based on tandem repeats with a second oligonucleotide based on a conserved tRNA region, specific for ascomycetes. Tandem repeats are randomly dispersed in all eukaryotic genomes and tRNA genes are conserved and present in several copies in different chromosomes. As an example, the method was applied to discriminate native M. pulcherrima strains but it could be extended to differentiate strains from other non-Saccharomyces species. The biodiversity of species and strains found in the grape ecosystem is a potential source of new enzymes, fungicides and/or novel sustainable methods for biological control of phytopathogens.
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Affiliation(s)
- Marianne Barquet
- Molecular Biology Department, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), 11600, Montevideo, Uruguay
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Detection and identification of microorganisms in wine: a review of molecular techniques. J Ind Microbiol Biotechnol 2011; 38:1619-34. [DOI: 10.1007/s10295-011-1020-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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Esteve-Zarzoso B, Hierro N, Mas A, Guillamón JM. A new simplified AFLP method for wine yeast strain typing. Lebensm Wiss Technol 2010. [DOI: 10.1016/j.lwt.2010.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Daniel HM, Prasad GS. The role of culture collections as an interface between providers and users: the example of yeasts. Res Microbiol 2010; 161:488-96. [PMID: 20197089 DOI: 10.1016/j.resmic.2010.01.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/13/2010] [Accepted: 01/28/2010] [Indexed: 11/26/2022]
Abstract
The importance and species diversity of yeasts in food production are described, including a listing of agricultural applications. Two yeast species were selected for case studies on distribution patterns from microbial culture collections: the high representation of Saccharomyces cerevisiae in culture collections enabled global comparison, while Dekkera bruxellensis deposits and distributions were analyzed from the perspective of a single culture collection. In conclusion, culture collections need to cover temporal gaps between deposit and application of strains. The further development of culture collections in countries of high but underexplored species diversity should facilitate the conservation and management of microbial resources.
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Affiliation(s)
- Heide-Marie Daniel
- Mycothèque de l'Université catholique de Louvain (MUCL), Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
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Coulon J, Perello MC, Lonvaud-Funel A, de Revel G, Renouf V. Brettanomyces bruxellensis evolution and volatile phenols production in red wines during storage in bottles. J Appl Microbiol 2009; 108:1450-8. [PMID: 19840180 DOI: 10.1111/j.1365-2672.2009.04561.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The presence of Brettanomyces bruxellensis is an important issue during winemaking because of its volatile phenols production capacities. The aim of this study is to provide information on the ability of residual B. bruxellensis populations to multiply and spoil finished wines during storage in bottles. METHODS AND RESULTS Several finished wines were studied. Brettanomyces bruxellensis populations were monitored during two and a half months, and volatile phenols as well as chemical parameters regularly determined. Variable growth and volatile phenols synthesis capacities were evidenced, in particularly when cells are in a noncultivable state. In addition, the volatile phenol production was clearly shown to be a two-step procedure that could strongly be correlated to the physiological state of the yeast population. CONCLUSIONS This study underlines the importance of minimizing B. bruxellensis populations at the end of wine ageing to reduce volatile phenols production risk once the wine in bottle. Moreover, the physiological state of the yeast seems to have an important impact on ethyl-phenols production, hence demonstrating the importance of taking into account this parameter when analysing wine spoilage risks. SIGNIFICANCE AND IMPACT OF THE STUDY Little data exist about the survival of B. bruxellensis once the wine in bottle. This study provides information on the alteration risks encountered during wine storage in bottle and reveals the importance of carrying on further studies to increase the knowledge on B. bruxellensis physiology.
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Affiliation(s)
- J Coulon
- MICROFLORA, ISVV, Université de Bordeaux, Villenave d'Ornon, France.
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Renault P, Miot-Sertier C, Marullo P, Hernández-Orte P, Lagarrigue L, Lonvaud-Funel A, Bely M. Genetic characterization and phenotypic variability in Torulaspora delbrueckii species: Potential applications in the wine industry. Int J Food Microbiol 2009; 134:201-10. [DOI: 10.1016/j.ijfoodmicro.2009.06.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 06/16/2009] [Accepted: 06/20/2009] [Indexed: 11/17/2022]
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Agnolucci M, Vigentini I, Capurso G, Merico A, Tirelli A, Compagno C, Foschino R, Nuti M. Genetic diversity and physiological traits of Brettanomyces bruxellensis strains isolated from Tuscan Sangiovese wines. Int J Food Microbiol 2009; 130:238-44. [DOI: 10.1016/j.ijfoodmicro.2009.01.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 01/08/2009] [Accepted: 01/25/2009] [Indexed: 11/17/2022]
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Vigentini I, Fracassetti D, Picozzi C, Foschino R. Polymorphisms of Saccharomyces cerevisiae genes involved in wine production. Curr Microbiol 2008; 58:211-8. [PMID: 19005725 DOI: 10.1007/s00284-008-9310-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 10/02/2008] [Accepted: 10/09/2008] [Indexed: 11/30/2022]
Abstract
The setting up of new molecular methods for Saccharomyces cerevisiae typing is valuable in enology. Actually, the ability to discriminate different strains in wine making can have a benefit both for the control of the fermentation process and for the preservation of wine typicity. This study focused on the screening of single-nucleotide polymorphisms in genes involved in wine production that could evolve rapidly considering the selective pressure of the isolation environment. Preliminary screening of 30 genes in silico was performed, followed by the selection of 10 loci belonging to 8 genes. The sequence analysis showed a low polymorphism and a degree of heterozygosity. However, a new potential molecular target was recognized in the TPS1 gene coding for the trehalose-6-phosphate synthase enzyme involved in the ethanol resistance mechanism. This gene showed a 1.42% sequence diversity with seven different nucleotide substitutions. Moreover, classic techniques were applied to a collection of 50 S. cerevisiae isolates, mostly with enologic origin. Our results confirmed that the wine making was not carried out only by the inoculated commercial starter because indigenous strains of S. cerevisiae present during fermentation were detected. In addition, a high genetic relationship among some commercial cultures was found, highlighting imprecision or fraudulent practices by starter manufacturers.
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Affiliation(s)
- Ileana Vigentini
- Dipartimento di Scienze e Tecnologie Alimentari e Microbiologiche, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
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Renouf V, Strehaiano P, Lonvaud-Funel A. Effectiveness of dimethlydicarbonate to prevent Brettanomyces bruxellensis growth in wine. Food Control 2008. [DOI: 10.1016/j.foodcont.2007.03.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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