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Jallet A, Friedrich A, Schacherer J. Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids. G3 (BETHESDA, MD.) 2023; 13:jkad115. [PMID: 37226280 PMCID: PMC10320193 DOI: 10.1093/g3journal/jkad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/21/2023] [Accepted: 05/18/2023] [Indexed: 05/26/2023]
Abstract
Gene expression variation can provide an overview of the changes in regulatory networks that underlie phenotypic diversity. Certain evolutionary trajectories such as polyploidization events can have an impact on the transcriptional landscape. Interestingly, the evolution of the yeast species Brettanomyces bruxellensis has been punctuated by diverse allopolyploidization events leading to the coexistence of a primary diploid genome associated with various haploid acquired genomes. To assess the impact of these events on gene expression, we generated and compared the transcriptomes of a set of 87 B. bruxellensis isolates, selected as being representative of the genomic diversity of this species. Our analysis revealed that acquired subgenomes strongly impact the transcriptional patterns and allow discrimination of allopolyploid populations. In addition, clear transcriptional signatures related to specific populations have been revealed. The transcriptional variations observed are related to some specific biological processes such as transmembrane transport and amino acids metabolism. Moreover, we also found that the acquired subgenome causes the overexpression of some genes involved in the production of flavor-impacting secondary metabolites, especially in isolates of the beer population.
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Affiliation(s)
- Arthur Jallet
- CNRS, GMGM UMR 7156, Université de Strasbourg, 67000 Strasbourg, France
| | - Anne Friedrich
- CNRS, GMGM UMR 7156, Université de Strasbourg, 67000 Strasbourg, France
| | - Joseph Schacherer
- CNRS, GMGM UMR 7156, Université de Strasbourg, 67000 Strasbourg, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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2
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Le Montagner P, Guilbaud M, Miot-Sertier C, Brocard L, Albertin W, Ballestra P, Dols-Lafargue M, Renouf V, Moine V, Bellon-Fontaine MN, Masneuf-Pomarède I. High intraspecific variation of the cell surface physico-chemical and bioadhesion properties in Brettanomyces bruxellensis. Food Microbiol 2023; 112:104217. [PMID: 36906300 DOI: 10.1016/j.fm.2023.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
Brettanomyces bruxellensis is the most damaging spoilage yeast in the wine industry because of its negative impact on the wine organoleptic qualities. The strain persistence in cellars over several years associated with recurrent wine contamination suggest specific properties to persist and survive in the environment through bioadhesion phenomena. In this work, the physico-chemical surface properties, morphology and ability to adhere to stainless steel were studied both on synthetic medium and on wine. More than 50 strains representative of the genetic diversity of the species were considered. Microscopy techniques made it possible to highlight a high morphological diversity of the cells with the presence of pseudohyphae forms for some genetic groups. Analysis of the physico-chemical properties of the cell surface reveals contrasting behaviors: most of the strains display a negative surface charge and hydrophilic behavior while the Beer 1 genetic group has a hydrophobic behavior. All strains showed bioadhesion abilities on stainless steel after only 3 h with differences in the concentration of bioadhered cells ranging from 2.2 × 102 cell/cm2 to 7.6 × 106 cell/cm2. Finally, our results show high variability of the bioadhesion properties, the first step in the biofilm formation, according to the genetic group with the most marked bioadhesion capacity for the beer group.
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Affiliation(s)
- Paul Le Montagner
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Laboratoire EXCELL, Floirac, France; Biolaffort, Floirac, France.
| | - Morgan Guilbaud
- Univ. Paris-Saclay, SayFood, AgroParisTech, INRAE UMR 782, 91300, Massy, France
| | - Cécile Miot-Sertier
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Lysiane Brocard
- Univ. Bordeaux, Plant Imaging Platform, Bordeaux Imaging Center, UMS 3420, CNRS, 33000, Bordeaux, France
| | - Warren Albertin
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSCBP, Bordeaux INP, 33600, Pessac, France
| | - Patricia Ballestra
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France
| | - Marguerite Dols-Lafargue
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; ENSCBP, Bordeaux INP, 33600, Pessac, France
| | | | | | | | - Isabelle Masneuf-Pomarède
- Univ. Bordeaux, INRAE, Bordeaux INP, Bordeaux Sciences Agro, OENO, UMR 1366, ISVV, 33140, Villenave d'Ornon, France; Bordeaux Sciences Agro, 33175, Gradignan, France
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3
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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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4
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Evaluating the influence of operational parameters of pulsed light on wine related yeasts: focus on inter- and intra-specific variability sensitivity. Food Microbiol 2022; 109:104121. [DOI: 10.1016/j.fm.2022.104121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022]
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5
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The teenage years of yeast population genomics trace history, admixing and getting wilder. Curr Opin Genet Dev 2022; 75:101942. [PMID: 35753210 DOI: 10.1016/j.gde.2022.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/22/2022]
Abstract
Population genomics studies the evolutionary processes that shape intraspecies genetic variations. In this review, I explore the insights into yeast-population genomics that have emerged from recent advances in sequencing. Genomes of the model Saccharomyces cerevisiae and many new yeast species from around the world are being used to address various aspects of population biology, including geographical origin, the level of introgression, domestication signatures, and outcrossing frequency. New long-read sequencing has enabled a greater capacity to quantify these variations at a finer resolution from complete de novo genomes at the population scale to phasing subgenomes of different origins. These resources provide a platform to dissect the relationship between phenotypes across environmental niches.
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6
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Varela C, Borneman AR. Molecular approaches improving our understanding of Brettanomyces physiology. FEMS Yeast Res 2022; 22:6585649. [PMID: 35561744 DOI: 10.1093/femsyr/foac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/20/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Brettanomyces species and particularly B. bruxellensis as the most studied representative, are strongly linked to industrial fermentation processes. This association is considered either positive or undesirable depending on the industry. While in some brewing applications and in kombucha production Brettanomyces yeasts contribute to the flavour and aroma profile of these beverages, in winemaking and bioethanol production Brettanomyces is considered a spoilage or contaminant microorganism. Nevertheless, understanding Brettanomyces biology and metabolism in detail will benefit all industries. This review discusses recent molecular biology tools including genomics, transcriptomics and genetic engineering techniques that can improve our understanding of Brettanomyces physiology and how these approaches can be used to make the industrial potential of this species a reality.
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Affiliation(s)
- Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia.,School of Agriculture, Food & Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Anthony R Borneman
- The Australian Wine Research Institute, PO Box 197, Glen Osmond, Adelaide, SA 5064, Australia.,School of Agriculture, Food & Wine, Faculty of Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
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7
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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: 8] [Impact Index Per Article: 4.0] [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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8
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9
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Eberlein C, Abou Saada O, Friedrich A, Albertin W, Schacherer J. Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species. Genome Res 2021; 31:2316-2326. [PMID: 34815309 PMCID: PMC8647821 DOI: 10.1101/gr.275380.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/25/2021] [Indexed: 01/01/2023]
Abstract
Polyploidization events are observed across the tree of life and occur in many fungi, plant, and animal species. During evolution, polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origin of polyploid populations is not always clear, and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced 71 strains from the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g., beer, contaminant of wine, kombucha, and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence <1%) or diverged copies (>3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations and exclude the known Brettanomyces sister species as possible donors. Finally, loss of heterozygosity events has shaped the structure of these polyploid genomes and underline their dynamics. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within the same species.
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Affiliation(s)
- Chris Eberlein
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Omar Abou Saada
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
| | - Warren Albertin
- Université de Bordeaux, ISVV, Unité de Recherche Œnologie EA 4577, USC 1366 INRA, Bordeaux INP, F-33140 Villenave d'Ornon, France
- ENSCBP, Bordeaux INP, 33600 Pessac, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, 67000 Strasbourg, France
- Institut Universitaire de France (IUF), 75231 Paris, France
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10
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Dutta A, Dutreux F, Schacherer J. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. eLife 2021; 10:70339. [PMID: 34159898 PMCID: PMC8245132 DOI: 10.7554/elife.70339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss of heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1% to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, that is, tracts extending to the end of the chromosome (n = 3168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.
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Affiliation(s)
- Abhishek Dutta
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Fabien Dutreux
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France.,Institut Universitaire de France (IUF), Paris, France
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11
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Paulin M, Miot-Sertier C, Dutilh L, Brasselet C, Delattre C, Pierre G, Dubessay P, Michaud P, Doco T, Ballestra P, Albertin W, Masneuf-Pomarède I, Moine V, Coulon J, Vallet-Courbin A, Maupeu J, Dols-Lafargue M. + Brettanomyces bruxellensis Displays Variable Susceptibility to Chitosan Treatment in Wine. Front Microbiol 2020; 11:571067. [PMID: 33013803 PMCID: PMC7498638 DOI: 10.3389/fmicb.2020.571067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/17/2020] [Indexed: 11/13/2022] Open
Abstract
Brettanomyces bruxellensis is the main spoilage microbial agent in red wines. The use of fungal chitosan has been authorized since 2009 as a curative treatment to eliminate this yeast in conventional wines and in 2018 in organic wines. As this species is known to exhibit great genetic and phenotypic diversity, we examined whether all the strains responded the same way to chitosan treatment. A collection of 53 strains of B. bruxellensis was used. In the conditions of the reference test, all were at least temporarily affected by the addition of chitosan to wine, with significant decrease of cultivable population. Some (41%) were very sensitive and no cultivable yeast was detected in wine or lees after 3 days of treatment, while others (13%) were tolerant and, after a slight drop in cultivability, resumed growth between 3 and 10 days and remained able to produce spoilage compounds. There were also many strains with intermediate behavior. The strain behavior was only partially linked to the strain genetic group. This behavior was little modulated by the physiological state of the strain or the dose of chitosan used (within the limits of the authorized doses). On the other hand, for a given strain, the sensitivity to chitosan treatment was modulated by the chitosan used and by the properties of the wine in which the treatment was carried out.
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Affiliation(s)
- Margot Paulin
- EA 4577 OEnologie, INRA, USC 1366, ISVV, Bordeaux INP, Université de Bordeaux, Bordeaux, France
| | - Cécile Miot-Sertier
- EA 4577 OEnologie, INRA, USC 1366, ISVV, Bordeaux INP, Université de Bordeaux, Bordeaux, France
| | - Lucie Dutilh
- Microflora-ADERA, EA 4577 OEnologie, ISVV, Bordeaux, France
| | - Clément Brasselet
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Cédric Delattre
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France.,Institut Universitaire de France, Paris, France
| | - Guillaume Pierre
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pascal Dubessay
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Philippe Michaud
- CNRS, SIGMA Clermont, Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thierry Doco
- INRA, SupAgro, UM1, UMR 1083, UMR Sciences pour l'Oenologie, Montpellier, France
| | - Patricia Ballestra
- EA 4577 OEnologie, INRA, USC 1366, ISVV, Bordeaux INP, Université de Bordeaux, Bordeaux, France
| | - Warren Albertin
- EA 4577 OEnologie, INRA, USC 1366, ISVV, Bordeaux INP, Université de Bordeaux, Bordeaux, France
| | | | | | | | | | - Julie Maupeu
- Microflora-ADERA, EA 4577 OEnologie, ISVV, Bordeaux, France
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12
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Colomer MS, Chailyan A, Fennessy RT, Olsson KF, Johnsen L, Solodovnikova N, Forster J. Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications. Front Microbiol 2020; 11:637. [PMID: 32373090 PMCID: PMC7177047 DOI: 10.3389/fmicb.2020.00637] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Brettanomyces yeasts have gained popularity in many sectors of the biotechnological industry, specifically in the field of beer production, but also in wine and ethanol production. Their unique properties enable Brettanomyces to outcompete conventional brewer’s yeast in industrially relevant traits such as production of ethanol and pleasant flavors. Recent advances in next-generation sequencing (NGS) and high-throughput screening techniques have facilitated large population studies allowing the selection of appropriate yeast strains with improved traits. In order to get a better understanding of Brettanomyces species and its potential for beer production, we sequenced the whole genome of 84 strains, which we make available to the scientific community and carried out several in vitro assays for brewing-relevant properties. The collection includes isolates from different substrates and geographical origin. Additionally, we have included two of the oldest Carlsberg Research Laboratory isolates. In this study, we reveal the phylogenetic pattern of Brettanomyces species by comparing the predicted proteomes of each strain. Furthermore, we show that the Brettanomyces collection is well described using similarity in genomic organization, and that there is a direct correlation between genomic background and phenotypic characteristics. Particularly, genomic patterns affecting flavor production, maltose assimilation, beta-glucosidase activity, and phenolic off-flavor (POF) production are reported. This knowledge yields new insights into Brettanomyces population survival strategies, artificial selection pressure, and loss of carbon assimilation traits. On a species-specific level, we have identified for the first time a POF negative Brettanomyces anomalus strain, without the main spoilage character of Brettanomyces species. This strain (CRL-90) has lost DaPAD1, making it incapable of converting ferulic acid to 4-ethylguaiacol (4-EG) and 4-ethylphenol (4-EP). This loss of function makes CRL-90 a good candidate for the production of characteristic Brettanomyces flavors in beverages, without the contaminant increase in POF. Overall, this study displays the potential of exploring Brettanomyces yeast species biodiversity to find strains with relevant properties applicable to the brewing industry.
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Affiliation(s)
- Marc Serra Colomer
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark.,National Institute for Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Chailyan
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Ross T Fennessy
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Kim Friis Olsson
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | | | | | - Jochen Forster
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
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