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De Guidi I, Galeote V, Blondin B, Legras JL. Copper-based grape pest management has impacted wine aroma. Sci Rep 2024; 14:10124. [PMID: 38698114 PMCID: PMC11066116 DOI: 10.1038/s41598-024-60335-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Despite the high energetic cost of the reduction of sulfate to H2S, required for the synthesis of sulfur-containing amino acids, some wine Saccharomyces cerevisiae strains have been reported to produce excessive amounts of H2S during alcoholic fermentation, which is detrimental to wine quality. Surprisingly, in the presence of sulfite, used as a preservative, wine strains produce more H2S than wild (oak) or wine velum (flor) isolates during fermentation. Since copper resistance caused by the amplification of the sulfur rich protein Cup1p is a specific adaptation trait of wine strains, we analyzed the link between copper resistance mechanism, sulfur metabolism and H2S production. We show that a higher content of copper in the must increases the production of H2S, and that SO2 increases the resistance to copper. Using a set of 51 strains we observed a positive and then negative relation between the number of copies of CUP1 and H2S production during fermentation. This complex pattern could be mimicked using a multicopy plasmid carrying CUP1, confirming the relation between copper resistance and H2S production. The massive use of copper for vine sanitary management has led to the selection of resistant strains at the cost of a metabolic tradeoff: the overproduction of H2S, resulting in a decrease in wine quality.
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Affiliation(s)
- Irene De Guidi
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Virginie Galeote
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Bruno Blondin
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France
| | - Jean-Luc Legras
- SPO, INRAE, Institut Agro, Université de Montpellier, 34060, Montpellier, France.
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2
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Tellini N, De Chiara M, Mozzachiodi S, Tattini L, Vischioni C, Naumova ES, Warringer J, Bergström A, Liti G. Ancient and recent origins of shared polymorphisms in yeast. Nat Ecol Evol 2024; 8:761-776. [PMID: 38472432 DOI: 10.1038/s41559-024-02352-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Shared genetic polymorphisms between populations and species can be ascribed to ancestral variation or to more recent gene flow. Here, we mapped shared polymorphisms in Saccharomyces cerevisiae and its sister species Saccharomyces paradoxus, which diverged 4-6 million years ago. We used a dense map of single-nucleotide diagnostic markers (mean distance 15.6 base pairs) in 1,673 sequenced S. cerevisiae isolates to catalogue 3,852 sequence blocks (≥5 consecutive markers) introgressed from S. paradoxus, with most being recent and clade-specific. The highly diverged wild Chinese S. cerevisiae lineages were depleted of introgressed blocks but retained an excess of individual ancestral polymorphisms derived from incomplete lineage sorting, perhaps due to less dramatic population bottlenecks. In the non-Chinese S. cerevisiae lineages, we inferred major hybridization events and detected cases of overlapping introgressed blocks across distinct clades due to either shared histories or convergent evolution. We experimentally engineered, in otherwise isogenic backgrounds, the introgressed PAD1-FDC1 gene pair that independently arose in two S. cerevisiae clades and revealed that it increases resistance against diverse antifungal drugs. Overall, our study retraces the histories of divergence and secondary contacts across S. cerevisiae and S. paradoxus populations and unveils a functional outcome.
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Affiliation(s)
- Nicolò Tellini
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France
| | | | | | | | | | - Elena S Naumova
- Kurchatov Complex for Genetic Research (GosNIIgenetika), National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Gianni Liti
- CNRS, INSERM, IRCAN, Côte d'Azur University, Nice, France.
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3
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Campos ACS, Araújo TM, Moraes L, Corrêa dos Santos RA, Goldman GH, Riano-Pachon DM, Oliveira JVDC, Squina FM, Castro IDM, Trópia MJM, da Cunha AC, Rosse IC, Brandão RL. Selected cachaça yeast strains share a genomic profile related to traits relevant to industrial fermentation processes. Appl Environ Microbiol 2024; 90:e0175923. [PMID: 38112453 PMCID: PMC10807443 DOI: 10.1128/aem.01759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 12/21/2023] Open
Abstract
The isolation and selection of yeast strains to improve the quality of the cachaça-Brazilian Spirit-have been studied in our research group. Our strategy considers Saccharomyces cerevisiae as the predominant species involved in sugarcane juice fermentation and the presence of different stressors (osmolarity, temperature, ethanol content, and competition with other microorganisms). It also considers producing balanced concentrations of volatile compounds (higher alcohols and acetate and/or ethyl esters), flocculation capacity, and ethanol production. Since the genetic bases behind these traits of interest are not fully established, the whole genome sequencing of 11 different Saccharomyces cerevisiae strains isolated and selected from different places was analyzed to identify the presence of a specific genetic variation common to cachaça yeast strains. We have identified 20,128 single-nucleotide variants shared by all genomes. Of these shared variants, 37 were new variants (being six missenses), and 4,451 were identified as missenses. We performed a detailed functional annotation (using enrichment analysis, protein-protein interaction network analysis, and database and in-depth literature searches) of these new and missense variants. Many genes carrying these variations were involved in the phenotypes of flocculation, tolerance to fermentative stresses, and production of volatile compounds and ethanol. These results demonstrate the existence of a genetic profile shared by the 11 strains under study that could be associated with the applied selective strategy. Thus, this study points out genes and variants that may be used as molecular markers for selecting strains well suited to the fermentation process, including genetic improvement by genome editing, ultimately producing high-quality beverages and adding value.IMPORTANCEThis work demonstrates the existence of new genetic markers related to different phenotypes used to select yeast strains and mutations in genes directly involved in producing flavoring compounds and ethanol, and others related to flocculation and stress resistance.
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Affiliation(s)
- Anna Clara Silva Campos
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Thalita Macedo Araújo
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Área de Ciências Biológicas, Instituto Federal de Minas Gerais, Campus Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Lauro Moraes
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renato Augusto Corrêa dos Santos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Gustavo Henrique Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Diego Maurício Riano-Pachon
- Laboratório de Biologia Computacional, Evolutiva e de Sistemas, Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | | | | | - Ieso de Miranda Castro
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Maria José Magalhães Trópia
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
| | - Aureliano Claret da Cunha
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório de Engenharia de Alimentos, Departamento de Alimentos, Escola de Nutrição, Salvador, Brazil
| | - Izinara C. Rosse
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
- Laboratório Multiusuário de Bioinformática, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Rogelio Lopes Brandão
- Laboratório de Biologia Celular e Molecular, Departamento de Farmácia, Escola de Farmácia, Ouro Preto, Brazil
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4
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Daute M, Jack F, Walker G. The potential for Scotch Malt Whisky flavour diversification by yeast. FEMS Yeast Res 2024; 24:foae017. [PMID: 38684485 PMCID: PMC11095643 DOI: 10.1093/femsyr/foae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/13/2024] [Accepted: 04/28/2024] [Indexed: 05/02/2024] Open
Abstract
Scotch Whisky, a product of high importance to Scotland, has gained global approval for its distinctive qualities derived from the traditional production process, which is defined in law. However, ongoing research continuously enhances Scotch Whisky production and is fostering a diversification of flavour profiles. To be classified as Scotch Whisky, the final spirit needs to retain the aroma and taste of 'Scotch'. While each production step contributes significantly to whisky flavour-from malt preparation and mashing to fermentation, distillation, and maturation-the impact of yeast during fermentation is crucially important. Not only does the yeast convert the sugar to alcohol, it also produces important volatile compounds, e.g. esters and higher alcohols, that contribute to the final flavour profile of whisky. The yeast chosen for whisky fermentations can significantly influence whisky flavour, so the yeast strain employed is of high importance. This review explores the role of yeast in Scotch Whisky production and its influence on flavour diversification. Furthermore, an extensive examination of nonconventional yeasts employed in brewing and winemaking is undertaken to assess their potential suitability for adoption as Scotch Whisky yeast strains, followed by a review of methods for evaluating new yeast strains.
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Affiliation(s)
- Martina Daute
- Division of Engineering and Food Sciences, School of Applied Sciences, Abertay University, Bell St, DD1 1HG, Dundee, Scotland
- The Scotch Whisky Research Institute, Research Ave N, EH14 4AP, Edinburgh, Scotland
| | - Frances Jack
- The Scotch Whisky Research Institute, Research Ave N, EH14 4AP, Edinburgh, Scotland
| | - Graeme Walker
- Division of Engineering and Food Sciences, School of Applied Sciences, Abertay University, Bell St, DD1 1HG, Dundee, Scotland
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5
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Chen J, Garfinkel DJ, Bergman CM. Horizontal transfer and recombination fuel Ty4 retrotransposon evolution in Saccharomyces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572574. [PMID: 38187645 PMCID: PMC10769310 DOI: 10.1101/2023.12.20.572574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Horizontal transposon transfer (HTT) plays an important role in the evolution of eukaryotic genomes, however the detailed evolutionary history and impact of most HTT events remain to be elucidated. To better understand the process of HTT in closely-related microbial eukaryotes, we studied Ty4 retrotransposon subfamily content and sequence evolution across the genus Saccharomyces using short- and long-read whole genome sequence data, including new PacBio genome assemblies for two S. mikatae strains. We find evidence for multiple independent HTT events introducing the Tsu4 subfamily into specific lineages of S. paradoxus, S. cerevisiae, S. eubayanus, S. kudriavzevii and the ancestor of the S. mikatae/S. jurei species pair. In both S. mikatae and S. kudriavzevii, we identified novel Ty4 clades that were independently generated through recombination between resident and horizontally-transferred subfamilies. Our results reveal that recurrent HTT and lineage-specific extinction events lead to a complex pattern of Ty4 subfamily content across the genus Saccharomyces. Moreover, our results demonstrate how HTT can lead to coexistence of related retrotransposon subfamilies in the same genome that can fuel evolution of new retrotransposon clades via recombination.
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Affiliation(s)
- Jingxuan Chen
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - David J. Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Casey M. Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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6
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Rosa CA, Lachance MA, Limtong S, Santos ARO, Landell MF, Gombert AK, Morais PB, Sampaio JP, Gonçalves C, Gonçalves P, Góes-Neto A, Santa-Brígida R, Martins MB, Janzen DH, Hallwachs W. Yeasts from tropical forests: Biodiversity, ecological interactions, and as sources of bioinnovation. Yeast 2023; 40:511-539. [PMID: 37921426 DOI: 10.1002/yea.3903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Tropical rainforests and related biomes are found in Asia, Australia, Africa, Central and South America, Mexico, and many Pacific Islands. These biomes encompass less than 20% of Earth's terrestrial area, may contain about 50% of the planet's biodiversity, and are endangered regions vulnerable to deforestation. Tropical rainforests have a great diversity of substrates that can be colonized by yeasts. These unicellular fungi contribute to the recycling of organic matter, may serve as a food source for other organisms, or have ecological interactions that benefit or harm plants, animals, and other fungi. In this review, we summarize the most important studies of yeast biodiversity carried out in these biomes, as well as new data, and discuss the ecology of yeast genera frequently isolated from tropical forests and the potential of these microorganisms as a source of bioinnovation. We show that tropical forest biomes represent a tremendous source of new yeast species. Although many studies, most using culture-dependent methods, have already been carried out in Central America, South America, and Asia, the tropical forest biomes of Africa and Australasia remain an underexplored source of novel yeasts. We hope that this review will encourage new researchers to study yeasts in unexplored tropical forest habitats.
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Affiliation(s)
- Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Biodiversity Center Kasetsart University, Kasetsart University, Bangkok, Thailand
- Academy of Science, Royal Society of Thailand, Bangkok, Thailand
| | - Ana R O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Melissa F Landell
- Setor de Genética, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas, Maceió, Alagoas, Brazil
| | - Andreas K Gombert
- Department of Engineering and Food Technology, School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Paula B Morais
- Laboratório de Microbiologia Ambiental e Biotecnologia, Campus de Palmas, Universidade Federal do Tocantins, Palmas, Tocantins, Brazil
| | - José P Sampaio
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Carla Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-i4HB, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Aristóteles Góes-Neto
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Paraíso F, Pontes A, Neves J, Lebani K, Hutzler M, Zhou N, Sampaio JP. Do microbes evade domestication? - Evaluating potential ferality among diastatic Saccharomyces cerevisiae. Food Microbiol 2023; 115:104320. [PMID: 37567630 DOI: 10.1016/j.fm.2023.104320] [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: 02/23/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 08/13/2023]
Abstract
Certain lineages of the wine, beer and bread yeast Saccharomyces cerevisiae have diastatic activity. They contain the chimeric gene STA1 that codes for an extracellular glucoamylase which enables the strains to degrade starch and dextrins. Beer contaminations by diastatic yeasts can be dangerous because they can cause super-attenuation due to the consumption of otherwise non-fermentable oligosaccharides, gushing and off-flavours. Given that diastatic yeasts can be used for beer fermentation it is important to understand the relationship between production and contaminant strains, their natural reservoirs and entry routes into the brewery. Here, we analyze real cases of contamination in a Portuguese craft brewery over a period of 18 months. By analyzing with whole genome sequencing several contaminants, we show that recurrent contaminations by diastatic yeasts are caused by environmental strains. Moreover, some beer contaminants were closely related to diastatic environmental strains isolated in Botswana. We observed the widespread presence of domestication signatures in diastatic strains. Moreover, the combined phylogeny of STA1 and its ancestor, SGA1, suggested a single STA1 origin, as ancient as the entire lineage of diastatic yeasts. Together, our results suggest that diastatic yeasts isolated in natural settings could be escaping from domestication settings and becoming feral.
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Affiliation(s)
- Francisca Paraíso
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Nova School of Science and Technology, Portugal
| | - Ana Pontes
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Nova School of Science and Technology, Portugal
| | - Joana Neves
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Nova School of Science and Technology, Portugal
| | - Kebaneilwe Lebani
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| | - Mathias Hutzler
- Technical University of Munich, Research Center Weihenstephan for Brewing and Food Quality, Alte Akademie 3, 85354 Freising, Germany
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| | - José Paulo Sampaio
- UCIBIO - Applied Molecular Biosciences Unit, Department of Life Sciences, Nova School of Science and Technology, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Nova School of Science and Technology, Portugal.
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Muller G, de Godoy VR, Dário MG, Duval EH, Alves-Jr SL, Bücker A, Rosa CA, Dunn B, Sherlock G, Stambuk BU. Improved Sugarcane-Based Fermentation Processes by an Industrial Fuel-Ethanol Yeast Strain. J Fungi (Basel) 2023; 9:803. [PMID: 37623574 PMCID: PMC10456111 DOI: 10.3390/jof9080803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
In Brazil, sucrose-rich broths (cane juice and/or molasses) are used to produce billions of liters of both fuel ethanol and cachaça per year using selected Saccharomyces cerevisiae industrial strains. Considering the important role of feedstock (sugar) prices in the overall process economics, to improve sucrose fermentation the genetic characteristics of a group of eight fuel-ethanol and five cachaça industrial yeasts that tend to dominate the fermentors during the production season were determined by array comparative genomic hybridization. The widespread presence of genes encoding invertase at multiple telomeres has been shown to be a common feature of both baker's and distillers' yeast strains, and is postulated to be an adaptation to sucrose-rich broths. Our results show that only two strains (one fuel-ethanol and one cachaça yeast) have amplification of genes encoding invertase, with high specific activity. The other industrial yeast strains had a single locus (SUC2) in their genome, with different patterns of invertase activity. These results indicate that invertase activity probably does not limit sucrose fermentation during fuel-ethanol and cachaça production by these industrial strains. Using this knowledge, we changed the mode of sucrose metabolism of an industrial strain by avoiding extracellular invertase activity, overexpressing the intracellular invertase, and increasing its transport through the AGT1 permease. This approach allowed the direct consumption of the disaccharide by the cells, without releasing glucose or fructose into the medium, and a 11% higher ethanol production from sucrose by the modified industrial yeast, when compared to its parental strain.
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Affiliation(s)
- Gabriela Muller
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Victor R. de Godoy
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Marcelo G. Dário
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Eduarda H. Duval
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Sergio L. Alves-Jr
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Augusto Bücker
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
| | - Carlos A. Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil;
| | - Barbara Dunn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; (B.D.); (G.S.)
| | - Boris U. Stambuk
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil; (G.M.); (V.R.d.G.); (M.G.D.); (E.H.D.); (S.L.A.-J.); (A.B.)
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9
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De Guidi I, Legras JL, Galeote V, Sicard D. Yeast domestication in fermented food and beverages: past research and new avenues. Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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10
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Díaz-Muñoz C, Verce M, De Vuyst L, Weckx S. Phylogenomics of a Saccharomyces cerevisiae cocoa strain reveals adaptation to a West African fermented food population. iScience 2022; 25:105309. [PMID: 36304120 PMCID: PMC9593892 DOI: 10.1016/j.isci.2022.105309] [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: 03/09/2022] [Revised: 07/22/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022] Open
Abstract
Various yeast strains have been proposed as candidate starter cultures for cocoa fermentation, especially strains of Saccharomyces cerevisiae. In the current study, the genome of the cocoa strain S. cerevisiae IMDO 050523 was unraveled based on a combination of long- and short-read sequencing. It consisted of 16 nuclear chromosomes and a mitochondrial chromosome, which were organized in 20 contigs, with only two small gaps. A phylogenomic analysis of this genome together with another 105 S cerevisiae genomes, among which 20 from cocoa strains showed a geographical distribution of the latter, including S. cerevisiae IMDO 050523. Its genome clustered together with that of a West African fermented food population, indicating a wider adaptation to West African food niches than cocoa. Furthermore, S. cerevisiae IMDO 050523 contained genetic signatures involved in sucrose hydrolysis, pectin degradation, osmotolerance, and conserved amino acid changes in key ester-producing enzymes that could point toward specific niche adaptations.
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Affiliation(s)
- Cristian Díaz-Muñoz
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marko Verce
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium,Corresponding author
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11
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García-Ríos E, Guillamón JM. Genomic Adaptations of Saccharomyces Genus to Wine Niche. Microorganisms 2022; 10:microorganisms10091811. [PMID: 36144411 PMCID: PMC9500811 DOI: 10.3390/microorganisms10091811] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Wine yeast have been exposed to harsh conditions for millennia, which have led to adaptive evolutionary strategies. Thus, wine yeasts from Saccharomyces genus are considered an interesting and highly valuable model to study human-drive domestication processes. The rise of whole-genome sequencing technologies together with new long reads platforms has provided new understanding about the population structure and the evolution of wine yeasts. Population genomics studies have indicated domestication fingerprints in wine yeast, including nucleotide variations, chromosomal rearrangements, horizontal gene transfer or hybridization, among others. These genetic changes contribute to genetically and phenotypically distinct strains. This review will summarize and discuss recent research on evolutionary trajectories of wine yeasts, highlighting the domestication hallmarks identified in this group of yeast.
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Affiliation(s)
- Estéfani García-Ríos
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
- Department of Science, Universidad Internacional de Valencia-VIU, Pintor Sorolla 21, 46002 Valencia, Spain
- Correspondence:
| | - José Manuel Guillamón
- Department of Food Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, 46980 Paterna, Spain
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12
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Silva M, Pontes A, Franco-Duarte R, Soares P, Sampaio JP, Sousa MJ, Brito PH. A glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast. Mol Ecol 2022; 32:2396-2412. [PMID: 35298044 DOI: 10.1111/mec.16428] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 11/28/2022]
Abstract
Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content, or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked with anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix - Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.
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Affiliation(s)
- Margarida Silva
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ana Pontes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Maria João Sousa
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Braga, Portugal
| | - Patrícia H Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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13
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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14
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Villarreal P, Quintrel PA, Olivares-Muñoz S, Ruiz JJ, Nespolo RF, Cubillos FA. Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia. Yeast 2021; 39:128-140. [PMID: 34406697 DOI: 10.1002/yea.3662] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/11/2022] Open
Abstract
The quest for new wild yeasts has increasingly gained attention because of their potential ability to provide unique organoleptic characters to fermented beverages. In this sense, Patagonia offers a wide diversity of ethanol-tolerant yeasts and stands out as a bioprospecting alternative. This study characterized the genetic and phenotypic diversity of yeast isolates obtained from Central Chilean Patagonia and analyzed their fermentation potential under different fermentative conditions. We recovered 125 colonies from Nothofagus spp. bark samples belonging to five yeast species: Saccharomyces eubayanus, Saccharomyces uvarum, Lachancea cidri, Kregervanrija delftensis, and Hanseniaspora valbyensis. High-throughput microcultivation assays demonstrated the extensive phenotypic diversity among Patagonian isolates, where Saccharomyces spp and L. cidri isolates exhibited the most outstanding fitness scores across the conditions tested. Fermentation performance assays under wine, mead, and beer conditions demonstrated the specific potential of the different species for each particular beverage. Saccharomyces spp. were the only isolates able to ferment beer wort. Interestingly, we found that L. cidri is a novel candidate species to ferment wine and mead, exceeding the fermentation capacity of a commercial strain. Unlike commercial strains, we found that L. cidri does not require nutritional supplements for efficient mead fermentation. In addition, L. cidri produces succinic and acetic acids, providing a distinct profile to the final fermented product. This work demonstrates the importance of bioprospecting efforts in Patagonia to isolate novel wild yeast strains with extraordinary biotechnological potential for the fermentation industry.
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Affiliation(s)
- Pablo Villarreal
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Pablo A Quintrel
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sebastián Olivares-Muñoz
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - José J Ruiz
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco A Cubillos
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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15
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Saccharomyces cerevisiae strains used industrially for bioethanol production. Essays Biochem 2021; 65:147-161. [PMID: 34156078 DOI: 10.1042/ebc20200160] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 01/21/2023]
Abstract
Fuel ethanol is produced by the yeast Saccharomyces cerevisiae mainly from corn starch in the United States and from sugarcane sucrose in Brazil, which together manufacture ∼85% of a global yearly production of 109.8 million m3 (in 2019). While in North America genetically engineered (GE) strains account for ∼80% of the ethanol produced, including strains that express amylases and are engineered to produce higher ethanol yields; in South America, mostly (>90%) non-GE strains are used in ethanol production, primarily as starters in non-aseptic fermentation systems with cell recycling. In spite of intensive research exploring lignocellulosic ethanol (or second generation ethanol), this option still accounts for <1% of global ethanol production. In this mini-review, we describe the main aspects of fuel ethanol production, emphasizing bioprocesses operating in North America and Brazil. We list and describe the main properties of several commercial yeast products (i.e., yeast strains) that are available worldwide to bioethanol producers, including GE strains with their respective genetic modifications. We also discuss recent studies that have started to shed light on the genes and traits that are important for the persistence and dominance of yeast strains in the non-aseptic process in Brazil. While Brazilian bioethanol yeast strains originated from a historical process of domestication for sugarcane fermentation, leading to a unique group with significant economic applications, in U.S.A., guided selection, breeding and genetic engineering approaches have driven the generation of new yeast products for the market.
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16
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Ruiz J, de Celis M, Martín-Santamaría M, Benito-Vázquez I, Pontes A, Lanza VF, Sampaio JP, Santos A, Belda I. Global distribution of IRC7 alleles in Saccharomyces cerevisiae populations: a genomic and phenotypic survey within the wine clade. Environ Microbiol 2021; 23:3182-3195. [PMID: 33973343 DOI: 10.1111/1462-2920.15540] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
The adaptation to the different biotic and abiotic factors of wine fermentation has led to the accumulation of numerous genomic hallmarks in Saccharomyces cerevisiae wine strains. IRC7, a gene encoding a cysteine-S-β-lyase enzyme related volatile thiols production in wines, has two alleles: a full-length allele (IRC7F ) and a mutated one (IRC7S ), harbouring a 38 bp-deletion. Interestingly, IRC7S -encoding a less active enzyme - appears widespread amongst wine populations. Studying the global distribution of the IRC7S allele in different yeast lineages, we confirmed its high prevalence in the Wine clade and demonstrated a minority presence in other domesticated clades (Wine-PDM, Beer and Bread) while it is completely missing in wild clades. Here, we show that IRC7S -homozygous (HS) strains exhibited both fitness and competitive advantages compared with IRC7F -homozygous (HF) strains. There are some pieces of evidence of the direct contribution of the IRC7S allele to the outstanding behaviour of HS strains (i.e., improved response to oxidative stress conditions and higher tolerance to high copper levels); however, we also identified a set of sequence variants with significant co-occurrence patterns with the IRC7S allele, which can be co-contributing to the fitness and competitive advantages of HS strains in wine fermentations.
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Affiliation(s)
- Javier Ruiz
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Miguel de Celis
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - María Martín-Santamaría
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Iván Benito-Vázquez
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ana Pontes
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Val F Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, IRYCIS, Madrid, 28034, Spain
| | - José Paulo Sampaio
- Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Antonio Santos
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology. Unit of Microbiology. Biology Faculty, Complutense University of Madrid, Madrid, 28040, Spain
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17
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Rácz HV, Mukhtar F, Imre A, Rádai Z, Gombert AK, Rátonyi T, Nagy J, Pócsi I, Pfliegler WP. How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes. Yeast 2021; 38:453-470. [PMID: 33844327 DOI: 10.1002/yea.3562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.
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Affiliation(s)
- Hanna Viktória Rácz
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Doctoral School of Nutrition and Food Sciences, University of Debrecen, Debrecen, Hungary
| | - Fezan Mukhtar
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Alexandra Imre
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary.,Kálmán Laki Doctoral School of Biomedical and Clinical Sciences, University of Debrecen, Debrecen, Hungary
| | - Zoltán Rádai
- MTA-ÖK Lendület Seed Ecology Research Group, Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | | | - Tamás Rátonyi
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - János Nagy
- Institute of Land Use, Technology and Regional Development, University of Debrecen, Debrecen, Hungary
| | - István Pócsi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
| | - Walter P Pfliegler
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, Debrecen, Hungary
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18
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Jacobus AP, Stephens TG, Youssef P, González-Pech R, Ciccotosto-Camp MM, Dougan KE, Chen Y, Basso LC, Frazzon J, Chan CX, Gross J. Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts. Front Microbiol 2021; 12:644089. [PMID: 33936002 PMCID: PMC8082247 DOI: 10.3389/fmicb.2021.644089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 01/05/2023] Open
Abstract
Ethanol production from sugarcane is a key renewable fuel industry in Brazil. Major drivers of this alcoholic fermentation are Saccharomyces cerevisiae strains that originally were contaminants to the system and yet prevail in the industrial process. Here we present newly sequenced genomes (using Illumina short-read and PacBio long-read data) of two monosporic isolates (H3 and H4) of the S. cerevisiae PE-2, a predominant bioethanol strain in Brazil. The assembled genomes of H3 and H4, together with 42 draft genomes of sugarcane-fermenting (fuel ethanol plus cachaça) strains, were compared against those of the reference S288C and diverse S. cerevisiae. All genomes of bioethanol yeasts have amplified SNO2(3)/SNZ2(3) gene clusters for vitamin B1/B6 biosynthesis, and display ubiquitous presence of a particular family of SAM-dependent methyl transferases, rare in S. cerevisiae. Widespread amplifications of quinone oxidoreductases YCR102C/YLR460C/YNL134C, and the structural or punctual variations among aquaporins and components of the iron homeostasis system, likely represent adaptations to industrial fermentation. Interesting is the pervasive presence among the bioethanol/cachaça strains of a five-gene cluster (Region B) that is a known phylogenetic signature of European wine yeasts. Combining genomes of H3, H4, and 195 yeast strains, we comprehensively assessed whole-genome phylogeny of these taxa using an alignment-free approach. The 197-genome phylogeny substantiates that bioethanol yeasts are monophyletic and closely related to the cachaça and wine strains. Our results support the hypothesis that biofuel-producing yeasts in Brazil may have been co-opted from a pool of yeasts that were pre-adapted to alcoholic fermentation of sugarcane for the distillation of cachaça spirit, which historically is a much older industry than the large-scale fuel ethanol production.
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Affiliation(s)
- Ana Paula Jacobus
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Pierre Youssef
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Raul González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Michael M Ciccotosto-Camp
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine E Dougan
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Luiz Carlos Basso
- Biological Science Department, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo (USP), Piracicaba, Brazil
| | - Jeverson Frazzon
- Institute of Food Science and Technology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jeferson Gross
- Laboratory for Genomics and Experimental Evolution of Yeasts, Institute for Bioenergy Research, São Paulo State University, Rio Claro, Brazil
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19
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Costa ACT, Hornick J, Antunes TFS, Santos AMC, Fernandes AAR, Broach JR, Fernandes PMB. Complete genome sequence and analysis of a Saccharomyces cerevisiae strain used for sugarcane spirit production. Braz J Microbiol 2021; 52:1087-1095. [PMID: 33835421 DOI: 10.1007/s42770-021-00444-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/02/2021] [Indexed: 12/01/2022] Open
Abstract
Distillation of fermented sugarcane juice produces both rum and cachaça, significant sources of revenue in Brazil and elsewhere. In this study, we provide a genomic analysis of a Saccharomyces cerevisiae strain isolated from a cachaça distillery in Brazil. We determined the complete genome sequence of a strain with high flocculation capacity, high tolerance to ethanol, osmotic and heat shock stress and high fermentation rates and compared the sequence with that of the reference S288c genome as well as those of two other cachaça strains. Single-nucleotide polymorphism analysis identified alterations in genes involved in nitrogen and organic compound metabolism, integrity of organelles and ion homeostasis. The strain exhibited fragmentation of several flocculation genes relative to the reference genome, as well as loss of a stop codon in the FLO8 gene, which encodes a transcription factor required for FLO gene expression. The strain contained no genes not present in the reference genome strain but did lack several genes, including asparaginase genes, maltose utilization loci, and several genes from the tandem array of the DUP240 family. The three cachaça strains lacked different sets of genes, but the asparaginase genes and several of the DUP240 genes were common deficiencies. This study provides new insights regarding the selective pressure of sugarcane fermentation on the genome of yeast strains and offers additional genetic resources for modern synthetic biology and genome editing tools.
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Affiliation(s)
- Ane Catarine Tosi Costa
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitoria, ES, 29040-090, Brazil
| | - Jacob Hornick
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Tathiana Ferreira Sá Antunes
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitoria, ES, 29040-090, Brazil
| | | | - A Alberto R Fernandes
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitoria, ES, 29040-090, Brazil
| | - James R Broach
- Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Patricia M B Fernandes
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitoria, ES, 29040-090, Brazil.
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20
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Bigey F, Segond D, Friedrich A, Guezenec S, Bourgais A, Huyghe L, Agier N, Nidelet T, Sicard D. Evidence for Two Main Domestication Trajectories in Saccharomyces cerevisiae Linked to Distinct Bread-Making Processes. Curr Biol 2021; 31:722-732.e5. [DOI: 10.1016/j.cub.2020.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/07/2020] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
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21
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Pontes A, Hutzler M, Brito PH, Sampaio JP. Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae-Phylogeny, Phenotypes, Ecology and Domestication. Microorganisms 2020; 8:E903. [PMID: 32549402 PMCID: PMC7356373 DOI: 10.3390/microorganisms8060903] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/02/2022] Open
Abstract
Saccharomyces cerevisiae-the most emblematic and industrially relevant yeast-has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
| | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, TU München, D-85354 Freising, Germany;
| | - Patrícia H. Brito
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
| | - José Paulo Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal; (A.P.); (P.H.B.)
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22
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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23
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Gibson B, Dahabieh M, Krogerus K, Jouhten P, Magalhães F, Pereira R, Siewers V, Vidgren V. Adaptive Laboratory Evolution of Ale and Lager Yeasts for Improved Brewing Efficiency and Beer Quality. Annu Rev Food Sci Technol 2020; 11:23-44. [DOI: 10.1146/annurev-food-032519-051715] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Yeasts directly impact the efficiency of brewery fermentations as well as the character of the beers produced. In recent years, there has been renewed interest in yeast selection and development inspired by the demand to utilize resources more efficiently and the need to differentiate beers in a competitive market. Reviewed here are the different, non-genetically modified (GM) approaches that have been considered, including bioprospecting, hybridization, and adaptive laboratory evolution (ALE). Particular emphasis is placed on the latter, which represents an extension of the processes that have led to the domestication of strains already used in commercial breweries. ALE can be used to accentuate the positive traits of brewing yeast as well as temper some of the traits that are less desirable from a modern brewer's perspective. This method has the added advantage of being non-GM and therefore suitable for food and beverage production.
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Affiliation(s)
- B. Gibson
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - M. Dahabieh
- Renaissance BioScience, Vancouver, British Columbia, Canada, V6T1Z3
| | - K. Krogerus
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - P. Jouhten
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - F. Magalhães
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - R. Pereira
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - V. Siewers
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - V. Vidgren
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
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24
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Evolution of Ty1 copy number control in yeast by horizontal transfer and recombination. PLoS Genet 2020; 16:e1008632. [PMID: 32084126 PMCID: PMC7055915 DOI: 10.1371/journal.pgen.1008632] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 03/04/2020] [Accepted: 01/27/2020] [Indexed: 01/04/2023] Open
Abstract
Transposable elements constitute a large fraction of most eukaryotic genomes. Insertion of mobile DNA sequences typically has deleterious effects on host fitness, and thus diverse mechanisms have evolved to control mobile element proliferation. Mobility of the Ty1 retrotransposon in Saccharomyces yeasts is regulated by copy number control (CNC) mediated by a self-encoded restriction factor derived from the Ty1 gag capsid gene that inhibits virus-like particle function. Here, we survey a panel of wild and human-associated strains of S. cerevisiae and S. paradoxus to investigate how genomic Ty1 content influences variation in Ty1 mobility. We observe high levels of mobility for a tester element with a gag sequence from the canonical Ty1 subfamily in permissive strains that either lack full-length Ty1 elements or only contain full-length copies of the Ty1' subfamily that have a divergent gag sequence. In contrast, low levels of canonical Ty1 mobility are observed in restrictive strains carrying full-length Ty1 elements containing a canonical gag sequence. Phylogenomic analysis of full-length Ty1 elements revealed that Ty1' is the ancestral subfamily present in wild strains of S. cerevisiae, and that canonical Ty1 in S. cerevisiae is a derived subfamily that acquired gag from S. paradoxus by horizontal transfer and recombination. Our results provide evidence that variation in the ability of S. cerevisiae and S. paradoxus strains to repress canonical Ty1 transposition via CNC is regulated by the genomic content of different Ty1 subfamilies, and that self-encoded forms of transposon control can spread across species boundaries by horizontal transfer.
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25
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Gallone B, Steensels J, Mertens S, Dzialo MC, Gordon JL, Wauters R, Theßeling FA, Bellinazzo F, Saels V, Herrera-Malaver B, Prahl T, White C, Hutzler M, Meußdoerffer F, Malcorps P, Souffriau B, Daenen L, Baele G, Maere S, Verstrepen KJ. Interspecific hybridization facilitates niche adaptation in beer yeast. Nat Ecol Evol 2019; 3:1562-1575. [PMID: 31636425 DOI: 10.1038/s41559-019-0997-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 09/02/2019] [Indexed: 11/09/2022]
Abstract
Hybridization between species often leads to non-viable or infertile offspring, yet examples of evolutionarily successful interspecific hybrids have been reported in all kingdoms of life. However, many questions on the ecological circumstances and evolutionary aftermath of interspecific hybridization remain unanswered. In this study, we sequenced and phenotyped a large set of interspecific yeast hybrids isolated from brewing environments to uncover the influence of interspecific hybridization in yeast adaptation and domestication. Our analyses demonstrate that several hybrids between Saccharomyces species originated and diversified in industrial environments by combining key traits of each parental species. Furthermore, posthybridization evolution within each hybrid lineage reflects subspecialization and adaptation to specific beer styles, a process that was accompanied by extensive chimerization between subgenomes. Our results reveal how interspecific hybridization provides an important evolutionary route that allows swift adaptation to novel environments.
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Affiliation(s)
- Brigida Gallone
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Stijn Mertens
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Maria C Dzialo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Jonathan L Gordon
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Ruben Wauters
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Florian A Theßeling
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Francesca Bellinazzo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | | | | | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | - Franz Meußdoerffer
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | | | | | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium. .,Leuven Institute for Beer Research, Leuven, Belgium.
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26
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Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol 2019; 3:1576-1586. [PMID: 31636426 DOI: 10.1038/s41559-019-0998-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022]
Abstract
The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.
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Affiliation(s)
- Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - EmilyClare P Baker
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ursula Bond
- Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. .,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. .,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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27
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Sampaio NMV, Watson RA, Argueso JL. Controlled Reduction of Genomic Heterozygosity in an Industrial Yeast Strain Reveals Wide Cryptic Phenotypic Variation. Front Genet 2019; 10:782. [PMID: 31572430 PMCID: PMC6749062 DOI: 10.3389/fgene.2019.00782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/24/2019] [Indexed: 01/12/2023] Open
Abstract
Abundant genomic heterozygosity can be found in wild strains of the budding yeast Saccharomyces cerevisiae isolated from industrial and clinical environments. The extent to which heterozygosity influences the phenotypes of these isolates is not fully understood. One such case is the PE-2/JAY270 strain, a natural hybrid widely adopted by sugarcane bioethanol distilleries for its ability to thrive under harsh biotic and abiotic stresses during industrial scale fermentation, however, it is not known whether or how the heterozygous configuration of the JAY270 genome contributes to its many desirable traits. In this study, we took a step toward exploring this question by conducting an initial functional characterization of JAY270’s heteroalleles. We manipulated the abundance and distribution of heterozygous alleles through inbreeding and targeted uniparental disomy (UPD). Unique combinations of homozygous alleles in each inbred strain revealed wide phenotypic variation for at least two important industrial traits: Heat stress tolerance and competitive growth. Quantitative trait loci analyses allowed the identification of broad genomic regions where genetic polymorphisms potentially impacted these traits, and there was no overlap between the loci associated with each. In addition, we adapted an approach to induce bidirectional UPD of three targeted pairs of chromosomes (IV, XIV, and XV), while heterozygosity was maintained elsewhere in the genome. In most cases UPD led to detectable phenotypic alterations, often in opposite directions between the two homozygous haplotypes in each UPD pair. Our results showed that both widespread and regional homozygosity could uncover cryptic phenotypic variation supported by the heteroalleles residing in the JAY270 genome. Interestingly, we characterized multiple examples of inbred and UPD strains that displayed heat tolerance or competitive growth phenotypes that were superior to their heterozygous parent. However, we propose that homozygosity for those regions may be associated with a decrease in overall fitness in the complex and dynamic distillery environment, and that may have contributed to slowing down the erosion of heterozygosity from the JAY270 genome. This study also laid a foundation for approaches that can be expanded to the identification of specific alleles of interest for industrial applications in this and other hybrid yeast strains.
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Affiliation(s)
- Nadia M V Sampaio
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.,Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, United States
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28
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Peltier E, Friedrich A, Schacherer J, Marullo P. Quantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains. Front Genet 2019; 10:683. [PMID: 31396264 PMCID: PMC6664092 DOI: 10.3389/fgene.2019.00683] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/01/2019] [Indexed: 11/13/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.
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Affiliation(s)
- Emilien Peltier
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
| | - Anne Friedrich
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department Micro-organismes, Génomes, Environnement, Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Philippe Marullo
- Department Sciences du vivant et de la sante, Université de Bordeaux, UR Œnologie EA 4577, Bordeaux, France
- Biolaffort, Bordeaux, France
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29
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Pontes A, Čadež N, Gonçalves P, Sampaio JP. A Quasi-Domesticate Relic Hybrid Population of Saccharomyces cerevisiae × S. paradoxus Adapted to Olive Brine. Front Genet 2019; 10:449. [PMID: 31191600 PMCID: PMC6548830 DOI: 10.3389/fgene.2019.00449] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/30/2019] [Indexed: 11/13/2022] Open
Abstract
The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages harboring some domestication signatures but that do not fit completely in the archetype of a domesticated yeast, by studying S. cerevisiae strains associated with processed olives, namely table olives, olive brine, olive oil, and alpechin. We confirmed earlier observations that reported that the Olives population results from a hybridization between S. cerevisiae and S. paradoxus. We concluded that the olive hybrids form a monophyletic lineage and that the S. cerevisiae progenitor belonged to the wine population of this species. We propose that homoploid hybridization gave rise to a diploid hybrid genome, which subsequently underwent the loss of most of the S. paradoxus sub-genome. Such a massive loss of heterozygosity was probably driven by adaptation to the new niche. We observed that olive strains are more fit to grow and survive in olive brine than control S. cerevisiae wine strains and that they appear to be adapted to cope with the presence of NaCl in olive brine through expansion of copy number of ENA genes. We also investigated whether the S. paradoxus HXT alleles retained by the Olives population were likely to contribute to the observed superior ability of these strains to consume sugars in brine. Our experiments indicate that sugar consumption profiles in the presence of NaCl are different between members of the Olives and Wine populations and only when cells are cultivated in nutritional conditions that support adaptation of their proteome to the high salt environment, which suggests that the observed differences are due to a better overall fitness of olives strains in the presence of high NaCl concentrations. Although relic olive hybrids exhibit several characteristics of a domesticated lineage, tangible benefits to humans cannot be associated with their phenotypes. These strains can be seen as a case of adaptation without positive or negative consequences to humans, that we define as a quasi-domestication.
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Affiliation(s)
- Ana Pontes
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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30
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Tra Bi CY, Amoikon TLS, Kouakou CA, Noemie J, Lucas M, Grondin C, Legras JL, N'guessan FK, Djeni TN, Djè MK, Casaregola S. Genetic diversity and population structure of Saccharomyces cerevisiae strains isolated from traditional alcoholic beverages of Côte d'Ivoire. Int J Food Microbiol 2019; 297:1-10. [PMID: 30852361 DOI: 10.1016/j.ijfoodmicro.2019.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 10/27/2022]
Abstract
In order to assess the genetic diversity and population structure of indigenous S. cerevisiae from Côte d'Ivoire, a total of 170 strains were isolated from four traditional alcoholic beverages through nine regions. Microsatellite analysis performed at 12 loci revealed that strains of palm oil and raffia wine were genetically related, unlike those of tchapalo and ron wine which formed two s from palm oil wine and raffia wine were clearly inbred. In comparison with the European, North American, Asian and others West African populations, Ivorian population was well defined, although most of these strains were admixed. Among these strains, only isolates from raffia wine appeared to have alleles in common to all populations.
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Affiliation(s)
- Charles Y Tra Bi
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire; Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Tiemele L S Amoikon
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire; Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Clémentine A Kouakou
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
| | - Jacques Noemie
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marine Lucas
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Cécile Grondin
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Luc Legras
- SPO, Université Montpellier INRA, Montpellier SupAgro, F-34060 Montpellier, France
| | - Florent K N'guessan
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
| | - Theodore N Djeni
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
| | - Marcellin K Djè
- Laboratoire de Biotechnologie et Microbiologie des Aliments, Unité de Formation et de Recherche en Sciences et Technologie des Aliments (UFR-STA), Université Nangui-Abrogoua, 02 BP 801 Abidjan 02, Côte d'Ivoire
| | - Serge Casaregola
- Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Cubillos FA, Gibson B, Grijalva-Vallejos N, Krogerus K, Nikulin J. Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast 2019; 36:383-398. [PMID: 30698853 DOI: 10.1002/yea.3380] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/29/2022] Open
Abstract
The burgeoning interest in archaic, traditional, and novel beer styles has coincided with a growing appreciation of the role of yeasts in determining beer character as well as a better understanding of the ecology and biogeography of yeasts. Multiple studies in recent years have highlighted the potential of wild Saccharomyces and non-Saccharomyces yeasts for production of beers with novel flavour profiles and other desirable properties. Yeasts isolated from spontaneously fermented beers as well as from other food systems (wine, bread, and kombucha) have shown promise for brewing application, and there is evidence that such cross-system transfers have occurred naturally in the past. We review here the available literature pertaining to the use of nonconventional yeasts in brewing, with a focus on the origins of these yeasts, including methods of isolation. Practical aspects of utilizing nondomesticated yeasts are discussed, and modern methods to facilitate discovery of yeasts with brewing potential are highlighted.
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Affiliation(s)
- Francisco A Cubillos
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.,Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Brian Gibson
- Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Nubia Grijalva-Vallejos
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Kristoffer Krogerus
- Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Espoo, Finland
| | - Jarkko Nikulin
- Industrial Biotechnology and Food Solutions, VTT Technical Research Centre of Finland Ltd, Espoo, Finland.,Chemical Process Engineering, Faculty of Technology, University of Oulu, Oulu, Finland
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