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Kessi-Pérez EI, Acuña E, Bastías C, Fundora L, Villalobos-Cid M, Romero A, Khaiwal S, De Chiara M, Liti G, Salinas F, Martínez C. Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains. Biol Res 2023; 56:43. [PMID: 37507753 PMCID: PMC10385942 DOI: 10.1186/s40659-023-00453-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
For more than 20 years, Saccharomyces cerevisiae has served as a model organism for genetic studies and molecular biology, as well as a platform for biotechnology (e.g., wine production). One of the important ecological niches of this yeast that has been extensively studied is wine fermentation, a complex microbiological process in which S. cerevisiae faces various stresses such as limited availability of nitrogen. Nitrogen deficiencies in grape juice impair fermentation rate and yeast biomass production, leading to sluggish or stuck fermentations, resulting in considerable economic losses for the wine industry. In the present work, we took advantage of the "1002 Yeast Genomes Project" population, the most complete catalogue of the genetic variation in the species and a powerful resource for genotype-phenotype correlations, to study the adaptation to nitrogen limitation in wild and domesticated yeast strains in the context of wine fermentation. We found that wild and domesticated yeast strains have different adaptations to nitrogen limitation, corroborating their different evolutionary trajectories. Using a combination of state-of-the-art bioinformatic (GWAS) and molecular biology (CRISPR-Cas9) methodologies, we validated that PNP1, RRT5 and PDR12 are implicated in wine fermentation, where RRT5 and PDR12 are also involved in yeast adaptation to nitrogen limitation. In addition, we validated SNPs in these genes leading to differences in fermentative capacities and adaptation to nitrogen limitation. Altogether, the mapped genetic variants have potential applications for the genetic improvement of industrial yeast strains.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Eric Acuña
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Camila Bastías
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Leyanis Fundora
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Manuel Villalobos-Cid
- Departamento de Ingeniería Informática, Program for the Development of Sustainable Production Systems (PDSPS), Facultad de Ingeniería, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Andrés Romero
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sakshi Khaiwal
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Gianni Liti
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | - Francisco Salinas
- Laboratorio de Genómica Funcional, Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID-Millennium Science Initiative-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.
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Aydın F, Günen TU, Kahve Hİ, Güler E, Özer G, Aktepe Y, Çakır İ. Molecular and Technological Characterization of Saccharomyces cerevisiae from Sourdough. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9040329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
DNA markers help detect the intraspecific genetic diversity of yeast strains. Eight ISSR (Inter Simple Sequence Repeats) primers were used to assess the intraspecific diversity of Saccharomyces cerevisiae (n = 96) from different populations (n = 3), evaluate the technological characteristics, and investigate trait-loci associations. The primers amplified 154 reproducible and scorable bands, of which 79.87% were polymorphic. The UPGMA (unweighted pair group method with arithmetic mean) dendrogram clustered 96 isolates into two main clusters, supported by STRUCTURE HARVESTER results (ΔK = 2). Analysis of molecular variance (AMOVA) indicated significant genetic differences between (15%) and within the populations (85%) (p < 0.001). Twenty-nine genetically distinct strains were selected for the technological characterization. Principal component analysis (PCA) revealed that five strains with high fermentation capacity, leavening activity, high growth index at 37 °C, and harsh growth conditions were technologically relevant. Trait-loci association analyses indicated that the highest correlation (r = 0.60) was recorded for the fermentation capacity on the 8th and 113th loci, amplified by ISSR-1 and ISSR-6 primers, respectively (p < 0.05). The strains yielding high performances and the associated loci amplified by ISSR markers possess a high potential to generate locus-specific primers to target the strains with high fermentation capacity.
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3
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Aydın F, Özer G, Alkan M, Çakır İ. Start Codon Targeted (SCoT) markers for the assessment of genetic diversity in yeast isolated from Turkish sourdough. Food Microbiol 2022; 107:104081. [DOI: 10.1016/j.fm.2022.104081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/28/2022]
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4
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Aydın F, Özer G, Alkan M, Çakır İ. Genetic diversity and population structure of Saccharomyces cerevisiae isolated from Turkish sourdough by iPBS-retrotransposons markers. Arch Microbiol 2022; 204:693. [PMCID: PMC9640837 DOI: 10.1007/s00203-022-03313-x] [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: 05/05/2022] [Revised: 09/30/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022]
Abstract
Molecular DNA markers are valuable tools for analyzing genetic variation among yeast from different populations to reveal the genetically different autochthonous strains. In this study, we employed inter-primer binding site (iPBS) retrotransposon polymorphism to assess the genetic variation and population structure of 96 Saccharomyces cerevisiae isolates from four different regions in Turkey. The nine selected iPBS primers amplified 102 reproducible and scorable bands, of which 95.10% were polymorphic with an average of 10.78 polymorphic fragments per primer. The average polymorphism information content and the resolving power were 0.26–3.58, respectively. Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) genetic differences within populations (88%) and between populations (12%). The unweighted pair group mean with arithmetic (UPGMA) dendrogram grouped 96 S. cerevisiae strains into two main clusters, where the highest probability of the data elucidating the population structure was obtained at ΔK = 2. There was not an obvious genetic discrimination of the populations according to geographical regions on UPGMA, supported by principal coordinate analysis. However, the individuals of the closer provinces in each population were more likely to group together or closely. The results indicate that iPBS polymorphism is a useful tool to reveal the genetically diverse autochthonous S. cerevisiae strains that may be important for the production of sourdough or baked goods.
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Affiliation(s)
- Furkan Aydın
- Department of Food Engineering, Faculty of Engineering, Aksaray University, 68100 Aksaray, Turkey
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey
| | - İbrahim Çakır
- Department of Food Engineering, Faculty of Engineering, Bolu Abant Izzet Baysal University, 14030 Bolu, Turkey
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5
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Oenological Potential of Autochthonous Saccharomyces cerevisiae Yeast Strains from the Greek Varieties of Agiorgitiko and Moschofilero. BEVERAGES 2021. [DOI: 10.3390/beverages7020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nemea and Mantinia are famous wine regions in Greece known for two indigenous grape varieties, Agiorgitiko and Moschofilero, which produce high quality PDO wines. In the present study, indigenous Saccharomyces cerevisiae yeast strains were isolated and identified from spontaneous alcoholic fermentation of Agiorgitiko and Moschofilero musts in order to evaluate their oenological potential. Random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) recovered the presence of five distinct profiles from a total of 430 yeast isolates. The five obtained strains were evaluated at microvinifications trials and tested for basic oenological and biochemical parameters including sulphur dioxide and ethanol tolerance as well as H2S production in sterile grape must. The selected autochthonous yeast strains named, Soi2 (Agiorgitiko wine) and L2M (Moschofilero wine), were evaluated also in industrial (4000L) fermentations to assess their sensorial and oenological characteristics. The volatile compounds of the produced wines were determined by GC-FID. Our results demonstrated the feasibility of using Soi2 and L2M strains in industrial fermentations for Agiorgitiko and Moschofilero grape musts, respectively.
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Mardones W, Villarroel CA, Abarca V, Urbina K, Peña TA, Molinet J, Nespolo RF, Cubillos FA. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb Biotechnol 2021; 15:967-984. [PMID: 33755311 PMCID: PMC8913853 DOI: 10.1111/1751-7915.13803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 01/02/2023] Open
Abstract
Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time‐course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off‐flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Carlos A Villarroel
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Valentina Abarca
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Kamila Urbina
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Tomás A Peña
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Jennifer Molinet
- Facultad de Química y Biología, Departamento de Biología, Universidad de Santiago de Chile, Santiago, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
| | - Roberto F Nespolo
- Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile.,Institute of Environmental and Evolutionary Science, Universidad Austral de Chile, Valdivia, 5110566, 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, 9170022, Chile.,Millennium Institute for Integrative Biology (iBio), ANID - Millennium Science Initiative Program, Santiago, 7500574, Chile
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7
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Higgins P, Grace CA, Lee SA, Goddard MR. Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion. G3-GENES GENOMES GENETICS 2021; 11:6044130. [PMID: 33561237 PMCID: PMC7849907 DOI: 10.1093/g3journal/jkaa027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/23/2020] [Indexed: 11/14/2022]
Abstract
Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.
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Affiliation(s)
- Peter Higgins
- The School of Life Sciences, College of Science, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK
| | - Cooper A Grace
- Department of Biology, York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK.,Department of Biological and Geographical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Soon A Lee
- The School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Matthew R Goddard
- The School of Life Sciences, College of Science, University of Lincoln, Brayford Pool, Lincoln, LN6 7TS, UK.,The School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
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Zabukovec P, Čadež N, Čuš F. Isolation and Identification of Indigenous Wine Yeasts and Their Use in Alcoholic Fermentation. Food Technol Biotechnol 2020; 58:337-347. [PMID: 33281489 PMCID: PMC7709452 DOI: 10.17113/ftb.58.03.20.6677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Research background In our study, spontaneous alcoholic fermentations were carried out to isolate non-Saccharomyces and Saccharomyces yeasts from grape must from different vine-growing regions in Slovenia. Additionally, the diversity of native Saccharomyces cerevisiae strains was evaluated during the process. Experimental approach During spontaneous alcoholic fermentations the yeast population of non-Saccharomyces and Saccharomyces yeasts was sampled. We used eleven microsatellite markers to determine the genetic diversity of S. cerevisiae strains. In addition, different ratios of the indigenous strains of S. cerevisiae, Hanseniaspora uvarum and Starmerella bacillaris were tested for their possible use in alcoholic fermentation with inoculated yeasts by monitoring its course and measuring the concentration of aroma compounds in wine. Results and conclusions Sequencing of the internal transcribed spacer (ITS) regions of ribosomal DNA showed that of 64 isolates, 46 strains represent S. cerevisiae and 18 strains belong to non-Saccharomyces yeasts. The identified non-Saccharomyces yeast species were H. uvarum, Pichia kudriavzevii, Saturnispora diversa and S. bacillaris. The dendrogram grouped S. cerevisiae strains into 14 groups. The number of S. cervisiae strains isolated from the musts was 10 (Posavje), 11 (Podravje) and 25 (Primorska vine-growing region). On the other hand, the alcoholic fermentation with inoculated yeasts, in which the native S. cerevisiae strain predominated over H. uvarum and S. bacillaris, gave the most promising result due to the highest alcoholvolume fraction, the lowest acetic acid concentration and significantly higher concentrations of volatile thiols 3-mercaptohexyl acetate (3MHA) and 3-mercaptohexan-1-ol (3MH), 2-methylpropanol, 2-methylbutanol, 3-methylbutanol and 2-phenylethanol) in the produced wine. Novelty and scientific contribution We confirmed the potential use of indigenous S. cerevisiae and non-Saccharomyces yeasts in alcoholic fermentation with inoculated yeasts, which allows the positive properties of the yeast strains to be expressed and good quality wines to be produced. Thus, the results are encouraging for winemakers to create different wine styles associated with a particular terroir using indigenous yeasts.
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Affiliation(s)
- Polona Zabukovec
- Agricultural Institute of Slovenia, Department of Fruit Growing, Viticulture and Oenology, Hacquetova ulica 17, 1000 Ljubljana, Slovenia
| | - Neža Čadež
- Department of Food Science and Technology, Chair of Biotechnology, Microbiology and Food Safety, Biotechnical Faculty, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Franc Čuš
- Agricultural Institute of Slovenia, Department of Fruit Growing, Viticulture and Oenology, Hacquetova ulica 17, 1000 Ljubljana, Slovenia
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G-Poblete C, Peña-Moreno IC, de Morais MA, Moreira S, Ganga MA. Biodiversity among Brettanomyces bruxellensis Strains Isolated from Different Wine Regions of Chile: Key Factors Revealed about its Tolerance to Sulphite. Microorganisms 2020; 8:E557. [PMID: 32295086 PMCID: PMC7232158 DOI: 10.3390/microorganisms8040557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
Brettanomyces bruxellensis is regarded as the main spoilage microorganism in the wine industry, owing to its production of off-flavours. It is difficult to eradicate owing to its high tolerance of adverse environmental conditions, such as low nutrient availability, low pH, and high levels of ethanol and SO2. In this study, the production of volatile phenols and the growth kinetics of isolates from various regions of Chile were evaluated under stressful conditions. Through randomly amplified polymorphic DNA (RAPD) analysis, 15 strains were identified. These were grown in the presence of p-coumaric acid, a natural antimicrobial and the main precursor of off-flavours, and molecular sulfur dioxide (mSO2), an antimicrobial synthetic used in the wine industry. When both compounds were used simultaneously, there were clear signs of an improvement in the fitness of most of the isolates, which showed an antagonistic interaction in which p-coumaric acid mitigates the effects of SO2. Fourteen strains were able to produce 4-vinylphenol, which showed signs of phenylacrylic acid decarboxylase activity, and most of them produced 4-ethylphenol as a result of active vinylphenol reductase. These results demonstrate for the first time the serious implications of using p-coumaric acid, not only for the production of off-flavours, but also for its protective action against the toxic effects of SO2.
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Affiliation(s)
- Camila G-Poblete
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
| | - Irina Charlot Peña-Moreno
- Department of Genetics, Biosciences Center, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (I.C.P.-M.); (M.A.d.M.J.)
| | - Marcos Antonio de Morais
- Department of Genetics, Biosciences Center, Universidade Federal de Pernambuco, Recife 50670-901, Brazil; (I.C.P.-M.); (M.A.d.M.J.)
| | - Sandra Moreira
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
| | - María Angélica Ganga
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad Tecnológica, Universidad de Santiago de Chile, Santiago 9170020, Chile; (C.G.-P.); (S.M.)
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10
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Kessi-Pérez EI, Molinet J, Martínez C. Disentangling the genetic bases of Saccharomyces cerevisiae nitrogen consumption and adaptation to low nitrogen environments in wine fermentation. Biol Res 2020; 53:2. [PMID: 31918759 PMCID: PMC6950849 DOI: 10.1186/s40659-019-0270-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/31/2019] [Indexed: 12/16/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been considered for more than 20 years as a premier model organism for biological sciences, also being the main microorganism used in wide industrial applications, like alcoholic fermentation in the winemaking process. Grape juice is a challenging environment for S. cerevisiae, with nitrogen deficiencies impairing fermentation rate and yeast biomass production, causing stuck or sluggish fermentations, thus generating sizeable economic losses for wine industry. In the present review, we summarize some recent efforts in the search of causative genes that account for yeast adaptation to low nitrogen environments, specially focused in wine fermentation conditions. We start presenting a brief perspective of yeast nitrogen utilization under wine fermentative conditions, highlighting yeast preference for some nitrogen sources above others. Then, we give an outlook of S. cerevisiae genetic diversity studies, paying special attention to efforts in genome sequencing for population structure determination and presenting QTL mapping as a powerful tool for phenotype-genotype correlations. Finally, we do a recapitulation of S. cerevisiae natural diversity related to low nitrogen adaptation, specially showing how different studies have left in evidence the central role of the TORC1 signalling pathway in nitrogen utilization and positioned wild S. cerevisiae strains as a reservoir of beneficial alleles with potential industrial applications (e.g. improvement of industrial yeasts for wine production). More studies focused in disentangling the genetic bases of S. cerevisiae adaptation in wine fermentation will be key to determine the domestication effects over low nitrogen adaptation, as well as to definitely proof that wild S. cerevisiae strains have potential genetic determinants for better adaptation to low nitrogen conditions.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Jennifer Molinet
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile.
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.
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11
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Liu D, Zhang P, Chen D, Howell K. From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine. Front Microbiol 2019; 10:2679. [PMID: 31824462 PMCID: PMC6880775 DOI: 10.3389/fmicb.2019.02679] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
Abstract
Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.
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Affiliation(s)
| | | | | | - Kate Howell
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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12
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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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Caldwell JM. Food Analysis Using Organelle DNA and the Effects of Processing on Assays. Annu Rev Food Sci Technol 2017; 8:57-74. [DOI: 10.1146/annurev-food-030216-030216] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Drumonde-Neves J, Franco-Duarte R, Lima T, Schuller D, Pais C. Association between Grape Yeast Communities and the Vineyard Ecosystems. PLoS One 2017; 12:e0169883. [PMID: 28085916 PMCID: PMC5234834 DOI: 10.1371/journal.pone.0169883] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/24/2016] [Indexed: 11/19/2022] Open
Abstract
The grape yeast biota from several wine-producing areas, with distinct soil types and grapevine training systems, was assessed on five islands of Azores Archipelago, and differences in yeast communities composition associated with the geographic origin of the grapes were explored. Fifty-seven grape samples belonging to the Vitis vinifera grapevine cultivars Verdelho dos Açores (Verdelho), Arinto da Terceira (Arinto) and Terrantez do Pico (Terrantez) were collected in two consecutive years and 40 spontaneous fermentations were achieved. A total of 1710 yeast isolates were obtained from freshly crushed grapes and 1200 from final stage of fermentations. Twenty-eight species were identified, Hanseniaspura uvarum, Pichia terricola and Metschnikowia pulcherrima being the three most representative species isolated. Candida carpophila was encountered for the first time as an inhabitant of grape or wine-associated environments. In both sampling years, a higher proportion of H. uvarum in fresh grapes from Verdelho cultivar was observed, in comparison with Arinto cultivar. Qualitatively significant differences were found among yeast communities from several locations on five islands of the Archipelago, particularly in locations with distinctive agro-ecological compositions. Our results are in agreement with the statement that grape-associated microbial biogeography is non-randomly associated with interactions of climate, soil, cultivar, and vine training systems in vineyard ecosystems. Our observations strongly support a possible linkage between grape yeast and wine typicality, reinforcing the statement that different viticultural terroirs harbor distinctive yeast biota, in particular in vineyards with very distinctive environmental conditions.
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Affiliation(s)
- João Drumonde-Neves
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Teresa Lima
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
| | - Dorit Schuller
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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Capece A, Granchi L, Guerrini S, Mangani S, Romaniello R, Vincenzini M, Romano P. Diversity of Saccharomyces cerevisiae Strains Isolated from Two Italian Wine-Producing Regions. Front Microbiol 2016; 7:1018. [PMID: 27446054 PMCID: PMC4928102 DOI: 10.3389/fmicb.2016.01018] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/15/2016] [Indexed: 11/13/2022] Open
Abstract
Numerous studies, based on different molecular techniques analyzing DNA polymorphism, have provided evidence that indigenous Saccharomyces cerevisiae populations display biogeographic patterns. Since the differentiated populations of S. cerevisiae seem to be responsible for the regional identity of wine, the aim of this work was to assess a possible relationship between the diversity and the geographical origin of indigenous S. cerevisiae isolates from two different Italian wine-producing regions (Tuscany and Basilicata). For this purpose, sixty-three isolates from Aglianico del Vulture grape must (main cultivar in the Basilicata region) and from Sangiovese grape must (main cultivar in the Tuscany region) were characterized genotypically, by mitochondrial DNA restriction analysis and MSP-PCR by using (GTG)5 primers, and phenotypically, by determining technological properties and metabolic compounds of oenological interest after alcoholic fermentation. All the S. cerevisiae isolates from each region were inoculated both in must obtained from Aglianico grape and in must obtained from Sangiovese grape to carry out fermentations at laboratory-scale. Numerical analysis of DNA patterns resulting from both molecular methods and principal component analysis of phenotypic data demonstrated a high diversity among the S. cerevisiae strains. Moreover, a correlation between genotypic and phenotypic groups and geographical origin of the strains was found, supporting the concept that there can be a microbial aspect to terroir. Therefore, exploring the diversity of indigenous S. cerevisiae strains can allow developing tailored strategies to select wine yeast strains better adapted to each viticultural area.
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Affiliation(s)
- Angela Capece
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, PotenzaItaly
| | - Lisa Granchi
- Department of Management of Agricultural, Food and Forestry Systems, University of Florence, FlorenceItaly
| | - Simona Guerrini
- Department of Management of Agricultural, Food and Forestry Systems, University of Florence, FlorenceItaly
| | - Silvia Mangani
- Department of Management of Agricultural, Food and Forestry Systems, University of Florence, FlorenceItaly
| | - Rossana Romaniello
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, PotenzaItaly
| | - Massimo Vincenzini
- Department of Management of Agricultural, Food and Forestry Systems, University of Florence, FlorenceItaly
| | - Patrizia Romano
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, PotenzaItaly
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Muñoz V, Beccaria B, Abreo E. Simultaneous and successive inoculations of yeasts and lactic acid bacteria on the fermentation of an unsulfited Tannat grape must. Braz J Microbiol 2014; 45:59-66. [PMID: 24948914 PMCID: PMC4059326 DOI: 10.1590/s1517-83822014000100009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Interactions between yeasts and lactic acid bacteria are strain specific, and their outcome is expected to change in simultaneous alcoholic--malolactic fermentations from the pattern observed in successive fermentations. One Oenococcus oeni strain Lalvin VP41™ was inoculated with two Saccharomyces cerevisiae strains either simultaneously, three days after the yeast inoculation, or when alcoholic fermentation was close to finish. Early bacterial inoculations with each yeast strain allowed for the growth of the bacterial populations, and the length of malolactic fermentation was reduced to six days. Alcoholic fermentation by Lalvin ICV D80® yeast strain left the highest residual sugar, suggesting a negative effect of the bacterial growth and malolactic activity on its performance. In sequential inoculations the bacterial populations did not show actual growth with either yeast strain. In this strategy, both yeast strains finished the alcoholic fermentations, and malolactic fermentations took longer to finish. Lalvin ICV D80® allowed for higher viability and activity of the bacterial strain than Fermicru UY4® under the three inoculation strategies. This was beneficial for the sequential completion of both fermentations, but negatively affected the completion of alcoholic fermentation by Lalvin ICV D80® in the early bacteria additions. Conversely, Fermicru UY4®, which was rather inhibitory towards the bacteria, favored the timely completion of both fermentations simultaneously. As bacteria in early inoculations with low or no SO2 addition can be expected to multiply and interact with fermenting yeasts, not only are the yeast-bacterium strains combination and time point of the inoculation to be considered, but also the amount of bacteria inoculated.
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Affiliation(s)
- Viviana Muñoz
- Laboratorio de Microbiología Enológica Escuela Superior de Vitivinicultura Canelones Uruguay
| | - Bruno Beccaria
- Laboratorio de Microbiología Enológica Escuela Superior de Vitivinicultura Canelones Uruguay
| | - Eduardo Abreo
- Laboratorio de Microbiología Enológica Escuela Superior de Vitivinicultura Canelones Uruguay
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18
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Tofalo R, Perpetuini G, Fasoli G, Schirone M, Corsetti A, Suzzi G. Biodiversity study of wine yeasts belonging to the “terroir” of Montepulciano d'Abruzzo “Colline Teramane” revealed Saccharomyces cerevisiae strains exhibiting atypical and unique 5.8S-ITS restriction patterns. Food Microbiol 2014; 39:7-12. [DOI: 10.1016/j.fm.2013.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/24/2013] [Accepted: 10/01/2013] [Indexed: 11/28/2022]
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19
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Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PLoS One 2014; 9:e86533. [PMID: 24466135 PMCID: PMC3897725 DOI: 10.1371/journal.pone.0086533] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/10/2013] [Indexed: 11/19/2022] Open
Abstract
Different populations within a species represent a rich reservoir of allelic variants, corresponding to an evolutionary signature of withstood environmental constraints. Saccharomyces cerevisiae strains are widely utilised in the fermentation of different kinds of alcoholic beverages, such as, wine and sake, each of them derived from must with distinct nutrient composition. Importantly, adequate nitrogen levels in the medium are essential for the fermentation process, however, a comprehensive understanding of the genetic variants determining variation in nitrogen consumption is lacking. Here, we assessed the genetic factors underlying variation in nitrogen consumption in a segregating population derived from a cross between two main fermenter yeasts, a Wine/European and a Sake isolate. By linkage analysis we identified 18 main effect QTLs for ammonium and amino acids sources. Interestingly, majority of QTLs were involved in more than a single trait, grouped based on amino acid structure and indicating high levels of pleiotropy across nitrogen sources, in agreement with the observed patterns of phenotypic co-variation. Accordingly, we performed reciprocal hemizygosity analysis validating an effect for three genes, GLT1, ASI1 and AGP1. Furthermore, we detected a widespread pleiotropic effect on these genes, with AGP1 affecting seven amino acids and nine in the case of GLT1 and ASI1. Based on sequence and comparative analysis, candidate causative mutations within these genes were also predicted. Altogether, the identification of these variants demonstrate how Sake and Wine/European genetic backgrounds differentially consume nitrogen sources, in part explaining independently evolved preferences for nitrogen assimilation and representing a niche of genetic diversity for the implementation of practical approaches towards more efficient strains for nitrogen metabolism.
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Tofalo R, Perpetuini G, Schirone M, Fasoli G, Aguzzi I, Corsetti A, Suzzi G. Biogeographical characterization of Saccharomyces cerevisiae wine yeast by molecular methods. Front Microbiol 2013; 4:166. [PMID: 23805132 PMCID: PMC3690337 DOI: 10.3389/fmicb.2013.00166] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/03/2013] [Indexed: 11/16/2022] Open
Abstract
Biogeography is the descriptive and explanatory study of spatial patterns and processes involved in the distribution of biodiversity. Without biogeography, it would be difficult to study the diversity of microorganisms because there would be no way to visualize patterns in variation. Saccharomyces cerevisiae, "the wine yeast," is the most important species involved in alcoholic fermentation, and in vineyard ecosystems, it follows the principle of "everything is everywhere." Agricultural practices such as farming (organic versus conventional) and floor management systems have selected different populations within this species that are phylogenetically distinct. In fact, recent ecological and geographic studies highlighted that unique strains are associated with particular grape varieties in specific geographical locations. These studies also highlighted that significant diversity and regional character, or 'terroir,' have been introduced into the winemaking process via this association. This diversity of wild strains preserves typicity, the high quality, and the unique flavor of wines. Recently, different molecular methods were developed to study population dynamics of S. cerevisiae strains in both vineyards and wineries. In this review, we will provide an update on the current molecular methods used to reveal the geographical distribution of S. cerevisiae wine yeast.
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Affiliation(s)
- Rosanna Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of TeramoMosciano Sant’Angelo, TE, Italy
| | | | | | | | | | | | - Giovanna Suzzi
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of TeramoMosciano Sant’Angelo, TE, Italy
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21
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Siesto G, Capece A, Sipiczki M, Csoma H, Romano P. Polymorphism detection among wild Saccharomyces cerevisiae strains of different wine origin. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0516-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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22
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Navarrete-Bolaños JL. Improving traditional fermented beverages: How to evolve from spontaneous to directed fermentation. Eng Life Sci 2012. [DOI: 10.1002/elsc.201100128] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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23
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Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. ISME JOURNAL 2011; 6:1281-90. [PMID: 22189497 DOI: 10.1038/ismej.2011.195] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Yeasts are a diverse seemingly ubiquitous group of eukaryotic microbes, and many are naturally associated with fruits. Humans have harnessed yeasts since the dawn of civilisation to make wine, and thus it is surprising that we know little of the distribution of yeast communities naturally associated with fruits. Previous reports of yeast community diversity have been descriptive only. Here we present, we believe, the first robust test for the geographic delineation of yeast communities. Humans have relatively recently employed Saccharomyces cerevisiae as a model research organism, and have long harnessed its ancient adaption to ferment even in the presence of oxygen. However, as far as we are aware, there has not been a rigorous test for the presence of regional differences in natural S. cerevisiae populations before. We combined these community- and population-level questions and surveyed replicate vineyards and corresponding spontaneous ferments from different regions on New Zealand's (NZ's) North Island and analysed the resulting data with community ecology and population genetic tests. We show that there are distinct regional delineations of yeast communities, but the picture for S. cerevisiae is more complex: there is evidence for region-specific sub-populations but there are also reasonable levels of gene flow among these regions in NZ. We believe this is the first demonstration of regional delineations of yeast populations and communities worldwide.
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Mercado L, Sturm ME, Rojo MC, Ciklic I, Martínez C, Combina M. Biodiversity of Saccharomyces cerevisiae populations in Malbec vineyards from the "Zona Alta del Río Mendoza" region in Argentina. Int J Food Microbiol 2011; 151:319-26. [PMID: 22056145 DOI: 10.1016/j.ijfoodmicro.2011.09.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 09/22/2011] [Accepted: 09/27/2011] [Indexed: 11/17/2022]
Abstract
The "Zona Alta del Río Mendoza" (ZARM) is the major Malbec grape viticulture region of Argentina. The aim of the present study was to explore Saccharomyces cerevisiae biodiversity in ZARM vineyards. Interdelta PCR and RFLP mtDNA molecular markers were applied to differentiate S. cerevisiae strains. The presence of commercial strains on ZARM vineyards was also assessed. Our results reveal a highly diverse, but genetically closely related, S. cerevisiae population (containing more than 190 molecular patterns among 590 S. cerevisiae isolates). According to the S. cerevisiae strain diversity found in vineyards, they were classified as vineyards with high and low polymorphic S. cerevisiae populations. Six vineyards showed a high polymorphic population, with more than 20 different S. cerevisiae molecular patterns. S. cerevisiae populations in these vineyards were diverse and irregularly distributed, with different strains in each vineyard site. Low polymorphic S. cerevisiae population vineyards displayed very low yeast diversity, with only 9 to 10 different S. cerevisiae strains and presence of two commercial strains widely distributed. Population diversity estimators were calculated to determine the population structure of S. cerevisiae in the ZARM vineyards. The obtained values support the hypothesis that the eight sampled subpopulations come indeed from a larger population.
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Affiliation(s)
- Laura Mercado
- Estación Experimental Agropecuaria Mendoza, Instituto Nacional de Tecnología Agropecuaria-INTA, San Martín 3853, Luján de Cuyo 5507, Mendoza, Argentina.
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Jeyaram K, Tamang JP, Capece A, Romano P. Geographical markers for Saccharomyces cerevisiae strains with similar technological origins domesticated for rice-based ethnic fermented beverages production in North East India. Antonie van Leeuwenhoek 2011; 100:569-78. [PMID: 21717205 DOI: 10.1007/s10482-011-9612-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Accepted: 06/14/2011] [Indexed: 11/28/2022]
Abstract
Autochthonous strains of Saccharomyces cerevisiae from traditional starters used for the production of rice-based ethnic fermented beverage in North East India were examined for their genetic polymorphism using mitochondrial DNA-RFLP and electrophoretic karyotyping. Mitochondrial DNA-RFLP analysis of S. cerevisiae strains with similar technological origins from hamei starter of Manipur and marcha starter of Sikkim revealed widely separated clusters based on their geographical origin. Electrophoretic karyotyping showed high polymorphism amongst the hamei strains within similar mitochondrial DNA-RFLP cluster and one unique karyotype of marcha strain was widely distributed in the Sikkim-Himalayan region. We conceptualized the possibility of separate domestication events for hamei strains in Manipur (located in the Indo-Burma biodiversity hotspot) and marcha strains in Sikkim (located in Himalayan biodiversity hotspot), as a consequence of less homogeneity in the genomic structure between these two groups, their clear separation being based on geographical origin, but not on technological origin and low strain level diversity within each group. The molecular markers developed based on HinfI-mtDNA-RFLP profile and the chromosomal doublets in chromosome VIII position of Sikkim-Himalayan strains could be effectively used as geographical markers for authenticating the above starter strains and differentiating them from other commercial strains.
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Affiliation(s)
- Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development, Takyelpat Institutional Area, Imphal, Manipur, India.
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26
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Chovanová K, Kraková L, Ženišová K, Turcovská V, Brežná B, Kuchta T, Pangallo D. Selection and identification of autochthonous yeasts in Slovakian wine samples using a rapid and reliable three-step approach. Lett Appl Microbiol 2011; 53:231-7. [DOI: 10.1111/j.1472-765x.2011.03097.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Massera A, Assof M, Sturm ME, Sari S, Jofré V, Cordero-Otero R, Combina M. Selection of indigenous Saccharomyces cerevisiae strains to ferment red musts at low temperature. ANN MICROBIOL 2011. [DOI: 10.1007/s13213-011-0271-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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28
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Capece A, Pietrafesa R, Romano P. Experimental approach for target selection of wild wine yeasts from spontaneous fermentation of “Inzolia” grapes. World J Microbiol Biotechnol 2011. [DOI: 10.1007/s11274-011-0753-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Diversity, variability and fast adaptive evolution of the wine yeast (Saccharomyces cerevisiae) genome—a review. ANN MICROBIOL 2010. [DOI: 10.1007/s13213-010-0086-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Salinas F, Mandaković D, Urzua U, Massera A, Miras S, Combina M, Angelica Ganga M, Martínez C. Genomic and phenotypic comparison between similar wine yeast strains ofSaccharomyces cerevisiaefrom different geographic origins. J Appl Microbiol 2010; 108:1850-8. [DOI: 10.1111/j.1365-2672.2010.04689.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Mercado L, Jubany S, Gaggero C, Masuelli RW, Combina M. Molecular Relationships Between Saccharomyces cerevisiae Strains Involved in Winemaking from Mendoza, Argentina. Curr Microbiol 2010; 61:506-14. [DOI: 10.1007/s00284-010-9645-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 03/26/2010] [Indexed: 11/24/2022]
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32
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Diversity and oenological characterization of indigenous Saccharomyces cerevisiae associated with Žilavka grapes. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0323-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tosi E, Azzolini M, Guzzo F, Zapparoli G. Evidence of different fermentation behaviours of two indigenous strains ofSaccharomyces cerevisiaeandSaccharomyces uvarumisolated from Amarone wine. J Appl Microbiol 2009; 107:210-8. [PMID: 19245401 DOI: 10.1111/j.1365-2672.2009.04196.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- E Tosi
- Centro per la Sperimentazione in Vitivinicoltura, Provincia di Verona, Servizio Agricoltura, San Floriano, Verona, Italy
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34
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Identification of yeast population dynamics of spontaneous fermentation in Beijing wine region, China. ANN MICROBIOL 2009. [DOI: 10.1007/bf03175601] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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35
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Charpentier C, Colin A, Alais A, Legras JL. French Jura flor yeasts: genotype and technological diversity. Antonie van Leeuwenhoek 2009; 95:263-73. [DOI: 10.1007/s10482-009-9309-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
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Cubillos FA, Vásquez C, Faugeron S, Ganga A, Martínez C. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations. FEMS Microbiol Ecol 2008; 67:162-70. [PMID: 19016866 DOI: 10.1111/j.1574-6941.2008.00600.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Saccharomyces cerevisiae is a model eukaryotic organism for classical genetics and genomics, and yet its ecology is still largely unknown. In this work, a population genetic analysis was performed on five yeast populations isolated from wine-making areas with different enological practices using simple sequence repeats and restriction fragment length polymorphism of mitochondrial DNA as molecular markers on 292 strains. In accordance with other studies, genome size estimation suggests that native S. cerevisiae strains are mainly homothallic and diploids. Analysis of mtDNA data showed that yeast populations from nonindustrial areas have 40% higher genetic diversity than populations isolated from industrial areas, demonstrating that industrial enological practices are likely to affect native yeast populations negatively by reducing its biodiversity. On the other hand, genetic differentiation analysis based on their microsatellite showed no correlation between genetic and geographic distance and a nonsignificant value when a Mantel test was applied. Finally, in the five populations studied, positive inbreeding (F(is)) values from 0.4 to 0.75, a low but significant level of linkage disequilibrium and a high number of multilocus genotypes were detected. These results strongly advocate that sexual reproduction is frequent enough to erase clonal signature in natural populations and that self-fertilization is the main mating system.
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Affiliation(s)
- Francisco A Cubillos
- Departamento de Ciencia y Tecnología de Alimentos, Universidad de Santiago de Chile, Estación Central, Santiago, Chile
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Abstract
International competition within the wine market, consumer demands for newer styles of wines and increasing concerns about the environmental sustainability of wine production are providing new challenges for innovation in wine fermentation. Within the total production chain, the alcoholic fermentation of grape juice by yeasts is a key process where winemakers can creatively engineer wine character and value through better yeast management and, thereby, strategically tailor wines to a changing market. This review considers the importance of yeast ecology and yeast metabolic reactions in determining wine quality, and then discusses new directions for exploiting yeasts in wine fermentation. It covers criteria for selecting and developing new commercial strains, the possibilities of using yeasts other than those in the genus of Saccharomyces, the prospects for mixed culture fermentations and explores the possibilities for high cell density, continuous fermentations.
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Affiliation(s)
- Graham H Fleet
- Food Science, School of Chemical Sciences and Engineering, University of New South Wales, Sydney, NSW, Australia.
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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