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Yeast Biodiversity in Fermented Doughs and Raw Cereal Matrices and the Study of Technological Traits of Selected Strains Isolated in Spain. Microorganisms 2020; 9:microorganisms9010047. [PMID: 33375367 PMCID: PMC7824024 DOI: 10.3390/microorganisms9010047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
Bakers use pure microorganisms and/or traditional sourdoughs as the leavening agent for making bread. The performance of each starter and the substances produced by the microorganisms greatly affect the dough rheology and features of breads. Modern sourdoughs inoculated with selected lactic acid bacteria and yeasts are microbiologically stable, safer than traditional sourdoughs, and easy to use. However, the commercial repertoire of baker’s yeasts is still limited. Therefore, there is a demand for new strains of yeast species, capable of conferring distinctive traits to breads made from a variety of agri-food matrices, in the design of innovative starters. In this context, we report the first comprehensive study on yeasts isolated from a wide range of fermented doughs, cereal flours, and grains of Spain. Nine yeast species were identified from 433 isolates, which were distributed among separate clades. Moreover, phenotypic traits of potential technological relevance were identified in selected yeast strains. Mother doughs (MDs) showed the greatest yeast biodiversity, whereas commercial Saccharomyces starters or related and wild strains often dominated the bakery doughs. A metataxonomic analysis of wheat and tritordeum MDs revealed a greater richness of yeast species and percentage variations related to the consistency, flour type, and fermentation time of MDs.
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Caridi A, Sidari R, Pulvirenti A, Blaiotta G. Genetic Improvement of wine yeasts for opposite adsorption activity of phenolics and ochratoxin A during red winemaking. FOOD BIOTECHNOL 2020. [DOI: 10.1080/08905436.2020.1850472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andrea Caridi
- Department of Agriculture, “Mediterranea” University, Reggio Calabria, Italy
| | - Rossana Sidari
- Department of Agriculture, “Mediterranea” University, Reggio Calabria, Italy
| | - Andrea Pulvirenti
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Blaiotta
- Department of Agricultural Sciences, Division of Vine and Wine Sciences, Federico II University of Napoli, Avellino, Italy
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Solieri L, Verspohl A, Bonciani T, Caggia C, Giudici P. Fast method for identifying inter- and intra-species Saccharomyces hybrids in extensive genetic improvement programs based on yeast breeding. J Appl Microbiol 2015; 119:149-61. [PMID: 25892524 DOI: 10.1111/jam.12827] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 01/05/2023]
Abstract
AIMS The present work proposes a two-step molecular strategy to select inter- and intra-species Saccharomyces hybrids obtained by spore-to-spore mating, one of the most used methods for generating improved hybrids from homothallic wine yeasts. METHODS AND RESULTS As low spore viability and haplo-selfing are the main causes of failed mating, at first, we used colony screening PCR (csPCR) of discriminative gene markers to select hybrids directly on dissection plate and discard homozygous diploid colonies arisen from one auto-diploidized progenitor. Then, pre-selected candidates were submitted to recursive streaking and conventional PCR in order to discriminate between the hybrids with stable genomic background and the false-positive admixtures of progenitor cells both undergone haplo-selfing. csPCRs of internal transcribed spacer (ITS) 1 or 2, and the subsequent digestion with diagnostic endonucleases HaeIII and RsaI, respectively, were efficient to select six new Saccharomyces cerevisiae × Saccharomyces uvarum hybrids from 64 crosses. Intragenic minisatellite regions in PIR3, HSP150, and DAN4 genes showed high inter-strain size variation detectable by cost-effective agarose gel electrophoresis and were successful to validate six new intra-species S. cerevisiae hybrids from 34 crosses. CONCLUSIONS Both protocols reduce significantly the number of massive DNA extractions, prevent misinterpretations caused by one or both progenitors undergone haplo-selfing, and can be easily implemented in yeast labs without any specific instrumentation. SIGNIFICANCE AND IMPACT OF THE STUDY The study provides a method for the marker-assisted selection of several inter- and intra-species yeast hybrids in a cost-effective, rapid and reproducible manner.
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Affiliation(s)
- L Solieri
- Department of Life Sciences, Unimore Microbial Culture Collection, Reggio Emilia, Italy
| | - A Verspohl
- Department of Life Sciences, Unimore Microbial Culture Collection, Reggio Emilia, Italy
| | - T Bonciani
- Department of Life Sciences, Unimore Microbial Culture Collection, Reggio Emilia, Italy
| | - C Caggia
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - P Giudici
- Department of Life Sciences, Unimore Microbial Culture Collection, Reggio Emilia, Italy
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Perrone B, Giacosa S, Rolle L, Cocolin L, Rantsiou K. Investigation of the dominance behavior of Saccharomyces cerevisiae strains during wine fermentation. Int J Food Microbiol 2013; 165:156-62. [PMID: 23728432 DOI: 10.1016/j.ijfoodmicro.2013.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/07/2013] [Accepted: 04/19/2013] [Indexed: 11/30/2022]
Abstract
During wine fermentation, different strains of Saccharomyces cerevisiae compete in the same fermenting must and dominance takes place when one strain overcomes all the others. The purpose of this study was to investigate this phenomenon by identifying S. cerevisiae strains endowed with this feature and to test them in laboratory fermentations. First, autochthonous S. cerevisiae from Nebbiolo fermentations were isolated, molecularly identified and characterized. Genetically diverse S. cerevisiae strains were subsequently subjected to physiological characterization and to micro-scale fermentation, the weight loss kinetics was measured and HPLC analysis was performed at the end of the fermentation. Then, the strains that presented good fermentation characteristics were chosen for further analysis and to determine the dominance feature. For this purpose, couples of strains were co-inoculated in Nebbiolo must and the fermentations were monitored by microbiological and chemical analysis. Two different inoculation approaches were used: co-fermentations in flasks with mixed cells and reactor co-fermentations, in which the cells from the two different strains were kept separate by means of a 0.45 μm filter membrane, which allowed the fermenting must to move freely between the two compartments. During the flask co-fermentations, a minisatellite PCR protocol was applied, in order to differentiate the two strains and determine which one was able to dominate. The protocol included a culture-dependent approach and an independent one. In the first case, DNA extraction was performed on all the colonies scraped off the plates after sampling. In the second case, DNA extraction was performed directly on the fermenting must. The strains that were able to dominate were tested against several S. cerevisiae in order to confirm this dominance behavior. Dominance was observed in the early stages of fermentation, as early as 3days. Combinations of dominant and not-dominant strains were subjected to further tests in a co-fermentation reactor system, in order to perform single-strain analysis so as to obtain a better understanding of the dominance behavior. Surprisingly, the results obtained in the flask co-fermentations were not confirmed. In fact, the two strains, one which was hypothesized to be dominant and the other not-dominant, coexisted throughout the fermentation period. The results of this study suggest that the dominant behavior of S. cerevisiae is only expressed when they sense other yeasts in the same environment.
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Affiliation(s)
- Benedetta Perrone
- Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Italy
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Capece A, Romaniello R, Siesto G, Romano P. Diversity of Saccharomyces cerevisiae yeasts associated to spontaneously fermenting grapes from an Italian “heroic vine-growing area”. Food Microbiol 2012; 31:159-66. [DOI: 10.1016/j.fm.2012.03.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 03/02/2012] [Accepted: 03/19/2012] [Indexed: 11/30/2022]
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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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Boveri S, Rainieri S, Pulvirenti A. Method for the validation of intraspecific crosses of Saccharomyces cerevisiae strains by minisatellite analysis. Can J Microbiol 2012; 58:350-8. [PMID: 22364492 DOI: 10.1139/w11-142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crossing of Saccharomyces strains by spore conjugation is one of the ways to obtain new starter cultures for the fermentation industry. One of the major difficulties of this practice is the identification of the newly formed hybrids. In this work we describe an effective molecular method for the validation of Saccharomyces intraspecific crosses. The method described is based in the hypothesis that hybrids constructed by spore conjugation contain the sum of the genomes of both parental strains. As a consequence, the conjugation of spores of two yeasts showing different genomic fingerprinting profiles will result in a hybrid culture that will show the sum of both profiles. We demonstrated that the detection of polymorphism in two genes containing minisatellite-like sequences, either SED1 or AGA1, is suitable for this purpose. Using this strategy we were able to validate 15 crosses out of 162 hybridization attempts.
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Affiliation(s)
- Silvio Boveri
- Department of Agriculture and Food Sciences - University of Modena and Reggio Emilia, Italy
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Oda Y, Mikumo D, Leo F, Urashima T. Discrimination of Saccharomyces cerevisiae and Saccharomyces paradoxus strains by the SUC2 gene sequences. J GEN APPL MICROBIOL 2010; 56:355-8. [PMID: 20953100 DOI: 10.2323/jgam.56.355] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuji Oda
- Department of Food Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.
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Zara G, Zara S, Pinna C, Marceddu S, Budroni M. FLO11 gene length and transcriptional level affect biofilm-forming ability of wild flor strains of Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2009; 155:3838-3846. [PMID: 19729408 DOI: 10.1099/mic.0.028738-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In Saccharomyces cerevisiae, FLO11 encodes an adhesin that is associated with different phenotypes, such as adherence to solid surfaces, hydrophobicity, mat and air-liquid biofilm formation. In the present study, we analysed FLO11 allelic polymorphisms and FLO11-associated phenotypes of 20 flor strains. We identified 13 alleles of different lengths, varying from 3.0 to 6.1 kb, thus demonstrating that FLO11 is highly polymorphic. Two alleles of 3.1 and 5.0 kb were cloned into strain BY4742 to compare the FLO11-associated phenotypes in the same genetic background. We show that there is a significant correlation between biofilm-forming ability and FLO11 length both in different and in the same genetic backgrounds. Moreover, we propose a multiple regression model that allows prediction of air-liquid biofilm-forming ability on the basis of transcription levels and lengths of FLO11 alleles in a population of S. cerevisiae flor strains. Considering that transcriptional differences are only partially explained by the differences in the promoter sequences, our results are consistent with the hypothesis that FLO11 transcription levels are strongly influenced by genetic background and affect biofilm-forming ability.
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Affiliation(s)
- Giacomo Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Severino Zara
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Claudia Pinna
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
| | - Salvatore Marceddu
- Istituto di Scienze delle Produzioni Alimentari (ISPA CNR Sassari), Via dei Mille 48, 07100 Sassari, Italy
| | - Marilena Budroni
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-alimentari (DISAABA), University of Sassari, Viale Italia 39, 07100 Sassari, Italy
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The β-tubulin gene as a molecular phylogenetic marker for classification and discrimination of the Saccharomyces sensu stricto complex. Antonie van Leeuwenhoek 2008; 95:135-42. [DOI: 10.1007/s10482-008-9296-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/02/2008] [Indexed: 11/26/2022]
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Ogihara F, Kitagaki H, Wang Q, Shimoi H. Common industrial sake yeast strains have three copies of the AQY1-ARR3 region of chromosome XVI in their genomes. Yeast 2008; 25:419-32. [PMID: 18509847 DOI: 10.1002/yea.1596] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Genomic analysis of industrial yeast strains is important for exploitation of their potential. We analysed the genomic structure of the most widely used sake yeast strain, Kyokai no. 7 (K7), by DNA microarray. Since the analysis suggested that the copy number of the AQY1-ARR3 region in the right arm of chromosome XVI was amplified, we performed Southern blot analysis using the AQY1 gene as a probe. The probe hybridized to three bands in the widely used sake strains derived from K7, but only to one band of 1.4 kb in the laboratory strains. Since the extra two bands were not observed in old sake strains, or in other industrial strains, the amplification of this region appeared to be specific for the widely used sake strains. The copy number of the AQY1-ARR3 region appeared to have increased by chromosomal translocation, since chromosomal Southern blot analysis revealed that the AQY1 probe hybridized to chromosomes IV and XIII, in addition to chromosome XVI, in which AQY1 of the laboratory strain is encoded. The chromosomal translocation was also confirmed by PCR analysis using primers that amplify the region containing the breakpoint. Cloning and sequencing of cosmids that encode the AQY1-ARR3 region revealed that this region is flanked by TG(1-3) repeats on the centromere-proximal side in chromosomes IV and XIII, suggesting that amplification of this region occurred by homologous recombination through TG(1-3) repeats. These results demonstrate the genomic characteristics of the modern widely used sake strains that discriminate them from other strains.
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Affiliation(s)
- Fukashi Ogihara
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashihiroshima 739-8530, Japan
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