Skip to main content
SpringerLink
Log in

Detection, Quantification, and Identification of Yeast in Winemaking

  • Chapter
  • First Online:
Yeasts in the Production of Wine

Abstract

Yeast have a fundamental role in winemaking. They carry out alcoholic fermentation and they contribute to the quality of the wine, although they can also cause spoilage during grape must transformation and in the final product. To detect and identify wine yeast and control their activities, a plethora of different methods can be utilized. As reported in the present chapter, these methods have different degrees of complexity and vary in terms of cost, rapidity and sensitivity. Those based on yeast isolation, namely culture-dependent methods, are widely utilized to define the composition of the microflora associated with wine-related environments and for yeast identification at the strain level, besides providing a means for ex-situ preservation of wine yeast biodiversity. Culture-independent methods bypass microorganisms cultivation, thus avoiding any bias introduced by their isolation and uncovering cell populations undetected by culture-dependent methods. These methods can be utilized to evaluate the impact of all of the components of the wine microbiota on the quality of the final product, to implement a quality control system based on real-time detection and quantification of specific targets, such as the inoculated starter (s) or the spoilage yeast, or to provide further insights into the composition of the microbial communities involved in the grape must transformation.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adt, I., Kohler, A., Gognies, S., Budin, J., Sandt, C., Belarbi, A., Manfait, M., & Sockalingum, G. D. (2010). FTIR spectroscopic discrimination of Saccharomyces cerevisiae and Saccharomyces bayanus strains. Canadian Journal of Microbiology, 56, 793–801.

    Article  CAS  PubMed  Google Scholar 

  • Agnolucci, M., Scarano, S., Santoro, S., Sassano, C., Toffanin, A., & Nuti, M. (2007). Genetic and phenotypic diversity of autochthonous Saccharomyces spp. strains associated to natural fermentation of ‘Malvasia delle Lipari’. Letters in Applied Microbiology, 45, 657–662.

    Article  CAS  PubMed  Google Scholar 

  • Agnolucci, M., Rea, F., Sbrana, C., Cristiani, C., Fracassetti, D., Tirelli, A., & Nuti, M. (2010). Sulphur dioxide affects culturability and volatile phenol production by Brettanomyces/ Dekkera bruxellensis. International Journal of Food Microbiology, 143, 76–80.

    Article  CAS  PubMed  Google Scholar 

  • Agnolucci, M., Cristani, C., Maggini, S., Rea, F., Cossu, A., Tirelli, A., & Nuti, M. (2013). Impact of sulphur dioxide on the viability, culturability, and volatile phenol production of Dekkera bruxellensis in wine. Annales de Microbiologie, 64, 653–659.

    Article  CAS  Google Scholar 

  • Albertin, W., Setati, M. E., Miot-Sertier, C., Mostert, T. T., Colonna-Ceccaldi, B., Coulon, J., et al. (2015). Hanseniaspora uvarum from winemaking environments show spatial and temporal genetic clustering. Frontiers in Microbiology, 6, 1569.

    PubMed  Google Scholar 

  • Amann, R., & Ludwig, W. (2000). Ribosomal RNA-target nucleic acid probes for studies in microbial ecology. FEMS Microbiology Reviews, 24, 555–565.

    Article  CAS  PubMed  Google Scholar 

  • Amann, R., Fuchs, B. M., & Behrens, S. (2001). The identification of microorganisms by fluorescence in situ hybridization. Current Opinion in Biotechnology, 12(3), 231–236.

    Article  CAS  PubMed  Google Scholar 

  • Andorrà, I., Landi, S., Mas, A., Guillamón, J. M., & Esteve-Zarzoso, B. (2008). Effect of oenological practices on microbial populations using culture independent techniques. Food Microbiology, 25, 849–856.

    Article  PubMed  CAS  Google Scholar 

  • Andorrà, I., Esteve-Zarzoso, B., Guillamon, J. M., & Mas, A. (2010). Determination of viable wine yeast using DNA binding dyes and quantitative PCR. International Journal of Food Microbiology, 144, 257–262.

    Article  PubMed  CAS  Google Scholar 

  • Andorrà, I., Monteiro, M., Esteve-Zarzoso, B., Albergaria, H., & Mas, A. (2011). Analysis and direct quantification of Saccharomyces cerevisiae and Hanseniaspora guilliermondii populations during alcoholic fermentation by fluorescence in situ hybridization, flow cytometry and quantitative PCR. Food Microbiology, 28, 1483–1149.

    Article  PubMed  CAS  Google Scholar 

  • Antunovics, Z., Irinyi, L., & Sipiczki, M. (2005a). Combined application of methods to taxonomic identification of Saccharomyces strains in fermenting botrytized grape must. Journal of Applied Microbiology, 98, 971–979.

    Article  CAS  PubMed  Google Scholar 

  • Antunovics, Z., Nguyen, H.-V., Gaillardin, C., & Sipiczki, M. (2005b). Gradual genome stabilization by progressive reduction of the Saccharomyces uvarum genome in an interspecific hybrid with Saccharomyces cerevisiae. FEMS Yeast Research, 5, 1141–1150.

    Article  CAS  PubMed  Google Scholar 

  • Arbefeville, S., Harris, A., & Ferrieri, P. (2017). Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species. Journal of Microbiological Methods, 140, 40–46.

    Article  CAS  PubMed  Google Scholar 

  • Attfield, P. V., Kletas, S., Veal, D. A., van Rooijen, R., & Bell, P. J. L. (2000). Use of flow cytometry to monitor cell damage and predict fermentation activity of dried yeasts. Journal of Applied Microbiology, 89, 207–214.

    Article  CAS  PubMed  Google Scholar 

  • Azumi, M., & Goto-Yamamoto, N. (2001). AFLP analysis of type strains and laboratory and industrial strains of Saccharomyces sensu stricto and its application to phenetic clustering. Yeast, 18, 1145–1154.

    Article  CAS  PubMed  Google Scholar 

  • Bagheri, B., Bauer, F. F., & Setati, M. E. (2017). The impact of Saccharomyces cerevisiae on a wine yeast consortium in natural and inoculated fermentations. Frontiers in Microbiology, 8, 1988.

    Article  PubMed  PubMed Central  Google Scholar 

  • Baleiras Couto, M. M., van der Vossen, J. M. B. M., Hofstra, H., & Huis in’t Veld, J. H. J. (1994). RAPD analysis: A rapid technique for differentiation of spoilage yeasts. International Journal of Food Microbiology, 24, 249–260.

    Article  CAS  PubMed  Google Scholar 

  • Balselga, I., Zafra, O., Pérez-Lago, E., Francisco-Álvarez, R., Rodriguez-Tarduchy, G., & Santos, C. (2017). An AFLP based method for the detection and identification of indigenous yeast in complex must samples without a microbiological culture. International Journal of Food Microbiology, 241, 89–97.

    Article  CAS  Google Scholar 

  • Barata, A., Malfeito-Ferreira, M., & Loureiro, V. (2012). The microbial ecology of wine grape berries. International Journal of Food Microbiology, 153, 243–259.

    Article  CAS  PubMed  Google Scholar 

  • Barbosa, C., Lage, P., Esteves, M., Chambel, L., Mendes-Faia, A., & Mendes-Ferreira, A. (2018). Molecular and phenotypic characterization of Metschnikowia pulcherrima strains from Douro wine region. Fermentation, 4, 8.

    Article  CAS  Google Scholar 

  • Barnett, J. A., Payne, R. W., & Yarrow, D. (2000a). Yeast. In Characteristics and identification (3rd ed.). England: Cambridge University Press.

    Google Scholar 

  • Barnett, J. A., Payne, R. W., & Yarrow, D. (2000b). Yeast. In Identification PC program (2nd ed.). England: Cambridge Micro Software, Cambridge University Press.

    Google Scholar 

  • Beh, A. L., Fleet, G. H., Prakichaiwattana, C., & Heard, G. M. (2006). Evaluation of molecular methods for the analyses of yeasts in foods and beverages. In A. D. Hocking, J. T. Pitt, R. A. Samson, & U. Thrane (Eds.), Advances in food mycology (pp. 69–106). Springer.

    Google Scholar 

  • Belda, I., Zarraonaindia, I., Perisin, M., Palacios, A., & Acedo, A. (2017). From vineyard soil to wine fermentation: Microbiome approximations to explain the “terroir” concept. Frontiers in Microbiology, 8, 821.

    Article  PubMed  PubMed Central  Google Scholar 

  • Beuchat, L. R., Copeland, F., Curiale, M. S., Danisavich, T., Gangar, V., King, B. W., Lawlis, T. C., Likin, R. O., Okwusoa, J., Smith, C. F., & Townsend, D. E. (1998). Comparison of the SimPlate, total plate count method with Petrifilm, Redigel, and conventional pour-plate methods for enumerating aerobic microorganisms in foods. Journal of Food Protection, 61, 14–18.

    Article  CAS  PubMed  Google Scholar 

  • Bisson, L. F., Joseph, C. M. L., & Domizio, P. (2017). Yeasts. In H. König, G. Unden, & J. Fröhlich (Eds.), Biology of microorganisms on grapes, in must and in wine (pp. 65–101). Cham: Springer.

    Chapter  Google Scholar 

  • Bokulich, N. A., & Mills, D. A. (2013). Improved selection of internal transcribed spacer-specific primers enables quantitative, ultrahigh-throughput profiling of fungal communities. Applied and Environmental Microbiology, 79, 2519–2526.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bokulich, N. A., Bamforth, C. W., & Mills, D. A. (2012a). A review of molecular methods for microbial community profiling of beer and wine. Journal of the American Society of Brewing Chemists, 70, 150–162.

    Article  CAS  Google Scholar 

  • Bokulich, N. A., Hwang, C. F., Liu, S., Boundy-Mills, K., & Mills, D. A. (2012b). Profiling the yeast communities of wine using terminal restriction fragment length polymorphism. American Journal of Enology and Viticulture, 63, 177–184.

    Article  CAS  Google Scholar 

  • Bokulich, N. A., Thorngate, J. H., Richardson, P. M., & Mills, D. A. (2014). Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proceedings of the National Academy of Sciences of the United States of America, 111, E139.

    Article  CAS  PubMed  Google Scholar 

  • Bokulich, N. A., Collins, T. S., Masarweh, C., Allen, G., Heymann, H., Ebeler, S. E., et al. (2016). Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio, 7, e00631–e00616.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bottari, B., Ercolini, D., Gatti, M., & Neviani, E. (2006). Application of FISH technology for microbiological analysis: Current state and prospects. Applied Microbiology and Biotechnology, 73, 485–494.

    Article  CAS  PubMed  Google Scholar 

  • Branco, P., Monteiro, M., Moura, P., & Albergaria, H. (2012). Survival rate of wine-related yeasts during alcoholic fermentation assessed by direct live/dead staining combined with fluorescence in situ hybridization. International Journal of Food Microbiology, 158, 49–57.

    Article  CAS  PubMed  Google Scholar 

  • Brinkman, N. E., Haugland, R. A., Wymer, L. J., Byappanahalli, M., Whitman, R. L., & Vesper, L. J. (2003). Evaluation of a rapid, quantitative real-time PCR method for enumeration of pathogenic Candida cells in water. Applied and Environmental Microbiology, 69, 1775–1782.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bustin, S. A., Benes, V., Nolan, T., & Pfaffl, M. W. (2005). Quantitative real-time RT-PCR- a perspective. Journal of Molecular Endocrinology, 34(3), 597–601.

    Article  CAS  PubMed  Google Scholar 

  • Cadez, N., Raspor, P., de Cock, A. W. A. M., Boekhout, T., & Smith, M. T. (2002). Molecular identification and genetic diversity within species of the genera Hanseniaspora and Kloeckera. FEMS Yeast Research, 1, 279–289.

    CAS  PubMed  Google Scholar 

  • Cameron, M., Siebrits, L., Du Toit, M., & Witthuhn, C. (2013). PCR-based DGGE fingerprinting and identification of the microbial population in South African red grape must and wine. OENO One, 47, 47–54.

    Article  CAS  Google Scholar 

  • Capece, A., Salzano, G., & Romano, P. (2003). Molecular typing techniques as a tool to differentiate non-Saccharomyces wine species. International Journal of Food Microbiology, 84, 33–39.

    Article  CAS  PubMed  Google Scholar 

  • Capozzi, V., Di Toro, M. R., Grieco, F., Michelotti, V., Salma, M., Lamontanara, A., Russo, P., Orrù, L., Alexandre, H., & Spano, G. (2016). Viable But Not Culturable (VBNC) state of Brettanomyces bruxellensis in wine: New insights of molecular basis of VBNC behavior using a transcriptomic approach. Food Microbiology, 59, 196–204.

    Article  CAS  PubMed  Google Scholar 

  • Cardinali, G., Liti, G., & Martini, A. (2000). Non-radioactive dot-blot DNA reassociation for unequivocal yeast identification. International Journal of Systematic and Evolutionary Microbiology, 50, 931–936.

    Article  PubMed  Google Scholar 

  • Carro, D., & Piňa, B. (2001). Genetic analysis of the karyotype instability in natural wine yeast strains. Yeast, 18, 1457–1470.

    Article  CAS  PubMed  Google Scholar 

  • Caruso, M., Capece, A., Salzano, G., & Romano, P. (2002). Typing of Saccharomyces cerevisiae and Kloeckera apiculata strains from Aglianico wine. Letters in Applied Microbiology, 34, 323–328.

    Article  CAS  PubMed  Google Scholar 

  • Casaregola, S., Nguyen, H., Lapathitis, G., Kotyk, A., & Gaillardin, C. (2001). Analysis of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. International Journal of Systematic and Evolutionary Microbiology, 51, 1607–1618.

    Article  CAS  PubMed  Google Scholar 

  • Casey, G. D., & Dobson, A. D. W. (2004). Potential of using real-time PCR-based detection of spoilage yeast in fruit juice – a preliminary study. International Journal of Food Microbiology, 91, 327–335.

    Article  CAS  PubMed  Google Scholar 

  • Chalupová, J., Raus, M., Sedlářová, M., & Šebela, M. (2014). Identification of fungal microorganisms by MALDI-TOF mass spectrometry. Biotechnology Advances, 32, 230–241.

    Article  PubMed  CAS  Google Scholar 

  • Christ, E., Kowalczyk, M., Zuchowska, M., Claus, H., Löwenstein, R., Szopinska-Morawska, A., Renaut, J., & Kònig, H. (2015). An exemplary model study for overcoming stuck fermentation during spontaneous fermentation with the aid of a Saccharomyces triple hybrid. Journal of Agricultural Science, 7, 18–34.

    Article  Google Scholar 

  • Cocolin, L., & Mills, D. A. (2003). Wine yeast inhibition by sulfur dioxide: A comparison of culture–dependent and independent methods. American Journal of Enology and Viticulture, 54, 125–130.

    CAS  Google Scholar 

  • Cocolin, L., Bisson, L. F., & Mills, D. (2000). Direct profiling of the dynamics in wine fermentation. FEMS Microbiology Letters, 189, 81–87.

    Article  CAS  PubMed  Google Scholar 

  • Cocolin, L., Rantsiou, K., Iacumin, L., Zironi, R., & Comi, G. (2004). Molecular detection and identification of Brettanomyces/Dekkera bruxellensis and Brettanomyces/Dekkera anomalus in spoiled wines. Applied and Environmental Microbiology, 70, 1347–1355.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cocolin, L., Campolongo, S., Alessandria, A., Dolci, P., & Rantsiou, K. (2011). Culture independent analyses and wine fermentation: An overview of achievements 10 years after first application. Annales de Microbiologie, 61, 17–23.

    Article  Google Scholar 

  • Corich, V., Mattiazzi, A., Soldati, E., Carraro, A., & Giacomini, A. (2005). Sau-PCR, a novel amplification technique for genetic fingerprinting of microorganisms. Applied and Environmental Microbiology, 71, 6401–6406.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Corredor, M., Davila, A.-M., Gaillardin, C., & Casaregola, S. (2000). DNA probes specific for the yeast species Debaryomyces hansenii: Useful tools for rapid identification. FEMS Microbiology Letters, 193, 171–177.

    Article  CAS  PubMed  Google Scholar 

  • Couto, J. A., Barbosa, A., & Hogg, T. (2005). A simple cultural method for the presumptive detection of the yeasts Brettanomyces/Dekkera in wines. Letters in Applied Microbiology, 41, 505–510.

    Article  CAS  PubMed  Google Scholar 

  • Curtin, C. D., Bellon, J. R., Henschke, P. A., Godden, P. W., & de Barros Lopes, M. A. (2007). Genetic diversity of Dekkera bruxellensis yeasts isolated from Australian wineries. FEMS Yeast Research, 7, 471–481.

    Article  CAS  PubMed  Google Scholar 

  • Daniel, H. M., & Meyer, W. (2003). Evaluation of ribosomal RNA and actin gene sequences for identification of ascomycetous yeasts. International Journal of Food Microbiology, 86, 71–78.

    Article  CAS  Google Scholar 

  • David, V., Terrat, S., Herzine, K., Claisse, O., Rousseaux, S., Tourdot-Maréchal, R., et al. (2014). High-throughput sequencing of amplicons for monitoring yeast biodiversity in must and during alcoholic fermentation. Journal of Industrial Microbiology & Biotechnology, 41, 811–821.

    Article  CAS  Google Scholar 

  • de Barros Lopes, M., Soden, A., Henschke, P. A., & Langridge, P. (1996). PCR differentiation of commercial yeast strains using intron splice primers. Applied and Environmental Microbiology, 62, 4514–4520.

    PubMed  PubMed Central  Google Scholar 

  • de Barros Lopes, M., Soden, A., Henschke, P. A., & Langridge, P. (1998). Differentiation and species identification of yeasts using PCR. International Journal of Systematic Bacteriology, 48, 279–286.

    Article  PubMed  Google Scholar 

  • de Barros Lopes, M., Raineri, S., Henschke, P. A., & Langridge, P. (1999). AFLP fingerprinting for analysis of yeast genetic variation. International Journal of Systematic Bacteriology, 49, 915–924.

    Article  PubMed  Google Scholar 

  • De Filippis, F., La Storia, A., & Blaiotta, G. (2017a). Monitoring the micobiota during Greco di Tufo and Anglianico wine fermentation by 18S rRNA gene sequencing. Food Microbiology, 63, 117–122.

    Article  PubMed  CAS  Google Scholar 

  • De Filippis, F., Parente, E., & Ercolini, D. (2017b). Metagenomics insights into food fermentations. Microbial Biotechnology, 10, 91–102.

    Article  PubMed  Google Scholar 

  • De Souza Liberal, A. T., Basilio, A. C. M., do Monte Resende, A., Brasileiro, B. T. V., da Silva-Filho, E. A., de Morais, J. O. F., Simoes, D. A., & de Morais, M. A., Jr. (2007). Identification of Dekkera bruxellensis as a major contaminant yeast in continuous fuel ethanol fermentation. Journal of Applied Microbiology, 102, 538–547.

    Article  PubMed  CAS  Google Scholar 

  • Deak, T. (2003). Detection, enumeration and isolation of yeasts. In T. Boekhout & V. Robert (Eds.), Yeasts in food, beneficial and detrimental aspects (pp. 39–64). Hamburg: Behr’s Verlag.

    Chapter  Google Scholar 

  • Deak, T. (2008). Handbook of food spoilage yeasts (2nd ed., p. 325). Boca Raton: CRC Press.

    Google Scholar 

  • Deak, T., & Beuchat, L. R. (1993). Comparison of the SIM, API20C, and ID32C systems for the identification of yeasts isolated from fruit juice concentrates and beverages. Journal of Food Protection, 56, 585–592.

    Article  CAS  PubMed  Google Scholar 

  • Di Maro, E., Ercolini, D., & Coppola, S. (2007). Yeast dynamics during spontaneous wine fermentation of the Catalanesca grape. International Journal of Food Microbiology, 117, 201–210.

    Article  PubMed  CAS  Google Scholar 

  • Divol, B., & Lonvaud-Funel, A. (2005). Evidence for viable but non-culturable yeasts in botrytis-affected wine. Journal of Applied Microbiology, 99, 85–93.

    Article  CAS  PubMed  Google Scholar 

  • Dlauchy, D., Tornai-Lehoczki, J., & Péter, G. (1999). Restriction enzyme analysis of PCR amplified rRNA as a taxonomic tool in yeast identification. Systematic and Applied Microbiology, 22, 445–453.

    Article  CAS  PubMed  Google Scholar 

  • Domizio, P., Romani, C., Lencioni, L., Comitini, F., Gobbi, M., Mannazzu, I., & Ciani, M. (2011). Outlining a future for non-Saccharomyces yeasts: Selection of putative spoilage wine strains to be used in association with Saccharomyces cerevisiae for grape juice fermentation. International Journal of Food Microbiology, 147, 170–180.

    Article  CAS  PubMed  Google Scholar 

  • Dowhanick, T., Sobczak, J., Russel, I., & Stewart, G. (1990). The rapid identification by protein fingerprinting of yeast and brewery contaminants. Journal of the American Society of Brewing Chemists, 48, 75–79.

    Article  CAS  Google Scholar 

  • Du Plessis, H. W., du Toit, M., Hoff, J. W., Hart, R. S., Ndimba, B. K., & Jolly, N. P. (2017). Characterization of non-Saccharomyces yeasts using different methodologies and evaluation of their compatibility with malolactic fermentation. South African Journal of Enology and Viticulture, 38, 46.63.

    Article  Google Scholar 

  • Duarte, F. L., & Baleiras-Couto, M. (2012). Evaluation of fermenting grape must yeast dynamics by SSCP profiles. Ciencia e Tecnica Vitivinicola, 27, 95–101.

    Google Scholar 

  • Egli, C. M., & Henick-Kling, T. (2001). Identification of Brettanomyces/Dekkera species based on polymorphism in the rRNA internal transcribed spacer region. American Journal of Enology and Viticulture, 52, 241–247.

    CAS  Google Scholar 

  • Entis, P., & Lerner, I. (1996). Two-day yeast and mold enumeration using the Iso-Grid® membrane filtration system in conjunction with YM-11 agar. Journal of Food Protection, 59, 416–419.

    Article  PubMed  Google Scholar 

  • Ercolini, D. (2004). PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. Journal of Microbiological Methods, 56, 297–314.

    Article  CAS  PubMed  Google Scholar 

  • Esteve-Zarzoso, B., Belloch, C., Uruburu, F., & Querol, A. (1999). Identification of yeasts by RFLP analysis of the 5.8S rRNA gene and the two ribosomal internal transcribed spacers. International Journal of Systematic Bacteriology, 49, 329–337.

    Article  CAS  PubMed  Google Scholar 

  • Fell, J. W., Boekhout, T., Fonseca, A., Scorzetti, G., & Statzell-Tallman, A. (2000). Biodiversity and systematics of basidiomycetous yeasts as determined by large subunit rD1/D2 domain sequence analysis. International Journal of Systematic and Environmental Microbiology, 50, 1351–1371.

    Article  CAS  Google Scholar 

  • Fernandes Lemos Junior, W. J., Bovo, B., Nadai, C., Crosato, G., Carlot, M., Favaron, F., Giacomini, A., & Corich, V. (2016). Biocontrol ability and action mechanism of Starmerella bacillaris (Synonym Candida zemplinina) isolated from wine musts against gray mold disease agent Botrytis cinerea on grape and their effects on alcoholic fermentation. Food Microbiology, 7, 1249.

    Google Scholar 

  • Fernández-Espinar, M. T., Esteve-Zarzoso, B., Querol, A., & Barrio, E. (2000). RFLP analysis of the ribosomal internal transcribed spacers and the 5.8S rRNA gene region of the genus Saccharomyces: a fast method for species identification of flor yeast. Antonie van Leeuwenhoek, 78, 87–97.

    Article  Google Scholar 

  • Fernández-Espinar, M. T., López, V., Ramón, D., Bartra, E., & Querol, A. (2001). Study of the authenticity of commercial wine yeast strains by molecular techniques. International Journal of Food Microbiology, 70, 1–10.

    Article  PubMed  Google Scholar 

  • Fernández-Espinar, M. T., Martorell, P., de Llanos, R., & Querol, A. (2006). Molecular methods to identify and characterise yeasts in foods and beverages. In A. Querol & G. H. Fleet (Eds.), Yeasts in food and beverages (pp. 55–82). Berlin: Springer.

    Chapter  Google Scholar 

  • Fernández-Espinar, M. T., Llopis, S., Querol, A., & Barrio, E. (2011). Chapter 5 – Molecular identification and characterization of wine yeasts. In A. V. Carrascosa, R. Munoz, & R. Gonzalez (Eds.), Molecular wine microbiology (pp. 111–141). San Diego: Academic.

    Chapter  Google Scholar 

  • Fröhlich, J., König, H., & Claus, H. (2017). Molecular methods for identification of wine microorganisms and yeast development. In H. König, G. Unden, & J. Fröhlich (Eds.), Biology of microorganisms on grapes, in must and in wine (pp. 517–548). Cham: Springer.

    Chapter  Google Scholar 

  • Fujita, S. H., Senda, Y., Nakaguchi, S., & Hashimoto, T. (2001). Multiplex PCR using internal transcribed spacer 1 and 2 regions for rapid detection and identification of yeast strains. Journal of Clinical Microbiology, 39, 3617–3622.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fung, D. (2002). Rapid methods and automation in microbiology. Comprehensive Reviews in Food Science and Food Safety, 1, 3–22.

    Article  CAS  Google Scholar 

  • Gallego, F. J., Perez, M. A., Martinez, I., & Hidalgo, P. (1998). Microsatellites obtained from database sequences are useful to characterize Saccharomyces cerevisiae strains. American Journal of Enology and Viticulture, 49, 350–351.

    CAS  Google Scholar 

  • Gallego, F. J., Perez, M. A., Nunez, Y., & Hidalgo, P. (2005). Comparison of RAPDs, AFLPs and SSR markers for the genetic analysis of yeast strains of Saccharomyces cerevisiae. Food Microbiology, 22, 561–568.

    Article  CAS  Google Scholar 

  • García, M., Esteve-Zarzoso, B., Crespo, J., Cabellos, J. M., & Arroyo, T. (2017). Yeast monitoring of wine mixed or sequential fermentations made by native strains from D.O. “Vinos de Madrid” using Real-Time Quantitative PCR. Frontiers in Microbiology, 8, 2520.

    Article  PubMed  PubMed Central  Google Scholar 

  • Gerbaux, V., & Thomas, J. (2009). Utilisations pratiques de la cytometrie de flux pour le suivi des levures en oenologie. Revue Francaise d'Oenologie, 8–13.

    Google Scholar 

  • Ghosh, S., Bagheri, B., Morgan, H. H., Divol, B., & Setati, M. E. (2015). Assessment of wine microbial diversity using ARISA and cultivation based methods. Annales de Microbiologie, 65, 4.

    Google Scholar 

  • Giesendorf, B. A. J., Quint, W. G. V., Vandamme, P., & van Belkum, A. (1996). Generation of DNA probes for detection of microorganisms by polymerase chain reaction fingerprinting. Zentbl Bakteriol Parasit Infekt Hyg Abt Orig, 283, 417–430.

    CAS  Google Scholar 

  • Giraffa, G. (2004). Studying the dynamics of microbial populations during food fermentation: Table 1. FEMS Microbiology Reviews, 28(2), 251–260.

    Article  CAS  PubMed  Google Scholar 

  • González, S. S., Barrio, E., Gafner, J., & Querol, A. (2006). Natural hybrids from Saccharomyces cereviseae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations. FEMS Yeast Research, 6(8), 1221–1234.

    Article  PubMed  CAS  Google Scholar 

  • Gori, A., Cerboneschi, M., & Tegli, S. (2012). High-resolution melting analysis as a powerful tool to discriminate and genotype Pseudomonas savastanoi pathovars and strains. PLoS ONE, 7, e30199.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grando, M. S., Ubeda, J., & Briones, A. I. (1994). RAPD analysis of wine Saccharomyces cerevisiae strains differentiated by pulsed field gel electrophoresis. Biotechnology Techniques, 8, 557–560.

    Article  CAS  Google Scholar 

  • Grangeteau, C., Gerhards, D., Rousseaux, S., von Wallbrunn, C., Alexandre, H., & Guilloux-Benatier, M. (2015). Diversity of yeast strains of the genus Hanseniaspora in the winery environment: What is their involvement in grape must fermentation? Food Microbiology, 50, 70–77.

    Article  CAS  PubMed  Google Scholar 

  • Grangeteau, C., Gerhards, D., Terrat, S., Dequiedt, S., Alexandre, H., Guilloux-Benatier, M., von Wallbrunn, C., & Rousseaux, S. (2016). FT-IR spectroscopy: A powerful tool for studying the inter- and intraspecific biodiversity of cultivable non-Saccharomyces yeasts isolated from grape must. Journal of Microbiological Methods, 121, 50–58.

    Article  CAS  PubMed  Google Scholar 

  • Grangeteau, C., Roullier-Gall, C., Rousseaux, S., Guogeon, R. D., Schmitt-Kopplin, P., Alexandre, H., et al. (2017). Wine microbiology is driven by vineyard and winery anthropogenic factors. Microbial Biotechnology, 10, 354–370.

    Article  CAS  PubMed  Google Scholar 

  • Guillamón, J. M., & Barrio, E. (2017). Genetic polymorphism in wine yeasts: Mechanisms and methods for its detection. Frontiers in Microbiology, 8, 806.

    Article  PubMed  PubMed Central  Google Scholar 

  • Guillamón, J. M., Barrio, E., Huerta, T., & Querol, A. (1994). Rapid characterization of four species of the Saccharomyces sensu stricto complex according to mitochondrial DNA patterns. International Journal of Systematic Bacteriology, 44, 708–714.

    Article  PubMed  Google Scholar 

  • Guillamón, J. M., Sabaté, J., Barrio, E., Cano, J., & Querol, A. (1998). Rapid identification of wine species based on RFLP analysis of the ribosomal ITS region. Archives of Microbiology, 169, 387–392.

    Article  PubMed  Google Scholar 

  • Gutiérrez, C., Gómez-Flechoso, M. A., Belda, I., Ruiz, J., Kayali, N., Polo, L., & Santos, A. (2017). Wine yeasts identification by MALDI-TOF MS: Optimization of the preanalytical steps and development of an extensible open-source platform for processing and analysis of an in-house MS database. International Journal of Food Microbiology, 254, 1–10.

    Article  PubMed  CAS  Google Scholar 

  • Hanna, S. E., Christopher, J. C., & Wang, H. H. (2005). Real-time polymerase chain reaction for the food microbiologist: Technologies, applications, and limitations. Journal of Food Science, 70(3), R49–R53.

    Article  CAS  Google Scholar 

  • Hayashi, N., Arai, R., Tada, S., Taguchi, H., & Ogawa, Y. (2007). Detection and identification of Brettanomyces / Dekkera sp. yeasts with a loop-mediated isothermal amplification method. Food Microbiology, 24, 778–785.

    Article  CAS  PubMed  Google Scholar 

  • Hayashi, N., Minato, T., Kanai, K., Ikushima, S., Yoshida, S., Tada, S., Taguchi, H., & Ogawa, Y. (2009). Differentiation of species belonging to Saccharomyces sensu stricto using a loop-mediated isothermal amplification method. Journal of the American Society of Brewing Chemists, 67, 118–126.

    Article  CAS  Google Scholar 

  • Hennequin, C., Thierry, A., Richard, G. F., Lecointre, G., Nguyen, H. V., Gaillardin, C., & Dujon, B. (2001). Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. Journal of Clinical Microbiology, 39, 551–559.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hierro, N., González, Á., Mas, A., & Guillamón, J. M. (2004). New PCR-based methods for yeast identification. Journal of Applied Microbiology, 97, 792–801.

    Article  CAS  PubMed  Google Scholar 

  • Hierro, N., González, Á., Mas, A., & Guillamón, J. M. (2006). Diversity and evolution of non-Saccharomyces yeast populations during wine fermentation: effect of grape ripeness and cold maceration. FEMS Yeast Research, 6, 102–111.

    Article  CAS  PubMed  Google Scholar 

  • Hierro, N., Esteve-Zarzoso, B., Mas, A., & Guillamón, J. M. (2007). Monitoring of Saccharomyces and Hanseniaspora populations during alcoholic fermentation by real-time quantitative PCR. FEMS Yeast Research, 7, 1340–1349.

    Article  CAS  PubMed  Google Scholar 

  • Howell, K. S., Bartowsky, E. J., Fleet, G. H., & Henschke, P. A. (2004). Microsatellite PCR profiling of Saccharomyces cerevisiae strains during wine fermentation. Letters in Applied Microbiology, 38, 315–320.

    Article  CAS  PubMed  Google Scholar 

  • Ibeas, J., Lozano, J., Perdigones, F., & Jimenez, J. (1996). Detection of Dekkera/Brettanomyces strains in sherry by a nested PCR method. Applied and Environmental Microbiology, 62, 998–1003.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ivey, M. L., & Phister, T. G. (2011). Detection and identification of microorganisms in wine: A review of molecular techniques. Journal of Industrial Microbiology and Biotechnology, 38(10), 1619–1634.

    Article  CAS  PubMed  Google Scholar 

  • Keisam, S., Romi, W., Ahmed, G., & Jeyaram, K. (2016). Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods. Scientific Reports, 6, 34155.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kopke, C., Cristovao, A., Prata, A. M., Silva Pereira, C., Figueiredo Marques, J. J., & San Romao, M. V. (2000). Microbiological control of wine. The application of epifluorescence microscopy method as a rapid technique. Food Microbiology, 17, 257–260.

    Article  Google Scholar 

  • Kurtzman, C. P., & Robnett, C. J. (1998). Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek, 73, 331–371.

    Article  CAS  PubMed  Google Scholar 

  • Kurtzman, C. P., & Robnett, C. J. (2003). Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses. FEMS Yeast Research, 3, 417–432.

    Article  CAS  PubMed  Google Scholar 

  • Landolfo, S., Zara, G., Zara, S., Budroni, M., Ciani, M., & Mannazzu, I. (2010). Oleic acid and ergosterol supplementation mitigates oxidative stress in wine strains of Saccharomyces cerevisiae. International Journal of Food Microbiology, 141, 229–235.

    Article  CAS  PubMed  Google Scholar 

  • Lavallée, F., Salvas, Y., Lamy, S., Thomas, D. Y., Degree, R., & Dulau, L. (1994). PCR and DNA fingerprinting used as quality control in the production of wine yeast strains. American Journal of Enology and Viticulture, 45, 86–91.

    Google Scholar 

  • Le Jeune, C., Lollier, M., Demuyter, C., Erny, C., Legras, J.-L., Aigle, M., & Masneuf-Pomarede, I. (2007). Characterization of natural hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum. FEMS Yeast Research, 7, 540–549.

    Article  PubMed  CAS  Google Scholar 

  • Legras, J. L., & Karst, F. (2003). Optimisation of interdelta analysis for Saccharomyces cerevisiae strain characterisation. FEMS Microbiology Letters, 221, 249–255.

    Article  CAS  PubMed  Google Scholar 

  • Legras, J. L., Ruh, O., Merdinoglu, D., & Karst, F. (2005). Selection of hypervariable microsatellite loci for the characterization of Saccharomyces cerevisiae strains. International Journal of Food Microbiology, 102, 73–83.

    Article  CAS  PubMed  Google Scholar 

  • Li, S. S., Cheng, C., Li, Z., Chen, J.-Y., Yan, B., Han, B.-Z., & Reeves, M. (2010). Yeast species associated with wine grapes in China. International Journal of Food Microbiology, 138, 85–90.

    Article  CAS  PubMed  Google Scholar 

  • Longin, C., Petitgonnet, C., Guilloux-Benatier, M., Rousseaux, S., & Alexandre, H. (2017). Application of flow cytometry to wine microorganisms. Food Microbiology, 62, 221–231.

    Article  CAS  PubMed  Google Scholar 

  • Lopandic, K., Gangl, H., Wallner, E., Tscheik, G., Leitner, G., Querol, A., Borth, N., Breitenbach, M., Prillinger, H., & Tiefenbrunner, W. (2007). Genetically different wine yeasts isolated from Austrian vine-growing regions influence wine aroma differently and contain putative hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii. FEMS Yeast Research, 7, 953–965.

    Article  CAS  PubMed  Google Scholar 

  • Lopes, C. A., van Broock, M., Querol, A., & Caballero, A. C. (2002). Saccharomyces cerevisiae wine yeast populations in a cold region in Argentiniean Patagonia. A study at different fermentation scales. Journal of Applied Microbiology, 93, 608–615.

    Article  CAS  PubMed  Google Scholar 

  • López, V., Fernández-Espinar, M. T., Barrio, E., Ramón, D., & Querol, A. (2003). A new PCR-based method for monitoring inoculated wine fermentation. International Journal of Food Microbiology, 81, 63–71.

    Article  PubMed  Google Scholar 

  • Loureiro, V., Malfeito-Ferreira, M., & Carreira, A. (2004). Detecting spoilage yeasts. In R. R. Steele (Ed.), Understanding and measuring the shelf-life of food (pp. 233–288). Cambridge: Woodhead.

    Chapter  Google Scholar 

  • Malacrino, P., Zapparoli, G., Torriani, S., & Dellaglio, F. (2001). Rapid detection of viable yeasts and bacteria in wine by flow cytometry. Journal of Microbiological Methods, 45, 127–134.

    Article  CAS  PubMed  Google Scholar 

  • Manavathu, E. K., Vakulenko, S. B., Obedeanu, N., & Lerner, S. A. (1996). Isolation and characterization of a species-specific DNA probe for the detetion of Candida krusei. Current Microbiology, 33, 147–151.

    Article  CAS  PubMed  Google Scholar 

  • Mannarelli, B. M., & Kurtzman, C. P. (1998). Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR. Journal of Clinical Microbiology, 36, 1634–1641.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mannazzu, I., Agelozzi, D., Belviso, S., Budroni, M., Farris, G. A., Goffrini, P., Lodi, T., Marzona, M., & Bardi, L. (2008). Behaviour of Saccharomyces cerevisiae wine strains during adaptation to unfavourable conditions of fermentation in synthetic medium: Cell lipid composition, membrane integrity, viability and fermentative activity. International Journal of Food Microbiology, 121, 84–91.

    Article  CAS  PubMed  Google Scholar 

  • Manzano, M., Medrala, D., Giusto, C., Bartolomeoli, I., Urso, R., & Comi, G. (2006). Classical and molecular analyses to characterize commercial dry yeasts used in wine fermentations. Journal of Applied Microbiology, 100, 599–607.

    Article  CAS  PubMed  Google Scholar 

  • Marcos, J. Y., & Pincus, D. H. (2013). Fungal diagnostics: Review of commercially available methods. In L. O’Connor & B. Glynn (Eds.), Fungal diagnostics. Methods in molecular biology (Methods and protocols) (Vol. 968). Totowa: Humana Press.

    Google Scholar 

  • Marinangeli, P., Angelozzi, D., Ciani, M., Clementi, F., & Mannazzu, I. (2004). Minisatellites in Saccharomyces cerevisiae genes encoding cell wall proteins: A new way towards wine strain characterisation. FEMS Yeast Research, 4, 427–435.

    Article  CAS  PubMed  Google Scholar 

  • Martinez, C., Cosgaya, P., Vásquez, C., Gac, S., & Ganga, A. (2007). High degree of correlation between molecular polymorphism and geographic origin of wine yeast strains. Journal of Applied Microbiology, 103, 2185–2195.

    Article  CAS  PubMed  Google Scholar 

  • Martins, G., Miot-Sertier, C., Lauga, B., Claisse, O., Lonvaud-Funel, A., Soulas, G., et al. (2012). Grape berry bacterial microbiota: Impact of the ripening process and the farming system. International Journal of Food Microbiology, 158, 93–100.

    Article  CAS  PubMed  Google Scholar 

  • Martins, G., Vallance, J., Mercier, A., Albertin, W., Stamatopoulos, P., Rey, P., et al. (2014). Influence of the farming system on the epiphytic yeasts and yeast like fungi colonizing grape berries during the ripening process. International Journal of Food Microbiology, 177, 21–28.

    Article  PubMed  Google Scholar 

  • Martorell, P., Querol, A., & Fernandez-Espinar, M. T. (2005). Rapid identification and enumeration of Saccharomyces cerevisiae cells in wine by real-time PCR. Applied and Environmental Microbiology, 71, 6823–6830.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mercado, L., Dalcero, A., Masuelli, R., & Combina, M. (2007). Diversity of Saccharomyces strains on grapes and winery surfaces: Analysis of their contribution to fermentative flora of malbec wine from Mendoza (Argentina) during two consecutive years. Food Microbiology, 24, 403–412.

    Article  CAS  PubMed  Google Scholar 

  • Millet, V., & Lonvaud-Funel, A. (2000). The viable but non-culturable state of wine micro-organisms during storage. Letters in Applied Microbiology, 30, 136–141.

    Article  CAS  PubMed  Google Scholar 

  • Mills, D. A., Johannsen, E. A., & Cocolin, L. (2002). Yeast diversity and persistence in botrytis-affected wine fermentation. Applied and Environmental Microbiology, 68, 4884–4893.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mitrakul, C. M., Henick-Kling, T., & Egli, C. M. (1999). Discrimination of Brettanomyces / Dekkera yeast isolates from wine by using various DNA finger-printing methods. Food Microbiology, 16, 3–14.

    Article  CAS  Google Scholar 

  • Morgan, H. H., du Toit, M., & Setati, M. E. (2017). The grapevine and wine microbiome: Insights from high-throughput amplicon sequencing. Food Microbiology, 8, 820.

    Google Scholar 

  • Morrison, T. B., Weiss, J. J., & Witter, C. T. (1998). Quantification of low-copy transcript by continuous SYBR Green monitoring during amplification. BioTechniques, 24, 954–962.

    CAS  PubMed  Google Scholar 

  • Morneau, A. D., Zuehlke, J. M., & Edwards, C. G. (2011). Comparison of media formulations used to selectively cultivate Dekkera/Brettanomyces. Letters in Applied Microbiology, 53(4), 460–465.

    Article  CAS  PubMed  Google Scholar 

  • Nadai, C., Bovo, B., Giacomini, A., & Corich, V. (2018). New rapid PCR protocol based on high-resolution melting analysis to identify Saccharomyces cerevisiae and other species within its genus. Journal of Applied Microbiology, 124, 1232–1242.

    Article  CAS  PubMed  Google Scholar 

  • Nardi, T., Carlot, M., De Bortoli, E., Corich, V., & Giacomini, A. (2006). A rapid method for differentiating Saccharomyces sensu stricto strains from other yeast species in an enological environment. FEMS Microbiology Letters, 264, 168–173.

    Article  CAS  PubMed  Google Scholar 

  • Naumov, G., Naumova, E., Gaillardin, C., Turakainen, H., & Korhola, M. (1994). Identification of new chromosomes of Saccharomyces bayanus using gene probes from S. cerevisiae. Hereditas, 120, 121–126.

    Article  CAS  PubMed  Google Scholar 

  • Naumov, G. I., Naumova, E. S., & Sniegowski, P. D. (1998). Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks. Canadian Journal of Microbiology, 44, 1045–1050.

    Article  CAS  PubMed  Google Scholar 

  • Ness, F., Lavallée, F., Dubourdieu, D., Aigle, M., & Dulau, L. (1993). Identification of yeast strains using the polymerase chain reaction. Journal of the Science of Food and Agriculture, 62, 89–94.

    Article  CAS  Google Scholar 

  • Nguyen, H. V., & Gaillardin, C. (2005). Evolutionary relationships between the former species Saccharomyces uvarum and the hybrids Saccharomyces bayanus and Saccharomyces pastorianus; reinstatement of Saccharomyces uvarum (Beijerinck) as a distinct species. FEMS Yeast Research, 5, 471–483.

    Article  CAS  PubMed  Google Scholar 

  • Nguyen, H. V., Lepingle, A., & Gaillardin, C. (2000). Molecular typing demonstrates homogeneity of Saccharomyces uvarum strains and reveals the existence of hybrids between S. uvarum and S. cerevisiae, including the S. bayanus Type strain CBS 380. Systematic and Applied Microbiology, 23, 71–85.

    Article  CAS  PubMed  Google Scholar 

  • Nisiotou, A. A., Spiropoulos, A. E., & Nychas, G.-J. E. (2007). Yeast community structures and dynamics in healthy and Botrytis-affected grape must fermentations. Applied and Environmental Microbiology, 73, 6705–6713.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nocker, A., & Camper, A. K. (2006). Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide. Applied and Environmental Microbiology, 72, 1997–2004.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28, 1–7.

    Article  Google Scholar 

  • Oelofse, A., Malherbe, S., Pretorius, I. S., & Du Toit, M. (2010). Preliminary evaluation of infrared spectroscopy for the differentiation of Brettanomyces bruxellensis strains isolated from red wines. International Journal of Food Microbiology, 143, 136–142.

    Article  CAS  PubMed  Google Scholar 

  • Oh, K. B., & Matsuoka, H. (2002). Rapid viability assessment of yeast cells using vital staining with2-NBDG, a fluorescent derivative of glucose. International Journal of Food Microbiology, 76, 47–53.

    Article  CAS  PubMed  Google Scholar 

  • Pallmann, C., Brown, J. A., Olineka, T. L., Cocolin, L., Mills, D., & Bisson, L. (2001). Use of WL medium to profile native flora fermentations. American Journal of Enology and Viticulture, 52, 198–203.

    CAS  Google Scholar 

  • Pataro, C., Guerra, J. B., Petrillo-Peixoto, M. L., Mendonca-Hagler, L. C., Linardi, V. R., & Rosa, C. A. (2000). Yeast communities and genetic polymorphism of Saccharomyces cerevisiae strains associated with artisanal fermentation in Brazil. Journal of Applied Microbiology, 89, 24–31.

    Article  CAS  PubMed  Google Scholar 

  • Paugham, A., Benchewtrit, M., Fiarce, A., Tourte-Schafer, C., & Dupouy-Camet, J. (1999). Comparison of four commercialized biochemical systems for clinical yeast identification by colour-producing reactions. Medical Mycology, 37, 11–17.

    Article  Google Scholar 

  • Pearson, B. M., & McKee, R. A. (1992). Rapid identification of Saccharomyces cerevisiae, Zygosaccharomyces bailii and Zygosaccharomyces rouxii. International Journal of Food Microbiology, 16, 63–67.

    Article  CAS  PubMed  Google Scholar 

  • Pérez, M. A., Gallego, F. J., & Hidalgo, P. (2001a). Evaluation of molecular techniques for the genetic characterization of Saccharomyces cerevisiae strains. FEMS Microbiology Letters, 205, 375–378.

    Article  PubMed  Google Scholar 

  • Pérez, M. A., Gallego, F. J., Martinez, I., & Hidalgo, P. (2001b). Detection, distribution and selection of microsatellites (SSRs) in the genome of the yeast Saccharomyces cerevisiae as molecular markers. Letters in Applied Microbiology, 33, 461–466.

    Article  PubMed  Google Scholar 

  • Pfannebecker, J., Schiffer-Hetz, C., Frohlich, J., & Becker, B. (2016). Culture medium optimization for osmotolerant yeasts by use of a parallel fermenter system and rapid microbiological testing. Journal of Microbiological Methods, 130, 14–22.

    Article  CAS  PubMed  Google Scholar 

  • Phister, T., & Mills, D. A. (2003). Real-time PCR assay for the detection and enumeration of Dekkera bruxellensis in wine. Applied and Environmental Microbiology, 69, 7430–7434.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Phister, G. T., Rawsthorne, H., Joseph, C. M. L., & Mills, D. A. (2007). Real-time PCR assay for detection and enumeration of Hanseniaspora species from wine and juice. American Journal of Enology and Viticulture, 58, 229–233.

    CAS  Google Scholar 

  • Piskur, J., & Langkjaer, R. B. (2004). Yeast genome sequencing: The power of comparative genomics. Molecular Microbiology, 53, 381–389.

    Article  CAS  PubMed  Google Scholar 

  • Povhe Jemec, K., Cadez, N., Zagorc, T., Bubic, V., Zupec, A., & Raspor, P. (2001). Yeast population dynamics in five spontaneous fermentations of Malvasia must. Food Microbiology, 18, 247–259.

    Article  CAS  Google Scholar 

  • Querol, A., & Ramón, D. (1996). The application of molecular techniques in wine microbiology. Trends in Food Science and Technology, 7, 73–78.

    Article  CAS  Google Scholar 

  • Querol, A., Barrio, E., & Ramon, D. (1992). A comparative study of different methods of yeast strain characterization. Systematic and Applied Microbiology, 15, 439–446.

    Article  Google Scholar 

  • Querol, A., Barrio, E., & Ramon, D. (1994). Population dynamics of natural Saccharomyces strains during wine fermenmtation. International Journal of Food Microbiology, 21, 315–323.

    Article  CAS  PubMed  Google Scholar 

  • Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017). Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35(9), 833–844.

    Article  CAS  PubMed  Google Scholar 

  • Ramìrez-Castrillòn, M., Mendes, S. D. C., Inostroza-Ponta, M., & Valente, P. (2014). (GTG)5 MSP-PCR fingerprinting as a technique for discrimination of wine associated yeasts? PLoS ONE, 9, e105870.

    Article  PubMed  PubMed Central  Google Scholar 

  • Rasmussen, R., Morrison, T., Herrmann, M., & Witter, C. (1998). Quantitative PCR by continuous fluorescence monitoring of double strand DNA specific binding dye. Biochemica, 2, 8–11.

    Google Scholar 

  • Raspor, P., Milek, D. M., Polanc, J., Smole Mozina, S., & Cadez, N. (2006). Yeasts isolated from three varieties of grapes cultivated in different locations of the Dolenjska vine-growing region, Slovenia. International Journal of Food Microbiology, 109, 97–102.

    Article  CAS  PubMed  Google Scholar 

  • Rawsthorne, H., & Phister, T. G. (2006). A real-time PCR assay for the enumeration and detection of Zygosaccharomyces bailii from wine and fruit juices. International Journal of Food Microbiology, 112, 1–7.

    Article  CAS  PubMed  Google Scholar 

  • Redzepovic, S., Orlic, S., Sikora, S., Majdak, A., & Pretorius, I. S. (2002). Identification and characterization of Saccharomyces cerevisiae and Saccharomyces paradoxus strains isolated from Croatioan vineyards. Letters in Applied Microbiology, 35, 305–310.

    Article  CAS  PubMed  Google Scholar 

  • Renouf, V., Falcou, M., Miot-Serier, C., Perello, M. C., De Revel, G., & Lonvaud-Funel, A. (2006a). Interactions between Brettanomyces bruxellensis and other yeast species during the initial stages of winemaking. Journal of Applied Microbiology, 100, 1208–1219.

    Article  CAS  PubMed  Google Scholar 

  • Renouf, V., Perello, M. C., Strehaiano, P., & Lonvaud-Funel, A. (2006b). Global survey of the microbial ecosystem during alcoholic fermentation in winemaking. Journal International des Sciences de la Vigne et du Vin, 40, 101–116.

    CAS  Google Scholar 

  • Ribeca, P., & Valiente, G. (2011). Computational challenges of sequence classification in microbiomic data. Briefings in Bioinformatics, 12(6), 614–625.

    Article  CAS  PubMed  Google Scholar 

  • Robert, V. (2000). BioloMICS a general system for identification, classification and archiving of strains and species data. www.bio-aware.com.

  • Robert, V. (2003). Data processing. In T. Boekhout & V. Robert (Eds.), Yeast in food. Beneficial and detrimental aspects (pp. 139–169). Hamburg: Behr’s Verlag.

    Chapter  Google Scholar 

  • Robert, V., Szoke, S., Jabas, B., Vu, D., Chouchen, O., Blom, E., & Cardinali, G. (2011). BioloMICS software: Biological data management, identification, classification and statistics. Open Applied Informatics Journal, 5, 87–98.

    Article  Google Scholar 

  • Röder, C., König, H., & Fröhlich, J. (2007). Species-specific identification of Dekkera / Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA. FEMS Yeast Research, 7, 1013–1026.

    Article  PubMed  CAS  Google Scholar 

  • Rodriguez, S. B., & Thornton, R. J. (2008). Use of flow cytometry with fluorescent antibodies in real-time monitoring of simultaneously inoculated alcoholic-malolactic fermentation of Chardonnay. Letters in Applied Microbiology, 46, 38–42.

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez-Porrata, B., Novo, M., Guillamón, J., Rozés, N., Mas, A., & Cordero Otero, R. (2009). Vitality enhancement of the rehydrated active dry wine yeast. International Journal of Food Microbiology, 126, 116–122.

    Article  CAS  Google Scholar 

  • Sabate, J., Cano, J., Querol, A., & Guillamón, J. M. (1998). Diversity of Saccharomyces strains in wine fermentations: Analysis for two consecutive years. Letters in Applied Microbiology, 26, 452–455.

    Article  CAS  PubMed  Google Scholar 

  • Salma, M., Rousseaux, S., Sequeira-Le Grand, A., Divol, B., & Alexandre, H. (2013). Characterization of the viable but nonculturable (VBNC) state in Saccharomyces cerevisiae. PLOS ONE, 8, e77600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Santamaria, M., Fosso, B., Consiglio, A., De Caro, G., Licciulli, F., Liuni, S., Marzano, M., Alonso-Alemany, D., Valiente, G., & Pesole, G. (2012). Reference databases for taxonomic assignment in metagenomics. Briefings in Bioinformatics, 13, 682–695.

    Article  CAS  PubMed  Google Scholar 

  • Schuller, D., Valero, E., Dequin, S., & Casal, M. (2004). Survey of molecular methods for the typing of wine yeast strains. FEMS Microbiology Letters, 231, 19–26.

    Article  CAS  PubMed  Google Scholar 

  • Senses-Ergul, S., Ágoston, R., Belák, Á., & Deak, T. (2006). Characterization of some yeasts isolated from foods by traditional and molecular tests. International Journal of Food Microbiology, 108, 120–124.

    Article  CAS  PubMed  Google Scholar 

  • Serpaggi, V., Remize, F., Suqueira-Le Grand, A., & Alexandre, H. (2010). Specific identification and quantification of the spoilage microorganism Brettanomyces in wine by flow cytometry: A useful tool for winemakers. Citometry Part A, 77A, 490–499.

    Google Scholar 

  • Serpaggi, V., Remize, F., Recorbet, G., Gaudot-Dumas, E., Suqueira-Le Grand, A., & Alexandre, H. (2012). Characterization of the “viable but nonculturable” (VBNC) state in the wine spoilage yeast Brettanomyces. Food Microbiology, 30, 438–447.

    Article  CAS  PubMed  Google Scholar 

  • Setati, M. E., Jacobson, D., & Bauer, F. F. (2015). Sequence-based analysis of the Vitis vinifera L. cv Cabernet Sauvignon grape must mycobiome in three South African vineyards employing distinct agronomic systems. Frontiers in Microbiology, 6, 1358.

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharpton, T. J. (2014). An introduction to the analysis of shotgun metagenomics data. Frontiers in Plant Science, 5, 209.

    Article  PubMed  PubMed Central  Google Scholar 

  • Smart, K. A., Chambers, K. M., Lambert, I., Jenkins, C., & Smart, C. A. (1999). The use of methylene violet staining procedures to determine yeast viability and vitality. Journal of the American Society of Brewing Chemists, 57, 18–23.

    Article  CAS  Google Scholar 

  • Smith, C. J., & Osborn, A. M. (2009). Advantages and limitations of quantitative PCR (QPCR)-based approaches in microbial ecology. FEMS Microbiology Ecology, 67(1), 6–20.

    Article  CAS  PubMed  Google Scholar 

  • Smole Možina, S., Dlauchy, D., Deak, T., & Raspor, P. (1997). Identification of Saccharomyces sensu stricto and Torulaspora yeasts by PCR ribotyping. Letters in Applied Microbiology, 24, 311–315.

    Article  PubMed  Google Scholar 

  • Soll, D. R. (2000). The ins and outs of DNA fingerprinting the infectious fungi. Clinical Microbiology Reviews, 13, 332–370.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Spangenberg, D. S., & Ingham, S. C. (2000). Comparison of methods for enumeration of yeasts and molds in shredded low-moisture part-skim mozzarella cheese. Journal of Food Protection, 63, 529–533.

    Article  CAS  PubMed  Google Scholar 

  • Stadlwieser, P., Domig, K. J., Kögler, B., Kneifel, W., Silhavy, K., & Mandl, K. (2006). Biochemische und molekularbiologische Characterisierung von Reinzuchthefen für die Weinbereitung. Mitt Klosterneuburg, 56, 213–223.

    CAS  Google Scholar 

  • Stender, H., Kurtzman, C., Hyldig-Nielsen, J. J., Sørensen, D., Broomer, A., Oliveira, K., Perry-O’Keefe, H., Sage, A., Young, B., & Coull, J. (2001). Identification of Dekkera bruxellensis (Brettanomyces) from wine by fluorescence in situ hybridization using peptide nucleic acid probes. Applied and Environmental Microbiology, 67, 938–941.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stender, H., Fiandaca, M., Hyldig-Nielsen, J. J., & Coull, J. (2002). PNA for rapid microbiology. Journal of Microbiological Methods, 48, 1–17.

    Article  CAS  PubMed  Google Scholar 

  • Sternes, P. R., Lee, D., Kutyna, D. R., & Borneman, A. R. (2017). A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation. GigaScience, 6, 1–10.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sun, Y., & Liu, Y. (2014). Investigating of yeast species in wine fermentation using terminal restriction fragment length polymorphism method. Food Microbiology, 38, 201–207.

    Article  CAS  PubMed  Google Scholar 

  • Taniwaki, M. H., da Silva, N., Banhe, A. A., & Iamanaka, B. T. (2001). Comparison of culture media, Simplate and Petrifilm for enumeration of yeasts and molds in food. Journal of Food Protection, 64, 1592–1596.

    Article  CAS  PubMed  Google Scholar 

  • Tessonnière, H., Vidal, S., Barnavon, L., Alexandre, H., & Remize, F. (2009). Design and performance testing of a real-time PCR assay for sensitive and reliable direct quantification of Brettanomyces in wine. International Journal of Food Microbiology, 129, 237–243.

    Article  PubMed  CAS  Google Scholar 

  • Tofalo, R., Schirone, M., Corsetti, A., & Suzzi, G. (2012). Detection of Brettanomyces spp. in red wines using real-time PCR. Journal of Food Science, 77, 545–549.

    Article  CAS  Google Scholar 

  • Urso, R., Rantsiou, K., Dolci, P., Rolle, L., Comi, G., & Cocolin, L. (2008). Yeast biodiversity and dynamics during sweet wine production as determined by molecular methods. FEMS Yeast Research, 8, 1053–1062.

    Article  CAS  PubMed  Google Scholar 

  • Valente, P., Ramos, J. P., & Leoncini, O. (1999). Sequencing as a tool in yeast molecular taxonomy. Canadian Journal of Microbiology, 45, 946–958.

    Article  Google Scholar 

  • Valero, E., Schuller, D., Cambon, B., Casal, M., & Dequin, S. (2005). Dissemination and survival of commercial wine yeast in the vineyard: A large-scale, three-years study. FEMS Yeast Research, 5, 959–969.

    Article  CAS  PubMed  Google Scholar 

  • Valero, E., Cambon, B., Schuller, D., Casal, M., & Dequin, S. (2007). Biodiversity of Saccharomyces yeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Research, 7, 317–329.

    Article  CAS  PubMed  Google Scholar 

  • Van der Vossen, J. M. B. M., Rahaoui, H., de Nijs, M. W. C. M., & Hartog, B. J. (2003). PCR methods for tracing and detection of yeasts in the food chain. In T. Boekhout & V. Robert (Eds.), Yeasts in food, beneficial and detrimental aspects (pp. 123–138). Hamburg: Behr’s Verlag.

    Chapter  Google Scholar 

  • Vaudano, E., & Garcia-Moruno, E. (2008). Discrimination of Saccharomyces cerevisiae wine strains using microsatellite multiplex PCR and band pattern analysis. Food Microbiology, 25, 56–64.

    Article  CAS  PubMed  Google Scholar 

  • Vaughan-Martini, A., Cardinali, G., & Martini, A. (1996). Differential killer sensitivity as a tool for fingerprintong wine-yeast strains of Saccharomyces cerevisiae. Journal of Industrial Microbiology, 17, 124–127.

    Article  CAS  PubMed  Google Scholar 

  • Vaughan-Martini, A., Angelini, P., & Cardinali, G. (2000). Use of conventional taxonomy, electrophoretic karyotyping and DNA-DNA hybridization for the classification fermentative apiculate yeasts. International Journal of Systematic and Evolutionary Microbiology, 50, 1665–1672.

    Article  CAS  PubMed  Google Scholar 

  • Velázquez, E., cruz-Sánchez, J. M., Rivas-Palá, T., Zurdo-Pineiro, J. L., Mateos, P. F., Monte, E., Martinez-Molina, E., & Chordi, A. (2001). YeastIdent-Food/ProleFood, a new system for the identification of food yeasts based on physiological and biochemical tests. Food Microbiology, 18, 637–646.

    Article  CAS  Google Scholar 

  • Versavaud, A., & Hallet, J. N. (1995). Pulsed-field gel electrophoresis combined with rare-cutting endonucleases for strain identification of Candida famata, Kloeckera apiculata and Schizosaccharomyces pombe with chromosome number and size estimation of the two former. Systematic and Applied Microbiology, 18, 303–309.

    Article  CAS  Google Scholar 

  • Wang, C., Esteve Zarzoso, B., & Mas, A. (2014). Monitoring of Saccharomyces cerevisiae, Hanseniaspora uvarum, and Starmerella bacillaris (synonym Candida zemplinina) populations during alcoholic fermentation by fluorescence in situ hybridization. International Journal of Food Microbiology, 191, 1–9.

    Article  CAS  PubMed  Google Scholar 

  • Wang, C., Esteve Zarzoso, B., Cocolin, L., Mas, A., & Rantsiou, K. (2015). Viable and culturable populations of Saccharomyces cerevisiae, Hanseniaspora uvarum and Starmerella bacillaris (synonym Candida zemplinina) during Barbera must fermentation. Food Research International, 78, 195–200.

    Article  CAS  PubMed  Google Scholar 

  • Wang, C., Mas, A., & Esteve-Zarzoso, B. (2016). The interaction between Saccharomyces cerevisiae and non-Saccharomyces yeast during alcoholic fermentation is species and strain specific. Frontiers in Microbiology, 7, 502. https://doi.org/10.3389/fmicb.2016.00502.

    Article  PubMed  PubMed Central  Google Scholar 

  • Welsh, J., & McClelland, M. (1990). Fingerprint genomes using PCR with arbitrary primers. Nucleic Acids Research, 18, 7213–7218.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. I. Sninsky, & T. J. White (Eds.), PCR protocols: A guide to methods and applications (pp. 315–322). San Diego: Academic.

    Google Scholar 

  • Willenburg, E., & Divol, B. (2012). Quantitative PCR: An appropriate tool to detect viable but not culturable Brettanomyces bruxellensis in wine. International Journal of Food Microbiology, 160, 131–136.

    Article  CAS  PubMed  Google Scholar 

  • Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 1631–1635.

    Article  Google Scholar 

  • Zara, G., Ciani, M., Domizio, P., Zara, S., Budroni, M., Carboni, A., & Mannazzu, I. (2013). A culture-independent PCR-based method for the detection of Lachancea thermotolerans in wine. Annales de Microbiologie, 64, 403–406.

    Article  CAS  Google Scholar 

  • Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., et al. (2015). The soil microbiome influences grapevine-associated microbiota. MBio, 6, e02527–e02514.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Agriculture, University of Sassari, Sassari, Italy

    Severino Zara & Ilaria Mannazzu

Authors
  1. Severino Zara
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ilaria Mannazzu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ilaria Mannazzu .

Editor information

Editors and Affiliations

  1. University of Basilicata, School of Agriculture, Forest, Food and Environmental Sciences, Potenza, Italy

    Patrizia Romano

  2. Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy

    Maurizio Ciani

  3. Food Science and Technology, University of New South Wales School of Chemical Engineering, Sydney, NSW, Australia

    Graham H. Fleet

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Science+Business Media, LLC, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Zara, S., Mannazzu, I. (2019). Detection, Quantification, and Identification of Yeast in Winemaking. In: Romano, P., Ciani, M., Fleet, G. (eds) Yeasts in the Production of Wine. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-9782-4_3

Download citation

Publish with us

Policies and ethics

Search

Navigation