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Applied Microbiology and Biotechnology

, Volume 97, Issue 10, pp 4597–4606 | Cite as

Differentiation of species of the genus Saccharomyces using biomolecular fingerprinting methods

  • V. Blättel
  • A. PetriEmail author
  • A. Rabenstein
  • J. Kuever
  • H. König
Methods and protocols

Abstract

The genus Saccharomyces comprises very closely related species. This high degree of relationship makes a simple identification and differentiation of strains difficult since these species are hardly discriminable by their morphological and physiological features. A sequence analysis of ribosomal DNA and the corresponding internal transcribed spacers can only rarely be successfully applied. In this study, we proved the applicability of a novel DNA fingerprinting method, the SAPD-PCR (specifically amplified polymorphic DNA) and of MALDI-TOF-MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) fingerprinting with the MALDI Biotyper for the differentiation of species belonging to the genus Saccharomyces. It was possible with SAPD-PCR to create specific banding patterns for all Saccharomyces species. Different strains of the same species produced nearly the same banding patterns. Specific and reproducible reference spectra could be generated for each of the strains with the MALDI Biotyper. Therefore, SAPD-PCR and MALDI-TOF-MS can be fast and reliable tools to identify these related Saccharomyces species which are applied in many biotechnological processes.

Keywords

Saccharomyces Identification Hybrids SAPD-PCR MALDI-TOF-MS MALDI Biotyper 

Notes

Acknowledgment

We thank the German Science Foundation for financial support (Ko 785/17-1).

References

  1. Antunovics Z, Irinyi L, Sipiczki M (2005) Combined application of methods to taxonomic identification of Saccharomyces strains in fermenting botrytized grape must. J Appl Microbiol 98:971–979CrossRefGoogle Scholar
  2. Blättel V (2012) Identifizierung, Quantifizierung und Hemmung von ausgewählten Hefen im Wein. Dissertation, Johannes Gutenberg-University MainzGoogle Scholar
  3. Brito dos Santos SK, Moreira Brasilio AC, Valente Brasileiro BTR, Simoes DA, Alves da Silva-Filho E, de Morais M (2007) Identification of yeasts within Saccharomyces sensu stricto complex by PCR-fingerprinting. World J Microbiol Biotechnol 23:1613–1620CrossRefGoogle Scholar
  4. De Barros Lopes M, Soden A, Martens AL, Henschke PA, Langridge P (1998) Differentiation and species identification of yeasts using PCR. Int J Syst Bacteriol 48:279–286CrossRefGoogle Scholar
  5. Demuyter C, Lollier M, Legras JL, Le Jeune C (2004) Predominance of Saccharomyces uvarum during spontaneous alcoholic fermentation, for three consecutive years, in an Alsatian winery. J Appl Microbiol 97:1140–1148CrossRefGoogle Scholar
  6. Dhiman N, Hall L, Wohlfiel SL, Buckwalter SP, Wengenack NL (2011) Performance and cost analysis of matrix-assisted laser desorption ionization-time of flight mass spectrometry for routine identification of yeast. J Clin Microbiol 49:1614–1616CrossRefGoogle Scholar
  7. Fernández-Espinar M, Barrio E, Querol A (2003) Analysis of the genetic variability in the species of the Saccharomyces sensu stricto complex. Yeast 20:1213–1226CrossRefGoogle Scholar
  8. Fröhlich J, Pfannebecker J (2007) Species-independent DNA fingerprint analysis with primers derived from the NotI identification sequence. Patent number: EP2027285 (A1)Google Scholar
  9. González SS, Barrio E, Gafner J, Querol A (2006) Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations. FEMS Yeast Res 6:1221–1234CrossRefGoogle Scholar
  10. González SS, Barrio E, Querol A (2008) Molecular characterization of new natural hybrids of Saccharomyces cerevisiae and S. kudriavzevii in brewing. Appl Environ Microbiol 74:2314–2320CrossRefGoogle Scholar
  11. Greig D (2009) Reproductive isolation in Saccharomyces. Heredity 102:39–44CrossRefGoogle Scholar
  12. Groth C, Hansen J, Piskur J (1999) A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol 49:1933–1938CrossRefGoogle Scholar
  13. Hadrys H, Balick M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1:55–63CrossRefGoogle Scholar
  14. Jensen RH, Arendrup MC (2011) Candida palmioleophila: characterization of a previously overlooked pathogen and its unique susceptibility profile in comparison with five related species. J Clin Microbiol 49:549–556CrossRefGoogle Scholar
  15. Kawahata M, Fujii T, Iefuji H (2007) Intraspecies diversity of the industrial yeast strains Saccharomyces cerevisiae and Saccharomyces pastorianus based on analysis of the sequences of the internal transcribed spacer (ITS) regions and the D1/D2 region of 26S rDNA. Biosci Biotechnol Biochem 71:1616–1620CrossRefGoogle Scholar
  16. Le Jeune C, Lollier M, Demuyter C, Erny C, Legras JL, Aigle M, Masneuf-Pomarède I (2007) Characterization of natural hybrids of Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum. FEMS Yeast Res 7:540–549CrossRefGoogle Scholar
  17. Libkind D, Hittinger CT, Valério E, Gonçalves C, Dover J, Johnston M, Gonçalves P, Sampaio J (2011) Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci USA 108:14539–14544CrossRefGoogle Scholar
  18. Liti G, Barton DB, Louis EJ (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174:839–850CrossRefGoogle Scholar
  19. 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 Res 7:953–965CrossRefGoogle Scholar
  20. Lopes CA, Barrio E, Querol A (2010) Natural hybrids of S. cerevisiae × S. kudriavzevii share alleles with European wild populations of Saccharomyces kudriavzevii. FEMS Yeast Res 10:412–421CrossRefGoogle Scholar
  21. Marklein G, Josten M, Klanke U, Müller E, Horré R, Maier T, Wenzel T, Kostrzewa M, Bierbaum G, Hoerauf A, Sahl H-G (2009) Matrix-assisted laser desorption ionization-time of flight mass spectrometry for fast reliable identification of clinical yeast isolates. J Clin Microbiol 47:2912–2917CrossRefGoogle Scholar
  22. Masneuf I, Hansen J, Groth C, Piskur J, Dubourdieu D (1998) New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol 64:3887–3892Google Scholar
  23. Masneuf-Pomarède I, Bely M, Marullo P, Lonvaud-Funel A, Dubourdieu D (2010) Reassessment of phenotypic traits for Saccharomyces bayanus var. uvarum wine yeast strains. Int J Food Microbiol 139:79–86CrossRefGoogle Scholar
  24. Mellmann A, Cloud J, Maier T, Keckevoet U, Ramminger I, Iwen P, Dunn J, Hall G, Wilson D, Lasala P, Kostrzewa M, Harmsen D (2008) Evaluation of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in comparison to 16S rRNA gene sequencing for species identification of nonfermenting bacteria. J Clin Microbiol 46:1946–1954CrossRefGoogle Scholar
  25. Montrocher R, Verner MC, Briolay J, Gautier C, Marmeisse R (1998) Phylogenetic analysis of the Saccharomyces cerevisiae group based on polymorphisms of rDNA spacer sequences. Int J Syst Bacteriol 48:295–303CrossRefGoogle Scholar
  26. Naumov GI, James SA, Naumova ES, Louis DJ, Roberts IN (2000) Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol 50:1931–1942Google Scholar
  27. Naumov GI, Lee C-F, Naumova ES (2013) Molecular genetic diversity of the Saccharomyces yeasts in Taiwan: S. arboricola, S. cerevisiae and S. kudriavzevii. Antonie van Leeuwenhoek 103:217–228CrossRefGoogle Scholar
  28. Naumova ES, Naumov GI, Masneuf-Pomarède I, Aigle M, Dubourdieu D (2005) Molecular genetic study of introgression between Saccharomyces bayanus and S. cerevisiae. Yeast 22:1099–1115CrossRefGoogle Scholar
  29. Page RDM (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358Google Scholar
  30. Pfannebecker J, Fröhlich J (2008) Use of a species-specific multiplex PCR for the identification of pediococci. Int J Food Microbiol 128:288–296CrossRefGoogle Scholar
  31. Querol A, Bond U (2009) The complex and dynamic genomes of industrial yeasts. FEMS Microbiol Lett 293:1–10CrossRefGoogle Scholar
  32. Rainieri S, Zambonelli C, Kaneko Y (2003) Saccharomyces sensu stricto: systematics, genetic diversity and evolution. J Biosci Bioeng 96:1–9Google Scholar
  33. Redzepović S, Orlić S, Sikora S, Majdak A, Pretorius IS (2002) Identification and characterization of Saccharomyces cerevisiae and Saccharomyces paradoxus strains isolated from Croatian vineyards. Lett Appl Microbiol 35:305–310CrossRefGoogle Scholar
  34. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  35. Sampaio JP, Gonçalves P (2008) Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Appl Environ Microbiol 74:2144–2152CrossRefGoogle Scholar
  36. Sebastian P, Herr P, Fischer U, König H (2011) Molecular identification of lactic acid bacteria occurring in must and wine. S Afr J Enol Vitic 32:300–309Google Scholar
  37. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier PE, Rolain JM, Raoult D (2009) Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49:543–551CrossRefGoogle Scholar
  38. Sicard D, Legras JL (2011) Bread, beer and wine: yeast domestication in the Saccharomyces sensu stricto complex. C R Biol 334:229–236CrossRefGoogle Scholar
  39. Sipiczki M (2008) Interspecies hybridization and recombination in Saccharomyces wine yeasts. FEMS Yeast Res 8:996–1007CrossRefGoogle Scholar
  40. Stevenson LG, Drake SK, Shea YR, Zelazny M, Murray PR (2010) Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J Clin Microbiol 48:3482–3486CrossRefGoogle Scholar
  41. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882CrossRefGoogle Scholar
  42. Tornai-Lehoczki J, Péter G, Dlauchy D, Deák T (1996) Some remarks on “a taxonomic key for the genus Saccharomyces” (Vaughan Martini and Martini 1993). Antonie van Leeuwenhoek 69:229–233CrossRefGoogle Scholar
  43. Torriani S, Zapparoli G, Suzzi G (1999) Genetic and phenotypic diversity of Saccharomyces sensu stricto strains isolated from Amarone wine. Diversity of Saccharomyces strains from Amarone wine. Antonie van Leeuwenhoek 75:207–215CrossRefGoogle Scholar
  44. Torriani S, Zapparoli G, Malacrinò P, Suzzi G, Dellaglio F (2004) Rapid identification and differentiation of Saccharomyces cerevisiae, Saccharomyces bayanus and their hybrids by multiplex PCR. Lett Appl Microbiol 38:239–244CrossRefGoogle Scholar
  45. Vaughan-Martini A, Martini A (2011) Saccharomyces Meyen ex Reess (1870). In: Kurtzman CP, Fell JW, Boekhout T (eds) The yeasts, a taxonomic study, 5th edn. Elsevier, Amsterdam, pp 733–746CrossRefGoogle Scholar
  46. Wang SA, Bai FY (2008) Saccharomyces arboricolus sp. nov., a yeast species from tree bark. Int J Syst Evol Microbiol 58:510–514CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • V. Blättel
    • 1
  • A. Petri
    • 1
    Email author
  • A. Rabenstein
    • 2
  • J. Kuever
    • 2
  • H. König
    • 1
  1. 1.Institute of Microbiology and Wine ResearchJohannes Gutenberg University MainzMainzGermany
  2. 2.Department of MicrobiologyBremen Institute for Materials TestingBremenGermany

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