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Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains

  • Applied microbial and cell physiology
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Abstract

Recent studies have suggested a correlation between genotype groups of Brettanomyces bruxellensis and their source of isolation. To further explore this relationship, the objective of this study was to assess metabolic differences in carbon and nitrogen assimilation between different B. bruxellensis strains from three beverages, including beer, wine, and soft drink, using Biolog Phenotype Microarrays. While some similarities of physiology were noted, many traits were variable among strains. Interestingly, some phenotypes were found that could be linked to strain origin, especially for the assimilation of particular α- and β-glycosides as well as α- and β-substituted monosaccharides. Based upon gene presence or absence, an α-glucosidase and β-glucosidase were found explaining the observed phenotypes. Further, using a PCR screen on a large number of isolates, we have been able to specifically link a genomic deletion to the beer strains, suggesting that this region may have a fitness cost for B. bruxellensis in certain fermentation systems such as brewing. More specifically, none of the beer strains were found to contain a β-glucosidase, which may have direct impacts on the ability for these strains to compete with other microbes or on flavor production.

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References

  • Albertin W, Panfili A, Miot-Sertier C, Goulielmakis A, Delcamp A, Salin F, Lonvaud-Funel A, Curtin C, Masneuf-Pomarède I (2014) Development of microsatellite markers for the rapid and reliable genotyping of Brettanomyces bruxellensis at strain level. Food Microbiol 42:188–195

    Article  CAS  PubMed  Google Scholar 

  • Bell SJ, Henschke PA (2005) Implications of nitrogen nutrition for grapes, fermentation and wine. Aust J Grape Wine Res 11:242–295

    Article  CAS  Google Scholar 

  • Bochner BR (2003) New technologies to assess genotype-phenotype relationships. Nat Rev 4:309–314

    Article  CAS  Google Scholar 

  • Borneman AR, Zeppel R, Chambers PJ, Curtin CD (2014) Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variation in ploidy and nutrient utilization potential amongst wine isolates. PLoS Genet 10, e1004161

    Article  PubMed Central  PubMed  Google Scholar 

  • Chatonnet P, Dubourdie D, Boidron J, Pons M (1992) The origin of ethylphenols in wines. J Sci Food Agric 60:165–178

  • Conterno L, Lucy Joseph CM, Arvik TJ, Henick-Kling T, Bisson LF (2006) Genetic and physiological characterization of Brettanomyces bruxellensis strains isolated from wines. Am J Enol Vitic 75:139–147

    Google Scholar 

  • Cosentino S, Fadda ME, Deplano M, Mulargia AF, Palmas F (2001) Yeasts associated with Sardinian ewe’s dairy products. Int J Food Microbiol 69:53–58

    Article  CAS  PubMed  Google Scholar 

  • Coton E, Coton M, Levert D, Casaregola S, Sohier D (2006) Yeast ecology in French cider and black olive natural fermentations. Int J Food Microbiol 108:130–135

    Article  CAS  PubMed  Google Scholar 

  • Crauwels S, Zhu B, Steensels J, Busschaert P, De Samblanx G, Marchal K, Willems KA, Verstrepen K, Lievens B (2014) Assesing genetic diversity among Brettanomyces yeast by DNA fingerprinting and whole genome sequencing. Appl Environ Microbiol 80:4398–4413

    Article  PubMed Central  PubMed  Google Scholar 

  • Curtin CD, Bellon JR, Henscke PA, Godden PW, de Barros Lopes MA (2007) Genetic diversity of Dekkera bruxellensis yeast isolated from Australian wineries. FEMS Yeast Res 7:471–481

    Article  CAS  PubMed  Google Scholar 

  • Curtin CD, Borneman AR, Chambers PJ, Pretorius IS (2012) De-novo assembly and analysis of the heterozygous triploid genome of the wine spoilage yeast Dekkera bruxellensis AWRI1499. PLoS ONE 7:1–10

    Article  Google Scholar 

  • Daenen L, Vanderhaegen B, Verachter H, Derdelinckx G (2004) Flavour enhancement in beer by yeast beta-glucosidase activity. Commun Agric Appl Biol Sci 69:73–76

    CAS  PubMed  Google Scholar 

  • de Barros Lopes M, Rainieri S, Henschke PA, Langridge P (1999) AFLP fingerprinting for analysis of yeast genetic variation. Int J Syst Bacteriol 49:915–924

    Article  PubMed  Google Scholar 

  • de Souza Liberal A, Basilio A, do Monte Resende A, Brasileiro B, da Silva-Filho E, de Morais J, Simoes D, de Morais M (2007) Identification of Dekkera bruxellensis as a major contaminant yeast in continuous fuel ethanol fermentation. J Appl Microbiol 102:538–547

  • Douglas H, Hawthorne D (1964) Enzymatic expression and genetic linkage of genes controlling galactose utilization in saccharomyces. Genetics 49:837–844.

  • Fugelsang KC (1997) Wine microbiology. Chapman and Hall, New York

    Book  Google Scholar 

  • Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A (2010) Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464:54–58

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199–D205

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kliewer WM (1967) Annual cyclic changes in the concentration of free amino acids in grapevines. Am J Enol Vitic 18:126–137

    CAS  Google Scholar 

  • Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Laureys D, De Vuyst L (2014) Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation. Appl Environ Microbiol 80:2564–2572

    Article  PubMed Central  PubMed  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The Sequence Alignment/Map (SAM) format and SAMtools. J Bioinforma 25:2078–2079

    Article  Google Scholar 

  • Licker JL, Acree TE, Henick-Kling T (1998) What is “Brett” (Brettanomyces) flavour? A preliminary investigation. In: Waterhouse AL, Ebeler SE (eds) Chemistry of wine flavour. Symposium series. American Chemical Society, Washington, DC, pp 96–115

    Chapter  Google Scholar 

  • Lievens B, Brouwer M, Vanachter ACRC, Lévesque CA, Cammue BPA, Thomma BPHJ (2003) Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiol Lett 223:113–122

    Article  CAS  PubMed  Google Scholar 

  • Loureiro V, Malfeito-Ferreira M (2003) Spoilage yeasts in the wine industry. Int J Food Microbiol 86:23–50

    Article  CAS  PubMed  Google Scholar 

  • Magasanik B, Kaiser CA (2002) Nitrogen regulation in Saccharomyces cerevisiae. Gene 290:1–18

    Article  CAS  PubMed  Google Scholar 

  • Martens H, Iserentant D, Verachtert H (1997) Microbial aspects of a mixed yeast-bacterial fermentation in the production of a special Belgian acidic ale. J Inst Brew 103:85–91

    Article  Google Scholar 

  • Martorell P, Barata A, Malfeito-Ferreira M, Fernandez-Espinar MT, Loureiro V, Querol A (2006) Molecular typing of the yeast species Dekkera bruxellensis and Pichia guilliermondii recovered from wine related sources. Int J Food Microbiol 106:79–84

    Article  CAS  PubMed  Google Scholar 

  • Miot-Sertier C, Lonvaud-Funel A (2007) Development of a molecular method for the typing of Brettanomyces bruxellensis (Dekkera bruxellensis) at the strain level. J Appl Microbiol 102:555–562

    Article  CAS  PubMed  Google Scholar 

  • Mitrakul CM, Henick-Kling T, Egli CM (1999) Discrimination of Brettanomyces/Dekkera yeast isolates from wine by using various DNA fingerprinting methods. Food Microbiol 16:3–4

    Article  CAS  Google Scholar 

  • Morrissey WF, Davenport B, Querol A, Dobson ADW (2004) The role of indigenous yeasts in traditional Irish cider fermentations. J Appl Microbiol 97:647–655

    Article  CAS  PubMed  Google Scholar 

  • Oelofse A, Lonvaud-Funel A, du Toit M (2009) Molecular identification of Brettanomyces bruxellensis strains isolated from red wines and volatile phenol production. Food Microbiol 26:377–385

    Article  CAS  PubMed  Google Scholar 

  • Passoth V, Blomqvist J, Schnürer J (2007) Dekkera bruxellensis and Lactobacillus vini form a stable ethanol producing consortium in a commercial alcohol production process. Appl Environ Microbiol 73:4354–4356

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Piskur J, Ling Z, Marcet-Houben M, Ishchuk O, Aerts A, LaButti K, Copeland A, Lindquist E, Barry K, Compagno C, Bisson L, Grigoriev I, Gabaldon T, Phister T (2012) The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. Int J Food Microbiol 157:202–209

  • Pogorzelski E, Wilkowska A (2007) Flavour enhancement through the enzymatic hydrolysis of glycosidic aroma precursors in juice and wine beverages: a review. Flavour Fragr J 22:251–254

    Article  CAS  Google Scholar 

  • Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • R Development Core Team (2006) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna

    Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:265–386

    Google Scholar 

  • Schifferdecker A, Dashko S, Ishchuk O, Piskur J (2014) The wine and beer yeast Dekkera bruxellensis. Yeast 31:323–332

  • Steensels J, Daenen L, Malcorps P, Derderlinckx G, Verachtert H, Verstrepen K (2015) Brettanomyces yeast- from spoilage organism to valuable contributors to industrial fermentation. Int J Food Microbiol 206:24–38

  • Teoh AL, Heard G, Cox J (2004) Yeast ecology of Kombucha fermentation. Int J Food Microbiol 95:119–126

    Article  CAS  PubMed  Google Scholar 

  • Ting SV, Rouseff RL (1979) Proline content in Florida frozen concentrated orange juice and canned grapefruit juice. Proc Fla State Hortic Soc 92:143–145

    CAS  Google Scholar 

  • Vaas LAI, Sikorsky J, Hofner B, Fiebig A, Buddruhs N, Klenk HPG, Göker M (2013) Opm: an R package for analysing OmniLog® Phenotype MicroArray Data. Bioinformatics 29:1823–1824

    Article  CAS  PubMed  Google Scholar 

  • Vanbeneden N, Gils F, Delvaux G, Delvaux FR (2008) Formation of 4-vinyl and 4-ethyl derivatives from hydroxycinnamic acids: occurrence of volatile phenolic flavour compounds in beer and distribution of Pad 1-activity among brewing yeasts. Food Chem 107:221–230

    Article  CAS  Google Scholar 

  • Vigentini I, De Lorenzis G, Picozzi C, Imazio S, Merico A, Galafassi S, Piskur J, Foschino R (2012) Intraspecific variations of Dekkera/Brettanomyces bruxellensis genome studied by capillary electrophoresis separation of the intron splice site profiles. Int J Food Microbiol 157:6–15

    Article  CAS  PubMed  Google Scholar 

  • Yamada Y, Matsuda M, Maeda K, Mikata K (1994) The phylogenetic relationships of species of the genus Dekkera Van Der Walt based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae). Biosci Biotechnol Biochem 58:1803–1808

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

We are grateful to everybody who provided us with Brettanomyces strains. Further, we are grateful to Sofie Malfliet for her help with compiling the tables.

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Disclosure of potential conflicts of interest/Research involving Human Participants and/or Animals/ Informed consent: not applicable for this study.

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Correspondence to B. Lievens.

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Crauwels, S., Van Assche, A., de Jonge, R. et al. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. Appl Microbiol Biotechnol 99, 9123–9134 (2015). https://doi.org/10.1007/s00253-015-6769-9

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  • DOI: https://doi.org/10.1007/s00253-015-6769-9

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