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Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity

  • 1.

    Romano, P., Ciani, M. & Fleet, G. Yeast Ecology of Wine Production in Yeast in the Production of Wine 2–31 (Springer, New York, 2020).

    Google Scholar 

  • 2.

    Zott, K., Miot-Sertier, C., Claisse, O., Lonvaud-Funel, A. & Masneuf-Pomarede, I. Dynamics and diversity of non-Saccharomyces yeasts during the early stages in winemaking. Int. J. Food Microbiol. 125(2), 197–203 (2008).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 3.

    Zott, K. et al. Characterization of the yeast ecosystem in grape must and wine using real-time PCR. Food Microbiol. 27(5), 559–567 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 4.

    Goddard, M. R. Quantifying the complexities of Saccharomyces cerevisiae’s ecosystem engineering via fermentation. Ecology 89(8), 2077–2082 (2008).

    PubMed  Article  PubMed Central  Google Scholar 

  • 5.

    Salvadó, Z., Arroyo-López, F. N., Barrio, E., Querol, A. & Guillamón, J. M. Quantifying the individual effects of ethanol and temperature on the fitness advantage of Saccharomyces cerevisiae. Food Microbiol. 28(6), 1155–1161 (2011).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  • 6.

    Mcgovern, P. E., Hartung, U., Badler, V. R., Glusker, D. L. & Exner, L. J. The Beginnings of Winemaking and Viticulture in the Ancient Near East and Egypt. Expedition 39(1), 3–21 (1997).

    Google Scholar 

  • 7.

    Cavalieri, D., McGovern, P. E., Hartl, D. L., Mortimer, R. & Polsinelli, M. Evidence for S. cerevisiae fermentation in ancient wine. J. Mol. Evol. 57(1), S226–S232 (2003).

    ADS  CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 8.

    Fay, J. C. & Benavides, J. A. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1(1), e5 (2005).

    PubMed Central  Article  CAS  Google Scholar 

  • 9.

    Legras, J. L., Merdinoglu, D., Cornuet, J. M. & Karst, F. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16(10), 2091–2102 (2007).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 10.

    Almeida, P. et al. A population genomics insight into the Mediterranean origins of wine yeast domestication. Mol. Ecol. 24(21), 5412–5427 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 11.

    Dubourdieu, D. et al. Identification de souches de levures de vin par l’analyse de leur AND mitochondrial. Connaissance Vigne Vin 4, 267–278 (1987).

    Google Scholar 

  • 12.

    Querol, A., Barrio, E., Huerta, T. & Ramón, D. Molecular monitoring of wine fermentations conducted by active dry yeast strains. Appl. Environ. Microbiol. 58(9), 2948–2953 (1992).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 13.

    Cappello, M. S., Bleve, G., Grieco, F., Dellaglio, F. & Zacheo, G. Characterization of Saccharomyces cerevisiae strains isolated from must of grape grown in experimental vineyard. J. Appl. Microbiol. 97(6), 1274–1280 (2004).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 14.

    Schuller, D., Alves, H., Dequin, S. & Casal, M. Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol. Ecol. 51(2), 167–177 (2005).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 15.

    Cubillos, F. A., Vásquez, C., Faugeron, S., Ganga, A. & Martínez, C. Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations. FEMS Microbiol. Ecol. 67(1), 162–170 (2009).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 16.

    Vezinhet, F., Blondin, B. & Hallet, J. N. Chromosomal DNA patterns and mitochondrial DNA polymorphism as tools for identification of enological strains of Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol. 32(5), 568–571 (1990).

    CAS  Article  Google Scholar 

  • 17.

    Frezier, V. & Dubourdieu, D. Ecology of yeast strains Saccharomyces cerevisiae during spontaneous fermentation in Bordeaux Winery. Am. J. Enol. Vitic. 43(4), 375–380 (1992).

    Google Scholar 

  • 18.

    Versavaud, A., Courcoux, P., Roulland, C., Dulau, L. & Hallet, J. N. Genetic diversity and geographical distribution of wild Saccharomyces cerevisiae strains from the wine-producing area of Charentes, France. Appl. Environ. Microbiol. 61(10), 3521–3529 (1995).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 19.

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

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 20.

    Ness, F., Lavalle, F., Dubourdieu, D., Aigle, M. & Dulau, L. Identification of yeast strains unsing polymerase chain reaction. J. Sci Food Agric. 62, 89–94 (1993).

    CAS  Google Scholar 

  • 21.

    Legras, J. L. & Karst, F. Optimisation of interdelta analysis for Saccharomyces cerevisiae strain characterisation. FEMS Microbiol. Lett. 221(2), 249–255 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 22.

    Ciani, M., Mannazzu, I., Marinangeli, P., Clementi, F. & Martini, A. Contribution of winery-resident Saccharomyces cerevisiae strains to spontaneous grape must fermentation. Antonie Van Leeuwenhoek 85(2), 159–164 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 23.

    Le Jeune, C., Erny, C., Demuyter, C. & Lollier, M. Evolution of the population of Saccharomyces cerevisiae from grape to wine in a spontaneous fermentation. Food Microbiol. 23(8), 709–716 (2006).

    PubMed  PubMed Central  Google Scholar 

  • 24.

    Vigentini, I. et al. The vintage effect overcomes the terroir effect: A three year survey on the wine yeast biodiversity in Franciacorta and Oltrepo Pavese, two Northern Italian Vine-Growing Areas. Microbiology 161(Pt_2), 362–373 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 25.

    Legras, J. L., Ruh, O., Merdinoglu, D. & Karst, F. Selection of hypervariable microsatellite loci for the characterization of Saccharomyces cerevisiae strains. Int. J. Food Microbiol. 102(1), 73–83 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 26.

    Schuller, D. et al. Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments. Yeast 24(8), 625–636 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 27.

    Schuller, D. et al. Genetic diversity and population structure of Saccharomyces cerevisiae strains isolated from different grape varieties and winemaking regions. PLoS ONE 7(2), e32507 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 28.

    Catlin, D. H. et al. Metapopulation viability of an endangered shorebird depends on dispersal and human-created habitats: Piping plovers (Charadrius melodus) and prairie rivers. Mov. Ecol. 4, 6 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 29.

    Knight, S. & Goddard, M. R. Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation. ISME J. 9(2), 361–370 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 30.

    Knight, S. J., Karon, O. & Goddard, M. R. Small scale fungal community differentiation in a vineyard system. Food Microbiol. 87, 103358 (2020).

    PubMed  Article  PubMed Central  Google Scholar 

  • 31.

    Goddard, M. R., Anfang, N., Tang, R., Gardner, R. C. & Jun, C. A Distinct population of Saccharomyces cerevisiae in New Zealand: Evidence for local dispersal by insects and human-aided global dispersal in Oak Barrels. Environ. Microbiol. 12(1), 63–73 (2010).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 32.

    Stefanini, I. et al. Role of social wasps in Saccharomyces cerevisiae ecology and evolution. Proc. Natl. Acad. Sci. U.S.A. 109(33), 13398–13403 (2012).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 33.

    Buser, C. C., Newcomb, R. D., Gaskett, A. C. & Goddard, M. R. Niche construction initiates the evolution of mutualistic interactions. Ecol. Lett. 17(10), 1257–1264 (2014).

    PubMed  Article  PubMed Central  Google Scholar 

  • 34.

    Francesca, N., Canale, D. E., Settanni, L. & Moschetti, G. Dissemination of Wine-Related Yeasts by Migratory Birds. Environmental Microbiology Reports 4(1), 105–112 (2012).

    PubMed  Article  PubMed Central  Google Scholar 

  • 35.

    Gayevskiy, V. & Goddard, M. R. Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. ISME J. 6(7), 1281–1290 (2012).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 36.

    Cordero-Bueso, G., Arroyo, T. & Valero, E. A long term field study of the effect of fungicides penconazole and sulfur on yeasts in the vineyard. Int. J. Food Microbiol. 189, 189–194 (2014).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 37.

    Oliva, J. et al. Influence of fungicides on grape yeast content and its evolution in the fermentation. Commun. Agric. Appl. Biol. Sci. 72, 181–189 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 38.

    Cordero-Bueso, G. et al. Influence of the farming system and vine variety on yeast communities associated with grape berries. Int. J. Food Microbiol. 145(1), 132–139 (2011).

    PubMed  Article  Google Scholar 

  • 39.

    Milanović, V., Comitini, F. & Ciani, M. Grape berry yeast communities: Influence of fungicide treatments. Int. J. Food Microbiol. 161, 240–246 (2013).

    PubMed  Article  CAS  Google Scholar 

  • 40.

    de Celis, M. et al. Diversity of Saccharomyces Cerevisiae yeasts associated to spontaneous and inoculated fermenting grapes from Spanish Vineyards. Lett. Appl. Microbiol. 68(6), 580–588 (2019).

    PubMed  Article  PubMed Central  Google Scholar 

  • 41.

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

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 42.

    Franco-Duarte, R. et al. Intrastrain genomic and phenotypic variability of the commercial Saccharomyces cerevisiae strain Zymaflore VL1 reveals microevolutionary adaptation to vineyard environments. FEMS Yeast Res. 15(6), fov063 (2015).

    PubMed  Article  CAS  PubMed Central  Google Scholar 

  • 43.

    Cordero-Bueso, G., Arroyo, T., Serrano, A. & Valero, E. Remanence and survival of commercial yeast in different ecological niches of the vineyard. FEMS Microbiol. Ecol. 77, 429–437 (2011).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 44.

    Mortimer, R. & Polsinelli, M. On the origins of wine yeast. Res. Microbiol. 150(3), 199–204 (1999).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 45.

    Rosini, G., Federici, F. & Martini, A. Yeast flora of grape berries during ripening. Microb. Ecol. 8(1), 83–89 (1982).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 46.

    Bokulich, N. A., Ohta, M., Richardson, P. M. & Mills, D. A. Monitoring seasonal changes in winery-resident microbiota. PLoS ONE 8(6), e66437 (2013).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 47.

    Dion, R. Aux origines du vignoble bordelais: La création du vignoble bordelais, Angers, Éditions de l’Ouest (1952).

  • 48.

    Aubin, G., Lavaud, R.P. (1996). Bordeaux: vignoble millénaire.Bordeaux : l’Horizon chimérique. 1, 215.

  • 49.

    Liti, G. et al. Population genomics of domestic and wild yeasts. Nature 458(7236), 337–341 (2009).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 50.

    Bruvo, R., Michiels, N. K., D’souza, T. G. & Schulenburg, H. A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level. Mol. Ecol. 13(7), 2101–2106 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 51.

    Gao, H., Williamson, S. & Bustamante, C. D. A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176(3), 1635–1651 (2007).

    PubMed  PubMed Central  Google Scholar 

  • 52.

    Gayevskiy, V., Klaere, S., Knight, S. & Goddard, M. R. ObStruct: A method to objectively analyse factors driving population structure using Bayesian ancestry profiles. PLoS ONE 9(1), e85196 (2014).

    ADS  PubMed  PubMed Central  Google Scholar 

  • 53.

    Sundqvist, L., Keenan, K., Zackrisson, M., Prodöhl, P. & Kleinhans, D. Directional genetic differentiation and relative migration. Ecol. Evol. 6, 3461–3475 (2016).

    PubMed  PubMed Central  Google Scholar 

  • 54.

    Gayevskiy, V., Lee, S. & Goddard, M. R. European derived Saccharomyces cerevisiae colonisation of New Zealand vineyards aided by humans retorius I, editor. FEMS Yeast Res. 16(7), 091 (2016).

    Google Scholar 

  • 55.

    Setati, M. E., Jacobson, D., Andong, U. C. & Bauer, F. The vineyard yeast microbiome, a mixed model microbial map. PLoS ONE 7(12), e52609 (2012).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 56.

    Cus, F. & Raspor, P. The Effect of Pyrimethanil on the Growth of Wine Yeasts. Lett. Appl. Microbiol. 47(1), 54–59 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 57.

    Viel, A. et al. The geographic distribution of Saccharomyces cerevisiae isolates within three italian neighboring winemaking regions reveals strong differences in yeast abundance, genetic diversity and industrial strain dissemination. Front Microbiol 8, 1595 (2017).

    PubMed  PubMed Central  Article  Google Scholar 

  • 58.

    Garijo, P. et al. The occurrence of fungi, yeasts and bacteria in the air of a Spanish winery during vintage. Int. J. Food Microbiol. 125(2), 141–145 (2008).

    CAS  PubMed  Article  PubMed Central  Google Scholar 

  • 59.

    Schacherer, J., Shapiro, J. A., Ruderfer, D. M. & Kruglyak, L. Comprehensive polymorphism survey elucidates population structure of S. cerevisiae. Nature 458(7236), 342–345 (2009).

    ADS  CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 60.

    White, T., Bruns, T., Lee, S., & Taylor, T. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications (eds Innis, M. et al.), 315–22. (Academic Press, Cambridge, 1990).

  • 61.

    Granchi, L., Bosco, M., Messini, A. & Vincenzini, M. Rapid detection and quantification of yeast species during spontaneous wine fermentation by PCR-RFLP analysis of the rDNA ITS region. J. Appl. Microbiol. 87(6), 949–956 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 62.

    Field, D. & Wills, C. Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc. Natl. Acad. Sci. U. S. A. 95(4), 1647–1652 (1998).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 63.

    González Techera, A., Jubany, S., Carrau, F. M. & Gaggero, C. Differentiation of industrial wine yeast strains using microsatellite markers. Lett. Appl. Microbiol. 33(1), 71–75 (2001).

    PubMed  PubMed Central  Google Scholar 

  • 64.

    Hennequin, C. et al. Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains. J. Clin. Microbiol. 39(2), 551–559 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 65.

    Pérez, M. A., Gallego, F. J., Martínez, I. & Hidalgo, P. Detection, distribution and selection of microsatellites (SSRs) in the genome of the yeast Saccharomyces cerevisiae as molecular markers. Lett. Appl. Microbiol. 33(6), 461–466 (2001).

    PubMed  PubMed Central  Google Scholar 

  • 66.

    Bradbury, J. E. et al. A homozygous diploid subset of commercial wine yeast strains. Antonie Van Leeuwenhoek 89(1), 27–37 (2005).

    PubMed  PubMed Central  Google Scholar 

  • 67.

    Colwell, R. K. Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85(10), 2717–2727 (2004).

    ADS  Google Scholar 

  • 68.

    Arnaud-Haond, S. & Belkhir, K. GENCLONE: A computer program to analyse genotypic data, test for clonality and describe spatial clonal organization. Mol. Ecol. Notes 7(1), 15–17 (2007).

    CAS  Google Scholar 

  • 69.

    Cormack, R. M. A review of classification. J. R. Stat. Soc. A 134, 321–367 (1971).

    MathSciNet  Google Scholar 

  • 70.

    Kamvar, Z. N., Tabima, J. F. & Grünwald, N. J. Poppr: An R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. Peer J 2, e281 (2014).

    PubMed  Article  PubMed Central  Google Scholar 

  • 71.

    Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).

    CAS  Article  Google Scholar 

  • 72.

    Legras, J. L. et al. Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication. Mol. Biol. Evol. 35(7), 1712–1727 (2018).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 73.

    Suzuki, R., & Shimodaira, H. R package: Pvclust: Hierarchical Clustering with P-values via multiscale bootstrap resampling. (2014).

  • 74.

    Mantel, N. The detection of disease clustering and a generalized regression approach. Cancer Res. 27(2 Part 1), 209–220 (1967).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 75.

    Peakall, R. & Smouse, P. E. GenAlEx 6.5: Genetic analysis in excel. Population genetic software for teaching and research—An update. Bioinformatics 28(19), 2537–2539 (2012).

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • 76.

    Diniz-Filho, J. A. et al. Mantel test in population genetics. Genet. Mol. Biol. 36(4), 475–485 (2013).

    PubMed  PubMed Central  Article  Google Scholar 

  • 77.

    Jost, L. GST and its relatives do not measure differentiation. Mol. Ecol. 17, 4015–4026 (2008).

    PubMed  Article  PubMed Central  Google Scholar 

  • 78.

    Beerli, P. & Michal, P. Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185(1), 313–326 (2010).

    PubMed  PubMed Central  Article  Google Scholar 


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