Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand

ISME Journal

Volumn 6, Issue 7, 2012, Pages 1281-1290

  Gayevskiy, Velimir ^a   Goddard, Matthew R ^a  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

biogeography; community ecology; population structure; Saccharomyces cerevisiae; yeast

Indexed keywords

BIOGEOGRAPHY; BIOTECHNOLOGY; CIVILIZATION; COMMUNITY ECOLOGY; FERMENTATION; FOOD INDUSTRY; GEOGRAPHICAL DISTRIBUTION; GEOGRAPHICAL VARIATION; MICROBIAL COMMUNITY; MICROBIAL ECOLOGY; OXYGEN; POPULATION STRUCTURE; SUBPOPULATION; VINE; YEAST;

ARTICLE; CLASSIFICATION; FERMENTATION; GENETICS; MICROBIOLOGY; NEW ZEALAND; PHYLOGENY; SACCHAROMYCES CEREVISIAE; VITIS; WINE; YEAST;

FERMENTATION; NEW ZEALAND; PHYLOGENY; SACCHAROMYCES CEREVISIAE; VITIS; WINE; YEASTS;

NEW ZEALAND;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84862589499     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2011.195     Document Type: Article

References (70)

1. Anfang N, Brajkovich M, Goddard MR. (2009). Cofermentation with Pichia kluyveri increases varietal thiol concentrations in Sauvignon Blanc. Aust J Grape Wine R 15: 1-8.
2. Beltran G, Torija MJ, Novo M, Ferrer N, Poblet M, Guillamon JM et al. (2002). Analysis of yeast populations during alcoholic fermentation: A six year followup study. Syst Appl Microbiol 25: 287-293. (Pubitemid 35014484)
3. Blanco P, Orriols I, Losada A. (2011). Survival of commercial yeasts in the winery environment and their prevalence during spontaneous fermentations. J Ind Microbiol Biot 38: 235-239.
4. Burke D, Dawson D, Stearns T. (2000). Methods in Yeast Genetics. A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Press: Cold Spring Harbor. Cadez N, Zupan J, Raspor P. (2010). The effect of fungicides on yeast communities associated with grape berries. FEMS Yeast Res 10: 619-630.
5. Chambers PJ, Pretorius IS. (2010). Fermenting knowledge: The history of winemaking, science and yeast research. EMBO Rep 11: 914-920.
6. Ciani M, Comitini F, Mannazzu I, Domizio P. (2010). Controlled mixed culture fermentation: A new perspective on the use of non-Saccharomyces yeasts in winemaking. FEMS Yeast Res 10: 123-133.
7. Clarke KR. (1993). Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18: 117-143. (Pubitemid 24409223)
8. Cordente AG, Swiegers JH, Hegardt FG, Pretorius IS. (2007). Modulating aroma compounds during wine fermentation by manipulating carnitine acetyltransferases in Saccharomyces cerevisiae. FEMS Microbiol Lett 267: 159-166. (Pubitemid 46114968)
9. Cordero-Bueso G, Arroyo T, Serrano A, Tello J, Aporta I, Velez MD et al. (2011). Influence of the farming system and vine variety on yeast communities associated with grape berries. Intl J Food Micro 145: 132-139.
10. Cox CB, Moore PD. (1993). Biogeography, an Ecological and Evolutionary Approach. Blackwell: London. Cubillos FA, Vasquez C, Faugeron S, Ganga A, Martinez C. (2009). Self-fertilization is the main sexual reproduction mechanism in native wine yeast populations. FEMS Microbiol Ecol 67: 162-170.
11. Drummond A.,Ashton B.,Cheung M.,Heled J.,Kearse M.,Moir R.,et al.Geneious v5.4 Available from http://www.geneious.com/
12. Drummond A, Ashton B, Cheung M, Heled J, Kearse M, Moir R et al. (2011). Geneious v5.4, Available from http://www.geneious.com/. Dujon B. (1996). The yeast genome project: What did we learn? Trends Genet 12: 263-270. (Pubitemid 26202681)
13. 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. Int J Syst Bacteriol 49: 329-337. (Pubitemid 29225895)
14. Ezov TK, Boger-Nadjar E, Frenkel Z, Katsperovski I, Kemeny S, Nevo E et al. (2006). Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from Evolution canyon: Microsatellite polymorphism, ploidy and controversial sexual status. Genetics 174: 1455-1468. (Pubitemid 44808314)
15. Falconer DS, Mackay TFC. (1996). Introduction to Quantitative Genetics, 4th edn. Pearson, Prentice Hall: New Jersey.
16. Falush D, Stephens M, Pritchard JK. (2003). Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164: 1567-1587. (Pubitemid 37102217)
17. Fay JC, Benavides JA. (2005). Evidence for domesticated and wild populations of Sacchoromyces cerevisiae. PLOS Genetics 1: 66-71.
18. Finlay BJ, Fenchel T. (2004). Cosmopolitan metapopulations of free-living microbial eukaryotes. Protist 155: 237-244. (Pubitemid 38889536)
19. Gao H, Williamson S, Bustamante CD. (2007). A Markov chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176: 1635-1651. (Pubitemid 47105223)
20. Gaston KJ. (2000). Global patterns in biodiversity. Nature 405: 220-227. (Pubitemid 30313545)
21. Goddard MR. (2008). Quantifying the complexities of Saccharomyces cerevisiae0s ecosystem engineering via fermentation. Ecology 89: 2077-2082.
22. Goddard MR, Anfang N, Tang R, Gardner RC, Jun C. (2010). 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: 63-73.
23. Goddard MR, Greig D, Burt A. (2001). Outcrossed sex allows a selfish gene to invade yeast populations. Proc R Soc Lond B-Biol Sci 268: 2537-2542. (Pubitemid 34107130)
24. Goode J. (2006). The Science of Wine. University of California Press: Berkeley.
25. Green JL, Holmes AJ, Westoby M, Oliver I, Briscoe D, Dangerfield M et al. (2004). Spatial scaling of microbial eukaryote diversity. Nature 432: 747-750. (Pubitemid 39656292)
26. Hamamoto M, Nakase T. (1996). Ballistosporous yeasts found on the surface of plant materials collected in New Zealand-The genera Bensingtonia and Bullera with descriptions of five new species. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 69: 279-291.
27. Hammer O, Harper DAT, Ryan PD. (2001). PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4 art. 4: 9 pp. (online only http://palaeo-electronica.org/2001-1/ past/issue1-01.htm).
28. Hartl DL, Clark AG. (1997). Principles of Population Genetics, III edn. Sinauer: Sunderland.
29. Howell KS, Cozzolino D, Bartowsky EJ, Fleet GH, Henschke PA. (2006). Metabolic profiling as a tool for revealing Saccharomyces interactions during wine fermentation. FEMS Yeast Res 6: 91-101.
30. Huelsenbeck JP, Andolfatto P. (2007). Inference of population structure under a Dirichlet process model. Genetics 175: 1787-1802. (Pubitemid 46789963)
31. Hugenholtz P, Goebel BM, Pace NR. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774. (Pubitemid 28429361)
32. Johnson H. (1998). The Story of Wine. Simon and Schuster: London.
33. Johnson LJ, Koufopanou V, Goddard MR, Hetherington R, Schafer SM, Burt A. (2004). Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166: 43-52. (Pubitemid 38364701)
34. Kalinowski ST. (2005). HP-RARE 1.0: A computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5: 187-189. (Pubitemid 40350919)
35. King ES, Kievit RL, Curtin C, Swiegers JH, Pretorius IS, Bastian SEP et al. (2010). The effect of multiple yeasts co-inoculations on Sauvignon Blanc wine aroma composition, sensory properties and consumer preference. Food Chem 122: 618-626.
36. King M. (2003). History of New Zealand. Penguin: Auckland.
37. Knop M. (2006). Evolution of the hemiascomycete yeasts: On life styles and the importance of inbreeding. Bioessays 28: 696-708. (Pubitemid 44257273)
38. Koufopanou V, Hughes J, Bell G, Burt A. (2006). The spatial scale of genetic differentiation in a model organism: The wild yeast Saccharomyces paradoxus. Philos T R Soc B 361: 1941-1946. (Pubitemid 44787029)
39. Kurtzman CP, Robnett CJ. (2003). Phylogenetic relationships among yeasts of the Saccharomyces complex determined from multigene sequence analyses. FEMS Yeast Res 3: 417-432. (Pubitemid 36570320)
40. Lachance MA, Lawrie D, Dobson J, Piggott J. (2008). Biogeography and population structure of the Neotropical endemic yeast species Metschnikowia lochheadii. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 94: 403-414.
41. Lachance MA, Starmer WT, Bowles JM, Phaff HJ, Rosa CA. (2000). Ribosomal DNA, species structure, and biogeography of the cactophilic yeast Clavispora opuntiae. Can J Microbiol 46: 195-210. (Pubitemid 30173600)
42. Lachance MA, Starmer WT, Rosa CA, Bowles JM, Barker JSF, Janzen DH. (2001). Biogeography of the yeasts of ephemeral flowers and their insects. FEMS Yeast Res 1: 1-8. (Pubitemid 34442288)
43. Lambrechts MG, Pretorius IS. (2000). Yeast and its importance to wine aroma-A review. S Afr J Enol Vitic 21: 97-129.
44. Landry CR, Townsend JP, Hartl DL, Cavalieri D. (2006). Ecological and evolutionary genomics of Saccharomyces cerevisiae. Mol Ecol 15: 575-591. (Pubitemid 43344777)
45. Legras JL, MerdinogluD, Cornuet JM, Karst F. (2007). Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol Ecol 16: 2091-2102. (Pubitemid 46718913)
46. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA et al. (2009). Population genomics of domestic and wild yeasts. Nature 458: 337-341.
47. Martinez C, Cosgaya P, Vasquez C, Gac S, Ganga A. (2007). High degree of correlation between molecular polymorphism and geographic origin of wine yeast strains. J Appl Microbiol 103: 2185-2195. (Pubitemid 350191187)
48. Martiny JBH, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL et al. (2006). Microbial biogeography: Putting microorganisms on the map. Nat Rev Microbiol 4: 102-112. (Pubitemid 43158153)
49. McGovern PE, Zhang J, Tang J, Zhang Z, Hall GR, Moreau RA et al. (2004). Fermented beverages of pre- and proto-historic China. Proc. Natl. Acad. Sci. USA 101: 17593-17598. (Pubitemid 40051931)
50. Nemergut DR, Costello EK, Hamady M, Lozupone C, Jiang L, Schmidt SK et al. (2011). Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13: 135-144.
51. Peakall R, Smouse PE. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295. (Pubitemid 43373825)
52. Pedros-Alio C. (2007). Dipping into the rare biosphere. Science 315: 192-193. (Pubitemid 46170317)
53. Piskur J, Rozpedowska E, Polakova S, Merico A, Compagno C. (2006). How did Saccharomyces evolve to become a good brewer? Trends Genet 22: 183-186.
54. Prakitchaiwattana CJ, Fleet GH, Heard GM. (2004). Application and evaluation of denaturing gradient gel electrophoresis to analyse the yeast ecology of wine grapes. FEMS Yeast Res 4: 865-877. (Pubitemid 39144378)
55. Pretorius IS. (2000). Tailoring wine yeast for the new millennium: Novel approaches to the ancient art of winemaking. Yeast 16: 675-729. (Pubitemid 30386786)
56. Replansky T, Koufopanou V, Greig D, Bell G. (2008). Saccharomyces sensu stricto as a model system for evolution and ecology. Trends Ecol Evol 23: 494-501.
57. Ribereau-Gayon P, Dobourdieu D, Doneche B, Lonvaud A. (2006). Handbook of Enology, Vol. 1 The Microbiology of Wine and Vinifications. John Wiley & Sons, Ltd: Chichetser, U.K.
58. Richards KD, Goddard MR, Gardner RC. (2009). A database of microsatellite genotypes for Saccharomyces cerevisiae. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 96: 355-359.
59. Romano P, Fiore C, Paraggio M, Caruso M, Capece A. (2003). Function of yeast species and strains in wine flavour. Intl J Food Micro 86: 169-180. (Pubitemid 36900416)
60. Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L. (2009). Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
61. Schuller D, Alves H, Dequin S, Casal M. (2005). Ecological survey of Saccharomyces cerevisiae strains from vineyards in the Vinho Verde Region of Portugal. FEMS Microbiol Ecol 51: 167-177. (Pubitemid 40038377)
62. Schuller D, Casal M. (2007). The genetic structure of fermentative vineyard-Associated Saccharomyces cerevisiae populations revealed by microsatellite analysis. Antonie Van Leeuwenhoek Int J. Gen. Mol. Microbiol. 91: 137-150.
63. Serjeant K, Tang R, Anfang N, Beggs JR, Goddard MR. (2008). Yeasts associated with the New Zealand Nothofagus honeydew system. New Zeal J Ecol 32: 209-213.
64. Swiegers JH, Pretorius IS. (2005). Yeast modulation of wine flavor. Adv Appl Microbiol 57: 131-175. (Pubitemid 40949519)
65. Swiegers JH, Pretorius IS. (2007). Modulation of volatile sulfur compounds by wine yeast. Appl Microbiol Biotechnol 74: 954-960. (Pubitemid 46434768)
66. Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP et al. (2005). Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet 37: 630-635. (Pubitemid 40770419)
67. Whitaker RJ, Grogan DW, Taylor JW. (2003). Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978. (Pubitemid 36994812)
68. Wolfe KH, Shields DC. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713. (Pubitemid 27270611)
69. Zhang HY, Lee SA, Bradbury JE, Warren RN, Seth H, Hooks D et al. (2010a). Yeasts isolated from New Zealand vineyards and wineries. Aust J Grape Wine R 16: 491-496.
70. Zhang HY, Skelton A, Gardner RC, Goddard MR. (2010b). Saccharomyces paradoxus and Saccharomyces cerevisiae reside on oak trees in New Zealand: Evidence for migration from Europe and interspecies hybrids. FEMS Yeast Res 10: 941-947.