Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests

Environmental Microbiology

Volumn 18, Issue 4, 2016, Pages 1137-1147

  Gayevskiy, Velimir ^a   Goddard, Matthew R ^a,b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF LINCOLN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; RNA, RIBOSOMAL, 26S;

ASIA; CLASSIFICATION; EVOLUTION; FOREST; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; MICROBIOLOGY; NEW ZEALAND; NUCLEOTIDE SEQUENCE; SACCHAROMYCES; SOUTH AMERICA;

ASIA; BASE SEQUENCE; BIOLOGICAL EVOLUTION; FORESTS; GENOTYPE; NEW ZEALAND; RNA, RIBOSOMAL; SACCHAROMYCES; SOIL MICROBIOLOGY; SOUTH AMERICA;

EID: 84953410740     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.13107     Document Type: Article

References (61)

1. Almeida, P., Gonçalves, C., Teixeira, S., Libkind, D., Bontrager, M., Masneuf-Pomarède, I., etal. (2014) A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun 5: 4044.
2. Andrews, S. (2012) FastQC: a quality control tool for high throughput sequence data.
3. Bergstrom, A., Simpson, J.T., Salinas, F., Barre, B., Parts, L., Zia, A., etal. (2014) A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol 31: 872-888.
4. Bing, J., Han, P.-J., Liu, W.-Q., Wang, Q.-M., and Bai, F.-Y. (2014) Evidence for a Far East Asian origin of lager beer yeast. Curr Biol 24: R380-R381.
5. Borneman, A.R., and Pretorius, I.S. (2015) Genomic insights into the Saccharomyces sensu stricto complex. Genetics 199: 281-291.
6. Cherry, J.M., Hong, E.L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E.T., etal. (2011) Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res 40: D700-D705.
7. Coton, E., Coton, M., Levert, D., Casaregola, S., and Sohier, D. (2006) Yeast ecology in French cider and black olive natural fermentations. Int J Food Microbiol 108: 130-135.
8. Darling, A.C.E., Mau, B., Blattner, F.R., and Perna, N.T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
9. Dashko, S., Zhou, N., Compagno, C., and Piskur, J. (2014) Why, when, and how did yeast evolve alcoholic fermentation? FEMS Yeast Res 14: 826-832.
10. Di Cagno, R., Pontonio, E., Buchin, S., De Angelis, M., Lattanzi, A., Valerio, F., etal. (2014) Diversity of the lactic acid bacterium and yeast microbiota in the switch from firm-to liquid-sourdough fermentation. Appl Environ Microbiol 80: 3161-3172.
11. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
12. Esteve-Zarzoso, B., Peris-Toran, M.J., Garcia-Maiquez, E., Uruburu, F., and Querol, A. (2001) Yeast population dynamics during the fermentation and biological aging of sherry wines. Appl Environ Microbiol 67: 2056-2061.
13. Ganga, M.A., and Martinez, C. (2004) Effect of wine yeast monoculture practice on the biodiversity of non-Saccharomyces yeasts. J Appl Microbiol 96: 76-83.
14. García-Alcalde, F., Okonechnikov, K., Carbonell, J., Cruz, L.M., Götz, S., Tarazona, S., etal. (2012) Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28: 2678-2679.
15. Gayevskiy, V., and Goddard, M.R. (2012) Geographic delineations of yeast communities and populations associated with vines and wines in New Zealand. ISME J 6: 1281-1290.
16. Goddard, M.R. (2008) Quantifying the complexities of Saccharomyces cerevisiae's ecosystem engineering via fermentation. Ecology 89: 2077-2082.
17. Goddard, M.R., and Greig, D. (2015) Saccharomyces cerevisiae: a nomadic yeast with no niche? FEMS Yeast Res 15: fov009.
18. Goddard, M.R., Anfang, N., Tang, R., Gardner, R.C., and 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.
19. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., etal. (1996) Life with 6000 Genes. Science 274: 546-567.
20. Guindon, S., and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
21. Hagman, A., Säll, T., Compagno, C., and Piskur, J. (2013) Yeast 'make-accumulate-consume' life strategy evolved as a multi-step process that predates the whole genome duplication. PLoS ONE 8: e68734.
22. Hittinger, C.T. (2013) Saccharomyces diversity and evolution: a budding model genus. Trends Genet 29: 309-317.
23. Hittinger, C.T., Gonçalves, P., Sampaio, J.P., Dover, J., Johnston, M., and Rokas, A. (2010) Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58.
24. Hurles, M.E., Matisoo-Smith, E., and Gray, R.D. (2003) Untangling Oceanic settlement: the edge of the knowable. Trends Ecol Evol 18: 531-540.
25. Hyma, K.E., and Fay, J.C. (2013) Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol Ecol 22: 2917-2930.
26. Johnson, L.J., Koufopanou, V., Goddard, M.R., Hetherington, R., Schäfer, S.M., and Burt, A. (2004) Population genetics of the wild yeast Saccharomyces paradoxus. Genetics 166: 43-52.
27. Kearse, M., Moir, R., Wilson, A., Stones-Hava, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., Thierer, T., Ashton, B., Mentjies, P., and Drummond, A. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649.
28. Knight, S., and Goddard, M.R. (2015) Quantifying separation and similarity in a Saccharomyces cerevisiae metapopulation. ISME J 9: 361-370.
29. Kobayashi, M., Kawamura, M., Kobayashi, A., Yamazaki, A., and Fukuda, M. (2013) Isolation of yeasts from kimchi and construction of a hydrostatic-pressure sensitive mutant. Rev High Press Sci Technol 23: 59-67.
30. Kurtzman, C.P. (2003) Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS Yeast Res 4: 233-245.
31. Lederer, M.A., Nielsen, D.S., Toldam-Ansersen, T.B., Herrmann, J.V., and Arneborg, N. (2013) Yeast species associated with different wine grape varieties in Denmark. Acta Agriculturae Scandinavica, Section B - Soil Plant Sci 61: 89-96.
32. Li, H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 1-3.
33. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., etal. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
34. Libkind, D., Hittinger, C.T., Valério, E., Gonçalves, C., Dover, J., Johnston, M., etal. (2011) Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. PNAS 108: 14539-14544.
35. Liti, G., Carter, D.M., Moses, A.M., Warringer, J., Parts, L., James, S.A., etal. (2009) Population genomics of domestic and wild yeasts. Nature 458: 337-341.
36. Liti, G., Ba, A.N.N., Blythe, M., Muller, C.A., Bergstrom, A., Cubillos, F.A., etal. (2013) High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics 14: 1-14.
37. McGovern, P.E., Zhang, J., Tang, J., Zhang, Z., Hall, G.R., Moreau, R.A., etal. (2004) Fermented beverages of pre-and proto-historic China. PNAS 101: 17593-17598.
38. Naumov, G.I., Naumova, E.S., and Sniegowski, P.D. (1997) Differentiation of European and Far East Asian populations of Saccharomyces paradoxus by allozyme analysis. Int J Syst Bacteriol 47: 341-344.
39. Naumov, G.I., Naumova, E.S., and Sniegowski, P.D. (1998) Saccharomyces paradoxus and Saccharomyces cerevisiae are associated with exudates of North American oaks. Can J Microbiol 44: 1045-1050.
40. Naumov, G.I., James, S.A., Naumova, E.S., Louis, E.J., and Roberts, I.N. (2000) Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol 50: 1931-1942.
41. Naumov, G.I., Lee, C.-F., and Naumova, E.S. (2013) Molecular genetic diversity of the Saccharomyces yeasts in Taiwan: Saccharomyces arboricola, Saccharomyces cerevisiae and Saccharomyces kudriavzevii. Antonie Van Leeuwenhoek 103: 217-228.
42. Peris, D., Sylvester, K., Libkind, D., Gonçalves, P., Sampaio, J.P., Alexander, W.G., and Hittinger, C.T. (2014) Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Mol Ecol 23: 2031-2045.
43. Pfeiffer, T., Schuster, S., and Bonhoeffer, S. (2001) Cooperation and competition in the evolution of ATP-producing pathways. Science 292: 504-507.
44. Piskur, J., Rozpedowska, E., Polakova, S., Merico, A., and Compagno, C. (2006) How did Saccharomyces evolve to become a good brewer? Trends Genet 22: 183-186.
45. Polz, M.F., and Cavanaugh, C.M. (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64: 3724-3730.
46. Rambaut, A. (2012) FigTree.
47. Replansky, T., Koufopanou, V., Greig, D., and Bell, G. (2008) Saccharomyces sensu stricto as a model system for evolution and ecology. Trends Ecol Evol 23: 494-501.
48. Rodríguez, M.E., Pérez-Través, L., Sangorrín, M.P., Barrio, E., and Lopes, C.A. (2014) Saccharomyces eubayanus and Saccharomyces uvarum associated with the fermentation of Araucaria araucana seeds in Patagonia. FEMS Yeast Res 14: 948-965.
49. Rokas, A., Williams, B.L., King, N., and Carroll, S.B. (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425: 798-804.
50. Rozpedowska, E., Hellborg, L., Ishchuk, O.P., Orhan, F., Galafassi, S., Merico, A., etal. (2011) Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts. Nat Commun 2: 302.
51. Salvado, Z., Arroyo-Lopez, F.N., Guillamon, J.M., Salazar, G., Querol, A., and Barrio, E. (2011) Temperature adaptation markedly determines evolution within the genus Saccharomyces. Appl Environ Microbiol 77: 2292-2302.
52. Scannell, D.R., Zill, O.A., Rokas, A., Payen, C., Dunham, M.J., Eisen, M.B., etal. (2011) The awesome power of yeast evolutionary genetics: new genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3: Genes, Genomes, Genetics 1: 11-25.
53. Serjeant, K., Tang, R., Anfang, N., Beggs, J.R., and Goddard, M.R. (2008) Yeasts associated with the New Zealand Nothofagus honeydew system. New Zeal J Ecol 32: 209-213.
54. Sniegowski, P.D., Dombrowski, P.G., and Fingerman, E. (2002) Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res 1: 299-306.
55. Spring, S., Lins, U., Amann, R., Schleifer, K.H., Ferreira, L., Esquivel, D., and Farina, M. (1998) Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusually large magnetosomes. Arch Microbiol 169: 136-147.
56. Tsai, I.J., Bensasson, D., Burt, A., and Koufopanou, V. (2008) Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle. PNAS 105: 4957-4962.
57. Wang, Q.-M., Liu, W.-Q., Liti, G., Wang, S.-A., and Bai, F.-Y. (2012) Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity. Mol Ecol 21: 5404-5417.
58. Wang, S.A., and Bai, F.Y. (2008) Saccharomyces arboricolus sp. nov., a yeast species from tree bark. Int J Syst Evol Microbiol 58: 510-514.
59. White, T.J., Bruns, T., Lee, S., and Taylor, J.W. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide Methods Appl 18: 315-322.
60. Zhang, H., Skelton, A., Gardner, R.C., and Goddard, M.R. (2010) 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.
61. Zhang, H., Richards, K.D., Wilson, S., Lee, S.A., Sheehan, H., Roncoroni, M., and Gardner, R.C. (2015) Genetic characterization of strains of Saccharomyces uvarum from New Zealand wineries. Food Microbiol 46: 92-99.