1887

Abstract

Five ascosporogenous yeast strains related to the genus were isolated. Two strains (CLIB 1764 and CLIB 1780) were isolated from French sourdoughs; three others (UFMG-CM-Y273, UFMG-CM-Y451 and UFMG-CM-Y452) were from rotting wood in Brazil. The sequences of the French and Brazilian strains differed by one and three substitutions, respectively, in the D1/D2 large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS). The D1/D2 LSU rRNA sequence of these strains differed by 0.5 and 0.7 % from , but their ITS sequences diverged by 8.1 and 8.3 %, respectively, from that of the closest described species . Analysis of protein coding sequences of , and distinguished the French from the Brazilian strains, with respectively 3.3, 6 and 11.7 % substitutions. Two novel species are described to accommodate these newly isolated strains: sp. nov. (type strain CLIB 1764=CBS 14374) and sp. nov. (type strain UFMG-CM-Y273=CLIB 1783=CBS 14236). Further analysis of culture collections revealed a strain previously assigned to the species, but having 3.8 % difference (22 substitutions and 2 indels) in its ITS with respect to . Hence, we describe a new taxon, sp. nov. (type strain CLIB 162=CBS 2141), to accommodate this strain. Finally, and are reassigned to the genus as new combinations. On the basis of sequence analysis, we also propose that and comb. nov. are conspecific.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001495
2016-12-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/12/5192.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001495&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [View Article][PubMed]
    [Google Scholar]
  2. Alvarez-Perez S., Mateos A., Dominguez L., Martinez-Nevado E., Rodriguez-Bertos A., Blanco J. L., Garcia M. E. 2012; First isolation of the anamorph of Kazachstania heterogenica from a fatal infection in a primate host. Med Mycol 50:193–196 [View Article][PubMed]
    [Google Scholar]
  3. Araújo F. V., Rosa C. A., Freitas L. F., Lachance M. A., Vaughan-Martini A., Mendonça-Hagler L. C., Hagler A. N. 2012; Kazachstania bromeliacearum sp. nov., a yeast species from water tanks of bromeliads. Int J Syst Evol Microbiol 62:1002–1006 [View Article][PubMed]
    [Google Scholar]
  4. Barnett J. A., Payne R. W., Yarrow D. 2000 Yeasts: Characteristics and Identification, 3rd edn. Cambridge: Cambridge University Press;
    [Google Scholar]
  5. Bon E., Neuvéglise C., Lépingle A., Wincker P., Artiguenave F., Gaillardin C., Casaregola S. 2000; Genomic exploration of the hemiascomycetous yeasts: 6. Saccharomyces exiguus . FEBS Lett 487:42–46 [View Article][PubMed]
    [Google Scholar]
  6. Cardinali G., Antonielli L., Corte L., Roscini L., Bagnetti A., Pelliccia C., Puddu G. 2012; Kazachstania ichnusensis sp. nov., a diploid homothallic ascomycetous yeast from Sardinian lentisk rhizosphere. Int J Syst Evol Microbiol 62:722–727 [View Article][PubMed]
    [Google Scholar]
  7. Chen R., Wei S. C., Jiang Y. M., Wang Q. M., Bai F. Y. 2010; Kazachstania taianensis sp. nov., a novel ascomycetous yeast species from orchard soil. Int J Syst Evol Microbiol 60:1473–1476 [View Article][PubMed]
    [Google Scholar]
  8. Cheng L., Luo J., Li P., Yu H., Huang J., Luo L. 2014; Microbial diversity and flavor formation in onion fermentation. Food Funct 5:2338–2347 [View Article][PubMed]
    [Google Scholar]
  9. De Vuyst L., Van Kerrebroeck S., Harth H., Huys G., Daniel H. M., Weckx S. 2014; Microbial ecology of sourdough fermentations: diverse or uniform?. Food Microbiol 37:11–29 [View Article][PubMed]
    [Google Scholar]
  10. Gordon J. L., Wolfe K. H. 2008; Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981. Yeast 25:449–456 [View Article][PubMed]
    [Google Scholar]
  11. Groenewald M., Daniel H. M., Robert V., Poot G. A., Smith M. T. 2008; Polyphasic re-examination of Debaryomyces hansenii strains and reinstatement of D. hansenii, D. fabryi and D. subglobosus . Persoonia 21:17–27 [View Article][PubMed]
    [Google Scholar]
  12. Hoffman C. S., Winston F. 1987; A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli . Gene 57:267–272 [View Article][PubMed]
    [Google Scholar]
  13. Jacques N., Mallet S., Casaregola S. 2009; Delimitation of the species of the Debaryomyces hansenii complex by intron sequence analysis. Int J Syst Evol Microbiol 59:1242–1251 [View Article][PubMed]
    [Google Scholar]
  14. Jacques N., Sacerdot C., Derkaoui M., Dujon B., Ozier-Kalogeropoulos O., Casaregola S. 2010; Population polymorphism of nuclear mitochondrial DNA insertions reveals widespread diploidy associated with loss of heterozygosity in Debaryomyces hansenii . Eukaryot Cell 9:449–459 [View Article][PubMed]
    [Google Scholar]
  15. James S. A., Carvajal Barriga E. J., Portero Barahona P., Nueno-Palop C., Cross K., Bond C. J., Roberts I. N. 2015; Kazachstania yasuniensis sp. nov., an ascomycetous yeast species found in mainland Ecuador and on the Galápagos. Int J Syst Evol Microbiol 65:1304–1309 [View Article][PubMed]
    [Google Scholar]
  16. Kabisch J., Honing C., Bohnlein C., Pichner R., Gareis M., Wenning M. 2013; Kazachstania psychrophila sp. nov., a novel psychrophilic yeast isolated from vacuum-packed beef. Antonie van Leeuwenhoek 104:925–931 [CrossRef]
    [Google Scholar]
  17. Katoh K., Standley D. M. 2016; A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics 32:1933–1942 [View Article][PubMed]
    [Google Scholar]
  18. 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[PubMed] [CrossRef]
    [Google Scholar]
  19. Kurtzman C. P., Robnett C. J. 1998; Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 73:331–371[PubMed] [CrossRef]
    [Google Scholar]
  20. Kurtzman C. P., Robnett C. J. 2003; Phylogenetic relationships among yeasts of the ‘Saccharomyces complex’ determined from multigene sequence analyses. FEMS Yeast Res 3:417–432 [View Article][PubMed]
    [Google Scholar]
  21. Lachance M.-A., Boekhout T., Scorzetti G., Fell J. W., Kurtzman C. P. 2011; Candida Berkhout. In The Yeast, a Taxonomic Study, 5th edn. vol. 2 pp. 987–1278 Edited by Kurtzman C. P., Boekhout T., Fell J. W. London: Elsevier; [CrossRef]
    [Google Scholar]
  22. Lee C. F., Yao C. H., Liu Y. R., Young S. S., Chang K. S. 2009; Kazachstania wufongensis sp. nov., an ascosporogenous yeast isolated from soil in Taiwan. Antonie van Leeuwenhoek 95:335–341 [View Article][PubMed]
    [Google Scholar]
  23. Lhomme E., Urien C., Legrand J., Dousset X., Onno B., Sicard D. 2016; Sourdough microbial community dynamics: an analysis during French organic bread-making processes. Food Microbiol 53:41–50 [View Article][PubMed]
    [Google Scholar]
  24. Liu Y. J., Whelen S., Hall B. D. 1999; Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Mol Biol Evol 16:1799–1808 [View Article][PubMed]
    [Google Scholar]
  25. Louis V. L., Despons L., Friedrich A., Martin T., Durrens P., Casarégola S., Neuvéglise C., Fairhead C., Marck C. et al. 2012; Pichia sorbitophila, an interspecies yeast hybrid, reveals early steps of genome resolution after polyploidization. G3 (Bethesda) 2:299–311 [View Article][PubMed]
    [Google Scholar]
  26. Mallet S., Weiss S., Jacques N., Leh-Louis V., Sacerdot C., Casaregola S. 2012; Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the Millerozyma (Pichia) farinosa species complex. PLoS One 7:e35842 [View Article][PubMed]
    [Google Scholar]
  27. Matheny P. B., Liu Y. J., Ammirati J. F., Hall B. D. 2002; Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am J Bot 89:688–698 [View Article][PubMed]
    [Google Scholar]
  28. McNeill J. 2012 International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code) Königstein: Koeltz Scientific Books;
    [Google Scholar]
  29. Minervini F., Lattanzi A., De Angelis M., Celano G., Gobbetti M. 2015; House microbiotas as sources of lactic acid bacteria and yeasts in traditional Italian sourdoughs. Food Microbiol 52:66–76 [View Article][PubMed]
    [Google Scholar]
  30. Nel E. E., van der Walt J. P. 1968; Torulopsis humilis, sp. n. Mycopathol Mycol Appl 36:94–96 [View Article][PubMed]
    [Google Scholar]
  31. Nguyen H. V., Gaillardin C., Neuvéglise C. 2009; Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis . FEMS Yeast Res 9:641–662 [View Article][PubMed]
    [Google Scholar]
  32. O'Donnell K. 1993; Fusarium and its relatives. In The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics pp. 225–233 Edited by Reynolds D. R., Taylor J. W. Wallingford, UK: CAB International;
    [Google Scholar]
  33. Perrière G., Gouy M. 1996; WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78:364–369 [View Article][PubMed]
    [Google Scholar]
  34. Pulvirenti A., Solieri L., Gullo M., De Vero L., Giudici P. 2004; Occurrence and dominance of yeast species in sourdough. Lett Appl Microbiol 38:113–117 [View Article][PubMed]
    [Google Scholar]
  35. Safar S. V., Gomes F. C., Marques A. R., Lachance M. A., Rosa C. A. 2013; Kazachstania rupicola sp. nov., a yeast species isolated from water tanks of a bromeliad in Brazil. Int J Syst Evol Microbiol 63:1165–1168 [View Article][PubMed]
    [Google Scholar]
  36. Solieri L., Dakal T. C., Croce M. A., Giudici P. 2013; Unravelling genomic diversity of Zygosaccharomyces rouxii complex with a link to its life cycle. FEMS Yeast Res 13:245–258 [View Article][PubMed]
    [Google Scholar]
  37. Suh S. O., Zhou J. J. 2011; Kazachstania intestinalis sp. nov., an ascosporogenous yeast from the gut of passalid beetle Odontotaenius disjunctus . Antonie van Leeuwenhoek 100:109–115 [View Article][PubMed]
    [Google Scholar]
  38. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  39. van der Walt J. P., Yarrow D. 1984; Methods for the isolation, maintenance, classification and identification of yeasts. In The Yeasts: A Taxonomic Study, 3rd edn. pp. 45–104 Edited by Kreger-van Rij N. J. W. Amsteredam: Elsevier; [CrossRef]
    [Google Scholar]
  40. Vardjan T., Mohar Lorbeg P., Rogelj I., Čanžek Majhenič A. 2013; Characterization and stability of lactobacilli and yeast microbiota in kefir grains. J Dairy Sci 96:2729–2736 [View Article][PubMed]
    [Google Scholar]
  41. Vaughan-Martini A. 1995; Saccharomyces barnetti and Saccharomyces spencerorum: two new species of Saccharomyces sensu lato (van der Walt). Antonie van Leeuwenhoek 68:111–118 [View Article][PubMed]
    [Google Scholar]
  42. Vaughan-Martini A., Lachance M.-A., Kurtzman C. P. 2011; Kazachstania Zubkova (1971). In The Yeast, a Taxonomic Study vol. 2 pp. 439–470 Edited by Kurtzman C. P., Boekhout T., Fell J. W. London: Elsevier; [CrossRef]
    [Google Scholar]
  43. Vigentini I., Antoniani D., Roscini L., Comasio A., Galafassi S., Picozzi C., Corte L., Compagno C., Dal Bello F. et al. 2014; Candida milleri species reveals intraspecific genetic and metabolic polymorphisms. Food Microbiol 42:72–81 [View Article][PubMed]
    [Google Scholar]
  44. Wang Q. M., Xu J., Wang H., Li J., Bai F. Y. 2009; Torulaspora quercuum sp. nov. and Candida pseudohumilis sp. nov., novel yeasts from human and forest habitats. FEMS Yeast Res 9:1322–1326 [View Article][PubMed]
    [Google Scholar]
  45. Weiss S., Samson F., Navarro D., Casaregola S. 2013; YeastIP: a database for identification and phylogeny of Saccharomycotina yeasts. FEMS Yeast Res 13:117–125 [View Article][PubMed]
    [Google Scholar]
  46. White T. J., Bruns T. D., Lee S., Taylor J. W. 1990; Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications pp. 315–322 Edited by Innis M. A., Gelfand D. H., Sninsky J., White T. J. San Diego: Academic press;
    [Google Scholar]
  47. Yarrow D. 1998; Methods for the isolation, maintenance and identification of yeasts. In The Yeasts, a Taxonomic Study pp. 77–100 Edited by Kurtzman C. P., Fell J. W. Amsterdam: Elsevier; [CrossRef]
    [Google Scholar]
  48. Yarrow D., Meyer S. A. 1978; Proposal for amendment of the diagnosis of the genus Candida berkhout nom. cons. Int J Syst Bacteriol 28:611–615 [View Article]
    [Google Scholar]
  49. Zubkova R. 1971; Genus novum Saccharomycetacearum e Kazachstania. Bot Mat Gerb Inst Bot an Kazahk SSR 7:53–56
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001495
Loading
/content/journal/ijsem/10.1099/ijsem.0.001495
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error