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f Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstania serrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov.

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  • Authors: Noémie Jacques1​ ,  Véronique Sarilar1​ ,  Charlotte Urien2​ ,  Mariana R. Lopes3​ ,  Camila G. Morais3​ ,  Ana Paula T. Uetanabaro4​ ,  Colin R. Tinsley1​ ,  Carlos A. Rosa3​ ,  Delphine Sicard5​ , Serge Casaregola1​
    • VIEW AFFILIATIONS
    • 1​ 1​Micalis Institute, INRA, AgroParisTech, CIRM-Levures, Université Paris-Saclay, 78350 Jouy-en-Josas, France 2​ 2​Génétique Quantitative et Evolution-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France 3​ 3​Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil 4​ 4​Departamento de Ciências Biológicas e Agroindústria, Universidade Estadual Santa Cruz, Ilhéus, BA 45662-900, Brazil 5​ 5​Sciences pour l’œnologie, INRA, Supagro, 34060 Montpellier, France
  • Correspondence Serge Casaregola [email protected]
  • First Published Online: 01 December 2016, International Journal of Systematic and Evolutionary Microbiology 66: 5192-5200, doi: 10.1099/ijsem.0.001495
  • Subject: New taxa - Eukaryotic micro-organisms
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Three novel ascomycetous yeast species of the Kazachstania clade, Kazachstania saulgeensis sp. nov., Kazachstania serrabonitensis sp. nov. and Kazachstania australis sp. nov. Reassignment of Candida humilis to Kazachstania humilis f.a. comb. nov. and Candida pseudohumilis to Kazachstania pseudohumilis f.a. comb. nov., Page 1 of 1

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  • Five ascosporogenous yeast strains related to the genus Kazachstania 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 Kazachstania exigua, but their ITS sequences diverged by 8.1 and 8.3 %, respectively, from that of the closest described species Kazachstania barnettii. Analysis of protein coding sequences of RPB1, RPB2 and EF-1α 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: Kazachstania saulgeensis sp. nov. (type strain CLIB 1764=CBS 14374) and Kazachstania serrabonitensis sp. nov. (type strain UFMG-CM-Y273=CLIB 1783=CBS 14236). Further analysis of culture collections revealed a strain previously assigned to the K. exigua species, but having 3.8 % difference (22 substitutions and 2 indels) in its ITS with respect to K. exigua. Hence, we describe a new taxon, Kazachstania australis sp. nov. (type strain CLIB 162=CBS 2141), to accommodate this strain. Finally, Candida humilis and Candida pseudohumilis are reassigned to the genus Kazachstania as new combinations. On the basis of sequence analysis, we also propose that Candida milleri and Kazachstania humilis comb. nov. are conspecific.

  • The GenBank/EMBL/DDBJ accession numbers for the sequences determined in this study are KF582608–KF582610, LT158238, LT158239, LT158241, LT158244, LT158246–LT158251, LT158253, LT158254, LT158258, LT158259, LT158261, LT158262, LT158264–LT158271, LT158273–LT158276, LT158278, LT158280, LT158282–LT158284 and LT594998–LT595004, see Table S1 (available in the online Supplementary Material) for details. The Mycobank (http://www.mycobank.org) accession numbers for Kazachstania saulgeensis sp. nov., Kazachstania serrabonitensis sp. nov., Kazachstania australis sp. nov., Kazachstania humilis f.a. comb. nov. and Kazachstania pseudohumilis f.a. comb. nov. are, respectively, MB 815524, MB 815525, MB 815523, MB 815526 and MB 815527.

  • Two supplementary tables are available with the online Supplementary Material.

  • Abbreviations:
    EF-1α translation elongation factor-1α
    ITS internal transcribed spacer
    LSU large subunit

© 2016 IUMS | Published by the Microbiology Society

  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • Barnett J. A., Payne R. W., Yarrow D..( 2000;). Yeasts: Characteristics and Identification, , 3rd edn.. Cambridge:: Cambridge University Press;.
     [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • Gordon J. L., Wolfe K. H..( 2008;). Recent allopolyploid origin of Zygosaccharomyces rouxii strain ATCC 42981. . Yeast 25: 449––456. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • Katoh K., Standley D. M..( 2016;). A simple method to control over-alignment in the MAFFT multiple sequence alignment program. . Bioinformatics 32: 1933––1942. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • 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]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • McNeill J..( 2012;). International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code) . Königstein:: Koeltz Scientific Books;.
     [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • Nel E. E., van der Walt J. P..( 1968;). Torulopsis humilis, sp. n. . Mycopathol Mycol Appl 36: 94––96. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • Perrière G., Gouy M..( 1996;). WWW-query: an on-line retrieval system for biological sequence banks. . Biochimie 78: 364––369. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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. [CrossRef] [PubMed]
    [Google Scholar]
  • 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]
  • 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]
  • 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. [CrossRef]
    [Google Scholar]
  • Zubkova R..( 1971;). Genus novum Saccharomycetacearum e Kazachstania. . Bot Mat Gerb Inst Bot an Kazahk SSR 7: 53––56.
     [Google Scholar]
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