sp. nov., a -xylose-fermenting species in the clade Free

Abstract

Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to , in a clade that also contains and . Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger / clade. One interpretation is that the genus is, in fact, paraphyletic. In conformity with this view, we propose the novel species sp. nov. to accommodate the isolates. The type strain of sp. nov. is UFMG-CM-Y306 (=CBS 13262). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002186
2017-10-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/10/3798.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002186&mimeType=html&fmt=ahah

References

  1. Nguyen NH, Suh S-O, Blackwell M. Spathaspora N. H. Nguyen, S.-O. Suh & M. Blackwell (2006). In Kurtzman CP, Fell JW, Boekhout T. (editors) The Yeasts: A Taxonomic Study Amsterdam: Elsevier Science; 2011 pp. 795–797 [Crossref]
    [Google Scholar]
  2. Daniel HM, Lachance MA, Kurtzman CP. On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription. Antonie van Leeuwenhoek 2014; 106:67–84 [View Article][PubMed]
    [Google Scholar]
  3. Lopes MR, Morais CG, Kominek J, Cadete RM, Soares MA et al. Genomic analysis and d-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov. FEMS Yeast Res 2016; 16:fow044 [View Article][PubMed]
    [Google Scholar]
  4. Cadete RM, Melo MA, Zilli JE, Vital MJ, Mouro A et al. Spathaspora brasiliensis sp. nov., Spathaspora suhii sp. nov., Spathaspora roraimanensis sp. nov. and Spathaspora xylofermentans sp. nov., four novel D-xylose-fermenting yeast species from Brazilian Amazonian forest. Antonie van Leeuwenhoek 2013; 103:421–431 [View Article][PubMed]
    [Google Scholar]
  5. Wang Y, Ren YC, Zhang ZT, Ke T, Hui FL. Spathaspora allomyrinae sp. nov., a D-xylose-fermenting yeast species isolated from a scarabeid beetle Allomyrina dichotoma . Int J Syst Evol Microbiol 2016; 66:2008–2012 [View Article][PubMed]
    [Google Scholar]
  6. Lachance MA. Paraphyly and (yeast) classification. Int J Syst Evol Microbiol 2016; 66:4924–4929 [View Article][PubMed]
    [Google Scholar]
  7. Guamán-Burneo MC, Dussán KJ, Cadete RM, Cheab MA, Portero P et al. Xylitol production by yeasts isolated from rotting wood in the Galápagos Islands, Ecuador, and description of Cyberlindnera galapagoensis f.a., sp. nov. Antonie van Leeuwenhoek 2015; 108:919–931 [View Article][PubMed]
    [Google Scholar]
  8. Kurtzman CP, Fell JW, Boekhout T, Roberts V. Methods for isolation, phenotypic characterization and maintenance of yeasts. In Kurtzman CP, Fell JW, Boekhout T. (editors) The Yeasts: A Taxonomic Study Amsterdam: Elsevier Science; 2011 pp. 87–110 [Crossref]
    [Google Scholar]
  9. Rosa CA, Lachance MA, Teixeira LC, Pimenta RS, Morais PB. Metschnikowia cerradonensis sp. nov., a yeast species isolated from ephemeral flowers and their nitidulid beetles in Brazil. Int J Syst Evol Microbiol 2007; 57:161–165 [View Article][PubMed]
    [Google Scholar]
  10. Kurtzman CP, Robnett CJ. Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species. FEMS Yeast Res 2013; 13:23–33 [View Article][PubMed]
    [Google Scholar]
  11. Lachance MA, Bowles JM, Starmer WT, Barker JS. Kodamaea kakaduensis and Candida tolerans, two new ascomycetous yeast species from Australian Hibiscus flowers. Can J Microbiol 1999; 45:172–177 [View Article][PubMed]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets Mol Biol Evol ; 2016; 331870–1874
  13. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  14. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  15. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007; 23:1061–1067 [View Article][PubMed]
    [Google Scholar]
  16. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 2015; 31:3210–3212 [View Article][PubMed]
    [Google Scholar]
  17. Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011; 12:491 [View Article][PubMed]
    [Google Scholar]
  18. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article][PubMed]
    [Google Scholar]
  19. Smit AFA, Hubley R, Green P. 2013; RepeatMasker Open 4.0. www.repeatmasker.org
  20. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  21. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
    [Google Scholar]
  22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  23. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article][PubMed]
    [Google Scholar]
  24. Cadete RM, de Las Heras AM, Sandström AG, Ferreira C, Gírio F et al. Exploring xylose metabolism in Spathaspora species: XYL1.2 from Spathaspora passalidarum as the key for efficient anaerobic xylose fermentation in metabolic engineered Saccharomyces cerevisiae . Biotechnol Biofuels 2016; 9:167 [View Article][PubMed]
    [Google Scholar]
  25. Kurtzman CP, Fell JW, Boekhout T, Roberts V. (editors) The Yeasts: A Taxonomic Study Amsterdam: Elsevier Science; 2011
    [Google Scholar]
  26. Cadete RM, Santos RO, Melo MA, Mouro A, Gonçalves DL et al. Spathaspora arborariae sp. nov., a D-xylose-fermenting yeast species isolated from rotting wood in Brazil. FEMS Yeast Res 2009; 9:1338–1342 [View Article][PubMed]
    [Google Scholar]
  27. Cadete RM, Melo MA, Dussán KJ, Rodrigues RC, Silva SS et al. Diversity and physiological characterization of D-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest. PLoS One 2012; 7:e43135 [View Article][PubMed]
    [Google Scholar]
  28. da Cunha-Pereira F, Hickert LR, Sehnem NT, de Souza-Cruz PB, Rosa CA et al. Conversion of sugars present in rice hull hydrolysates into ethanol by Spathaspora arborariae, Saccharomyces cerevisiae, and their co-fermentations. Bioresour Technol 2011; 102:4218–4225 [View Article][PubMed]
    [Google Scholar]
  29. Hickert LR, de Souza-Cruz PB, Rosa CA, Ayub MA. Simultaneous saccharification and co-fermentation of un-detoxified rice hull hydrolysate by Saccharomyces cerevisiae ICV D254 and Spathaspora arborariae NRRL Y-48658 for the production of ethanol and xylitol. Bioresour Technol 2013; 143:112–116 [View Article][PubMed]
    [Google Scholar]
  30. Nguyen NH, Suh SO, Marshall CJ, Blackwell M. Morphological and ecological similarities: wood-boring beetles associated with novel xylose-fermenting yeasts, Spathaspora passalidarum gen. sp. nov. and Candida Jeffriesii sp. nov. Mycol Res 2006; 110:1232–1241 [View Article][PubMed]
    [Google Scholar]
  31. Cadete RM, Cheab MA, Santos RO, Safar SV, Zilli JE et al. Cyberlindnera xylosilytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials. Int J Syst Evol Microbiol 2015; 65:2968–2974 [View Article][PubMed]
    [Google Scholar]
  32. Hou X. Anaerobic xylose fermentation by Spathaspora passalidarum . Appl Microbiol Biotechnol 2012; 94:205–214 [View Article][PubMed]
    [Google Scholar]
  33. Long TM, Su YK, Headman J, Higbee A, Willis LB et al. Cofermentation of glucose, xylose, and cellobiose by the beetle-associated yeast Spathaspora passalidarum . Appl Environ Microbiol 2012; 78:5492–5500 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002186
Loading
/content/journal/ijsem/10.1099/ijsem.0.002186
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed