1887

Abstract

Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade. The novel species, Scheffersomyces stambukii f.a., sp. nov., is proposed to accommodate these isolates. The type strain of Scheffersomyces stambukii sp. nov. is UFMG-CM-Y427 (=CBS 14217). The MycoBank number is MB 824093. In addition, we studied the xylose metabolism of this new species.

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2018-05-22
2019-10-23
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References

  1. Kurtzman CP, Suzuki M. Phylogenetic analysis of ascomycete yeasts that form coenzyme Q-9 and the proposal of the new genera Babjeviella, Meyerozyma, Millerozyma, Priceomyces, and Scheffersomyces. Mycoscience 2010; 51: 2– 14 [CrossRef]
    [Google Scholar]
  2. Suh SO, Houseknecht JL, Gujjari P, Zhou JJ. Scheffersomyces parashehatae f.a., sp. nov., Scheffersomyces xylosifermentans f.a., sp. nov., Candida broadrunensis sp. nov. and Candida manassasensis sp. nov., novel yeasts associated with wood-ingesting insects, and their ecological and biofuel implications. Int J Syst Evol Microbiol 2013; 63: 4330– 4339 [CrossRef] [PubMed]
    [Google Scholar]
  3. Liu XJ, Cao WN, Ren YC, Xu LL, Yi ZH et al. Taxonomy and physiological characterisation of Scheffersomyces titanus sp. nov., a new d-xylose-fermenting yeast species from China. Sci Rep 2016; 6: 32181 [CrossRef] [PubMed]
    [Google Scholar]
  4. Cadete RM, Lopes MR, Rosa CA. Yeasts associated with decomposing plant material and rotting wood. In Buzzini P, Lachance MA, Yurkov A. (editors) Yeasts in Natural Ecosystems: Diversity Cham: Springer; 2017; pp. 265– 292 [Crossref]
    [Google Scholar]
  5. Urbina H, Blackwell M. Multilocus phylogenetic study of the Scheffersomyces yeast clade and characterization of the N-terminal region of xylose reductase gene. PLoS One 2012; 7: e39128 [CrossRef] [PubMed]
    [Google Scholar]
  6. 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 [CrossRef] [PubMed]
    [Google Scholar]
  7. 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 [CrossRef] [PubMed]
    [Google Scholar]
  8. Kurtzman CP, Fell JW, Boekhout T, Robert V. Methods for isolation, phenotypic characterization and maintenance of yeasts. In Kurtzman CP, Fell JW, Boekhout T. (editors) The Yeasts, A Taxonomic Study, 5th ed. Amsterdam: Elsevier; 2011; pp. 87– 110 [Crossref]
    [Google Scholar]
  9. White TJ, Bruns T, Lee S, Taylor JW. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis MA, Gelfand DH, Sninsky JJ, White TJ. (editors) PCR Protocols: A Guide to Methods and Applications San Diego, CA: Academic Press; 1990; pp. 315– 322
    [Google Scholar]
  10. O'Donnell K. Fusarium and its near relatives. In Reynolds DR, Taylor JW. (editors) The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematic Oregon: CAB International; 1993; pp. 225– 233
    [Google Scholar]
  11. Kurtzman CP, Robnett CJ. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 1998; 73: 331– 371 [CrossRef] [PubMed]
    [Google Scholar]
  12. 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 [CrossRef] [PubMed]
    [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  14. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403– 410 [CrossRef] [PubMed]
    [Google Scholar]
  15. 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 [CrossRef] [PubMed]
    [Google Scholar]
  16. Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 2007; 23: 1061– 1067 [CrossRef] [PubMed]
    [Google Scholar]
  17. 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 [CrossRef] [PubMed]
    [Google Scholar]
  18. Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011; 12: 491 [CrossRef] [PubMed]
    [Google Scholar]
  19. 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 [CrossRef] [PubMed]
    [Google Scholar]
  20. Smit AFA, Hubley R, Green P. 2015; RepeatMasker Open 4.0. 2013–2015. Institute for Systems Biology www.repeatmasker.org
  21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32: 1792– 1797 [CrossRef] [PubMed]
    [Google Scholar]
  22. 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 [CrossRef] [PubMed]
    [Google Scholar]
  23. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30: 1312– 1313 [CrossRef] [PubMed]
    [Google Scholar]
  24. Lachance MA. Paraphyly and (yeast) classification. Int J Syst Evol Microbiol 2016; 66: 4924– 4929 [CrossRef] [PubMed]
    [Google Scholar]
  25. Morais CG, Batista TM, Kominek J, Borelli BM, Furtado C et al. Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade. Int J Syst Evol Microbiol 2017; 67: 3798– 3805 [CrossRef] [PubMed]
    [Google Scholar]
  26. 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 [CrossRef] [PubMed]
    [Google Scholar]
  27. Haase MAB, Kominek J, Langdon QK, Kurtzman CP, Hittinger CT. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis. FEMS Yeast Res 2107; 17: fox019
    [Google Scholar]
  28. Urbina H, Frank R, Blackwell M. Scheffersomyces cryptocercus: a new xylose-fermenting yeast associated with the gut of wood roaches and new combinations in the Sugiyamaella yeast clade. Mycologia 2013; 105: 650– 660 [CrossRef] [PubMed]
    [Google Scholar]
  29. Agbogbo FK, Coward-Kelly G. Cellulosic ethanol production using the naturally occurring xylose-fermenting yeast, Pichia stipitis. Biotechnol Lett 2008; 30: 1515– 1524 [CrossRef] [PubMed]
    [Google Scholar]
  30. Okonkwo CC, Azam MM, Ezeji TC, Qureshi N. Enhancing ethanol production from cellulosic sugars using Scheffersomyces (Pichia) stipitis. Bioprocess Biosyst Eng 2016; 39: 1023– 1032 [CrossRef] [PubMed]
    [Google Scholar]
  31. Santos SC, de Sousa AS, Dionísio SR, Tramontina R, Ruller R et al. Bioethanol production by recycled Scheffersomyces stipitis in sequential batch fermentations with high cell density using xylose and glucose mixture. Bioresour Technol 2016; 219: 319– 329 [CrossRef] [PubMed]
    [Google Scholar]
  32. Wang X, Lewis Liu Z, Zhang X, Ma M. A new source of resistance to 2-furaldehyde from Scheffersomyces (Pichia) stipitis for sustainable lignocellulose-to-biofuel conversion. Appl Microbiol Biotechnol 2017; 101: 4981– 4993 [CrossRef] [PubMed]
    [Google Scholar]
  33. Cadete RM, Melo-Cheab MA, Viana AL, Oliveira ES, Fonseca C et al. The yeast Scheffersomyces amazonensis is an efficient xylitol producer. World J Microbiol Biotechnol 2016; 32: 207 [CrossRef] [PubMed]
    [Google Scholar]
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