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Volume 73, Issue 10

sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome Open Access

Abstract

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus . A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing , , , , and , but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with , from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to and sp. TF2021a (=). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name sp. nov. is proposed to accommodate the novel species. The holotype of is CBS 16589. The MycoBank number is MB849369. was able to kill cells of by means of penetration with infection pegs, a trait common to most species of .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Amazonian Forest , predacious yeast , Saccharomycopsis praedatoria sp. nov. and soil
Funding
This study was supported by the:
  • Wisconsin Alumni Research Foundation
    • Principle Award Recipient: ChrisTodd Hittinger
  • National Institute of Food and Agriculture (Award 1020204)
    • Principle Award Recipient: ChrisTodd Hittinger
  • National Science Foundation (Award DEB-2110403)
    • Principle Award Recipient: ChrisTodd Hittinger
  • Great Lakes Bioenergy Research Center (Award DE-SC0018409)
    • Principle Award Recipient: ChrisTodd Hittinger
  • Natural Science and Engineering Research Council of Canada (Award Discovery Grants)
    • Principle Award Recipient: Marc-AndréLachance
  • Fundação de Amparo à Pesquisa do Estado de Minas Gerais (Award APQ-01525-14, APQ-01477-13 and APQ-02552-15)
    • Principle Award Recipient: CarlosA. Rosa
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (Award #406564/2022-1, 0457499/2014-1, 313088/2020-9, and 408733/2021)
    • Principle Award Recipient: CarlosA. Rosa
  • Fundação de Amparo à Pesquisa do Estado de Minas Gerais (Award APQ-01525-14, APQ-01477-13 and APQ-02552-15)
    • Principle Award Recipient: CarlosA. Rosa
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-10-31
2024-05-08
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References

  1. Kurtzman CP, Smith MT. Kurtzman CP, Fell JW, Boekhout T. Saccharomycopis Schioning (1903). In The Yeasts, a Taxonomic Study, 5th. edn Amsterdam: Elsevier; 2011 pp 751–763
     [Google Scholar]
  2. Jacques N, Louis-Mondesir C, Coton M, Coton E, Casaregola S. Two novel Saccharomycopsis species isolated from black olive brines and a tropical plant. Description of Saccharomycopsis olivae f. a., sp. nov. and Saccharomycopsis guyanensis f. a., sp. nov. Reassignment of Candida amapae to Saccharomycopsis amapae f. a., comb. nov., Candida lassenensis to Saccharomycopsis lassenensis f. a., comb. nov. and Arthroascus babjevae to Saccharomycopsis babjevae f. a., comb. nov.. Int J Syst Evol Microbiol. 2014; 64:2169–2175 [View Article] [PubMed]
     [Google Scholar]
  3. Yuan X, Peng K, Li C, Zhao Z, Zeng X et al. Complete genomic characterization and identification of Saccharomycopsisphalluae sp. nov., a novel pathogen causes yellow rot disease on Phallus rubrovolvatus. J Fungi 2021; 7:707 [View Article] [PubMed]
     [Google Scholar]
  4. Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen XX et al. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 2023; 105:181–202 [View Article]
     [Google Scholar]
  5. Pimenta RS, Silva JFM, Coelho CM, Morais PB, Rosa CA et al. Integrated control of Penicillium digitatum by the predacious yeast Saccharomycopsis crataegensis and sodium bicarbonate on oranges. Braz J Microbiol 2010; 41:404–410 [View Article] [PubMed]
     [Google Scholar]
  6. Iacumin L, Manzano M, Andyanto D, Comi G. Biocontrol of ochratoxigenic moulds (Aspergillus ochraceus and Penicillium nordicum) by Debaryomyces hansenii and Saccharomycopsis fibuligera during speck production. Food Microbiol 2017; 62:188–195 [View Article] [PubMed]
     [Google Scholar]
  7. Lachance MA, Pang WM. Predacious yeasts. Yeast 1997; 13:225–232 [View Article] [PubMed]
     [Google Scholar]
  8. Lachance MA, Pupovac-Velikonja A, Natarajan S, Schlag-Edler B. Nutrition and phylogeny of predacious yeasts. Can J Microbiol 2000; 46:495–505 [View Article] [PubMed]
     [Google Scholar]
  9. Lachance MA, Rosa CA, Carvajal EJ, Freitas LFD, Bowles JM. Saccharomycopsis fodiens sp. nov., a rare predacious yeast from three distant localities. Int J Syst Evol Microbiol 2012; 62:2793–2798 [View Article] [PubMed]
     [Google Scholar]
  10. Junker K, Bravo Ruiz G, Lorenz A, Walker L, Gow NAR et al. The mycoparasitic yeast Saccharomycopsis schoenii predates and kills multi-drug resistant Candida auris. Sci Rep 2018; 8:14959 [View Article] [PubMed]
     [Google Scholar]
  11. Barros KO, Alvarenga FBM, Magni G, Souza GFL, Abegg MA et al. The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species. Yeast 2023; 40:84–101 [View Article] [PubMed]
     [Google Scholar]
  12. Kurtzman CP, Fell JW, Boekhout T, Robert V. Methods for isolation, phenotypic characterization and maintenance of yeasts. In Kurtzman CP, Fell JW, Boekhout T. eds The Yeasts, a Taxonomic Study, 5th edn. Amsterdam: Elsevier; 2011 pp 87–110
     [Google Scholar]
  13. 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. eds PCR Protocols: A Guide to Methods and Applications San Diego: Academic Press; 1990 pp 315–322
     [Google Scholar]
  14. O’Donnell K. Fusarium and its near relatives. In Reynolds DR, Taylor JW. eds The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematic vol 604 Oregon: CAB International; 1993 pp 225–233
     [Google Scholar]
  15. Lachance MA, Bowles JM, Starmer WT, Barker JSF. 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]
  16. 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 [View Article] [PubMed]
     [Google Scholar]
  17. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic Local Alignment Search Tool. J Mol Biol 1990; 21:403–410 [View Article] [PubMed]
     [Google Scholar]
  19. Shen X-X, Opulente DA, Kominek J, Zhou X, Steenwyk JL et al. Tempo and mode of genome evolution in the budding yeast subphylum. Cell 2018; 175:1533–1545 [View Article] [PubMed]
     [Google Scholar]
  20. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Mikheenko A, Prjibelski A, Saveliev V, Antipov D, Gurevich A. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 2018; 34:i142–i150 [View Article] [PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 2021; 38:4647–4654 [View Article] [PubMed]
     [Google Scholar]
  26. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004; 5:113 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. Corrigendum to: IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
     [Google Scholar]
  29. Lachance M-A, Lee DK, Hsiang T. Delineating yeast species with genome average nucleotide identity: a calibration of ANI with haplontic, heterothallic Metschnikowia species. Antonie van Leeuwenhoek 2020; 113:2097–2106 [View Article] [PubMed]
     [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  31. Saraiva JP, Bartholomäus A, Toscan RB, Baldrian P, Nunes da Rocha U. Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes. Mol Ecol Resour 2023; 23:1066–1076 [View Article] [PubMed]
     [Google Scholar]
  32. Freitas LFD, Batista TM, Santos ARO, Hilário HO, Moreira RG et al. Yeast communities associated with cacti in Brazil and the description of Kluyveromyces starmeri sp. nov. based on phylogenomic analyses. Yeast 2020; 37:625–637 [View Article] [PubMed]
     [Google Scholar]
  33. Groenewald M, Lombard L, de Vries M, Lopez AG, Smith M et al. Diversity of yeast species from dutch garden soil and the description of six novel Ascomycetes. FEMS Yeast Res 2018; 18: [View Article] [PubMed]
     [Google Scholar]
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Saccharomycopsis praedatoria sp. nov., a predacious yeast isolated from soil and rotten wood in an Amazonian rainforest biome
Int J Syst Evol Microbiol 73, 006125 (2023); https://doi.org/10.1099/ijsem.0.006125
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