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Yeast diversity and novel yeast D1/D2 sequences from corn phylloplane obtained by a culture-independent approach

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Abstract

Culture-independent techniques have recently been used for evaluation of microbial diversity in the environment since it addresses the problem of unculturable microorganisms. In this study, the diversity of epiphytic yeasts from corn (Zea mays Linn.) phylloplanes in Thailand was investigated using this technique and sequence-based analysis of the D1/D2 domains of the large subunit ribosomal DNA sequences. Thirty-seven samples of corn leaf were collected randomly from 10 provinces. The DNA was extracted from leaf washing samples and the D1/D2 domains were amplified. The PCR products were cloned and then screened by colony PCR. A total of 1049 clones were obtained from 37 clone libraries. From this total, 329 clones (213 sequences) were closely related to yeast strains in the GenBank database, and they were clustered into 77 operational taxonomic units (OTUs) with a similarity threshold of 99 %. The majority of sequences (98.5 %) were classified into the phylum Basidiomycota. Sixteen known yeast species were identified. Interestingly, more than 65 % of the D1/D2 sequences obtained by this technique were suggested to be sequences from new yeast taxa. The predominant yeast sequences detected belonged to the order Ustilaginales with relative frequency of 68.0 %. The most common known yeast species detected on the leaf samples were Pseudozyma hubeiensis pro tem. and Moesziomyces antarcticus with frequency of occurrence of 24.3 and 21.6 %, respectively.

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Acknowledgments

Authors are grateful to Napakhwan Imklin for PCA analysis. We also thank Kevin Maskell for English language edition. This work was supported by the Thailand Research Fund and the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission.

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Authors and Affiliations

  1. Department of Biotechnology, Faculty of Engineering and Industrial Technology, Silpakorn University, Sanamchandra Palace Campus, Amphoe Muang, Nakhon Pathom, 73000, Thailand

    Rujikan Nasanit & Sopin Jaibangyang

  2. Central Laboratory and Greenhouse Complex, Faculty of Agriculture at Kamphaeng Sean, Kasetsart University, Kamphaeng Sean Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand

    Manee Tantirungkij

  3. Department of Microbiology, Faculty of Science, Kasetsart University, Jatujak, Bangkok, 10900, Thailand

    Savitree Limtong

  4. Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok, 10900, Thailand

    Savitree Limtong

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  1. Rujikan Nasanit
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  2. Sopin Jaibangyang
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  4. Savitree Limtong
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Correspondence to Savitree Limtong.

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Nasanit, R., Jaibangyang, S., Tantirungkij, M. et al. Yeast diversity and novel yeast D1/D2 sequences from corn phylloplane obtained by a culture-independent approach. Antonie van Leeuwenhoek 109, 1615–1634 (2016). https://doi.org/10.1007/s10482-016-0762-x

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