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Assessment of soil fungal communities using pyrosequencing

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Abstract

Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5′ region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.

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Authors and Affiliations

  1. National Institute of Biological Resource, Incheon, 404-708, Republic of Korea

    Young Woon Lim & Changmu Kim

  2. Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea

    Byung Kwon Kim

  3. School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 151-742, Republic of Korea

    Hack Sung Jung & Jongsik Chun

  4. Division of Microbiology, National Center for Toxicological Research/U.S.FDA, Jefferson, AR, 72079, USA

    Bong-Soo Kim

  5. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea

    Jae-Hak Lee & Jongsik Chun

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  1. Young Woon Lim
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Correspondence to Jongsik Chun.

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Lim, Y.W., Kim, B.K., Kim, C. et al. Assessment of soil fungal communities using pyrosequencing. J Microbiol. 48, 284–289 (2010). https://doi.org/10.1007/s12275-010-9369-5

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