- Assessment of Soil Fungal Communities Using Pyrosequencing
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Young Woon Lim , Byung Kwon Kim , Changmu Kim , Hack Sung Jung , Bong-Soo Kim , Jae-Hak Lee , Jongsik Chun
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J. Microbiol. 2010;48(3):284-289. Published online June 23, 2010
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DOI: https://doi.org/10.1007/s12275-010-9369-5
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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 (mitosporic Ascomycota). 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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- Phylogenetic Relationships of the Aphyllophorales Inferred from Sequence Analysis of Nuclear Small Subunit Ribosomal DNA
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Seon Young Kim , Hack Sung Jung
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J. Microbiol. 2000;38(3):122-131.
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Abstract
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Phylogenetic classification of the Aphyllophorales was conducted based on the analysis of nuclear small subunit ribosomal RNA gene (nuc SSU rDNA) sequences. Based on phylogenetic groupings and taxonomic characters, 16 families were recognized and discussed. Although many of the characters had more or less homoplasies, microscopic characters such as the mitic system and clamp, spore amyloidity and rot type appeared to be important in the classification of the Aphyllophorales. Phylogenetically significant families were newly defined to improve the classification of the order Aphyllophorales.
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