454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

Authors

  • Leho Tedersoo,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
    2. Natural History Museum of Tartu University, 46 Vanemuise Street, 51005 Tartu, Estonia
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    • These authors contributed equally to this work.

  • R. Henrik Nilsson,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
    2. Department of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
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    • These authors contributed equally to this work.

  • Kessy Abarenkov,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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  • Teele Jairus,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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  • Ave Sadam,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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  • Irja Saar,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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  • Mohammad Bahram,

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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  • Eneke Bechem,

    1. Department of Plant and Animal Sciences, University of Buea, PO Box 63, Buea, Cameroon
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  • George Chuyong,

    1. Department of Plant and Animal Sciences, University of Buea, PO Box 63, Buea, Cameroon
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  • Urmas Kõljalg

    1. Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
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Author for correspondence:
Leho Tedersoo
Tel: +372 7376222
Email: leho.tedersoo@ut.ee

Summary

  • Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood.
  • This study compares the performance of pyrosequencing and traditional sequencing for species’ recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses.
  • Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing.
  • Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz.

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