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Pooled samples bias fungal community descriptions

Authors

  • P. G. AVIS,

    1. Department of Biology, Indiana University Northwest, Gary, IN, USA
    2. Department of Botany, The Field Museum of Natural History, Chicago, IL, USA
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  • S. BRANCO,

    1. Department of Botany, The Field Museum of Natural History, Chicago, IL, USA
    2. Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, USA
    3. Centro de Investigação de Montanha, Bragança, Portugal
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  • Y. TANG,

    1. Department of Botany, The Field Museum of Natural History, Chicago, IL, USA
    2. School of Forestry and Environmental Studies, Yale University, New Haven, CT, USA
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  • G. M. MUELLER

    1. Department of Botany, The Field Museum of Natural History, Chicago, IL, USA
    2. Committee on Evolutionary Biology, The University of Chicago, Chicago, IL, USA
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Peter G. Avis, Fax: 219 980 7125; E-mail: pavis@iun.edu

Abstract

We tested the accuracy of molecular analyses for recovering the species richness and structure of pooled fungal communities of known composition. We constructed replicate pools of 2–20 species and analysed these pools by two separate pooling-DNA extraction procedures and three different molecular analyses (Automated Ribosomal Intergenic Spacer Analysis (ARISA), terminal restriction fragment length polymorphism (T-RFLP) and clone library-sequencing). None of the methods correctly described the known communities. Only clone library-sequencing with high sequencing per pool (∼100 clones) recovered reasonable estimates of richness. Frequency data were skewed with all procedures and analyses. These results indicate that the error introduced by pooling samples is significant and problematic for ecological studies of fungal communities.

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