Mycorrhiza

, Volume 16, Issue 8, pp 525–531

Rationalizing molecular analysis of field-collected roots for assessing diversity of arbuscular mycorrhizal fungi: to pool, or not to pool, that is the question

Original Paper

DOI: 10.1007/s00572-006-0067-4

Cite this article as:
Renker, C., Weißhuhn, K., Kellner, H. et al. Mycorrhiza (2006) 16: 525. doi:10.1007/s00572-006-0067-4

Abstract

For rationalizing molecular analysis of field-collected roots in diversity studies on arbuscular mycorrhiza, we compared three different approaches. After DNA extraction from 50 root samples of Plantago lanceolata grown on monoculture plots at a former arable field site, (1) DNAs were amplified separately by nested PCR and each amplicon was cloned separately; (2) DNAs were amplified separately by nested PCR, 1 μl of each amplicon was pooled, and a single cloning was made from the resulting amplicons mix; and (3) DNAs were pooled and the single amplicon derived from the nested PCR was cloned. Based on these three different methods, 109 nuclear ribosomal internal transcribed spacer sequences were obtained. Methods 1 and 2 enabled the detection of almost similar levels of arbuscular mycorrhizal fungal diversity. However, method 1 was expensive and time-consuming as much more cloning had to be done. Method 3 was completely biased by preferential amplification of nontarget organisms, which were only detected in low frequencies by the other methods.

Keywords

Arbuscular mycorrhizal fungi DNA extraction PCR bias Preferential amplification 

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • C. Renker
    • 1
    • 2
  • K. Weißhuhn
    • 1
    • 3
  • H. Kellner
    • 1
    • 2
  • F. Buscot
    • 1
    • 2
  1. 1.Terrestrial Ecology, Institute of Biology IUniversity of LeipzigLeipzigGermany
  2. 2.Department of Soil EcologyUFZ Centre for Environmental Research Leipzig-Halle Ltd.HalleGermany
  3. 3.Department of Community EcologyUFZ Centre for Environmental Research Leipzig-Halle Ltd.HalleGermany

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