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Analysis of Arbuscular Mycorrhizal Fungal Communities by Terminal Restriction Fragment Length Polymorphism (TRFLP)

  • Álvaro López-GarcíaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2146)

Abstract

Terminal restriction fragment length polymorphism (TRFLP) approaches enable the detection and identification of microbial taxa into samples coming from root or soil material DNA extraction. The low taxonomic diversity of arbuscular mycorrhizal (AM) fungi makes this technique a cheap and adequate method for fingerprinting their communities. Here, I describe the TRFLP database approach, a version of the technique in which the AM fungal taxa present in the sample pool is identified for, later, match their presence in the different samples contained in the experiment. A final AM fungal operational taxonomic unit x sample presence–absence matrix is obtained, which allows the subsequent multivariate statistical analysis of the experimental results.

Key words

Community assembly Fingerprinting Operational taxonomic units Phylogenetic analyses R software TRAMPR package 

Notes

Acknowledgments

The author was supported by Spanish government under the Plan Nacional de I+D+I (project CGL2015-69118-C2-2-P-COEXMED-II) and University of Jaén (Spain) under the Plan 6-UJA postdoctoral fellowship.

Supplementary material

470476_1_En_10_MOESM1_ESM.txt (57 kb)
Data 1 (TXT 57 kb)
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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Soil Microbiology and Symbiotic SystemsEstación Experimental del Zaidín, CSICGranadaSpain
  2. 2.Department of Animal Biology, Plant Biology and EcologyUniversidad de JaénJaénSpain

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