Analysis of Arbuscular Mycorrhizal Fungal Communities by Terminal Restriction Fragment Length Polymorphism (TRFLP)
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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 wordsCommunity assembly Fingerprinting Operational taxonomic units Phylogenetic analyses R software TRAMPR package
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.
- 8.López-García Á, Palenzuela J, Barea JM, Azcón-Aguilar C (2014) Life-history strategies of arbuscular mycorrhizal fungi determine succession into roots of Rosmarinus officinalis L., a characteristic woody perennial plant species from Mediterranean ecosystems. Plant Soil 379:247–260CrossRefGoogle Scholar
- 15.Oksanen J, Blanchet FG, Kindt R et al (2011) Vegan: community ecology package. R package version 2.0-1. R Project. http://CRAN.R-project.org/package=vegan
- 17.Huson DH, Rupp R, Scornavacca C (2011) Phylogenetic networks: concepts, algorithms and applications. Cambridge University Press, CambridgeGoogle Scholar