Barcoded NS31/AML2 Primers for Sequencing of Arbuscular Mycorrhizal Communities in Environmental Samples

Benjamin S.T. Morgan, Louise M. Egerton-Warburton*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


Premise of the study: Arbuscular mycorrhizal fungi (AMF) are globally important root symbioses that enhance plant growth and nutrition and influence ecosystem structure and function. To better characterize levels of AMF diversity relevant to ecosystem function, deeper sequencing depth in environmental samples is needed. In this study, Illumina barcoded primers and a bioinformatics pipeline were developed and applied to study AMF diversity and community structure in environmental samples. Methods: Libraries of small subunit ribosomal RNA fragment amplicons were amplified from environmental DNA using a singlestep PCR reaction with barcoded NS31/AML2 primers. Amplicons were sequenced on an Illumina MiSeq sequencer using version 2, 2 × 250-bp paired-end chemistry, and analyzed using QIIME and RDP Classifier. Results: Sequencing captured 196 to 6416 operational taxonomic units (OTUs; depending on clustering parameters) representing nine AMF genera. Regardless of clustering parameters, ∼20 OTUs dominated AMF communities (78-87% reads) with the remaining reads distributed among other OTUs. Analyses also showed significant biogeographic differences in AMF communities and that community composition could be linked to specific edaphic factors. Discussion: Barcoded NS31/AML2 primers and Illumina MiSeq sequencing provide a powerful approach to address AMF diversity and variations in fungal assemblages across host plants, ecosystems, and responses to environmental drivers including global change.

Original languageEnglish (US)
Article number1700017
JournalApplications in Plant Sciences
Issue number8
StatePublished - Aug 2017


  • Glomeromycota
  • arbuscular mycorrhizal fungi
  • barcoding
  • community composition
  • diversity
  • tropical dry forest

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Plant Science


Dive into the research topics of 'Barcoded NS31/AML2 Primers for Sequencing of Arbuscular Mycorrhizal Communities in Environmental Samples'. Together they form a unique fingerprint.

Cite this