TY - JOUR
T1 - Barcoded NS31/AML2 Primers for Sequencing of Arbuscular Mycorrhizal Communities in Environmental Samples
AU - Morgan, Benjamin S.T.
AU - Egerton-Warburton, Louise M.
N1 - Funding Information:
1Manuscript received 27 February 2017; revision accepted 17 June 2017. The authors thank M. Orvañanos, M. Lazcano Barrero, and L. Leal for site access; M. Öpik for sharing MaarjAM resources; and J. Gilbert and S. Owens (Argonne National Laboratory) for technical advice and Illumina sequencing, respectively. This research was funded by a grant to L.M.E.W. from the Institute for Sustainability and Energy at Northwestern University. 4Author for correspondence: lwarburton@chicagobotanic.org
PY - 2017/8
Y1 - 2017/8
N2 - 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.
AB - 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.
KW - Glomeromycota
KW - arbuscular mycorrhizal fungi
KW - barcoding
KW - community composition
KW - diversity
KW - tropical dry forest
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U2 - 10.3732/apps.1700017
DO - 10.3732/apps.1700017
M3 - Article
C2 - 28924511
AN - SCOPUS:85028325621
VL - 5
JO - Applications in Plant Sciences
JF - Applications in Plant Sciences
SN - 2168-0450
IS - 8
M1 - 1700017
ER -