Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi.
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.
Biology University of British Columbia Okanagan, Kelowna, BC, Canada.
Miranda M
MM
Hart
Biology University of British Columbia Okanagan, Kelowna, BC, Canada.
Kristin
K
Aleklett
Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada.
Pierre-Luc
PL
Chagnon
Biology University of British Columbia Okanagan, Kelowna, BC, Canada.
Cameron
C
Egan
Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy.
Stefano
http://orcid.org/0000-0002-2033-2286
S
Ghignone
Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
Thorunn
T
Helgason
MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA.
Ylva
Y
Lekberg
Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia.
Maarja
http://orcid.org/0000-0001-8025-7460
M
Öpik
Biology University of British Columbia Okanagan, Kelowna, BC, Canada.
Brian J
BJ
Pickles
Division of Biological Sciences, University of Montana, Missoula, MT, USA.
Lauren
L
Waller
D058448:Biota / Q000235:genetics*; D019295:Computational Biology; D004271:DNA, Fungal / Q000235:genetics; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008954:Models, Biological; D038821:Mycorrhizae / Q000235:genetics*; D013048:Specimen Handling
D004271:DNA, Fungal
PCR; arbuscular mycorrhizal fungi (AMF); bioinformatics; environmental sequencing; next generation sequencing (NGS)