title: High-resolution community profiling of arbuscular mycorrhizal fungi.
abstract: Community analyses of arbuscular mycorrhizal fungi (AMF) using ribosomal small subunit (SSU) or internal transcribed spacer (ITS) DNA sequences often suffer from low resolution or coverage. We developed a novel sequencing based approach for a highly resolving and specific profiling of AMF communities. We took advantage of previously established AMF-specific PCR primers that amplify a c. 1.5-kb long fragment covering parts of SSU, ITS and parts of the large ribosomal subunit (LSU), and we sequenced the resulting amplicons with single molecule real-time (SMRT) sequencing. The method was applicable to soil and root samples, detected all major AMF families and successfully discriminated closely related AMF species, which would not be discernible using SSU sequences. In inoculation tests we could trace the introduced AMF inoculum at the molecular level. One of the introduced strains almost replaced the local strain(s), revealing that AMF inoculation can have a profound impact on the native community. The methodology presented offers researchers a powerful new tool for AMF community analysis because it unifies improved specificity and enhanced resolution, whereas the drawback of medium sequencing throughput appears of lesser importance for low-diversity groups such as AMF.
authors.affiliation: Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland. klaus.schlaeppi@agroscope.admin.ch.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schlaeppi
authors.affiliation: Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
authors.forename: S Franz
authors.initials: SF
authors.lastname: Bender
authors.affiliation: Plant Breeding and Genetic Resources, Institute for Plant Production Sciences, Agroscope, Route de Duillier 50, 1260, Nyon, Switzerland.
authors.forename: Fabio
authors.initials: F
authors.lastname: Mascher
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Russo
authors.affiliation: Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Patrignani
authors.affiliation: Plant Ecology, Institute of Biology, Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.|Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.
authors.forename: Tessa
authors.initials: T
authors.lastname: Camenzind
authors.affiliation: Plant Ecology, Institute of Biology, Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.|Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hempel
authors.affiliation: Plant Ecology, Institute of Biology, Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.|Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Freie Universität Berlin, Altensteinstraße 6, 14195, Berlin, Germany.
authors.forename: Matthias C
authors.initials: MC
authors.lastname: Rillig
authors.affiliation: Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland. marcel.vanderheijden@agroscope.admin.ch.|Plant-Microbe-Interactions, Department of Biology, Utrecht University, 3508TB, Utrecht, the Netherlands. marcel.vanderheijden@agroscope.admin.ch.|Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. marcel.vanderheijden@agroscope.admin.ch.
authors.forename: Marcel G A
authors.initials: MG
authors.lastname: van der Heijden
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D055137:Glomeromycota / Q000502:physiology*; D038821:Mycorrhizae / Q000502:physiology*; D009876:Operon / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D004271:DNA, Fungal; D012335:RNA, Ribosomal
keywords: AMF community analyses; AMF inoculation; Glomeromycota diversity; arbuscular mycorrhizal fungi (AMF); microbiome; single molecule real-time (SMRT) sequencing