K SCHLAEPPI¹, F BENDER¹, M VAN DER HEIJDEN<sup>1

1</sup>Plant-Soil-Interactions, Institute for Sustainability Sciences, Agroscope, Zürich, Switzerland

Community analyses of arbuscular mycorrhizal fungal (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 AMF-specific PCR primers that amplify an ~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 discriminated successfully closely related AMF species, which would not be discernible using SSU sequences. In inoculation tests we could separate the strain of the introduced AMF species (Rhizoglomus irregulare) from the strains of the native community, indicating resolution at strain level. Further, the introduced strain almost replaced the local strain(s) revealing that AMF inoculation can have a profound impact on the native community. The presented methodology offers researchers a powerful new tool for AMF community analysis because it unifies high specificity and enhanced resolution while the drawback of medium sequencing throughput appears of lesser importance for low-diversity groups such as AMF.