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High‐resolution community profiling of arbuscular mycorrhizal fungi
Author(s) -
Schlaeppi Klaus,
Bender S. Franz,
Mascher Fabio,
Russo Giancarlo,
Patrignani Andrea,
Camenzind Tessa,
Hempel Stefan,
Rillig Matthias C.,
Heijden Marcel G. A.
Publication year - 2016
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.14070
Subject(s) - biology , amplicon , ribosomal dna , dna sequencing , internal transcribed spacer , ribosomal rna , arbuscular mycorrhizal fungi , computational biology , amplicon sequencing , fungal diversity , botany , genetics , inoculation , dna , polymerase chain reaction , gene , phylogenetics , 16s ribosomal rna , horticulture
Summary 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 .