ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards

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DOI

  • Andrea Berruti, UOS Torino, Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP-CNR), Natl Res Council, Inst Sustainable Plant Protect
  • ,
  • Alessandro Desiro, Michigan State Univ, Michigan State University, Dept Plant Soil & Microbial Sci
  • ,
  • Stefano Visentin
  • ,
  • Odoardo Zecca, Inst Agr Reg
  • ,
  • Paola Bonfante, Univ Turin, University of Turin, Dept Life Sci & Syst Biol

ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here, we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs. soil) and environment. Both methodologies made it possible to detect the same alpha-diversity trend among the locations under study but not between root and soil transects. We show that the ITS2 primer system for fungal barcoding provides a good estimate of both AMF community structure and relation to environmental variables. However, this primer system does not fit in with cross-compartment surveys (roots vs. soil) as it can underestimate AMF diversity in soil samples. When specifically focusing on AMF, the 18S primer system resulted in wide coverage and marginal non-target amplification.

Original languageEnglish
JournalEnvironmental Microbiology Reports
Volume9
Issue5
Pages (from-to)658-667
Number of pages10
ISSN1758-2229
DOIs
Publication statusPublished - Oct 2017

    Research areas

  • ARBUSCULAR MYCORRHIZAL FUNGI, INTERNAL TRANSCRIBED SPACER, GIGASPORA-MARGARITA, MOLECULAR DIVERSITY, SEQUENCE VARIATION, COMMUNITIES, GLOMEROMYCOTA, IDENTIFICATION, REGION, CLASSIFICATION

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