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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ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards. / Berruti, Andrea; Desiro, Alessandro; Visentin, Stefano; Zecca, Odoardo; Bonfante, Paola.

I: Environmental Microbiology Reports, Bind 9, Nr. 5, 10.2017, s. 658-667.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Berruti, A, Desiro, A, Visentin, S, Zecca, O & Bonfante, P 2017, 'ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards', Environmental Microbiology Reports, bind 9, nr. 5, s. 658-667. https://doi.org/10.1111/1758-2229.12574

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Berruti, Andrea ; Desiro, Alessandro ; Visentin, Stefano ; Zecca, Odoardo ; Bonfante, Paola. / ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards. I: Environmental Microbiology Reports. 2017 ; Bind 9, Nr. 5. s. 658-667.

Bibtex

@article{249bcca99b8b48b1888bce8ea9d13bca,
title = "ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards",
abstract = "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.",
keywords = "ARBUSCULAR MYCORRHIZAL FUNGI, INTERNAL TRANSCRIBED SPACER, GIGASPORA-MARGARITA, MOLECULAR DIVERSITY, SEQUENCE VARIATION, COMMUNITIES, GLOMEROMYCOTA, IDENTIFICATION, REGION, CLASSIFICATION",
author = "Andrea Berruti and Alessandro Desiro and Stefano Visentin and Odoardo Zecca and Paola Bonfante",
year = "2017",
month = "10",
doi = "10.1111/1758-2229.12574",
language = "English",
volume = "9",
pages = "658--667",
journal = "Environmental Microbiology Reports",
issn = "1758-2229",
publisher = "John Wiley & Sons, Inc.",
number = "5",

}

RIS

TY - JOUR

T1 - ITS fungal barcoding primers versus 18S AMF-specific primers reveal similar AMF-based diversity patterns in roots and soils of three mountain vineyards

AU - Berruti, Andrea

AU - Desiro, Alessandro

AU - Visentin, Stefano

AU - Zecca, Odoardo

AU - Bonfante, Paola

PY - 2017/10

Y1 - 2017/10

N2 - 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.

AB - 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.

KW - ARBUSCULAR MYCORRHIZAL FUNGI

KW - INTERNAL TRANSCRIBED SPACER

KW - GIGASPORA-MARGARITA

KW - MOLECULAR DIVERSITY

KW - SEQUENCE VARIATION

KW - COMMUNITIES

KW - GLOMEROMYCOTA

KW - IDENTIFICATION

KW - REGION

KW - CLASSIFICATION

U2 - 10.1111/1758-2229.12574

DO - 10.1111/1758-2229.12574

M3 - Journal article

C2 - 28799720

VL - 9

SP - 658

EP - 667

JO - Environmental Microbiology Reports

JF - Environmental Microbiology Reports

SN - 1758-2229

IS - 5

ER -