MycorrhizaeV1, Main, Corpus, bibRecord, 001706

What goes in must come out: testing for biases in molecular analysis of arbuscular mycorrhizal fungal communities.

Identifieur interne : 001706 ( Main/Corpus ); précédent : 001705; suivant : 001707

What goes in must come out: testing for biases in molecular analysis of arbuscular mycorrhizal fungal communities.

Auteurs : T E Anne Cotton ; Alex J. Dumbrell ; Thorunn Helgason

Source :

PloS one [ 1932-6203 ] ; 2014.

RBID : pubmed:25275629

English descriptors

KwdEn :
- Genes, Fungal (MeSH), Mycorrhizae (genetics), Polymorphism, Restriction Fragment Length (MeSH).
MESH :
- genetics : Mycorrhizae.
- Genes, Fungal, Polymorphism, Restriction Fragment Length.

Abstract

Arbuscular mycorrhizal (AM) fungi are widely distributed microbes that form obligate symbioses with the majority of terrestrial plants, altering nutrient transfers between soils and plants, thereby profoundly affecting plant growth and ecosystem properties. Molecular methods are commonly used in the study of AM fungal communities. However, the biases associated with PCR amplification of these organisms and their ability to be utilized quantitatively has never been fully tested. We used Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis to characterise artificial community templates containing known quantities of defined AM fungal genotypes. This was compared to a parallel in silico analysis that predicted the results of this experiment in the absence of bias. The data suggest that when used quantitatively the TRFLP protocol tested is a powerful, repeatable method for AM fungal community analysis. However, we suggest some limitations to its use for population-level analyses. We found no evidence of PCR bias, supporting the quantitative use of other PCR-based methods for the study of AM fungi such as next generation amplicon sequencing. This finding greatly improves our confidence in methods that quantitatively examine AM fungal communities, providing a greater understanding of the ecology of these important fungi.

DOI: 10.1371/journal.pone.0109234
PubMed: 25275629
PubMed Central: PMC4183568

Links to Exploration step

pubmed:25275629

Le document en format XML

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<author><name sortKey="Cotton, T E Anne" sort="Cotton, T E Anne" uniqKey="Cotton T" first="T E Anne" last="Cotton">T E Anne Cotton</name>
<affiliation><nlm:affiliation>Department of Biology, University of York, York, United Kingdom; School of Biological Sciences, University of Essex, Colchester, United Kingdom.</nlm:affiliation>
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<author><name sortKey="Dumbrell, Alex J" sort="Dumbrell, Alex J" uniqKey="Dumbrell A" first="Alex J" last="Dumbrell">Alex J. Dumbrell</name>
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<author><name sortKey="Helgason, Thorunn" sort="Helgason, Thorunn" uniqKey="Helgason T" first="Thorunn" last="Helgason">Thorunn Helgason</name>
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<front><div type="abstract" xml:lang="en">Arbuscular mycorrhizal (AM) fungi are widely distributed microbes that form obligate symbioses with the majority of terrestrial plants, altering nutrient transfers between soils and plants, thereby profoundly affecting plant growth and ecosystem properties. Molecular methods are commonly used in the study of AM fungal communities. However, the biases associated with PCR amplification of these organisms and their ability to be utilized quantitatively has never been fully tested. We used Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis to characterise artificial community templates containing known quantities of defined AM fungal genotypes. This was compared to a parallel in silico analysis that predicted the results of this experiment in the absence of bias. The data suggest that when used quantitatively the TRFLP protocol tested is a powerful, repeatable method for AM fungal community analysis. However, we suggest some limitations to its use for population-level analyses. We found no evidence of PCR bias, supporting the quantitative use of other PCR-based methods for the study of AM fungi such as next generation amplicon sequencing. This finding greatly improves our confidence in methods that quantitatively examine AM fungal communities, providing a greater understanding of the ecology of these important fungi. </div>
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What goes in must come out: testing for biases in molecular analysis of arbuscular mycorrhizal fungal communities.

What goes in must come out: testing for biases in molecular analysis of arbuscular mycorrhizal fungal communities.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki