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From the same journal

What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities

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What Goes in Must Come out : Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities. / Cotton, T E Anne; Dumbrell, Alex J; Helgason, Thorunn.

In: PLoS ONE, Vol. 9, No. 10, e109234, 2014.

Research output: Contribution to journalArticle

Harvard

Cotton, TEA, Dumbrell, AJ & Helgason, T 2014, 'What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities', PLoS ONE, vol. 9, no. 10, e109234. https://doi.org/10.1371/journal.pone.0109234

APA

Cotton, T. E. A., Dumbrell, A. J., & Helgason, T. (2014). What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities. PLoS ONE, 9(10), [e109234]. https://doi.org/10.1371/journal.pone.0109234

Vancouver

Cotton TEA, Dumbrell AJ, Helgason T. What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities. PLoS ONE. 2014;9(10). e109234. https://doi.org/10.1371/journal.pone.0109234

Author

Cotton, T E Anne ; Dumbrell, Alex J ; Helgason, Thorunn. / What Goes in Must Come out : Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities. In: PLoS ONE. 2014 ; Vol. 9, No. 10.

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@article{8b02e9e45f8d47839e573fc397ec75c2,
title = "What Goes in Must Come out: Testing for Biases in Molecular Analysis of Arbuscular Mycorrhizal Fungal Communities",
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.",
author = "Cotton, {T E Anne} and Dumbrell, {Alex J} and Thorunn Helgason",
year = "2014",
doi = "10.1371/journal.pone.0109234",
language = "English",
volume = "9",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - What Goes in Must Come out

T2 - PLoS ONE

AU - Cotton, T E Anne

AU - Dumbrell, Alex J

AU - Helgason, Thorunn

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

U2 - 10.1371/journal.pone.0109234

DO - 10.1371/journal.pone.0109234

M3 - Article

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 10

M1 - e109234

ER -