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

Cotton, TEA and Dumbrell, AJ and Helgason, T (2014) 'What goes in must come out: Testing for biases in molecular analysis of arbuscular mycorrhizal fungal communities.' PLoS ONE, 9 (10). ISSN 1932-6203

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Abstract

© 2014 Cotton et al. 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.

Item Type: Article
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Science and Health > Life Sciences, School of
Depositing User: Jim Jamieson
Date Deposited: 10 Feb 2015 12:24
Last Modified: 29 Aug 2019 21:15
URI: http://repository.essex.ac.uk/id/eprint/12775

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