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