Development and validation of an oligonucleotide microarray to characterise ectomycorrhizal fungal communities.

BMC Microbiology
Marlis ReichMarc Buée

Abstract

In forest ecosystems, communities of ectomycorrhizal fungi (ECM) are influenced by several biotic and abiotic factors. To understand their underlying dynamics, ECM communities have been surveyed with ribosomal DNA-based sequencing methods. However, most identification methods are both time-consuming and limited by the number of samples that can be treated in a realistic time frame. As a result of ongoing implementation, the array technique has gained throughput capacity in terms of the number of samples and the capacity for parallel identification of several species. Thus far, although phylochips (microarrays that are used to detect species) have been mostly developed to trace bacterial communities or groups of specific fungi, no phylochip has been developed to carry oligonucleotides for several ectomycorrhizal species that belong to different genera. We have constructed a custom ribosomal DNA phylochip to identify ECM fungi. Specific oligonucleotide probes were targeted to the nuclear internal transcribed spacer (ITS) regions from 95 fungal species belonging to 21 ECM fungal genera. The phylochip was first validated using PCR amplicons of reference species. Ninety-nine percent of the tested oligonucleotides generated positive ...Continue Reading

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Citations

Nov 28, 2012·Environmental Science and Pollution Research International·Jessica U KegelLinda K Medlin
Oct 26, 2010·Trends in Microbiology·Francesca CappitelliClaudia Sorlini
Nov 18, 2018·Nature Reviews. Microbiology·R Henrik NilssonLeho Tedersoo

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Datasets Mentioned

BETA
FN545289
545352
GSM162978

Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

Analytic Rarefaction
phylochip
Phylochips
MultAlin
GenePix Pro
MEGAN
BLASTN
AmplifX
Sequencher

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