Comparison of 454 and Illumina sequencing methods to study arbuscular mycorrhizal fungal community diversity

We identified AMF in root samples by sequencing metagenomic DNA without prior PCR amplification. 1 ng of sample DNA was processed for the sequencing libraries using the Illumina Nextera XT sample preparation kit (Illumina, San Diego, USA) following the manufacturer’s protocol. This approach uses tagmentation to enzymatically fragment and tag the sample DNA with adapters in random positions. Libraries were pooled and sequenced on MiSeq with 2 x 250 bp paired-end reads. Metagenomic Illumina sequencing yielded very few AMF reads and taxa and was dominated by plant DNA, suggesting that AMF DNA is present at low abundance in colonised root samples.