Arbuscular mycorrhizal fungal SSU, isolated from roots
The amplified PCR product then underwent a short second PCR to attach the Illumina Nextera XT v2 index set (Illumina Australia, Melbourne, Australia), as per manufacturers instructions (https://support.illumina.com).  Each reaction consisted of 3.8l of Q5 High-Fidelity DNA Polymerase 2x master mix (NEB), 1.5l of each index (Illumina) and 2.3l of PCR product, total reaction volume was 7.6l. The amplicons were then diluted and again assessed using the Qunat-iT  PicoGreen (ThermoFisher Scientific) assay and normalised library pools were constructed using the Eppendorf epMotion.  The libraries were cleaned-up and prepared for sequencing following the Illumina MiSeq protocol. Sequencing was performed on the Illumina MiSeq platform using the Illumina MiSeq reagent kit v3 2x 300bps paired-end chemistry as per manufacturers instructions.