Illumina sequencing of AMF
AMF from root,  rhizosphere and soil samples were targeted with a nested PCR, using the  AMF-discriminating primers pair AML1/AML2 for the first amplification and  nu-SSU-0450-5/ nu-SSU-0899-3 for the second. The PCR products were purified  from residual dNTPs, primers and buffer using Agencourt AMPure XP beads with  a Sciclone liquid handler. The purified amplicons were indexed (index length  = 8 bp) using the Nextera index kit. The purification with magnetic beads and  normalization of the concentrations were done as described above. The  quantitation of the purified indexed amplicons was performed using the  LightCycler 480 system. The concentrations estimated by qPCR were used to  determine the volume of each sample to make up a 1 nM amplicon pool for library  preparation. The quality of the library was checked on 4200 TapeStation  system, using the High Sensitivity D1000 assay. Paired-end sequencing (2   250 bp) was carried out using the Illumina MiSeq sequencer for 500 cycles .