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 .