Evidence for niche differentiation in the environmental responses of co-occurring mucoromycotinian fine root endophytes and glomeromycotinian arbuscular mycorrhizal fungi
two T. subterraneum plants were carefully removed and processed. DNA was extracted from approximately 20 mg of fresh root material using the PowerSoil DNA isolation kit (Mo Bio Laboratories, USA). For each DNA sample (116 in total), 15 ng of DNA were used to amplify approximately 260 bp of the 18S rRNA gene using the AMF primer set AMV4.5NF (5-AAGCTCGTAGTTGAATTTCG-3) and AMDGR (5-CCCAACTATCCCTATTAATCAT-3) (Sato et al. 2005) with Nextera XT Index Kit v2 adapters (Illumina). The libraries were sequenced using the MiSeq Reagent Kit v3 600-cycle (Illumina). Following sequencing, VSEARCH (Enns et al. 1990) was used to merge paired-end reads and remove low quality bases, chimeras and low abundance sequences (< 10). After a quality check, sequences were clustered into OTUs at a 97% identity threshold. Then, consensus OTUs were queried against the SILVA 18S rRNA database (Quast et al. 2012). Given the unknown diversity of FRE, we took a conservative approach for the classification of OTUs. Any OTU matching an Endogonales (within Mucoromycotina) species was classified as FRE, and any OTU matching a Glomeromycotina species was classified as AMF (> 95% match to reference sequence and > 90% query cover). Seven samples failed to amplify DNA and were removed from the dataset, leaving 109 samples