DNA extraction and sequencing
Microbial community DNA was extracted from soil, root, and leaf samples
using the FastDNA® Spin Kit for Soil (MP Biomedicals), following the
manufacturer’s instructions. The hypervariable region ITS of the fungal
gene was amplified using the primer pairs ITS1F
(5’-CTTGGTCATTTAGAGGAAGTAA-3’) and ITS2R (5’-GCTGCGTTCTTCATCGATGC-3’)
(Adams et al., 2013). Sequencing was conducted on the Illumina MiSeq
platform, following standard protocols. All samples were pooled in
equimolar concentrations and subjected to paired-end sequencing on the
Illumina MiSeq platform. The paired-end sequences were merged to
generate single sequences of approximately 300 bp. These sequences were
then quality-filtered (maximum expected error = 0.2), and singletons
were removed using USEARCH v.10. (Edgar, 2010). The raw reads obtained
from the sequencing were deposited into the NCBI Sequence Read Archive
(SRA) database (Accession Number: SRP342019).