## 2 Materials and Methods
### Fungal High-Throughput Illumina Sequencing and Analysis  
The total DNA of each aliquot (L1, L2, L3 and L4) was extracted using a Powersoil DNA Isolation Kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions with minor modifications. Samples were prepared for Illumina Sequencing by Internal Transcribed Spacer 2 region amplification of the microbial community. The DNA was amplified for the hypervariable region with specific primers and further reamplified in a limited-cycle PCR reaction to add sequencing adapters and dual indexes. First PCR reactions were performed for each sample using a KAPA HiFi HotStart PCR Kit (Kapa Biosystems, Roche, Basel, Switzerland) according to the manufacturer's suggestions: 0.3 uM of each PCR primer of a pool of forward primers ITS3 NGS1_F 5'-CATCGATGAAGAACGAG-3', ITS3 NGS2_F 5'-CAACGATGAAGAACCGCAG-3', ITS3 NGS3_F 5'-CACCGATGAAGAACCGCAG-3', ITS3 NGS4_F 5'-CATCGATGAAGAACGTG-3', ITS3 NGS5_F 5'-CATCGATGAAGAACGTG-3', and ITS3 NGS10_F 5'-CATCGATGAAGAACGTG-3' and reverse primer ITS4 NGS001_R 5'-TCCTSCGCTTATTGTATGTAC-3' [45] and 5 uL of template DNA in a total volume of 25 uL. The PCR conditions involved a 3 min denaturation at 95 \({}^{\circ}\)C, followed by 35 cycles of 98 \({}^{\circ}\)C for 20 s, 60 \({}^{\circ}\)C for 30 s and 72 \({}^{\circ}\)C for 30 s and a final extension at 72 \({}^{\circ}\)C for 5 min. Second PCR reactions added indexes and sequencing adapters to both ends of the amplified target region according to the manufacturer's recommendations [46]. Negative PCR controls were included for all amplification procedures. PCR products were then one-step purified and normalized using a SegualPrep 96-well plate kit (ThermoFisher Scientific, Waltham, MA, USA) [47], pooled and pair-end sequenced in the Illumina MiSeq(r) sequencer with the MiSeq Reagent Kit v3 (600 cycles), according to the manufacturer's instructions (Illumina, San Diego, CA, USA) at Genoinseq, Next Generation Sequencing Unit of CNC/Biocant (Cantanhede, Portugal).  
Treatment of metabarcoding raw data, clustering and taxonomic analyses were performed at Genoinseq, Next Generation Sequencing Unit of CNC/Biocant (Cantanhede, Portugal). Raw reads were extracted from an Illumina MiSeq(r) System in fastq format and quality filtered with a PRINSEQ version 0.20.4 [48] to remove sequencing adapters, trim bases with an average quality lower than Q25 in a window of five bases and eliminate reads with fewer than 100 bases. The forward and reverse reads were merged by overlapping paired end reads with an AdapterRemoval version 2.1.5 [49] using default parameters. The QIIME2 package version 2020.2 [50] was used for operational taxonomic unit (OTU) generation, taxonomic identification, sample diversity and richness indices calculation. Sample IDs were assigned to the merged reads and converted to FASTA format. Chimeric merged reads were detected and removed using UCHIME [51] against the UNITE/QIIME ITS database version 8.2 [52]. The ITSx version 1.1.2 [53] was used to extract the highly variable fungal ITS2 subregion from the merged reads. OTUs were selected at 97% similarity threshold using the open reference strategy and those with fewer than two reads were removed from the OTU table. A representative sequence of each OTU was then selected for taxonomy assignment using the referred database. All metagenomic data were deposited in the international SRA database with the reference PRJNA875387.