V4 Fluidigm Pool
All DNA samples were initially quantified using the Qubit Fluorometer 2.0 (Thermo Fisher Scientific). Polymerase Chain Reaction (PCR) amplification was performed using three primer sets (as found in the metadata): two primer sets for amplification of two variable regions (V3-V5 and V4) of the bacterial 16S ribosomal RNA (rRNA), and a primer set for amplification of a portion of the nuclear ribosomal Internal Transcribed Spacer (ITS) region (ITS 3-4) in fungi. A 48.48 Fluidigm Access Array (Fluidigm Corporation, South San Francisco, USA) was used for amplification and library construction.  PCR products were harvested from the PCR chambers from the Post-PCR IFC Controller AX.  Amplicons containing sample-specific barcodes and Illumina adapter sequencers were quantified with a Fragment Analyzer Automated CE System (Advanced Analytical) and pooled in equimolar ratios into two Eppendorf tubes; DNA bands in the size range of 350-1000 bp were selected and excised following gel electrophoresis corresponding to equal amplicon size of V3-V5, V4 and ITS3-4 products. DNA was purified with a Mini Elute Gel Extraction Kit (Qiagen), then analyzed and quantitated.