Bacterial 16S V3-V4 regions were amplified by PCR using universal primers derived from DBact-0341-b-S-17 and S-d-Bact-0785-a-A-21 (29 (link)) containing unique adapters for the Nextera XT indexing kit according to the manufacturer's instructions (Illumina Inc., San Diego, CA). Fungal ITS2 regions were amplified using separate adapter primers derived from IST3_KYO1 and IST4_KYO1 (30 (link)). After adding unique indices, each sample's DNA concentration was determined using the Quant-iT PicoGreen kit (Molecular Probes, Inc., Eugene, OR) and equal mass portions of each were pooled prior to sequencing.
The amplicon pools were paired-end sequenced (250 cycles) using the MiSeq platform (Illumina Inc.) at either the Interdisciplinary Center for Biotechnology Research (year 1 data set, University of Florida, Gainesville, FL) or the UCF Genomics & Bioinformatics Cluster (year 2 data set, University of Central Florida, Orlando, FL).
The amplicon pools were paired-end sequenced (250 cycles) using the MiSeq platform (Illumina Inc.) at either the Interdisciplinary Center for Biotechnology Research (year 1 data set, University of Florida, Gainesville, FL) or the UCF Genomics & Bioinformatics Cluster (year 2 data set, University of Central Florida, Orlando, FL).
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