Marina proximity 16S rRNA gene amplicon analysis

During the summer of 2013, Sofie Voerman collected leaf, root, water and sediment samples for microbiome analysis from 0.25 m2 quadrats (n = 3) located near the marina (2 m from the marina wall), at an intermediate distance halfway into the patch (20 m from the marina wall), and at the farthest side of the patch from the harbor (40 m from the marina wall and 2 m from the outer edge of the patch) in Bodega Bay, CA. Bacterial and archaeal 16S rRNA genes were amplified from DNA extracted from these samples using 515F and 806R primers. Sequencing was performed by the DNA Technologies Core facility in the Genome Center (http://dnatech.genomecenter.ucdavis.edu/) on an Illumina MiSeq (250 bp paired-end reads). The resulting fastq files were deposited at GenBank under the accession no. PRJNA350006. This RMarkdown notebook describes the analysis of that 16S rRNA gene dataset.