V4 region 18S rRNA gene: photosynthetic-EBPR bioreactor
The twenty-one genomic DNA samples were submitted to the University of Wisconsin-Madison Biotechnology Center. Samples were prepared as described in the 16S Metagenomic Sequencing Library Preparation Protocol, Part #15044223 Rev. B (Illumina Inc., San Diego, California, USA) with the following modifications: The 16S rRNA gene V3/V4 variable region was amplified using S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 forward and reverse primers (Herlemann et al., 2011).  The 18S rRNA gene V4 variable region was amplified using the Euk_1391f and EukBr-7R primers based on the protocol outlined by the Earth Microbiome Project initiative (http://www.earthmicrobiome.org/emp-standard-protocols/18S/) (Caporaso et al., 2012). Both sets of primers were modified to add Illumina adapter overhang nucleotide sequences to the gene_specific sequences. Following initial amplification, library size was verified on an Agilent DNA1000 chip, and cleaned using a 1x volume of AxyPrep Mag PCR clean-up beads (Axygen Biosciences, Union City, CA).