16SrRNA of clam biodeposit
DNA was extracted using the Qiagen DNeasy PowerSoil DNA extraction kit following the manufacturers protocol. DNA extractions were quantified fluorometrically using a Qubit 3.0 (ThermoFisher, Waltham, MA) and were normalized to 3 ng/l prior to PCR. General bacterial primers, 515F and 806R (Caporaso et al. 2011), were used to amplify the 16S rRNA gene; the primers had appropriate Illumina adaptors and individual 12-bp GoLay barcodes were attached to the reverse primers for demultiplexing. Each sample was amplified in triplicate using PCR conditions described in Caporaso et al. (2011), and included a negative control. Libraries were confirmed with gel electrophoresis and size selection was completed by gel cutting and purification using the Qiagen QIAquick gel extraction kit (Qiagen, Valencia, CA). Libraries were quantified with the Qubit 3.0 and pooled in equal molar concentrations for sequencing on the Illumina MiSeq platform using the paired-end 500-cyle kit and V2 chemistry.