16S rRNA amplicon seq of marine biofilm: PDMS surface 4
Experimental panels were attached to a metal frame using cable ties and deployed to the anchored University of Portsmouth raft in Langstone Harbour UK. Frames were immersed vertically to the seawater surface at 0.5-1 m depth for a period of 119 days from April 6th until August 3rd, 2018. The biofilms samples were collected (n=4 per coating) from panels using sterile swabs. The swab was passed 10 times over the panel with circular movements for biofilm collection. During sampling, the frames were manually removed from the seawater and exposed to air during collection, for approximately 5-15 min. Between sampling, all panels were hydrated with surrounding seawater. After biofilm collection, each swab was placed into a sterile Eppendorf tube and the breakpoint was cut out using sterile scissors. Samples were then immediately snap frozen in liquid nitrogen (in the field), transferred to the laboratory and stored at -80 degrees C within 4 hours. DNA extraction took place within 2 months from sampling. Genomic DNA was extracted using the QIAGEN DNeasy PowerBiofilm Kit. The quantity and partial quality of nucleic acid samples were assessed based on absorbance spectrums using a Nanodrop 1000 spectrophotometer. High-throughput amplicon sequencing covering the V4-V5 region of the 16S rRNA gene was performed by the Molecular Research DNA Lab (TX, USA) on an Illumina Miseq 2x300 paired-end platform using the universal primers 515F/926R following the manufacturers guidelines.
PDMS4