Samples were collected from the icebreaker CCGS 'Amundsen' into Franklin Bay from fall 2003 to summer 2004 at depth between 160 m and 200 m with a Seabird rosette system equipped with 12 l Niskin-type bottles and a Seabird 911+ CTD probe (salinity, temperature, depth). Fluorescence (Seapoint), transmissivity (WetLabs C-Star Transmissometer), photosynthetically available radiation (PAR; Biospherical Biospherical Instruments), and relative nitrate concentrations (Satlantic MBARI ISUS) were also recorded. Water for DNA analyses was sequentially filtered through a 100 um mesh, a 3 um pore size filter and a 0.2 um pore size Sterivex unit by positive displacement using a peristaltic pump. These DNA analysis were performed on the 3 um filters (large fraction) and the 0.2 um Sterivex units (small fraction): DNA extraction, PCR amplification of sample DNA, DGGE analyses, PCR amplification of 18s rRNA genes, clone libraries construction, taxonomic affiliation and phylogenetic analyses. Sequences from this study are available from GenBank under accession numbers FJ169684 to FJ169852 and FJ775605 to FJ775666.
