Sample collection: The sampling was part of the Canadian Arctic Shelf Exchange Study (CASES) in which CCGS Amundsen was frozen in Franklin Bay in the coastal Beaufort Sea (Station FB/200) during winter. Upper mixed-layer microbial plankton communities were sampled 5m below the water surface using the ship CTD rosette system equipped with 12L Niskins during openwater conditions. During the time that the ship was frozen in Franklin Bay from December 2003 to early June 2004, samples were taken using a 5L Niskin bottle from 3m below the bottom ice through a 300mm hole that had been drilled 500m upstream of the ship. HPLC pigment analysis: One to two liter samples of water were filtered onto Whatman GF/F filters and stored frozen at -80C until analysis. Phytoplankton pigments on the GF/Fs were extracted in 3mL of 95 percent MeOH and 100 uL of the extracts was injected into a Varian ProStar HPLC equipped with a Symmetry C8 column. The HPLC peaks were detected by diode-array spectroscopy (350-750nm) and absorbance chromatograms were obtained at 440 (for chls) and 450nm (for carotenoids). Chlorophylls were also detected by fluorescence (excitation: 440nm; emission: 650nm). The HPLC solvent protocol was based on gradient dilution with two solvent mixtures (Zapata et al. 2000): a methanol, acetonitrile, and aqueous pyridine (50:25:25 v:v:v) solution; and a methanol, acetonitrile, and acetone (20:60:20 v:v:v) solution. The flow rate was 1mL/ min, and the equilibration time was 7min.

Sinking export of organic material was investigated during the fall of 2007, using free-drifting, short-term particle interceptor traps . The particle interceptor traps were deployed at 6 stations along a transect spanning between the North Water polynya (Baffin Bay) and the Beaufort Sea. The traps were deployed from the CCGS Amundsen at three depths below the euphotic zone (50, 100 and 150 m) for a period between 8 and 22 hours. The analyses on the sinking material included total chlorophyll a and phaopigments (fluorometric determination), particulate organic carbon and nitrogen, biogenic silica, cell composition and abundance and fecal pellet abundance.

Samples were collected from nine sites distributed across the study region in 2008 and 2009. To avoid confounding influence of seasons, the same sites were sampled in the same season each year. Sampling was conducted onboard the CCGS Amundsen between July and October during the Circumpolar Flaw Lead Study, ArcticNet expeditions in collaboration with the Canadian Healthy Ocean Network and the Malina project. Locations were chosen to study both hotspots and coldspots in the Canadian Arctic. At each sampling station, an USNEL box corer was deployed for seafloor sediment collection. From each box core, three to five sub-cores of 10 cm diameter and approximately 20 cm sediment depth were taken for assessing benthic remineralisation function in shipboard microcosm incubations. After incubation, the same sediment cores were passed through a 0.5 mm mesh sieve under slow running seawater. The sieve residues were preserved in a 4% seawater-formaldehyde solution for later analyses of species diversity and abundance under a dissection microscope.

Sinking export of organic material was investigated during the fall of 2006, using free-drifting, short-term particle interceptor traps . The particle interceptor traps were deployed at 9 stations along a transect spanning between the North Water polynya (Baffin Bay) and the Beaufort Sea. The traps were deployed from the CCGS Amundsen at three depths below the euphotic zone (50, 100 and 150 m) for a period between 8 and 29 hours. The analyses on the sinking material included total chlorophyll a and phaopigments (fluorometric determination), particulate organic carbon and nitrogen, biogenic silica, cell composition and abundance and fecal pellet abundance.

Benthic fauna were sampled at 78 stations between June and October from 2007 to 2011 onboard the Canadian research icebreaker CCGS Amundsen. Station depths ranged from 34 to 1024 m, all below the average ice scouring zone. All faunal samples were collected with an Agassiz trawl (effective opening of 1.5 m and a 40 mm net mesh size, with a 5 mm cod end liner) with average trawling time and speed of 5 min and 1.5 knots, respectively.