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.

This dataset consists of vertical profiles of discrete depth sampled weekly at a fixed station under the ice in Franklin Bay (Southeastern Beaufort Sea) for chlorophyll a concentration of different size fractions: >0.7µm and >5µm. Sampling took place from December 2003 to May 2004 through the moon-pool of the CCGS Amundsen for depth ranging from 10m to the bottom and through a hole in the ice cover for the surface depth (3-10m). Chlorophyll a concentrations were determined by fluorimetry.

Field observations were made in the southern Beaufort Sea and the Amundsen Gulf as part of CASES 2003 expedition. Samples were collected during the first two legs of the expedition from 13 September to 14 October 2003 (open water) and from 15 October to 25 November 2003 (newly formed sea ice) onboard the Canadian icebreaker CCGS Amundsen. Temperature and salinity profiles were obtained using a SeaBird 911 Conductivity¿Temperature¿Depth (CTD) probe. Nutrient concentrations (nitrate plus nitrite, phosphate, and silicate) were determined on fresh samples (within 1 h of sampling) using standard colorimetric methodologies adapted for use on an Auto-Analyzer 3 (Bran þ Luebbe). A RAMSES ASC scalar hyperspectral irradiance sensor (TriOS) was mounted on the flight bridge to measure downwelling irradiance with 1 nm intervals during the day. A total of 50 and 102 discrete water samples were collected over the euphotic zone at 13 and 20 stations for legs 1 and 2, respectively for fluorometrically chlorophyll a measurements and absorption analysis of phytoplankton, non-algal particules (NAP) and colored dissolved organic matter (CDOM). Water samples (preserved in acidic Lugol solution) were enumerated and identified to the lowest possible taxonomic rank using an inverted microscope. Concentrations of chlorophyll a and chlorophyll b were obtained by HPLC measurements and these two pigments were used for the calculation of the ratios of chl b to chl a.

Sampling took place on legs 6, 7, 8b, and 9 of the CFL project on the CCGS Amundsen (2008). Zooplankton were sampled with a 1x1m2 (200 µm mesh) net through the moon-pool and with a 1m diameter (200 µm mesh) ring net on the ice at ice covered stations. In open water, samples were collected with 2x1 sq.m (500 µm mesh), 4x1 sq.m (500 and 200 µm mesh), and rectangular mid-water trawl (1600 µm mesh). Samples were live sorted to species and frozen at -25C. Algae were collected from the bottom ice via ice cores and the dive program, from the ice interface/surface water with a Hg clean Niskin and a hose and pump on a 1m arm, and from the chlorophyll a maximum depth via the rosette. Samples in ice were frozen in the dark, while samples in water were filtered via dual filtration following Morrison and Watras (1999) and filters were frozen at -25C. Zooplankton species Calanus glacialis and Calanus hyperboreus were analyzed for total mercury using CVAAS; C. hyperboreus was also analyzed for methyl mercury via Gas Chromatography Atomic Fluorescence Spectrophotometry (GC AFS). The algae samples were analyzed for THg using cold vapour atomic absorption spectrometry (CVAAS) and MeHg using cold vapour atomic fluorescence spectroscopy (CVAFS).

As part of the ArcticNet expeditions (http://www.arcticnet.ulaval.ca) on the CCGS Amundsen in 2008-2019, we collected water samples from stations throughout the Canadian Arctic. Cruise tracks varied from year to year, but always included a transect of northern Baffin Bay, and sometimes sampling in Lancaster Sound, the Beaufort Sea, and/or along the east coast of Baffin Island. The sampling period ranged from summer to autumn. Samples were collected by CTD-rosette from 2-8 depths corresponding to water column features such as surface water, the subsurface chlorophyll maximum, the nitracline, or Atlantic Water. To collect samples for DNA/RNA, water was filtered through 3-µm filters and 0.2 µm cartridges, which were conserved in a buffer at -80°C. These have been used for high-throughput sequencing for amplicon-based surveys, metagenomics, and other molecular techniques. Samples for flow cytometry (to enumerate bacterial and/or pigmented cells), microscopy (with a fluorescent DAPI stain, or using FNU preservative for identifying larger cells), fluorescent in-situ hybridization (another microscopy technique), chlorophyll a (to quantify photosynthetic organisms), and HPLC pigment analysis (to identify different algae taxa), were also collected. Samples from which nucleic acids have been extracted and sequenced in many projects. Samples from which nucleic acids have been extracted and sequenced can be found in the GenBank Short Read Archive under the project accession numbers PRJNA202104, PRJNA283142, PRJNA283296, PRJNA383398, and SRX037894-SRX037896

An incubation experiment was conducted on board of the Canadian research icebreaker CCGS Amundsen between 6 and 15 August 2015. The water was collected near the nitracline at 38 m depth in Baffin Bay using 12-L Niskin-type bottles deployed on a CTD rosette system. A natural Arctic plankton community in a pre-bloom stage (initial high nutrient-low Chl a concentrations) was exposed over 9 days to reduced pH conditions under two contrasting light regimes. The two light regimes were designed to simulate the mean irradiance in an ice-free 5-m thick surface mixed layer (HL, marginal ice bloom conditions) and the mean irradiance at 5 m depth under a melting ponded ice pack (LL, under-ice bloom/ subsurface chlorophyll maximum conditions). The pH gradient comprised 6 levels covering the range of pH expected between the present and the year 2300. During the incubation, a phytoplankton bloom developed in every incubation bag and diatoms dominated the biomass (Chaetoceros spp.). Temporal variations of pH, dissolved inorganic carbon, total alkalinity, chlorophyll a, macronutrients, DMS(P), flow cytometry (nano- and pico-phytoplankton, bacteria, virus), taxonomy, salinity and incubator's temperature are available.

We are seeking answers to two key questions regarding the influence of marine processes on Arctic climate: 1) How will the increased flow of Pacific waters through the Canadian Archipelago affect the dynamics of climate-active gases in the ocean, and 2) How will these gases be affected by a reduction of sea-ice cover, and increased areas of open water? These questions have been addressed by our multidisciplinary team during two expeditions on the Canadian research ice-breaker Amundsen as part of the International Polar Year. The expeditions took place during the fall of 2007 and 2008. Eleven (2007) and ten (2008) Arctic SOLAS scientists from 7 Canadian institutions participated to these expeditions which allowed a unique and extensive longitudinal survey of these trace gases and aerosols in the High Canadian Arctic, from Baffin Bay to the Beaufort Sea. The missions enabled us to collect new oceanographic and atmospheric data on the distribution and cycling of DMS, N2O, and VOCs across the Canadian Archipelago and to relate these measurements to the distribution and chemical characteristics of aerosol particles. Activities of this program where coordinated with those of the IPY programs CFL, the Canadian program ArcticNet, and the international programs OASIS and SOLAS.

DMSP and DMS water concentrations were determine at fixed depths and at selected stations (ArcticNet stations) along a transect beginning in the North Water Polynya, going through the Lancaster Sound and the Northwest Passage, and terminating in the Beaufort Sea. During transit time, near surface DMS measurements were conducted every 2 hours from the pumping system of the CCGS Amundsen. In all cases, DMSP and DMS measurements were done following the methods of Kiene and Slezak 2006 (Limnol. Oceanogr.: Methods 4: 80-95). At selected stations, DMSP and DMS microbial cycling was determined during onboard incubations following the 35S-DMSP protocol (Merzouk et al. 2006, Deep Sea Res. 53:2370-2383).