The datasets present new data from microscopic counts and selected nutrient and physical data assembled from the following missions. Aboard the CCGS Louis St-Laurent: IPY Canada's Three Oceans 2007. Aboard the CCGS Amundsen: International Polar Year (IPY) Circumpolar Flaw Lead Study 2008; ArcticNet 2008. Temporal coverage is July-September. Cell density of the three sub-clades MAST-1A, MAST-1B and MAST-1C was measured by cell-counts using fluorescent in situ hybridization with taxa-specific probe. Biomass of phototrophic organisms, of different size classes, was obtained by counts of DAPI-stained cells under epifluorescence microscopy. Samples for total chlorophyll a (chl a) were filtered onto GF/F filters, extracted in either ethanol or acetone and analysed by spectrofluorometry. Chl a was also measured for the < 3 µm size fraction, and chl a in the < 3 µm size fraction was calculate by simple substraction. CCGS Amundsen data: Temperature, salinity, transmissivity, oxygen, and photosynthetically active radiation were provided by Dr. Y. Gratton (Institut National de la Recherche Scientifique, Québec). Nitrate and Phosphate concentrations were provided by Dr. J.-É. Tremblay (Université Laval, Québec). CCGS Louis St-Laurent data were supplied by Drs. E.C. Carmack and J. Nelson (Institute of Ocean Sciences, Sidney, B.C.). Distance to ice edge was obtained from the Canadian Ice Services (http://ice-glaces.ec.gc.ca).

The datasets present new data from microscopic counts and selected nutrient and physical data assembled from the following cruises. Aboard the CCGS Amundsen: ArcticNet Expeditions 2006, 2008, 2009, 2010; International Polar Year (IPY) Circumpolar Flaw Lead Study 2008 and MALINA Project 2009 (French IPY project headed by Dr. M. Babin). Aboard the CCGS Louis St-Laurent: IPY Canada's Three Oceans 2007. Temporal coverage is Feb.-Nov., but varies by year, with the greatest sampling effort in July-Oct. Cryothecomonas abundance was measured by cell-counts using fluorescent in situ hybridization with a taxon-specific probe. Biomass of phototrophic and heterotrophic organisms, of different size classes, was obtained by counts of DAPI-stained cells under epifluorescence microscopy. Samples for total chlorophyll a (chl a) were filtered onto GF/F filters, extracted in either ethanol or acetone and analysed by spectrofluorometry. Chl a was also measured for the < 3 µm size fraction. CCGS Amundsen data: Temperature, salinity, oxygen, and photosynthetically active radiation were provided by Dr. Y. Gratton (Institut National de la Recherche Scientifique, Québec). Nitrate and Phosphate concentrations were provided by Dr. J.-É. Tremblay (Université Laval, Québec). CCGS Louis St-Laurent data were supplied by Drs. EC Carmack and John Nelson (Institute of Ocean Sciences, Sidney, B.C.). Distance to ice edge was obtained from the Canadian Ice Services (http://ice-glaces.ec.gc.ca).

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