Multidisciplinary field campaigns were carried out in the Fram Strait region during late summer 2019 (JR18007, 04/08/2019 to 28/08/2019) aboard RRS James Clark Ross. A motion-compensated Bongo net fitted with 200 um mesh was deployed at all locations to a maximum depth of 200 m or to within 10 m of the seabed.In the Arctic and sub-Arctic sectors adjacent to the Atlantic, three species of Calanus co-occur. However, their respective core distributions align with different water masses, with Calanus hyperboreus being a high-Arctic oceanic species, C. glacialis being associated with Arctic shelf waters, and C. finmarchicus dominating inflowing Atlantic Water.The proportions of these three species in each deployment was established through molecular analysis of the paired ethanol preserved sample. Subsamples of the ethanol sample were analysed using a 16S ribosomal RNA gene barcode (16SAR, 16SB2R primers) following an adapted protocol. Amplified DNA was sequenced using llumina high-throughput sequencing (HTS) platform. Resultant sequences processed through the Qiime pipeline, clustered into Operational Taxonomic Units at 97% homology and taxonomy was assigned using BLASTn (NCBI). Funded by UKRI Natural Environment Research Council (NERC; NE/P006213/1, NE/P006353/1, NE/P006302/1, NE/ P005985/1 amongst others).

Mesozooplankton were collected with a motion-compensated Bongo net (61 cm mouth diameter, 100 and 200 micrometre meshes) and a mini- Bongo net (18 cm mouth diameter, 50 micrometre mesh nets). Both nets fished to a maximum depth of 400 m but sometimes shallower. Specimens were categorised to the lowest possible taxonomic level, which in some cases encompassed developmental stages but in other cases was limited to higher order taxa. Each taxa was enumerated to determine abundance in units of individuals m-2. The dataset allows examination of the distribution and abundance of these species within the Atlantic sector of the Southern Ocean over a number of years and covering much of the productive season from spring to autumn. The data for the North Atlantic and Arctic covers one season only (summer) and is limited to providing a spatial perspective on the distribution and abundance of mesozooplankton.

Macrozooplankton and nekton were collected with a Rectangular Midwater Trawl 25 (RMT25) at locations within the Benguela Current region in May and June 2018. The work was carried out as part of the NERC Large Grant, COMICS (Controls on Mesopelagic Interior Carbon) on board the RRS Discovery (cruise DY090). Depth-discrete samples were collected across four time stations (BS1, BN1-3) between 0-750 m at intervals of 750-500m, 500-250m, 250-125m and 125-10 m. At each time station, two RMT25 hauls were deployed in the hours of darkness and two in daylight, with 16 deployments being undertaken overall. The RMT25 was operated via a downwire net monitor and was equipped with a flow meter, and temperature and salinity sensors. Nets in the deep strata (750-500m and 500-250m) were sampled for approximately 40 mins. and nets in the shallow strata (250-125m, 125-10m) for approximately 20mins. Catches were immediately sorted on board and identified to the lowest taxonomic level feasible. All fishes and subsamples of the other parts of the catch were retained (frozen), principally for subsequent biochemical and physiological analyses. In total, 1917 fish were caught and preserved (not including Cyclothone spp.). Catches were dominated by the myctophids and various other mesopelagic fish species. The water column below 250m was dominated by Bathylagus spp. and genus Melamphidae spp. The most numerous fish overall were the Cyclothone spp. which occurred in large numbers below 500m. In deeper depth intervals (250m-750m), the macrozooplankton component of the RMT25 net catches was mostly dominated by Decapoda and hydromedusae of the genus Atolla spp.. Salps, smaller hydromedusa species and small euphausiids Euphausia hanseni and Nematocelis megalops dominated the shallower depths (10-250m).

Macrozooplankton and nekton were collected with a Rectangular Midwater Trawl 25 (RMT25) over several visits to the sustained observation location P3 (52.70 S, 40.26 W) in the northern Scotia Sea during November and December 2017. The work was carried out as part of the NERC Large Grant, COMICS (Controls on Mesopelagic Interior Carbon) on board the RRS Discovery (cruise DY086). The RMT25 net hauls sampled between 10 and 500 m depth, with the water column divided into 2 depth intervals (10-250 m and 250-500 m). A total of 6 hauls were obtained during 3 separate visits to station P3, each visit comprising a pair of hauls, of which one was carried out in nominal daytime and the other in nominal nighttime. Catches were immediately sorted on board and identified to the lowest taxonomic level feasible. Subsamples of the catches were retained, principally for subsequent biochemical and physiological analyses. In total, 777 fish were caught, belonging to at least 23 species, with catches dominated by the myctophids Krefftichthys anderssoni, Gymnoscopelus braueri, Electrona antarctica and Protomyctophum tenesoni. The water column below 250m was dominated by Bathylagus spp. Temperate myctophid species, such as Protomyctophum parallelum and Protomyctophum andreyeshevi were also caught in small numbers. With regards macrozooplankton, the 250m-500m depth interval was dominated by the jellyfish, Atolla and Periphylla. The tunicate Salpa thompsoni and the euphausiids Euphausia triacantha and Thysanoessa spp. were also relatively abundant. Jellyfish still dominated catches in shallower waters (250m-10m), closely followed by euphausiids and Salpa thompsoni and chaetognaths. Themisto gaudichaudii and Parandania boecki were the most numerous amphipod species caught. Decapods were only caught in the deeper depth interval, both day and night.

Mesozooplankton were collected with a MOCNESS net system during the oceanographic cruise JR16003 (Dec 2016 to Jan 2017). The MOCNESS comprised 9 separate nets which opened in sequence such that the closing of one net opened the next; net 1 was open during the descent of the net to its maximum depth (1000 m) while the remaining 8 depths opened at regular intervals during the reascent to the surface. All catches were immediately preserved in 4% buffered formaldehyde. Identification of taxa was performed by the Morski Institute (Poland). Specimens were categorised to the lowest possible taxonomic level, which, in some cases, encompassed developmental stages but, in other cases, was limited to higher order taxa. Each taxa was enumerated to determine abundance in units of individuals m-3. The dataset allows examination of the distribution and abundance of these species across Polar Frontal Zone in Southern Ocean Atlantic sector. The survey was funded by The UK Natural Environment Research Council (NERC) and carried out as part of the POETS Wester Core Box and SCOOBIES programmes at British Antarctic Survey. The time of Geraint Tarling and the analysis of the MOCNESS nets was funded by the NERC grant "SeaDNA - Assessing marine biodiversity and structure using environmental DNA: from groundtruthing to food web structure and stability" NE/N00616X/1 PI: Stefano Mariani.

Here, for the first time in the Southern Ocean, this dataset contains the seasonal occurrence of the zooplankton assemblage in the Northeast Scotia Sea using a sediment trap deployed throughout 2018 (P3 observation site, 52.80 degrees S, 40.14 degrees W). Southern Ocean zooplankton provide globally significant ecosystem services through their role in carbon sequestration, nutrient cycling and food webs. The remote and extreme nature of the Southern Ocean creates significant logistical difficulties for studying zooplankton all year round and there is a significant paucity in winter data. Sediment traps are able to sample throughout the year, providing much needed insight into the seasonality of zooplankton in the Southern Ocean. The dataset is accompanied by temperature data at depth 200 m from the CTD instrument mounted on the P3 observation site mooring. Clara Manno was supported by UK Research and Innovation Future Leaders Fellowships project CUPIDO (MR/T020962/1). Work was carried out as part of the Ecosystems programme at the British Antarctic Survey and the Scotia Sea Open Ocean Laboratories (SCOOBIES) sustained observation programme at the British Antarctic Survey in the frame of a Western Core Box-POETS survey cruise (https://www.bas.ac.uk/project/scoobies/).