CTD sensor and related bottle data analyses from RRS Discovery cruise DY086 at site P3

Physical, chemical and biogeochemical measurements derived from CTD-rosette deployments during three visits to site P3 (November to December, 2017) in the South Atlantic. Measurements were made during COMICS cruise DY086 on the RRS Discovery using a trace metal free Titanium Rosette (events 4, 7, 15, 19, 24, 26, 29) and a Stainless Steel Rosette (all other events). Physical parameters include temperature, salinity, density, photosynthetically active radiation and turbulence; chemical parameters include dissolved oxygen, dissolved oxygen saturation, nitrate, phosphate and silicate; biogeochemical parameters include turbidity, beam transmittance, beam attenuation, fluorescence, particulate organic carbon (POC), dissolved organic carbon (DOC), chlorophyll-a, net primary productivity (NPP), ambient leucine assimilation and bacterial cell count. To determine turbulence, a downward facing lowered acoustic doppler current profiler (LADCP, Teledyne Workhorse Monitor 300 kHz ADCP) was attached to the CTD frame. Shear and strain, which are obtained from velocity and density measurements, were used to estimate the dissipation rate of turbulent kinetic energy and the diapycnal eddy diffusivity from a fine-scale parameterisation. Estimates are calculated by parameterising internal wave-wave interactions and assuming that wave breaking modulates turbulent mixing. A detailed description of the method for calculating diffusivity from LADCP and CTD can be found in Kunze et al. (2006). Two datasets with different vertical resolutions were produced: one in which the shear is integrated from 150 to 300 m and the strain over 20-150 m, and one in which the shear is integrated from 70 to 200 m and the strain over 30-200 m. Nutrients (nitrate, phosphate, silicate) were determined via colourimetric analysis (see cruise report, Giering and Sanders, 2019), POC was determined as described in Giering et al. (2023), DOC and DOC flux were determined as described in Lovecchio et al. (2023), NPP was determined as described in Poulton et al. (2019), and ambient leucine assimilation and bacterial cell count were determined as described in Rayne et al. (2024). Bacterial abundance and leucine assimilation were made from bottle samples of six CTD casts of the stainless-steel rosette. Water was collected at six depths (6 m, deep-chlorophyll maximum, mixed layer depth + 10, 100, 250 and 500 m). Acid-cleaned HDPE carboys and tubing were used for sampling. Samples were then stored in the dark and at in-situ temperature prior to on-board laboratory sample preparation or analysis. Flow cytometry was used to measure bacterial abundance. Room temperature paraformaldehyde was used to fix 1.6 ml samples for 30 minutes. Then, using liquid nitrogen, the samples were flash frozen and stored at -80°C. Samples were then defrosted before being stained using SYBR Green I and run through the flow cytometer (BD FACSort™). The method of Hill et al. (2013) was applied to determine prokaryotic leucine assimilation using L-[4,5-³H] leucine which has a specific activity of 89.3 Ci/mmol­. In the mixed and upper layers of the water column, the protocol in Zubkov et al. (2007) was followed. Below the mixed layer, adaptions to the method included reducing the concentration of ³H-Leucine to 0.005, 0.01, 0.025, 0.04 and 0.05 nM; increasing experimental volumes to 30 ml; enhancing incubation times to 30, 60, 90 and 120 min. These adaptions were made to improve accuracy where lower rates of leucine assimilation were expected. Data were provided by the British Oceanographic Data Centre and funded by the National Environment Research Council.