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.

本数据集源自2017年11月至12月对南大西洋P3站点的3次温盐深采水架（CTD-rosette）部署作业，获取了物理、化学与生物地球化学测量数据。本次测量由英国皇家研究舰“发现号”（RRS Discovery）执行的COMICS航次DY086完成，分别采用无痕量金属钛合金采水架（对应事件4、7、15、19、24、26、29）与不锈钢采水架（其余所有事件）实施测量。其中物理参数涵盖温度、盐度、密度、光合有效辐射及湍流参数；化学参数涵盖溶解氧、溶解氧饱和度、硝酸盐、磷酸盐与硅酸盐；生物地球化学参数涵盖浊度、光束透过率、光束衰减系数、荧光、颗粒有机碳（POC）、溶解有机碳（DOC）、叶绿素a、净初级生产力（NPP）、原位亮氨酸同化速率与细菌细胞计数。为获取湍流相关数据，CTD框架上搭载了向下观测的下放式声学多普勒海流剖面仪（LADCP, Teledyne Workhorse Monitor 300 kHz ADCP）。基于流速与密度测量得到的剪切力与应变量，通过细尺度参数化方法可估算湍流动能耗散率与斜压涡扩散系数，该方法通过参数化内波-内波相互作用并假设波浪破碎调控湍流混合实现。Kunze等人（2006）详细阐述了基于LADCP与CTD数据计算扩散系数的方法。本数据集包含两组不同垂直分辨率的结果：一组的剪切力积分区间为150~300 m，应变量积分区间为20~150 m；另一组的剪切力积分区间为70~200 m，应变量积分区间为30~200 m。营养盐（硝酸盐、磷酸盐、硅酸盐）采用比色法测定（详见航次报告Giering与Sanders, 2019）；颗粒有机碳的测定方法参见Giering等人（2023）；溶解有机碳及其通量的测定方法参见Lovecchio等人（2023）；净初级生产力的测定方法参见Poulton等人（2019）；原位亮氨酸同化速率与细菌细胞计数的测定方法参见Rayne等人（2024）。细菌丰度与亮氨酸同化速率的测量样本取自不锈钢采水架的6个CTD站位的瓶采样品，采样深度分别为6 m、深层叶绿素最大值层、混合层深度+10 m、100 m、250 m与500 m。采样使用经酸清洗的高密度聚乙烯（HDPE）储液桶与管路采集水样，样品在黑暗环境与原位温度下保存，直至船载实验室完成样品前处理或分析。采用流式细胞术测量细菌丰度：取1.6 ml样品，使用室温多聚甲醛固定30分钟，随后经液氮快速冷冻并保存于-80℃。分析前将样品解冻，使用SYBR Green I染色后通过流式细胞仪（BD FACSort™）上机检测。采用Hill等人（2013）的方法，利用比活度为89.3 Ci/mmol的L-[4,5-³H]亮氨酸测定原核生物亮氨酸同化速率。在水层混合层与上层水体中，遵循Zubkov等人（2007）的实验流程；在混合层以下水体中，对方法进行了优化调整：将³H-亮氨酸的浓度设置为0.005、0.01、0.025、0.04与0.05 nM，将实验体积提升至30 ml，将孵育时间延长至30、60、90与120分钟，以在预期亮氨酸同化速率较低的场景下提升测量准确性。本数据集由英国海洋数据中心提供，资助方为英国国家环境研究委员会。