Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary in-situ observations focusing on a shallow seamount in the oligotrophic ocean. In this dataset, we report high-resolution hydrographic and biochemical observational data from both sectional observations and time-series stations observations.

Xianbei Seamount is located in the central SCS basin and is an isolated and steep shallow seamount with a summit elevation of 208 m. The transverse section of the seamount is roughly elliptical, with a long axis of about 60 km and a short axis of 40 km. Field observations were conducted onboard the R/V ShenKuo from 14–24 September 2021, and a section parallel to the flow direction was designed to conduct comprehensive field observations. Besides, four time-series stations stretched about 25 h with an interval of 4 h, located at the upstream slope, summit, downstream slope, and downstream bottom. The temperature, salinity, depth, fluorescence, and nitrate were measured using a Seabird 911 plus CTD sensor (frequency, 24 Hz) equipped with a fluorometer and Seabird Deep-Suna (1 Hz). The Photosynthetically active radiation (PAR) was measured with a PAR sensor. The current and particle size spectrum were derived from an RDI 300 kHz LADCP and Hydroptic Underwater Version Profiler 5 (UVP5, maximum frequency 20 Hz), respectively.

The Thorpe-scale method was used to evaluate the strength of the mixing with reference to the mature data processing procedure. Before applying the Thorpe-scale method for calculation, the original CTD data underwent preprocessing through a standardized procedure. This involved utilizing Seabird processing software to perform tasks such as minimizing thermal lag, removing salinity spiking, identifying occasionally reversed signs, eliminating extremely abnormal data points, and averaging at regular depth intervals. The turbulence dissipation rate  can be estimated based on the Thorpe displacement and the stratification. Then, the diapycnal diffusivity K_ρ was calculated. Finally, according to Fick’s law, the vertical nitrate gradient and the diapycnal diffusivity K_ρ were multiplied to estimate the vertical turbulent nitrate flux.

The UVP5 HD allows for the in-situ quantifications of all objects >100 μm, including both non-living particles and living organisms with high vertical resolution. The size and gray level of every object larger than 100 μm were recorded, but only large objects larger than 600 μm were stored as images in the instrument for subsequent analysis. After the instrument was retrieved, all images >600 μm were extracted using the ImageJ-based ZooProcess macro set and uploaded to Exotaxa website for the automated classification, and the classifications were validated by experts. Thus, the size information was obtained for each particle and each copepod zooplankton, and the volume of each object was calculated based on the equivalent sphere diameter d. The abundance and biovolume of the copepod zooplankton were both binned into 5-m intervals for further analysis. The POC flux was estimated based on the carbon-based particle size approach. The distribution of particle size follows a power law in particle size ranging from micrometers to millimeters.