DOI: 10.5061/dryad.rr4xgxdfx
title: Data from: Seamounts generate efficient active transport loops to nourish the twilight ecosystem

description: 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.
description: 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<em> ShenKuo </em>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 <em>Seabird</em> 911 plus CTD sensor (frequency, 24
 Hz) equipped with a fluorometer and <em>Seabird</em> 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
 <em>RDI</em> 300 kHz LADCP and <em>Hydroptic</em>
 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<sub>ρ</sub> was calculated. Finally, according to Fick’s
 law, the vertical nitrate gradient and the diapycnal diffusivity
 K<sub>ρ</sub> were multiplied to estimate the vertical
 turbulent nitrate flux. The UVP5 HD allows for the
 in-situ quantifications of all objects &gt;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 &gt;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.
description: # **Date from: Seamounts Generate Efficient Active Transport Loops to
 Nourish the Twilight Ecosystem** 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. **Description of the data and file structure**
 **File Structure** We have submitted our raw data including the
 **Cross-section observational data** (1. Sectional_data.xlsx),
 **Time-series observational data** (2. Timeseries \_data.xlsx), and **UVP
 observational data** (3. Particle_and \_Zooplankton_data_UVP.xlsx). **1)
 Cross-section observational data:** a)        *Hydro_biochem_data*:
 hydrological and biochemical data at 1-m depth intervals * *Lon.*:
 Longitude (°E) * *Lat.*: Latitude (°N) * *Bot. depth*: depth of bottom
 topography (m) * *Depth:* observation depth (m) * *Temperature*: potential
 temperature (℃) * *Salinity*: practical salinity unit (psu) * *Nitrate*:
 nitrate concentration (μmol L−1) * *Chl-a*: Chlorophyll-*a* concentration
 (μg L−1) * *Particle abundance*: particle abundance in seawater
 (individual L−1) b)        *Nitrate_Diffusive_flux*: mixing intensity and
 diffusive nitrate flux at 5-m depth intervals * *ε*: turbulent dissipation
 rate calculated by thorpe scale method (W kg−1) * *Kρ* : diffusion
 coefficients (m2 s−1) * *NO3− Diffusive Flux*: nitrate diffusion flux
 based on 1st Fick’s law (mmol m2 day−1) c)        *Vel_LADCP*: current
 velocity observed by Lowered ADCP at 8-m depth intervals * *u*: eastward
 current velocity (m s−1) * *v*: northward current velocity (m s−1)
 d)        *vertical shear*: * *S2*: vertical shear square at 8-m depth
 intervals (s−2) **2) Time-series observational data:** Data from four
 time-series stations including observation time, depth, temperature,
 nitrate, chlorophyll, and backward scattering data. a)       
 *Hydro_biochem_data*: hydrological and biochemical data * *Lon.*:
 Longitude (°E) * *Lat.*: Latitude (°N) * *Date*: observation date
 (yyyy-mm-dd) * *Time*: local time (hh:mm) * *Temperature*: potential
 temperature (℃) * *Chl-a*: Chlorophyll-*a* concentration (μg L−1)
 b)        *Backscattering_intensity*: Backscattering intensity at
 nighttime/daytime (db re1 m−1) **3) UVP observational data:** Particle
 abundance at various particle size classes, total particle volume, and
 abundance and volume of copepods from UVP observations at four-time series
 stations. All datasets contain missing values marked as “NaN”. * *Lon.*:
 Longitude (°E) * *Lat.*: Latitude (°N) * *Date*: observation date
 (yyyy-mm-dd) * *Time*: local time (hh:mm) * *Bot. depth*: depth of bottom
 topography (m) * *Depth:* observation depth (m) * *Particle abundance*:
 particle abundance in seawater at 5-m depth intervals (individual L−1) *
 *Total Volume*: total particle volume per cubic meter of seawater (mm3
 m−3) * *POC flux*: POC flux at 5-m depth intervals (mgC m−3 day−1) *
 *Copepods abundance*: copepods abundance per litre of seawater (ind L−1) *
 *Copepods biovolume*: total copepods volume per cubic meter of seawater
 (mm3 m−3) * *Part conc*: particle concentration per litre of seawater at
 specific size range (ind L−1)