Metadata Report for BODC Series Reference Number 1816659

• Metadata Summary

• Problem Reports

• Data Access Policy

• Narrative Documents

• Project Information

• Data Activity or Cruise Information

• Fixed Station Information

• BODC Quality Flags

• SeaDataNet Quality Flags

Metadata Summary

Problem Reports

Trapped bubbles are potentially affecting the transmissometer readings from the start of the series with an exhibited decrease trend. All values have been flagged. (BODC assessment)

Trapped bubbles are potentially affecting the transmissometer readings from the start of the series with an exhibited decrease trend. All values have been flagged. (BODC assessment)

Trapped bubbles are potentially affecting the transmissometer readings from the start of the series with an exhibited decrease trend. All values have been flagged. (BODC assessment)

RRS James Cook JC088 surface hydrography quality control report

General comments

The Non-toxic water supply was turned off and the sensors cleaned at intervals throughout the cruise details below. Transmissometer readings were taken after cleaning with the sensor in open air and closed off to light, readings are also below. All channels were flagged when the pump for the non-toxic supply was temporarily switched off.

Temperature and Salinity

Strong variations in sea surface temperatures (measured at the raw water inlet and in the housing; Temp_r, Temp_h) and Salinity, were observed. Subsequently, the sensors were switched off and on, on 11th July 2013 at 12:30 GMT, however this had no effect on the data. It was noted that these variations coincided with the beginning of the MSS (microstructure) profiling, during which the ship's speed was reduced to 0.5-1 kn. Increasing atmospheric pressure and rising air temperatures were also observed during this period, and subsequently a strong thermocline developed in the surface layer. It was concluded that the vertical motion of the ship through the stratified surface layer caused the strong variations in observed sea surface temperatures. (Originators assessment)

Chlorophyll

The manufacturers calibrated chlorophyll should be treated with caution. Calibration of underway fluorimetry is notoriously difficult because of daytime fluorescence quenching in surface waters. (Originators assessment)

Data Access Policy

Open Data supplied by Natural Environment Research Council (NERC)

You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."

Narrative Documents

SeaBird Digital Oceanographic Thermometer SBE38

The SBE38 is an ultra-stable thermistor that can be integrated as a remote temperature sensor with an SBE21 Thermosalinograph or an SBE 45 Micro TSG, or as a secondary temperature sensor with an SBE 16 plus, 16plus-IM, 16plus V2, 16plus-IM V2 or 19plus V2 SEACAT CTD.

Temperature is determined by applying an AC excitation to reference resistances and an ultra-stable aged thermistor. The reference resistor is a hermetically sealed VISHAY. AC excitation and ratiometric comparison using a common processing channel removes measurement errors due to parasitic thermocouples, offset voltages, leakage currents and gain errors.

The SBE38 can operate in polled sampling, where it takes one sample and transmits the data, or in continuous sampling.

Specifications

Further details can be found in the manufacturer's specification sheet.

WET Labs WETStar Fluorometers

WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.

Specifications

By model:

All models:

Further details can be found in the manufacturer's specification sheet, and in the instrument manual.

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.

Specifications

Further details are available in the manufacturer's specification sheet or user guide.

RRS James Cook JC088 Surface Hydrography Instrumentation

Instrumentation

The sea surface hydrographical suite of sensors was fed by the pumped-seawater, non-toxic supply. The depth of the seawater intake was at 5.5 m.

The following surface hydrology sensors were fitted:

SeaBird MicroTSG Thermosalinograph SBE 45

The SBE45 MicroTSG is an externally powered instrument designed for shipboard measurement of temperature and conductivity of pumped near-surface water samples. The instrument can also compute salinity and sound velocity internally.

The MicroTSG comprises a platinum-electrode glass conductivity cell and a stable, pressure-protected thermistor temperature sensor. It also contains an RS-232 port for appending the output of a remote temperature sensor, allowing for direct measurement of sea surface temperature.

The instrument can operate in Polled, Autonomous and Serial Line Sync sampling modes:

• Polled sampling: the instrument takes one sample on command
• Autonomous sampling: the instrument samples at preprogrammed intervals and does not enter quiescence (sleep) state between samples
• Serial Line Sync: a pulse on the serial line causes the instrument to wake up, sample and re-enter quiescent state automatically

Specifications

Further details can be found in the manufacturer's specification sheet.

RRS James Cook JC088 Surface Hydrography processing procedures

Originator's Data Processing

The data were logged by the TECHSAS (TECHnical and Scientific sensors Acquisition System) system into daily NetCDF files. The TECHSAS system is used as the main data logging system on NMF-SS operated research vessels. Data were additionally logged into the RVS Level-C format files.

Each Level-C file was read into Matlab so that further processing, calibration and quality control could be performed on selected variables.

Samples from the ships underway water supply were taken every 6 hours up until 25th June 2012, and then every 4 hours thereafter, in order to provide calibration for salinity and chlorophyll concentration.

Salinity

A total of 136 useable salinity samples were analyzed using a Guildline Autosal salinometer (S/N 60839) against standard seawater. After the residuals were calculated, three distinct step changes were detected in the data. These coincided with the weekly non-toxic cleaning of the underway data. As a result, four periods were chosen to be analysed separately.

These periods were:
1st: 28th June - 4th July 2013
2nd: 4th - 12th July 2013
3rd: 12th - 19th July 2013
4th: 19th - 22nd July 2013

During the first period a total of 25 samples were used from which the mean and standard deviation of residuals (Sample SBE45) is - 0.0045 ±0.0011. An offset of -0.0045 has therefore been applied to the SBE45 underway salinity during this period.

During the second period 39 samples were used from which the mean and standard deviation of residuals (Sample SBE45) is - 0.0086 ±0.0014. An offset of -0.0086 has therefore been applied to the SBE45 underway salinity during this period.

During the third period 32 samples were used from which the mean and standard deviation of residuals (Sample SBE45) is - 0.0191 ±0.0014. An offset of -0.0191 has therefore been applied to the SBE45 underway salinity during this period.

During the last period 10 samples were used from which the mean and standard deviation of residuals (Sample SBE45) is - 0.0242 ±0.000712. An offset of -0.0242 has therefore been applied to the SBE45 underway salinity during this period.

Chlorophyll

A chlorophyll calibration was not attempted while at sea. The voltage (Fluor) and manufacturer calibration (CHL in µg/l) were provided to BODC in the .mat files but should be treated with caution.

Calibration of underway fluorimetry is notoriously difficult because of daytime fluorescence quenching in surface waters. During the day when the amount of incoming solar radiation is highest, light levels exceed the amount that phytoplankton cells in the surface can process and the excess energy is dissipated as heat rather than fluorescence. In this situation, the amount of fluorescence measured, relative to the amount of chlorophyll pigment present is decreased. In-situ measurements of chlorophyll concentration would therefore not show the same amount of chlorophyll present in the water. Other factors that can add significant variability in the relationship between fluorescence and pigment concentration are: community composition, light history of the cells (changes in mixed layer depth or stratification caused for example by a wind event), and nutrient limitation.

The worst spiking from a number of channels was removed, by identifying measurements falling beyond x standard deviations of the median within a Δt second window. In exceptional cases, spikes were identified and removed manually.

The Matlab surface hydrography files provided to BODC were used for BODC processing. Data were additionally logged into the RVS Level-C format files and TECHSAS which have been archived at BODC.

For more detailed information on the Originator's underway data processing, please see the cruise report

Files delivered to BODC

BODC Data Processing

The files were reformatted to BODC internal format using standard data banking procedures. All files were reduced to 60 second intervals. The following table shows how the variables within the files were mapped to appropriate BODC parameter codes:

JC88_SURF1_1s.mat

JC88_SURF2_1s.mat

Screening

All the reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag.

Calibration

Field Calibrations

Salinity was calibrated as described in the originators processing section above.

Manufacturers Calibrations

Transmissometer

The transmissometer voltage channel was converted to beam transmission ( beamtrans ) and beam attenuation ( atten ) by the originator as follows:

beamtrans [%] = ([ volts - Vdark ] / [ Vref - Vdark ])100

atten [per m] = (-1/ pathlength ) ln( beamtrans /100)

where Vdark = 0.060 V, Vref = 4.665 V and pathlength = 0.25 m.

Fluorometer

The fluorescence voltage channel was converted to engineering units ( chla ) by the originator using the following calibration:

chla [µg/L]= SF ( volts - CWO )

where SF = 12.7 µg/L/V and CWO = 0.057 V.

Project Information

Fluxes Across Sloping Topography of the North East Atlantic (FASTNEt)

Background

The FASTNEt consortium was funded to deliver NERC's Ocean Shelf Edge Exchange Programme. Commencing in October 2011, this four year study aims to couple established observational techniques, such as moorings and CTDs, with the very latest in autonomous sampling initiatives - including use of Autosub Long Range and gliders. With the aid of novel model techniques, these observations will be utilised to construct a new paradigm of Ocean/Shelf exchange.

Shelf edge regions mark the gateway between the world's deep oceans and shallower coastal seas, linking terrestrial, atmospheric and oceanic carbon pools and influencing biogeochemical fluxes. Shelf edge processes can influence near-shore productivity (and fisheries) and ultimately affect global climate.

FASTNEt brings together researchers from multiple UK organisations. Further collaboration has been established with five Project Partners: the UK Met Office, Marine Scotland Science, Agri-Food and Biosciences Institute, Marine Institute Ireland and Scripps Institution of Oceanography.

Scientific Objectives

• To determine the seasonality of physical gradients and exchange across the shelf edge by deploying new observational technologies (gliders, Autosub Long Range) and established techniques (long term moorings, drifters)
• To quantify key exchange mechanisms and to collect new data targeted at testing and improving high resolution models of the shelf edge, by carrying out detailed process studies in contrasting regions of the shelf edge of the NE Atlantic margin
• To develop a new parameterisation of shelf edge exchange processes suitable for regional-scale models, using improved resolution numerical, and new empirical models constrained by the observations
• To test the new parameterisations in a regional model in the context of making an assessment of inter-annual variability of ocean-shelf exchange.

Fieldwork

Three survey sites on the UK shelf edge have been selected for FASTNEt. These are a) the Celtic Sea shelf edge, b) Malin shelf and c) North Scotland shelf. Fieldwork is centred around two research cruises. The first, to the Celtic Sea, on RRS Discovery in June 2012. The second cruise visits the Malin shelf on RRS James Cook, during summer 2013. In addition to these dedicated cruises, opportunist cruise activity to the North Scotland shelf has been agreed with project partner Marine Scotland Science. Autonomous technologies will complement observations made during the cruises and provide knowledge of seasonal and inter-annual variability in exchange processes.

Instrumentation

Types of instruments/measurements:

• Gliders
• Autosub Long Range
• Drifter buoys
• Scanfish
• Microstructure profilers
• Moored CTD/CT loggers and ADCPs
• Shipboard measurements: CTD, underway, nutrients (and other discrete sampling), LADCP, ADCP.

Contacts

Data Activity or Cruise Information

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

No Fixed Station Information held for the Series

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle: