Metadata Report for BODC Series Reference Number 2012266

• 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

No Problem Report Found in the Database

James Clark Ross Cruise AMT28 (JR18001) CTD Data Quality Document

Temperature, salinity, potential temperature and sigma-theta: Entrainment features were visible in a number of casts, both in the frame mounted (primary) and vane mounted (secondary channels). These features were apparent throughout the thermocline/pycnocline and continued down to varying depths. The level of entrainment can be indicated by a variation between data points of around 0.2 to 0.3 °C in the temperature, of 0.04-0.05 in the salinity and 0.02 kg m^-3in sigma-theta. Overall, the secondary temperature, salinity and density channels were deemed to be of better quality and were retained for banking in the NODB, while primary channels were discarded.

Chlorophyll: Uncalibrated chlorophyll values were frequently negative and have therefore been flagged, however values that have had the manufacturers calibration look to be good quality.

Down and up-welling PAR irradiance: Optics casts were taken pre-dawn and at solar noon. Therefore, for almost half the casts, the PAR values are negligible as they were recorded in the dark.

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

Sea-Bird Dissolved Oxygen Sensor SBE 43 and SBE 43F

The SBE 43 is a dissolved oxygen sensor designed for marine applications. It incorporates a high-performance Clark polarographic membrane with a pump that continuously plumbs water through it, preventing algal growth and the development of anoxic conditions when the sensor is taking measurements.

Two configurations are available: SBE 43 produces a voltage output and can be incorporated with any Sea-Bird CTD that accepts input from a 0-5 volt auxiliary sensor, while the SBE 43F produces a frequency output and can be integrated with an SBE 52-MP (Moored Profiler CTD) or used for OEM applications. The specifications below are common to both.

Specifications

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

RRS James Clark Ross JR18001 CTD Instrumentation

A stainless steel Sea-Bird 911 plus CTD system was used on cruise JR18001. This was mounted on a SBE-32 carousel water sampler holding 24 x 20-litre Niskin bottles. The CTD was fitted with the following scientific sensors:

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus, that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus.

Specifications

Specifications for the SBE 9 plus underwater unit are listed below:

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

Chelsea Technologies Group Aquatracka MKIII fluorometer

The Chelsea Technologies Group Aquatracka MKIII is a logarithmic response fluorometer. Filters are available to enable the instrument to measure chlorophyll, rhodamine, fluorescein and turbidity.

It uses a pulsed (5.5 Hz) xenon light source discharging along two signal paths to eliminate variations in the flashlamp intensity. The reference path measures the intensity of the light source whilst the signal path measures the intensity of the light emitted from the specimen under test. The reference signal and the emitted light signals are then applied to a ratiometric circuit. In this circuit, the ratio of returned signal to reference signal is computed and scaled logarithmically to achieve a wide dynamic range. The logarithmic conversion accuracy is maintained at better than one percent of the reading over the full output range of the instrument.

Two variants of the instrument are available, both manufactured in titanium, capable of operating in depths from shallow water down to 2000 m and 6000 m respectively. The optical characteristics of the instrument in its different detection modes are visible below:

* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.

The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l^-1 to 100 µg l^-1. The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).

The instrument accuracy is ± 0.02 µg l^-1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).

Further details are available from the Aquatracka MKIII specification sheet.

Biospherical Instruments QSP-2350 underwater PAR sensor

Quantum Scalar Irradiance PAR Sensor. Developed for data loggers with limited dynamic range. It uses a scalar irradiance collector to obtain a uniform directional response over 3.6-pi steradians. A stainless���steel encased optical light pipe guides flux from the collector to a filtered silicon pho���todetector, resultng in a flat quantum response over the PAR spectral region (400���700 nm). The sensor produces a logarithmically compressed analog voltage output and BH���4���MP connector Operates in waters depths up to 2000 m.

For more information, please see this document: https://www.bodc.ac.uk/data/documents/nodb/pdf/Biospherical_QSP_2300_2350_series_brochure.pdf

Tritech Digital Precision Altimeter PA200

This altimeter is a sonar ranging device that gives the height above the sea bed when mounted vertically. When mounted in any other attitude the sensor provides a subsea distance. It can be configured to operate on its own or under control from an external unit and can be supplied with simultaneous analogue and digital outputs, allowing them to interface to PC devices, data loggers, telemetry systems and multiplexers.

These instruments can be supplied with different housings, stainless steel, plastic and aluminum, which will limit the depth rating. There are three models available: the PA200-20S, PA200-10L and the PA500-6S, whose transducer options differ slightly.

Specifications

Common specifications are presented below

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

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.

Originators Data Processing of CTD casts from cruise JR18001 (AMT28)

Sampling Strategy

In total, 63 CTD casts along the cruise transect were deployed to obtain profiles of the water column from a range of sensors. All casts were conventional profiling casts with 24 x 20L Ocean Test Equipment (OTE) Niskin bottles for sampling water. CTDs were deployed pre-dawn at ~04:30am and noon ~1.00pm ship time each day, from 25th September 2018 until 27th October 2018. Profiles were down to 500 metres depth twice a day, with two 5000 m CTDs and one 1500 m CTD. Sensors on the CTD included pressure, temperature, conductivity, oxygen, fluorescence, PAR, turbidity, transmittance and attenuance.

Data Processing

The Sea-bird data collection software Seasave-Win32 recorded the raw data output from the CTD casts. Processing the raw data occurred daily, following the BODC recommended guidelines using SBE Data Processing-Win32 v7.26.7. Subsequently, the following processing routines were run to convert the raw CTD data into CNV files, each routine is named after each stage in brackets < >:

• Data conversion - converted raw binary Sea-Bird files to ASCII files (CNV) containing the 24 Hz data for up and down casts <DatCnv>.
• Generation of bottle files for each cast containing the mean values of all the variables at the time of bottle firing events <Bottle Summary>.
• Using the CNV files, processing routines were applied to remove pressure spikes <WildEdit>.
• The oxygen sensor was then shifted relative to the pressure by 2 seconds, to compensate for the lag in the sensor response time <AlignCTD> .
• The effect of thermal 'initia' on the conductivity cells was removed <CellTM>.
• Identification of the surface soak for each cast using <Seaplot>, removed manually and then LoopEdit run.
• Salinity and oxygen concentration were re-derived and density (sigma-theta) values were derived after the corrections for sensor lag and thermal inertia had been applied <Derive>.
• The CTD files produced from Sea-Bird processing were converted from 24Hz ascii files into 1 dbar downcast files for calibration and visualisation on-board <BinAverage>.
• Removal of the initial salinity and oxygen channels produced at the DatCnv stage, along with the conductivity, voltage and altimeter channels from the 1-dbar downcast files <Strip>.

Prior to processing the xmlcon files were checked to against the instrument calibration sheets to ensure the correct set up details were used.

Data were then processed using the Mexec processing suite (a set of Matlab and shell scripts developed by Brian King (NOC) and updated by numerous users, including substantial recent updates by Yvonne Firing). All CTD processing and calibration for JR18001 was executed using Mexec v3.2.

Calibrations

Collation of the sensor values at bottle firing generated by the <Bottle Summary> routine formed the dataset for calibrating the two CTD salinity sensors and oxygen sensor against discrete bench salinometer measurements and oxygen Winkler measurements, respectively. The fluorometer sensor was calibrated post-cruise using AC-9 data calibrated against HPLC data. The CNV files were converted to ODV format and calibrations were applied using ODV software.

To generate a calibration, an offset between the discrete water sample measurement (salinity/oxygen) and the nominal value from the sensor at bottle firing was calculated. Outliers were identified using plots of offset against the discrete sample values and a linear regression was applied.

Where the regression was strong and significant the calibration equation was derived by rearranging the regression equation:

Offset = a * Discrete sample + b

Where: offset = Discrete sample - Sensor value

To give: Calibrated value = 1/(1-a) * Sensor value + b/(1-a)

Where the regression was not significant the mean value of the offset was applied. All calibration datasets are available upon request from BODC post cruise.

Salinity

The salinity channels were calibrated against bench salinometer measurements from five samples on average collected from CTD casts every few days. Further details of these measurements can be found in the salinity sampling cruise report section.

For the primary CTD salinity sensor, there was a weak but significant relationship between bench salinity and offset. Applying a regression did not improve the dataset so the mean offset was applied.

The secondary CTD salinity sensor was calibrated against discrete salinity measurements. Again, there was a weak but significant relationship between bench salinity and offset. Applying a regression did not improve the dataset, so the mean offset was applied.

Oxygen

Calibration of the SBE 43 oxygen sensor against discrete oxygen Winkler titration measurements used five depths collected from the pre-dawn and noon CTDs. Further details of these measurements can be found in the oxygen sampling cruise report section. The oxygen sensor operated without problems throughout the the cruise. Several data points did not fit the pattern observed with the data from the other casts and so were excluded from the calibration data set. There was a strong, significant relationship between the offset and the discrete oxygen data, so the trend below was applied to the CTD oxygen data.

Fluorometer

The CTD fluorometer operated without problem during the cruise. Calibration of the CTD fluorometer sensor against sample data will be carried out after the cruise against AC-9 and HPLC data.

RRS James Clark Ross JR18001 CTD BODC Processing

The CTD data were supplied to BODC as one ODV file which was converted to a .txt file and then transferred to the BODC internal format.

During transfer the originator's variables were mapped to unique BODC parameter codes. The following table shows the parameter mapping.

ODV flags applied during originators processing were transferred as 'K' flags

Following transfer the data were screened using BODC in-house visualisation software. Improbable data values were assigned the appropriate BODC data quality flag. Missing data values, where present, were changed to the missing data value and assigned a BODC data quality flag.

Parameters found in the file and that were not transferred are available upon request. Second sensor parameters have been removed from the final file but can also be provided on request.

Project Information

Marine LTSS: CLASS (Climate Linked Atlantic Sector Science)

Introduction

CLASS is a five year (2018 to 2023) programme, funded by the Natural Environment Research Council (NERC) and extended until March 2024.

Scientific Rationale

The ocean plays a vital role in sustaining life on planet Earth, providing us with both living resources and climate regulation. The trajectory of anthropogenically driven climate change will be substantially controlled by the ocean due to its absorption of excess heat and carbon from the atmosphere, with consequent impacts on ocean resources that remain poorly understood. In an era of rapid planetary change, expanding global population and intense resource exploitation, it is vital that there are internationally coordinated ocean observing and prediction systems so policy makers can make sound evidence-based decisions about how to manage our interaction with the ocean. CLASS will underpin the UK contribution to these systems, documenting and understanding change in the marine environment, evaluating the impact of climate change and effectiveness of conservation measures and predicting the future evolution of marine environments. Over the five-year period CLASS will enhance the cost-effectiveness of observing systems by migrating them towards cutting edge autonomous technologies and developing new sensors. Finally, CLASS will create effective engagement activities ensuring academic partners have transparent access to NERC marine science capability through graduate training partnerships and access to shipborne, lab based and autonomous facilities, and modelling capabilities.

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: