Metadata Report for BODC Series Reference Number 1733404

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• 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 AMT25 (JR15001) 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 primary temperature, salinity and density channels were deemed to be of better quality and were retained for banking in the NODB, while secondary channels were discarded.

Chlorophyll: In circumstances where data were collected at pressures typically > 150 dbar, negative concentrations were frequently visible. These were flagged as anomalous. These resulted from the chlorophyll calibration being optimised for the euphotic zone, in particular the fluorescence/chlorophyll maximum.

Dissolved oxygen concentration and oxygen saturation: Several deep casts exhibited strong variability in the deeper water around 2000 m depth.

Attenuance and transmissance: Casts 003, 004, 006 and 055 had some values outside the parameter range (0-400 m^-1) and (0-100%) which were flagged as anomalous. In some cases, the whole profile was flagged. This may be due to a suspect manufacturer's calibration. Although the values should be teated with caution, the shape of the profiles are still representative of the parameter.

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 Cruise JR15001 AMT25 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911 plus system, consisting of an SBE 11 plus deck unit and a 9 plus underwater unit. The CTD was fitted with an altimeter, a downwelling PAR sensor, transmissometer, backscatter sensor and a fluorometer as auxilliary sensors. All instruments were attached to a 24 position stainless steel Sea-Bird SBE 32 carousel water sampler equipped with 24 Ocean Test Equipment 20L water samplers. The table below lists more detailed information about the various 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 Log Quantum Cosine Irradiance Sensor QCD-905L

The QCD-905L is a submersible radiometer designed to measure irradiance over Photosynthetically Active Radiation (PAR) wavelengths (400-700 nm). It features a cosine directional response when fully immersed in water.

The sensor is a blue-enhanced high stability silicon photovoltaic detector with dielectric and absorbing glass filter assembly, and produces a logarithmic output. Normal output range is -1 to 6 volts with 1 volt per decade. Typically, the instrument outputs 5 volts for full sunlight and has a minimum output of 0.001% full sunlight, where typical noon solar irradiance is 1.5 to 2 x 10¹⁷ quanta cm^-2 s^-1. The instrument can be calibrated with constants for µE cm^-2 s^-1 or quanta cm^-2 s^-1.

The QCD-905L can be coupled to a fixed range data acquisition system like a CTD (Conductivity-Temperature-Depth) profiler or current meter. It has an aluminium and PET housing, and a depth rating of 7000 m.

Specifications

Further details can be found in the manufacturer's manual.

WETLabs Single-angle Backscattering Meter ECO BB

An optical scattering sensor that measures scattering at 117°. This angle was determined as a minimum convergence point for variations in the volume scattering function induced by suspended materials and water. The measured signal is less determined by the type and size of the materials in the water and is more directly correlated to their concentration.

Several versions are available, with minor differences in their specifications:

• ECO BB(RT)provides analog or RS-232 serial output with 4000 count range
• ECO BB(RT)D adds the possibility of being deployed in depths up to 6000 m while keeping the capabilities of ECO BB(RT)
• ECO BB provides the capabilities of ECO BB(RT) with periodic sampling
• ECO BBB is similar to ECO BB but with internal batteries for autonomous operation
• ECO BBS is similar to ECO BB but with an integrated anti-fouling bio-wiper
• ECO BBSB has the capabilities of ECO BBS but with internal batteries for autonomous operation

Specifications

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.

RRS James Clark Ross Cruise JR15001 AMT25 CTD Processing Document

Sampling Protocol for Data Acquisition and Analysis

A total of 74 CTD casts (casts 001 to 081 but excluding casts 049 to 054) were completed during the AMT25 cruise. The cruise departed from Immingham, UK on 15th September 2016 and arrived in Port Stanley, Falkland Islands on 04th November 2016. The ship docked at Portsmouth to take on fuel at approximately 07:00 on 17th September 2015 and then departed Portsmouth on 17th September 2015 at 16:00. The ship briefly stopped at the Azores on 24th September 2015 (did not dock) to exchange personnel and made a port call at Praia, Cape Verde on 07th October 2015 for several hours, departing the same day. A change of personnel from AMT to BAS scientists occurred at Ascension Island on 15th to 18th October 2015. CTD data collected during the phase around Ascension Island are available as part of a BAS funded project and consisted of CTD's 049 to 054. All casts were conventional stainless steel profiling casts with water sampling by 24 x 20L OTE Niskin bottles. Casts were carried out at around 04:00-05:00 and around 13:00-14:00 ship time each day weather permitting.

BODC Cruise Processing

CTD casts were recorded using the Sea-Bird data collection software Seasave-Win32. The software outputs were then processed following the BODC recommended guidelines using SBE Data Processing-Win32 v7.23.2; the processing routines are named after each stage in brackets < >. The software applied the calibrations as appropriate through the instrument configuration file to the data in engineering units output by the CTD hardware.

An ASCII file (CNV) containing the 24 Hz data for up and down casts was generated from the binary Sea-Bird files for each cast <DatCnv>. Files were created for each cast containing the mean values of all the variables at the 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> and the effect of thermal 'inertia' on the conductivity cells was removed <CellTM>. The surface soak was identified for each cast, removed and LoopEdit run. Salinity and oxygen concentration were re-derived and density (sigma-theta) values were derived <Derive> after the corrections for sensor lag and thermal 'inertia' had been applied. The CTD files produced from Sea-Bird processing were converted from 24 Hz ASCII files into 1 dbar downcast files for calibration and visualisation onboard <BinAverage>. The initial salinity and oxygen channels produced at the DatCnv stage, along with the conductivity, voltage and altimeter channels were removed from the 1 dbar downcast files <Strip>.

The sensor values at bottle firing produced by the Bottle Summary routine were collated and used to generate calibrations for the salinity, oxygen and fluorometer channels where appropriate. Water samples were collected from each cast for measurement of salinity (bench salinometer) and chlorophyll-a (filtration, acetone extraction and fluorometer measurement) and from the pre-dawn cast each day for oxygen (Winkler titration).

The table below shows the parameters available in the final processed CNV files provided to BODC and the channel names in the final ODV file. Calibrated salinity, oxygen and fluorometer channels were then added to the profiles where appropraite using calibration equations derived from the bottle file data compared against discrete samples collected from the CTD water bottles on each cast.

Calibrations

The method used for calibration was to generate an offset between the discrete water sample measurement (salinity/oxygen/chl-a) and the nominal value from the sensor at bottle firing. The offsets were then plotted against the discrete sample values and a linear regression applied.

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 if appropriate. All calibration datasets are available upon request from BODC post cruise.

Temperature

There were no independent measurements of temperature made during the cruise and the sensors on the rig returned consistent data. No further calibration of these sensors has been carried out.

Salinity

The salinity channels were calibrated against bench salinometer measurements from 2 - 4 samples collected from each cast. Further details of these measurements can be found in the documentation for the discrete salinity dataset.

The regression for both salinity sensors was not significant and so was not applied. The mean offset for both sensors was also not applied as the standard deviation of the offsets was larger than the average offset.

Primary Conductivity Sensor SBE 4C-2248: n = 106; r² = 0.011; p = 0.2885; mean offset = 0.0010; standard deviation of offsets = 0.0130

Secondary Conductivity Sensor SBE 4C-4471: n = 107; r² = 0.0011; p = 0.7367; mean offset=0.0064; standard deviation of offsets = 0.0148

Oxygen

The oxygen sensor was calibrated against discrete oxygen sample Winkler titration measurements from up to 18 samples collected from the pre-dawn and solar noon CTD's.

The oxygen sensor operated without problem throughout the cruise

Several Winkler titration samples did not fit the pattern observed with the data from the other casts and were excluded from the calibration dataset.

The calibration equation was:

Calibrated O_{2 (in µmol/l)} = 1.0526 * sensor O_{2 (in µmol/l)} + 12.9936 (n=664; r²=0.137; p < 0.001);

Fluorescence

The CTD deployed Chelsea AQUAtracka MkIII fluorometer was calibrated against extracted chlorophyll-a measurements made on seawater collected by Niskin bottles on each cast. Calibrations were derived individually for each cast where appropriate as shown in the table below. Samples of seawater from CTD niskin bottles were collected to calibrate the CTD fluorometer with the analytical method following Welschmeyer (1994). Samples were collected at 74 stations from up to 10 depths including light depths from 97, 55, 33, 14, 7, 1 and 0.1%. Each sample of 250 ml was filtered through 47 mm 0.2 µm polycarbonate filters. The filters were then placed in a vial with 10 ml 90% acetone and left in a freezer for 24 hours. The samples were then analysed on a pre-calibrated Turner Designs Trilogy fluorometer with a non-acidified chl module (CHL NA #046) fitted. The pre-calibrated fluorometer produced anomalous results during analysis throughout the cruise, however as there were no dilutions of pure chlorophyll stock available, the calibration was not checked or modified. To compensate for this, the fluorometer was back-calibrated at PML after the cruise and the results were updated based on the new fluorometer calibration. The regression analysis was not significant for casts 3, 4, 5, 44, 46, 76 and 78 and so the fluorometer channel on these casts were not calibrated.

The Chelsea AQUAtracka MkIII fluorometer attached to the CTD rig operated without problem.

References

Welschmeyer N.A., 1994. Fluorometric analysis of chlorophyll-a in the presence of chlorophyll-b and phaeopigments. Limnology and Oceanography, 39(8), 1985-1992.

BODC post-processing and screening

Reformatting

The data were converted from tab delimited ODV format into BODC internal format using BODC transfer function 480. Final calibrated channels have been transferred were possible, but where a calibration was not possible, the uncalibrated channel has been transferred. The following table shows how each variable was mapped to appropriate BODC parameter codes. Oxygen saturation, sigma-theta and potential temperature were derived and added to the profiles during the transfer process.

References

Benson, B.B. and Krause, D., 1984. The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. Limnology and Oceanography, 29(3), pp. 620-632.

Fofonoff, N.P. and Millard, R.C., 1983. Algorithms for computations of fundamental properties of seawater. UNESCO Technical Papers in Marine Science No. 44, pp. 53

Screening

Reformatted CTD data were transferred onto a graphics work station for visualisation using the in-house editor EDSERPLO. No data values were edited or deleted. Flagging was achieved by modification of the associated BODC quality control flag for suspect or null values.

Project Information

No Project Information held for the Series

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: