Metadata Report for BODC Series Reference Number 1747909

• 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

Attenuation due to backscatter channels in all casts is problematic and BODC advise caution if looking at these data. The complete channels have been flagged for every CTD profile as the channels are frequently constant at around zero, the data do not appear reasonable or realistic.

AMT23 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 approximately 200 dbar. The level of entrainment can be indicated by a variation between data points of 0.2 °C in the temperature, of 0.02-0.03 in the salinity and 0.1 kg m^-3 in sigma-theta. The vane mounted sensors should theoretically be of better quality than the frame mounted sensors as they are held outside the water mass being carried down within the CTD frame structure, however there was a lot of spiking with spurious data that was not present on the primary channels. Therefore the primary temperature, salinity and density were retained for banking in the NODB, while secondary channels were discarded.

Chlorophyll: In circumstances where data were collected at pressures > 200 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. Only the BAS casts have a calibrated chlorophyll channel.

Dissolved oxygen concentration and oxygen saturation: Overall profiles appear good and few flags were applied. Only the BAS casts have a calibrated oxygen channel.

Attenuance and transmissance: A few spikes were flagged where the values appeared improbable. On most casts, below ~100 m the values go outside of the expected range for the parameter (either over 100% for transmittance or negative for attenuance). These values have been flagged and caution is recommended when using these data.

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. Some intermittent flags have been applied to values outside the parameter range.

Backscatter: These channels should be used with caution as the values are unrealistic. All channels have been completely flagged as improbable

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 JR300 AMT23 BAS CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911plus 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, two BB-RTD sensors (one red light and one green light), a transmissometer, dissolved oxygen sensor and a fluorometer as auxilliary sensors. All instruments were attached to a 24 position stainless steel Sea-Bird SBE 32 carousel water sampler (S/N 3246833-0636) equipped with 24 x 20 litre Ocean Test Equipment 20L ES-120B water samplers, (s/n's 1A -12A, 15A-21A, 24A, 26A, 34A, 45A, 47A). 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 JR300 AMT23 BODC CTD Processing

BODC CTD processing

BODC received the CTD profiles from the originator in ODV format, in a combined file for all casts performed during the cruise. The data were converted from tab delimited ODV format into BODC internal format using BODC transfer function 480. Only the final calibrated channels were transferred to BODC format. The following table shows how the original ODV variables were mapped to appropriate BODC parameter codes. Oxygen saturation and sigma-theta were derived internally by BODC and added to the profiles during the transfer.

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.

The vane mounted sensors suffered more from spiking and spuious data values than did the sensors in the frame and therefore the primary temperature, salinity and density were retained for banking in the NODB, while the secondary channels were discarded.

Banking

The profiles were banked to the National Oceanographic Database (NODB) following BODC procedures.

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), 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, 53pp.

RRS James Clark Ross Cruise JR300 AMT23 Originators CTD Processing

Sampling strategy

A total of 65 CTD casts were completed during the cruise. All casts were conventional profiling casts using a stainless steel (SS) CTD frame. 54 casts (BAS casts) were deployed with water sampling by 24 x 20L OTE Niskin bottles. The remaining 11 casts (NOC casts) were deployed with water sampling by 24 x 10L OTE Niskin bottles. CTD deplopyments were typically carried out at pre-dawn (~5.00 GMT) and solar noon (~13:00 GMT) each day, with one deployment at each station. On eleven occations, a second CTD deployment using the NOC frame was performed for collection of large water volumes. On 04 November 2013 the noon station was cancelled due to rough weather. A total of 65 casts were completed for water bottle sampling during the cruise, and the CTD's operated without any issues.

Cruise processing

Data from the CTD casts were recorded using the Sea-Bird data collection software Seasave-Win32 (Seasave V 7.22.3). The software outputs were processed following the BODC recommended guidelines using SBE Data Processing-Win32 v7.22.5; the processing routines are named after each stage in brackets < >. The software applied the calibrations as appropriate through the instrument configuration files 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) 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 2 Hz ascii files of the complete cast (down and upcasts) with all channels for archive at BODC and also to 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 Sea-Bird 1 dbar downcast files were converted from the Sea-Bird CNV format to the tab delimited ODV format using the mapping described below:

Field Calibrations

The sensor values at bottle firing produced by the Bottle Summary routine were collated and used to generate calibration datasets for the salinity, oxygen and fluorometer channels. Discrete 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). Discrete chlorophyll and oxygen samples were taken from the BAS casts only. Discrete salinity samples were taken from both rigs.

Calibrated salinity, oxygen and fluorometer channels were then added to the ODV profiles using the calibration equations derived and shown below. Once the calibrations were applied to the files in ODV, a combined ODV file containing all casts was extracted and provided to BODC.

Pressure

No adjustments were made to the values resulting from application of manufacturer's coefficients during the initial processing.

Temperature

Temperature readings from the two temperature sensors were almost identical outside of entrainment features and no other independent measurements of better quality were available. No further correction was therefore applied to the data.

Salinity

BAS Rig

The salinity data were calibrated by comparing the sensor readings from the up-cast at the point when the bottles were fired with the discrete salinity data measured using the bench salinometer on water samples collected from fired bottles. The samples collected were from four to six depths for each cast. Offsets were generated between the salinometer and CTD sensor values and plotted against cast and salinometer values. The linear regressions from the offset against bench salinometer data were not significant for sensor 1 or 2 so the mean offset was applied. The RMS residual showed a reduction from 0.00049 to 0.00025 for sensor 1 after calibration indicating an improved fit to the sample data. No change occurred in the RMS residual for sensor 2 (0.00016).

NOC rig

The linear regressions from the offset against bench salinometer data were not significant for both sensors, so the mean offset was applied. The RMS residual remained the same after applying the mean offset for both sensors (0.00007 for both sensor 1 and 2).

Dissolved oxygen

The oxygen sensors were calibrated by comparing the SBE43 sensor readings from the CTD up-cast at the point when the bottles were fired with the dissolved oxygen concentrations from Winkler titrations on water samples collected from the fired bottles. The samples collected were from six or seven depths from the pre-dawn CTD casts throughout the cruise. The linear regressions from the offset (Winkler titration data - SBE43 data) against Winkler titration data was significant (r = 0.40353).

The reduction in the RMS residual (uncalibrated = 0.45681, calibrated = 0.35051) indicated an improved match to the Winkler titration dataset after calibration.

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, shown 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 54 stations from an average of 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 Chelsea AQUAtracka MkIII fluorometer attached to the CTD rig operated without problem.

The reduction in the RMS residual (uncalibrated = 0.269309, calibrated = 0.146539) indicated an improved match to the extracted chl-a sample dataset after calibration.

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.

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: