Metadata Report for BODC Series Reference Number 1147595

• 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

RSS James Clark Ross Cruise JR20130109/JR274 CTD Data Quality Document

Cast76s contains some anomalous data for several of the channels such as chlorophyll and oxygen concentration, therefore the data should be used with caution.

Attenuance (ATTNDR01)

Attenuance data are only available from the stainless steel CTD casts.

Downwelling Irradiance (DWIRPP01)

These profiles are only available for the titanium CTD casts. Many of the profiles are constant with values of zero. Casts CTD39t and CTD48t were deployed at night in the dark so values of zero would be expected. All other casts with consistant values of zero however, were not deployed in the dark and so have been flagged as suspect. Several of the series have data points that are beyond the acceptable range of the parameter (0-500 W m^-2). These data points have been flagged as suspect.

Downwelling Irradiance (IRRDUV01)

Several of the series have data points that are beyond the acceptable range of the parameter (0-2500 µE m^-2s^-1). These data points have been flagged as suspect.

Chlorophyll concentration (CPHLPM01)

Several of the series have data points that are beyond the acceptable range of the parameter (0-999 mg m^-3). These data points have been flagged as suspect.

Oxygen concentration (DOXYSC01 and DOXYSU01)

Several of the series have data points that are beyond the acceptable range of the parameter (0-600 µmol L^-1). These data points have been flagged as suspect.

Data Access Policy

Public domain data

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

The recommended acknowledgment is

"This study uses data from the data source/organisation/programme, provided by the British Oceanographic Data Centre and funded by the funding body."

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.

Instrument Description JR20130109 Stainless Steel Frame

Standard Rosette CTD Unit and Auxiliary Sensors

Two CTD systems were used during this cruise; a stainless steel frame and a titanium frame. This document outlines the instrument description of the stainless steel frame.

A 24-way stainless steel frame (s/n SBE CTD6), with a Sea-Bird 9 plus CTD underwater unit (SN 09P-30856-0707) and SBE 11 plus deck unit (s/n 11P-20391-0502) was used throughout the cruise. All auxiliary instruments were attached to a Sea-Bird 32 24-way carousel (s/n 32-46833-0636) with Ocean Test Equipment 20L water samplers (s/n 1A -12A, 15A-21A, 24A, 26A, 34A, 45A, 47A).

The table below provides further information on the CTD sensors.

Instrument Description JR20130109 Titanium Frame

Standard Rosette CTD Unit and Auxiliary Sensors

Two CTD systems were used during this cruise; a stainless steel frame and a titanium frame. This document outlines the instrument description of the titanium frame.

The Titanium CTD system used an 11 plus deck unit (s/n 11P-20391-0502) with SBE 9plus underwater unit (s/n 09P-39607-0803). A 24-way titanium frame (s/n SBE CTD TITA1), with secondary temperature and conductivity sensors was used throughout the cruise. All other instruments were attached to a Sea-Bird 32 24-way carousel (for casts 001t through 045t, s/n 32-24680-0346; for casts 048t through 077t, s/n 32-34173-0493), with Ocean Test Equipment 10L TMF water samplers (s/n 1T through 24T).

The table below provides further detail on the sensors included in the CTD unit.

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 QCP-2300 & QCP-2350

The QCP-2300 is a submersible cosine-collector radiometer designed to measure irradiance over Photosynthetically Active Radiation (PAR) wavelengths. It features a constant (better than ±10%) quantum response from 400 to 700 nm with the response being sharply attenuated above 700 nm and below 400 nm.

The sensor is a blue-enhanced high stability silicon photovoltaic detector with dielectric and absorbing glass filter assembly. The output is a DC voltage typically between 0 and 5 VDC that is proportional to the log of the incident irradiance.

The QCP-2300 is specifically designed for integration with 12-bit CTD systems and dataloggers requiring a limited-range of signal input.

Specifications

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

Paroscientific Absolute Pressure Transducers Series 3000 and 4000

Paroscientific Series 3000 and 4000 pressure transducers use a Digiquartz pressure sensor to provide high accuracy and precision data. The sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

The 3000 series of transducers includes one model, the 31K-101, whereas the 4000 series includes several models, listed in the table below. All transducers exhibit repeatability of better than ±0.01% full pressure scale, hysteresis of better than ±0.02% full scale and acceleration sensitivity of ±0.008% full scale /g (three axis average). Pressure resolution is better than 0.0001% and accuracy is typically 0.01% over a broad range of temperatures.

Differences between the models lie in their pressure and operating temperature ranges, as detailed 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.

UK Ocean Acidification (UKOA) cruise JR20130109 CTD processing

Sampling strategy

A total of 78 successful CTD casts were made during the cruise using both a titanium and stainless steel frame. Three data files for each cast were supplied to BODC, one for the downcast, upcast and one from the combined down and upcast. One exception was cast 42 of the titanium rosette, where no upcast was recorded. Rosette bottles were fired throughout the water column on the upcast of most profiles. Data were measured by a PC running Seasave V 7.21d, Sea-Bird's data acquisition software. The raw data files were supplied to BODC after the cruise.

Originator's processing

The initial Sea-Bird processing of the CTD profiles was carried out by the data originators at NOCL.

Sea-Bird processing

The raw data files have the appendices: .hex, .HDR, .bl and .CON. The .CON files for each cast contain the calibration coefficients for the instrument. The .HDR files contain the header information for each data file. The .hex files are the data files for each cast and are in hex format. The .bl files contain CTD scans that were collected while the water bottles were being closed.

A few issues were identified with the data during Sea-Bird processing. Soaks were missing from casts 09s, 10s, 28s, 47s and 76s of the stainless steel rosette and casts 05t, 06t, 07t, 08t, 48t, 50t, 57t and 77t of the titanium rosette. In some cases, due to the missing soaks, a large amount of surface data had to be removed. Also, in cast 72t, there was a spike in the pressure channel at about 4058 seconds that was not removed during WILDEDIT processing. This led to null data in most of the other channels, all of which were flagged as null.

Data were processed following established BODC procedures and the following SeaBird routines were carried out: DATCNV, BOTTLESUM, WILDEDIT, FILTER, ALIGNCTD, CELLTM, LOOPEDIT, DERIVE and BINAVERAGE. In the first instance, each raw CTD file was converted to ASCII format using the latest available version of the SeaBird Processing software, SBE Data Conversion (DATCNV). Further details of the BODC routines applied follow.

• DATCNV was run on all raw files. For the conversion of oxygen concentration, a window size of 2 was used, and tau and hysteresis corrections were applied.

• WILDEDIT was run to remove spikes in the pressure and depth channels of each cast. Flags were applied where values differed from the mean by more than two standard deviations on the first pass, or more than 20 standard deviations on the second pass, using 100 scans per block. The conductivity channel contained large spikes in many of the casts in both the primary and secondary channels. These spikes were removed by hand and replaced with the mean of the adjacent conductivity values. When a large number of data had to be removed, the conductivity values were flagged rather than replaced with a mean value.

• ALIGNCTD was run on the temperature and conductivity channels from both CTD's to ensure data were obtained from the same body of water, for any later derivations. Three randomly selected casts from each CTD were used to identify whether any sudden changes in one channel were aligned to any other channel. This process was also carried out on the secondary temperature and conductivity channels. No correction was required for either the primary or secondary temperature channel of the stainless steel CTD or of the titanium CTD, as the changes in conductivity were well aligned with those in temperature. To ensure the oxygen concentration corresponded to the correct pressure, the alignment of the oxygen channel was checked for both CTDs. For the stainless steel CTD, the differences between the up and downcast were least when the oxygen channel was adjusted by 4.0 seconds. Using SBE Align, a correction of four seconds was applied to the oxygen channel of each stainless steel CTD cast. For casts 19 and 40 of the titanium CTD, the difference between the up and downcast was least when the oxygen channel was adjusted by 3.8 seconds. Using SBE Align, a correction of 3.8 seconds was applied to the oxygen channel of each titanium CTD cast.

• CELLTM was used to remove conductivity cell thermal mass effects from the primary and secondary conductivity channels. The values used for the thermal anomaly amplitude and thermal anomaly constant were 0.03 and 7 respectively.

• DERIVE was used to obtain depth, nitrogen saturation, oxygen concentration, primary and secondary practical salinity, primary and secondary density and the primary and secondary sigma t values. For the derivation of oxygen, a window size of 2 was used and tau and hysteresis corrections were applied.

• BINAVERAGE was used to separate the data into 1 m bins. For each cast, the surface bin minimum value used was 1 m. The exceptions were casts: 3t (14m used for the downcast), 16s (4m used for the downcast), 46s (5m used for both the down- and the upcast), 51s (5m used for the downcast) and 52s (6m used for the downcast). These minimum surface bin values were used instead due to unreliable data for the derived variables being observed below 1m.

• STRIP was used to remove the surplus oxygen, depth and nitrogen saturation channels.

Field calibrations

Calibration of the oxygen sensor

Oxygen data were calibrated against discrete sample data. There was no significant drift in the stainless steel CTD oxygen sensor, only an offset. Ignoring the upper and lower 10% of the error, a mean offset of 0.293 was calculated and used to correct the oxygen channel on the stainless steel CTD. Due to ambiguity in the station and bottle numbers recorded for the titanium CTD, it was not possible to calibrate the oxygen channel for the titanium casts.

Salinity calibration

There was a consistent drift in the salinity channel of the stainless steel CTD so a correction was applied to both the primary and secondary salinity channels. To calculate the drift and offset in the data, a first order polynomial regression was used. To prevent any anomalous values affecting the corrections, the regression was only used once the lower and upper 10% of the error had been disregarded since the increase in the error was reasonably constant between these points. Where day is the number of days since the first cast, the corrected primary salinity was calculated as follows.

• Corrected Salinity = Salinity + 1.44 * 10^-4 * Day + 0.0118

The corrected secondary salinity was calculated as follows.

• Corrected salinity = salinity + 1.894 * 10^-4 * Day + 0.00939.

There was also a consistent drift in the salinity channel of the titanium CTD so a correction was applied to both the primary and secondary salinity channels. A first order polynomial regression was used again, ignoring the upper and lower 10% of errors. The corrected primary salinity was calculated as follows.

• Corrected Salinity = Salinity + 4.090 * 10^-5 * Day + 0.00160

The corrected secondary salinity was calculated as follows.

• Corrected Salinity = Salinity - 2.768 * 10^-5 * Day + 8.713 * 10^-4.

BODC Reformatting

The data were converted from Sea-Bird ASCII format into BODC internal format using BODC transfer function 357. The following tables show how the variables within the Sea-Bird files were mapped to appropriate BODC parameter codes. Oxygen saturation, sigma-theta and potential temperature were derived and added to the profiles during the transfer.

For the stainless steel casts

For the titanium casts

Screening

Reformatted CTD data were visualised using the in-house graphical editor EDSERPLO. No data values were edited or deleted, and all spurious and null data were flagged with BODC quality control flags.

Titanium cast PAR

Comparison between the voltage values and PAR values provided in the files with the calibration certificates showed that the data were by a factor of 0.04234 for the PAR values derived from voltages. This is a recurring problem with the way coefficients are entered into the Sea-Bird .CON files onboard the ship. A correction factor of /0.04234 was applied to the DWIRPP01 channel.

Banking

Once quality control screening was complete, the CTD downcasts were banked.

References

Benson, B.B., and Krausse Jr, D., 1984. The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. The American Society of Limnology and Oceanography, 29 (3), p.620 - 637.

Fofonoff, N.P., and Millard, R.C., 1983. Algorithms for computations of fundamental properties of seawater. UNESCO Technical Papers in Marine Science, 44, p. 53.

UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science, 38, p. 192.

Project Information

UKOARP Theme B: Ocean acidification impacts on sea surface biology, biogeochemistry and climate

The overall aim of this theme is to obtain a quantitative understanding of the impact of ocean acidification (OA) on the surface ocean biology and ecosystem and on the role of the surface ocean within the overall Earth System.

The aims of the theme are:

• To ascertain the impact of OA on planktonic organisms (in terms of physiological impacts, morphology, population abundances and community composition).
• To quantify the impacts of OA on biogeochemical processes affecting the ocean carbon cycle (both directly and indirectly, such as via availability of bio-limiting nutrients).
• To quantify the impacts of OA on the air-sea flux of climate active gases (DMS and N₂O in particular).

The main consortium activities will consist of in-situ measurements on three dedicated cruises, as well as on-deck bioassay experiments probing the response of the in-situ community to elevated CO₂. Most of the planned work will be carried out on the three cruises to locations with strong gradients in seawater carbon chemistry and pH; the Arctic Ocean, around the British Isles and the Southern Ocean.

Weblink: http://www.oceanacidification.org.uk/research_programme/surface_ocean.aspx

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: