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Metadata Report for BODC Series Reference Number 1050067

Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
Sea-Bird SBE 43 Dissolved Oxygen Sensor  dissolved gas sensors
Sea-Bird SBE 911plus CTD  CTD; water temperature sensor; salinity sensor
Paroscientific 410K Pressure Transducer  water temperature sensor; water pressure sensors
Sea-Bird SBE 3plus (SBE 3P) temperature sensor  water temperature sensor
Sea-Bird SBE 4C conductivity sensor  salinity sensor
Chelsea Technologies Group Aquatracka III fluorometer  fluorometers
Chelsea Technologies Group Alphatracka II transmissometer  transmissometers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Prof Tim Jickells
Originating Organization University of East Anglia School of Environmental Sciences
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Atlantic Meridional Transect Phase2(AMT)

Data Identifiers

Originator's Identifier AMT12_54
BODC Series Reference 1050067

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2003-06-07 05:34
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 1.0 decibars

Spatial Co-ordinates

Latitude 26.46067 N ( 26° 27.6' N )
Longitude 30.16217 W ( 30° 9.7' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 3.48 m
Maximum Sensor or Sampling Depth 302.29 m
Minimum Sensor or Sampling Height 5307.21 m
Maximum Sensor or Sampling Height 5606.02 m
Sea Floor Depth 5609.5 m
Sea Floor Depth Source -
Sensor or Sampling Distribution Variable common depth - All sensors are grouped effectively at the same depth, but this depth varies significantly during the series
Sensor or Sampling Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface


BODC CODERankUnitsTitle
ATTNDR011per metreAttenuation (red light wavelength) per unit length of the water body by 25cm path length red light transmissometer
CPHLPM011Milligrams per cubic metreConcentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and manufacturer's calibration applied
CPHLPS011Milligrams per cubic metreConcentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and calibration against sample data
DOXYSC011Micromoles per litreConcentration of oxygen {O2 CAS 7782-44-7} per unit volume of the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data
OXYSSC011PercentSaturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data and computation from concentration using Benson and Krause algorithm
POTMCV011Degrees CelsiusPotential temperature of the water body by computation using UNESCO 1983 algorithm
PRESPR011DecibarsPressure (spatial coordinate) exerted by the water body by profiling pressure sensor and correction to read zero at sea level
PSALCC011DimensionlessPractical salinity of the water body by CTD and computation using UNESCO 1983 algorithm and calibration against independent measurements
SIGTPR011Kilograms per cubic metreSigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm
TEMPCU011Degrees CelsiusTemperature of the water body by CTD and NO verification against independent measurements

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

Problem Reports

Problem Report

Beam attenuance

The transmissometers suffered from operational difficulties due to the high temperature; casts 20 to 44 appeared to be affected, and users should take account of quality control flags. Where data are binned to 1 decibar, there will be large sections of these casts where the data are null, due to the absence of good quality data for each bin.

The transmissometer has been calibrated with pure water as the reference for 100% transmission and therefore beam attenuation values in clear water should be close to 0 m-1. Chelsea Instruments advise that ALPHAtracka is calibrated at the factory at 20°C in distilled water with an electrical conductivity less than one µS cm-1 and filtered to better than 5 µm and that it is possible that the user will encounter water which is purer than that used during the calibration. Indeed the minimum attenuance values for the both sensors were lower then 0 m-1, suggesting that the calibration procedure recommended by Sea-Bird and Chelsea Instruments may need adjusting to use deep clear oceanic water as the reference for 100% transmission. The data from both sensors will need further offset correction to bring them in line with recognised values. Whether this should be done for the dataset as a whole or on a cast by cast basis is for the user to decide based on their requirements.

RSS James Clark Ross Cruise AMT12 CTD Data Quality Document

Fluorescence (Chelsea Technology Group (CTG) Aquatracka MKIII fluorometer)

The nominal chlorophyll-a values have been calculated from the CTG Aquatracka MKIII fluorometer data (with manufacturer's calibration applied) from the up-cast at bottle firing and the fluorometric chlorophyll-a data from sampled bottles. Where samples were not supplied or too few to generate a calibration and could not be grouped with other casts, the fluorometer profiles have not been calibrated. The sampling strategy for the extracted chlorophyll-a dataset used to calibrate the fluorometer focused on the upper water column, therefore the calibration is biased towards these depths. The calibration may not be as reliable below depths ~150m. Casts AMT12_01, AMT12_02, AMT12_03, AMT12_04, AMT12_06, AMT12_09, AMT12_68 and AMT12_69 have not been calibrated. The extracted chlorophyll-a dataset is available for users to derive their own calibrations should they wish.


Due to transmissometer calibration issues, many of the attenuance values were negative (beyond the range of the parameter). All negative values were flagged 'M'. This does not necessarily mean that the data are scientifically useless, just that the calibration coefficients may be slightly out. Where previous 'T' flags were overwritten, the original flagged data are available on request. There is no attenuance data for cast AMT12_05.

Salinity and temperature

Salinity and temperature data for casts AMT12_40, AMT12_42, AMT12_43, AMT12_45 and AMT12_47 were affected by problems with the pumps and should be used with caution. In addition the secondary salinity channel was suspect for casts AMT12_33, AMT12_34 and AMT12_36.

Data Access Policy

Open 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.

If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:

"Contains public sector information licensed under the Open Government Licence v1.0."

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.


Housing Plastic or titanium

0.5 mil- fast response, typical for profile applications

1 mil- slower response, typical for moored applications

Depth rating

600 m (plastic) or 7000 m (titanium)

10500 m titanium housing available on request

Measurement range 120% of surface saturation
Initial accuracy 2% of saturation
Typical stability 0.5% per 1000 h

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

James Clarke Ross Cruise AMT12 CTD Instrumentation for the stainless steel rig

Two different CTD frames were used - a stainless steel frame and a titanium frame used for trace metal sampling. This document is for the instrumentation on the stainless steel rig.

Stainless Steel

The CTD unit was a Sea-Bird Electronics 911plus system, with dissolved oxygen sensor. The CTD was fitted with a transmissometer and a fluorometer. All instruments were attached to a Sea-Bird SBE 32 carousel. The table below lists more detailed information about the various sensors.

Sensor Model Serial Number Calibration Comments
Pressure transducer Digiquartz temperature compensated pressure sensor 83008 09/01/2001 -
Conductivity sensor 1 SBE 4C 2637 13/09/2002 -
Conductivity sensor 2 SBE 4C 2407 13/09/2002 -
Temperature sensor 1 SBE 3P 2919 14/09/2002 -
Temperature sensor 2 SBE 3P 2758 14/09/2002 -
Dissolved oxygen SBE 43 43B-0363 06/02/2003 -
Transmissometer Chelsea MkII Alphatracka 161-2642-03 05/09/1996 0.25 m path
Fluorometer Chelsea MkIII Aquatracka 088-242 28/04/2001 -

Change of sensors during cruise: None reported.

Sampling device

Rosette sampling system equipped with 24 x 20 l sampling bottles (manufactured by Ocean Test Equipment Inc.).

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 for the SBE 9 plus underwater unit are listed below:

Parameter Range Initial accuracy Resolution at 24 Hz Response time
Temperature -5 to 35°C 0.001°C 0.0002°C 0.065 sec
Conductivity 0 to 7 S m-1 0.0003 S m-1 0.00004 S m-1 0.065 sec (pumped)
Pressure 0 to full scale (1400, 2000, 4200, 6800 or 10500 m) 0.015% of full scale 0.001% of full scale 0.015 sec

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:

Excitation Chlorophyll a Rhodamine Fluorescein Turbidity
Wavelength (nm) 430 500 485 440*
Bandwidth (nm) 105 70 22 80*
Emission Chlorophyll a Rhodamine Fluorescein Turbidity
Wavelength (nm) 685 590 530 440*
Bandwidth (nm) 30 45 30 80*

* 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.

Chelsea Technologies Group ALPHAtracka and ALPHAtracka II transmissometers

The Chelsea Technologies Group ALPHAtracka (the Mark I) and its successor, the ALPHAtracka II (the Mark II), are both accurate (< 0.3 % fullscale) transmissometers that measure the beam attenuation coefficient at 660 nm. Green (565 nm), yellow (590 nm) and blue (470 nm) wavelength variants are available on special order.

The instrument consists of a Transmitter/Reference Assembly and a Detector Assembly aligned and spaced apart by an open support frame. The housing and frame are both manufactured in titanium and are pressure rated to 6000 m depth.

The Transmitter/Reference housing is sealed by an end cap. Inside the housing an LED light source emits a collimated beam through a sealed window. The Detector housing is also sealed by an end cap. A signal photodiode is placed behind a sealed window to receive the collimated beam from the Transmitter.

The primary difference between the ALPHAtracka and ALPHAtracka II is that the Alphatracka II is implemented with surface-mount technology; this has enabled a much smaller diameter pressure housing to be used while retaining exactly the same optical train as in the Mark I. Data from the Mark II version are thus fully compatible with that already obtained with the Mark I. The performance of the Mark II is further enhanced by two electronic developments from Chelsea Technologies Group - firstly, all items are locked in a signal nulling loop of near infinite gain and, secondly, the signal output linearity is inherently defined by digital circuitry only.

Among other advantages noted above, these features ensure that the optical intensity of the Mark II, indicated by the output voltage, is accurately represented by a straight line interpolation between a reading near full-scale under known conditions and a zero reading when blanked off.

For optimum measurements in a wide range of environmental conditions, the Mark I and Mark II are available in 5 cm, 10 cm and 25 cm path length versions. Output is default factory set to 2.5 volts but can be adjusted to 5 volts on request.

Further details about the Mark II instrument are available from the Chelsea Technologies Group ALPHAtrackaII specification sheet.

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:

Model Max. pressure (psia) Max. pressure (MPa) Temperature range (°C)
31K-101 1000 6.9 -54 to 107
42K-101 2000 13.8 0 to 125
43K-101 3000 20.7 0 to 125
46K-101 6000 41.4 0 to 125
410K-101 10000 68.9 0 to 125
415K-101 15000 103 0 to 50
420K-101 20000 138 0 to 50
430K-101 30000 207 0 to 50
440K-101 40000 276 0 to 50

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

James Clarke Ross Cruise AMT12 CTD Processing

Sampling strategy

A total of 69 successful CTD casts were made during the cruise. Rosette bottles were fired throughout the water column on the upcast of most profiles. Data were measured at 24 Hz by a PC running SEASAVE, Sea-Bird's data acquisition software. The raw data files were supplied to BODC after the cruise.

Originator's processing

Only a subset of files had been partially processed on board during the cruise. The raw data were therefore reprocessed at BODC to produce and homogeneous set of CTD data files for this cruise. BODC used the latest version of the SeaBird Processing software available at the time to process the raw binary data files (DAT files) based on information held in the sensor configuration files (CON files), and bottle firing files (BL).

BODC post-processing and screening

  • Sea-Bird processing

    The CON files were first checked for any changes which may have occurred during the cruise, with the exception of the transmissometer coefficients that changed on a cast by cast basis to account for source decay, none were made. The information was also cross checked against information held in the sensors' calibration reports.

    The following SeaBird routines were then carried out using SBE Data Processing software version 5.30a: DATCNV, CELLTM, FILTER, LOOPEDIT, DERIVE, BINAVG, STRIP. After CELLTM was run, tests were carried out to check whether an alignment of the conductivity sensor was necessary. No lag was observed. Details of the routines and settings used were as follows:

    DATCNV converts the raw data into engineering units. Both down and upcasts were selected. All channels were selected for transfer.

    The manufacturer's calibration for the fluorometer was applied during Sea-Bird processing as follows:

    Stainless Steel Nominal chl-a conc (µg/l) = (0.009 * 10voltage) - 0.016
    Titanium Nominal chl-a conc (µg/l) = (0.00864 * 10voltage) - 0.0201

    CELLTM was run on the DATCNV output using SeaBird's recommended settings of alpha= 0.03 and Tau=7.

    FILTER was run on pressure using a low pass time constant of 0.15 seconds.

    LOOPEDIT was run in order to minimise the marked wake effect linked to ship rolling observed on recent cruises.

    DERIVE, BINAVG and STRIP were then run to derive the salinity and oxygen concentration, reduce the data to 2Hz and strip redundant channels from the final sets of ASCII files.

    Conversion of transmissometer voltages to beam attenuation

    There were air and blocked path readings along the cruise track available for this cruise. The transmissometer profiles were corrected for source decay through the calculation of coefficients M and B following SeaBird Application Note 7.

    M = (Tw / (W0 - Y0) * (A0 - Y0) / (A1 - Y1)
    B = -M * Y1


    Stainless steel Titanium
    Tw = % transmission for pure water 100% 100%
    W0 = voltage output in pure water 4.205 V 4.213 V
    A0 = manufacturer's air voltage 4.660 V 4.514 V
    Y0 = manufacturer's blocked path voltage 0.027 V 0.021 V
    A1 = current air voltage cruise logsheet - cast specific
    Y1 = current blocked path voltage cruise logsheet - cast specific
  • Reformatting

    The data were converted from Sea-Bird ASCII format into BODC internal format (QXF) using BODC transfer function 357. The following table shows how the variables within the Sea-Bird files were mapped to appropriate BODC parameter codes:

    Sea-Bird Parameter Name Units Description BODC Parameter Code Units Comments
    Pressure, Digiquartz dbar CTD pressure PRESPR01 dbar -
    Temperature [ITS-90] °C Temperature of water column by CTD sensor 1 TEMPCU01 °C -
    Temperature, 2 [ITS-90] °C Temperature of water column by CTD sensor 2 TEMPCU02 °C -
    Salinity - Practical salinity of the water body by CTD sensor 1 PSALCU01 - -
    Salinity, 2 - Practical salinity of the water body by CTD sensor 2 PSALCU02 - -
    Oxygen µmol kg-1 Dissolved oxygen concentration DOXYSU01 µmol l-1 Converted from µmol kg-1 to µmol l-1 using sigma-T during transfer
    Fluorescence mg m-3 Nominal chl-a concentration CPHLPM01 mg m-3 Manufacturer's calibration applied during processing
    Beam Attn m-1 Beam attenuance ATTNDR01 m-1 Generated using manufacturer's calibration corrected for source decay
    - - Practical salinity of the water body by CTD sensor 1 - sample calibrated PSALCC01 - PSALCU01 calibrated against bench salinometer data
    - - Practical salinity of the water body by CTD sensor 2 - sample calibrated PSALCC02 - PSALCU02 calibrated against bench salinometer data
    - - Dissolved oxygen concentration - sample calibrated DOXYSC01 µmol l-1 DOXYSU01 calibrated against Winkler titration data
    - - Fluorometer - sample calibrated CPHLPS01 mg m-3 CPHLPM01 calibrated against fluorometric chlorophyll-a data
    - - Oxygen saturation OXYSSC01 % Generated by BODC using the Benson and Krause (1984) algorithm wioth parameters DOXYSC01, PSALCC01 and TEMPCU01
    - - Potential temperature POTMCV01 °C Generated by BODC using UNESCO Report 38 (1981) algorithm with parameters PRESPR01, PSALCC01 and TEMPCU01
    - - Sigma-theta SIGTPR01 kg m-3 Generated by BODC using the Fofonoff and Millard (1982) algorithm with parameters PSALCC01 and POTMCV01
  • 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. Limnol. Oceanogr., 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.

    UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science No. 38, 192pp

  • Screening

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

    There were leaking connectors/corroding pins on the stainless steel CTD system due to damage caused on the previous cruise. This caused noise and loss of pumps on primary and secondary temperature and conductivity sensors for AMT12_40, 42, 43, 45 and 47.

  • Screening notes regarding specific casts:

    Salinity: The secondary salinity channel (PSALST02) was suspect for casts AMT12_33, 34 and 36.

    Dissolved oxygen: The dissolved oxygen signal for AMT12_02 was suspect between 170 - 270 db. For AMT12_24, the downcast concentration was high relative to the upcast below 2000m.

    Beam attenuance: The Chelsea Alphatracka Mk II transmissometers are designed to operate in a temperature range of 1 to 25 °C. Where they encountered higher air and water temperatures, they suffered from hysteresis which affected the up- and downcasts. The severity of the problem depended on the degree of heating on the deck and in the water, and also on the pressure. Jeff Benson noted that the casts between AMT12_27 and AMT12_36 were affected. During screening of the CTD data, it appeared that the transmissometers were affected for more of the casts than originally thought. The worst affected casts were from AMT12_27 to AMT12_36 as identified by UKORS. However, the upcast and downcast signals were very different for casts from AMT12_20 to AMT12_26 and for AMT12_37 to AMT12_44. Minimum beam attenuation values were too low and require further calibration and correction. See the data quality section for more details.

  • Banking

    Once quality control screening was complete, the CTD downcasts were banked. Finally, the data were binned against pressure at 1 dbar increments with flagged data excluded from the bin averaging. The primary salinity, temperature, density and potential temperature channels were retained as the best quality data channels from the two sensors.

Field Calibrations

  • Pressure

    There were no casts where the CTD pressure was logging in air. 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 and no other independent measurements of better quality were available. No further correction was therefore applied to the data.

  • Salinity

    There were 71 CTD bottle samples from the stainless steel casts and 73 samples from the titanium casts that were analysed on the bench salinometer. These have been compared with CTD values at the depth of bottle firing during the CTD upcast. The data were extracted from Sea-Bird bottle files created during processing. They were also compared with CTD values at the same depths taken from the CTD downcast. This additional information was used to remove outliers from the calibration data set.

    Despite the large calibration set, there was still a high degree of variability in the relationship between the CTD sensor data and the salinometer data.

    Stainless steel frame

    Samples from casts AMT12_40, 42, 43, 45 and 47 were excluded from the data set due to the quality problems described above.

    The mean offset between the primary and sceondary sensors showed a significant change over the cruise. Comparison with the bench salinometer data suggested that primary sensor was drifting over time. The casts have been split into two groups for the calibration of PSALCU01. The offset between bench salinometer data and secondary sensor values was consistent throughout the cruise. One calibration was, therefore, applied to produce PSALCC02 and this should be used in preference to PSALCC01.

    Sensor Stainless Steel Casts Calibration N stddev BODC cal ref
    Primary AMT12_01 to AMT12_27 PSALCC01 = PSALCU01 + 0.002113 35 0.002 2768
    Primary AMT12_29 to AMT12_67 PSALCC01 = PSALCU01 + 0.008350 25 0.004 2767
    Secondary All PSALCC02 = PSALCU02 + 0.003734 62 0.003 2766

    Titanium frame

    The mean offset between the primary and sceondary sensors was -0.0055 with a standard deviation of 0.0024. However, it was noted that there was a trend of increasing offset over time. The CTD casts were split into two groups - from AMT12_09 to AMT12_39 and from AMT12_44 to AMT12_69. The offsets between the salinometer and CTD data for both sensors were calculated separately for the two groups of data. For the primary sensor, there was no significant change between the two groups, so one calibration has been applied to both sensors. The standard deviation was higher than the mean offset. However, this was due to a general noisiness of the data set throughout the cruise, rather than a changing offset over time. For the secondary sensor, there was a change in the offset, suggesting that this sensor showed a slight drift with time.

    Sensor Titanium Casts Calibration N stddev BODC cal ref
    Primary All PSALCC01 = PSALCU01 + 0.00267 67 0.0055 2763
    Secondary AMT12_09 to AMT12_39 PSALCC02 = PSALCU01 - 0.00433 42 0.002 2764
    Secondary AMT12_44 to AMT12_69 PSALCC02 = PSALCU01 - 0.00716 29 0.001 2765
  • Dissolved oxygen

    The dissolved oxygen channels have been calibrated against water bottle Winkler data from Nikki Gist and Carol Robinson, Plymouth Marine Laboratory.

    Stainless steel frame

    The oxygen sensor on the stainless steel CTD frame was calibrated in three groups. This was due to an apparent drift of the sensor after 02/06/2003.

    Stainless Steel Casts Calibration N R2 BODC cal ref
    AMT12_01 to AMT12_40 DOXYSC01 = 1.00232 * DOXYSU01 + 12.8242 120 0.998 3245
    AMT12_42, 43, 45 (suspect data) and 47 DOXYSC01 = 1.06772 * DOXYSU01 + 7.826 16 0.999 3246
    AMT12_49 to AMT12_67 DOXYSC01 = 1.08694 * DOXYSU01 + 7.289 70 0.992 3247

    Titanium frame

    The oxygen sensor on the titanium frame showed no drift throughout the cruise. However, cast AMT12_11 deviated from the rest of the data set, so a separate calibration was obtained.

    Titanium Casts Calibration N R2 BODC cal ref
    AMT12_03 to AMT12_69 (AMT12_11 excluded) DOXYSC01 = 1.16848 * DOXYSU01 + 5.1 47 0.997 3243
    AMT12_11 DOXYSC01 = 1.1626 * DOXYSU01 + 20.07 10 0.935 3244
  • Fluorescence

    The nominal chlorophyll-a values have been calculated from the fluorometer data (with manufacturer's calibration applied) from the up-cast at bottle firing and the fluorometric chlorophyll-a data from sampled bottles. There was some drift in the sensor at the end of the transect and the calibrations have been split to take this into account. There were some casts without sample data at the start and end of the cruise and without these data to quantify the level of drift, these fluorometer profiles were not calibrated.

    Stainless steel frame

    There were no sample data for casts 1 and 3, so no calibrations were applied to these profiles.

    Stainless Steel Casts Calibration N R2 BODC cal ref
    AMT12_05 to AMT12_58 CPHLPS01 = 1.3531 * CPHLPM01 + 0.0112 107 0.375 6630
    AMT12_60 to AMT12_67 CPHLPS01 = 0.6722 * CPHLPM01 + 0.0339 20 0.508 6631

    Titanium frame

    There were no sample data for casts 2, 4, 6, 9, 68 and 69, so no calibrations were applied to these profiles.

    Titanium Casts Calibration N R2 BODC cal ref
    AMT12_11 to AMT12_62 CPHLPS01 = 1.5561 * CPHLPM01 + 0.0184 82 0.640 6632
    AMT12_64 and AMT12_66 CPHLPS01 = CPHLPM01 + 0.0309 (±0.0182) 5 - 6633

Project Information

The Atlantic Meridional Transect - Phase 2 (2002-2006)

Who was involved in the project?

The Atlantic Meridional Transect Phase 2 was designed by and implemented by a number of UK research centres and universities. The programme was hosted by Plymouth Marine Laboratory in collaboration with the National Oceanography Centre, Southampton. The universities involved were:

  • University of Liverpool
  • University of Newcastle
  • University of Plymouth
  • University of Southampton
  • University of East Anglia

What was the project about?

AMT began in 1995, with scientific aims to assess mesoscale to basin scale phytoplankton processes, the functional interpretation of bio-optical signatures and the seasonal, regional and latitudinal variations in mesozooplankton dynamics. In 2002, when the programme restarted, the scientific aims were broadened to address a suite of cross-disciplinary questions concerning ocean plankton ecology and biogeochemistry and the links to atmospheric processes.

The objectives included the determination of:

  • how the structure, functional properties and trophic status of the major planktonic ecosystems vary in space and time
  • how physical processes control the rates of nutrient supply to the planktonic ecosystem
  • how atmosphere-ocean exchange and photo-degradation influence the formation and fate of organic matter

The data were collected with the aim of being distributed for use in the development of models to describe the interactions between the global climate system and ocean biogeochemistry.

When was the project active?

The second phase of funding allowed the project to continue for the period 2002 to 2006 and consisted of six research cruises. The first phase of the AMT programme ran from 1995 to 2000.

Brief summary of the project fieldwork/data

The fieldwork on the first three cruises was carried out along transects from the UK to the Falkland Islands in September and from the Falkland Islands to the UK in April. The last three cruises followed a cruise track between the UK and South Africa, only deviating from the traditional transect in the southern hemisphere. During this phase the research cruises sampled further into the centre of the North and South Atlantic Ocean and also along the north-west coast of Africa where upwelled nutrient rich water is known to provide a significant source of climatically important gases.

Who funded the project?

Natural Environment Research Council (NERC)

Data Activity or Cruise Information


Cruise Name JR20030512 (AMT12, JR102, JR88, JR90)
Departure Date 2003-05-12
Arrival Date 2003-06-17
Principal Scientist(s)Tim Jickells (University of East Anglia School of Environmental Sciences)
Ship RRS James Clark Ross

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:

Flag Description
Blank Unqualified
< Below detection limit
> In excess of quoted value
A Taxonomic flag for affinis (aff.)
B Beginning of CTD Down/Up Cast
C Taxonomic flag for confer (cf.)
D Thermometric depth
E End of CTD Down/Up Cast
G Non-taxonomic biological characteristic uncertainty
H Extrapolated value
I Taxonomic flag for single species (sp.)
K Improbable value - unknown quality control source
L Improbable value - originator's quality control
M Improbable value - BODC quality control
N Null value
O Improbable value - user quality control
P Trace/calm
Q Indeterminate
R Replacement value
S Estimated value
T Interpolated value
U Uncalibrated
W Control value
X Excessive difference

SeaDataNet Quality Control Flags

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

Flag Description
0 no quality control
1 good value
2 probably good value
3 probably bad value
4 bad value
5 changed value
6 value below detection
7 value in excess
8 interpolated value
9 missing value
A value phenomenon uncertain
B nominal value
Q value below limit of quantification