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Metadata Report for BODC Series Reference Number 1054449


Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
NameCategories
Sea-Bird SBE 43 Dissolved Oxygen Sensor  dissolved gas sensors
Chelsea Technologies Group 2-pi PAR irradiance sensor  radiometers
Sea-Bird SBE 911plus CTD  CTD; water temperature sensor; salinity sensor
Turner Designs Cyclops-7 phycoerythrin cyanobacteria fluorometer  fluorometers
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 Patrick Holligan
Originating Organization University of Southampton School of Ocean and Earth Science
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 AMT14_89
BODC Series Reference 1054449
 

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2004-05-30 11:40
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 1.0 decibars
 

Spatial Co-ordinates

Latitude 49.25733 N ( 49° 15.4' N )
Longitude 6.60783 W ( 6° 36.5' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 0.5 m
Maximum Sensor or Sampling Depth 91.69 m
Minimum Sensor or Sampling Height 29.92 m
Maximum Sensor or Sampling Height 121.11 m
Sea Floor Depth 121.61 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 Chart reference - Depth extracted from available chart
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
 

Parameters

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
FVLTPELN1VoltsRaw signal (voltage) of instrument output by linear-response phycoerythrin fluorometer
IRRDPP011MicroEinsteins per square metre per secondDownwelling 2-pi scalar irradiance as photons of electromagnetic radiation (PAR wavelengths) in the water body by 2-pi scalar radiometer
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 38 to 54 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.

There were no air/dark readings supplied from the cruise and the values generated from the instrument voltage based on manufacturer's readings are frequently larger than would be expected. The absolute attenuation values are therefore questionable but the relative profile should be reliable except for profiles where hysteresis was a problem.

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. The attenuance data will need further offset correction relative to the profile minimum values 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. The absolute attenuation values are therefore questionable but the relative profile should be reliable except for profiles where hysteresis was a problem.

RSS James Clark Ross Cruise AMT14 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. 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. All values outside the range of the parameter were flagged 'M'. Where previous 'T' flags were overwritten, the original flagged data are available on request. The chlorophyll channels are constant for cast AMT14_11, however this is a shallow cast at around 300 m, so is unlikely the sensor would have been removed. Casts AMT14_01, AMT14_12 and AMT14_13 were very noisy and the 1Hz data were heavily flagged based on comparison with upcast data. Data from these profiles should be used with caution.

Attenuance

Some spikes in the data were flagged on series AMT14_08, AMT14_66, AMT14_71 and AMT14_88.

Downwelling and upwelling sub-surface PAR irradiance

The downwelling and upwelling PAR channels in series AMT14_14 are constant. This is not a particularly shallow cast at around 1000 m depth but this cast was taken at night. Upwelling and downwelling PAR sensors were only deployed on shallow casts. The downwelling profiles show some variablility for the shallower part of the profile, which may be a result of shading from the vessel.

Cyclops 7 fluorometer voltage (FVLTPELN)

No calibration details were provided so only the raw voltage is available. Data are only available from 08 May 2004 (cast AMT_026 onwards) when the sensor was added in place of the PAR upwelling sensor. The profiles have been flagged for noise in surface waters.

Salinity

Cast AMT14_87 the quality of the salinity profile is poor, although most bad data and spikes have been flagged prior to binning, users should be advised that the profile should be used with caution.

Oxygen

The profiles have been flagged for noise and spikes but are generally of good quality.

For all channels, cast 11 has bad data in the upper 15 db.


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

Housing Plastic or titanium
Membrane

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 AMT14 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911plus system, with dissolved oxygen sensor. The CTD was fitted with a transmissometer, a fluorometer, down and up welling PAR sensors. 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 73299 08/05/2002 -
Conductivity sensor 1 SBE 4C 2580 03/02/2004 -
Conductivity sensor 2 SBE 4C 2841 09/10/2003 -
Temperature sensor 1 SBE 3P 4301 02/10/2003 -
Temperature sensor 2 SBE 3P 4151 20/09/2003 -
Dissolved oxygen SBE 43 43B-0363 06/02/2003 -
Transmissometer Chelsea MkII Alphatracka 161045 28/04/2001 0.25 m path
Fluorometer Chelsea MkIII Aquatracka 88/2050/95 13/11/2002 -
PAR - upwelling Chelsea PAR sensor 10 05/05/1999 -
PAR - downwelling Chelsea PAR sensor 11 05/05/1999 -
Light Back-Scatter Sea Tech Light Scatter Sensor 339 16/04/1997 -

Change of sensors during cruise: The upwelling PAR sensor was replaced with a Turner Design Cyclops-7 fluorometer (s/n 'n/a' calibration date 'n/a') on 8th May 2004.

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

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.

Turner Designs Cyclops-7 Submersible Sensors

The Cyclops-7 series of sensors is designed for integration into multi-parameter platforms, providing measurements of in vivo chlorophyll-a, cyanobacteria (phycocyanin and phycoerythrin), rhodamine and fluorescein dyes, optical brighteners, coloured dissolved organic matter (CDOM), crude oil and refined fuels, BTEX (benzene, toluene, ethylbenzene, and xylenes) or turbidity.

The voltage output of the sensor can be correlated with in situ concentration by calibration with a standard of known concentration. The excitation wavelength varies, depending on the environmental variable of interest, with visible wavelengths being used for chlorophyll, rhodamine, fluorescein and cyanobacteria; UV being used for CDOM, oil, optical brighteners and refined fuels; and IR being used for turbidity. The photodiode detector operates over the range 300-1100 nm. Custom optics over the range 260-900 nm are also available.

The Cyclops-7 operates over an ambient temperature range of 0 to 50°C and a water temperature range of -2 to 50°C. It has a depth rating of 600 m and displays a linearity of 0.99 R2 over the full range.

Specifications

Application Minimum detection limit Dynamic range
Chlorophyll-a 0.025 µg L-1 0 to 500 µg L-1
CDOM 0.4 ppb QS* 0 to 2500 ppb QS*
Crude Oil 0.02 ppb QS* 0 to 1500 ppb QS*
Cyanobacteria 150 cells mL-1 0 to 150000 cells mL-1
Optical Brighteners 1 ppb QS* 0 to 15000 ppb QS*
Fluorescein Dye 0.01 ppb 0 to 500 ppb
Rhodamine Dye 0.01 ppb 0 to 1000 ppb
Turbidity 0.05 NTU 0 to 3000 NTU
Refined Fuels 2 ppb NS** 0 to 10000 ppb NS**
BTEX 0.1 ppm > 2500 ppm

*QS - Quinine Sulphate

**NS - 1,5 Napthalene Disulfonic Disodium Salt

Further details can be found in the manufacturer's 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.

Chelsea Technologies Photosynthetically Active Radiation (PAR) Irradiance Sensor

This sensor was originally designed to assist the study of marine photosynthesis. With the use of logarithmic amplication, the sensor covers a range of 6 orders of magnitude, which avoids setting up the sensor range for the expected signal level for different ambient conditions.

The sensor consists of a hollow PTFE 2-pi collector supported by a clear acetal dome diverting light to a filter and photodiode from which a cosine response is obtained. The sensor can be used in moorings, profiling or deployed in towed vehicles and can measure both upwelling and downwelling light.

Specifications

Operation depth 1000 m
Range 2000 to 0.002 µE m-2 s-1
Angular Detection Range ± 130° from normal incidence
Relative Spectral Sensitivity

flat to ± 3% from 450 to 700 nm

down 8% of 400 nm and 36% at 350 nm

Further details can be found in the manufacturer's 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 AMT14 CTD Processing

Sampling strategy

A total of 89 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. None were made. The information was also crosschecked 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. For reasons which have not been documented output from the LSS6000 sensor and from the secondary temperature and conductivity sensors were omitted from the list of channels output by DATCNV. All other channels were selected. Although DATCNV has since been run again to obtain and preserve an ASCII version of data recorded by the full suite of sensors deployed on the CTD package, the fully processed and QCed version of this CTD dataset does not include data from the secondary sensors nor from the light scatter sensor.

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

    Nominal chl-a conc (µg/l) = (0.0113 * 10voltage) - 0.032

    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 no air and blocked path readings available for this cruise. As a result, the transmissometer reading could not be corrected for source decay and users are advised caution when using absolute attenuance values for this cruise. The calculation of coefficients M and B followed SeaBird Application Note 7with the most recent dark/air voltages being those provided by the manufacturer.

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

    where

    Stainless steel
    Tw = % transmission for pure water 100%
    W0 = voltage output in pure water 4.2220 V
    A0 = manufacturer's air voltage 4.4045 V
    Y0 = manufacturer's blocked path voltage 0.0185 V
    A1 = cruise air voltage not available - used A0
    Y1 = cruise blocked path voltage not available - used Y0
  • Reformatting

    The data were converted from Sea-Bird ASCII format into BODC internal format (PXF) using BODC transfer function 357. The data were converted to PXF, a BODC internal format. The data were processed from 2Hz averaged down- and upcast data. Sigma-theta was calculated and output from the primary temperature and salinity data channels according to the UNESCO method during the conversion to PXF format. This was used to aid screening of the salinity and temperature data. 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 - - Not transferred during BODC processing
    Salinity - Practical salinity of the water body by CTD sensor 1 PSALCU01 - -
    Salinity, 2 - Practical salinity of the water body by CTD sensor 2 - - Not transferred during BODC processing
    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
    Voltage 4 V Upwelling PAR sensor voltage LVLTPU01 V Removed on 8th May 2004
    Voltage 4 V Downwelling PAR sensor voltage LVLTPD01 V Replaced upwelling PAR sensor from 8th May 2004
    Voltage 5 V Downwelling PAR sensor voltage LVLTPD01 V Moved to Voltage 4 on 8th May 2004
    Voltage 5 V Cyclops 7 fluorometer voltage FVLTPELN V Added on 8th May 2004
    Voltage 6 V Light Back-Scattering Sensor voltage - - Not transferred during BODC processing
    Beam Attenuance m-1 Beam attenuance ATTNDR01 m-1 Manufacturer's calibration applied during processing
    - - Practical salinity of the water body by CTD sensor 1 - sample calibrated PSALCC01 - PSALCU01 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
    - - Downwelling sub-surface PAR irradiance IRRDPP01 µE m-2 s-1 Generated using manufacturer's calibration
    - - Upwelling sub-surface PAR irradiance IRRUPP01 µE m-2 s-1 Generated using manufacturer's calibration
    - - 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

    The PXF data were compared with the original data files to ensure that no errors had been introduced during the conversion process. The data channels were then screened on a graphics workstation using in-house visualisation software. This allows multiple channels to be viewed simultaneously. The start and end-points of the downcast were marked. All spurious and null data were flagged with BODC quality control flags.

    The CTD profiles were generally of good quality. However, cast 11 has bad data in the upper 15 db and for cast 87 the quality of the salinity profile is poor, although most bad data and spikes have been flagged prior to binning, users should be advised that the profile should be used with caution.

    Oxygen sensor

    The profiles have been flagged for noise and spikes but are generally of good quality.

    Fluorometer - generally good with the exceptions:

    Cast 11: The raw data were constant and negative. So there will be no fluorometer data for that cast.

    Casts 1, 12 and 13 were very noisy and the 1Hz data were heavily flagged based on comparison with upcast data. Data from these profiles should be used with caution.

    Transmissometer

    The transmissometer data are not accurately calibrated as no dark and air voltages were recorded during the cruise to account for source decay along the cruise track. The attenuance values should not be used as absolute values. Casts 12 and 86 have had spikes and anomalous data flagged throughout the water column.

    As experienced in AMT12 and 13, the transmissometer malfunctioned in high temperatures and produced poor data. The casts affected were from 39 to 54 and the suspect profiles show large but smooth attenuance maximum at depth as well as strong drifts. The problem is likely related to environmental conditions, for example if temperature or temperature gradients were beyond an acceptable threshold. It is telling that the anomalies are not depth or sensor related but seems to be invariably related to the depth of the thermocline i.e. anomalies are consistently observed at the base of the strong thermocline. The anomalies observed are likely due to a severe case of hysteresis produced by air and water temperature in excess of the instruments operating range (1 to 25 °C).

    Up-welling and Down-welling irradiance

    Only 8 casts have data for the up-welling PAR sensor.

    The down-welling data from casts 19, 44, 71 and 77 were very noisy and the data have been flagged accordingly.

    Phycoerythrin fluorometer

    Data recorded from cast 26 onwards. The profiles have been flagged for noise in surface waters but in the absence of a calibration sheet are only present as the raw voltage.

  • Banking

    Once quality control screening was complete, the CTD downcasts were banked. Finally, the data were binned against pressure at 1 dbar increments.

Voltage conversions

  • PAR sub-surface irradiance

    The PAR sensor raw voltages have been converted to PAR irradiance values in units of µE m-2 s-1 using supplied manufacturer's calibration coefficients.

    Sensor s/n Calibration BODC cal ref
    11 IRRDPP01 = 0.0423 * exp (LVLTDP01 * 5.331 - 9.267) 3924
    10 IRRUPP01 = 0.0423 * exp (LVLTUP01 * 5.195 - 9.036) 3920

Field Calibrations

  • Pressure

    The pressure sensor has not been calibrated as no values were record in air.

  • Temperature

    No reversing thermometer data were available for AMT14, so the CTD sensor data have not been calibrated against another dataset. 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

    Bench salinometer data were provided by UKORS.

    The salinometer data were compared with CTD values from primary sensor on the upcast at the time of bottle firing. Analysis of the data showed that, with the exclusion of 2 outliers, the samples measured on-board produced consistent relationships with the CTD sensor data. A regression analysis was run on the data and showed that there was no linear trend in the data at the 95% confidence level. A simple mean offset, significant at the same confidence level, was applied to the CTD salinities.

    Casts Calibration N BODC cal ref
    All PSALCC01 = PSALCU01 + 0.0026 76 3775
  • Dissolved oxygen

    Oxygen calibrations have been carried out using dissolved oxygen data from Winkler titrations (provided by Niki Gist, Plymouth Marine Laboratory). Examination of the calibration data set showed a good correlation with the sensor throughout the cruise.

    Casts Calibration N R2 BODC cal ref
    All DOXYSC01 = 1.0314 * DOXYSU01 + 5.3147 248 0.994 3794
  • Fluorescence

    The CTD fluorometer was calibrated against chlorophyll a concentration extracted from water samples and determined by fluorometric analysis (data originator: A. Poulton, SOC). Nominal chlorophyll concentration recorded on the upcast by the CTD fluorometer at bottle firing depth were extracted from the SeaBird bottle files and compared with extracted values, after exclusion of 6 spurious CTD values and 2 suspect extracted values.

    Casts Calibration N R2 BODC cal ref
    All CPHLPS01 = 1.66 * CPHLPM01 + 0.09 456 0.673 3918

    Residuals (CTD-Extracted) from this calibration ranged between -0.95 and 0.50 mg chl m-3 and 80% of the calibrated CTD fluorometer values were within 0.25 mg chl m-3of the extracted value. The largest residuals (>0.4 mg chl m-3) were observed in the northern and southern part of the transect, outside the subtropical gyres region, and in the upper 50 m of the water column. It is possible that the accuracy of the calibration be improved by splitting the datasets into subgroups. However, an initial attempt to do this by isolating datapoints from stations 15 to 50, had little effect on the quality of the calibration. It was therefore decided in a first instance to apply only one calibration equation for the entire cruise. This calibration was first applied to the data on 10-dec-2004.


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

Cruise Name JR20040428 (AMT14, JR101)
Departure Date 2004-04-28
Arrival Date 2004-06-01
Principal Scientist(s)Patrick M Holligan (University of Southampton School of Ocean and Earth Science)
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
Q value below limit of quantification