Metadata Report for BODC Series Reference Number 1069240
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RSS James Clark Ross Cruise AMT11 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 extracted chlorophyll-a dataset is available for users to derive their own calibrations should they wish.
Downwelling sub-surface PAR irradiance
For downwelling PAR, some data points were beyond the maximum range of the parameter and so were flagged as suspect. Cast AMT11-01 has no irradiance data.
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."
James Clark Ross Cruise AMT11 CTD Instrumentation
Sea Bird Electronics 911plus CTD (with SBE9 CTD and SBE11 deck unit)
Rosette fitted with 12 30-litre Niskin water bottles
Chelsea Aquatracka fluorometer MkIII (#AQU3598, 6000m), S/N 88216
Biospherical Instruments PAR sensor model QCD905L, SN7235
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.
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.
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:
* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.
The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l-1 to 100 µg l-1. The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).
The instrument accuracy is ± 0.02 µg l-1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).
Further details are available from the Aquatracka MKIII specification sheet.
Biospherical Instruments Log Quantum Cosine Irradiance Sensor QCD-905L
The QCD-905L is a submersible radiometer designed to measure irradiance over Photosynthetically Active Radiation (PAR) wavelengths (400-700 nm). It features a cosine directional response when fully immersed in water.
The sensor is a blue-enhanced high stability silicon photovoltaic detector with dielectric and absorbing glass filter assembly, and produces a logarithmic output. Normal output range is -1 to 6 volts with 1 volt per decade. Typically, the instrument outputs 5 volts for full sunlight and has a minimum output of 0.001% full sunlight, where typical noon solar irradiance is 1.5 to 2 x 1017 quanta cm-2 s-1. The instrument can be calibrated with constants for µE cm-2 s-1 or quanta cm-2 s-1.
The QCD-905L can be coupled to a fixed range data acquisition system like a CTD (Conductivity-Temperature-Depth) profiler or current meter. It has an aluminium and PET housing, and a depth rating of 7000 m.
|Wavelength||400 to 700 nm|
|Output range||-1 to 6 V, with 1 V decade-1|
|Operating temperature||-2 to 35°C|
|Depth range||0 - 7000 m|
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:
|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 Clark Ross Cruise AMT11 CTD Processing
The CTD profiles were processed onboard using Sea-Bird's data processing software.
BODC data processing
The data files were sent to BODC in Sea-Bird's data processing software output. All available channels were listed into ASCII format. Non-null channels were then converted to PXF, a BODC internal format. The data were processed from 1Hz averaged down- and upcast data. Sigma-theta was calculated and output from the raw data during the conversion to PXF format.
Originator's Parameter Originator's Units Description BODC code BODC Units Comments Pressure decibars Pressure PRESPR01 decibars - Temperature °C Temperature TEMPCU01 °C - Temperature, 2 °C Temperature TEMPCU02 °C - Salinity - Salinity PSALCU01 - - Salinity, 2 - Salinity PSALCU02 - - Voltage 0 V Fluorometer voltage FVLTAQ01 V - Voltage 2 V 2 pi-PAR meter voltage LVLTBD01 V - - - Salinity - calibrated PSALCC01 - PSALCU01 calibrated against bottle samples - - Salinity - calibrated PSALCC02 - PSALCU02 calibrated against bottle samples - - Calibrated fluorescence CPHLPS01 mg m-3 Calibrated against bottle HPLC chl-a data - - Downwelling PAR irradiance IRRDPP01 µE m-2 s-1 Calculated from PAR meter voltage using manufacturer's coefficients - - Potential temperature POTMCV01 °C Computed using UNESCO POTEMP function (using primary T and S) - - Sigma-theta SIGTPR01 kg m-3 Computed using UNESCO SVAN function
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. The pressure ranges over which bottles were fired were also marked. The bottle firing events were identified by disturbances in CTD parameters on the upcast profiles. All spurious and null data were flagged with appropriate BODC quality control flags.The secondary temperature and salinity channels were used to aid screening of the primary channels only. The primary channels should be used in preference to the secondary channel as they have been quality controlled.
The following notes were made during the screening of AMT11 CTD data.
For the first cast (AMT11-01), the fluorescence signal was suspect - the fluorometer had either not been attached to the CTD frame, or had not been configured correctly.
The PAR sensor showed fairly noisy data throughout the cruise, but particularly AMT11-27, AMT11-28 and AMT11-43.
Loading into the BODC database
After the data had been screened and quality controlled, the data were loaded into the BODC database under the Oracle RDBMS.
46 entries were made in table EVENT, which stores metadata for the CTD casts. The start and end times were taken from the data files. The position was taken from the ship's navigation stored in the underway file at the start time of the CTD cast.
The data from all 46 casts were loaded into the data tables.
The pressure sensor had a mean reading of -0.51 decibar while the CTD was logging in air - this was identified during BODC processing. A pressure correction was, therefore, applied to the data when they were listed from the BODC database.
PRESPR01(corr) = PRESPR01(raw) + 0.51 decibar (BODC calibration 2303).
No reversing thermometer data were available for AMT11, so the CTD sensor data have not been calibrated against another data set. However, the Sea-Bird sensors were tested and calibrated before and after the cruise, and manufacturer's calibrations were applied during Sea-Bird processing. No further correction has been applied to the data at BODC.
There were a limited number (26) of CTD bottle samples that were analysed on the bench salinometer. These have been compared with CTD values at the depth of bottle firing. The offset between bench salinometer and CTD salinity data was quite variable throughout the cruise. Two samples were removed from the data set due to high standard deviation of CTD measurements at that point. The mean offset for sensor 1 was 0.03336 PSU with a standard deviation of 0.03291. The mean offset for sensor 2 was 0.03346 with a standard deviation of 0.0329. These offsets have been applied to the data. Note that the moderately high standard deviations mean that the accuracy of the salinity channel cannot be may be up to 0.0329 PSU out.
PSALCC01 = PSALCU01 + 0.03336 (BODC calibration 2705)
PSALCC02 = PSALCU02 + 0.03346 (BODC calibration 2706)
The fluorometer on AMT11 was a Chelsea Instruments Aquatracka. The manufacturer's calibrations of the instrument indicated a relationship of the form:
Chl-a conc (µg/l) = 0.00945 * 10voltage - 0.0172
The fluorescence data is stored as the raw voltages. A chlorophyll-a channel was created by comparing the voltages at bottle firing depths on the upcast with HPLC data obtained from those bottles. The HPLC data included HPLC chlorophyll-a, chlorophyll-a allomer, chlorophyll-a epimer and divinyl chlorophyll-a. The sum of these was used to calibrated the fluorometer.
The data for AMT11 did not follow the same relationship throughout the cruise. This is likely to be due to the presence of different species populations in different areas along the cruise track. The CTD casts were separated into two groups, based on two sample populations that could be identified in the plot of the whole data set. Some outlying values were removed from the data set.
Two calibration equations were produced and they have been applied as follows:
AMT11-02 to -15 and AMT11-20 to -35:
CPHLPS01 = 0.00783 * 10FVLTAQ01 - 0.0480 (BODC calibration 2863; r2 = 0.889; N = 69)
AMT11-16 to -19 and AMT11-36 to -46:
CPHLPS01 = 0.0170 * 10FVLTAQ01 - 0.145 (BODC calibration 2883; r2 = 0.776; N = 26)
The calibrations were applied, and the concentrations in the surface mixed layer, the chlorophyll maximum and at maximum depths were checked against the bottle HPLC data and fluorometric chlorophyll-a (the sum of size-fractions>0.2 m). The results showed good agreement. The exception appeared to be the final cast, AMT11-46 - the calibration produced concentrations that appeared slightly too high.
Irradiance = 10 lightmeter voltage * (104 * calibration factor), where the wet calibration factor = 1.88 * 10-6 µEinsteins cm-2sec-1.
The Atlantic Meridional Transect (AMT) - Phase 1 (1995-2000)
Who was involved in the project?
The Atlantic Meridional Transect (AMT) programme was designed by and implemented as a collaboration between Plymouth Marine Laboratory (PML) and Southampton Oceanography Centre (SOC). The programme was hosted by Plymouth Marine Laboratory and involved additional researchers from UK and international universities throughout its duration.
What was the project about?
When AMT began in 1995 the programme provided a platform for international scientific collaboration, including the calibration and validation of SeaWiFs measurements and products. The programme provided an exceptional opportunity for nationally and internationally driven collaborative research and provided a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, the data collected by the AMT consortium informed on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.
The scientific aims were to assess:
- mesoscale to basin scale phytoplankton processes
- the functional interpretation of bio-optical signatures
- the seasonal, regional and latitudinal variations in mesozooplankton dynamics
When was the project active?
The first phase of the AMT programme ran from 1995 to 2000 and consisted of a total of 12 cruises. A second phase of funding allowed the project to continue for the period 2002 to 2006 with a further 6 cruises.
Brief summary of the project fieldwork/data
The AMT programme undertook biological, chemical and physical oceanographic research during the annual return passage of the RRS James Clark Ross between the UK and the Falkland Islands or the RRS Discovery between the UK and Cape Town, a distance of up to 13,500 km. This transect crossed a range of ecosystems from sub-polar to tropical and from euphotic shelf seas and upwelling systems to oligotrophic mid-ocean gyres. The transect route was covered north-south in September/October and south-north in April/May of each year.
The measurements of hydrographic and bio-optical properties, plankton community structure and primary production completed on the first 12 transects (1995-2000) represent the most coherent set of repeated biogeochemical observations over ocean basin scales. This unique dataset has led to several important discoveries concerning the identification of oceanic provinces, validation of ocean colour algorithms, distributions of picoplankton, identifying new regional sinks of pCO2 and variability in rates of primary production and respiration.
Who funded the project?
The programme was funded by the Natural Environment Research Council (NERC) and further support was received from the National Aeronautics and Space Administration (NASA) with equipment and funding from the Sea-viewing Wild Field-of-view Sensor (SeaWiFS) project.
|Cruise Name||JR20000912 (AMT11, JR52 Leg1, JR53)|
|Principal Scientist(s)||E Malcolm S Woodward (Plymouth Marine Laboratory)|
|Ship||RRS James Clark Ross|
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|<||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.)|
|E||End of CTD Down/Up Cast|
|G||Non-taxonomic biological characteristic uncertainty|
|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|
|O||Improbable value - user quality control|
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|0||no quality control|
|2||probably good value|
|3||probably bad value|
|6||value below detection|
|7||value in excess|
|A||value phenomenon uncertain|
|Q||value below limit of quantification|