Metadata Report for BODC Series Reference Number 1148224
Metadata Summary
Problem Reports
Data Access Policy
Narrative Documents
Project Information
Data Activity or Cruise Information
Fixed Station Information
BODC Quality Flags
SeaDataNet Quality Flags
Metadata Summary
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Problem Reports
No Problem Report Found in the Database
Data Quality Report - D352 Scanfish tow 6
The originator has reported that on survey six a number of data drop outs occurred. This culminated in the eventual failure of the underwater termination after some thirty six hours of the survey. The cable was re-terminated and the survey run was completed at the end of the cruise.
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.
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.
D352 Scanfish instrumentation
The Scanfish package contained a SeaBird 911 plus unit, complimented by a SeaBird 43 Oxygen sensor and a Chelsea Aqua 3 Fluorometer. The table below details the calibration dates and serial numbers of the instruments fitted to the Scanfish:
| Sensor | Serial Number | Last factory calibration dates | Mounting |
|---|---|---|---|
| SeaBird 9 temperature sensor | 4782 | 12 February 2010 | Port cheek wing |
| SeaBird 9 conductivity sensor | 2450 | 10 February 2010 | Port cheek wing |
| Digiquartz pressure sensor with TC | 110557 | 26 April 2009 | Mounted internally |
| SeaBird 43 Oxygen sensor | 0621 | 20 March 2010 | Mounted internally |
| Fluorometer, Chelsea Aqua 3 | 088126 | 02 January 2007 | - |
Originator's data processing - D352 Scanfish
Sampling Strategy
The Scanfish towed undulator was deployed behind the ship for eight survey runs over the duration of cruise D352 in order to profile the water column. This resulted in approximately five and a half days of time spent in the water.
Data Processing
The Scanfish tows were recorded using the SeaBird data collection software SeaSave-Win32. This software output three files for each run which had extensions .HEX (raw data files), .CON (data configuration file), and .HDR (header file). These files were backed up on the ships network and processing was done using SeaBird Software Processing, Version 7.18c (SBEDataProcessing-Win32).
DATCNV was used to convert raw data files from engineering units producing .CNV files. FILTER was used to run a low-pass filter on each column of the data, smoothing high frequency, rapidly changing data. The pressure channel was filtered with a time constant of 0.15 seconds. ALIGNCTD was then used to shift the dissolved oxygen sensor output relative to the pressure by 4 seconds to compensate for lags in the sensor response time. The effect of thermal inertia on conductivity cells was removed by CELLTM and data were averaged using time with a 0.5 second bin size for up and downcasts using BINAVERAGE. Oxygen concentration, salinity and density were calculated by DERIVE.
Data cycles sampled whilst the instrument was at the surface of the water column have been trimmed from the beginning and end of the files; so that only the data when the Scanfish was actively diving and resurfacing were supplied to BODC. Data have also been loaded in to MATLAB and .mat files created for each run except for runs 4 and 6 where there was so much data that it was decided to split these in to 3 and 2 files respectively. Calibrations have been applied to some parameters using data from a calibration run of the Scanfish and CTD casts taken just before and just after this run.
For more information about the originator's processing and calibration methods please see pages 31 - 40 of the cruise report
The final dataset
The final dataset supplied to BODC included the following parameters:
| Parameter ID | Parameter | Units | Comments |
|---|---|---|---|
| Chloro | Concentration of chlorophyll-a | µg l-1 | |
| Chloro_calib | Calibrated concentration of chlorophyll-a | µg l-1 | Scanfish concentration of chlorophyll calibrated with D352 Ship CTD data (which has been calibrated with in-situ sample data) |
| Cond1 | Conductivity | S m-1 | |
| Descent_rate | The vertical rate of decent of the Scanfish | m s-1 | |
| Density | Density | kg m-3 | |
| Density_calib | Calibrated Density | kg m-3 | Density derived from calibrated temperature and salinity data |
| Distance_run | The horizontal distance travelled since the start of each run | km | Distance run derived from the positional latitude and longitude data |
| Flag | Data quality flag assigned by originator | ||
| Lat | Latitude | Degrees | |
| Lon | Longitude | Degrees | |
| O2_con_mll | Oxygen concentration | ml l-1 | |
| O2_con_mll_calib | Calibrated oxygen concentration | ml l-1 | Oxygen concentration data calibrated with D352 Ship CTD data (which has been calibrated with independent oxygen data from a SeaBird 43 Oxygen sensor) |
| O2_con_umolkg | Oxygen concentration | µmol kg-1 | |
| O2_saturation | Oxygen saturation | % | |
| Pressure | Pressure | dbar | |
| Salinity1 | Salinity | dimensionless | |
| Salinity1_calib | Calibrated salinity | dimensionless | Salinity data calibrated with D352 Ship CTD data (which has been calibrated with in-situ water samples). Originator identified this as the variable to be used in the final dataset to be processed by BODC instead of the filtered version. |
| Salinity1_calib_ft | Calibrated salinity which has been filtered | dimensionless | Salinity data calibrated with D352 Ship CTD data (which has been calibrated with in-situ water samples) and then median filtered with 4 second window |
| Scans | Scan number since start of run | ||
| Sigma_theta | Sigma-theta | Kg m-3 | |
| Sigma_theta_calib | Calibrated sigma-theta | Kg m-3 | Sigma theta data derived from calibrated temperature and salinity data |
| Starttime | Start time of data file | Date and time formatted as: mmm dd yyyy HH:MM:SS | |
| Temp1 | Temperature | °C | |
| Temp1_calib | Calibrated temperature | °C | Temperature data calibrated with D352 Ship CTD data |
| Time | Time elapsed since start time | seconds |
Processing undertaken by BODC - D352 Scanfish
Data arrived at BODC as a series of (.mat) MATLAB files. Together, these files represented data collected from the eight Scanfish surveys conducted during D352 and processed by the originator. Data were reformatted to BODC's internal format.
The following table shows the mapping of variables within the MATLAB files to appropriate BODC parameter codes:
| Originator' Variable | Units | Description | BODC Parameter Code | Units | Comments |
|---|---|---|---|---|---|
| Latitude (lat) | Degrees | Latitude north (WGS84) by unspecified GPS system | ALATGP01 | Degrees | |
| Longitude (lon) | Degrees | Longitude east (WGS84) by unspecified GPS system | ALONGP01 | Degrees | |
| Pressure (pressure) | dbar | Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level | PRESPR01 | dbar | |
| Calibrated salinity (salinity1_calib) | dimensionless | Practical salinity of the water body by CTD and computation using UNESCO 1983 algorithm and calibration against independent measurements | PSALCC01 | dimensionless | |
| Calibrated temperature (temp1_calib) | °C | Temperature of the water body by CTD and verification against independent measurements | TEMPCC01 | °C | |
| Conductivity (cond1) | S m-1 | Electrical conductivity of the water body by CTD | CNDCST01 | S m-1 | |
| Calibrated oxygen concentration (O2_con_mll_calib) | ml l-1 | Concentration of oxygen {O2} per unit volume of the water body [dissolved phase] by Sea-Bird SBE 43 sensor and calibration against sample data | DOXYSC01 | µmol l-1 | Conversion by * 44.66 |
| Oxygen saturation (O2_saturation) | % | Saturation of oxygen {O2} in the water body [dissolved phase] | OXYSZZ01 | % | |
| Calibrated chlorophyll (chloro_calib) | ug l-1 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate phase] by in-situ chlorophyll fluorometer. In-situ fluorometer with manufacturer, laboratory or sample calibration applied. | CPHLPR01 | mg m-3 | No conversion required, ug l-1 = mg m-3 |
| Descent rate (descent_rate) | m s-1 | Downward velocity of sensor package in the water body | CTDLOWRT | m s-1 | |
| Distance run (distance_run) | km | Distance travelled | DSRNCV01 | km | |
| Sigma-theta | Sigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm | SIGTPR01 | kg m-3 | Derived by BODC | |
| Potential temperature | Potential temperature of the water body by computation using UNESCO 1983 algorithm | POTMCV01 | kg m-3 | Derived by BODC |
The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, and missing data marked by both setting the data to an appropriate value and setting the quality control flag.
Finally, detailed metadata are loaded to the BODC database and linked to each data series so that the information is readily available to future users.
References
Fofonoff, NP and Millard, RC (1983). Algorithms for computations of fundamental properties of seawater. UNESCO Technical Papers in Marine Science No. 44, 53pp.
Project Information
NERC Responsive Mode Project: A Thermocline Nutrient Pump
Project Partners and Duration
NERC Responsive Mode research project NE/F002432/1 ("A Thermocline Nutrient Pump") was jointly awarded to Bangor University (Principal Investigator: Dr. Tom Rippeth) and the Proudman Oceanographic Laboratory [since April 2010, part of the National Oceanography Centre] (Principal Scientist: Prof. Jonathan Sharples, since January 2010 based at the University of Liverpool). The project runs from 2008 to 2013.
Background
The seasonal thermocline in temperate shelf seas acts as a critical interface in the shelf sea system. It is a physical barrier to vertical exchange, controlling biological growth through the summer and enabling the sequestration of atmospheric CO2.
Once the spring bloom is over, the seasonal thermocline separates the sun drenched but nutrient depleted surface waters from the dark nutrient rich deep water. The vertical mixing of nutrients across the seasonal thermocline acts to couple this well-lit surface zone with the deep water nutrient supply, leading to the formation of a layer of phytoplankton within the thermocline (the subsurface chlorophyll maxima). This phenomenon is estimated to account for about half of the annual carbon fixation in seasonally stratified shelf seas, and yet the controlling physics is only just being unravelled. The identification and parameterisation of the physical processes which are responsible for the vertical mixing of nutrients across the thermocline is a vital prerequisite to the understanding of shelf sea ecosystems.
Project Aim
This project aim is to investigate the role of wind driven inertial oscillations in driving vertical mixing across the seasonal thermocline, identifying the mechanisms and processes responsible for their generation and dissipation on both special and temporal scales. This is to be achieved through an observational campaign closely integrated with numerical model predictions using both 1D and 3D numerical models.
Specific Hypotheses to be tested:
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A significant fraction of the total turbulent mixing at the thermocline is the result of episodic spikes in inertial shear.
-
Inertial shear events are sensitive to local stratification and tidal conditions.
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Inertial mixing events have significant horizontal variability.
Project Objectives
1. Acquisition of long time series of well-resolved current and temperature profiles to quantify the episodic nature of the shear events and investigate their relationship with surface winds, tides and stratification. This objective contributes to testing of Hypothesis 1.
2. Investigate spatial variability of the generation/dissipation of inertial shear events caused by horizontal variations in wind forcing, tidal characteristics and horizontal patchiness in density structure. This contributes to testing of Hypothesis 2.
3. Determination of the spatial connectivity of inertial shear events as a mechanism for non-local generation, transfer and dissipation of intertial energy. This contributes to testing of Hypotheses 2 and 3.
4. Determination of consistent discrepancies between modelled sequences of intertial events and direct observations and identification of possible causes. This will identify deficiencies in the current modelling physics.
5. Investigate the link between inertial mixing and vertical nitrate fluxes into the thermocline and the consequences of incorrect modelling of the episodic nature of this mixing process.
Fieldwork Schedule
| Cruise | Location | Dates | Main Activities |
|---|---|---|---|
| RV Prince Madog cruise PD20_09 | Western Irish Sea | 2009-05-18 to 2009-05-22 |
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| RV Prince Madog cruise PD27_09 | Western Irish Sea | 2009-07-06 to 2009-07-10 |
|
| RV Prince Madog cruise (ID not available at this time) | Western Irish Sea | May 2010 (exact dates not available at present) |
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| RRS Discovery cruise D352 | Firth of Clyde, Irish Sea and Celtic Sea | 2010-06-02 to 2010-06-26 |
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| RV Prince Madog cruise (ID not available at this time) | Western Irish Sea | July 2010 (exact dates not available at present) |
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| RV Prince Madog cruise (ID not available at this time) | Western Irish Sea | September 2010 (exact dates not available at present) |
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Key:
VMP: Vertical Microstructure Profiler
CTD: Conductivity, temperature and depth sensor
ADCP: Acoustic Doppler Current Profiler
SAPS: Stand-alone Pump Sampling
VMADCP: Vessel Mounted ADCP
LADCP: Lowered ADCP
RAS: Remote Access Sampler
Data Activity or Cruise Information
Cruise
| Cruise Name | D352 |
| Departure Date | 2010-06-02 |
| Arrival Date | 2010-06-26 |
| Principal Scientist(s) | Jonathan Sharples (National Oceanography Centre, Liverpool) |
| Ship | RRS Discovery |
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 |
