Metadata Report for BODC Series Reference Number 979142

• Metadata Summary

• Problem Reports

• Data Access Policy

• Narrative Documents

• Project Information

• Data Activity or Cruise Information

• Fixed Station Information

• BODC Quality Flags

• SeaDataNet Quality Flags

Metadata Summary

Problem Reports

Dissolved Oxygen

All data from this channel should be used with caution as the values measured were unrealistic during this and several other cruises. Readings taken by the probe indicated that the sensor was constantly saturated.

Data quality notes

LISST transmission and scattering

Users should be aware that the clear water values measured on different cruises are observed to increase and decrease at times, which is not consistent behaviour. In addition, the clear water scattering values are also sometimes less than and sometimes greater than those measured by the manufacturer at the time of last calibration (October 2006). This may be due to a problem with the instrument or the method in which the clear water values are measured.

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 Electronics SBE13 Dissolved Oxygen Sensor

The SBE 13 was designed as an auxiliary sensor for Sea Bird SBE 9plus, but can fitted in custom instrumentation applications. When used with the SBE 9 Underwater Unit, a flow-through plenum improves the data quality, as the pumping water over the sensor membrane reduces the errors caused by oxygen depletion during the periods of slow or intermittent flushing and also reduces exposure to biofouling.

The output voltage is proportional to membrane current (oxygen current) and to the sensor element's membrane temperature (oxygen temperature), which is used for internal temperature compensation.

Two versions of the SBE 13 are available: the SBE 13Y uses a YSI polarographic element with replaceable membranes to provide in situ measurements up to 2000 m depth and the SBE 13B uses a Beckman polarographic element to provide in situ measurements up to 10500 m depth, depending on the sensor casing. This sensor includes a replaceable sealed electrolyte membrane cartridge.

The SBE 13 instrument has been out of production since 2001 and has been superseded by the SBE 43.

Specifications

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

Prince Madog Cruise PD02_07 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911plus system (SN P23655-0620), with dissolved oxygen sensor. The CTD was fitted with a red (660 nm) beam transmissometer, a fluorometer, a Sequoia Scientific Laser In-Situ Scattering and Transmissometry (LISST) particle analyser and a LI-COR Underwater Quantum Sensor. Also attached was a Sea-Bird SBE-35 Temperature Logger to supply an independent check of temperature. All instruments were attached to a Sea-Bird 32 compact carousel. The table below lists more detailed information about the various sensors.

Change of sensors during cruise: None reported.

Sampling device

Rosette sampling system equipped with 5 l sampling bottles (Sea-Bird Improved PVC Sample Bottles based on design of Ocean Test Equipment Inc. model 110 bottle).

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus, that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus.

Specifications

Specifications for the SBE 9 plus underwater unit are listed below:

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

Turner Designs Self-Contained Underwater Fluorescence Apparatus (SCUFA)

The Turner Designs SCUFA is a submersible fluorometer for chlorophyll and dye tracing operations that has been designed to operate in a wide range of concentrations, environmental conditions as well as operational modes (profiling or moored deployments). The instrument includes an integrated temperature probe and software which allow for automatic correction of fluorescence data from temperature effects. The superior ambient light rejection eliminates the effects of sunlight and allows the SCUFA to be used in surface waters without the need for external pumps or light shields.

Each instrument can be customised to meet user requirements. Users can choose one of the following channels: chlorophyll a, cyanobacteria (phycocyanin or phycoerythrin pigments), rhodamine WT, fluorescein and turbidity. Instrument options include turbidity, internal data logging and automatic temperature correction.

Three versions of the SCUFA are available: SCUFA I, II and III. SCUFA I and II are used for chlorophyll a applications, while SCUFA III is used for Rhodamine WT. Models II and III include a turbidity channel that is not present on model I. The SCUFA has been out of production since 2008.

Specifications

The table below presents the specifications for the different channels.

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

LI-COR LI-192 Underwater Quantum Sensor

The LI-192 Underwater Quantum Sensor is used to measure photosynthetic photon flux density and is cosine corrected. The sensor is often referred to as LI-192SA or LI-192SB (the LI-192SB model was superseded by LI-192SA). One of the main differences is that the LI-192SA model includes a built-in voltage output for interfacing with NexSens iSIC and SDL data loggers.

Sensor specifications, current at January 2012, are given in the table below. More information can be found in the manufacturer's LI-192SA andLI-192SB specification sheets.

Sensor Specifications

(Specifications apply to both models unless otherwise stated)

SeaTech Transmissometer

Introduction

The transmissometer is designed to accurately measure the the amount of light transmitted by a modulated Light Emitting Diode (LED) through a fixed-length in-situ water column to a synchronous detector.

Specifications

• Water path length: 5 cm (for use in turbid waters) to 1 m (for use in clear ocean waters).
• Beam diameter: 15 mm
• Transmitted beam collimation: <3 milliradians
• Receiver acceptance angle (in water): <18 milliradians
• Light source wavelength: usually (but not exclusively) 660 nm (red light)

Notes

The instrument can be interfaced to Aanderaa RCM7 current meters. This is achieved by fitting the transmissometer in a slot cut into a customized RCM4-type vane.

A red LED (660 nm) is used for general applications looking at water column sediment load. However, green or blue LEDs can be fitted for specilised optics applications. The light source used is identified by the BODC parameter code.

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

Sequoia Laser In-situ Sediment Size Transmissometer (LISST)

The Sequoia LISST measures particle size distribution of suspended sediments by laser diffraction. This technique allows particles of various compositions to be measured with a single device and, because the particle volume is roughly of the same order for all sizes, the required dynamic range of the sensors is reduced compared with single-particle counters.

The instrument includes optics for producing a collimated laser beam, a detector array, electronics for signal amplification and processing, a data storage and scheduling computer and a battery system. The primary measurement is the scattering of laser light at a number of angles, which is mathematically inverted to give a grain size distribution, and also scaled to obtain the volume scattering function. The size distribution is presented as concentration in each of 32 logarithmically-spaced grain-size class bins. Optical transmission, water depth and temperature are recorded as supporting measurements.

Several models are available and although the principals of operation are the same, their specifications vary slightly. The specifications for model LISST-100 are provided below.

Specifications

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

Prince Madog Cruise PD02_07 CTD Processing

Sampling Strategy

A total of 35 CTD casts were performed during the cruise throughout Liverpool Bay. Rosette bottles were fired near-bed on numerous profiles in order to obtain independent temperature and salinity samples, the results of which were sent to BODC. Water bottle samples were also taken from the near-surface and near-bed bottle and frozen for nutrient analysis (nitrates, phosphate, silicate) at the National Oceanography Centre, Southampton. Additionally, the near-surface samples were filtered to determine suspended sediment load by the School of Ocean Sciences. Some filtrate was preserved by mercuric chloride for nutrient analysis by CEFAS at station 1 (twice), stations 5-8 and 11.

Data Processing

Data were logged at 24 Hz onto a PC running SEASAVE, Sea-Bird's data acquisition software. The raw Sea-Bird data, configuration and bottle files were supplied to BODC for further processing.

Sea-Bird Processing

The raw CTD files were processed through the Sea-Bird SBE Data Processing software version 5.35. Binary (.DAT) files were converted to engineering units and ASCII format (.CNV) using the DATCNV program. Sea-Bird bottle files (.BTL), with information on pressure and other logged readings at the time of bottle firing, were also generated during the data conversion process.

Sea-Bird software program ALIGNCTD was run to advance conductivity by 0s and oxygen by 3s (within the typical range given in the Sea-Bird manual). No adjustment was made to the temperature channel as the fast sensor response time renders this unnecessary, according to the Sea-Bird literature.

To compensate for conductivity cell thermal mass effects, the data files were run through CELLTM, using alpha = 0.03, 1/beta = 7, typical values for this CTD model given in the Sea-Bird literature. After running WILD EDIT, FILTER was run on the pressure channel using the recommended time filter of 0.15 seconds. Next, a minimum CTD velocity of 0.0 m s^-1 was used for LOOP EDIT in order to exclude scans where the CTD was travelling backwards due to ship's heave. Salinity, density and oxygen concentration were then calculated and added to the output files using the DERIVE program. The files were then averaged to 0.5 second intervals using BINAVERAGE.

Reformatting

The data were converted from ASCII format into BODC internal format (QXF). The following table shows the mapping of variables within the original files to appropriate BODC parameter codes:

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 quality control flag to 'M' for suspect values and 'N' for nulls.

Banking

Once quality control screening was complete, CTD downcasts for all casts were binned against pressure at 0.5 dbar increments. During binning, BODC exclude flagged data and generate interpolated values to fill in gaps in the increment sequence, where necessary. Finally, the CTD downcasts were banked.

Calibrations

Salinity

37 independent salinity samples, obtained from the CTD rosette, were used to calibrate the CTD. Three points were deemed to be outliers (casts C001, C018 and C022) and were removed from the analysis. The salinity offset (bottle salinity - CTD salinity) was examined to see if it varied with pressure, attenuation or bottle salinity. No significant relationships at 95% confidence could be found between offset and any other parameter. Therefore, a calibration equation was derived from the mean offset as follows, based on 32 observations:

• calibrated salinity = CTD salinity + 0.0086

The calibration residuals ranged from -0.191 to 0.3301.

Temperature

115 independent temperature values were compared to pressure and CTD temperature. Two points were identified as outliers (casts C001 at depth 20.26m, C018 at depth 13.19m) and were removed from the analysis. The offset between CTD temperature and SBE-35 temperature was found not to be significantly different from zero at 95% confidence. Therefore, there was no adjustment to the CTD temperature resulting from the application of manufacturer's coefficients during initial processing.

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.

Beam attenuation

Coefficients M and B were calculated, allowing calibration of the transmissometer with air readings taken during the cruise. M and B are calculated according to SBE Application Note No. 7:

Where Tw is the percent transmission for pure water for the instrument (92.98%); W0 is the voltage output in pure water (4.649 volts); A0 is the manufacturer's air voltage (4.661 volts); Y0 is the manufacturer's blocked path voltage (0.000 volts); A1 is the cruise maximum air voltage (4.558 volts); Y1 is the current blocked path voltage (0.0000 volts). For this cruise, M and B were calculated to be 20.4520 and 0, respectively.

M and B are then inserted into the following equations (from SBE Application Note No. 7) to obtain calibrated beam attenuation:

Where M and B are the calibration coefficients, z is the transmissometer path length (0.2m), light transmission[decimal] is light transmission [%] divided by 100, c = beam attenuation (m-1)

LISST transmission and scattering

The data are currently supplied as voltages due to concerns about the observed variability in the clean water readings over time. With reliable clean water readings, the voltages can be calibrated to give optical transmission, beam attenuation, total volume concentration and Sauter mean diameter according to the following manufacturer's constants and calculations:

Where, the coefficients supplied here are from clear water readings taken during the most recent manufacturer calibration (October 2006) as follows:

• V_T = measured transmission output V
• V_Toff = transmission output offset = 0.007 V
• V_TO = clear water transmission output = 2.828 V
• cal = total volume concentration calibration constant = 630
• V_S = measured scattering output V
• V_Soff = scattering output offset = 0.004 V
• V_SO = clear water scattering output = 0.155 V
• a = Sauter mean diameter calibration constant = 0.075

Ideally the manufacturer's clear water values should be substituted by values determined by the LISST calibration cast, during which the instrument is placed in a tank of clean water. However, there is suspicion that these values may not be accurate.

The clean water transmission and scattering voltages can be seen to both increase and decrease with time, showing inconsistency in either the instrument performance or the calibration dip method. Therefore, manufacturer's values have been quoted along with values measured by the instrument during previous cruises since the last manufacturer's calibration. Users are advised to use their own discretion in deciding which coefficients to apply.

PAR

During instrument deployment, no effort was made to avoid data collection possibly being affected by ship shadowing. The LI-COR LI-192SB sensor number 33 was calibrated from raw voltages using the CEFAS supplied equation:

• PAR = 0.157508*exp(volts*3.42410)

Project Information

Proudman Oceanographic Laboratory Coastal Observatory

The Coastal Observatory was established by Proudman Oceanographic Laboratory as a coastal zone real time observing and monitoring system. The main objective is to understand a coastal sea's response both to natural forcing and to the consequences of human activity. Near real-time measurements will be integrated with coupled models into a pre-operational coastal prediction system whose results will be displayed on the World Wide Web.

The Observatory is expected to grow and evolve as resources and technology allow, all the while building up long time series. A site selection pilot study was carried out in September 2001 and the Observatory became operational in August 2002.

The site is located in Liverpool Bay and is subject to typical coastal sea processes, with strong tides, occasional large storm surges and waves, freshwater input, stable and unstable stratification, high suspended sediment concentration and biogeochemical interaction. Measurements and monitoring will focus on the impacts of storms, variations in river discharge (especially the Mersey), seasonality and blooms in Liverpool Bay.

A variety of methods will be used to obtain measurements, including:

1. Moored instruments for in situ time series of currents, temperature and salinity profiles, and surface waves and meteorology. It is hoped that turbidity and chlorophyll measurements will be made at another site as the Observatory progresses;
2. The Cefas Smartbuoy for surface properties such as nutrients and chlorophyll, starting late 2002;
3. R.V. Prince Madog to carry out spatial surveys and service moorings;
4. Instrumented ferries for near surface temperature, salinity, turbidity, chlorophyll and nutrients. The first route will be Liverpool to Douglas, Isle of Man, starting late 2002;
5. Drifters for surface currents and properties such as temperature and salinity, starting in 2004;
6. Tide gauges, with sensors for meteorology, waves, temperature and salinity, where appropriate;
7. Meteorological data from Bidston Observatory and Hilbre Island, HF radar and tide gauge sites;
8. Shore-based HF radar measuring waves and surface currents out to a range of 50 km, starting in 2003;
9. Satellite data, with infrared for sea surface temperature and visible for chlorophyll and suspended sediment.

The partners currently involved with the project are listed below:

• Proudman Oceanographic Laboratory
• British Oceanographic Data Centre
• UK Meteorological Office
• Centre for Environment, Fisheries and Aquaculture Science
• Environment Agency
• Liverpool University and Port Erin Marine Laboratory
• Bangor University School of Ocean Sciences
• National Oceanography Centre Southampton
• Department of Agriculture and Rural Development in Northern Ireland

A summary of Coastal Observatory cruises to date on R.V. Prince Madog is given in the table below:

Data Activity or Cruise Information

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

Fixed Station Information

Liverpool Bay Coastal Observatory Site 7

This station is one of 34 stations regularly visited by the Proudman Oceanographic Laboratory (POL) as part of the Liverpool Bay Coastal Observatory. During each site visit, CTD profiles are taken. The station lies within a box of mean water depth 23 m with the following co-ordinates:

The position of this station relative to the other POL Coastal Observatory sites can be seen from the figure below.

CTD Sampling History

The CTD instrument package for these cruises was a Sea-Bird 911plus, with beam transmissometer, fluorometer, LICOR PAR sensor, LISST-25, and oxygen sensor.

Related Fixed Station activities are detailed in Appendix 1

BODC Quality Control Flags

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

SeaDataNet Quality Control Flags

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

Appendix 1: Coastal Observatory Site 7

Related series for this Fixed Station are presented in the table below. Further information can be found by following the appropriate links.

If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.