Metadata Report for BODC Series Reference Number 1807693

• 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

No Problem Report Found in the Database

RRS James Cook Cruise JC073 CTD Data Quality Document

Spikes in the CTD casts have been looked at in closer detail and flagged suspect if necessary. When these spikes are part of wider variability the spikes have been left unflagged.

TEMPST01 and PSALST01

There is variability at depth in both TEMPST01 and PSALST01 in casts over the Logachev mounds. From the cruise report, this variation is likely due to different current influences washing over the reef and potentially creating complex eddy dynamics along the slope and so this variability has not been flagged as suspect. This variability was also seen in the SIGTPR01 channel as SIGTPR01 was derived using TEMPST01 and PSALST01.

DWIRPP01

Many of the profiles are constant with values of zero. The majority of these casts were deployed at night in the dark so values of zero would be expected. All other casts with constant values of zero however, were not deployed in the dark and so have been flagged as suspect.

CPHLPM01

There are several data points in Cast 24 that are negative which have been flagged suspect.

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

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

RRS James Cook cruise JC073 Instrumentation

Standard Rosette CTD Unit and Auxiliary Sensors;

The CTD system configuration used a Sea-Bird Electronics 11plus deck unit (s/n: 11P-19817-0495) and Sea-Bird 9plus underwater unit, (s/n: 09P-46253-0869) with dissolved oxygen sensor. The CTD was fitted with an altimeter, turbidity sensor, PAR irradiance sensor, fluorometer and transmissometer as auxilliary sensors. All instruments were attached to a stainless steel frame (s/n: SBE CTD1) Sea-Bird 24-position Carousel, (s/n: 32-31240-0423) with 24 x Ocean Test Equipment 10 L water samplers, (s/n: 01B to 24B). A secondary SBE 11plus CTD deck unit (s/n: 11P-24680-0587) was also fitted.

The table below provides more information on the CTD unit configuration.

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.

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.

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

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

WETLabs Single-angle Backscattering Meter ECO BB

An optical scattering sensor that measures scattering at 117°. This angle was determined as a minimum convergence point for variations in the volume scattering function induced by suspended materials and water. The measured signal is less determined by the type and size of the materials in the water and is more directly correlated to their concentration.

Several versions are available, with minor differences in their specifications:

• ECO BB(RT)provides analog or RS-232 serial output with 4000 count range
• ECO BB(RT)D adds the possibility of being deployed in depths up to 6000 m while keeping the capabilities of ECO BB(RT)
• ECO BB provides the capabilities of ECO BB(RT) with periodic sampling
• ECO BBB is similar to ECO BB but with internal batteries for autonomous operation
• ECO BBS is similar to ECO BB but with an integrated anti-fouling bio-wiper
• ECO BBSB has the capabilities of ECO BBS but with internal batteries for autonomous operation

Specifications

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

RRS James Cook UK Ocean Acidification (UKOA) cruise JC073 CTD Data processing

Sampling strategy

As part of the UK Ocean Acidification (UKOA) Programme the RRS James Cook JC073 "Changing Oceans" expedition took place from May to June 2012 to study the functional ecology of cold-water coral habitats at contrasting sites in the North Atlantic west of Scotland and Ireland.

A total of 58 CTD casts were obtained using a Sea-Bird Electronics (SBE) 911plus/917plus CTD. The CTD was equipped with a 24 bottle rosette except during casts when a Stand Alone Pump (SAP) was attached to the CTD rig. The rosette bottles were fired during the upcast period of profiling the water column. The cast data were measured by a PC running Seasave V 7.20g, Sea-Bird's data acquisition software.

Originator's processing

The CTD casts obtained were processed using the SBE Data Processing (V7.21g) software and converted to ASCII (CNV). The raw data files were processed using recommended BODC on-board data processing guidelines for SBE-911 CTD (version 1.0, October 2010).

As part of the SBE processing procedure the following steps took place

• DATCNV (data conversion) was run to convert the raw data into ASCII format.
• BOTTLESUM was run to generate the data at bottle firing depths
• FILTER was run on the pressure channel to smoothe out response-time issues in the sensors.
• ALIGNCTD was run to apply a correction to the oxygen and conductivity channels to remove any time lag.
• CELLTM (cell thermal mass) was used to remove conductivity cell thermal mass effects from the conductivity channels.
• LOOPEDIT was used to mark scans with a bad flag wherever there is a pressure slowdown or reversal.
• DERIVE was used to obtain depth, nitrogen saturation, oxygen concentration, practical salinity, density and sigma t values.
• BINAVERAGE was used to separate the temperature, salinity, pressure, depth, oxygen, fluorescence and turbidity data into 0.5 m bins.

The data were saved in ASCII format and imported into Microsoft Excel for quality controlling. The Sea-Bird files in CNV format were converted to tab delimited ODV format. Initial visualisation and plots of CTD data were carried out in Ocean Data View (V4).

Field calibrations

Oxygen

Water samples were obtained in order to measure oxygen concentrations and compare these to the CTD measurements. Dissolved oxygen was measured using the automated Winkler titration, with a polarographic electrode sensor using standard methods outlined in Hansen, 1999. Calibrations took place at the beginning and end of the cruise. The data showed that all casts, apart from cast 11 at 15m, had lower oxygen concentrations to that sampled from the discrete bottles. The best quality version of the oxygen channel was supplied to BODC.

Salinity

Discrete salinity samples were taken from the CTD's in order to compare to the CTD salinity sensor data. A salinometer 8400B (serial number 65764) was used to analyse the salinity samples and was sited in the electronics workshop due to low temperature work in the CT lab. Salinity samples were taken at irregular intervals throughout the cruise, based around scientific requirements. Only 24 samples were taken. The best quality version of the CTD salinity channel was supplied to BODC.

BODC Processing

Reformatting

A total of 56 processed CTD cast files, including seven yo-yo casts for CTD003 were submitted to BODC (Casts 001 to 049). Processed data for Casts 050 and 051 were not provided. The data were submitted in ODV file format and due to incorrect station labelling, the file was updated and modified at BODC to accurately represent the data.

The variables provided in the originators files were reformatted using BODC transfer procedures and can be found in the table below.

The variables which were not reformatted include Depth, Density, TimeJ, activity, Latitude [degrees_north] and Longitude [degrees_east]. Oxygen saturation and sigma-theta were re-derived during transfer. The aforementioned are metadata/derived parameters and hence not measured environmental data but are available upon request.

Parameters derived during the reformatting procedure can be seen in the table below. As the below are derived, there is no originator variable name.

Screening

Reformatted CTD data were visualized using the in-house graphical editor EDSERPLO. No data values were edited or deleted. All spurious and null data were flagged with BODC quality control flags. An originator's flag was also mapped to the PSALST01 channel during screening.

Banking

Once quality control screening was complete the CTD downcasts were banked.

Project Information

UKOARP Theme B: Ocean acidification impacts on sea surface biology, biogeochemistry and climate

The overall aim of this theme is to obtain a quantitative understanding of the impact of ocean acidification (OA) on the surface ocean biology and ecosystem and on the role of the surface ocean within the overall Earth System.

The aims of the theme are:

• To ascertain the impact of OA on planktonic organisms (in terms of physiological impacts, morphology, population abundances and community composition).
• To quantify the impacts of OA on biogeochemical processes affecting the ocean carbon cycle (both directly and indirectly, such as via availability of bio-limiting nutrients).
• To quantify the impacts of OA on the air-sea flux of climate active gases (DMS and N₂O in particular).

The main consortium activities will consist of in-situ measurements on three dedicated cruises, as well as on-deck bioassay experiments probing the response of the in-situ community to elevated CO₂. Most of the planned work will be carried out on the three cruises to locations with strong gradients in seawater carbon chemistry and pH; the Arctic Ocean, around the British Isles and the Southern Ocean.

Weblink: http://www.oceanacidification.org.uk/research_programme/surface_ocean.aspx

Data Activity or Cruise Information

Cruise

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:

SeaDataNet Quality Control Flags

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