Metadata Report for BODC Series Reference Number 954996

• 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

Data Quality Report

Series metadata suggest that the CTD cast depth is greater than the seafloor depth. This is the result of uncorrected seafloor depths, from the ship's precision echosounder, appearing in the originator's data header files.

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.

D340B CTD Instrumentation

CTD unit and auxiliary sensors

The CTD system used on cruise D340B was the Sea-Bird 911 plus. This was mounted on a stainless steel rosette frame, equipped with 24 10-litre Niskin bottles. The CTD was fitted with the following scientific sensors:

It should be noted that for the CTD cast C089 the dual PAR sensor was removed because the depth to which the CTD was deployed was greater than the PAR sensor pressure rating.

The salinity samples from the CTD were analysed during the cruise in a constant temperature laboratory using the Guildline Autosal model 8400B. Dissolved oxygen concentrations were determined using a Winkler titration technique

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.

Aquatracka fluorometer

The Chelsea Instruments Aquatracka is a logarithmic response fluorometer. It uses a pulsed (5.5 Hz) xenon light source discharging between 320 and 800 nm through a blue filter with a peak transmission of 420 nm and a bandwidth at half maximum of 100 nm. A red filter with sharp cut off, 10% transmission at 664 nm and 678 nm, is used to pass chlorophyll-a fluorescence to the sample photodiode.

The instrument may be deployed either in a through-flow tank, on a CTD frame or moored with a data logging package.

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.

D340B CTD Originator Processing

Sampling Strategy

A total of 15 CTD casts were performed during the cruise which sailed between Dunstaffnage on the west coast of Scotland to Govan via Barra Head and the surrounding shelf. All of the CTD casts deployed during the cruise were housed in a stainless steel frame equipped with dual temperature and conductivity sensors. The CTDs were located within and near the bottom of the rosette frame which held 24 10-litre Niskin water sampling bottles.

Data Processing

Following the completion of each CTD cast the data were saved to the deck unit PC and transferred over the network to a Unix data disk. SBE Seasave Win32 V 5.35 software was used to perform all processing steps.

Raw data files were converted to engineering units and binary .CNV files using the DATCNV program. Sea-Bird bottle data files (.BTL), with information on pressure and other readings logged at the time of bottle firing, were also generated during the data conversion process. The WILDEDIT program was run to remove any large pressure spikes and then the SeaSoft program ALIGNCTD was run to advance the oxygen measurements by 3 seconds ensuring the calculations of dissolved oxygen concentration are made using measurements from the same parcel of water. CELLTM was run, according to Sea-Bird's recommendations, to remove conductivity cell thermal mass effects from the measured conductivity and FILTER was run on the pressure channel using a low-pass filter value of 0.2 to smooth the rapidly changing data. Finally twin salinities, twin density and depth were calculated using the DERIVE program and TRANSLATE wrote the data to an ASCII output .CNV file. Despiking of the pressure, oxygen, temperature and salinity data was carried out by visualising the data in MATLAB. If a spike occurs in pressure, temperature or salinity the whole corresponding scan is deleted. If the spike occurs in the other channels, the value is set to NaN and all remaining channels are left unedited. Following despiking of the data in MATLAB the module BINAVERAGE averaged the 24 Hz data into 2db-bins, using the downcast data only.

Comparison between primary and secondary temperature and conductivity sensors on the stainless steel casts showed strong agreement during the downcast but showed a noticeable difference during the upcast especially during bottle firings and in the thermocline zone.

Calibrations

For the salinity calibration data were incorporated into a set including data from CTD073 to CTD085 of the preceeding cruise D340A which took place in the Scottish shelf seas to provide a more reliable calibration. This produced the following calibration equations;

• Sal1_calibrated = 0.9978 Sal1_uncalibrated + 0.0802 (primary sensors - attached to CTD vane)
• Sal2_calibrated = 0.9993 Sal2_uncalibrated + 0.0275 (secondary sensors - situated within rosette frame)

It should be noted that the originators favoured the vane CTD sensor data for this cruise and data from these sensors alone were chosen when generating the definitive WOCE-standard CTD data files.

The oxygen data were later calibrated with the following equations;

• Ox_calibrated = 0.9326 Ox_uncalibrated + 0.8173 (units: mg l^-1)

References

Inall M. E, 2009. Cruise D340B Dunstaffnage to Govan via Barra Head and the Surrounding Shelf. Internal Report No 265. Scottish Association for Marine Science.

Available - Cruise D430B Internal Report

D340B CTD Processing undertaken by BODC

Data arrived at BODC in a total of 15 ASCII, WHP (WOCE Hydrographic Program) standard files representing the CTD casts from the stainless steel frame deployed during cruise D340B. These files contain 2db-bin averaged data including temperature, salinity and dissolved oxygen channels processed to WOCE standards alongside concurrent fluorometer and transmissometer data.

24 Hz ASCII versions of these data are also available from BODC, upon request. These files are held in their original format and, although containing additional parameters, have undergone less quality control by the originator and remain uncalibrated.

The lodged WHP standard casts were reformatted to BODC's internal QXF format. The following table shows the mapping of variables within the ASCII files to appropriate BODC parameter codes:

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.

Project Information

Oceans 2025 Theme 3, Work Package 3.8: Pelagic and Benthic Biogeochemical Processes: Response to Spatial Variability in Topographically Controlled Mixing

This Work Package (WP) is managed by the Scottish Association for Marine Science (SAMS) and focuses on improving understanding of the processes governing carbon cycling on the shelf. The biological processes governing the fixation and transfer and fate of carbon on the shelf are poorly quantified. This is a major impediment to biogeochemical modelling of carbon flux. An improved understanding of the physical and nutrient controls of different planktonic functional groups in terms of their rates of growth, the grazing pressure they experience, trophic transfer and export flux is critical to better understanding of ecosystem function and carbon cycling in shelf seas.

The specific objectives are:

• To determine how topographically generated horizontal and vertical mixing and its influence on nutrient ratios will influence the distribution and density of different phytoplankton, bacterial and micro/meso zooplankton functional groups and hence the rate and quantity of primary production, trophic transfer and the quantity and quality of carbon deposition to the benthos
• To assess the role of inputs of high quality labile carbon associated with specific topographical features in fuelling high rates of benthic particle reworking and solute transport, promoting microbial mediated remineralisation and increased rates of benthic recycling of inorganic nutrients
• To investigate the role of sea bed topography in modifying cross shelf carbon transport processes, creating areas of enhanced deposition and erosion

More detailed information on this WP is available at pages 15 - 17 of the official Oceans 2025 Theme 3 document: Oceans 2025 Theme 3

Weblink: http://www.oceans2025.org/

Oceans 2025 Theme 3, Work Package 3.2: Horizontal Patchiness in Vertical Mixing in Stratified Shelf Seas

In this Work Package, the Proudman Oceanographic Laboratory (POL) aim to address vertical mixing processes at the thermocline that are either poorly understood or have inadequate parameterisations in models. This is important because, as a boundary to vertical mixing, the thermocline affects much of the ecology and biochemistry of seasonally-stratifying shelf seas. Horizontal patchiness of vertical mixing is now known to be driven by varying seabed topography, indicating a need for a non-hydrostatic approach. This work is an expansion of the research carried out by POL during project Physical-Biological Control of New Production within the Seasonal Thermocline.

The specific objectives of Work Package 3.2 are:

• Quantify discrepancies between the Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) numerical model and observations of thermocline depths/strengths and diapycnal fluxes.
• Determine the causes of these discrepancies in terms of modelled and observed responses to meteorological forcing and in terms of the potential for patchy internal mixing.
• Quantify the importance of non-hydrostatic processes at the thermocline over typical shelf topographies.
• Carry out ship-based process studies focusing on the patchiness of mixing through the shelf thermocline.
• Quantify the consequences of thermocline patchiness over a whole shelf sea, alongside recommendations for process, bathymetry, and model resolution required to simulate the more important consequences.

More detailed information on this Work Package is available at pages 7 - 8 of the official Oceans 2025 Theme 3 document: Oceans 2025 Theme 3

Weblink: http://www.oceans2025.org/

Cruise Schedule

Moorings

Oceans 2025 Theme 3, Work Package 3.7: Role of Topography in Determining the Spatial Variability in Horizontal Dispersion

Tracer and budget studies show that mixing and exchange of oceanic and coastal water take place on the shelf. Topographic features, such as banks, slopes and troughs enhance horizontal and vertical mixing on scales of a few kilometres. This is presently too small to be fully resolved by existing shelf models but not by the next generation. However, for this to occur, processes that drive the mixing between terrestrial runoff and oceanic water, e.g. tidal stirring and straining, inertial currents, eddy activity and internal waves need to be explicitly included or parameterised.

Internal waves are assumed to dominate velocity and density variations on scales <100 m. Two-dimensional geostrophic horizontal turbulence ("vortical modes") exists at similar and larger scales and is relatively well understood, in isolation. However, the dispersive effects of interactions between vortical modes and internal wave mixing are poorly understood. Both internal waves and vortical mode activity are influenced by topography. Work Package (WP) 3.7, managed by the Scottish Association for Marine Science (SAMS) aims to investigate topographic regime control on horizontal dispersion mediated by internal wave/vortical mode interactions on the continental shelf.

The specific objectives are:

• Assess and quantify how horizontal dispersion through shelf seas is affected by irregular seabed topography
• Deliver an understanding on what the rate limiting processes are in the horizontal dispersion and exchange and mixing rates of stratified shelf waters

More detailed information on this WP is available at pages 14 - 15 of the official Oceans 2025 Theme 3 document: Oceans 2025 Theme 3

Weblink: http://www.oceans2025.org/

Oceans 2025 - The NERC Marine Centres' Strategic Research Programme 2007-2012

Who funds the programme?

The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).

Who is involved in the programme?

The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:

• National Oceanography Centre, Southampton (NOCS)
• Plymouth Marine Laboratory (PML)
• Marine Biological Association (MBA)
• Sir Alister Hardy Foundation for Marine Science (SAHFOS)
• Proudman Oceanographic Laboratory (POL)
• Scottish Association for Marine Science (SAMS)
• Sea Mammal Research Unit (SMRU)

Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:

• British Oceanographic Data Centre (BODC), hosted at POL
• Permanent Service for Mean Sea Level (PSMSL), hosted at POL
• Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS

The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.

What is the programme about?

Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:

• improve knowledge of how the seas behave, not just now but in the future;
• help assess what that might mean for the Earth system and for society;
• assist in developing sustainable solutions for the management of marine resources for future generations;
• enhance the research capabilities and facilities available for UK marine science.

In order to address these aims there are nine science themes supported by the Oceans 2025 programme:

• Climate, circulation and sea level (Theme 1)
• Marine biogeochemical cycles (Theme 2)
• Shelf and coastal processes (Theme 3)
• Biodiversity and ecosystem functioning (Theme 4)
• Continental margins and deep ocean (Theme 5)
• Sustainable marine resources (Theme 6)
• Technology development (Theme 8)
• Next generation ocean prediction (Theme 9)
• Integration of sustained observations in the marine environment (Theme 10)

In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.

When is the programme active?

The programme started in April 2007 with funding for 5 years.

Brief summary of the programme fieldwork/data

Programme fieldwork and data collection are to be achieved through:

• physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;
• the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';
• physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;
• coastal and shelf sea observatory data (Liverpool Bay Coastal Observatory (LBCO) and Western Channel Observatory (WCO)) using the RV Prince Madog and RV Quest.

The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.

Oceans 2025 Theme 3: Shelf and Coastal Processes

Over the next 20 years, UK local marine environments are predicted to experience ever-increasing rates of change - including increased temperature and seawater acidity, changing freshwater run-off, changes in sea level, and a likely increase in flooding events - causing great concern for those charged with their management and protection. The future quality, health and sustainability of UK marine waters require improved appreciation of the complex interactions that occur not only within the coastal and shelf environment, but also between the environment and human actions. This knowledge must primarily be provided by whole-system operational numerical models, able to provide reliable predictions of short and long-term system responses to change.

However, such tools are only viable if scientists understand the underlying processes they are attempting to model and can interpret the resulting data. Many fundamental processes in shelf edge, shelf, coastal and estuarine systems, particularly across key interfaces in the environment, are not fully understood.

Theme 3 addresses the following broad questions:

• How do biological, physical and chemical processes interact within shelf, coastal and estuarine systems, particularly at key environmental interfaces (e.g. coastline, sediment-water interface, thermocline, fronts and the shelf edge)?
• What are the consequences of these interactions on the functioning of the whole coastal system, including its sensitivity and/or resilience to change?
• Ultimately, what changes should be expected to be seen in the UK coastal environment over the next 50 years and beyond and how might these changes be transmitted into the open ocean?

Within Oceans 2025, Theme 3 will develop the necessary understanding of interacting processes to enable the consequences of environmental and anthropogenic change on UK shelf seas, coasts and estuaries to be predicted. Theme 3 will also provide knowledge that can improve the forecasting capability of models being used for the operational management of human activities in the coastal marine environment. Theme 3 is therefore directly relevant to all three of NERC's current strategic priorities; Earth's Life-Support Systems, Climate Change, and Sustainable Economies

The official Oceans 2025 documentation for this Theme is available from the following link: Oceans 2025 Theme 3

Weblink: http://www.oceans2025.org/

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: