Metadata Report for BODC Series Reference Number 1029852

• 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

Pressure

Towards the end of the scanfish deployment the pressure record becomes highly variable with a large number of (both positive and negative) points. These have been flagged and should be viewed with caution.

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.

JC025 Scanfish Instrumentation

The scanfish package contained a Sea-Bird 911 plus unit, complimented by a Chelsea Aquatracka III Rhodamine Fluorometer. An additional small Turner Designs chlorophyll fluorometer was attached to the outside of the vehicle. The table below details all scientific sensors fitted to the scanfish:

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.

Turner Designs Cyclops-7 Submersible Sensors

The Cyclops-7 series of sensors is designed for integration into multi-parameter platforms, providing measurements of in vivo chlorophyll-a, cyanobacteria (phycocyanin and phycoerythrin), rhodamine and fluorescein dyes, optical brighteners, coloured dissolved organic matter (CDOM), crude oil and refined fuels, BTEX (benzene, toluene, ethylbenzene, and xylenes) or turbidity.

The voltage output of the sensor can be correlated with in situ concentration by calibration with a standard of known concentration. The excitation wavelength varies, depending on the environmental variable of interest, with visible wavelengths being used for chlorophyll, rhodamine, fluorescein and cyanobacteria; UV being used for CDOM, oil, optical brighteners and refined fuels; and IR being used for turbidity. The photodiode detector operates over the range 300-1100 nm. Custom optics over the range 260-900 nm are also available.

The Cyclops-7 operates over an ambient temperature range of 0 to 50°C and a water temperature range of -2 to 50°C. It has a depth rating of 600 m and displays a linearity of 0.99 R² over the full range.

Specifications

*QS - Quinine Sulphate

**NS - 1,5 Napthalene Disulfonic Disodium Salt

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

JC025 Scanfish Originator Processing

Sampling Strategy

Two dye releases were made during the cruise using Rhodamine WT, diluted with propan-2-ol. The releases were made into the seasonal thermocline at a depth of approximately 35 m from tanks on deck though a 25 mm diameter hose lowered from the stern.

Following each dye release the scanfish was deployed and used in a dye tracking capacity by utilising a Chelsea Aquatraka III Rhodamine-tuned fluorometer fitted to the package.

Data Processing

Following the completion of each scanfish survey the data were saved to the deck unit PC and transferred over the ship network to a Unix data disk. Sea-Bird SBE logging software (Seasave V7) writes 3 files per series with the following extensions: .HEX (raw data files), .CON (data configuration file), and .HDR (header file). SBE Seasave Win32 V 5.37e software was later used to perform all processing steps. CTD data were combined with ship navigation data to calculate the scanfish position in the water using the ship as a reference.

DATCNV was used to convert raw data files from engineering units producing .CNV files containing 24Hz down and up cast data. 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 0.5 seconds. ALIGNCTD was then used to shift the dissolved oxygen sensor output relative to the pressure by 5 seconds to compensate for lags in the sensor response time. In addition shifts equal to 0.5 seconds were also applied to the temperature and conductivity sensor outputs. The effect of thermal inertia on conductivity cells was removed by CELLTM and data were averaged using pressure with a 1m bin size for up and downcasts using BINAVERAGE. Depth, potential temperature, salinity and Specific Volume Anomaly were calculated by DERIVE and finally the binary .CNV files were converted into ASCII format .CNV files by ASCIIOUT.

Calibrations

Experimental calibration of the temperature, salinity and chlorophyll fluorescence channels was carried out by profiling the scanfish vertically at 13:45 17/07/2008 and then comparing the data with 1 dbar binned data from CTD profiles carried out immediately before and after this profile (CTD024 and CTD025). Offsets were derived for salinity and temperature channels using data between 57 and 80 dbar, with a chlorophyll calibration being performed using the upper 37 dbar of the water column. It should be noted, however, that the scanfish data provided to BODC have not had these calibrations applied, but further details are available in the cruise report.

JC025 Scanfish Processing undertaken by BODC

Data arrived at BODC as a series of ASCII (.cnv) files output from the Seasave software. Together, these files represented data collected from the six dye tracking scanfish surveys conducted during JC025. Multiple files supplied for individual surveys were appended together and reformatted to BODC's internal format, a netCDF subset.

The following table shows the mapping of variables within the ASCII (.cnv) 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. The deployment and recovery periods have been flagged suspect.

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.

Project Information

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/

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 - 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.

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: