Metadata Report for BODC Series Reference Number 909168

• 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 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.

Benthos Programmable Sonar Altimeter (PSA) 916 and 916T

The PSA 916 is a submersible altimeter that uses the travel time of an acoustic signal to determine the distance of the instrument from a target surface. It provides the user with high resolution altitude or range data while simultaneously outputting data through a digital serial port. A wide beam angle provides for reliable and accurate range measurements under the most severe operational conditions. The instrument is electronically isolated to eliminate any potential signal interference with host instrument sensors. The PSA 916 is an upgrade of the PSA 900.

The standard model (PSA 916) has an operational depth range of 0 - 6000 m, while the titanium PSA 916T has a depth range of 0 - 10000 m. All other specifications for the two versions are the same.

Specifications

Further details can be found in the manufacturer's specification sheets for the PSA 916 and the PSA 916T.

Instrument Description

CTD Unit and Auxiliary Sensors

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.

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.

BODC Processing

The data arrived at BODC in a series of pstar files, representing all 74 CTD casts taken during the cruise. The following table shows how the variables were mapped to the appropriate BODC parameter codes.

There were duplicate potential temperature channels in the original data. Only one set of these was transferred.

The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag.

References

Benson B.B. and Krause D. 1984. The concentration and isotopic fractionation of oxygen dissolved in fresh water and sea water in equilibrium with the atmosphere. Limnol. Oceanogr. 29 pp.620-632.

D332 CTD Data Quality Report

Chlorophyll (CPHLPM01)

Throughout many of the 74 casts, the transfer automatically placed 'M' flags on chlorophyll values where the supplied concentrations were negative. The most likely cause is that the instrument calibration was out.

Transmittance (POPTDR01)

A number of data values in the transmittance channel exceed 100%. All such values have been flagged. The most likely cause is that the instrument calibration was out.

Dissolved oxygen

The dissolved oxygen sensor, SBE43-0619, failed early during the downcast of station 071. This had an effect on both of the conductivity channels, but does not appear to have affected temperature or pressure. A repeat of station 071 was made as station 073.

This data is also held by ICES, who have chosen to add additional data quality flags to the oxygen data. BODC have not added these additional flags to the BODC data.

Altimeter (AHSFZZ01)

This altimeter only reliably measures depth within 100m of the sea floor. Therefore, all values above 100m were flagged. Throughout these casts the altimeter gave a good return within 80m from the bottom in low sediment areas and 35m from the bottom when a lot of sediment was present.

In calm seas the CTD was worked to around 10m from the bottom, which increased to 15m from the bottom in swell. During shelf stations in large currents it was not possible to work the CTD close to the bottom.

Salinity

This data is also held by ICES, who have chosen to add additional data quality flags to the salinity data. BODC have not added these additional flags to the BODC data.

Originator's Data Processing

Sampling Strategy

A total of 74 CTD stations were completed during D332. These included three casts for calibration of the NIOZ MMP moorings.

CTD

The only CTD sensor failure during the cruise was the dissolved oxygen (DO) sensor SBE43-0619.

This failed very early during the downcast of CTD071. Unusually this also had an effect on both conductivity channels, but none on either temperature or pressure. The DO sensor is an analogue 0-5V sensor, whereas the T, C and P sensors are frequency devices, hence the failed sensor was probably pulling down the instrument power supply and the conductivity cells may be particularly sensitive to supply voltage. A repeat of this station was made as CTD073.

Altimetry

The Benthos altimeter worked very reliably, obtaining a good bottom return within 80m of the bottom in low sediment areas and 35m from the bottom when a lot of sediment was present. The NMF pinger was also used both as a backup and as a double check on proximity to the bottom.

The pinger was visualised using the EA500 PES display. In calm seas the CTD was worked to around 10m from the bottom. This was increased to approximately 15m from the bottom in swell. During shelf stations in large currents, it was not possible to work the CTD close to the bottom. Rapid shallowing of 200-800m was observed in the matter of minutes.

Data Processing

The CTD package comprised the following instruments: Seabird 911+ CTD with dual temperature and conductivity sensors; Seabird carousel type SBE 32; RDI 300kHz workhorse ADCPs, one upward looking and one downward looking; Chelsea instruments Alphatracka (transmissometer) and Aquatracka (fluorometer); Wetlabs light back sensor type BBRTD; Benthos altimeter type 915T; twenty four 20 litre Ocean Test Equipment water bottles. The Seabird primary T/C duct had an inline Seabird oxygen sensor type SBE 43 fitted and was mounted on the stabilising vane for casts 1-14. The first cast (14) with the Lebus Portable Hydrographic Winch showed excessive rotation of the package and subsequently the vane was removed, necessitating attaching of the primary sensors to the main body of the CTD. 74 full casts were completed

The logging software produced four files per CTD cast with the following extensions:

• .hex (raw data file),
• .con (data configuration file),
• .bl (contained record of bottle firing locations),
• .hdr (a header file).

The raw data files were then processed using SeaBird's own CTD data processing software, SBE.DataProcessing-Win32: v.7.18. SeaBird CTD processing routines were used as follows.

• DatCnv: The Data Conversion routine read in the raw CTD data file (D332nnn.hex). This contained the raw CTD data in engineering units output by the SeaBird hardware on the CTD rosette. DatCnv requires a configuration file that defines the calibrated CTD data output so that it is in the correct form to be read into the pstar format on the UNIX system. The output file (D332nnn.cnv) format was set to binary and to include both up and down casts. A second output file (D309nnn.ros) contained bottle firing information, taking the output data at the instant of bottle firing.
• AlignCTD: This program read in D332nnn.cnv and was set to shift the Oxygen sensor relative to the pressure data by 5 seconds compensating for lags in the sensor response time. Input and output files are the same.
• WildEdit: A de-spiking routine. The data was scanned twice calculating the standard deviation of a set number of scans, setting values that are outside a set number of standard deviations (sd) of the mean to bad data values. On this cruise, the scan range was set to 500, with 2 sd's on the first pass and 10 sd's on the second.
• CellTM: The effect of thermal 'inertia' on the conductivity cells was removed using the routine CellTM. It should be noted that this routine must only be run after WildEdit or any other editing of bad data values as this routine uses the temperature variable to adjust the conductivity values, and if spikes exist in the former they are amplified in the latter.
• Translate: Finally, the D332nnn.cnv file was converted from binary into ASCII format.

The following c-shell UNIX scripts were used to process the data.

• ctd0: This script read in the SeaBird processed ascii file (.cnv) and converted it into pstar format, also setting header information. Information from the header was extracted from the SeaBird ascii file where possible. The latitude and longitude of the ship when the CTD was at the bottom were typed in manually and added to the header, although later in the cruise this information was omitted and the position read in from latitude and longitude values in the data stream. The output file contained the data averaged to 24hz.
• ctd1: This script operated on the .24hz file and used the PEXEC program pmdian to remove residual spikes from all of the variables. The data were then averaged into a 1hz file using pavrge. Absent data values in the pressure data were interpolated across using pintrp. Salinity, potential temperature, sigma0 and sigma2 (referenced to 2000 db) were calculated using peos83 and finally a 10 second averaged file was also created.
• ctd2: This script carried out a head and tail crop of the .1hz file to select the relevant data cycles for just the up and down casts of the CTD. Before running ctd2, the .1hz files were examined in mlist to determine the data cycles for i.) the shallowest depth of the CTD rosette after the initial soaking at 10m, ii.) the greatest depth, and iii.) the last good point before the CTD is removed from the water. These values were then manually entered at the correct screen prompts in ctd2. The data were then cut out with pcopya and the files ctd332nn.ctu created. Finally, the data were averaged into two decibar pressure bins creating the files ctd332nn.2db. Position information was extracted for the start data cycle of the downcast file and written to the header.
• ctd3: The script ctd3 was used to produce plots from the .ctu files.
• fir0: This script converted the .ros file into pstar format. It then took the relevant data cycles from the .10s averaged file (secondary output from ctd1) and pasted it into a new file fir332nn containing the mean values of all variables at the bottle firing locations.
• samfir: This script created the file, sam332nn containing selected variables from fir332nn so that the results from the bottle sampling analysis could be added. Modification to the standard processing was needed to convert the oxygen variable from ml/l output from the SeaBird system to mol/kg. Further modifications were required on D332 as not all bottles were fired on all casts due to the problems encountered with the winch. The changes involved inserting a bottle number variable into the file, reading in the number of each bottle fired from the .bl file then using ppaste with a control variable rather than assuming that the record numbers in the donor and recipient files match.

Once salinity bottle data had been processed and excel files were created for each ctd. The following scripts were then run:

• sal0: Read in the sample bottle excel files, that had been saved as tab delimited text only files, and converted some PC unique characters into UNIX friendly characters. Then sal0 created pstar format files with pascin.
• sal1: (previously passal). Pasted bottle file (sal332nn.bot) values into sam332nn files.
• sal2: (previously botcond). Calculated conductivity for bottle salinities using peos83 and primary temperature.
• ctdcondcal: This script was used to calibrate the .ctu and .2db files and recalculate salinity, potential temperature and sigma0/sigma2.

Field Calibrations

The following field calibrations were used:

Conductivity

These were calculated using the mean square of the conductivity values and the mean product of the bottle and CTD conductivity values, giving the following calibrations:

• conductivity1 = 1.00004361*conductivity1
• conductivity2 = 0.99998671*conductivity2

Oxygen

For stations 1-70 the following field calibrations were applied:

oxygen_bottle-oxygen_ctd = 16.662+0.001558*pressure

For stations 72-74 there was not enough data for a separate calibration of the new oxygen sensor. However, there was no evidence of significantly different behaviour to the previous sensor, so the same calibrations were applied.

Project Information

Oceans 2025 Theme 1: Climate, Ocean Circulation and Sea Level

Through fieldwork, analysis and modelling, Theme 1 will provide detailed knowledge of how the Atlantic, Arctic and Southern Oceans are responding to, and driving, climate change. In combination with geodetic studies, it will also improve our ability to predict global sea level and UK land movements in the century ahead.

The official Oceans 2025 documentation for this Theme is available from the following link: Oceans 2025 Theme 1

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

Oceans 2025 Theme 1, Work Package 1.3: Physical-biogeochemical budgets and mixing in the Southern Ocean

This Work Package is run by the National Oceanography Centre, Southampton (NOCS) and aims to establish regional budgets of heat, freshwater and carbon, and to develop more accurate parameterisations for predictive ocean models by quantitatively investigating diapycnal and isopycnal transport processes using observations.

Vast, though poorly quantified, amounts of anthropogenic CO2 (~20 Pg) are believed to have been absorbed into the Antarctic mode and intermediate waters. Much of this uptake is achieved in the Antarctic Circumpolar Current (ACC), involving the upwelling of North Atlantic Deep Water, its northward transport by a delicate balance between Ekman drift and eddies, followed by subduction as mode waters. Models suggest that the rate of CO2 uptake is sensitive to changes in the wind and to changes to the eddy fluxes (Mignone et al., 2005).

To predict climate change, it is essential that the size of this carbon sink be known, and the processes that control it be understood. Even the exchanges of heat and freshwater between the Atlantic and Southern Oceans are poorly known. NOCS will combine observations and modelling to quantify and understand the processes controlling property fluxes and trends in the Atlantic sector of the Southern Ocean, where the Atlantic overturning circulation is partially closed as it meets the ACC. The observational effort will be fully integrated with the international Climate Variability and Predictability (CLIVAR)/Carbon repeat hydrography program, and with the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) initiative to study mixing rates and processes; this work has been accepted as a contribution to the International Polar Year. The budgets and mixing rates inferred from field measurements will be used to both evaluate and improve numerical models.

More detailed information on this Work Package is available at pages 10 - 11 of the official Oceans 2025 Theme 1 document: Oceans 2025 Theme 1

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

References

Mignone B., Gnanadesikan A., Sarmiento JL., and Slater RD., 2005. Central role of Southern Hemisphere winds and eddies in modulating the oceanic uptake of anthropogenic carbon, Geophys Res Lett, 32 doi:101029/2005Gl024464

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: