Metadata Report for BODC Series Reference Number 2012021

• 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

JR18005 CTD Data Quality Report

Screening and Quality Control

During BODC quality control, data were screened using in house visualisation software and any obvious outliers and spikes were looked at in closer detail and flagged if necessary.

Any values beyond the parameter minimum or maximum were flagged as M (improbable). This was the case for a number of series in the POPTDR01 and BB117NIR channels. In addition, the BB117NIR channels from two series were entirely flagged M as each of the series had a constant value that is below the parameter minimum. Both of these channels were deleted accordingly

AHSFZZ01

The altimeter only collects good data within 100 m of the seabed and so any values that were beyond this range i.e. constant values or not decreasing with depth, have been flagged M.

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.

JR18005 CTD Instrumentation

The Sea-Bird Scientific SBE911plus CTD was mounted on a rosette with a SBE32 carousel water sampler and 24 12-litre Niskin bottles. The CTD was fitted with the following scientific 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.

SeaBird SBE35 Deep Ocean Standards Thermometer

The SBE 35 is a high precision thermometer that can be used in fixed point cells or at depths up to 6800 m. It is not affected by shock and vibration, allowing it to be used in calibration laboratories and for thermodynamic measurement of hydro turbine efficiency.

The SBE35 can be used with the SBE32 Carousel Water Sampler and with a real-time or autonomous CTD system. In this case, an SBE35 temperature measurement is collected each time a bottle is fired and the value is stored in EEPROM (Electrically Erasable Programmable Read-Only Memory), eliminating the need for reversing thermometers while providing a high accuracy temperature reading.

The SBE35 is standardized in water triple point (0.0100 °C) and gallium melting point (29.7646 °C) cells, following the methodology applied to the Standard-Grade Platinum Resistance Thermometer (SPRT). However, it does not need a resistance bridge, making it more cost-efficient than an SPRT.

Temperature is determined by applying an AC excitation to reference resistances and an ultrastable aged thermistor. Each of the resulting outputs is digitized by a 20-bit A/D converter. The AC excitation and ratiometric comparison uses a common processing channel, which removes measurement errors due to parasitic thermocouples, offset voltages, leakage currents and gain errors.

Specifications

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

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.

Biospherical Instruments QCP-2350 [underwater] PAR sensor

A cosine-corrected PAR quantum irradiance profiling sensor. For use in underwater applications with 24 bit ADC systems. Measures light available for photosynthesis on a flat surface. Operation is by a single channel compressed analog output voltage that is proportional to the log of incident PAR (400-700 nm) irradiance. The sensor is designed for operation in waters to depths of up to 2,000 m (standard) or 6,800 m (optional).

For more information, please see this document: https://www.bodc.ac.uk/data/documents/nodb/pdf/Biospherical_QCP2300_QCP2350_Apr2014.pdf

WETLabs ECO FLBB-RTD scattering and fluorescence sensor

A dual-optical-sensor that carries a single-wavelength chlorophyll fluorometer (470nm ex/695nm em) and backscattering sensor (700 nm) designed to measure chlorophyll and particle concentration. The instrument is capable of various combinations of backscatter, turbidity and fluorescence measurements. These include blue, green or red scattering, Chlorophyll-a, FDOM, Phycocyanin, Phycoerythrin, or Rhodamine fluorescence. It operates by using blue (470nm) and red (700 nm) LEDs that alternately flash. The blue LED stimulates chlorophyll fluorescence in plants while the red light illuminates the total particle field. It features active anti-fouling due to its copper faceplate and wiper, plus internal batteries, enabling long-term deployments. It also produces real-time data outputs. The fluorometer can typically measure phytoplankton concentrations in the range 0-30 ug/l, with a sensitivity of 0.025 ug/l. The backscattering sensor can measure within the range 0-3 m-1, with a sensitivity of 0.002 m-1. It is rated to 6000m depth.

For more information, please see this document: https://www.bodc.ac.uk/data/documents/nodb/pdf/ECO_FLBB_RTD.pdf

Tritech Digital Precision Altimeter PA200

This altimeter is a sonar ranging device that gives the height above the sea bed when mounted vertically. When mounted in any other attitude the sensor provides a subsea distance. It can be configured to operate on its own or under control from an external unit and can be supplied with simultaneous analogue and digital outputs, allowing them to interface to PC devices, data loggers, telemetry systems and multiplexers.

These instruments can be supplied with different housings, stainless steel, plastic and aluminum, which will limit the depth rating. There are three models available: the PA200-20S, PA200-10L and the PA500-6S, whose transducer options differ slightly.

Specifications

Common specifications are presented below

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

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.

Specifications

Further details are available in the manufacturer's specification sheet or user guide.

JR18005 ORCHESTRA CTD Data: Processing by BODC

The CTD data were supplied to BODC as 99 Matlab files and were converted to the BODC internal format.

During transfer the originator's variables were mapped to unique BODC parameter codes. The following table shows the parameter mapping.

Following transfer the data were screened using BODC in-house visualisation software. Improbable data values were assigned the appropriate BODC data quality flag. Missing data values, where present, were changed to the missing data value and assigned a BODC data quality flag.

Second sensor parameters have been removed from the final file but can be provided on request.

JR18005 ORCHESTRA Originator's CTD Data Processing

Sampling Strategy

A Conductivity-Temperature-Depth (CTD) unit was used to vertically profile the water column. The Sea-Bird Scientific SBE9plus CTD was mounted on a rosette with a SBE32 carousel water sampler and 24 12-litre Niskin bottles, and was connected through the sea cable to a SBE11plus deck unit.

The JR18005 cruise saw 105 CTDs carried out in total, with 99 of these being fully successful. Further information on the JR18005 CTD sampling can be found on page 30 of the JR18005 cruise report.

Originator's processing

CTD data were collected at 24 Hz and logged via the deck unit to a PC running Seasave version 7.22.3 (Sea-Bird Scientific), which allows real-time viewing of the data. The procedure was to start data logging during deployment of the CTD, then stop the instrument at 10 m wire out, where the CTD package was left for at least two minutes to allow the conductivity-activated pumps to switch on and the sensors to equilibrate with ambient conditions. The pumps consistently switched on 60 seconds after the instrument entered the water.

The CTD data were recorded using Seasave version 7.22.3, which created four files:

JR18005_[NNN].hex - hex data file

JR18005_[NNN].XMLCON - ascii configuration file containing calibration information

JR18005_[NNN].hdr - ascii header file containing sensor information

JR18005_[NNN].bl - ascii file containing bottle fire information where NNN is the CTD number

The SBE Data Processing module Datcnv was used to convert the hex file to ascii. Align was then used to account for the time lag of the oxygen sensor, with data being advanced by 5 seconds. The cell thermal mass (celltm) module was then used to remove the conductivity cell thermal mass effects from the measured conductivity. This rederives the pressure and conductivity, taking into account the temperature of the pressure sensor and the action of pressure on the conductivity cell. The output of this process is an ascii file, named as JR18005_[NNN]_align_ctm.cnv.

Further processing of CTD data was carried out in Matlab where the data was stored in Matlab arrays and a series of scripts were run to:

• Remove the 10-m soak prior to the CTD cast, through finding the minimum pressure after the soak and asking for user confirmation after displaying the full pressure plot for the cast.
• Graphically remove data collected at the end of the upcast when the CTD was out of the water.
• Averaging data from a 24hz CTD profile to 1 hz for LADCP processing.
• Splitting CTD data into upcast and downcast.
• Flagging points on the downcast where pressure is less than one previously recorded or if the fall rate is less than 0.25 ms^-1.This process results in smoother density profiles with fewer apparent overturns.
• Padding data with NaNs to 5999dbar, thereby ensuring that arrays for all CTDs are the same size.
• Extracting CTD pressure, temperature (1 & 2), conductivity (1 & 2), transmission, fluorescence, oxygen and PAR for each bottle fired.
• Calculating the standard deviation for pressure, temperature and conductivity, and writing a warning to the screen if those for temperature and conductivity are greater than 0.001.
• Applying any temperature and conductivity offset and recalculating salinity once the scripts have been run for all CTD casts.

A detailed description of the scripts that were run on for all CTD casts can be found on page 31 & 32 of the JR18005 cruise report.

Calibration

Sea-water samples for CTD calibration were collected using Niskin bottles fired at various depths during a CTD cast. The depths at which samples were taken were decided by the CTD operator, but tended to be chosen where there were low salinity gradients. For most CTD casts 8 samples were collected. Once the salinity samples were run, a series of Matlab scripts extracted CTD pressure, temperature (1 & 2), conductivity (1 & 2), transmission, fluorescence, oxygen and PAR for each bottle fired. It also calculated the standard deviation for pressure, temperature and conductivity, and writes a warning to the screen if those for temperature and conductivity are greater than 0.001.

Once the batch of scripts were run for all CTD casts, the temperature and conductivity offset was applied and salinity recalculated. The chosen calibrations were linear pressure-dependent offsets for the two temperature sensors, while two different piecewise linear offsets, were chosen for the three conductivity sensors. The offsets were to be compatible with the sensor differences and the calibration can then be checked by plotting T1-T2 and C1-C2 for relevant casts through the cruise.

Further details on the sea-water sampling proceedures usedfor the CTD calibration can be found on page 43 & 44 of the JR18005 cruise report.

Problems

On cast 032 an offset was observed in T1/T2 and C1/C2 values, which increased when hauling and settled when stopped. This was thought likely to be an issue with pump 1 and a pump was replaced after the cast. Due to confusion over which side was duct 1, pump 2 was inadvertently replaced; however, the problem did not occur again and bench-testing of the removed pump was successful. There may have been an external factor which caused the pump to stall which has not repeated."

Conductivity cell 1 started drifting on cast 065 so the decision was taken to replace it this is when the aforementioned misidentification of the duct numbers was noticed, as C2 was replaced instead of the faulty C1. In all cases, C2 produced good data while C1 produced bad data for casts 065 and 066.

Otherwise, there are no significant issues to report regarding the CTD from this cruise.

Project Information

Ocean Regulation of Climate by Heat and Carbon Sequestration and Transports (ORCHESTRA)

The Ocean Regulation of Climate by Heat and Carbon Sequestration and Transports (ORCHESTRA) is a £8.4 million, five year (2016-2021) research programme funded by the Natural Environment Research Council (NERC). The aim of the research is to to advance the understanding of, and capability to predict, the Southern Ocean's impact on climate change via its uptake and storage of heat and carbon. The programme will significantly reduce uncertainties concerning how this uptake and storage by the ocean influences global climate, by conducting a series of unique fieldwork campaigns and innovative model developments.

Background

ORCHESTRA represents the first fully-unified activity by NERC institutes to address these challenges, and will draw in national and international partners to provide community coherence, and to build a legacy in knowledge and capability that will transcend the timescale of the programme itself.

It brings together science teams from six UK research institutions to investigate the role that the Southern Ocean plays in our changing climate and atmospheric carbon draw-down. It is led by British Antarctic Survey, in partnership with National Oceanography Centre, British Geological Survey, Plymouth Marine Laboratory, the Centre for Polar Observation and Modelling and the Sea Mammal Research Unit.

The oceans around Antarctica play a critical a key role in drawing down and storing large amounts of carbon and vast quantities of heat from from the atmosphere. Due to its remoteness and harsh environment, the Southern Ocean is the world's biggest data desert, and one of the hardest places to get right in climate models. The ORCHESTRA programme will make unique and important new measurements in the Southern Ocean using a range of techniques, including use of the world-class UK research vessel fleet, and deployments of innovative underwater robots. The new understanding obtained will guide key improvements to the current generation of computer models, and will enhance greatly our ability to predict climate into the future.

The scope of the programme includes interaction of the Southern Ocean with the atmosphere, exchange between the upper ocean mixed layer and the interior and exchange between the Southern Ocean and the global ocean.

Further details are available on the ORCHESTRA page.

Participants

Six different organisations are directly involved in research for ORCHESTRA. These institutions are:

• British Antarctic Survey (BAS)
• National Oceanography Centre (NOC)
• Plymouth Marine Laboratory (PML)
• British Geological Survey (BGS)
• Centre for Polar Observation and Modelling (CPOM)
• Sea Mammal Research Unit (SMRU)

GO-SHIP are a third party organisation that, although not directly involved with the programme, will conduct ship based observations that will also be used by ORCHESTRA.

Research details

Three Work Packages have been funded by the ORCHESTRA programme. These are described in brief below:

• Work Package 1: Interaction of the Southern ocean with the atmosphere
  WP1 will use new observations of surface fluxes and their controlling parameters in order to better constrain the exchanges of heat and carbon loss across the surface of the Southern Ocean.

• Work Package 2: Exchange between the upper ocean mixed layer and the interior.
  This work package will combine observationally-derived data and model simulations to determine and understand the exchanges between the ocean mixed layer and its interior.

• Work Package 3: Exchange between the Southern Ocean and the global ocean .
  This WP will use budget analyses of the hydrographic/tracer sections to diagnose the three-dimensional velocity field of the waters entering, leaving and recirculating within the Southern Atlantic sector of the Southern ocean.

• Fieldwork and data collection

  The campaign consists of 12 core cruises on board the NERC research vessels RRS James Clark Ross and RRS James Cook and will include hydrographic/tracer sections conducted across Drake Passage (SR1b), the northern Weddell Sea/Scotia Sea (A23), the northern rim of the Weddell Gyre (ANDREXII) and across the South Atlantic (24S). Section I6S will be performed by GO-SHIP Project Partners. Measurements will include temperature, salinity, dissolved oxygen, velocity, dissolved inorganic carbon, total alkalinity, inorganic nutrients, oxygen and carbon isotopes, and underway meteorological and surface ocean observations including pCO₂.

  Tags will be deployed on 30 Weddel seals and these will provide temperature and salinity profiles that can be used alongside the Argo data.

  Autonomous underwater ocean gliders will conduct multi-month missions and will deliver data on ocean stratification, heat content, mixed layer depth and turbulent mixing over the upper 1 km, with previously-unobtainable temporal resolution. These gliders will be deployed in the Weddell Gyre and the ACC.

  Field campaigns with the MASIN meteorological aircrafts will be conducted flying out of Rothera and Halley research stations and the Falkland Islands. These campaigns will deliver information on key variables relating to air-sea fluxes (surface and air temperature, wind, humidity, atmospheric CO₂, radiation, turbulent fluxes of heat, momentum and CO₂), in different sea ice conditions and oceanic regimes.

  Eart Observation datasets will be used to inform the programme on the properties of the ocean, sea ice and atmosphere and on interactions between them.

  A cluster of 6 deep ocean moorings in the Orkney Passage will collect year round series of AABW temperatre and transport. This work connects to the NERC funded project Dynamics of the Orkney Passage Outflow (DYNOPO).

  The UK Earth System model (UKESM) and underlying physical model will be used to conduct analyses of heat and carbon uptake and transport by the Southern Ocean and their links to wider climate on decadal timescales.

  An eddy-resolving (1/12°) sector model of the ocean south of 30°S with 75 vertical levels, will be built using the NEMO model coupled to the Los Alamos sea ice (CICE) model. The improvements on the ocean boundary layer will be based from the results from the NERC-funded OSMOSIS project and the inclusion of tides.

  20-5 year runs of an adjoint model will be conducted to determine how key forcings and model states affect the uptake and subduction of heat and carbon by the ocean.

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: