Metadata Report for BODC Series Reference Number 681432

• 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

The primary temperature, conductivity, and salinity channels are suspect and should not be used. The primary temperature, conductivity and dissolved oxygen sensors were unreliable for the duration of the cruise (oxygen channel subsequently dropped by BODC). The problem is evident as excessive noise in the profiles. Some profiles are only noisy in places while other profiles are affected throughout. Derived density profiles where the data are noisy also appear unphysical. The secondary channels are much more reliable and appear normal.

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.

Instrumentation

The CTD on-board the D300 consisted of a 12-way stainless steel frame carrying a Sea-Bird 9+ underwater unit, SBE32 24-way rosette and associated sensors linked via a torque balanced conducting cable and auxillary deck cabling to a Sea-Bird 11plus Deck unit and dual PC system where incoming data was monitored, stored and from where water sampling was controlled. The following instruments made up the CTD system:

RRS Discovery 300 CTD Data Documentation

Originator's processing

Ten CTD casts were conducted as part of Discovery cruise D300. More details on the cruise can be found in the cruise summary report. Casts commenced on-deck where the Sea-Bird system was activated and data recording began. The package was held at 10 m depth until the pumps had begun and the instruments had stabilised. The CTD package was then raised to the surface waters before the downcast commenced. The package was veered at a nominal rate of 60 m/min to a depth within the vicinity of 12 - 20 m of the sea floor.

Data was processed using the SBE data processing program. The CTD data was output into individual PStar files. Bottle samples were also taken to allow the CTD to be calibrated. There were a pair of temperature and conductivity sensors on the CTD package which were arbitraily assigned to primary and secondary. The primary sensors were often noisy during casts so only salinity from the secondary sensors has been calibrated. Comparisons with the bottle data showed that salinity calculated from the CTD was approximately 0.002 too high. A constant offset of 0.002 was applied to the secondary salinity channel.

No samples were taken to calibrate the oxygen or fluorometer channels.

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.

BODC processing

The files were provided to BODC in Pstar format with a separate file for each cast. Seven files for each cast were supplied representing a complete set of CTD data from the cruise. Some of the files included in the submission were the full 24 Hz CTD files, 2 db binned CTD data and the bottle firing files. Data was converted to QXF format using BODC generated Matlab code. This transfer involved mapping the measured variables to BODC parameter codes. The parameter mapping is described below

Data was inspected visually using in-house software. Suspect data points were flagged with the appropriate BODC data quality control flag.

Project Information

CROZET (Benthic CROZEX)

The CROZET project was a multidisciplinary Benthic study that compliments the CROZet natural iron bloom EXport experiment (CROZEX). It was a Natural Environment Research Council (NERC) funded project (grant number NER/A/S/2003/00573).

The principle objective of CROZET was "To assess how biogeochemical composition and flux of Organic Matter (OM) to the deep-sea floor drive benthic community structure, dynamics and diversity at two sites with contrasting primary production regimes".

Specific hypotheses tested were:

1. That the variability in biogeochemical composition as well as the total flux of OM reaching the abyssal seafloor is dependent on the productivity of the overlying surface waters.
2. That the biogeochemical composition of incoming OM is imprinted on the biochemistry of key detritovores.
3. That key nano-nutrients are critical for the reproduction of some deep-sea species and thus variations in OM flux affect sediment community structure and diversity.
4. That variations in total OM flux also influence benthic rate processes (e.g. faunal activity).

The University of Liverpool Department of Earth Science hosted the project with particiption from another seven research centres/universities.

The project ran from December 2005 to September 2008 with the primary marine data collection during RRS Discovery cruise D300 between 1^st December 2005 and 14^th January 2006. The sediment trap moorings for this project were deployed during the RRS Discovery CROZEX cruises D285 and D286 one year previously.

The cruise primarily sampled stations M5 (an eutrophic region subject to photoplankton blooms) and M6 (to the south of the Crozet Islands and an oligotrophic High Nutrient Low Chlorophyll (HNLC) area) previously occupied during the CROZEX cruises and described in Pollard et al. (2007). The two contrast regions allowed a comparison of the benthic communities that were:

1. At the same depth.
2. In the same physical setting (topographic and hydrographic).
3. Interconnected (with no physical barrier between them).

Where possible the following observations were conducted at each major station:

• Underway navigation, surface, meteorology and bathymetry throughout the cruise
• Underway sampling of:
  • Salinity
  • Nutrients (Nitrogen and Phosphorus)
  • Chlorophyll-a
  • Dissolved Iron
• 150kHz Vessel-Mounted Acoustic Doppler Current Profiller (VMADCP) data throughout the cruise
• Full water column CTD stations for salinity, temperature, chlorophyll and dissolved oxygen. CTD rig included a Lowered Acoustic Doppler Current Profiller (LADCP). CTD water bottles were sampled for:
  • Salinity
  • Particulate Organic Carbon (POC)
  • Particulate Organic Nitrogen (PON)
  • Bacterial biomass and community structure using DNA analyses
  • MPN enumeration and isolation of marine bacteria
  • Particulate iron
  • Chloropyhll-a
• Stand Alone Pumps with analyses of:
  • Organic biogeochemistry
  • Bacterial biomass and community structure using DNA analyses
  • MPN enumeration and isolation of marine bacteria
  • Archael bacteria
  • Particulate Organic Carbon (POC)
  • Particulate Organic Nitrogen (PON)
  • Particulate iron
• Megacoring with analyses of:
  • Total Organic Carbon (TOC)
  • Total Nitrogen (TN)
  • Hydrolysable amino acids
  • Bacterial biomass and community structure using DNA analyses
  • MPN enumeration and isolation of marine bacteria
  • Nematodes
  • Polychaetes
  • Pigments
  • Pigment degradation
  • Meiofauna
  • Foraminifera
  • Macrofauna
  • Pore fluid geochemistry
  • Biomarkers
  • Lipids
  • Solid phase geochemistry
  • Bacteria
• Holothurian sample photography
• WASP sea floor photography and video for study of benthic megafaunal populations
• Fish RESPirometry Lander (FRESP) deployments
• RObust BIOdiversity Lander (ROBIO) deployments (included a current meter)
• Demersal ichthyofauna sampling with analyses of:
  • Species
  • Wet weight
  • Length (total, standard, head and pre-anal)
• Demersal ichthyofauna macrouridae (Rattail) sex, stomach weight, liver (weight, fullness) and sexual maturity
• Bacterial long-term enrichment incubations
• SPRATS Sampling pressure retaining system deployments
• Holothurian pigment analysis (gut and gonad)
• Holothurian - molecular (DNA) analysis
• Holothurian Bacterial samples (gut and cloaca)
• Holothurian lipid analysis

The project has produced significant findings including the discovery of six new species of fish. Further information on the project can be found in the D300 cruise report and the CROZET project web pages.

References

Pollard R., Sanders R., Lucas M. and Statham P., 2007. The Crozet natural iron bloom and export experiment (CROZEX). Deep-Sea Research II, 54, 1905-1914.

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: