Metadata Report for BODC Series Reference Number 1760684

• 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

Problem report

Fluorometer

The fluorometer channel reports consistently similar values throughout the duration of the cruise and should therefore be used with caution. The fluorometer on the JCR is known to have an issue and should only be used to give an indication and not a finite reading.

RRS James Clark Ross Cruise JR20081003 (AMT18) Surface Hydrographic Quality Control Report

Quality control report

TSG Flow rate, salinity and temperature

The flow rate through the non-toxic supply was very unstable and varied erratically throughout the cruise. This affected the quality of some of the measurements from the non-toxic water supply system and notably salinity. The salinity record has a large amount of noise throughout the cruise. This was due to many small increasing and decreasing steps in its signal of the order of 0.2-0.3 PSU which were generally coincident with irregularities in the flow rate and which could not be corrected for through the calibration.

The temperature measurements from the non-toxic water supply available for this cruise (temperature of the conductivity measurements and temperature from the fluorometer) seemed to be affected by the problem in flow rate and should therefore be used with caution. The fluorometer temperature in particular is of poor quality.

Hull temperature

The quality of the sea surface temperature from the hull mounted sensor did not seem to have suffered from this problem of flow rate.

Fluorometer

The quality of the fluorometer record was also affected by the variation in flow rate probably due to bubbles being formed and interfering with the sensor. These periods were initially flagged as suspect during screening. However when the fluorometer data were compared with concentration of chlorophyll extracted from samples taken every 4-5 hours for the duration of the cruise, it became clear that the fluorometer was not responding to changes in chlorophyll levels at the equator and in the northern and southern gyre regions. The decision was taken to flag the entire channel as suspect; the extracted chlorophyll dataset should be used for surface chlorophyll data along the cruise track.

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

Turner Designs 10AU Field Fluorometer

The Turner Designs 10AU is designed for continuous-flow monitoring or discrete sample analyses of fluorescent species. A variety of optical kits with appropriate filters and lamps are available for a wide range of applications. Individual filters and lamps are also available for customised applications.

Standard optical kits include those for chlorophyll-a (extracted and/or in vivo), phycocyanin, phycoerythrin, CDOM, ammonium, rhodamine and fluorescein dye tracing, crude oil, refined oil, histamine and optical brighteners.

The instrument's light source is a 4 watt lamp and the detector is a photomultiplier tube with a standard detection range of 300-650 nm. A red-sensitive version with a detetion range of 185-970 nm is also available.

Specifications

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

Litre Meter flow meter

A flow meter used to monitor water flow rates for pumped systems such as ships' continuous seawater supplies.

RRS James Clark Ross Cruise JR20081003 (AMT18) Surface Hydrographic Instrumentation

The sea surface hydrography suite of sensors was fed by the pumped-seawater, non-toxic supply. Sensors have been identified where possible from the BAS JCR data dictionary and a list of underway sensors that were present on the JCR at the start of 2008, which have been provided to BODC by BAS.The following surface hydrology sensors were fitted:

SeaBird MicroTSG Thermosalinograph SBE 45

The SBE45 MicroTSG is an externally powered instrument designed for shipboard measurement of temperature and conductivity of pumped near-surface water samples. The instrument can also compute salinity and sound velocity internally.

The MicroTSG comprises a platinum-electrode glass conductivity cell and a stable, pressure-protected thermistor temperature sensor. It also contains an RS-232 port for appending the output of a remote temperature sensor, allowing for direct measurement of sea surface temperature.

The instrument can operate in Polled, Autonomous and Serial Line Sync sampling modes:

• Polled sampling: the instrument takes one sample on command
• Autonomous sampling: the instrument samples at preprogrammed intervals and does not enter quiescence (sleep) state between samples
• Serial Line Sync: a pulse on the serial line causes the instrument to wake up, sample and re-enter quiescent state automatically

Specifications

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

RRS James Clark Ross Cruise JR20081003 (AMT18) Surface Hydrographic Data Processing Procedures

Originator's Data Processing

The non-toxic supply draws water from a depth 6.5 m below the surface and the hull sensor is mounted just inside the inlet. The thermosalinograph is situated in the lab with the fluorometer downstream. The data from the non-toxic supply and atmospheric sensors were logged by the RVS Surfmet system during the cruise. The processing of the underway data was completed daily using two PSTAR routines. The first 'oceanlog0' converted the RVS format data into PSTAR format. Then 'oceanlog1' set the unrealistic values of variables to absent, converted conductivity into mS/cm and merged time, lat, lon and distance run into the file from the Bestnav navigation (abnv2181). The daily processed data was saved to as a file 'olg.218xx' and the file 'olg.master' was appended with the data each day of the cruise.

BODC Data Processing

Underway hydrography data from processed PSTAR format files were transferred to BODCs NetCDF format (QXF) under the BODC Underway Data System (BUDS). This transfer involved reducing the data by averaging to 60 second intervals. Directional data were reduced by averaging using a unit circle.

The logged measurements from the ships non-toxic underway system (SST, salinity, chl-a) were loaded from the PSTAR files generated from the RVS Surfmet system. BODC were advised by the data processors that the file 'olg.master' was appended with the data each day of the cruise, with the exception of the last days data and this data was loaded from the daily file 'olg.21837'. At BODC after loading the 'olg.master' and 'olg.21837' files and screening the input, data from 10/10/2008 was found to be missing and was subsequently loaded from the daily file 'olg.21808'.

Screening

Each data channel was inspected on a graphics workstation using BODC screening software EDSERPLO and any spikes or periods of dubious data were flagged using BODC quality control flag system ('M' for suspect value). Impossible values were checked carefully and flagged null only if believed to be genuine missing or bad data. EDSERPLO was used to carry out comparative screening checks between channels by overlaying data channels. A map of the cruise track was simultaneously displayed in order to take account of the oceanographic context. The table below shows the parameters loaded from the original meteorological data files and the BODC code they have been mapped to.

Calibrations

Salinity

Salinity data from the thermosalinograph (TSG) were compared with bench salinometer readings from samples taken from the ships non-toxic pump supply. An offset between the bench salinometer and the TSG data was calculated. A regression between the offset and decimalised time was carried out, which was found to be significant. This indicates a slight drift in the TSG sensor over time. The calibration equation relating the offset to decimalised time was used to generate the offset at the start and end of the underway data and applied through the BODC calibration database.

The root mean square (RMS) error was calculated for the comparison of bench salinometer salinity with uncalibrated TSG salinity and the newly calibrated salinity. The decrease in the residual range and the RMS error is small but indicates the calibration equation improves the match between the bench salinometer and the TSG sensor. The Max residual, Min residual and RMS error are as follows for uncalibrated and calobrated salinity respectively (0.410, -0.064, 0.0849) and (0.349, -0.116, 0.0690).

Temperature

The temperature from the hull sensor in the BUDS file was compared with the surface temperatures recorded by the CTD sensor. The data from the CTD profiles were averaged over 7 decibars at the surface. Data values with high standard deviations were removed from the calibration set and an offset calculated between CTD and hull sensor temperature. The offset was then plotted against time and CTD temperature. There was a significant regression with CTD temperature and the regression against time was not significant. The calibration equation was derived from the regression of the offset against CTD temperature.

The root mean square (RMS) error was calculated for the comparison of surface temperature from SeaBird CTD with the uncalibrated TSG temperature and the newly calibrated temperature. The Max residual, Min residual and RMS error are as follows for uncalibrated and calibrated salinity respectively (-0.350, -0.601, 0.449921) and (0.0753, -0.1482, 0.037687).

The decrease in the residual range and the RMS error indicates the calibration equation improves the match between the CTD temperature and the hull temperature sensors.

Chlorophyll

Once the underway fluorometer readings were compared with the extracted chlorophyll samples collected during the cruise it was observed that the fluorometer showed limited response to changes in surface chlorophyll levels in oceanic regions. Therefore the fluorometer data have not been calibrated and BODC recommends the use of the underway sampled extracted chlorophyll dataset, which provides good coverage along the cruise track.

Project Information

Oceans 2025 Theme 10, Sustained Observation Activity 1: The Atlantic Meridional Transect (AMT)

The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.

The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:

• give early warning of any fundamental change in Atlantic ecosystem functionng
• improve forecasts of the future ocean state and associated socio-economic impacts
• provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.

The specific objectives are:

• To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands
• To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems
• To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases

The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).

More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10

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: