Metadata Report for BODC Series Reference Number 1760659

• 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

Transmittance and Attenuance

The transmittance and attenuance channels are very noisy with many spikes observed. This is probably due to passing bubbles with the trapped bubbles causing the data to arbitrarily decline. The signal increases when the sensor is cleaned but it is not clear which are the good data. Users should use caution when interpreting the attenuance and transmittance channels.

AMT RRS James Cook Cruise JC039 surface hydrography quality control report

The underway log sheets were used as a guide to the times when the non-toxic flow was switched off, dropped low or was adjusted during the cruise. Where there was noise in the channel at these times the data were flagged suspect. If there was no noise or spiking the data remain unflagged.

The sample calibrations applied to the TSG salinity and hull sensor temperature channels appear reasonable and did not produce suspect data in the calibrated channels.

Fluorometer

The data for period from 28/10/2009 12:00 to 31/10/2010 12:00 should be considered suspect. There was a step up in sensor values at 28/10/2009 12:00, which decreased back to values before the step over the next 2-3 days. The calibration appeared to correct for some of this drift but users should be aware that the calibrated data may still not be reliable for this period as the number of discrete samples were small for this period. The first diel station (29/10/2009 03:59 - 30/10/2009 11:15) coincides with this period and the data show little variation for this period as might be anticipated since the vessel is not underway. There appeared to be drift in the sensor for the period 10/11/2009 19:00 to 14/11/2009 19:56, possibly from not being cleaned for a number of days however the calibration was able to correct for this drift.

The calibrated fluorometer data exhibit large amounts of variability towards the end of the cruise in the southern Atlantic Ocean. The calibration in this area is not as closely matched to the sample data for this reason. Users should keep this in mind when using the sample calibrated fluorometer data.

Attenuance and transmittance

Throughout the cruise track there was intermittent noise in the transmissometer channels. It is possible bubbles were becoming trapped in the transmissometer and building up to a point before being flushed past the lens. There are also a few steps in the data of which users should be aware. Users should use caution when interpreting the attenuance and transmittance channels.

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

SeaBird Digital Oceanographic Thermometer SBE38

The SBE38 is an ultra-stable thermistor that can be integrated as a remote temperature sensor with an SBE21 Thermosalinograph or an SBE 45 Micro TSG, or as a secondary temperature sensor with an SBE 16 plus, 16plus-IM, 16plus V2, 16plus-IM V2 or 19plus V2 SEACAT CTD.

Temperature is determined by applying an AC excitation to reference resistances and an ultra-stable aged thermistor. The reference resistor is a hermetically sealed VISHAY. AC excitation and ratiometric comparison using a common processing channel removes measurement errors due to parasitic thermocouples, offset voltages, leakage currents and gain errors.

The SBE38 can operate in polled sampling, where it takes one sample and transmits the data, or in continuous sampling.

Specifications

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

WET Labs WETStar Fluorometers

WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.

Specifications

By model:

All models:

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

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.

AMT RRS James Cook Cruise JC039 surface hydrographic instrumentation

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.

AMT RRS James Cook Cruise JC039 surface hydrography data processing procedures

Originator's Data Processing

The surface water component consisted of a flow through system with a pumped pickup at approximately 5 m depth. TSG flow was approximately 18 litres per minute whilst fluorometer and transmissometer flow was approximately 1.5 litres per minute. Flow to instruments was degassed using a debubbler with 24 litres per minute inflow and 10 litres per minute waste flow. The non-toxic system ran throughout the cruise except when entering within 200 nautical miles of the Azores, Falklands and Argentina.

The data from the non-toxic supply were logged by the TECHSAS system during the cruise and combined in RVS Level-C format to produce the files 'surfmet' and 'sbe45'. The following instruments were logged during the cruise:
1) Wetlabs C-star 25 cm pathlength transmissometer (logged to RVS format in surfmet)
2) Wetlabs WetStar fluorometer (logged to RVS format in surfmet)
3) Seabird SBE38 Temperature sensor (logged to RVS format in sbe45)
4) Seabird SBE45 MicroTSG (logged to RVS format in sbe45)

The table below shows the files delivered to BODC.

BODC Data Processing

Reformatting

Underway seawater data from the raw RVS files were transferred to BODC's 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 'surfmet' and 'sbe45' files were used as the source data for transfer.

The table below shows how originator's variables were mapped to the appropriate BODC parameter codes.

surfmet

sbe45

* NMF technician confirmed the fluorometer and transmissometer channels had been reversed during logging.

Calibrations

Manufacturer's calibrations

The coefficients from the calibration sheets provided for the transmissometer were used to generate the calibration equation to convert the raw voltage to transmittance and then to attenuance.

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. 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.

Sample Calibrations

The hull temperature sensor data were calibrated against the CTD profile temperature. The data from the hull sensor at the CTD start time were compared with the temperature from the CTD averaged over the surface 5 decibars. The temperature offsets (CTD - Hull) were plotted against date/time and CTD sensor temperature and outliers identified and removed from the calibration dataset. The relationships in the offset between sensors were then compared to the date/time and the CTD sensor temperature in separate linear regressions. There was a significant relationship with CTD sensor temperature (R² = 0.067; n = 108; F = 7.58; p = 0.007) and also a significant regression of offset with date/time (R² = 0.079; n = 108; F = 9.09; p = 0.003).

Applying the significant regression equation with the greater F ratio, offsets were generated at the date/time when the non-toxic underway system was switched on (17/10/2009 08:11:00 offset =-0.0027) and when switched off at the end of the cruise (29/11/2009 13:41:00 offset = -0.0219). The offset was applied for the period in-between by linear interpolation of these offsets through the BODC BUDS calibration routine (BODC ICALRF 6436).

The SBE45 salinity data were calibrated against bench salinometer data from samples collected from the underway system during the cruise. The data from the SBE45 TSG at the discrete sampling times were compared with the bench salinometer measurements. The salinity offsets (bench - TSG) were plotted against date/time and bench salinity and outliers identified. The relationships in the offset between TSG and bench salinometer were then compared to the date/time and the bench salinity in separate linear regressions. There was a significant relationship of offset with date/time (R² = 0.060; n = 179; F = 11.33; p = 0.001) and also with bench salinity (R² = 0.022; n = 179; F = 4.03; p = 0.046).

Applying the significant equation from the date/time regression, the offset was generated at the date/time when the non-toxic underway system was switched on (17/10/2009 08:11:00 offset = 0.0409) and when switched off at the end of the cruise (29/11/2009 13:41:00 offset = 0.0241). The offset was applied for the period in-between by linear interpolation of these offsets through the BODC BUDS calibration routine (BODC ICALRF 6437).

The fluorometer voltage data were calibrated against extracted chlorophyll-a data from samples collected from the underway system during the cruise. Samples of seawater collected and extracted chlorophyll-a measurements made following Welschmeyer (1994). Each sample of 250 ml was filtered through a 47 mm 0.2 µm polycarbonate filter. The filters were then placed in a vial with 10 ml 90% acetone and left in a freezer for 24 hours. The samples were then analysed on a pre-calibrated Turner Designs Trilogy fluorometer with a non-acidified chl module (CHL NA #046) fitted. The bench fluorometer calibration was checked against dilutions of pure chlorophyll stock during the cruise and no modifications to the calibration were necessary.

The raw voltage data from the fluorometer were compared with the extracted chlorophyll-a measurements. The offsets (extracted chl-a - voltage) were plotted against date/time and extracted chlorophyll-a and outliers identified. The calibration dataset was split into a number of sections to correct for different periods of drift in the sensor and oceanographic regions. These changes were related to different sections of the cruise where the non-toxic system had been turned off/on and/or cleaned.

References

Welschmeyer N.A., 1994. Fluorometric analysis of chlorophyll-a in the presence of chlorophyll-b and phaeopigments. Limnology and Oceanography, 39:1985-1992.

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: