Metadata Report for BODC Series Reference Number 1889827

• 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

Niskin Bottle

The Niskin bottle is a device used by oceanographers to collect subsurface seawater samples. It is a plastic bottle with caps and rubber seals at each end and is deployed with the caps held open, allowing free-flushing of the bottle as it moves through the water column.

Standard Niskin

The standard version of the bottle includes a plastic-coated metal spring or elastic cord running through the interior of the bottle that joins the two caps, and the caps are held open against the spring by plastic lanyards. When the bottle reaches the desired depth the lanyards are released by a pressure-actuated switch, command signal or messenger weight and the caps are forced shut and sealed, trapping the seawater sample.

Lever Action Niskin

The Lever Action Niskin Bottle differs from the standard version, in that the caps are held open during deployment by externally mounted stainless steel springs rather than an internal spring or cord. Lever Action Niskins are recommended for applications where a completely clear sample chamber is critical or for use in deep cold water.

Clean Sampling

A modified version of the standard Niskin bottle has been developed for clean sampling. This is teflon-coated and uses a latex cord to close the caps rather than a metal spring. The clean version of the Levered Action Niskin bottle is also teflon-coated and uses epoxy covered springs in place of the stainless steel springs. These bottles are specifically designed to minimise metal contamination when sampling trace metals.

Deployment

Bottles may be deployed singly clamped to a wire or in groups of up to 48 on a rosette. Standard bottles and Lever Action bottles have a capacity between 1.7 and 30 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.

AMT19 (JC039) pigment composition by HPLC analysis from CTD bottle samples

Data Acquisition and Analysis

Samples (1-2L) were vacuum filtered onto GF/F filters, flash frozen in liquid nitrogen and stored at -80°C on board ship. Samples were shipped back to UK on dry ice. On receipt at PML, a small amount of dry ice remained around samples. At PML, samples were stored at -80°C until analysis. Pigments were extracted from the sample filters into 2 mL 100% acetone using an ultrasonic probe (35 s; 50W). An internal standard was used (Trans-B-Apo-8'-carotenal) to correct for water content of filters. Extracts were centrifuged to remove filter and cell debris (5 min at 4000 rpm) and analysed by reversed phase HPLC, using a method based on Barlow et al. 1997. Analyses were performed using a Thermo Accela Series HPLC system with chilled autosampler (4°C) and photodiode array detector. The HPLC was calibrated using a suite of standards purchased from DHI (Denmark). Pigments were identified based on retention time and spectral match using photo-diode array.

Instrumentation Description

Thermo Accela Series HPLC system

BODC Data Processing Procedures

These data supersede data previously supplied to BODC without quality assurance (see the Data Quality Report section for more details). Data were submitted to BODC in Microsoft Excel spreadsheet format and saved to the archive with reference PML130050. The file was provided to BODC with date, latitude, longitude, station number and depth as metadata. Sample metadata were checked against information held in the database - there were no discrepancies.

The following parameters were provided in the file but only the parameters that were not derived from the summation of other parameters in the dataset were loaded into the database. The absent data value was recorded as the effective limit of detection (LOD). The effective limits of detection, calculated for a filter volume of 3L are given in the table below.

There were duplicate data provided for 12 samples (cast 5s, depth 1 m and 5 m; cast 8s, depths 1 m, 10 m, 17 m and 38 m; cast 15t, depths 1 m, 10 m and 20 m; cast 71s, depths 10 m, 20 m and 35 m) and the mean and standard deviation for these values were entered into the database for each sample.

Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below. The data were provided in µg l^-1 units that were converted to ng l^-1 for all parameters but chlorophyll-a.

Data loaded into BODC's database without any further changes.

Data Quality Report

Dataset originally obtained using inadequate quality assurance (QA) procedures (for an example of adequate QA procedures during pigment analysis, see Van Heukelem and Hooker (2011)). A series of duplicate samples spanning the chl-a concentration range observed in the dataset were analysed using a quality assured, validated HPLC method by an experienced pigment scientist. A comparison between the original and duplicate sample pigment concentrations was performed, and systematic errors for individual pigments identified. The AMT19 pigment dataset was corrected for the systematic errors identified, and validated against surface pigment samples collected during AMT19, and analysed independently by a validated pigment method in a NASA laboratory (Hornpoint). The root mean square deviation (RMSD) of the two sample sets (PML and Hornpoint) was determined and normalized to the concentration range for each pigment. The average normalized root mean square deviation (NRMSD) for the primary pigments was 7.9% (see table below). Notably, the highest NRMSD value for the primary pigments was observed for diatoxanthin, which was present at low concentration in all but one of the compared samples.

The precision for replicate filters (gives whole method precision, from filtering to analysis) was provided in a separate file and is available on request to BODC. The average coefficients of variation (CV%) were 7.97 and 15.04 for [TChl a] and [TPig], respectively.

Samples values provided with the effective LOD were flagged '<' for each parameter in the database.

Problem Report

This section is not relevant to this data set.

References Cited

Barlow R.G., Cummings D.G. and Gibb S.W., 1997. Improved resolution of mono- and divinyl chlorophylls a and b and zeaxanthin and lutein in phytoplankton extracts using reverse phase C8 HPLC. Marine Ecology Progress Series, 161 , 303-307.

Van Heukelem L. and Hooker S.B. 2011. The importance of a quality assurance plan for method validation and minimizing uncertainties in the HPLC analysis of phytoplankton pigments. In: Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography, eds. Suzanne Roy, Carole A. Llewellyn, Einar Skarstad Egeland and Geir Johnsen. Cambridge University Press.

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

Data Activity

BODC Sample Metadata Report for JC039_CTD_CTD083T

Please note:the supplied parameters may not have been sampled from all the bottle firings described in the table above. Cross-match the Sample Reference Number above against the SAMPRFNM value in the data file to identify the relevant metadata.

Related Data Activity activities are detailed in Appendix 1

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:

Appendix 1: JC039_CTD_CTD083T

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