Metadata Report for BODC Series Reference Number 2296692

• 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

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:

"Contains public sector information licensed under the Open Government Licence v1.0."

Narrative Documents

Thermo Scientific Accela High Performance Liquid Chromatograph

The Accela high performance liquid chromatography system provides fast separations at pressures of up to 18,130 psi and at flow rates of 1 to 5000 µL/min. The system consists of an analytical pump, an autosampler, an optional PDA detector or UV/Vis detector and a solvent platform.

There is a choice of three analytical pumps to use with the system (the Accela Pump, Accela 600 Pump and Accela 1250 Pump) with each pump having a built-in degassing unit which is remotely controlled from the data system computer via USB. The autosampler automates sample injections and sample preparation and includes a built-in column oven, with a temperature range of 5 to 95°C, and a sample temperature control (0 to 60°C). Within the autosampler there is the capacity for 200 samples across five sample trays. There is a choice to use a PDA detector which in combination with the 5 or 1 cm LightPipe flowcell, provides the highest level of sensitivity available in photodiode array detection for HPLC. The second detector that can be used is a UV/Vis detector which can monitor two wavelength channels. Both detectors have a dual-lamp optical bench that covers the UV-visible spectrum from 190 to 800 nm. The solvent platform is located on top of the system stack and holds four 1 L solvent reservoir bottles and one 1 L wash bottle.

Please see the manufacturer's user's guide and product sheet for further details.

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.

AMT25 (JR15001) pigment composition by HPLC analysis from CTD bottle and underway samples

Originator's Protocol for Data Acquisition and Analysis

Seawater samples were collected from both CTD casts (predawn and noon) and the underway supply and stored in 9.5 L polypropylene carboys that were covered in black plastic in order to keep out light. The samples were then vacuum filtered through GF/F filters in volumes of 1 - 4 L depending on phytoplankton biomass. Samples were filtered using a low-medium vacuum setting on the vacuum pump. When the last of the water passed through the filter paper, taps on the vacuum pump were closed and the resulting sample filters were folded into 2 mL cryovials. There was not a liquid nitrogen generator on board the ship and so samples were immediately stored in a freezer at -80°C. For each CTD cast, two samples were collected at the surface (2-5 m) and one at the subsurface chlorophyll maximum. Duplicate HPLC measurements were taken at all depths at each station with the exception of when a CTD bottle misfired and there was not enough water for the duplicate. Two daily samples were also taken from the underway supply around the time of each CTD cast. The frequency of the underway samples was increased to nine samples during a phytoplankton bloom at the start of the cruise. The frozen samples were transported back to Plymouth Marine Laboratory (PML) where they were analysed using HPLC methods.

The pigments were extracted from the filters into 2 mL 90% acetone using an ultrasonic probe (35 s; 50 W). Extracts were clarified and analysed by reversed phase HPLC 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, following the methods in Zapata et al. (2000).

References Cited

Zapata, M., Rodriguez, F., Garrido, J.L., 2000. Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C8 column and pyridine-containing mobile phases. Marine Ecology Progress Series, 195, 29-45.

Instrumentation Description

Thermo Accela Series HPLC system

BODC Data Processing Procedures

Data were submitted to BODC in Microsoft Excel spreadsheet format and saved to the archive following BODC procedure. The file was provided to BODC with cruise, sample ID, volume filtered, sequential day of year and depth as metadata. Sample metadata were checked against information held in the database and no discrepancies were found. In addition to the data, a second Excel spreadsheet was submitted containing a description of the dataset; the effective limits of detection; quality assurance check and a summary of the methods. The methods were also described in a Word document which contained: the dataset title; name of data file; dataset creators and institute; dataset period; dataset abstract; sampling methodology and description of analytical techniques and data quality comments.

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.

The data to be loaded were reformatted and assigned BODC parameter codes in units ng L^-1 with the exception of chlorophyll-a (mg m^-3). The data were provided in μg L^-1 units and so the data were converted to ng L^-1 for all parameters, apart from chlorophyll-a, by multiplying by 1000. Duplicate data were provided for CTD casts 1, 16, 20, 28, 29, 38, 53 and 66 and so the mean and standard deviation were calculated for these casts. Data were loaded in BODC's samples database under Oracle Relational Database Management System using established BODC data banking procedures without any further changes.

The originator's parameters were mapped to BODC parameter codes as follows:

The standard deviation parameter codes were only used where there were any duplicate data from one depth of a CTD cast and were calculated by BODC. The standard deviation parameter codes were not used during the process of the underway samples.

Data Quality Report

Quality assurance procedures for pigment analysis are in place at PML and values of precision were given where replicate samples were available. The whole dataset conforms to the quality assurance criteria set out in Aiken et al. 2009. For this pigment analysis, the absent data value is considered to be the effective limit of detection.

The pigment profile of AMT25 surface samples frequently contained an unknown component with an absorption maximum at 418 nm, that coeluted with [Chl c3]. The unknown component, when present, affected the quantification of [Chl c3]. The originator highlighted the data affected and during BODC processing these data were flagged L. If [Chl c3] was affected by the unknown component when calculating the average and standard deviations of duplicates, the affected value was omitted and so the measurement would be the unaffected value within the pair. In these cases standard deviations were not calculated. In cases where both values were affected the average and standard deviation were calculated with the average flagged L.

References Cited

Aiken J., Pradhan Y., Barlow R., Lavender S., Poulton A.J., Holligan P.M. and Hardman-Mountford N.J., 2009 Phytoplankton pigments and functional types in the Atlantic Ocean: A decadal assessment, 1995-2005. Deep Sea Research Part II, 56 (15), 899-917.

Project Information

PML National Capability

The Plymouth Marine Laboratory National Capability focuses on long term science concerned with basin/decadal variability of the Ocean.

Data Activity or Cruise Information

Data Activity

BODC Sample Metadata Report for JR15001_CTD_CTD_S017

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: JR15001_CTD_CTD_S017

Related series for this Data Activity are presented in the table below. Further information can be found by following the appropriate links.

If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.