Metadata Report for BODC Series Reference Number 2277805

• 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

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.

AMT16 Pico-plankton, nano-plankton and bacteria abundance from AFC analysis of samples collected from CTD bottle samples during AMT16

Originator's Protocol for Data Acquisition and Analysis

This data originates from analyses on samples collected from CTD casts during the cruise. Samples were taken from the pre-dawn CTD cast (~0200 - 0400h local time) and from the late morning 'optics' cast (1100h local time).

Seawater samples were collected in HCl washed 50ml polypropylene tubes from each depth on 3am and 11am casts. Samples were stored in a refrigerator and analysed within 1-2 hours of collection.

Another set of samples were stained with Sybr Green I nucleic acid stain, with the addition of 0.5 µm beads as an internal standard and a potassium citrate buffer and left in the dark at 35^oC for at least 1 hour before analysis by flow cytometry onboard ship. The data were stored on disk and analysed back in the UK.

Additional subsamples were fixed with paraformaldehyde (1% final concentration) and flash frozen in liquid nitrogen for approximately 1 minute and then placed in the -60^oC freezer for post-cruise flow cytometric analysis of autotrophic and heterotrophic picoplankton abundance.

Fresh samples were measured using a Becton Dickinson FACSort flow cytometer, which characterised and enumerated Prochlorococcus spp. andSynechococcus spp. (both cyanobacteria), pico-eukaryotes, cryptophytes, coccolithophores and other nano-phytoplnkton based on their light scattering and autofluorescence properties.

After sample analysis, a density plot of particle light scatter vs green fluorescence, which is due to the Sybr Green I dye was plotted. The dye binds to the DNA in cells (including phytoplankton and viruses) and, the data originator advised that through experience, a protocol has been developed to specifically analyse bacteria. The density plots clearly show different clusters with different light scattering and green fluorescence properties and regions can be drawn around the different clusters and the numbers within them obtained to provide abundances for heterotrophic bacteria with low or high nucleic acid content.

A similar technique was applied to the Synechococcus spp. based on the bright/dim orange fluorescence of the phycoerythrin proteins in the cells.

The frozen samples were analysed post-cruise using flow cytometric analysis. This data was used to compare the effects of fixation, preservation and time on abundance estimates obtained by flow cytometry.

References Cited

Instrumentation Description

Becton Dickinson FACSort instrument

BODC Data Processing Procedures

Data were submitted via email in an Excel spreadsheet archived under BODC's accession number PML060508. Sample metadata in the file (lat, lon, depth, cast) were checked against information held in the database. There were no discrepancies.

There were a number of cells in the worksheet with '#VALUE!' or '#N/A' suggesting a problem with a formula or the data for these samples. The data originator clarified these cells should be treated as no data collected.

Since the data originator was unclear on the exact biological significance of the division between bright and dim orange fluorescence Synechococcus spp. abundance, these were combined to totalSynechococcus spp. abundance for loading into the database. This is consistent with theSynechococcus spp. data returned from other AMT cruise. BODC retains the split data in the archived file and this can be provided if requested.

The data were provided in cell abundance per millilitre. These units were consistent with the BODC parameter code units and no conversions were necessary.

The data were reformatted and loaded in BODC's samples database under Oracle Relational Database Management System. Data were marked up with BODC parameter codes and loaded into the database. Individual samples were matched through rosette sampling bottle and depth.

A parameter mapping table is provided below;

Data Quality Report

BODC were not advised of specific quality checks carried out by the data originators. There were no standout values in the sample data provided to BODC.

Problem Report

Not relevant to this data set.

Project Information

The Atlantic Meridional Transect - Phase 2 (2002-2006)

Who was involved in the project?

The Atlantic Meridional Transect Phase 2 was designed by and implemented by a number of UK research centres and universities. The programme was hosted by Plymouth Marine Laboratory in collaboration with the National Oceanography Centre, Southampton. The universities involved were:

• University of Liverpool
• University of Newcastle
• University of Plymouth
• University of Southampton
• University of East Anglia

What was the project about?

AMT began in 1995, with scientific aims to assess mesoscale to basin scale phytoplankton processes, the functional interpretation of bio-optical signatures and the seasonal, regional and latitudinal variations in mesozooplankton dynamics. In 2002, when the programme restarted, the scientific aims were broadened to address a suite of cross-disciplinary questions concerning ocean plankton ecology and biogeochemistry and the links to atmospheric processes.

The objectives included the determination of:

• how the structure, functional properties and trophic status of the major planktonic ecosystems vary in space and time
• how physical processes control the rates of nutrient supply to the planktonic ecosystem
• how atmosphere-ocean exchange and photo-degradation influence the formation and fate of organic matter

The data were collected with the aim of being distributed for use in the development of models to describe the interactions between the global climate system and ocean biogeochemistry.

When was the project active?

The second phase of funding allowed the project to continue for the period 2002 to 2006 and consisted of six research cruises. The first phase of the AMT programme ran from 1995 to 2000.

Brief summary of the project fieldwork/data

The fieldwork on the first three cruises was carried out along transects from the UK to the Falkland Islands in September and from the Falkland Islands to the UK in April. The last three cruises followed a cruise track between the UK and South Africa, only deviating from the traditional transect in the southern hemisphere. During this phase the research cruises sampled further into the centre of the North and South Atlantic Ocean and also along the north-west coast of Africa where upwelled nutrient rich water is known to provide a significant source of climatically important gases.

Who funded the project?

Natural Environment Research Council (NERC)

Data Activity or Cruise Information

Data Activity

BODC Sample Metadata Report for AMT16_CTD_CTD029s

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: AMT16_CTD_CTD029s

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.