Metadata Report for BODC Series Reference Number 1705010


Metadata Summary

Data Description

Data Category Water sample data
Instrument Type
NameCategories
Niskin bottle  discrete water samplers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Alex Poulton
Originating Organization Southampton Oceanography Centre (now National Oceanography Centre, Southampton)
Processing Status banked
Project(s) Atlantic Meridional Transect Phase2(AMT)
 

Data Identifiers

Originator's Identifier AMT13_CTD_PIGX_215:A13_42
BODC Series Reference 1705010
 

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2003-09-29 12:21
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval -
 

Spatial Co-ordinates

Latitude 3.83265 S ( 3° 50.0' S )
Longitude 24.99662 W ( 24° 59.8' W )
Positional Uncertainty Unspecified
Minimum Sensor Depth 0.9 m
Maximum Sensor Depth 99.9 m
Minimum Sensor Height 5358.0 m
Maximum Sensor Height 5457.0 m
Sea Floor Depth 5457.9 m
Sensor Distribution Unspecified -
Sensor Depth Datum Unspecified -
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
 

Parameters

BODC CODE Rank Units Short Title Title
ADEPZZ01 1 Metres DepBelowSurf Depth below surface of the water body
ALLOHPP1 1 Nanograms per litre alloxanthin_water>GF/F_HPLC Concentration of alloxanthin {CAS 28380-31-6} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
BBCAHPP1 1 Nanograms per litre BB-carotene_water>GF/F_HPLC Concentration of beta,beta-carotene {beta-carotene CAS 7235-40-7} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
BOTTFLAG 1 Dimensionless C22_flag Sampling process quality flag (BODC C22)
BUTAHPP1 1 Nanograms per litre 19'-butanoyloxyfucoxanthin_water>GF/F_HPLC Concentration of 19'-butanoyloxyfucoxanthin per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
CHLBHPP1 1 Nanograms per litre chl-b_water>GF/F_HPLC Concentration of chlorophyll-b {chl-b CAS 519-62-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
CLC2HPP1 1 Nanograms per litre chl-c2_water>GF/F_HPLC Concentration of chlorophyll-c2 {chl-c2} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
CLC3HPP1 1 Nanograms per litre chl-c3_water>GF/F_HPLC Concentration of chlorophyll-c3 {chl-c3} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
CPHLFLP1 1 Milligrams per cubic metre chl-a_water>GF/F_fluor Concentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and fluorometry
CPHLHPP1 1 Milligrams per cubic metre chl-a_water>GF/F_HPLC Concentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
DIADHPP1 1 Nanograms per litre diadinoxanthin_water>GF/F_HPLC Concentration of diadinoxanthin {CAS 18457-54-0} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
DVCAHPP1 1 Nanograms per litre DVchl-a_water>GF/F_HPLC Concentration of divinyl chlorophyll-a per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
DVCBHPP1 1 Nanograms per litre DVchl-b_water>GF/F_HPLC Concentration of divinyl chlorophyll-b per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
FIRSEQID 1 Dimensionless FireSeqNo Bottle firing sequence number
FUCXHPP1 1 Nanograms per litre fucoxanthin_water>GF/F_HPLC Concentration of fucoxanthin {CAS 3351-86-8} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
HEXOHPP1 1 Nanograms per litre 19'-hexanoyloxyfucoxanthin_water>GF/F_HPLC Concentration of 19'-hexanoyloxyfucoxanthin {CAS 60147-85-5} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
PERIHPP1 1 Nanograms per litre peridinin_water>GF/F_HPLC Concentration of peridinin {CAS 33281-81-1} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
ROSPOSID 1 Dimensionless RosPos Bottle rosette position identifier
SAMPRFNM 1 Dimensionless SampRef Sample reference number
VILXHPP1 1 Nanograms per litre violaxanthin_water>GF/F_HPLC Concentration of violaxanthin {CAS 126-29-4} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
ZEOXHPP1 1 Nanograms per litre zeaxanthin_water>GF/F_HPLC Concentration of zeaxanthin {CAS 144-68-3} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC)
 

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

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 have a capacity between 1.7 and 30 L, while Lever Action bottles have a capacity between 1.7 and 12 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.

AMT13 extracted chlorophyll-a (total and size-fractionated) measured fluormetrically from CTD bottle and underway samples

Data Acquisition and Analysis

Total chlorophyll was analysed on samples collected from both the CTD rosette sampler and from a small number of underway samples collected from the ship's non-toxic water supply. Water-column sampling during AMT13 concentrated around 5 or 6 light depths from the predawn CTD cast (~0200 - 0400h local time), with a reduced set of depths from the late morning 'optics' cast (1100h local time).

Water samples from the 5-6 main light depths were collected from CTD bottles and underway samples from the ship's non-toxic supply and these samples were filtered on 25 mm GFF filters. Filters were extracted in 90% acetone for 10-24 hrs and total chlorophyll-a measured with a TD-700 Turner Designs fluorometer following the procedure of Welschmeyer (1994) which minimises interference by chlorophyll-b. The fluorometer was calibrated with dilutions of a solution of pure chlorophyll-a (Sigma, UK) in 90% acetone, the concentration of which was determined spectrophotometrically after the cruise.

Size-fractionation of chlorophyll was carried out for samples collected on the pre-dawn cast. Size-fractionated chlorophyll distribution was determined by serial filtration onto 10, 5, 2 and 0.2 µm polycarbonate membrane filters (Poretics, UK). The filters were treated identically to the GF/F used for total chlorophyll and were soaked in 10-ml 90% acetone (HPLC grade) for 10-24 hours prior to reading on the bench fluorometer.

References Cited

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

Instrumentation Description

Not relevant to this dataset.

BODC Data Processing Procedures

Data were submitted to BODC in an Excel spreadsheet and were accessioned under BODC archive SOC040010. Sample metadata provided (CTD cast, date, time, lat/lon and depth) were checked against information held in the database. There were no discrepancies noted.

Parameter codes defined in BODC parameter dictionary were assigned to the variable. The units supplied in the spreadsheet were mg m -3 , which match the Parameter Dictionary units so no unit conversions were necessary.

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

A parameter mapping table is provided below;

Originator's Parameter Units Description BODC Parameter Code Units Comments
Chlorophyll-a mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and fluorometry CPHLFLP1 mg m -3 n/a
0.2-2µm mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate 0.2-2µm phase] by filtration, acetone extraction and fluorometry SCHLFLPF mg m -3 n/a
2-5µm mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate 2-5µm phase] by filtration, acetone extraction and fluorometry SCHLFLPC mg m -3 n/a
>5µm mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >5µm phase] by filtration, acetone extraction and fluorometry SCHLFLPA mg m -3 n/a
5-10µm mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate 5-10µm phase] by filtration, acetone extraction and fluorometry SCHLFLPX mg m -3 n/a
>10µm mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >10µm phase] by filtration, acetone extraction and fluorometry SCHLFLPO mg m -3 n/a
Total mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >0.2µm phase] by filtration, acetone extraction, fluorometry and summation of size-fractionated values CPHLFLP4 mg m -3 n/a

Data Quality Report

The data originator removed any suspect data before submission to BODC.

Problem Report

Not relevant to this dataset.

AMT13 pigment composition by HPLC analysis from CTD bottle samples

Data Acquisition and Analysis

Fresh seawater samples from upto five light depths were collected from 57 stations during the cruise. The main sampling was conducted on the pre-dawn cast each day with a reduced set of samples from the midday cast. All samples and replicates were stored at -80 °C and were returned to SOC in liquid-N for analysis.

HPLC analysis was carried out according to Barlow et al. (1997).

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.

Instrumentation Description

Section not relevant.

BODC Data Processing Procedures

Data were submitted to BODC in Microsoft Excel spreadsheet format and saved to the archive with reference SOC040134. The file was provided to BODC with CTD cast number, date, and bottle depth as metadata.

Sample metadata were checked against information held in the database - there was one minor depth discrepancy. Data were provided from a sample collected from 160m during cast 21, but no bottle was fired at this depth instead bottles were fired at 150m and the data were loaded against this depth.

Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below. Values were multiplied by one thousand where appropriate for conversion into nanograms per litre. Cells where a value was logged as 'Present' were changed to 0 and the flag '<' was added to show values were below the detection level of the instrument. Column headings were substituted for the appropriate BODC parameter code except for Tpigm and Tchla, which were derived from the summation of all pigment values and ChlA and Dv ChlA values repectively. These derived values were not loaded into the database.

Data loaded into BODC's database without any changes.

Originator's Parameter Units Description BODC Parameter Code Units Comments
Chl c3 mg m -3 Concentration of chlorophyll-c3 {chl-c3} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) CLC3HPP1 ng l -1 Unit conversion x1000 applied
Chl c2 mg m -3 Concentration of chlorophyll-c2 {chl-c2} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) CLC2HPP1 ng l -1 Unit conversion x1000 applied
Peridinin mg m -3 Concentration of peridinin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) PERIHPP1 ng l -1 Unit conversion x1000 applied
19'But mg m -3 Concentration of 19'-butanoyloxyfucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) BUTAHPP1 ng l -1 Unit conversion x1000 applied
Fucox mg m -3 Concentration of fucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) FUCXHPP1 ng l -1 Unit conversion x1000 applied
19'Hex mg m -3 Concentration of 19'-hexanoyloxyfucoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) HEXOHPP1 ng l -1 Unit conversion x1000 applied
Violax mg m -3 Concentration of violaxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) VILXHPP1 ng l -1 Unit conversion x1000 applied
Diadinox mg m -3 Concentration of diadinoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) DIADHPP1 ng l -1 Unit conversion x1000 applied
Allox mg m -3 Concentration of alloxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) ALLOHPP1 ng l -1 Unit conversion x1000 applied
Zeax mg m -3 Concentration of zeaxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) ZEOXHPP1 ng l -1 Unit conversion x1000 applied
Dv ChlB mg m -3 Concentration of divinyl chlorophyll-b per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) DVCBHPP1 ng l -1 Unit conversion x1000 applied
Chl B mg m -3 Concentration of chlorophyll-b per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) CHLBHPP1 ng l -1 Unit conversion x1000 applied
Dv ChlA mg m -3 Concentration of divinyl chlorophyll-a per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) DVCAHPP1 ng l -1 Unit conversion x1000 applied
ChlA mg m -3 Concentration of chlorophyll-a {chl-a} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) CPHLHPP1 mg m -3 n/a
B-Carot mg m -3 Concentration of beta-carotene {beta,beta-carotene} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) BCARHPP1 ng l -1 Unit conversion x1000 applied

Data Quality Report

The following values were reported as suspect by the originator and were flagged 'L' in the database: AMT13_30, 12m: Value for DV ChlA too low. AMT13_65, 52m: Value for DV ChlA too high.

Problem Report

This section is 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:

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:

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

Start Date (yyyy-mm-dd) 2003-09-29
End Date (yyyy-mm-dd) 2003-09-29
Organization Undertaking ActivityPlymouth Marine Laboratory
Country of OrganizationUnited Kingdom
Originator's Data Activity IdentifierAMT13_CTD_A13_42
Platform Categorylowered unmanned submersible

BODC Sample Metadata Report for AMT13_CTD_A13_42

Sample reference number Nominal collection volume(l) Bottle rosette position Bottle firing sequence number Minimum pressure sampled (dbar) Maximum pressure sampled (dbar) Depth of sampling point (m) Bottle type Sample quality flag Bottle reference Comments
509329 20.0 24 1   303.20   303.50   300.20 Niskin bottle No problem reported    
509330 20.0 23 2   253.30   253.60   250.70 Niskin bottle No problem reported    
509331 20.0 22 3   202.30   202.80   200.10 Niskin bottle No problem reported    
509332 20.0 20 5   122.10   122.40   120.30 Niskin bottle No problem reported    
509333 20.0 19 6   101.50   101.90     99.90 Niskin bottle No problem reported    
509334 20.0 18 7     81.80     82.20     80.30 Niskin bottle No problem reported    
509335 20.0 15 9     79.50     79.80     78.00 Niskin bottle No problem reported    
509336 20.0 16 10     80.20     80.40     78.60 Niskin bottle No problem reported    
509337 20.0 17 11     79.80     79.90     78.10 Niskin bottle No problem reported    
509338 20.0 12 13     75.70     75.90     74.10 Niskin bottle Bottle misfire   did not fire according to nutrient log
509339 20.0 11 14     72.00     72.10     70.40 Niskin bottle Bottle misfire   did not fire according to nutrient log
509340 20.0 10 15     69.90     70.20     68.40 Niskin bottle No problem reported    
509341 20.0 8 17     51.90     52.20     50.50 Niskin bottle Bottle misfire   did not fire according to nutrient log
509342 20.0 7 18     35.90     36.20     34.60 Niskin bottle No problem reported    
509343 20.0 6 19     21.80     22.50     20.80 Niskin bottle No problem reported    
509344 20.0 4 21     11.70     11.90     10.50 Niskin bottle No problem reported    
509345 20.0 5 22     11.80     12.20     10.70 Niskin bottle No problem reported    
509346 20.0 1 24       1.90       2.40         .90 Niskin bottle No problem reported    
510204 20.0 21 4   152.50   152.50   150.40 Niskin bottle No problem reported    
510205 20.0 14 8     79.80     80.40     78.40 Niskin bottle No problem reported    
510206 20.0 13 12     77.90     78.10     76.30 Niskin bottle No problem reported    
510207 20.0 9 16     62.20     62.50     60.80 Niskin bottle No problem reported    
510208 20.0 3 20     11.80     12.30     10.70 Niskin bottle No problem reported    
510209 20.0 2 23       8.10       8.40       7.00 Niskin bottle No problem reported    

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.

Other Series linked to this Data Activity - 1130891

Cruise

Cruise Name JR20030910 (AMT13, JR91)
Departure Date 2003-09-10
Arrival Date 2003-10-14
Principal Scientist(s)Carol Robinson (Plymouth Marine Laboratory)
Ship RRS James Clark Ross

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:

Flag Description
Blank Unqualified
< Below detection limit
> In excess of quoted value
A Taxonomic flag for affinis (aff.)
B Beginning of CTD Down/Up Cast
C Taxonomic flag for confer (cf.)
D Thermometric depth
E End of CTD Down/Up Cast
G Non-taxonomic biological characteristic uncertainty
H Extrapolated value
I Taxonomic flag for single species (sp.)
K Improbable value - unknown quality control source
L Improbable value - originator's quality control
M Improbable value - BODC quality control
N Null value
O Improbable value - user quality control
P Trace/calm
Q Indeterminate
R Replacement value
S Estimated value
T Interpolated value
U Uncalibrated
W Control value
X Excessive difference

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Flag Description
0 no quality control
1 good value
2 probably good value
3 probably bad value
4 bad value
5 changed value
6 value below detection
7 value in excess
8 interpolated value
9 missing value
A value phenomenon uncertain