Metadata Report for BODC Series Reference Number 1870305
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
Data Description |
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Data Identifiers |
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Time Co-ordinates(UT) |
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Spatial Co-ordinates | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Parameters |
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Definition of BOTTFLAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BOTTFLAG | Definition |
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0 | The sampling event occurred without any incident being reported to BODC. |
1 | The filter in an in-situ sampling pump physically ruptured during sample resulting in an unquantifiable loss of sampled material. |
2 | Analytical evidence (e.g. surface water salinity measured on a sample collected at depth) indicates that the water sample has been contaminated by water from depths other than the depths of sampling. |
3 | The feedback indicator on the deck unit reported that the bottle closure command had failed. General Oceanics deck units used on NERC vessels in the 80s and 90s were renowned for reporting misfires when the bottle had been closed. This flag is also suitable for when a trigger command is mistakenly sent to a bottle that has previously been fired. |
4 | During the sampling deployment the bottle was fired in an order other than incrementing rosette position. Indicative of the potential for errors in the assignment of bottle firing depth, especially with General Oceanics rosettes. |
5 | Water was reported to be escaping from the bottle as the rosette was being recovered. |
6 | The bottle seals were observed to be incorrectly seated and the bottle was only part full of water on recovery. |
7 | Either the bottle was found to contain no sample on recovery or there was no bottle fitted to the rosette position fired (but SBE35 record may exist). |
8 | There is reason to doubt the accuracy of the sampling depth associated with the sample. |
9 | The bottle air vent had not been closed prior to deployment giving rise to a risk of sample contamination through leakage. |
Definition of Rank |
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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.
AMT5 pigment composition by HPLC analysis from CTD bottle and discrete underway samples
Data Acquisition and Analysis
Seawater samples from up to ten light depths were collected from 28 stations during the cruise. Samples were also collected from the ships non-toxic supply at 7 m depth. All samples were filtered through G/F filters, which were stored at -80 °C and returned to PML 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 PML020061. The file was provided to BODC with CTD cast number, date, time, latitude, longitude and bottle depth as metadata.
Sample metadata were checked against information held in the database - there were two depth discrepancies. Data were provided from samples collected from 50 and 100m during cast 20, but no bottle was fired at this depth instead bottles were fired at 20 and 60m and the data were loaded against these depth respectively.
Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below. Chloophyll-a values were divided by one thousand for conversion from nanograms per litre into milligrams per cubic metre. All data columns were loaded to the database except for tot CHLa, which were derived from the summation of ChlA+Dv ChlA values. 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 |
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Chlorophyll c3 | ng l-1 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate <GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CLC3HPP1 | ng l-1 | - |
Chlorophyll c2 | ng l-1 | 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 | - |
Peridinin | ng l-1 | 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 | - |
But-fucoxanthin | ng l-1 | 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 | - |
Fucoxanthin | ng l-1 | 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 | - |
Hex-fucoxanthin | ng l-1 | 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 | - |
Violaxanthin | ng l-1 | 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 | - |
Diadinoxanthin | ng l-1 | 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 | - |
Diatoxanthin | ng l-1 | Concentration of diatoxanthin per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | DIATHPP1 | ng l-1 | - |
Alloxanthin | ng l-1 | 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 | - |
Zeaxanthin | ng l-1 | 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 | - |
Lutein | ng l-1 | Concentration of lutein per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | LUTNHPP1 | ng l-1 | - |
dv Chlorophyll b | ng l-1 | 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 | - |
Chlorophyll b | ng l-1 | 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 | - |
dv Chlorophyll a | ng l-1 | 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 | - |
Chlorophyll a | ng l-1 | 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 | Unit conversion /1000 applied |
Beta-carotene | ng l-1 | Concentration of beta,beta-carotene per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BBCAHPP1 | ng l-1 | - |
pheophytin a | ng l-1 | Concentration of phaeophytin-a per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PTAXHPP1 | ng l-1 | - |
pheophorbide a | ng l-1 | Concentration of phaeophorbide-a per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PBAXHPP1 | ng l-1 | - |
pyro- pheophytin a | ng l-1 | Concentration of pyrophaeophytin-a {pyro-a} per unit volume of the water column [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PYPTHPP1 | ng l-1 | - |
Data Quality Report
The originator advised the sample bottles in the region of the Deep Chlorophyll Maximum (DCM) may have become mixed up for cast 13.
Problem Report
This section is not relevant to this data set.
Project Information
The Atlantic Meridional Transect (AMT) - Phase 1 (1995-2000)
Who was involved in the project?
The Atlantic Meridional Transect (AMT) programme was designed by and implemented as a collaboration between Plymouth Marine Laboratory (PML) and Southampton Oceanography Centre (SOC). The programme was hosted by Plymouth Marine Laboratory and involved additional researchers from UK and international universities throughout its duration.
What was the project about?
When AMT began in 1995 the programme provided a platform for international scientific collaboration, including the calibration and validation of SeaWiFs measurements and products. The programme provided an exceptional opportunity for nationally and internationally driven collaborative research and provided a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, the data collected by the AMT consortium informed on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.
The scientific aims were to assess:
- mesoscale to basin scale phytoplankton processes
- the functional interpretation of bio-optical signatures
- the seasonal, regional and latitudinal variations in mesozooplankton dynamics
When was the project active?
The first phase of the AMT programme ran from 1995 to 2000 and consisted of a total of 12 cruises. A second phase of funding allowed the project to continue for the period 2002 to 2006 with a further 6 cruises.
Brief summary of the project fieldwork/data
The AMT programme undertook biological, chemical and physical oceanographic research during the annual return passage of the RRS James Clark Ross between the UK and the Falkland Islands or the RRS Discovery between the UK and Cape Town, a distance of up to 13,500 km. This transect crossed a range of ecosystems from sub-polar to tropical and from euphotic shelf seas and upwelling systems to oligotrophic mid-ocean gyres. The transect route was covered north-south in September/October and south-north in April/May of each year.
The measurements of hydrographic and bio-optical properties, plankton community structure and primary production completed on the first 12 transects (1995-2000) represent the most coherent set of repeated biogeochemical observations over ocean basin scales. This unique dataset has led to several important discoveries concerning the identification of oceanic provinces, validation of ocean colour algorithms, distributions of picoplankton, identifying new regional sinks of pCO2 and variability in rates of primary production and respiration.
Who funded the project?
The programme was funded by the Natural Environment Research Council (NERC) and further support was received from the National Aeronautics and Space Administration (NASA) with equipment and funding from the Sea-viewing Wild Field-of-view Sensor (SeaWiFS) project.
Data Activity or Cruise Information
Data Activity
Start Date (yyyy-mm-dd) | 1997-10-08 |
End Date (yyyy-mm-dd) | 1997-10-08 |
Organization Undertaking Activity | Plymouth Marine Laboratory |
Country of Organization | United Kingdom |
Originator's Data Activity Identifier | AMT5_CTD_AMT5020 |
Platform Category | lowered unmanned submersible |
BODC Sample Metadata Report for AMT5_CTD_AMT5020
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 |
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503357 | 30.00 | 252.20 | 253.40 | 251.00 | Niskin bottle | No problem reported | ||||
503358 | 30.00 | 201.60 | 202.50 | 200.10 | Niskin bottle | No problem reported | ||||
503359 | 30.00 | 180.60 | 181.90 | 180.00 | Niskin bottle | No problem reported | ||||
503360 | 30.00 | 161.40 | 162.50 | 160.50 | Niskin bottle | No problem reported | ||||
503361 | 30.00 | 146.10 | 147.00 | 145.60 | Niskin bottle | No problem reported | ||||
503362 | 30.00 | 138.60 | 139.60 | 137.60 | Niskin bottle | No problem reported | ||||
503363 | 30.00 | 125.90 | 126.70 | 125.40 | Niskin bottle | No problem reported | ||||
503364 | 30.00 | 110.80 | 111.70 | 110.60 | Niskin bottle | No problem reported | ||||
503365 | 30.00 | 60.40 | 61.30 | 60.80 | Niskin bottle | No problem reported | ||||
503366 | 30.00 | 19.60 | 20.60 | 20.40 | Niskin bottle | No problem reported | ||||
503367 | 30.00 | 1.60 | 2.60 | 2.10 | 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.
Related Data Activity activities are detailed in Appendix 1
Cruise
Cruise Name | JR19970914 (AMT5, JR23) |
Departure Date | 1997-09-14 |
Arrival Date | 1997-10-17 |
Principal Scientist(s) | James Aiken (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 |
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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 |
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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 |
B | nominal value |
Q | value below limit of quantification |
Appendix 1: AMT5_CTD_AMT5020
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.
Series Identifier | Data Category | Start date/time | Start position | Cruise |
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1631967 | Water sample data | 1997-10-08 12:08:00 | 20.66221 S, 34.22468 W | RRS James Clark Ross JR19970914 (AMT5, JR23) |
1870587 | Water sample data | 1997-10-08 12:08:00 | 20.66221 S, 34.22468 W | RRS James Clark Ross JR19970914 (AMT5, JR23) |