Metadata Report for BODC Series Reference Number 1890392
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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Parameters |
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Definition of BOTTFLAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BOTTFLAG | Definition |
---|---|
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 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.
AMT1-6 and 11 size-fractionated extracted chlorophyll-a measured fluorometrically from CTD bottle samples
Data Acquisition and Analysis
These data originate from analyses on samples collected from CTD rosette bottles and the measurements were made concurrently with the depths sampled for the primary production (14C) incubations carried out during each cruise.
Water samples from the 5-7 main light depths were collected from CTD bottles. For AMT1 all samples were filtered through 0.2 µm filters only. For AMTs 2-6 and 11 size-fractionated chlorophyll-a concentrations were determined fluorometrically after sequential filtration of a 200 - 300 ml seawater sample through 20 µm, 2 µm and 0.2 µm polycarbonate filters. All filters were placed in 90% acetone at -20°C for pigment extraction.
Instrumentation Description
Turner Designs 10-AU fluorometer
BODC Data Processing Procedures
Data were submitted to BODC in an Excel spreadsheet with the Primary Production incubation data and were saved to the BODC archive with reference UVI020056. Sample metadata provided (CTD cast, latitude and depth) were checked against information held in the database. There were no discrepancies.
Where chl-a values were provided with no size fractioned data, the data were loaded under a separate parameter for total chl-a collected on a 0.2 µm filter, not a summation of different filter sizes.
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 |
---|---|---|---|---|---|
Chl 0.2-2 µm | 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 |
Chl 2-20 µm | 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 | SCHLFLPG | mg m-3 | n/a |
Chl >20 µm | mg m-3 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >20µm phase] by filtration, acetone extraction and fluorometry | SCHLFLPQ | mg m-3 | n/a |
Chlorophyll-a | 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 |
Chl >2 µm | mg m-3 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >2µm phase] by filtration, acetone extraction and fluorometry | SCHLFLPB | mg m-3 | n/a |
Chl >0.2 µm | mg m-3 | Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >0.2µm phase] by filtration, acetone extraction and fluorometry | CPHLFLP5 | mg m-3 | n/a |
Data Quality Report
BODC were not advised of any data quality checks made by the data originator prior to submission of the dataset.
Problem Report
Not relevant to this dataset.
AMT11 pigment composition by HPLC analysis (CTD bottles)
Data Acquisition and Analysis
For vertical profiling samples were taken from five depths down to 250 m and 1.5-3 litres were filtered through 0.2 µm glass fibre filters. Pigment samples were stored at -80 oC until analysis by HPLC. Pigments were extracted in acetone using ultrasonication, and centrifugation to remove debris, and analysed using the method of 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 BODC archive with reference PML030067. The file was provided to BODC with CTD cast number and depth as metadata. Sample metadata were checked against information held in the database - there were no discrepancies.
There were three samples provided with null data values for all pigments (cast 7 depth 70 m; cast 27 depth 80 m; cast 46 depth 80 m). It was unclear if these were measured null values or no data because of a lost filter and these data were not loaded to the database.
The data were provided in units of micrograms per litre. The units associated with the parameter codes in the BODC Parameter Dictionary were nanograms per litre, with the exception of chlorophyll-a which was in units of milligrams per cubic metre. All data had a unit conversion factor applied (x 1000) except the chl-a data where the units are equivalent.
Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below.
Data loaded into BODC's database without any changes.
Originator's Parameter | Units | Description | BODC Parameter Code | Units | Comments |
---|---|---|---|---|---|
Chl c3 | µg l-1 | 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 applied (x 1000) |
Chl c2 | µg l-1 | 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) | CLC2HPP1 | ng l-1 | Unit conversion applied (x 1000) |
Perid | µg 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 | Unit conversion applied (x 1000) |
Butfuco | µg 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 | Unit conversion applied (x 1000) |
Fuco | µg 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 | Unit conversion applied (x 1000) |
Hexfuco | µg 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 | Unit conversion applied (x 1000) |
Viola | µg 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 | Unit conversion applied (x 1000) |
Diadino | µg 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 | Unit conversion applied (x 1000) |
Allo | µg 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 | Unit conversion applied (x 1000) |
Prasino | µg l-1 | Concentration of prasinoxanthin per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | PRSXHPP1 | ng l-1 | Unit conversion applied (x 1000) |
Zea | µg 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 | Unit conversion applied (x 1000) |
Lut | µg 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 | Unit conversion applied (x 1000) |
DV Chl b + Chl b | µg l-1 | Concentration of chlorophyll-b+divinyl chlorophyll-b per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CBDVHPP1 | ng l-1 | Unit conversion applied (x 1000) |
Neo | µg l-1 | Concentration of neoxanthin per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | NEOXHPP1 | ng l-1 | Unit conversion applied (x 1000) |
DV Chl a | µg 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 | Unit conversion applied (x 1000) |
4keto- Hexfuco | µg l-1 | Concentration of 4-keto-hexanoylfucoxanthin per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | K4HXHPP1 | ng l-1 | Unit conversion applied (x 1000) |
β,β-Caro | µg l-1 | Concentration of beta,beta-carotene per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BBCAHPP1 | ng l-1 | Unit conversion applied (x 1000) |
β,epsilon-Caro | µg l-1 | Concentration of beta,epsilon-carotene per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | BECAHPP1 | ng l-1 | Unit conversion applied (x 1000) |
MgDVP | µg l-1 | Concentration of Mg-2,4-divinyl pheoporphyrin a5 monomethyl ester per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | MDVPHPP1 | ng l-1 | Unit conversion applied (x 1000) |
Chl a allom | µg l-1 | Concentration of chlorophyll-a allomer per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CLAAHPP1 | ng l-1 | Unit conversion applied (x 1000) |
Chla epim | µg l-1 | Concentration of chlorophyll-a epimer per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | CLAEHPP1 | ng l-1 | Unit conversion applied (x 1000) |
Chlc2-MGDG (C.polylepis) | µg l-1 | Concentration of chlorophyll-c2 monogalactosyldiacylglyceride ester (C. polylepsis type) per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | C2MEHPC1 | ng l-1 | Unit conversion applied (x 1000) |
Chlc2-MGDG (E.huxleyi) | µg l-1 | Concentration of chlorophyll-c2 monogalactosyldiacylglyceride ester (E. huxleyi type) per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | C2MEHPE1 | ng l-1 | Unit conversion applied (x 1000) |
MVChl c3 | µg l-1 | Concentration of monovinyl chlorophyll-c3 per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and high performance liquid chromatography (HPLC) | MVC3HPP1 | ng l-1 | Unit conversion applied (x 1000) |
Chl a | µg 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 | - |
Data Quality Report
BODC were not advised by the data originator of any quality control processes applied to the data set.
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) | 2000-09-15 |
End Date (yyyy-mm-dd) | 2000-09-15 |
Organization Undertaking Activity | Plymouth Marine Laboratory |
Country of Organization | United Kingdom |
Originator's Data Activity Identifier | AMT11_CTD_AMT11-03 |
Platform Category | lowered unmanned submersible |
BODC Sample Metadata Report for AMT11_CTD_AMT11-03
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 |
---|---|---|---|---|---|---|---|---|---|---|
506012 | 162.70 | 163.40 | 162.10 | Niskin bottle | No problem reported | |||||
506013 | 122.80 | 123.90 | 122.80 | Niskin bottle | No problem reported | |||||
506014 | 92.10 | 92.80 | 92.20 | Niskin bottle | No problem reported | |||||
506015 | 62.00 | 62.80 | 62.40 | Niskin bottle | No problem reported | |||||
506016 | 41.70 | 42.90 | 42.40 | Niskin bottle | No problem reported | |||||
506017 | 31.80 | 32.70 | 32.50 | Niskin bottle | No problem reported | |||||
506018 | 21.80 | 22.60 | 22.50 | Niskin bottle | No problem reported | |||||
506093 | 254.00 | 255.00 | 252.70 | Niskin bottle | No problem reported | |||||
506094 | 5.80 | 6.60 | 6.70 | 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 | JR20000912 (AMT11, JR52 Leg1, JR53) |
Departure Date | 2000-09-12 |
Arrival Date | 2000-10-11 |
Principal Scientist(s) | E Malcolm S Woodward (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 |
B | nominal value |
Q | value below limit of quantification |
Appendix 1: AMT11_CTD_AMT11-03
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 |
---|---|---|---|---|
1095399 | Water sample data | 2000-09-15 09:56:00 | 47.13436 N, 11.5845 W | RRS James Clark Ross JR20000912 (AMT11, JR52 Leg1, JR53) |
1632749 | Water sample data | 2000-09-15 09:56:00 | 47.13436 N, 11.5845 W | RRS James Clark Ross JR20000912 (AMT11, JR52 Leg1, JR53) |
1853117 | Water sample data | 2000-09-15 09:56:00 | 47.13436 N, 11.5845 W | RRS James Clark Ross JR20000912 (AMT11, JR52 Leg1, JR53) |