Metadata Report for BODC Series Reference Number 2136350
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 |
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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 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
Becton Dickinson FACSort Flow Cytometer
The Becton Dickinson FACSort Flow Cytometer is a benchtop, five-detector, flow cytometer that is designed to analyse cells as they travel, one by one, in a moving fluid stream, through a focused, air-cooled, argon-ion laser beam. Samples are introduced through a stainless steel injection tube equipped with an outer droplet containment sleeve. As the cell passes through the laser, a mechanical catcher tube located in the upper portion of the flow cell, moves in and out of the sample stream to collect desired cells at a rate of up to 300 per second. The physical characteristics of the cells, which pertain to how the cell scatters the laser light and emits fluorescence are then analysed. This provides information about the cell's size, internal complexity and relative fluorescence intensity. Up to five parameters can be measured at once by the FACSort including forward light scatter, side light scatter, three fluorescence parameters, pulse height and width of each fluorescence parameter. FACSort can be operated with any Macintosh computer, where the information is output to. The FACSort system includes CELLQuest software for acquisition and analysis and FACSComp software for daily setup and quality control.
Droplet formation of sheath fluid as it backflows from the injection tube is eliminated by the use of the containment sleeve in conjunction with a vacuum pump. Fluid controls allow the user to select the fluidics mode and sample flow rate. As a mechanical device is used to sort cells, no side streams are formed so aerosol formation is completely eliminated. The laser alignment and stream velocity are fixed so the time it takes for desired cells to reach the catcher tube is constant so no setup calculations are required. As no optical alignment is required, daily setup can be performed quickly and consistently. Between one and three cell collection tubes can be installed and the instrument will automatically determine the maximum volume of sample to collect.
Specifications
Excitation: Laser | Cyonics 15 mW, 488 nm, air-cooled, argon-ion laser (Class I). Life expectancy >5000 hours. |
Excitation: Beam Geometry | Prismatic expander and spherical lens provide 20 x 64 µm elliptical beam. |
Optics: Alignment | Fixed, no user adjustments necessary or available. |
Optics: Dichroics | 560/22.5 ° (blue/orange-red); 640 LP (orange/red) |
Optics: Filters | FL1: 530/30; FL2: 585/42; FL3: 650 LP |
Photomultipliers | FL1, FL2, FL3: R1477, SSC: 1P28 |
Fluidics: Flow Rates | Three selectable flow rates: LO (12 µL ±3 µL/min); MED (35 µL ±5 µL/min); HI (60 µL ±7 µL/min) |
Fluidics: Quartz Cuvette | Internal cross-section is rectangular 430 x 180 µm. External surfaces are anti reflection coated. |
Fluidics: Air Pressure | Internal air pump provides sheath pressure of 4.5 psig and sample pressures of 4.6, 4.8 and 5.0 psig. |
Electronics: Parameters | Seven data channels available for acquisition: FSC, SSC, FL1, FL2, FL3, FLX-W, FLX-A (X=DDM parameter) |
Electronics: Acquisition speed | 20 µs approximate processing time while sorting; acquires up to 10000 cells/sec. |
Electronics: Sort rate | 300 cells/sec maximum in Single Cell sort mode. |
Signal Processing: measurement resolution | 256 or 1024 channels on all 5 parameters (Seven when acquiring with DDM). |
Signal Processing: signal modes | Any combination of logarithmic or linear selections for each detector. |
Signal Processing: Dynamic range | Four decades are provided by logarithmic amplifiers for each of the 5 parameters. |
Signal Processing: Fluorescence sensitivity | 1000 molecules of equivalent soluble fluorescein. |
Further details can be found in the manufacturer's specification sheet.
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.
D321A Microbial community data
Originator's Protocol for Data Acquisition and Analysis
Water samples were collected from the 6 light depths (1, 4.5, 7, 14, 33 and 55% of surface light) and either one or two depths below the euphotic zone. Samples from CTDs coinciding with bacterivory experiments were analysed immediately by flow cytometry to determine microbial abundance and composition. Samples from all other CTD stations were preserved and frozen at -80°C for post-cruise analysis. Fresh seawater samples were collected in clean 250 mL polycarbonate bottles from a Seabird CTD system containing either 24 x 20 L Niskin bottles. Samples were stored in a refrigerator and analysed within 1-2 hours of collection. Fresh samples were measured using a Becton Dickinson FACSort instrument, which characterised and enumerated Synechococcus spp. (cyanobacteria), picoeukaryotes, cryptophytes, coccolithophores and other nanophytoplankton based on their light scattering and autofluorescence properties. Microorganisms were also preserved with paraformaldehyde (1% final concentration) and then stained with SYBR Green I nucleic acid stain. The samples were then left in the dark at room temperature for at least 1 hour before enumeration of bacterioplankton, heterotrophic and phototrophic flagellates by flow cytometry. Samples for post-cruise analysis were collected in 50 mL polypropylene centrifuge tubes and stored in a refrigerator for up to 4 h before fixing with paraformaldehyde (1% final concentration). Samples were then left to fix in a refrigerator for a minimum of 1 hour before being frozen and stored in a -80°C freezer.
BODC Data Processing Procedures
Data received were loaded into the BODC database using established BODC data banking procedures. Originators parameters were mapped to BODCs parameters as follows:
Originator's Parameter | Unit | Description | BODC Parameter Code | BODC Unit | Comments |
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SYN | Cells/ml | Synechococcus spp., cyanobacteria | P700A90Z | #/ml | - |
PEUK | Cells/ml | Picoeukaryote phytoplankton flagellates </2 µm | PU00A02A | #/ml | - |
NEUK | Cells/ml | Nanoeukaryote phytoplankton flagellates, approx. 2-12 µm | X726A86B | #/ml | - |
COCCO | Cells/ml | Coccolithophores, calcified | P490A00Z | #/ml | - |
Bacteria HNA | Cells/ml | High nucleic acid, relative | NA016999 | #/ml | - |
Bacteria LNA | Cells/ml | Low nucleic acid, relative | P5B29926 | #/ml | - |
HFLAGs | Cells/ml | Heterotrophic flagellates | NANFHETR | #/ml | - |
Project Information
Oceans 2025 - The NERC Marine Centres' Strategic Research Programme 2007-2012
Who funds the programme?
The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).
Who is involved in the programme?
The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:
- National Oceanography Centre, Southampton (NOCS)
- Plymouth Marine Laboratory (PML)
- Marine Biological Association (MBA)
- Sir Alister Hardy Foundation for Marine Science (SAHFOS)
- Proudman Oceanographic Laboratory (POL)
- Scottish Association for Marine Science (SAMS)
- Sea Mammal Research Unit (SMRU)
Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:
- British Oceanographic Data Centre (BODC), hosted at POL
- Permanent Service for Mean Sea Level (PSMSL), hosted at POL
- Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS
The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.
What is the programme about?
Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:
- improve knowledge of how the seas behave, not just now but in the future;
- help assess what that might mean for the Earth system and for society;
- assist in developing sustainable solutions for the management of marine resources for future generations;
- enhance the research capabilities and facilities available for UK marine science.
In order to address these aims there are nine science themes supported by the Oceans 2025 programme:
- Climate, circulation and sea level (Theme 1)
- Marine biogeochemical cycles (Theme 2)
- Shelf and coastal processes (Theme 3)
- Biodiversity and ecosystem functioning (Theme 4)
- Continental margins and deep ocean (Theme 5)
- Sustainable marine resources (Theme 6)
- Technology development (Theme 8)
- Next generation ocean prediction (Theme 9)
- Integration of sustained observations in the marine environment (Theme 10)
In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.
When is the programme active?
The programme started in April 2007 with funding for 5 years.
Brief summary of the programme fieldwork/data
Programme fieldwork and data collection are to be achieved through:
- physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;
- the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';
- physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;
- coastal and shelf sea observatory data (Liverpool Bay Coastal Observatory (LBCO) and Western Channel Observatory (WCO)) using the RV Prince Madog and RV Quest.
The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.
Data Activity or Cruise Information
Data Activity
Start Date (yyyy-mm-dd) | 2007-08-10 |
End Date (yyyy-mm-dd) | 2007-08-10 |
Organization Undertaking Activity | National Oceanography Centre, Southampton |
Country of Organization | United Kingdom |
Originator's Data Activity Identifier | D321A_CTD_16247B |
Platform Category | lowered unmanned submersible |
BODC Sample Metadata Report for D321A_CTD_16247B
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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177983 | 10.00 | 19 | 19 | 6.80 | 8.00 | 7.30 | Niskin bottle | No problem reported | ||
177984 | 10.00 | 20 | 20 | 7.30 | 7.70 | 7.40 | Niskin bottle | No problem reported | ||
177985 | 10.00 | 21 | 21 | 7.00 | 7.80 | 7.30 | Niskin bottle | No problem reported | ||
177986 | 10.00 | 22 | 22 | 7.20 | 7.50 | 7.30 | Niskin bottle | No problem reported | ||
177987 | 10.00 | 23 | 23 | 7.30 | 7.70 | 7.40 | Niskin bottle | No problem reported | ||
177988 | 10.00 | 24 | 24 | 7.30 | 7.70 | 7.40 | Niskin bottle | No problem reported | ||
178131 | 10.00 | 15 | 10 | 34.40 | 34.90 | 34.30 | Niskin bottle | No problem reported | ||
178132 | 10.00 | 11 | 17 | 7.10 | 8.00 | 7.50 | Niskin bottle | No problem reported | ||
178338 | 10.00 | 1 | 1 | 810.70 | 811.80 | 802.00 | Niskin bottle | No problem reported | ||
178339 | 10.00 | 2 | 2 | 405.80 | 406.80 | 402.10 | Niskin bottle | No problem reported | ||
178340 | 10.00 | 3 | 3 | 128.40 | 129.20 | 127.50 | Niskin bottle | No problem reported | ||
178341 | 10.00 | 4 | 4 | 77.40 | 78.30 | 77.10 | Niskin bottle | No problem reported | ||
178342 | 10.00 | 13 | 5 | 77.50 | 78.00 | 77.00 | Niskin bottle | No problem reported | ||
178343 | 10.00 | 5 | 6 | 49.30 | 50.20 | 49.30 | Niskin bottle | No problem reported | ||
178344 | 10.00 | 6 | 7 | 48.90 | 50.10 | 49.00 | Niskin bottle | No problem reported | ||
178345 | 10.00 | 14 | 8 | 49.20 | 50.00 | 49.10 | Niskin bottle | No problem reported | ||
178346 | 10.00 | 7 | 9 | 34.00 | 34.90 | 34.10 | Niskin bottle | No problem reported | ||
178347 | 10.00 | 8 | 11 | 29.60 | 29.80 | 29.40 | Niskin bottle | No problem reported | ||
178348 | 10.00 | 16 | 12 | 29.20 | 30.10 | 29.40 | Niskin bottle | No problem reported | ||
178349 | 10.00 | 9 | 13 | 22.30 | 23.00 | 22.40 | Niskin bottle | No problem reported | ||
178350 | 10.00 | 17 | 14 | 22.40 | 22.80 | 22.40 | Niskin bottle | No problem reported | ||
178351 | 10.00 | 10 | 15 | 12.10 | 12.80 | 12.30 | Niskin bottle | No problem reported | ||
178352 | 10.00 | 18 | 16 | 12.00 | 12.80 | 12.30 | Niskin bottle | No problem reported | ||
178353 | 10.00 | 12 | 18 | 7.10 | 8.00 | 7.50 | 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 | D321 (D321A) |
Departure Date | 2007-07-24 |
Arrival Date | 2007-08-23 |
Principal Scientist(s) | John T Allen (National Oceanography Centre, Southampton) |
Ship | RRS Discovery |
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: D321A_CTD_16247B
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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2137501 | Water sample data | 2007-08-10 02:43:30 | 59.98947 N, 20.47579 W | RRS Discovery D321 (D321A) |
1349543 | Water sample data | 2007-08-10 02:44:00 | 59.98947 N, 20.47579 W | RRS Discovery D321 (D321A) |
1854157 | Water sample data | 2007-08-10 02:44:00 | 59.98947 N, 20.47579 W | RRS Discovery D321 (D321A) |