Metadata Report for BODC Series Reference Number 2008058
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 |
|||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||
Data Identifiers |
|||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||
Time Co-ordinates(UT) |
|||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||
Spatial Co-ordinates | |||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||
Parameters |
|||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||
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 |
|
|
Problem Reports
No Problem Report Found in the Database
Data Access Policy
Public domain 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.
The recommended acknowledgment is
"This study uses data from the data source/organisation/programme, provided by the British Oceanographic Data Centre and funded by the funding body."
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.
Abundance of microbial phytoplankton through the water column by analytical flow cytometry (AFC) analysis of samples collected from CTD casts during AMT25 (JR20150916/JR15001).
Originator's Protocol for Data Acquisition and Analysis
These data originate from analyses on fresh seawater samples collected from 200 m to the surface, using a Seabird CTD system containing a 24 bottle rosette of 20 L Niskin bottles. Samples were collected from the predawn and were stored in a refrigerator and analysed within 3 hours of collection. Fresh samples were measured using a Becton Dickinson FACSort flow cytometer which characterised and enumerated Prochlorococcus sp. and Synechococcus sp. (cyanobacteria) and pico- and eucaryote phytoplankton, based on their light scattering and autofluorescence properties. Data were saved in listmode format and analysed onboard during the cruise.
References Cited
Instrumentation Description
Becton Dickinson FACSort flow cytometer
BODC Data Processing Procedures
Data were submitted via email in an Excel spreadsheet archived under BODC's accession number PML160002. Sample metadata including cruise, station, sampling gear, date, CTD cast, time on deck, latitude, longitude, Niskin bottle number and depth were checked against information held in the database and matched according to cast, rosette bottle number and depth.
The data were provided in cell abundance per millilitre. These units were consistent with the BODC parameter code units so no conversions were necessary.
The data were reformatted and marked up with BODC parameter codes. Data were loaded to into BODC's samples database under Oracle Relational Database Management System using established BODC data banking procedures.
A parameter mapping table is provided below;
| Originator's Parameter | Units | Description | BODC Parameter Code | Units | Comments |
|---|---|---|---|---|---|
| Synechococcus sp. cyanobacteria | cell abundance ml-1 | Abundance of Synechococcus (ITIS: 773: WoRMS 160572) per unit volume of the water body by automated flow cytometry | P700A90Z | cell abundance ml-1 | n/a |
| Prochlorococcus sp. cyanobacteria | cell abundance ml-1 | Abundance of Prochlorococcus (ITIS: 610076: WoRMS 345515) per unit volume of the water body by automated flow cytometry | P701A90Z | cell abundance ml-1 | n/a |
| Picoeukaryote phytoplankton (<3 µm) | cell abundance ml-1 | Abundance of Picoeukaryotic cells per unit volume of the water body by automated flow cytometry | PYEUA00A | cell abundance ml-1 | n/a |
| Cryptophytes (a specific group of nanoeukaryote phytoplankton) | cell abundance ml-1 | Abundance of Cryptophyceae (ITIS: 10598: WoRMS 17639) per unit volume of the water body by automated flow cytometry | J79A0596 | cell abundance ml-1 | n/a |
| Coccolithophores (a specific group of nanoeukaryote phytoplankton) | cell abundance ml-1 | Abundance of Prymnesiophyceae (ITIS: 2135: WoRMS 115057) [Subgroup: coccolithophores] per unit volume of the water body by automated flow cytometry | P490A00Z | cell abundance ml-1 | n/a |
| Nanoeukaryote phytoplankton (approx. 3-12 µm) excluding coccolithophores and cryptophytes | cell abundance ml-1 | Abundance of nanoeukaryotic cells [Size: 2-12 µm] per unit volume of the water body by automated flow cytometry | X726A86B | cell abundance ml-1 | n/a |
Data Quality Report
BODC were not advised of specific quality checks carried out by the data originators. There were no stand out values in the sample data provided to BODC.
Problem Report
Not relevant to this data set.
Project Information
PML National Capability
The Plymouth Marine Laboratory National Capability focuses on long term science concerned with basin/decadal variability of the Ocean.
Data Activity or Cruise Information
Data Activity
| Start Date (yyyy-mm-dd) | 2015-09-19 |
| End Date (yyyy-mm-dd) | 2015-09-19 |
| Organization Undertaking Activity | British Antarctic Survey |
| Country of Organization | United Kingdom |
| Originator's Data Activity Identifier | JR15001_CTD_CTD_S003 |
| Platform Category | lowered unmanned submersible |
No Document Information Held for the Series
Related Data Activity activities are detailed in Appendix 1
Cruise
| Cruise Name | JR15001 (AMT25, JR864) |
| Departure Date | 2015-09-15 |
| Arrival Date | 2015-11-04 |
| Principal Scientist(s) | David Barnes (British Antarctic Survey), Jonathan Sharples (University of Liverpool Department of Earth, Ocean and Ecological Sciences), Tim Smyth (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: JR15001_CTD_CTD_S003
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 |
|---|---|---|---|---|
| 1968098 | Water sample data | 2015-09-19 13:30:00 | 47.50954 N, 11.06232 W | RRS James Clark Ross JR15001 (AMT25, JR864) |
