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Metadata Report for BODC Series Reference Number 1710699

Metadata Summary

Data Description

Data Category Water sample data
Instrument Type
Niskin bottle  discrete water samplers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Anna Hickman
Originating Organization National Oceanography Centre, Southampton
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Seasonal Thermocline Production Control

Data Identifiers

Originator's Identifier CD173_CTD_PIGX_229:CTD076
BODC Series Reference 1710699

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2005-07-29 07:06
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval -

Spatial Co-ordinates

Latitude 49.86374 N ( 49° 51.8' N )
Longitude 7.95276 W ( 7° 57.2' W )
Positional Uncertainty Unspecified
Minimum Sensor or Sampling Depth 0.5 m
Maximum Sensor or Sampling Depth 69.8 m
Minimum Sensor or Sampling Height 3.2 m
Maximum Sensor or Sampling Height 72.5 m
Sea Floor Depth 73.0 m
Sea Floor Depth Source -
Sensor or Sampling Distribution Unspecified -
Sensor or Sampling Depth Datum Unspecified -
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface


BODC CODERankUnitsTitle
ADEPZZ011MetresDepth (spatial coordinate) relative to water surface in the water body
BOTTFLAG1Not applicableSampling process quality flag (BODC C22)
CPHLFLP11Milligrams per cubic metreConcentration 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
FIRSEQID1DimensionlessBottle firing sequence number
ROSPOSID1DimensionlessBottle rosette position identifier
SAMPRFNM1DimensionlessSample reference number

Definition of BOTTFLAG

0The sampling event occurred without any incident being reported to BODC.
1The filter in an in-situ sampling pump physically ruptured during sample resulting in an unquantifiable loss of sampled material.
2Analytical 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.
3The 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.
4During 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.
5Water was reported to be escaping from the bottle as the rosette was being recovered.
6The bottle seals were observed to be incorrectly seated and the bottle was only part full of water on recovery.
7Either 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).
8There is reason to doubt the accuracy of the sampling depth associated with the sample.
9The bottle air vent had not been closed prior to deployment giving rise to a risk of sample contamination through leakage.

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

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

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.


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.

CD173 Discrete Chlorophyll Sampling Document

Originator's Protocol for Data Acquisition and Analysis

488 water samples were taken to determine the concentration of chlorophyll-a during RRS Charles Darwin cruise CD173, which was conducted in the Celtic Sea, from 15 July 2005 to 06 August 2005. These samples were collected from the water bottle rosette mounted on the lowered CTD during 82 casts. Samples were collected from between four to ten rosette bottles fired at depths within the surface mixed layer and depths within the thermocline corresponsding to the peak and the upper slope of the deep chlorophyll maximum.

All measurements for chlorophyll-a were made following the fluoresence method of Welschmeyer (1994) using GF/F filters extracted in 90% acetone at 4°C in the dark for a minimum of 24 hours. The chlorophyll solution in acetone was analysed in a Turner A-10 fluorometer which had been calibrated against a standard solution of pure chlorophyll-a (Sigma Chemical Company). Chlorophyll-a values were obtained by applying a calibration factor of 0.1585 to the fluorometer output. The calibration factor was obtained from a calibration done at sea combined with a check on the standards using the following formula;

CHL = (FLSample - FLBlank) x R x (VOLAcetone / VOLSeawater)

FLSample = fluorescence reading for sample
FLBlank = fluorescence reading for acetone blank
R = calibration factor = 0.1585
VOLAcetone = volume of acetone used in pigment extraction = 10 ml
VOLSeawater = volume of seawater filtered through GF/F filter = 100 ml

References Cited

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

BODC Data Processing Procedures

The chlorophyll data were supplied to BODC in Microsoft Excel format. Values were extracted from this and saved in ASCII format prior to being loaded into BODC's Samples Database under the ORACLE Relational Database Management System. This was done by matching the sample's station and bottle identifiers and depth with the information already held in the database for this cruise.

The source file from the Data Originator included a record of samples taken at bottle position 7 during casts 40 (sample depth = 55 m) and 104 (sample depth = 2 m). However, an inspection of the logsheets for these casts showed no bottles were fired at position 7, but bottles were fired at position 9 at the depth which was recorded as the collection depth in the spreadsheet. In each case, the bottle fired at position 9 was 7th in the bottle triggering sequence for that cast. BODC have therefore made the assumption that the bottle position record actually relates to the firing sequence order in these two cases, meaning the samples actually came from bottle position 9. They have been linked accordingly.

During this extraction, it was found that 8 of the samples were replicates: 4 samples were taken at 30 m depth during cast 110, and 4 samples were taken at 45 m depth during cast 120. For these replicate samples, the mean and standard deviations were obtained and loaded instead, giving a total number of 484 entries to the BODC database. Methodology and units were checked against information held in the BODC parameter dictionary and an approriate parameter code was attributed to each variable. Data that were considered unrealistic were flagged suspect.

Content of data series

Originator's Parameter Unit Description BODC Parameter code BODC Unit Comments
Calib. Chl a µg l-1 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 No unit conversion necessary as
µg l-1 = mg m-3
- - Concentration standard deviation of chlorophyll-a {chl-a} per unit volume of the water body [particulate >GF/F phase] by filtration, acetone extraction and fluorometry CLSDFLP1 mg m-3 Calculated by BODC for instances where replicate samples were taken


The Data Originator highlighted that a number of the chlorophyll-a samples collected from CTD water bottles may have been contaminated. These values have subsequently been flagged accordingly and should be used with caution.

Project Information

Physical-Biological Control of New Production within the Seasonal Thermocline

This project was a NERC responsive-mode project which was co-funded by the Defence Science and Technology Laboratory and ran from 2003 to 2006. The key institutes and scientists involved were:

Institute Scientific personnel
Proudman Oceanographic Laboratory (POL) Jonathan Sharples
National Oceanography Centre, Southampton (NOCS) Patrick Holligan
Mark Moore
University of Wales, Bangor (UWB) John Simpson
Tom Rippeth

Research Aim

The main aim of this research was to investigate the generation and dissipation of turbulence in the thermocline, and to quantify how the resulting mixing (supplying nutrients and controlling the light experienced by the algae) affected the growth of phytoplankton within the sub-surface chlorophyll maximum (SCM).

Research Objectives

The objective of the research was to test the general hypothesis that, in seasonally-stratified shelf waters, temporal and spatial variability of the rate of 'new' production is determined by the degree of coupling between physical and biological processes within the seasonal thermocline. In particular it has been suggested that physiological adaptation by phytoplankton making up the subsurface chlorophyll maximum drives a biological pump for extracting nitrate from the bottom mixed layer that is sensitive to internal mixing and to external climatological factors.

Research Approach

The sampling and experimental strategy was based on established methods for obtaining compatible, high-resolution vertical profiles (alternate CTD and FLY) and sections (SeaSoar) of physical, chemical, and biological parameters, allowing quantification of vertical fluxes and primary production on tidal and internal wave time scales. The cruise schedule (with associated mooring deployments) for the project is below.

Cruise Schedule

Cruise ID Ship Sampling Region Cruise Dates Main measurements
JR98 RRS James Clark Ross St Georges Channel, Celtic Sea and shelf edge 25/07/03 - 14/08/03 CTD casts, SeaSoar transects (CTD, chlorophyll, fluorescence), FRRF, ship ADCP, primary productivity, nutrients, trace metals, phytoplankton uptake rates, algal photophysiology, oxygen concentration, particle size, optics, mooring deployments
PD32_03 RV Prince Madog Celtic Sea and shelf edge 27/07/03 - 13/08/03 5 x FLY 25 hour tidal cycle stations, particle size analysis, particle settling velocity, CTD casts, mooring deployments
CD173 RRS Charles Darwin Celtic Sea and shelf edge 15/07/05 - 06/08/05 CTD casts, chlorophyll, oxygen concentration, FLY profiles, SeaSoar tows (CTD, chlorophyll, FRRF), phytoplankton pigments, nutrients, primary productivity, phytoplankton uptake rates, FRRF profiles, optics, particle size analysis, mooring deployments
PD27_05 RV Prince Madog Celtic Sea and shelf edge 22/07/05 - 06/08/05 FLY profiles, mooring deployments


Station ID Latitude Longitude Depth (m) Mooring Deployment date Recovery date Deployment vessel
CS3 51.471 -6.428 95 Seabed frame 300 kHz ADCP 01/08/03 11/08/03 RV Prince Madog
CS3 51.471 -6.428 95 Seabed frame 1200 kHz ADCP 01/08/03 11/08/03 RV Prince Madog
CS3 51.474 -6.437 95 Mid-water subsurface 300 kHz ADCP 01/08/03 11/08/03 RV Prince Madog
CS3 51.469 -6.437 95 Thermistor chain from 5 - 45 m depth 01/08/03 11/08/03 RV Prince Madog
ACW 51.266 -5.741 85 Seabed frame 300 kHz ADCP 06/08/03 08/08/03 RV Prince Madog
CS2 48.532 -9.463 200 Surface temperature toroid 28/07/03 12/08/03 RRS James Clark Ross
CS2 48.532 -9.463 200 Thermistor chain throughout water column 28/07/03 12/08/03 RRS James Clark Ross
CS2 48.532 -9.463 200 Sub-suface 600 kHz ADCP (90 m) 28/07/03 12/08/03 RRS James Clark Ross
CS2 48.532 -9.463 200 Aanderaa RCM7 current meter/CTD (12 mab)* 28/07/03 12/08/03 RRS James Clark Ross
CS2 48.532 -9.463 200 Seabed frame 150 kHz ADCP 28/07/03 12/08/03 RRS James Clark Ross
CS2 48.532 -9.463 200 Seabed frame 300 kHz ADCP 28/07/03 12/08/03 RRS James Clark Ross
U2 49.236 -6.166 121 Sub-suface 300 kHz ADCP (5 mab)* 15/07/05 03/08/05 RRS Charles Darwin
U2 49.233 -6.167 120 Thermistor chain throughout water column 19/07/05 Mooring lost RRS Charles Darwin
CS2 48.571 -9.509 200 Thermistor chain throughout water column 17/07/05 24/07/05 RRS Charles Darwin
CS2 48.573 -9.51 194 Sub-suface 300 kHz ADCP (100 m) 17/07/05 24/07/05 RRS Charles Darwin
CS2 48.572 -9.508 196 Seabed frame 300 kHz ADCP 17/07/05 24/07/05 RRS Charles Darwin
CS2 48.571 -9.507 202 Seabed frame 150 kHz ADCP 17/07/05 24/07/05 RRS Charles Darwin
Bank 1 49.938 -7.792 118 Thermistor chain throughout water column 26/07/05 Mooring lost RRS Charles Darwin
Bank 1 49.936 -7.792 118 Seabed frame 300 kHz ADCP 27/07/05 Recovered by trawler 29/07/05 RRS Charles Darwin
Bank 2 49.895 -7.872 114 Thermistor chain throughout water column 20/07/05 04/08/05 RRS Charles Darwin
Bank 2 49.876 -7.897 112 Sub-surface 600 kHz ADCP (56 m) 26/07/05 04/08/05 RRS Charles Darwin
Bank 2 49.894 -7.873 110 Seabed frame 300 kHz ADCP 26/07/05 04/08/05 RRS Charles Darwin
Bank 3 49.851 -7.952 78 Thermistor chain throughout water column 26/07/05 03/08/05 RV Prince Madog
Bank 3 49.854 -7.948 78 Seabed frame 300 kHz ADCP 26/07/05 Mooring lost RV Prince Madog

* = metres above seabed

Project Outcomes

The main products of the research were:

  • The first large scale interdisciplinary study of the dynamic processes that determine the properties of the SCM in NW European shelf waters.
  • Substantive advances in quantifying internal mixing in NW European shelf seas, and in understanding how primary production is controlled by this small-scale turbulence.
  • New parameterisations for internal vertical mixing, and the response of primary production, for use in coupled numerical models.
  • Improved capability for estimating primary productivity in stratified waters by satellite remote sensing (ocean colour, sea surface temperature, wind mixing etc.)
  • An overall development of our understanding of the dynamics of ecosystems that support important fisheries, and of our abilities in predicting ecological and biogeochemical responses to variations and changes in the climate of the marine environment.

Data Activity or Cruise Information

Data Activity

Start Date (yyyy-mm-dd) 2005-07-29
End Date (yyyy-mm-dd) Ongoing
Organization Undertaking ActivityProudman Oceanographic Laboratory (now National Oceanography Centre, Liverpool)
Country of OrganizationUnited Kingdom
Originator's Data Activity IdentifierCD173_CTD_CTD076
Platform Categorylowered unmanned submersible

BODC Sample Metadata Report for CD173_CTD_CTD076

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
436451   20.00 1 1   71.10   72.10   69.80 Niskin bottle No problem reported    
436452   20.00 2 2   51.60   52.60   50.50 Niskin bottle No problem reported    
436453   20.00 3 3   41.30   42.30   40.30 Niskin bottle No problem reported    
436454   20.00 4 4   26.50   27.50   25.60 Niskin bottle No problem reported    
436455   20.00 5 5   11.30   12.30   10.60 Niskin bottle No problem reported    
436456   20.00 8 6    1.10    2.10     .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 Name CD173
Departure Date 2005-07-15
Arrival Date 2005-08-06
Principal Scientist(s)Jonathan Sharples (Proudman Oceanographic Laboratory)
Ship RRS Charles Darwin

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: CD173_CTD_CTD076

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 IdentifierData CategoryStart date/timeStart positionCruise
1352237Water sample data2005-07-29 07:06:0049.86374 N, 7.95276 WRRS Charles Darwin CD173
2081562Water sample data2005-07-29 07:06:0049.86374 N, 7.95276 WRRS Charles Darwin CD173