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Metadata Report for BODC Series Reference Number 2103909

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 Mr Malcolm Woodward
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Shelf Sea Biogeochemistry (SSB)

Data Identifiers

Originator's Identifier JC105_CTD_NUTS_62:040
BODC Series Reference 2103909

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2014-06-20 16:49
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval -

Spatial Co-ordinates

Latitude 48.37695 N ( 48° 22.6' N )
Longitude 9.56822 W ( 9° 34.1' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 11.9 m
Maximum Sensor or Sampling Depth 499.4 m
Minimum Sensor or Sampling Height 26.4 m
Maximum Sensor or Sampling Height 513.9 m
Sea Floor Depth 525.8 m
Sea Floor Depth Source BUDS
Sensor or Sampling Distribution Unspecified -
Sensor or Sampling Depth Datum Unspecified -
Sea Floor Depth Datum Unspecified -


BODC CODERankUnitsTitle
ADEPZZ011MetresDepth (spatial coordinate) relative to water surface in the water body
AMONAAD51Micromoles per litreConcentration of ammonium {NH4+ CAS 14798-03-9} per unit volume of the water body [dissolved plus reactive particulate <0.2um phase] by filtration and colorimetric autoanalysis
BOTTFLAG1Not applicableSampling process quality flag (BODC C22)
FIRSEQID1DimensionlessBottle firing sequence number
NTRIAAD51Micromoles per litreConcentration of nitrite {NO2- CAS 14797-65-0} per unit volume of the water body [dissolved plus reactive particulate <0.2um phase] by filtration and colorimetric autoanalysis
NTRZAAD51Micromoles per litreConcentration of nitrate+nitrite {NO3+NO2} per unit volume of the water body [dissolved plus reactive particulate <0.2um phase] by filtration and colorimetric autoanalysis
PHOSAAD51Micromoles per litreConcentration of phosphate {PO43- CAS 14265-44-2} per unit volume of the water body [dissolved plus reactive particulate <0.2um phase] by filtration and colorimetric autoanalysis
ROSPOSID1DimensionlessBottle rosette position identifier
SAMPRFNM1DimensionlessSample reference number
SLCAAAD51Micromoles per litreConcentration of silicate {SiO44- CAS 17181-37-2} per unit volume of the water body [dissolved plus reactive particulate <0.2um phase] by filtration and colorimetric autoanalysis

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

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.


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.

Discrete inorganic nutrient samples from CTD bottles and underway supply during RRS James Cook cruise JC105

Originator's Protocol for Data Acquisition and Analysis

Sampling strategy

Discrete samples were collected from 21 CTD casts carried out with the stainless steel CTD package that was fitted with a Sea-Bird SBE 911plus underwater CTD and deck unit (s/n 09P-46253-0869 and 11P-22559-0532, respectively), a Sea-Bird SBE 32, twenty-four way carousel (s/n 32-19817-0243) and 24 x 10 L Ocean Test Equipment (OTE) niskin bottles. Samples were withdrawn from 2 to 6 depths, spanning the entire water column. Six samples were also collected from the non-toxic, pumped seawater supply (intake approximately 5.5 m below sea level). The water sample was transferred from either the CTD or underway supply to 60 ml HDPE Nalgene bottles (acid washed and cleaned) using silicone tubing and acrodisc filter (0.2 µm), with the sample bottle being washed three times before the final sample was taken. The sample was immediately stored at -20 °C. Samples were defrosted at room temperature prior to analysis. Gloves and other clean handling protocols were adopted following the GO-SHIP protocols.

Sample Analysis

The inorganic nutrient samples were analysed using a 5 channel (nitrate, nitrite, phosphate, silicate and ammonium) Bran and Luebbe AAIII segmented flow, colorimetric, autoanalyser. The data were calibrated against home nutrient standards and then compared against Certified Nutrient Reference Materials, from KANSO Technos, Japan.

The analytical chemical methodologies used were according to Brewer and Riley (1965) for nitrate, Grasshoff (1976) for nitrite, Kirkwood (1989) for phosphate and silicate, and Mantoura and Woodward (1983) for ammonium. The detection limits were 0.01 µmol l-1 (nitrite), 0.02 µmol l-1 (nitrate+nitrite), 0.03 µmol l-1 (ammonium) and 0.02 µmol l-1(phosphate). There was no limit for silicate.


Kirkwood D., 1989. Simultaneous determination of selected nutrients in seawater. ICES CM 1989/C:29.

Brewer and Riley, 1965. The automatic determination of nitrate in sea water. Deep Sea Research, 12, 765-72.

Grasshoff K., 1976. Methods of seawater analysis. Verlag Chemie, Weiheim and New York, 317pp.

Mantoura R.F.C and Woodward E.M.S, 1983. Optimization of the indophenol blue method for the automated determination of ammonia in estuarine waters. Estuarine Coastal and Shelf Science, 17, 219-24.

BODC Data Processing Procedures

The data arrived at BODC in one Excel (.xlsx) file containing all the discrete inorganic nutrient samples collected from CTD bottles and underway non-toxic, pumped-seawater supply during JC105. Data received were loaded into the BODC database using established BODC data banking procedures without any further changes. Originator's variables were mapped to appropriate BODC parameter codes as follows:

Originator's Parameter Originator's Unit Description BODC Parameter Code BODC Unit
Nitrite µmol l-1 Concentration of nitrite {NO2} NTRIAAD5 µmol l-1
Nitrate+Nit µmol l-1 Concentration of nitrate+nitrite {NO3+NO2} NTRZAAD5 µmol l-1
Ammonium µmol l-1 Concentration of ammonium {NH4} AMONAAD5 µmol l-1
Silicate µmol l-1 Concentration of silicate {SiO4} SLCAAAD5 µmol l-1
Phosphate µmol l-1 Concentration of phosphate {PO4} PHOSAAD5 µmol l-1

Data Quality Report

None. (BODC assessment)

Problem Report

None. (BODC assessment)

Project Information

Shelf Sea Biogeochemistry (SSB) Programme

Shelf Sea Biogeochemistry (SSB) is a £10.5 million, six-year (2011-2017) research programme, jointly funded by the Natural Environment Research Council (NERC) and the Department for Environment, Food and Rural Affairs (DEFRA). The aim of the research is to reduce the uncertainty in our understanding of nutrient and carbon cycling within the shelf seas, and of their role in global biogeochemical cycles. SSB will also provide effective policy advice and make a significant contribution to the Living with Environmental Change programme.


The Shelf Sea Biogeochemistry research programme directly relates to the delivery of the NERC Earth system science theme and aims to provide evidence that supports a number of marine policy areas and statutory requirements, such as the Marine Strategy Framework Directive and Marine and Climate Acts.

The shelf seas are highly productive compared to the open ocean, a productivity that underpins more than 90 per cent of global fisheries. Their importance to society extends beyond food production to include issues of biodiversity, carbon cycling and storage, waste disposal, nutrient cycling, recreation and renewable energy resources.

The shelf seas have been estimated to be the most valuable biome on Earth, but they are under considerable stress, as a result of anthropogenic nutrient loading, overfishing, habitat disturbance, climate change and other impacts.

However, even within the relatively well-studied European shelf seas, fundamental biogeochemical processes are poorly understood. For example: the role of shelf seas in carbon storage; in the global cycles of key nutrients (nitrogen, phosphorus, silicon and iron); and in determining primary and secondary production, and thereby underpinning the future delivery of many other ecosystem services.

Improved knowledge of such factors is not only required by marine policymakers; it also has the potential to increase the quality and cost-effectiveness of management decisions at the local, national and international levels under conditions of climate change.

The Shelf Sea Biogeochemistry research programme will take a holistic approach to the cycling of nutrients and carbon and the controls on primary and secondary production in UK and European shelf seas, to increase understanding of these processes and their role in wider biogeochemical cycles. It will thereby significantly improve predictive marine biogeochemical and ecosystem models over a range of scales.

The scope of the programme includes exchanges with the open ocean (transport on and off the shelf to a depth of around 500m), together with cycling, storage and release processes on the shelf slope, and air-sea exchange of greenhouse gases (carbon dioxide and nitrous oxide).

Further details are available on the SSB website.


15 different organisations are directly involved in research for SSB. These institutions are

  • Centre for Environment, Fisheries and Aquaculture Science (Cefas)
  • Meteorological Office
  • National Oceanography Centre (NOC)
  • Plymouth Marine Laboratory (PML)
  • Scottish Association for Marine Science (SAMS) / Scottish Marine Institute (SMI)
  • University of Aberdeen
  • University of Bangor
  • University of East Anglia (UEA)
  • University of Edinburgh
  • University of Essex
  • University of Liverpool
  • University of Oxford
  • Plymouth University
  • University of Portsmouth
  • University of Southampton

In addition, there are third party institutions carrying out sampling work for SSB, but who are not involved in the programme itself. These are:

  • The Agri-Food and Biosciences Institute (AFBI)
  • Irish Marine Institute (MI)
  • Marine Science Scotland (MSS)

Research details

Overall, five Work Packages have been funded by the SSB programme. These are described in brief below:

  • Work Package 1: Carbon and Nutrient Dynamics and Fluxes over Shelf Systems (CaNDyFloSS).
    This work package aims to perform a comprehensive study of the cycling of nutrients and carbon throughout the water column over the whole north-west European shelf. This will allow the fluxes of nutrients and carbon between the shelf and the deep ocean and atmosphere to be quantified, establishing the role of the north-west European continental shelf in the global carbon cycle.

  • Work Package 2: Biogeochemistry, macronutrient and carbon cycling in the benthic layer.
    This work package aims are to map the sensitivity and status of seabed habitats, based on physical conditions, ecological community structure and the size and dynamics of the nitrogen and carbon pools found there. This information will be used, in conjunction with some laboratory-based work, to generate an understanding of the potential impacts on the benthic community as a result of changing environmental conditions, such as rising CO2 levels.

  • Work Package 3: The supply of iron from shelf sediments to the ocean.
    The research for this work package addresses the question of how currents, tides, weather and marine chemistry allow new iron to be transported away from the shallow shelf waters around the United Kingdom (UK), to the nearby open ocean. This will ultimately allow an improved understanding of how the transport of iron in shelf waters and shelf sediments influences phytoplankton growth in open oceans. This in turn improves the understanding of carbon dioxide uptake by phytoplankton.

  • Work Package 4: Integrative modelling for Shelf Seas Biogeochemistry.
    The aim of this work package is the development of a new shelf seas biogeochemical model system, coupled to a state of the art physical model, that is capable of predicting regional impacts of environmental change of timescales from days to decades. It is envisaged that the combination of predictive tools and new knowledge developed in this work package will underpin development and implementation of marine policy and marine forecasting systems.

  • Work Package 5: Data synthesis and management of marine and coastal carbon (DSMMAC).
    This work package is funded by Defra and is also known by the name 'Blue Carbon'. The aim is to provide a process-based, quantitative assessment of the role of UK coastal waters and shelf seas in carbon storage and release, using existing data and understanding, and also emerging results from SSB fieldwork, experiments and modelling. Particular emphasis will be given to processes that may be influenced by human activities, and hence the opportunity for management interventions to enhance carbon sequestration.

Fieldwork and data collection

The campaign consists of the core cruises in the table below, to the marine shelf (and shelf-edge) of the Celtic Sea on board the NERC research vessels RRS Discovery and RRS James Cook. These cruises will focus on the physics and biogeochemistry of the benthic and pelagic zones of the water column, primarily around four main sampling sites in this area.

Cruise identifier Research ship Cruise dates Work packages
DY008 RRS Discovery March 2014 WP 2 and WP 3
JC105 RRS James Cook June 2014 WP 1, WP 2 and WP 3
DY026 RRS Discovery August 2014 WP1, WP 2 and WP 3
DY018 RRS Discovery November - December 2014 WP 1 and WP 3
DY021 (also known as DY008b) RRS Discovery March 2015 WP 2 and WP 3
DY029 RRS Discovery April 2015 WP 1 and WP 3
DY030 RRS Discovery May 2015 WP 2 and WP 3
DY033 RRS Discovery July 2015 WP 1 and WP 3
DY034 RRS Discovery August 2015 WP 2 and WP 3

Core cruises will be supplemented by partner cruises led by Cefas, MI, MSS, Bangor University and AFBI, spanning the shelf seas and shelf-edges around United Kingdom and Republic of Ireland.

Activities will include coring, Conductivity Temperature and Depth (CTD) deployments, Acoustic Doppler Current Profilers (ADCP) surveys, moorings and wire-walker deployments, benthic lander observatories, autonomous gliders and submersible surveys, Marine Snow Catcher particulate matter analysis, plankton net hauls, in-situ sediment flume investigations and laboratory incubations with core and sea water samples.

Data Activity or Cruise Information

Data Activity

Start Date (yyyy-mm-dd) 2014-06-20
End Date (yyyy-mm-dd) 2014-06-20
Organization Undertaking ActivityNational Oceanography Centre, Liverpool
Country of OrganizationUnited Kingdom
Originator's Data Activity IdentifierJC105_CTD_040
Platform Categorylowered unmanned submersible

No Document Information Held for the Series

Related Data Activity activities are detailed in Appendix 1


Cruise Name JC105
Departure Date 2014-06-15
Arrival Date 2014-06-24
Principal Scientist(s)Jo Hopkins (National Oceanography Centre, Liverpool)
Ship RRS James Cook

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: JC105_CTD_040

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
2108152Water sample data2014-06-20 16:49:3048.37695 N, 9.56822 WRRS James Cook JC105
2143162Water sample data2014-06-20 16:49:3048.37695 N, 9.56822 WRRS James Cook JC105