Metadata Report for BODC Series Reference Number 1349414
Definition of BOTTFLAG
|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
No Problem Report Found in the Database
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."
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.
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.
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 have a capacity between 1.7 and 30 L, while Lever Action bottles have a capacity between 1.7 and 12 L. Reversing thermometers may be attached to a spring-loaded disk that rotates through 180° on bottle closure.
RRS Discovery Cruise D321 (D321A) Discrete inorganic nutrient (nitrate, silicate and phosphate) concentrations from CTD OTE bottles
Content Of Data Series
|Parameter||Units||BODC Parameter code||No. of Samples||Comments|
|Inorganic nitrate||µmol l-1||NTRZAATX||1453a||Nitrate = nitrate+nitrite|
|Inorganic silicate||µmol l-1||SLCAAATX||1453a|
|Inorganic phosphate||µmol l-1||PHOSAATX||1453a|
aPlease note: 1502 CTD samples were reported to have been taken in the cruise report (p201), however, a number of these were duplicate/triplicate analyses made from the same CTD OTE niskin bottle. Replicate analyses were subsequently averaged during BODC data processing (see BODC processing) resulting in a lower number of CTD samples.
Originator's Data Acquisition and Processing
Inorganic nutrient samples were taken from 92 CTD casts throughout cruise D321A. Of these, 7 CTD casts were taken as part of the Extended Ellet Line, 27 as part of CTD survey 1, 32 were part of CTD survey 2, 19 of SeaSoar survey 1 and 9 were taken as part of SeaSoar survey 2a. Samples were taken from the majority of depths from each cast.
aThis totals 94 CTD casts, however site C1A3 (part of CTD survey 1) was also site IB12 (part of the Extended Ellet Line). Site C1A3/IB12 was visited twice during the cruise (stations 16204A and 16204B), therefore only 92 CTD casts were actually sampled for inorganic nutrients.
Materials and Methodology
Water for analysis was collected from depth using two different CTD systems. A 'standard' stainless steel unit (A) for physics and general sampling, and a titanium unit (B) for trace metal and productivity sampling. The stainless steel unit comprised of a SBE32 Seabird carousel (S/N 32-37898-0518) fitted with a 911+ Seabird CTD (S/N 0636) and twenty four, 20 litre OTE niskin bottles. The titanium unit comprised of a SBE32 Seabird carousel (S/N 32-34173-0493) fitted with a 911+ Seabird CTD (S/N 0637) and twenty four, 10 litre OTE trace metal niskin bottles. Nutrient concentration was determined using a Scalar Sanplus Autoanalyser following the methods described by Kirkwood (1996) (1) with the exception that the pump rates through the phosphate line are increased by a factor of 1.5. Further information on methodology and the performance of the autoanalyser can be found from p201 of the cruise report.
Data processing was undertaken using Skalar propriety software and was done within 72 hours of the run being finished. The limits of detection were defined as twice the level of background noise averaged out over the course of the cruise. The background noise levels in digital units (the arbitrary unit used by the skalar autoanalyser software) were measured at the start and at the end of 10 of the 37 runs performed during the cruise. These were then averaged to give an averaged background noise level for the whole cruise. This number was then multiplied by 2. The concentration per digital unit was taken from the calculations used to determine the blank nutrient level in the artificial seawater matrix. Multiplying this number by the concentration per unit gives the limit of detection as follows.
|Chemistry||Limit of Detection (µmol l-1)|
b The limit of detection for nitrate and silicate can be taken as 0.1 µmol l-1 as visual inspection of the peaks clearly indicates that peaks down to this level are attributable to samples rather than fluctuations in the noise. This is because of the length of time over which the samples are analysed.
The errors for the nutrient analysis were worked out using a duplicate set of samples run during each analysis. A drift sample was included in each analysis to indicate if the baseline moves over the course of the run. These drift samples are included in pairs, i.e. 2 drift samples from the same batch are run one after the other. The first pair of these drifts was used as the duplicate samples in each of the 18 analyses. The error for the each analysis was determined using equation (1) where A is the largest of the duplicates and B is the smallest. These errors were then averaged over the cruise to obtain the error for the whole cruise.
Table of errors:
|Chemistry||Error in data (%)|
BODC Data Processing
Data arrived at BODC in a Microsoft Excel spreadsheet containing all the samples taken during the cruise. The spreadsheet was initially converted into a Comma Separated Values format file (.csv) and appropriate BODC parameter codes were subsequently assigned. The following table shows how the variables supplied were mapped to BODC parameter codes.
|Originator's Parameter||Originator's Units||Parameter description||BODC Parameter code||BODC Units||Comments|
|N||µmol l-1||Inorganic nitrate via segmented flow autoanalyser and colourimetric detection||NTRZAATX||µmol l-1||Nitrate=nitrate+nitrite|
|Si||µmol l-1||Inorganic silicate via segmented flow autoanalyser and colourimetric detection||SLCAAATX||µmol l-1|
|P||µmol l-1||Inorganic phosphate via segmented flow autoanalyser and colourimetric detection||PHOSAATX||µmol l-1|
Data below the detction limit specified by the data originator were flagged '<'. Duplicate and triplicate analyses from the same CTD bottle were averaged. The averaged products were subsequently flagged 'M' if the error (%) between replicates was high and the precursor data values were clearly above the detection limits. Data points were dropped from the calculation where replicates contained a suspect data point or data below the detection limit. In cases where replicate values differed greatly, a suspect data point could be determined by comparison to measurements from other CTD niskin bottles fired at similar depths. The overall result was a .csv file containing only one phosphate, nitrate and silicate measurement per CTD OTE bottle sampled.
The data were loaded from the .csv file into an Oracle database where measurements were linked to corresponding depths through the CTD rosette bottle no. (supplied by the originator)and the CTD rosette bottle no. obtained from electronic Seabird CTD logs (which contained accurate pressure readings for each bottle fired). This was achieved via BODC unique bottle identifiers (IBTTLE) which were already associated with each CTD OTE bottle fired during the cruise. Depth (m) was calculated from the average pressure and latitidue using BODC function DEPSET.
Two rosette bottle numbers in the originator's file did not match entries in the CTD electronic logs. For cast 16202A, the originator collected from bottle 24 whereas only bottles 1-23 were fired according to the CTD logs. Checks were made against the written Seabird CTD logs which also reported that bottles 1-23 were fired. These sample values were similar in value to the other surface samples (7-12 m, bottles 23-18) suggesting it is from the surface. This was especially so for nitrate where bottle 24 = 1.76 µmol l-1 and bottles 23-18 were 1.34 - 1.77 µmol l-1. This could suggest it was a replicate from one of the other surface bottles. Alternatively, bottle 24 could have been fired by accident. Similarly for cast 16203A, the originator collected from bottle 24 whereas only bottles 1-23 were fired acording to the electronic CTD logs. Likewise, only 23 bottles were reported in the Seabird hand-written CTD logs. However, these sample values (0.26, 0.06 and 0.01 µmol l-1 N, Si, P respectively) were much lower than other sample values measured for the cast (N = 1.64-18.34, Si = 0.19-11.82, P = 0.11-1.23 µmol l-1). This could suggest that a bottle was fired higher up in the water column. Alternatively, it could just be a bad replicate from one of the other surface bottles.
In order to resolve the issue, checks were made on preceding and subsequent casts. Bottle number 24 was fired on subsequent and preceding stainless steel casts suggesting there was not a problem with this bottle. No further information about bottle 24 could be found in the cruise report or technical notes. The pressure channel from the corresponding .cnv files were plotted. By viewing changes in pressure during cast 16203A, it could be seen that the CTD was held at ~7.5 db for 2 min then at ~0.7 db for around 5 min before the file ended. Similar observations were found for cast 16202A. This did not resolve the problem as a bottle could have been fired at 0.7 db (although this is likely the holding depth before lifting the CTD out of the water).
In a final attempt, the originator was contacted to see if he had any further information about these samples. He indicated that the label '24' was likely a mistake in both cases. For cast 16202A, the originator suggested that bottle 24 was a replicate analysis of the sample withdrawn from bottle 23. For cast 16203A, the originator suggested that bottle 24 was a blank analyses based on the low concentrations measured. Consequently, he suggested it was best to drop both of these samples from the dataset. Therefore, both measurements were dropped from the database.
Discrepancies between the originator's written depth (where supplied) and depth independently loaded in the database were checked. There was only one major discrepancy. For cast 16212B (rosette bottle 8) the depth supplied was 33 m whereas the rosette bottle depth was ~28 m. Despite this, the data looked plausible for a measurement from 28 m and not 33 m. This was determined by comparison to bottle 16 also fired at ~28 m and measurements from ~28 m made on the 'A' cast taken at the same station.
The data were then visually checked in Microsoft Excel by plotting the depth profile of each cast. Flags were added as appropriate. Absent data were updated to the absent data value '-1' and flagged. According to the originator, absent data were samples that were lost during analysis. The samples would have been taken but there may have been an error during analysis that affected these samples, e.g. a bubble getting in the system and stick in the flowcell and so giving erroneous results.
Data Quality Report
(1) Kirkwood, D (1996) Nutrients: Practical notes on their determination in sea water. ICES techniques in marine environmental sciences. No. 17, 25pp.
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.
|Start Date (yyyy-mm-dd)||2007-08-06|
|End Date (yyyy-mm-dd)||2007-08-06|
|Organization Undertaking Activity||National Oceanography Centre, Southampton|
|Country of Organization||United Kingdom|
|Originator's Data Activity Identifier||D321A_CTD_16234A|
|Platform Category||lowered unmanned submersible|
BODC Sample Metadata Report for D321A_CTD_16234A
|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|
|179020||20.00||1||1||810.80||811.40||801.90||Niskin bottle||Bottle misfire||Bottle misfire reported|
|179021||20.00||2||2||608.70||609.70||602.60||Niskin bottle||No problem reported|
|179022||20.00||3||3||406.80||407.10||402.70||Niskin bottle||No problem reported|
|179023||20.00||4||4||204.70||205.30||203.00||Niskin bottle||No problem reported|
|179024||20.00||5||5||129.00||129.30||127.90||Niskin bottle||Bottle misfire||Bottle misfire reported|
|179025||20.00||6||6||78.30||78.70||77.80||Niskin bottle||No problem reported|
|179026||20.00||7||7||49.80||50.40||49.60||Niskin bottle||No problem reported|
|179027||20.00||8||8||34.50||34.90||34.40||Niskin bottle||No problem reported|
|179028||20.00||9||9||29.20||30.00||29.30||Niskin bottle||No problem reported|
|179029||20.00||10||10||22.40||22.90||22.40||Niskin bottle||No problem reported|
|179030||20.00||11||11||10.90||11.40||11.00||Niskin bottle||No problem reported|
|179031||20.00||12||12||5.10||5.70||5.30||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.
|Cruise Name||D321 (D321A)|
|Principal Scientist(s)||John T Allen (National Oceanography Centre, Southampton)|
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|<||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.)|
|E||End of CTD Down/Up Cast|
|G||Non-taxonomic biological characteristic uncertainty|
|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|
|O||Improbable value - user quality control|
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|0||no quality control|
|2||probably good value|
|3||probably bad value|
|6||value below detection|
|7||value in excess|
|A||value phenomenon uncertain|
|Q||value below limit of quantification|