Metadata Report for BODC Series Reference Number 2112857

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 Category

Water sample data

Instrument Type

Name	Categories
Niskin bottle	discrete water samplers
Becton Dickinson FACSort Flow Cytometer	flow cytometers

Instrument Mounting

lowered unmanned submersible

Originating Country

United Kingdom

Originator

Dr Glen Tarran

Originating Organization

Plymouth Marine Laboratory

Processing Status

banked

Online delivery of data

Download available - Ocean Data View (ODV) format

Project(s)

Oceans 2025 Theme 10 SO1:AMT

Data Identifiers

Originator's Identifier	JC079_CTD_AFCX_104:CTD56
BODC Series Reference	2112857

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm)	2012-11-10 05:03
End Time (yyyy-mm-dd hh:mm)	-
Nominal Cycle Interval	-

Spatial Co-ordinates

Latitude	25.74984 S ( 25° 45.0' S )
Longitude	24.98978 W ( 24° 59.4' W )
Positional Uncertainty	0.05 to 0.1 n.miles
Minimum Sensor or Sampling Depth	1.5 m
Maximum Sensor or Sampling Depth	200.3 m
Minimum Sensor or Sampling Height	4377.5 m
Maximum Sensor or Sampling Height	4576.3 m
Sea Floor Depth	4577.8 m
Sea Floor Depth Source	PEVENT
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

Parameters

BODC CODE	Rank	Units	Title
ADEPZZ01	1	Metres	Depth (spatial coordinate) relative to water surface in the water body
BOTTFLAG	1	Not applicable	Sampling process quality flag (BODC C22)
FIRSEQID	1	Dimensionless	Bottle firing sequence number
J79A0596	1	Number per millilitre	Abundance of Cryptophyceae (ITIS: 10598: WoRMS 17639) per unit volume of the water body by flow cytometry
P490A00Z	1	Number per millilitre	Abundance of Prymnesiophyceae (ITIS: 2135: WoRMS 115057) [Subgroup: coccolithophores] per unit volume of the water body by flow cytometry
P700A90Z	1	Number per millilitre	Abundance of Synechococcus (ITIS: 773: WoRMS 160572) per unit volume of the water body by flow cytometry
P701A90Z	1	Number per millilitre	Abundance of Prochlorococcus (ITIS: 610076: WoRMS 345515) per unit volume of the water body by flow cytometry
PYEUA00A	1	Number per millilitre	Abundance of picoeukaryotic cells per unit volume of the water body by flow cytometry
ROSPOSID	1	Dimensionless	Bottle rosette position identifier
SAMPRFNM	1	Dimensionless	Sample reference number
X726A86B	1	Number per millilitre	Abundance of nanoeukaryotic cells [Size: 2-12um] per unit volume of the water body by flow cytometry

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
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 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.

Abundance of microbial phytoplankton through the water column by analytical flow cytometry (AFC) analysis of samples collected from CTD casts during AMT22 (JC079)

Originator's Protocol for Data Acquisition and Analysis

These data originate from analyses on fresh seawater samples from 200 m to the surface, collected from CTD casts during the cruise. Samples were collected in clean 250 mL polycarbonate bottles from the predawn and solar noon CTD casts and were stored in a refrigerator then 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 eukaryote phytoplankton, based on their light scattering and autofluorescence properties. Data were saved in listmode format and analysed onboard during the cruise.

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 PML130200. Sample metadata (Cruise, station, type, CTD, time on deck, latitude, longitude, Niskin bottle number and depth) were checked against information held in the database. There were some discrepancies between the depths provided by the originator for several Niskin bottles, and those in the database and CTD logsheets. These discrepancies were resolved with the originator prior to loading in to the database. All individual samples were matched to metadata in the database through rosette sampling bottle 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 spp.	cell abundance ml^-1	Abundance of Synechococcus spp. (ITIS: 773: WoRMS 160572) per unit volume of the water body by automated flow cytometry	P700A90Z	cell abundance ml^-1	n/a
Prochlorococcus spp.	cell abundance ml^-1	Abundance of Prochlorococcus spp. (ITIS: 610076: WoRMS 345515) per unit volume of the water body by automated flow cytometry	P701A90Z	cell abundance ml^-1	n/a
Pico-eukaryote phytoplankton (<2 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	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	cell abundance ml^-1	Abundance of Coccosphaerales (ITIS: 610061: WoRMS 115059) [Subgroup: coccolithophore] per unit volume of the water body by automated flow cytometry	P490A00Z	cell abundance ml^-1	n/a
Nanoeukaryote phytoplankton (approx. 2-12 µm)	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

Oceans 2025 Theme 10, Sustained Observation Activity 1: The Atlantic Meridional Transect (AMT)

The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.

The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:

give early warning of any fundamental change in Atlantic ecosystem functionng
improve forecasts of the future ocean state and associated socio-economic impacts
provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.

The specific objectives are:

To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands
To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems
To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases

The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).

More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10

Weblink: http://www.oceans2025.org/

Data Activity or Cruise Information

Data Activity

Start Date (yyyy-mm-dd)	2012-11-10
End Date (yyyy-mm-dd)	2012-11-10
Organization Undertaking Activity	Plymouth Marine Laboratory
Country of Organization	United Kingdom
Originator's Data Activity Identifier	JC079_CTD_CTD56
Platform Category	lowered unmanned submersible

BODC Sample Metadata Report for JC079_CTD_CTD56

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

678104	20.00	1	1	503.10	504.40	499.10	Niskin bottle	No problem reported
678107	20.00	2	2	302.40	303.20	299.90	Niskin bottle	No problem reported
678110	20.00	3	3	201.60	203.30	200.30	Niskin bottle	No problem reported
678113	20.00	4	4	183.30	183.70	181.50	Niskin bottle	No problem reported
678116	20.00	5	5	183.30	184.00	181.60	Niskin bottle	No problem reported
678119	20.00	6	6	159.30	160.10	157.90	Niskin bottle	No problem reported
678122	20.00	7	7	159.10	160.10	157.80	Niskin bottle	No problem reported
678125	20.00	8	8	159.00	160.30	157.80	Niskin bottle	No problem reported
678128	20.00	9	9	140.90	142.00	139.70	Niskin bottle	No problem reported
678131	20.00	10	10	120.70	122.80	120.20	Niskin bottle	No problem reported
678134	20.00	11	11	121.60	122.60	120.50	Niskin bottle	No problem reported
678137	20.00	12	12	105.90	106.50	104.70	Niskin bottle	No problem reported
678140	20.00	13	13	92.50	93.90	91.80	Niskin bottle	No problem reported
678143	20.00	14	14	92.30	93.80	91.70	Niskin bottle	No problem reported
678146	20.00	15	15	71.00	71.30	69.90	Niskin bottle	No problem reported
678149	20.00	16	16	52.60	53.00	51.70	Niskin bottle	No problem reported
678152	20.00	17	17	29.30	30.40	28.90	Niskin bottle	No problem reported
678155	20.00	18	18	29.30	30.10	28.80	Niskin bottle	No problem reported
678158	20.00	19	19	20.10	21.60	20.00	Niskin bottle	No problem reported
678161	20.00	20	20	20.80	21.00	20.00	Niskin bottle	No problem reported
678164	20.00	21	21	16.40	17.20	15.90	Niskin bottle	No problem reported
678167	20.00	22	22	4.90	5.20	4.30	Niskin bottle	No problem reported
678170	20.00	23	23	1.80	3.10	1.70	Niskin bottle	No problem reported
678173	20.00	24	24	1.60	3.00	1.50	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	JC079 (AMT22)
Departure Date	2012-10-10
Arrival Date	2012-11-24
Principal Scientist(s)	Glen A Tarran (Plymouth Marine Laboratory)
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