Metadata Report for BODC Series Reference Number 2137709

• 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

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

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.

Pico-plankton, nano-plankton and heterotrophic bacteria abundance from Analytical Flow Cytometry (AFC) analysis of samples collected from CTD casts during DY018 (SSB)

Originator's Protocol for Data Acquisition and Analysis

Samples for enumeration of plankton, approx. < 20 µm were collected CTD Niskin bottles into clean 125 mL polycarbonate bottles. Subsamples were then pipetted into 2 mL microcentrifuge tubes and fixed with glutaraldehyde (50%, TEM grade, 1% final concentration) within half an hour of surfacing. Samples were left to fix in a refrigerator for between 1-12 h, and then stored at -80° C. Samples were analysed ashore as follows. For phytoplankton, samples were thawed at room temperature and then analysed using a Becton Dickinson FACSort flow cytometer to characterise and enumerate Synechococcus sp. (cyanobacteria) and    pico-  and eucaryote phytoplankton, based on their light scattering and autofluorescence properties. Samples for bacteria and heterotrophic nanoflagellates were thawed and then stained with the DNA stain SYBR Green I (Invitrogen) in order to separate particles in suspension based on DNA content and light scattering properties. Further information on the protocol can be found in the following link.

Instrumentation Description

Becton Dickinson FACSort flow cytometer

BODC Data Processing Procedures

Data were submitted by originator via email in an Excel spreadsheet. 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;

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

Shelf Sea Biogeochemistry (SSB) Programme Work Package 1: CaNDyFloSS

Carbon and Nutrient Dynamics and Fluxes over Shelf Systems (CaNDyFloSS) is a £2.76 million component of the Natural Environment Research Council (NERC) Shelf Sea Biogeochemistry (SSB) research programme, running from 2013 to 2017. It is jointly funded by NERC and the Department for Environment, Food and Rural Affairs (DEFRA). The aim of the research is 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.

Background

Shelf seas are the primary regions of human marine resource exploitation, including both renewable and fossil fuel energy sources, recreation, trade and food production. They provide 90% of global fish catches which form an important source of food to much of the global population. They also play an important role in the ecosystem services provided by the oceans as a whole, in particular in storing carbon away from the atmosphere.

Physical and biochemical processes in shelf seas influence the removal of CO₂ from the atmosphere and the subsequent storage of carbon in the deep ocean. Biological growth draws carbon out of the water, which is then replaced by carbon in CO₂ from the atmosphere. In the shelf seas this growth is supported by terrestrial and open ocean sources of nutrients, implying intimate roles for both the terrestrial biosphere and the open ocean environment in regulating shelf sea climate services. The oceans can also be a major source or sink for other greenhouse gases, including nitrous oxide (N₂O), with the shallow shelf sea thought to play a key role.

The spatial extent of the submerged continental shelves varies greatly. The NW European shelf sea is one of the largest and hence is likely to play a significant role in marine biogeochemical cycling, alongside providing a useful model for other systems. However, even in this relatively well studied region, there is a lack of detailed understanding of the principal controls on the cycling of carbon and the major nutrient elements, nitrogen, phosphorus and silicon. Consequently it is also difficult to predict how the cycling of these elements and hence the carbon removal they support may be altered by ongoing and potential future global change. This work package aims to address these uncertainties through a comprehensive study of the cycling of the major nutrients and carbon throughout the water column over the NW European shelf sea system.

Further details are available on the SSB website.

Participants

9 different organisations are directly involved in research for SSB Work Package 1. These institutions are

• Centre for Environment, Fisheries and Aquaculture Science (Cefas)
• 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 Liverpool
• University of Southampton

In addition, there are third party institutions carrying out sampling work for SSB Work Package 1, 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)

Objectives

Two overarching objectives are defined for this Work Package.

• Objective 1: Estimate the size of the continental shelf carbon pump over the whole north-west European shelf.
  This will consist of two principal activities. (1) Over a 12 month period, observations of air-sea CO₂ fluxes will be made to provide a synoptic estimate of the magnitude of carbon update by the whole shelf system. (2) Concentrations of carbon (C), nitrogen (N), phosphate (P) and silicate (Si) will be estimated in water flowing on and off the shelf. These estimates will be coupled to estimates of flow and dispersion along the shelf edge, through collaboration with the NERC Fluxes across Sloping Topography of the North East Atlantic (FASTNEt) programme to allow an observational estimate of the net off-shelf transport of C, N, P and Si.

• Objective 2: Determine the relative importance of external nutrient sources and internal biogeochemical cycling in maintaining the continental shelf pump.
  Estimates of the flux of nutrients and carbon generated in Objective 1 will be used to determine the estimation of any excess of on-shelf nutrient supply, relative to that of carbon. Work Package 1 will then quantify the processes which govern internal biogeochemical cycling by measuring the uptake ratios of N, P, Si and C into phytoplankton and the element and energy balance of organic matter production by autotrophs. Potential modifications to the relative concentrations and uptake of C, N, P and Si in the thermocline and sediment food webs will also be assessed, as will the relative importance of microbial and zooplankton turnover in controlling C, N, P and Si.

Fieldwork and data collection

Data for Objective 1 will be provided using pCO₂ systems aboard third party vessels and ferry boxes, along with measurements made through the FASTNEt programme and through the Work Package 1 process cruises detailed below. The third party cruises will be undertaken by Cefas, MI, MSS, University of Bangor and AFBI, spanning the shelf seas and shelf-edges around the United Kingdom and the Republic of Ireland.

The Work Package 1 process cruises will provide data for Objective 1 and Objective 2 and are listed in the table below. The study area is the marine shelf (and shelf-edge) of the Celtic Sea. Work will be carried out 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.

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

Data Activity or Cruise Information

Data Activity

No Document Information Held for the Series

Related Data Activity activities are detailed in Appendix 1

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

Fixed Station Information

Western Channel Observatory station E1

The Western Channel Observatory (WCO) is situated in the Western English Channel and comprises of sustained long-term observations at a number of stations.

Station E1 is located south-west of Plymouth at 50°2.00'N, 4°22.00'W.

More information can be found on the Western Channel Observatory website.

Related Fixed Station activities are detailed in Appendix 2

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Appendix 1: DY018_UCCTD_261

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.

Appendix 2: Western Channel Observatory E1

Related series for this Fixed Station 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.