Metadata Report for BODC Series Reference Number 1736198

• 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

RRS Discovery DY033 surface hydrography quality control report

General comments

The non-toxic, pumped seawater supply was switched on at 20:26 on 11/07/2015 at the start of the cruise, and was turned off at 12:00 on 02/08/2015, towards the end of the cruise; all housing measurements recorded outside this time span were flagged.

The originator noted that the flow rate needed frequent adjustment throughout the cruise, and the data that had been compromised as a result were removed. BODC proceeded to flag the suspicious housing data that had been left unflagged at these times.

The underway system was switched off for cleaning on several occasions throughout the cruise. BODC flagged the affected housing parameters that had been left unflagged by the originator during these periods.

Fluorescence and chlorophyll

BODC noted that the average chlorophyll and fluorescence measurements experienced a drop to lower values following the reported cleaning of the underway pumped system at 08:00 on 29/07/2015.

Raw transmittance, transmission and beam attenuation

The originator recommends to treat transmissometer derived data with caution, as the instrument output was severely affected by the frequent presence of trapped bubbles throughout the cruise. BODC noticed several instances in which enhanced noise in the data may either represent natural variability or result from bubbles in the system, and no flags were thus applied; one such example was recorded on 14/07/2015 between 09:40 and 10:00. On the other hand, more isolated cases of drops in the signal were flagged.

BODC noticed a drift in transmissometer derived data on at least three occasions, shortly prior to the time at which the underway system was switched off for cleaning: on 26/07/2015 from 16:08, on 29/07/2015 from 08:24, and on 01/08/2015 from 12:22. These drifts likely result from pressure losses, which were reported to take place frequently during the cruise. Please treat the reported data with caution.

Housing temperature, conductivity and salinity

TSG parameters seemed to drift to adjustment levels for a short time period after the underway system had been switched on. BODC flagged as suspect such drifts between 20:26 and 20:34 on 11/07/2016, and between 08:56 and 09:12 on 29/07.

Regular positive spikes in TSG parameters were flagged from 25/07/2015 at 08:41 until the end of the cruise. These may result from the underway system cleaning operations.

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

SeaBird Digital Oceanographic Thermometer SBE38

The SBE38 is an ultra-stable thermistor that can be integrated as a remote temperature sensor with an SBE21 Thermosalinograph or an SBE 45 Micro TSG, or as a secondary temperature sensor with an SBE 16 plus, 16plus-IM, 16plus V2, 16plus-IM V2 or 19plus V2 SEACAT CTD.

Temperature is determined by applying an AC excitation to reference resistances and an ultra-stable aged thermistor. The reference resistor is a hermetically sealed VISHAY. AC excitation and ratiometric comparison using a common processing channel removes measurement errors due to parasitic thermocouples, offset voltages, leakage currents and gain errors.

The SBE38 can operate in polled sampling, where it takes one sample and transmits the data, or in continuous sampling.

Specifications

Further details can be found in the manufacturer's specification sheet.

WET Labs WETStar Fluorometers

WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.

Specifications

By model:

All models:

Further details can be found in the manufacturer's specification sheet, and in the instrument manual.

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.

Specifications

Further details are available in the manufacturer's specification sheet or user guide.

RRS Discovery DY033 surface hydrographic instrumentation

The sea surface hydrographical suite of sensors was fed by the pumped-seawater, non-toxic supply. The seawater intake was located approximately 6 m below the sea surface.

The following surface hydrology sensors were fitted:

SeaBird MicroTSG Thermosalinograph SBE 45

The SBE45 MicroTSG is an externally powered instrument designed for shipboard measurement of temperature and conductivity of pumped near-surface water samples. The instrument can also compute salinity and sound velocity internally.

The MicroTSG comprises a platinum-electrode glass conductivity cell and a stable, pressure-protected thermistor temperature sensor. It also contains an RS-232 port for appending the output of a remote temperature sensor, allowing for direct measurement of sea surface temperature.

The instrument can operate in Polled, Autonomous and Serial Line Sync sampling modes:

• Polled sampling: the instrument takes one sample on command
• Autonomous sampling: the instrument samples at preprogrammed intervals and does not enter quiescence (sleep) state between samples
• Serial Line Sync: a pulse on the serial line causes the instrument to wake up, sample and re-enter quiescent state automatically

Specifications

Further details can be found in the manufacturer's specification sheet.

RRS Discovery DY033 surface hydrography data processing procedures

Originator's Data Processing

The data were logged by the TECHSAS (TECHnical and Scientific sensors Acquisition System) system into NetCDF, pseudo-TECHSAS ascii and UKORS RVS Level-C format files. All subsequent processing was carried out using internally developed Matlab routines.

The data were submitted to BODC in ascii format for post-cruise processing and data banking.

Sea surface temperature (SBE38), housing temperature and salinity (SBE45)

The daily pseudo-TECHSAS ascii files from the sbe45 data stream were reformatted and appended. The data were then filtered of noise, by applying a moving average window of 60 seconds. All data points outside two standard deviations of the filtering average were removed.

Fluorescence, Chlorophyll-a, transmission and beam attenuation

The daily pseudo-TECHSAS ascii files were reformatted, and manufacturers calibrations applied to each file before being appended. Suspect data were then removed, and a moving average filters with a window of 120 seconds were applied. All data points outside 1.5 standard deviations of the filtering average were removed.

The following manufacturer's calibration was applied to fluorescence data to derive chlorophyll-a concentration:

Which includes the raw chlorophyll fluorescence data (raw), the clean water output coefficient (a) = 0.068 V, the scale factor (b) = 5.5 µg L^-1V^-1. Note: 1 µg L^-1 = 1 mg m^-3.

No air and dark calibration values were measured on the ship, therefore the manufacturer's calibration equation including the factory's readings only was used to derive light transmission (%) from raw transmittance voltage outputs:

Which includes the raw transmittance data (raw), the manufacturer's dark voltage reading (Vdark) = 0.058 V, and the manufacturer's voltage output in pure water (Vref) = 4.623 V.

The following manufacturer's equation was applied to derive beam attenuation from transmission values:

Which includes the path length (a) = 0.25 m, and the decimal transmission (Tr) = transmission (%) / 100.

For more detailed information on the Originator's underway data processing, please see the cruise report, p27-38.

Files delivered to BODC

Note: each file was split in two by the originator due to storage problems linked to file size.

BODC Data Processing

Reformatting

Underway data files were reformatted to NetCDF using BODC standard data banking procedures, and merged into a single file using time as the primary linking key. The time span of the reformatted file is 11/07/2015 16:43:42 to 02/08/2015 13:40:12, with a sampling interval of 30 seconds.

The following tables show how the variables within the files were mapped to appropriate BODC parameter codes:

DY033_OPTF_master_filt_110715_200715, DY033_OPTF_master_filt_210715_020815

DY033_OPTT_master_filt_110715_200715, DY033_OPTT_master_filt_210715_020815

DY033_TSG_master_filt_110715_200715, DY033_TSG_master_filt_210715_020815

Screening

All reformatted data were inspected on a graphics workstation, and any spikes or dubious data were flagged. The workstation software also allowed comparative screening checks between channels, carried out by overlaying data channels.

Data processing, correction and calibration

Salinity

Salinity was computed from housing temperature and conductivity using the UNESCO 1978 Practical Salinity Scale (Fofonoff and Millard, 1982), and calibrated against independent bottle salinity samples. Underway salinity data were extracted at the time of collection of bottle salinity data using BODC standard procedures. Of the 72 discrete underway salinity samples collected during the cruise, 19 were excluded from the calculation of the calibration equations. This is due either to: a) a flagged matching thermosalinograph data cycle; b) a flagged bottle salinity data value following BODC assessment of Salinometer output data; c) outliers revealed from regression analysis.

Three calibration equations had to be applied to separate portions of the data, due to noticeably different trends and average offsets affecting different data collection periods. This inconsistency may be explained by a change in instrument outputs following underway system cleaning operations, as well as by offsets possibly introduced to salinity bottle data processed in batches by different people and at different times on the Salinometer.

Below are the three calibration equations applied to the original underway data over the time spans indicated. Note that the first calibration equation results from a trend in time of the difference between bottle and thermosalinograph salinity measurements.

Where 'new_salinity' is the calibrated salinity, 'old_salinity' is the thermosalinograph salinity, and 'day' is the decimal day of the year.

Sea surface temperature (SST)

SST was calibrated against the primary CTD temperature sensor. CTD temperature (interpolated to 6 m depth) and corresponding SST data values were extracted using standard BODC procedures. Sixteen out of a total of eighty-eight CTD and SBE38 temperature measurements matching in time were excluded from the calculation of the calibration equation, as they resulted to be outliers from regression analysis. No significant trend of temperature offset (CTD - SBE38) with time was found, therefore the average offset was used to correct the underway sea surface temperature measurement:

Where 'new_temperature' is the calibrated underway raw inlet temperature, 'old_temperature' is the raw inlet underway temperature.

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.

Background

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.

Participants

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.

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.

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

Cruise

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:

SeaDataNet Quality Control Flags

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