Metadata Report for BODC Series Reference Number 1850955

• 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

Shelf Sea Biogeochemistry RRS James Cook Cruise JC105 underway sea surface hydrography quality control report

Quality control report

Sea surface temperature

Strong surface temperature gradients (up to 0.5 °C) were observed in the CTD temperature profiles from the cruise. Thus, the calibration of this sensor against CTD temperature should be treated with caution. (BODC and data originator assessment).

General comments

All surface hydrography data were flagged from the start of the cruise up to 15/06/2014 10:49:00 as values were considered anomalous. M flags were also applied from 23/06/2014 17:17:30 to the end of the cruise. (BODC and NMF assessment)

Transmissometer

Data arising from the transmissometer (voltage, transmittance and attenuation) were flagged for trapped bubbles that occurred sporadically throughout the cruise. In addition, one continuous period was flagged between 17/06/2014 08:06:00 - 12:22:00. (BODC assessment).

One data point in the voltage channel that was below the manufacturer blank reading (Vdark = 0.060 V) was set to the absent data value and flagged accordingly. The data point was recorded on the 23/06/2014 17:26:30. (BODC assessment).

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.

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.

Shelf Sea Biogeochemistry RRS James Cook Cruise JC105 underway sea surface hydrography instrumentation

Instrumentation

The sea surface hydrographical suite of sensors was fed by the pumped-seawater, non-toxic supply. The seawater intake was located approximately 5.5 m below the sea surface. The SBE 38 sea surface temperature sensor was located towards the hull near the seawater intake. All other sensors were located in the clean seawater laboratory on the main deck, directly above the intake pipe.

Shelf Sea Biogeochemistry RRS James Cook Cruise JC105 underway sea surface hydrography data processing procedures

Data Processing Procedures

Originator's Data Processing

All underway sensors/instruments were initially logged via the Ifremer TECHSAS (TECHnical and Scientific sensors Acquisition System) system. The data were then broadcast in UDP/IP frames via the on-board LAN. Data were broadcast in two formats: NMEA broadcasting format and XML broadcasting format. The XML broadcast was used to create TECHSAS NetCDF files while the NMEA broadcast was used to transfer data to the RVS Level-C UNIX system where it was parsed into RVS data streams (RVS format files).

Files delivered to BODC

BODC Data Processing

sbe45 and surfmet were selected for transfer into BODC format since they contained the most processed sea surface hydrography data. The TSG (salinity, housing temperature and conductivity) and sea surface temperature data were sourced from the sbe45 data stream since the same variables in surfmet may be delayed in time. The files were reformatted to NetCDF using BODC standard data banking procedures. The following table shows how variables within the file were mapped to appropriate BODC parameter codes:

sbe45

surfmet

All the reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, missing data by both setting the data to an appropriate value and setting the quality control flag.

Chlorophyll-a

The following manufacturer's calibration was applied to the fluorometer to derive chlorophyll-a concentration:

where 'a' is the raw voltage output, the scale factor (SF) = 4.8 µg V^-1 and the clean water offset (CWO) = 13.2 µg l ^-1 V ^-1 (1 µg L ^-1 = 1 mg m ^-3)

Transmittance and beam attenuation

The following manufacturer's calibration was applied to the transmissometer to derive transmittance and beam attenuation:

where M = ( Tw / [W0 - Y0] ) (A0 - Y0) / (A1 - Y1) = 21.7155 and B = - M x Y1 = -1.3029.

The following manufacturer's equation was applied to transmittance to derive beam attenuation:

where a is the pathlength in metres (=0.25 m) and Tr is the decimal transmittance (=light transmission(%)/100).

Field calibrations

Sea surface temperature (SST)

SST was calibrated against the primary temperature sensor on CTD casts deployed during the cruise. CTD temperature (interpolated to 6 m depth) and corresponding SST data values were extracted using standard BODC procedures (n = 31). Strong surface temperature gradients were observed in the CTD temperature profiles causing high variability in the temperature of the extracted CTD data. The standard deviation of sample points extracted per CTD cast ranged from 0.0002 - 0.364 °C ( n = 7-12 sample points extracted per CTD cast). Indeed, visual examination showed temperatures could change by up to 0.5 °C in the top 6 m on some casts. As a result, the calibration dataset had to be reduced to only include calibration points where the standard deviation of the extracted CTD temperature was < 0.02 °C. This limit was comparable to the typical standard deviations encountered in the calibration of previous SSB cruises. However, it meant there were only 8 viable calibration data points. Subsequently, the temperature offset was calculated (CTD temperature - UW temperature) and no further outliers needed to be removed.

No significant trend was found between the temperature offset (CTD - UW) and time (R² adj = 0.162, P > 0.05, n = 8). No significant trend was found between the temperature offset and CTD temperature (R ² adj = 0.077, P > 0.05, n = 8). However, a significant offset was observed. Therefore, underway SST was calibrated with a mean offset as follows:

Please note: The spread of the data around the mean offset is greater than the offset itself (0.041 > 0.013) and is likely due to the strong surface temperature gradients observed in the CTD profiles. Thus, this calibration should be treated with caution.

Salinity

Salinity was calibrated against the primary salinity sensor on CTD casts deployed during the cruise in preference to the salinity bottle samples collected from the TSG. This was because there were only 10 viable bottle samples collected during the cruise. CTD salinity (interpolated to 6 m) and corresponding underway salinity data values were extracted using standard BODC procedures (n = 31). Two outliers were removed because they were more than twice the standard deviation around the mean. A significant but weak relationship was found between the salinity offset (CTD - UW) and time ( R2 = 0.2861, n = 29, P < 0.05). Similarly, there was a significant but weak relationship was found between the salinity offset and CTD salinity (R2 = 0.1482, n = 29, P < 0.05). The mean salinity offset was also found to be significant (0.0033 PSU ±0.0025 S.D., n = 29, P < 0.001). Both trends and offset were applied to the data and all were found to suitably adjust the data. However, given the weak relationships found in regressions with time and CTD salinity, the mean offset was used to calibrate the underway salinity as follows::

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: