Metadata Report for BODC Series Reference Number 2202735

• 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

Attenuation

At least 44% of cycles within the originator's attenuation channels are extremely low ( < 0/m) for all 6 CTD (Conductivity Temperature Depth profiling instrument) casts. For 2 casts (3 and 4), all cycles were < 0/m. Values for attenuation below 0/m are outside of BODC parameter limits, indicating there may be a problem with the data. These recorded values were caused by an issue with the instrument calibration, confirmed by the originator. All values within this channel were flagged 'M' by BODC as a result.

Transmittance

At least 44% of cycles within the originator's transmittance channels are extremely high ( > 100%) for all 6 CTD casts. For 2 casts (3 and 4), all cycles were > 100%. Values for transmittance above 100% are outside of BODC parameter limits, indicating there may be a problem with the data. These recorded values were caused by an issue with the instrument calibration, confirmed by the originator. All values within this channel were flagged 'M' by BODC as a result.

Both attenuation and transmittance were recorded by the same instrument: Chelsea Technologies Group Alphatracka II transmissometer.

RRS James Cook JC036 CTD Data Quality Report

BODC flag M is applied to a single spike in chlorophyll concentration data (CPHLPM01) found in cast 1 (420m).

BODC flag M is applied to all attenuation data (ATTNMR01). At least 44% of cycles within the originator's attenuation channels are extremely low ( < 0/m) for all 6 CTD (Conductivity Temperature Depth profiling instrument) casts. For 2 casts (3 and 4), all cycles were < 0/m. Values for attenuation below 0/m are outside of BODC parameter limits, indicating there may be a problem with the data. These recorded values were caused by an issue with the instrument calibration, confirmed by the originator.

BODC flag M is applied to all transmittance data (POPTDR01). At least 44% of cycles within the originator's transmittance channels are extremely high ( > 100%) for all 6 CTD casts. For 2 casts (3 and 4), all cycles were > 100%. Values for transmittance above 100% are outside of BODC parameter limits, indicating there may be a problem with the data. These recorded values were caused by an issue with the instrument calibration, confirmed by the originator.

Both attenuation and transmittance were recorded by the same instrument: Chelsea Technologies Group Alphatracka II transmissometer.

Data Access Policy

Open Data

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:

"Contains public sector information licensed under the Open Government Licence v1.0."

Narrative Documents

Sea-Bird Dissolved Oxygen Sensor SBE 43 and SBE 43F

The SBE 43 is a dissolved oxygen sensor designed for marine applications. It incorporates a high-performance Clark polarographic membrane with a pump that continuously plumbs water through it, preventing algal growth and the development of anoxic conditions when the sensor is taking measurements.

Two configurations are available: SBE 43 produces a voltage output and can be incorporated with any Sea-Bird CTD that accepts input from a 0-5 volt auxiliary sensor, while the SBE 43F produces a frequency output and can be integrated with an SBE 52-MP (Moored Profiler CTD) or used for OEM applications. The specifications below are common to both.

Specifications

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

JC036 CTD Instrumentation

The Sea-Bird Scientific SBE911plus CTD (Conductivity Temperature Depth profiling instrument) was mounted on a rosette. Please see the JC036 cruise report for further information on the CTD configuration. The CTD was fitted with the following scientific sensors:

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus, that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus.

Specifications

Specifications for the SBE 9 plus underwater unit are listed below:

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

Chelsea Technologies Group Aquatracka MKIII fluorometer

The Chelsea Technologies Group Aquatracka MKIII is a logarithmic response fluorometer. Filters are available to enable the instrument to measure chlorophyll, rhodamine, fluorescein and turbidity.

It uses a pulsed (5.5 Hz) xenon light source discharging along two signal paths to eliminate variations in the flashlamp intensity. The reference path measures the intensity of the light source whilst the signal path measures the intensity of the light emitted from the specimen under test. The reference signal and the emitted light signals are then applied to a ratiometric circuit. In this circuit, the ratio of returned signal to reference signal is computed and scaled logarithmically to achieve a wide dynamic range. The logarithmic conversion accuracy is maintained at better than one percent of the reading over the full output range of the instrument.

Two variants of the instrument are available, both manufactured in titanium, capable of operating in depths from shallow water down to 2000 m and 6000 m respectively. The optical characteristics of the instrument in its different detection modes are visible below:

* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.

The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l^-1 to 100 µg l^-1. The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).

The instrument accuracy is ± 0.02 µg l^-1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).

Further details are available from the Aquatracka MKIII specification sheet.

Chelsea Technologies Group ALPHAtracka and ALPHAtracka II transmissometers

The Chelsea Technologies Group ALPHAtracka (the Mark I) and its successor, the ALPHAtracka II (the Mark II), are both accurate (< 0.3 % fullscale) transmissometers that measure the beam attenuation coefficient at 660 nm. Green (565 nm), yellow (590 nm) and blue (470 nm) wavelength variants are available on special order.

The instrument consists of a Transmitter/Reference Assembly and a Detector Assembly aligned and spaced apart by an open support frame. The housing and frame are both manufactured in titanium and are pressure rated to 6000 m depth.

The Transmitter/Reference housing is sealed by an end cap. Inside the housing an LED light source emits a collimated beam through a sealed window. The Detector housing is also sealed by an end cap. A signal photodiode is placed behind a sealed window to receive the collimated beam from the Transmitter.

The primary difference between the ALPHAtracka and ALPHAtracka II is that the Alphatracka II is implemented with surface-mount technology; this has enabled a much smaller diameter pressure housing to be used while retaining exactly the same optical train as in the Mark I. Data from the Mark II version are thus fully compatible with that already obtained with the Mark I. The performance of the Mark II is further enhanced by two electronic developments from Chelsea Technologies Group - firstly, all items are locked in a signal nulling loop of near infinite gain and, secondly, the signal output linearity is inherently defined by digital circuitry only.

Among other advantages noted above, these features ensure that the optical intensity of the Mark II, indicated by the output voltage, is accurately represented by a straight line interpolation between a reading near full-scale under known conditions and a zero reading when blanked off.

For optimum measurements in a wide range of environmental conditions, the Mark I and Mark II are available in 5 cm, 10 cm and 25 cm path length versions. Output is default factory set to 2.5 volts but can be adjusted to 5 volts on request.

Further details about the Mark II instrument are available from the Chelsea Technologies Group ALPHAtrackaII specification sheet.

Chelsea Technologies Photosynthetically Active Radiation (PAR) Irradiance Sensor

This sensor was originally designed to assist the study of marine photosynthesis. With the use of logarithmic amplication, the sensor covers a range of 6 orders of magnitude, which avoids setting up the sensor range for the expected signal level for different ambient conditions.

The sensor consists of a hollow PTFE 2-pi collector supported by a clear acetal dome diverting light to a filter and photodiode from which a cosine response is obtained. The sensor can be used in moorings, profiling or deployed in towed vehicles and can measure both upwelling and downwelling light.

Specifications

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

WETLabs Single-angle Backscattering Meter ECO BB

An optical scattering sensor that measures scattering at 117°. This angle was determined as a minimum convergence point for variations in the volume scattering function induced by suspended materials and water. The measured signal is less determined by the type and size of the materials in the water and is more directly correlated to their concentration.

Several versions are available, with minor differences in their specifications:

• ECO BB(RT)provides analog or RS-232 serial output with 4000 count range
• ECO BB(RT)D adds the possibility of being deployed in depths up to 6000 m while keeping the capabilities of ECO BB(RT)
• ECO BB provides the capabilities of ECO BB(RT) with periodic sampling
• ECO BBB is similar to ECO BB but with internal batteries for autonomous operation
• ECO BBS is similar to ECO BB but with an integrated anti-fouling bio-wiper
• ECO BBSB has the capabilities of ECO BBS but with internal batteries for autonomous operation

Specifications

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

JC036 CTD BODC Processing

The Conductivity Temperature Depth profiling instrument (CTD) data were supplied to BODC as 6 MATLAB files and converted to the BODC internal format.

During transfer, the originator's variables were mapped to unique BODC parameter codes. The following table shows the parameter mapping:

Following transfer the data were screened using BODC in-house visualisation software.

Originator's Data Processing of CTD casts from cruise JC036

Sampling Strategy

Six Conductivity Temperature Depth profiling instrument (CTD) cast deployments were used to obtain profiles of the water column, with a range of sensors, at six different stations. These stations were located in Whittard Canyon, northern slope of the Bay of Biscay. The sensors used include temperature, conductivity, pressure, oxygen, fluorescence, altitude, irradiance, backscatter, and attenuance. During JC036, stand-alone pump system (SAPS) surveys were also completed alongside the CTD deployments, where the CTD was deployed first to determine the structure of the water body. CTDs were deployed from 22^nd June 2009 to 26^th July 2009. The deepest cast was deployed at station 008 (cast 1), where the depth was recorded at 3589m. The shallowest cast was at station 108 (cast 6), which descended to 1415m. Please see the JC036 cruise report for further information.

Initial Data Processing

For processing of the data, the Sea-Bird data collection software Seasave v7.18 were used to record the raw data output from the CTD casts. Processing the raw data followed the BODC recommended guidelines, using SBE Data processing-Win32 v7.23.2 software.

Further Data Processing

During reprocessing, the CTD data from all casts were averaged (median value) into 2 m bins for the downcast, the upcast and the downcast and upcast combined. The data were output into MATLAB files. These data were reprocessed together with the data from the later Whittard Canyon cruises JC125 and JC237.

Project Information

Oceans 2025 Theme 5: Continental Margins and the Deep Ocean

The deep ocean and the seafloor beneath it are the largest yet least known environments on our planet. They profoundly influence the way in which the Earth reacts to climate change, provide vital resources, and can cause natural catastrophes (with significant risks to the UK). A better understanding of the biodiversity and resource potential of the deep ocean, its geophysics and its complex interactions with the global carbon cycle are all urgently required.

The overall aim of Theme 5 is to deliver coordinated, multidisciplinary research on the functioning of the deep ocean from the photic zone to the sub-seabed, encompassing biology, physics, geology, chemistry and mathematical modelling. Such an integrated deep-sea programme is unique in the UK and will ensure the provision of knowledge essential for underpinning UK policy in conserving marine biodiversity, controlling the effects of global change, managing ocean resources in a sustainable manner, and mitigating the effects of geohazards.

The specific objectives of Theme 5 are:

• To understand the processes controlling the vertical flux of carbon between the base of the photic zone and the seabed and to quantify this flux.
• To quantify fluxes of carbon and fluids from the sub-seabed into the deep ocean and their contribution to global carbon budgets.
• To determine how the carbon flow interacts with deep-ocean pelagic and benthic communities in the open ocean and on the continental slope.
• To investigate how benthic ecosystems on continental margins and in the deep ocean respond to spatial and temporal variation in environmental parameters.
• To understand the causes, frequency and predictability of submarine geohazards.
• To apply scientific knowledge to the sustainable management of the ocean and its resources.

Theme 5 combines two Research Units, on Continental Margins and on the Biochemistry of the Deep Ocean. Ultimately the science of the two activities will be combined, but because the methods of study and the resources needed are largely different, the work has been planned within two groups.

In Continental Margins, the physical processes regulating the transport of sediment is investigated as well as the transport of hydrocarbons and aqueous fluids from the seafloor. The effect of both of these major processes on the landscape ecology of the continental slope will be assessed. In addition, the causes, mechanisms and frequency of submarine geohazards will be studied, particularly those that potentially could have a devastating effect on coastal communities, such as earthquake and landslide-induced tsunamis. Carbon flux from the geosphere into the ocean will be assessed. The information will be used to advise on whole ecosystem management strategies, including policy issues relating to Marine Protected Areas and international treaties on the development of open ocean resources.

In Biogeochemistry of the Deep Ocean, the flux of particles through the 'twilight zone' in order to reduce the large uncertainties in our knowledge of the magnitude of the downward flux in various biogeochemical provinces of the global ocean will be studied. The twilight zone is a large biogeochemical reactor influencing the supply of nutrients to the euphotic zone and the fate of materials consigned to the deep seafloor. Theme 5 will study how zooplankton and microbes repackage and breakdown particles, and how these processes influence carbon transfer. Direct observations and experimental approaches will provide data to drive stoichiometric models of heterotrophic OM utilisation. The impact on the deep-sea benthos of repackaged OM, and the of part of surface production that by-passes twilight zone processes, will be assessed by analysing global patterns and through ROV in situ experimentation. Proven modelling expertise in upper ocean systems will be extended to benthic ecosystems utilising the information generated by bentho-pelagic coupling observations and experimental approaches.

The official Oceans 2025 documentation for this Theme is available from the following link: Oceans 2025 Theme 5

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

Hotspot Ecosystem Research and Man's Impact on European seas (HERMIONE)

Background

The HERMIONE project is designed to make a major advance in our knowledge of the functioning of deep-sea ecosystems and their contribution to the production of goods and services.

The project set out to investigate ecosystems at critical sites on Europe's deep-ocean margin including submarine canyons, seamounts, cold seeps, open slopes, and deep basins in the Arctic, North Atlantic Ocean, and Mediterranean Sea. It included scientists from a wide range of disciplines (including biologists, ecologists, microbiologists, biogeochemists, sedimentologists, physical oceanographers, modelers and socio-economists) who researched the natural dynamics and interconnections of ecosystems as well as how these contribute to the goods and services we rely on, and how they are affected by natural and anthropogenic change.

A major aim of HERMIONE was to use the knowledge gained during the project to contribute to EU environmental policies, by integrating socio-economic research with natural science. This information can be used to create effective management plans that will help to protect our oceans for the future.

The objectives of HERMIONE were:

1. To investigate the dimensions, distribution and interconnection of deep-sea ecosystems;
2. To understand changes in deep-sea ecosystems related to key factors including climate change, human impacts and the impact of large-scale episodic events;
3. To understand the biological capacities and specific adaptations of deep-sea organisms, and investigate the importance of biodiversity in the functioning of deep-water ecosystems;
4. To provide stakeholders and policy-makers with scientific knowledge to support deep-sea governance aimed at the sustainable management of resources and the conservation of ecosystems.

HERMIONE will enhance the education and public perception of the deep-ocean issues, assisted by the involvement of some of the major EU aquaria and through GEOSS databases that will create a platform for discussion between a range of stakeholders, and contribute to EU environmental policies.

Fieldwork

Fieldwork was carried out on 93 research cruises of which 69 were longer than 5 days. The project in total consisted of 1094 days of ship time.

Participants

• Natural Environment Research Council, United Kingdom
• Institut Francais De Recherche Pour L'exploitation De La Mer, France
• Stichting Nioz, Koninklijk Nederlands Instituut Voor Onderzoek Der Zee, Netherlands
• Universitat De Barcelona, Spain
• Hellenic Centre For Marine Research, Greece
• Leibniz-Institut Fuer Meereswissenschaften An Der Universitaet Kiel, Germany
• Consiglio Nazionale Delle Ricerche, Italy
• Alfred-Wegener-Institut Helmholtz-Zentrum Fur Polar- Und Meeresforschung, Germany
• Universitetet I Tromsoe - Norges Arktiske Universitet, Norway
• National University Of Ireland Galway, Ireland
• Friedrich-Alexander-Universitaet Erlangen-Nuernberg , Germany
• Universiteit Gent, Belgium
• Agencia Estatal Consejo Superior De Investigaciones Cientificas, Spain
• Consorzio Nazionale Interuniversitario Per Le Scienze Del Mare Associazione, Italy
• Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften Ev, Germany
• Centre National De La Recherche Scientifique CNRS, France
• Instituto Hidrografico, Portugal
• Jacobs University Bremen GGMBH, Germany
• Universitaet Bremen, Germany
• Cardiff University, United Kingdom
• Havforskningsinstituttet, Norway
• Goeteborgs Universitet, Sweden
• University Of Southampton, United Kingdom
• Koninklijke Nederlandse Akademie Van Wetenschappen - Knaw, Netherlands
• The University Court Of The University Of Aberdeen, United Kingdom
• The University Of Liverpool, United Kingdom
• The Scottish Association For Marine Science LBG, United Kingdom
• Universidade De Aveiro, Portugal
• Universite Pierre Et Marie Curie - Paris 6, France
• P.P. Shirshov Institute Of Oceanology Of Russian Academy Of Sciences, Russia
• United Nations Environment Programme , Kenya
• Universidade Dos Acores, Portugal
• Median SCP, Spain
• Archimedix, Möckl & Munzel GbR, Germany
• Panepistimio Thessalias, Greece
• University College Cork - National University Of Ireland, Cork, Ireland
• National Marine Aquarium Ltd., United Kingdom
• Costa Edutainment S.P.A, Italy
• Heriot-Watt University, United Kingdom
• Senckenberg Gesellschaft Fur Naturforschung, Germany
• WCMC LBG, United Kingdom

Funding

The project was funded under the EU Commission Seventh Framework Programme, FP7 (2007-2013), grant agreement ID 226354. It ran from 1^st April 2009 to 30^th September 2012. Ship time was largely funded outside of the project by National funds. The project was coordinated by the Natural Environment Research Council (NERC), UK. More information can be found here and in the newsletters.

Data Activity or Cruise Information

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

Fixed Station Information

Fixed Station - Whittard Canyon - The Canyons Marine Conservation Zone

The Canyons MCZ is located in the far south-west corner of the UK continental shelf, more than 330 km from Land's End, Cornwall. It encompasses the steep part of the shelf break where the seabed drops from a depth of 100 m to the oceanic abyssal plain at 2000 m. It is unique within the context of England's largely shallow seas due to its depth, sea-bed topography and the coral features it contains.

There are two large canyons within the site, which add to its topographic complexity: the Explorer Canyon to the north and the Dangaard Canyon below it. The wider Whittard Canyon area encapsulates the Canyons MCZ and also includes a network of submarine canyons to the West. The MCZ, also known as a Marine Protected Area (MPA), was designated in November 2013 under the Marine and Coastal Access Act (2009). The Canyons MCZ covers an area of 661 km², which extends to approximately 5200 km² when Whittard Canyon is included.

On the northernmost wall of the Explorer Canyon is a patch of live Cold-water coral reef (Lophelia pertusa) and Coral gardens, both of which are a OSPAR threatened and/or declining habitat. This is the only known example of living Cold-water coral reef recorded within England's seas, making it unique in these waters.

Cold-water corals and Coral gardens typically support a range of other organisms. The coral provides a three-dimensional structure and a variety of microhabitats that provide shelter and an attachment surface for other species. Both Cold-water corals and Coral gardens can be long-lived but are extremely slow growing (at about 6 mm a year), making protection important for their conservation. Another reef-forming cold-water coral, Madrepora oculata, is also present in the site.

The variety of deep-sea bed communities present are indicative of the range of substrates found in and around the canyons, including bedrock, biogenic reef, coral rubble, coarse sediment, mud and sand. These biological communities include cold-water coral communities (Lophelia pertusa and Madrepora oculata), Coral gardens, feather star (Leptometra celtica) assemblages and Sea-pen and burrowing megafauna communities (including, burrowing anemone fields, squat lobster (Munida sp.) assemblages, barnacle assemblages and deep-sea sea-pen (Kophobelemnon sp.) fields).

Sampling History

Related Fixed Station activities are detailed in Appendix 1

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: Whittard Canyon - The Canyons Marine Conservation Zone

Related series for this Fixed Station are presented in the table below. Further information can be found by following the appropriate links.

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