Metadata Report for BODC Series Reference Number 2012101

• 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 James Cook Cruise JC136 sea surface hydrography data quality report

Further to the data processing documentation, data quality issues concerning meteorology data were noted.

All parameters

Throughout the duration of data collection there were instances of equipment failure as well as periods where the systems were turned off. These gaps have been flagged.

Transmittance, Beam Transmission and Attenuance

These channels contained intermittent spiking which has been flagged where necessary.

Chlorophyll and Fluorescence

Flags have been placed in areas where readings are consistent for long periods due to the sensor output getting stuck.

The non-toxic, pumped seawater supply was switched on at 12:20 on 15/05/2016, and was turned off at 09:25 on 22/06/2016, towards the end of the cruise; all housing measurements recorded outside this time span were flagged. The supply was also switched off whilst in port at Stornoway from 05:45 on 03/06/2016 until 08:00 on 04/06/2016. The housing measurements were flagged, other then during a coinciding prolonged period of unrealistic values until Techsas froze and restarted at 05:32 on 04/06/2016, where these values were set to null.

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 James Cook JC136 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 5.5 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 James Cook JC136 surface hydrography data processing procedures

Originator's Data Processing

The data were logged by the TECHSAS (TECHnical and Scientific sensors Acquisition System) system into daily NetCDF files. The TECHSAS system is used as the main data logging system on NMF-SS operated reserach vessels. The daily TECHSAS NetCDF navigation and bathymetry files provided to BODC were used for BODC processing. Data were additionally logged into the RVS Level-C format files which have been archived at BODC. A portion of the data were then processed daily using the National Oceanography Centre MSTAR data procesing routines (mstar_version_v3).

Files delivered to BODC

BODC Data Processing

The files were reformatted to BODC internal format using standard data banking procedures. The following table shows how the variables within the files were mapped to appropriate BODC parameter codes:

*-*-Surf-DY-SM_DY1.SURFMETv3

*-*-SBE45-SBE45_DY1.TSG

All the reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag.

Manufacturers Calibrations

Transmissometer

The transmissometer voltage channel was converted to beam transmission ( beamtrans ) and beam attenuation ( atten ) as follows:

beamtrans [%] = ([Volts - Vdark] / [Vref - Vdark])*100

atten [per m] = (-1/pathlength) * ln(beamtrans)

where Vdark = 0.058 V, Vref = 4.685 V and pathlength = 0.25 m.

Fluorometer

The fluorescence voltage channel was converted to engineering units (chla) using the following calibration:

chla [µg/L] = SF (volts - CWO)

where SF = 5.6 µg/L/V and CWO = 0.064 V.

Processing

All reformatted data were visualised using the in-house EDSERPLO software. Where calibrations had been applied, only the calibrated versions of those parameters were screened. Suspect data were marked by adding an appropriate quality control flag.

Field Calibrations

No calibration against independent variables were applied to these data.

Project Information

Deep Links: Influence of population connectivity on depth-dependent diversity of deep-sea marine benthic biota

Background

Species populations are connected to each other through both movement of adults (migration) and eggs, larvae and juveniles (dispersal). If populations become isolated from one another (i.e. are no longer connected), then through genetic mutation, drift and natural selection, they may become so different that they evolve into new biological species. Understanding how populations become isolated is critical to understanding the process of speciation. In the marine environment many species do not move as adults (e.g. corals) or move very slowly (sea urchins). This means that for different adult populations to remain connected they rely on dispersal of early life history stages. Most marine species have a larval stage that lives in the plankton for a period of time, moving with the currents, before settling in a new area. It is larval dispersal that keeps distant populations connected. So understanding patterns of larval dispersal is important to understanding connectivity.

In the deep-sea (>200m) the bathyal region of the continental slope has been identified as supporting high species richness and being an area where the rate of origination of new species may also be high. The reasons for this are not clear, but given the importance of connectivity to population isolation and speciation, it follows that the key to understanding patterns of species diversity in this region lies in understanding connectivity. New research has suggested that because the speed of the currents that carry larvae decreases as you go deeper, larvae might not be able to travel as far, leading to a greater tendency for populations at bathyal depths to become isolated over a given distance, and thus increasing the chances of speciation.

This study aims to test this theory by investigating how patterns of connectivity vary with depth. This will be done in 3 ways:

1. Using genetic analysis (similar to DNA fingerprinting) to compare how related distant populations are and if they become less closely related as you go deeper
2. Using a model of ocean currents to simulate the movement of larvae between sites
3. Io look at the range and abundance of species present at distant locations to see if those at shallower depths are more similar to each-other than those at bathyal depths.

Fieldwork

Data were collected on James Cook cruise JC136 between 14^th May and 23^rd June 2016. During the cruise, 5 sites in the North East Atlantic (Rockall Bank, George Bligh Bank, Anton Dohrn Seamount, Wyville-Thomson Ridge, and Rosemary Bank) were visited undertaking 27 ROV dives, 12 AUV missions, 43 CTD casts, 2 mooring deployments. 3630 biological samples were obtained from sufficient depth and site coverage for molecular analysis for 3 target species.

Participants

• Dr Kerry Howell (Principal Investigator - Parent Grant) University of Plymouth
• Dr Andy Foggo (Co-Investigator) University of Plymouth
• Dr Alex Nimmo-Smith (Co-Investigator) University of Plymouth
• Dr Vasyl Vlasenko (Co-Investigator) University of Plymouth
• Professor Alex Rogers (Principal Investigator - Child Grant) University of Oxford

Funding

This project was funded by Natural Environment Research Council parent and child grants NE/K011855/1 and NE/K013513/1, entitled 'Influence of population connectivity on depth-dependent diversity of deep-sea marine benthic biota', with the former, parent grant led by Dr Kerry Howell, University of Plymouth, and the latter child grant led by Professor Alex Rogers, University of Oxford. The project was also in partnership with the Joint Nature Conservation Committee (JNCC) and the British Geological Survey (BGS). The project was active between 16^th November 2015 and 31^st December 2019.

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: