CRUISE REPORT: AR07
(Updated NOV 2019)






HIGHLIGHTS



                        CRUISE SUMMARY INFORMATION


               Section Designation  AR07
Expedition designation (ExpoCodes)  74JC20140606
                  Chief Scientists  B.A. King/NOC and N.P. Holliday/NOC
                             Dates  2014 JUN 06 – 2014 JUL 21
                              Ship  RRS James Clark Ross
                     Ports of call  St Johns, Newfoundland, Canada to 
                                    Immingham, UK,

                                                  63°19.02' N
             Geographic Boundaries  55°33.91' W                 6°7.98' W
                                                    52°0' N

                          Stations  280 CTD Stations
      Floats and drifters deployed  8 Argo floats deployed
    Moorings deployed or recovered  0

                           Contact Information:

                              N.P. Holliday
   National Oceanography Centre, Southampton University of Southampton 
      Waterfront Campus European Way • Southampton Hants SO14 3ZH UK
       Tel:  +44 (0)23  8059 6206 • Email: penny.holliday@noc.ac.uk

 









              Final report assembly by Jerry Kappa, SIO/UCSD





National 
Oceanography Centre
Natural Environment Research Council








            National Oceanography Centre Cruise Report No. 35
                     RRS James Clark Ross Cruise 302
                          06 JUN - 21 JUL 2014
                      The 2015 RAGNARRoC, OSNAP and
                    Extended Ellett Line cruise report


                           Principal Scientists
                       B A King  and N P Holliday






                                   2015





















National Oceanography Centre, Southampton University of Southampton 
Waterfront Campus European Way
Southampton Hants SO14 3ZH UK

Tel:  +44 (0)23  8059 6206
Email: penny.holliday@noc.ac.uk
©  National Oceanography Centre, 2015



DOCUMENT DATA SHEET

AUTHOR                                                      PUBLICATION 
      KING, B A  &  HOLLIDAY, N P  et al                    DATE     2015

TITLE
      RRS James Clark Ross Cruise 302, 06 Jun - 21 Jul 2014, 
      The 2015 RAGNARRoC, OSNAP AND Extended Ellett Line cruise report

REFERENCE
      Southampton, UK: National Oceanography Centre, Southampton, 76pp.
      (National Oceanography Centre Cruise Report, No. 35)

ABSTRACT
      Cruise JR302 was an NERC-NC funded cruise aiming to complete a full 
      CTD section across the subpolar gyre, from Canada to Greenland to 
      Scotland. The CTD section was located along the OSNAP track 
      (www.ukosnap.org), providing a high quality and high resolution 
      synoptic survey for the start of that programme. The objectives 
      included a full suite of biogeochemistry measurements under the 
      RAGNARRoC programmes.

      Finally, the eastern part of the section included the 2014 
      occupation of the Extended Ellett Line 
      (projects.noc.ac.uk/ExtendedEllettLine) between Scotland and 
      Iceland. Additional sections were made around the Cape Farewell 
      region with the objective of measuring transport and the movement 
      of water away from the boundary currents.

      Additional objectives included deploying eight Met Office Argo 
      floats, and recovering one SAMS glider. Two new instruments were 
      trialled by deploying them on the CTD frame; the IMP and RBR.

All objectives were successfully completed.



KEYWORDS

ISSUING ORGANISATION  National  Oceanography  Centre
                      University of Southampton Waterfront Campus
                      European Way
                      Southampton SO14 3ZH  UK
                      Tel: +44(0)23 80596116  Email: nol@noc.soton.ac.uk

            A pdf of this report is available for download at:
                       http://eprints.soton.ac.uk



Contents

Scientific Personnel

Ship's Personnel

1. Overview
   1.1  Itinerary
   1.2  Objectives

2. Profile Measurements
   2.1  CTD Sensors
   2.2  CTD Data processing
   2.3  CTD calibrations
        2.3.1  Oxygen
        2.3.2  Salinity
   2.4  LADCP
        2.4.1  Instrument technical details
        2.4.2  Data Processing
        2.4.3  IMP
   2.5  RBR Concerto CTD

3. Water Sample Measurements
   3.1  Salinity
   3.2  Dissolved Oxygen
   3.3  Total Dissolved and Dissolved Inorganic Nutrients
   3.4  Carbonate system measurements
   3.5  CFCs
   3.6  Methane and Nitrous Oxide
   3.7  Surfactants, CDOM and Pigments
   3.8  Trace Metals
   3.9  Phytoplankton community structure and species identification
   3.10 Iodine Isotope sampling

4. Underway Measurements
   4.1  SCS data streams
   4.2  VMADCP
   4.3  Pumped seawater: underway carbon

5. Autonomous Platforms
   5.1  Floats
   5.2  Seaglider

6. Outreach

CCHDO Data Processing Notes








Scientific Personnel

Ian Brown             PML
Jen Clarke            NOC/Southampton University PhD student
Damien Desbruyeres    NOC
Hannah Donald         NOC/Southampton University PhD student
Andy England          BAS
Claudia Fry           NOC/Southampton University PhD student
Becky Garley          Bermuda
Stefan Gary           SAMS
Carolyn Graves        NOC/Southampton University PhD student
Alex Griffiths        NOC
Lilo Henke            Exeter University PhD student
Penny Holliday        NOC
Brian King            NOC
Jonathan Lawrence     NOC/Southampton University PhD student
Peter Mead            Exeter University
Marie-Jose Messias    Exeter University
Gary Murphy           Exeter University
Bita Sabbaghzadeh     Newcastle University
Mark Stinchcombe      NOC
Seth Thomas           BAS
Sinhue Torres Valdes  NOC
Tobia Tudino          Exeter University PhD student
Eithne Tynan          Southampton University
Felicity Williams     NOC/Southampton University PhD student
John Wynar            NOC


Ship's Personnel

CHAPMAN Graham P      Master
EVANS Simon D         Ch Officer
HIPSEY Christopher W  2nd Officer
DELPH Georgina M      3rd Off
WADDICOR Charles A    ETO (Coms)
PARNELL Luke T        Ch Eng
COLLARD Glynn         2nd Eng
HARDY Aleksandr J     3rd Eng
EADIE Steven J        4th Eng
WRIGHT Simon A        Deck Eng
DUNBAR Nicholas J     ETO (Eng)
KLEPACKI Julian       Suppny ETO
GIBSON James S        Purser
MULLANEY Clifford     Bosun SciOps
O'DUFFY John P        Bosun
LEGGETT Colin J       SG1
DYER Martyn P         SG1
PHELPS Kenneth J      SG1
WAYLETT Graham L      SG1
BELL Shaun            SG1
FAULKNER Leslie J     SG1
WILSON Paul S         MG1
HERBERT Ian B         MG1
WALKER Keith A        Cook
MOLLOY Padraig G      2nd Cook
WESTON Kenneth        Sr Stwd
NEWALL James          Stwd
LEE Derek W           Stwd
PATTERSON Thomas R    Stwd

 

1.  OVERVIEW

1.1  Itinerary

St Johns, Newfoundland, Canada to Immingham, UK, 6 Jun - 21 Jul 2014


Figure 1.1.1: The JR302 station positions and track line
Figure 1.1.2: Station positions and numbers for the OSNAP West line
Figure 1.1.3: Station positions and numbers for stations around Greenland
Figure 1.1.4: Station positions and numbers for OSNAP East (part 1).
Figure 1.1.5: Station positions and numbers for OSNAP East (part 2).
Figure 1.1.6: Station positions and numbers for Extended Ellett Line.

 
1.2  Objectives

Cruise JR302 was an NERC-NC funded cruise aiming to complete a full CTD 
section across the subpolar gyre, from Canada to Greenland to Scotland. 
The CTD section was located along the OSNAP track, providing a high 
quality and high-resolution synoptic survey for the start of that 
programme. The objectives included a full suite of biogeochemistry 
measurements under the RAGNARRoC programmes. Finally, the eastern part of 
the section included the 2014 occupation of the Extended Ellett Line 
between Scotland and Iceland. Additional sections were made around the 
Cape Farewell region with the objective of measuring transport and the 
movement of water away from the boundary currents.

Additional objectives included deploying eight Met Office Argo floats, 
and recovering one SAMS glider. Two new instruments were trialed by 
deploying them on the CTD frame; the IMP and RBR.


Figure 1.2.1: The scientific personnel of JR302

Team Physics

  Penny Holliday
  Damien Desbruyères
  Jonathan Lawrence
  Stefan Gary
  Felicity Williams

Methane & Nitrous oxide

  Ian Brown

Team Carbon
  
  Alex Griffiths
  Eithne Tynan
  Claudia Fry
  Jen Clarke
  Becky Gorley

CTD Engineer

  John Wynar

Principal Scientist

  Brian King

Support Engineer
 
  Seth Thomas

IT Engineer

  Andy England

Team Nutrients/Oxygen

  Sinhue Torres-Valdes
  Hannah Donald
  Carolyn Graves
  Mark Stinchcome

Team CFCs

  Marie-Jose Messias
  Peter Mead
  Gary Murphy
  Lilo Henke
  Tobia Tudino

Surfactants & chlorophyll
  
  Bita Sabbaghzadeh





2.  PROFILE MEASUREMENTS

2.1  CTD Sensors

Seth Thomas
SBE_Instrument Configuration SB_ConfigCTD_FileVersion="7.22.0.2" 

Name SBE 911plus
    Frequency Channels Suppressed        0
    Voltage Words Suppressed             0
    Computer Interface                   0
!-- 1 == SBE11plus Firmware Version 5.0 --- 
    Deck Unit Version                    0
    Scans To Average                     1
    Surface Par Voltage Added            0
    Scan Time Added                      0
    Nmea Position DataAdded              1
    Nmea Depth Data Added                0
    Nmea Time Added                      0
    Nmea Device ConnectedToPC            1

Sensor index="0" Sensor ID="55" 
    Temperature Sensor Sensor ID="55"
      Serial Number                    03P-4472
      Calibration Date                 30 August 2012 
      G               4.41398102e-003
      H               6.42799011e-004
      I               2.19747460e-005
      J               1.88664616e-006
      F            1000.000
      Slope           1.00000000
      Offset          0.0000

Sensor index="1" SensorID="3" 
    Conductivity Sensor SensorID="3"
      Serial Number                    2875
      Calibration Date                 19 March 2013 
      G              -1.01639718e+001
      H               1.40355804e+000
      I               8.86145233e-005
      J               5.99096076e-005
      CPcor          -9.57000000e-008
      CTcor           3.2500e-006

Sensor index="2" SensorID="45" 
    Pressure Sensor SensorID="45"
      Serial Number                    89973
      Calibration Date                 22 August 2012 
      C             1-4.925971e+004
      C2             -2.136250e-001
      C3              9.435710e-003
      D1              3.900400e-002
      D2              0.000000e+000
      T1              2.983458e+001
      T2             -3.883229e-004
      T3              3.262440e-006
      T4              3.429810e-009
      Slope           1.00010000
      Offset         -1.27140
      T5              0.000000e+000 
      AD590M          1.277500e-002 
      AD590B         -9.391460e+000
      
Sensor index="3" SensorID="55" 
    Temperature Sensor SensorID="55"
      Serial Number                    03P-2366
      Calibration Date                 30 August 2012 
      G               4.31974772e-003
      H               6.44172106e-004
      I               2.35210024e-005
      J               2.26433319e-006
      F           01000.000
      Slope           1.00000000
      Offset          0.0000

Sensor index="4" SensorID="3" 
    ConductivitySensor SensorID="3" 
      SerialNumber                     04C-2289
      CalibrationDate                  21 August 2012 
      G              -1.04066323e+001
      H               1.38729309e+000
      I              -2.46034773e-003
      J               2.40168672e-004
      CPcor          -9.57000000e-008
      CTcor           3.2500e-006
      Slope           1.00000000
      Offset          0.00000

Sensor index="5" SensorID="71" 
    WET_LabsCStar SensorID="71"
      SerialNumber                     CST-846DR
      CalibrationDate                  13 March 2013
      M              21.6360
      B              -1.2938
      PathLength      0.250

Sensor index="6" SensorID="5" 
    FluoroChelseaAqua3Sensor SensorID="5" 
      SerialNumber                     088216
      CalibrationDate                  19 February 2013
      VB              0.219400
      V1              2.068800
      Vacetone        0.228700
      ScaleFactor     1.000000
      Slope           1.000000
      Offset          0.000000

Sensor index="7" SensorID="42" 
    PAR_BiosphericalLicorChelseaSensor SensorID="42" 
      SerialNumber                     7235
      CalibrationDate                  24 April 2013
      M               1.00000000
      B               0.00000000
      CalibrationConstant              33557046980.00000000
      Multiplier      1.00000000
      Offset         -0.04219064

Sensor index="8" SensorID="0" 
    AltimeterSensor SensorID="0"
      SerialNumber                     244740
      CalibrationDate                  16 May 2012
      ScaleFactor    15.000
      Offset          0.000

Sensor index="9" SensorID="38" 
    OxygenSensor SensorID="38" 
      SerialNumber                     0676
      CalibrationDate                  28-Aug-12 
      Soc             4.4589e-001
      offset         -0.4962
      A              -8.8979e-004
      B               6.4609e-005
      C              -5.1722e-007
      D0              2.5826e+000
      D1              1.92634e-004
      D2             -4.64803e-002
      E               3.6000e-002
      Tau          20 1.1700
      H1             -3.3000e-002
      H2              5.0000e+003
      H3              1.4500e+003
      

 
2.2  CTD Data processing

Brian King, Damien Desbruyeres, Penny Holliday

CTD data processing followed the usual mexec path described in previous 
cruise reports, as follows.

2.2.1  Sea Bird Data processing

• Preparation at the start of the cruise
  The first step is to select the SBE output variables. It is essential 
  that the output variables include scan and pressure temperature.  For 
  example (JR302):
    # name 0 = timeS: Time, Elapsed [seconds]
    # name 1 = depSM: Depth [salt water, m]
    # name 2 = prDM: Pressure, Digiquartz [db]
    # name 3 = t090C: Temperature [ITS-90, deg C]
    # name 4 = t190C: Temperature, 2 [ITS-90, deg C]
    # name 5 = c0mS/cm: Conductivity [mS/cm]
    # name 6 = c1mS/cm: Conductivity, 2 [mS/cm]
    # name 7 = sal00: Salinity, Practical [PSU]
    # name 8 = sal11: Salinity, Practical, 2 [PSU]
    # name 9 = sbeox0V: Oxygen raw, SBE 43 [V]
    # name 10 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/Kg]
    # name 11 = sbeox0ML/L: Oxygen, SBE 43 [ml/l]
    # name 12 = xmiss: Beam Transmission, Chelsea/Seatech/WET Labs CStar[%]
    # name 13 = flC: Fluorescence, Chelsea Aqua 3 Chl Con [ug/l]
    # name 14 = turbWETbb0: Turbidity, WET Labs ECO BB [m^-1/sr]
    # name 15 = altM: Altimeter [m]
    # name 16 = scan: Scan Count
    # name 17 = ptempC: Pressure Temperature [deg C]
    # name 18 = pumps: Pump Status
    # name 19 = latitude: Latitude [deg]
    # name 20 = longitude: Longitude [deg]
    # name 21 = flag: 0.000e+00

    - Oxygen hysteresis correction: decide whether to use the SBE oxygen 
      hysteresis correction using standard parameters, or whether to 
      derive your own. Look at options in the SBE data conversion 
      program: it is here that the hysteresis correction is applied and 
      you can uncheck that option. Make sure that mstar script moxy_02b 
      is edited to match your requirement.
• SBE Data Processing
  On the CTD logging computer, the SBE Data Processing software was used 
  for initial processing when the cast was finished, by running the 
  following:
    Data Conversion to convert the raw frequency and voltage data to 
    engineering units as appropriate by applying the manufacturer's 
    calibrations stored in the CON file and save both downcast and upcast 
    to an ASCII format file. Can include hysteresis correction using SBE 
    parameters.

    Align CTD to align the oxygen sensor in time relative to pressure.

    Cell Thermal Mass to correct the pressure and conductivity. Output 
    File: JC86_NNN_actm.cnv
 
2.2.2 MSTAR Data Processing

• Preparation at the start of the cruise
    - Data are retrieved from the ship's data directories by the use of 
      symbolic links in ctd_linkscript
    - Edit ctd_linkscript to pick up the files using the symbolic links, 
      check format of lines that extract information from SBE filenames 
      to create the standard mstar names. The script only picks up data 
      files not already copied to the ASCII_FILE directory.
      Edit the list of variable names that you require for your sample 
      file. This will vary from cruise to cruise depending on which 
      samples are being collected.  The list of variables is contained in 
      the file /data/templates/sam_jr302_varlist.csv.
    - Create a template csv file in which you will input information 
      about bottle firing, ready for pasting into the master sample file 
      later. It is useful to create a blank master file with all bottles 
      set to flag 2 (No problems noted), to be edited after each cast 
      when bottles are either not fired (flag 9), or don't trip correctly 
      (flag 4) etc. File: /data/ctd/ASCII_FILES/bot_jr302_001.csv.
• ctd_linkscript was used to copy the data from the ship's network drive 
  to the NOCS Sun workstation FOLA. The files are copied with their 
  original names, then a symbolic link created for each one with the name 
  in the format expected by standard mstar scripts.
• MatLab was opened and 'm_setup' run to setup the environment for mexec 
  processing.
  The MSTAR processing was split into several phases. 'ctd_all_part1' 
  included the following:
• msam_01 creates an empty sam file sam_jr302_NNN.nc (make sure that the 
  list of variable contains the expected channels);
• mctd_01 reads in 24Hz CTD data into ctd_jr302_NNN_raw.nc;
• mctd_02a renames SeaBird variable names in ctd_jr302_NNN_raw.nc ;
• mctd_02b carries out oxygen hysteresis correction using SBE default 
  parameters or users preferred parameters (edit as appropriate, check it 
  matches your decision for SEBE data processing). Creates 
  ctd_jr302_NNN_24hz;
• mctd_03 averages data to 1Hz (output to ctd_jr302_NNN_1hz.nc) and 
  calculates derived variables (output to ctd_jr302_NNN_psal.nc);
• mdcs_01 creates empty dcs file which will store information about 
  start, bottom and end of good data in CTD file;
• mdcs_02 populates dcs file with data to identify bottom of cast.
• mdcs_03g allows the user to decide which scan numbers mark the start of 
  the downcast and the end of the upcast. This is a graphical interface. 
  The start of the downcast was selected to be the lowest pressure after 
  the CTD had soaked and been brought to the surface before descending.   
  The end of the downcast was selected as the last scan for which there 
  was good in-water oxygen, temperature, conductivity and salinity data 
  (note that oxygen data becomes out-of-water before the other variables 
  because the different sensor response times). Output to 
  dcs_jr302_nnn.nc.
  Phase 3 routines grouped under 'ctd_all_part2' ran the following:
• mctd_04 extract downcast data from psal file using index information 
  from dcs file; sort, interpolate gaps and average to 2db (output to 
  ctd_jr302_NNN_2db.nc);
• mdcs_04 merge positions of start, bottom and end cast from navigation 
  file into dcs file;
• mfir_01 read in information from SeaBird .bl file and create netCDF fir 
  file;
• mfir_02 merge time from ctd  file  onto  fir  file  using  scan  number  
  (output  to  fir_jr302_NNN_time.nc);
• mfir_03 merge CTD upcast data onto fir file;
• mfir_04 paste CTD fir data into sam file and output to 
  sam_jr302_NNN.nc;
• mwin_01  creates win file  which will hold winch data and extracts 
  times from start and end of 1Hz ctd  file;
• mwin_03 merge winch wire out data onto fir file;
• mwin_04 paste winch fir data into sam file; At this point the data can 
  be examined using some scripts to generate standard plots:
• mctd_checkplots and mctd_rawshow generate a series of plots of raw, 1hz 
  and 2db data. mctd_checkplots allows a series of previous casts to be 
  plotted also. The plots should be examined for data quality.
• mctd_rawedit is a graphical interface that allows the user to manually 
  select bad data cycles in temp, cond and oxygen. Preserves original raw 
  file as ctd_jr302_nnn_raw_original.nc and outputs new file 
  ctd_jr302_nnn_raw_cleaned.nc. The cleaned file is linked by a new 
  symbolic link called ctd_jr302_nnn_raw.nc so that following scripts 
  work on the cleaned version if it exists.
  The editing is done on the raw data file so that edits are preserved 
  throughout all derived files. So after the edits are finished, the 
  derived files need to be re-generated. This is done in steps mctd_02b, 
  mctd_03, mctd_04, mfir_03, mfir_04. These scripts can be run manually 
  or using smallscript.m (check and edit this first).
• list_ctd_1hz(nnn) generates and ascii listing of the 1hz file ready for 
  use in the LADCP processing. Each file was saved in /data/ctd and a 
  symbolic link created to it from the LADCP directory 
  (/data/ladcp/ix/data/CTD/)
• mbot_01.m takes bottle firing quality flags manually set in 
  bot_jr302_001.csv.  Output: bot_jr302_nnn.nc.
• mbot_02.m pastes the bottle firing codes into sam jr302_nnn.nc
  As header information for the CTD data files becomes available, the 
  information in the files can be updated through the following steps:
• mdep_01.m requires a matlab file (station_depth_jr302.mat) containing 
  water depth in variable 'bestdeps'. On JR302 this information came from 
  the LADCP data files where it existed, or from the bathymetry file 
  (saved as ascii file ctd_depths.csv). Where there was neither LADCP or 
  bathymetry data (one station) the depth was left as NaN.  mdep_01.m 
  pastes this information into headers of all CTD files.
• mdcs_04.m takes the lat and lon from the navigation (pos_jr302_01) at 
  the time of start, bottom and end  of each cast and pastes into 
  dcs_jr302_nnn_pos.nc.
• mdcs_05.m pastes the lat and lon for the bottom of the cast into the 
  headers of all CTD files.


2.3  CTD calibrations

Penny Holliday, Brian King, Damien Desbruyères

2.3.1  Oxygen

When oxygen bottle data had been pasted into the CTD sample files, and 
the individual station sample files had been appended (sam_jr302_all), 
the data were used to examine the performance of the CTD oxygen sensor. 
First the relationship between the bottle oxygen and uncalibrated CTD 
oxygen was derived (bottle sample units were converted to umol/kg using 
the calibrated CTD salinity). The standard procedure is to define an 
initial correction to the data (linear or quadratic), then apply further 
temperature- and/or pressure- dependent corrections if the calibrated 
residuals suggest one is required. For JR302 data, a linear initial fit 
followed by a pressure correction was applied.  The fit was used to 
define coefficients as follows:

    CTD_oxycal  = a*CTD_oxygen + b

where a = 1.0633 and b = 16.91. The subsequent pressure correction 
applied was a linear offset defined by interpolations between offset-
pressure pairs (-1, 0), (0, 1000) and (4, 3800). These coefficients are 
specified in function oxy_apply_cal.m called by mctd_oxycal.m

In mstar:

• mctd_oxycal: used to apply these calibrations to the CTD files 
(ctd_jr302_nnn_24hz). After calibrations have been applied, subsequent 
steps need to be repeated (mctd_03, mctd_04, mfir_03, mfir_04) this was 
done by editing and running smallscript.m. All sam_jr302_nnn files were 
re-appended to create a new version of sam_jr302_all.nc that contained 
the calibrated CTD conductivity, salinity and oxygen.

The calibration was initially determined from the first 30 stations of 
the cruise and subsequently monitored against newer samples. The CTD 
oxygen sensor was remarkably stable and this calibration was used 
unchanged for the rest of the cruise. Variations in the oxygen bottle 
residuals were associated with new batches of reagents used in the 
titrations up to station 179. The offsets between batches of chemicals 
was order 2 umol/kg and this can be considered to be the level of 
uncertainty associated with the samples.

From station 180 onwards however, there is an issue with the bottle 
oxygen samples that led us to label them all as "suspect data" (coloured 
red in Fig. 2.3.1). Those samples were not used to correct the CTD 
sensor. Examination of the CTD temperature-oxygen relationship before and 
after station 180 has led us to conclude there was no observable drift in 
the sensor to the end of the cruise.

The mean of the oxygen residuals (good samples from stations 1-180, and 
excluding outliers) was -1.1 ± 2.5 umol/kg.

 
Figure 2.3.1: Distribution of bottles fired (cyan) and "good" oxygen 
              samples (black). Samples from stations 180 onwards are 
              shown as red.
Figure 2.3.2: Calibrated CTD oxygen against bottle oxygen. Samples from 
              stations 180 onwards are shown as red.
Figure 2.3.3: Calibrated oxygen residuals against station number. 
              Samples from stations 180 onwards are shown as red.
Figure 2.3.4: Calibrated oxygen residuals against pressure. Samples from 
              stations 180 onwards are shown as red.


2.3.2  Salinity Calibration

CTD conductivity was calibrated with the water sample bottles (see 
section 3.1).



2.4  LADCP

2.4.1  Instrument technical details

A downward looking 300 kHz Workshorse LADCP was attached to the CTD frame 
for JR302. The configuration was 16x10m bins with data collected in beam 
co-ordinates and rotated to earth co-ordinates during processing. The 
LADCP was connected to a charger and by a serial cable to a BAS AME-
supplied laptop in the Chem Lab for programming and testing prior to each 
data, and data download after each station, using BB-talk. Data 
downloaded after each station were copied to the network legdata drive, 
along with the pre-deployment logs.

Command file: 

CR1
RN J302M 
WM15 TC2
LP1
TB 00:00:02.80
TP 00:00.00
TE 00:00:01.30 
LN25
LS0800 LF0 
LW1 
LV400 SM1 
SA011 SB0 
SW5500 
SI0
EZ0011101 
EX00100 
CF11101 CK
CS


2.4.2  Data Processing

Data from each station were processed on workstation FOLA using two 
software packages; the University of Hawaii software, and the Lamont-
Doherty IX software.

2.4.3  IMP

John Wynar

The IMP mk 3 consists of a Raspberry Pi (RPi) micro computer, and 
separate clock and 3-axis tilt/magnetic field sensor boards. 
Communication with the device is achieved wirelessly. Initially, when 
these boards were connected together and 5V power applied from a Farnell 
PSU, communication could not be established. However, subsequent testing 
using a proprietary PSU was successful and the system functions 
validated. The boards were then assembled together with a dc/dc converter 
which would provide the 5V necessary to power the system, stepped down 
from the 50V (approximately) of the LADCP battery pack. With the long 
antenna fitted, wireless communication with the IMP was easily achieved 
even when fitted into its pressure case and on the CTD frame. The 
pressure case was tested on the CTD frame to a depth of over 3000m 
without the IMP inside to ensure its water tight integrity.
 
Calibration of the IMP inside the pressure case was carried out in the 
lab as per the instructions and the data logged. As the IMP sensor board 
was to be kept to near horizontal when fitted, a line was drawn on the 
end cap to show the orientation of the boards when in the pressure case.

In actual operation, communication with the IMP was carried out using a 
laptop in the laboratory adjoining the CTD annexe. Logging (and other 
house-keeping tasks) was initiated and terminated using the Tera Term 
terminal software. Data were copied and backed up onto a network drive 
using WinSCP. Start and stop times were written onto a log sheet and 
referenced to the station number.

Problems only occurred on two occasions, the first after some 26 days of 
operation, when communication with the IMP could not be established. On 
the first occasion, power cycling the unit was attempted but without 
success. The next step was to remove the IMP from its pressure case and 
investigate further. Bench testing did not reveal any fault so the system 
was re-assembled and fitted back into the CTD frame and operation 
continued. The system “hung up” again two days later. This time simple 
power cycling re-booted the IMP and communication re-established. It is 
possible that insufficient time was given on the first occasion between 
disconnecting and re-applying power for a re-boot to take effect.

The data collected from the IMP during the cruise will be sent to the 
designer, Andreas Thurnherr, for analysis.



2.5  RBR Concerto CTD

John Wynar

The instrument (S/N 065583) was attached to brackets fitted to a vertical 
stanchion on the CTD frame (constructed of stainless steel) with the 
plastic clamps provided (Figure 2.5.1). This gave a separation of about 
50mm between the conductivity cell and the metalwork of the frame. This 
position was the best compromise which could be attained considering the 
aspects of (i) accessibility (to switch on logging), (ii) safety (to 
prevent accidental damage), (iii) free uncontaminated current flow 
through the cell, and (iv) proximity to the frame (affecting the cell’s 
external field).

The unit was depth rated for 2000 m, hence it was necessary to remove the 
instrument for CTD casts in excess of this. For the sake of convenience, 
it was also removed prior to the final shallow casts near to the Scottish 
coast. In any case, by then the instrument had logged over a hundred 
“dives” which was deemed sufficient for the purpose intended. The 
instrument’s logging could be initiated without using a computer which 
made it very simple to use. The end cap was simply twisted to a point 
where two marks lined up, the starting of logging confirmed by a slight 
and short period of vibration coming from inside the unit. To disable 
logging, the end cap was twisted to come in line with a different mark, 
again confirmed by a period of vibration.

The instrument was downloaded several times using the Ruskin software 
when it was convenient to do so, for instance when it had to be removed 
for deeper stations. On the first occasion, logging was disabled (for no 
particular reason). However, it was unknown at that point that when 
logging was re-enabled this would mean that the memory would be erased. 
It might be beneficial in a future revision of the software to allow 
logging to be enabled without erasing the memory. Also on this occasion, 
the clock was corrected to GPS time (albeit it was only 1 second slow) 
and the battery voltage recorded as 11.81V as displayed in the Ruskin 
software. On successive occasions, the battery voltage was noted as not 
being less than 12.0V, the fifth and final value being 12.02V. (The 
author also suggests that a channel displaying the battery voltage during 
deployment would be useful.) After re-setting the onboard clock during 
the first download, the clock was found to be 5 seconds slow some 29 days 
later. Total memory used at this point was 45.14MB although there was no 
numerical display of the memory remaining. There was, however, a sliding 
bar giving a graphical representation of unused memory.

 
Figure 2.5.1: The RBR concerto CTD attached to the stainless steel frame.





3.  WATER SAMPLE MEASUREMENTS

3.1  Salinity

Team: Brian King, Penny Holliday, Stefan Gary, Damien Desbruyères, 
      Jonathan Lawrence, Felicity Williams, John Wynar

Water samples from CTD casts and TSG underway measurements were analysed 
with a salinometer to retrieve accurate estimates of the conductivity 
ratio for further calibration of the CTD/TSG data. Crates of water 
samples and sea water standards (batch P156; K15 = 0.99984) were stored 
at the same temperature for at least 24 hours in the laboratory room 
before being analysed following the usual procedure of 3 rinsing – 3 
reading – average for each sample and standards. One (sometimes two) 
standard seawater (SSW) samples were run before and after each crate of 
samples. All readings were numerically recorded and saved in Excel and 
csv files as “sal_jr302_stationnumber” before being merged together in 
“sal_jr302_01.csv”.

The lab temperature fluctuated between about 20 and 23.5 °C. The same 
salinometer was used for most of the analysis (serial number 68959) and 
showed a satisfactory behaviour (light cycling, constant temperature, 
stability) during the whole cruise. A drift (probably electronically-
related) in the standard conductivity ratio was however revealed from 
standard 25 to standard 100 (see Figure 3.1.1). This initiated the use of 
a secondary machine (serial number 63360), which was yet aborted after 
noticing an inconsistency between the machine reading and the software 
display (station 66/67). The drift disappeared at about station 100 and 
standard conductivity ratio stabilized around 1.99980, although some 
“short-term” spreading around this value continued to be observed (e.g. 
higher ratios for standards 170 to 180, lower ratios for standards 230 to 
239).


Figure 3.1.1: The difference between the salinometer-measured conduc-
              tivity ratio and the label ratio of SSW samples (x10-5).
Figure 3.1.2: The offsets applied to all bottle conductivity ratios 
              (derived from Figure 3.1.1, see also Table 3.1.1) (black) 
              and the residuals after corrections applied.


By visually inspecting the temporal behaviour of the standard 
conductivity ratios, a correction was applied to sets of station samples. 
These offsets are given in the table below. The resulting calibrated 
bottle salinities were then used to adjust the CTD data.
 

Table 3.1.1: Offset applied to conductivity ratio, derived from SSW 
             analysis

     Station number  Offset applied to conductivity ratio (*10-5)
     ——————————————  ————————————————————————————————————————————
        1 to 20                            0
       21 to 30                           -1
       31 to 32                           -2
       33 to 36                           -3
       37 to 40                           -4
       41 to 46                           -5
       47 to 54                           -6
       55 to 60                           -7
       61 to 63                           -8
       64 to 65                           -9
       66 to 67                            0
       67 to 74                           -9
       75 to 79                          -10
       80 to 90                          -11



3.2 Dissolved Oxygen

Team: Hannah Donald, Carolyn Graves, Mark Stinchcombe and 
      Sinhue Torres-Valdes


All stations (except where no bottles were fired and one occasion when 
the night shift carried out a safety drill) occupied during JR302 were 
sampled for dissolved oxygen (DO). Sampling for DO was done just after 
CFCs and surfactants were sampled, or first when CFCs and surfactants 
were not sampled. Seawater was collected directly into pre-calibrated 
glass flasks using a Tygon® tube. Before the sample was drawn, bottles 
were flushed with seawater for several seconds (for about 3 times the 
volume of the bottle) and the temperature of the water was recorded 
simultaneously using a hand-held thermometer. The fixing reagents 
(manganese chloride and sodium hydroxide/sodium iodide solutions) were 
then added. Care was taken to avoid bubbles inside the sampling tube and 
sampling bottle, and a water seal was used after the sample was fixed and 
stoppered. Samples were thoroughly mixed following the addition of the 
fixing reagents and were then kept in a dark plastic crate for 30-40 min 
to allow the precipitate to settle to <50% the volume of the bottle. Once 
the precipitate had settled all samples were thoroughly mixed for a 
second time in order to maximize the efficiency of the reaction. Analyses 
were carried out within 2-4 h of sample collection.

Methods

DO determinations were made following the Winkler method using a 
potentiometric Ω-Metrohm titration unit (916 Ti-Touch, with electronic 
burettes). Chemical reagents were previously prepared at NOCS following 
the procedures described by Dickson (1994). Recommendations given by 
Dickson (1994) and by Holley and Hydes (1994) were adopted.

Oxygen calibration

Titrations were carried out with a thiosulphate solution which was 
prepared at least 24 hours before use (50 g dissolved in 1 L of Milli-Q 
water). Its concentration was determined by the use of certified OSIL 
standards of known molarity (1.667 mmol L-1). Typically, calibrations 
were carried out every 3-4 days to monitor potential changes in the 
concentration of the thiosulphate. Calculation of oxygen concentrations 
were facilitated by the use of an Excel spreadsheet set up with unique 
flask calibrated volumes and reagent dispenser volumes. When a new 
calibration was done, calculation sheets were updated with the latest 
numbers and oxygen concentrations determined with those results until a 
new calibration was completed. By examining the results of the 
calibrations carried out for a given batch of thiosulphate we determined 
that there was no significant drift in the concentration, and that the 
slight differences in the calibration results are likely due to 
instrument sensitivity and analytical noise. Hence, it was decided that 
an average of the calibrations done for a specific batch of thiosulphate 
was the best option to produce consistent results for oxygen 
concentration in samples as determined by plotting the difference between 
oxygen measurements against the CTD sensor data (residuals). Table 3.2.1 
lists the calibrations carried out during JR302 separated by thiosulphate 
batch, showing the results of the blank and standard, as well as the 
averages for a given thiosulphate batch.

For every cast replicates were taken from randomly selected Niskin 
bottles to assess reproducibility of the analysis. Figure 3.2.1 shows the 
results of replicates (same Niskin bottle sampled twice) selected 
randomly in every cast. Overall (except values flagged as bad), 
reproducibility was between 0.3 and 1 umol L-1.

Problems encountered

From CTD cast 180-200, a drift was noted in the residuals. Examination of 
CTD data suggested that the oxygen sensor was not responsible for this 
drift, and given that no chemical reagents or thiosulphate solution were 
changed during these measurements, we believe that the titration probe 
may be responsible for this drift for reasons we do not understand; all 
of a sudden the amount of thiosulphate added to titrate a sample at a 
specific depth increased relative to neighbouring stations at similar 
depths. The addition of thiosulphate was determined potentiometrically by 
the probe, and just as the problem appeared, it also disappeared. By the 
time this report was completed, this issue remained unresolved.


Figure 3.2.1: The absolute replicate difference for the oxygen bottles in 
              each CTD cast (n=236). The mean (0.96 mmol L-1) and the 
              standard deviation of –all values in the plot considered- 
              are specified with solid and dash line respectively (± 1.4 
              mmol L-1). Green symbols show replicate values flagged as 
              good (0 - 0.3 mmol L-1), yellow symbols show replicate 
              values flagged as good (0.3 - 1.1 mmol L-1) and red symbols 
              show remaining data, including values flagged as dubious or 
              bad (1.1 mmol L-1 and above).


References

Dickson, A.G. (1994) Determination of dissolved oxygen in seawater by 
    Winkler titration. Technical report, WOCE operations manual, WOCE 
    report 68/91 Revision 1 November 1994.

Holley, S.E. and Hydes, D.J. (1994) Procedures for the determination of 
    dissolved oxygen in seawater. Technical report, James Rennell Centre 
    for Ocean Circulation.


Table 3.2.1: JR302 Dissolved O2 analysis calibrations; showing number of 
             casts analysed with a given thiosulphate batch, dates on 
             which calibrations were carried out, stations for which 
             concentrations were originally calculated with a given 
             calibration, mean blank titre volume (BLK) per calibration 
             and per thiosulphate batch, standard titre volume (STD) per 
             calibration and per thiosulphate batch, STD minus BLK, 
             molarity of thiosulphate per calibration and per 
             thiosulphate batch, standard deviation (stdev) of average 
             molarity and stdev as percent of the mean molarity. 

No.     Date        Station     Blank    Blank    Standard  Standard  STD-    Molarity  Average  Stdev       % 
Casts               No.                  AVERAGE            AVERAGE   BLK
——————  ——————————  ——————————  ———————  ———————  ————————  ————————  ——————  ————————  ———————  ————————  —————
        04/06/2014  training    0.01190           0.51920             0.5073  0.199 

        07/06/2014  CTD001-003  0.01326           0.51520             0.5019  0.2010 
   001  10/06/2014  CTD004-026  0.01335           0.51622             0.5029  0.2006 
42  -   14/06/2014  CTD027-37   0.01320           0.51763             0.5044  0.2000 
   042  16/06/2014              0.01310           0.51532             0.5022  0.2008 
        16/06/2014  CTD040-42   0.01274  0.01311  0.51410   0.51521   0.5014  0.2012    0.2007   0.000468  0.23 

   043- 17/06/2014  CTD043-62   0.01476           0.51210             0.4973  0.2028 
33 076  21/06/2014  CTD063-76   0.01328  0.01402  0.51268   0.51239   0.4994  0.2020    0.2024   0.000593  0.29 

   077  24/06/2014  CTD077-96   0.01358           0.51524             0.5017  0.2011 
37  -   27/06/2014  CTD097-111  0.01364           0.51870             0.5051  0.1997 
   115  30/06/2014  CTD112-115  0.01336  0.01353  0.51746   0.51713   0.5041  0.2001    0.2003   0.00070   0.35 

   116  01/07/2014  CTD116-130  0.01392           0.51700             0.5031  0.2005 
62  -   04/07/2014  CTD132-177  0.01396           0.51570             0.5017  0.2010 
   177  10/07/2014              0.01296  0.01361  0.51626   0.51632   0.5033  0.2004    0.2006   0.000337  0.17 

   180- 10/07/2014  CTD180-205  0.01438           0.51460             0.5002  0.2016 
54 234  15/07/2014  CTD206-234  0.01330  0.01384  0.51516   0.51488   0.5019  0.2010    0.2013   0.000467  0.23 
 


3.3  Total Dissolved and Dissolved Inorganic Nutrients

Team: Hannah Donald, Carolyn Graves, Mark Stinchcombe and 
      Sinhue Torres-Valdes 


Lab Set up

A 7-channel Seal Analytical AA3 autoanalyser was set up in the main lab 
of the JCR for the analysis of micro-molar concentrations of dissolved 
inorganic nutrients (silicate, phosphate, nitrate plus nitrite-hereafter 
nitrate-, nitrite and ammonium) and total nutrients (total dissolved 
phosphorus and total dissolved nitrogen). Two members of the team (CG and 
ST) arrived on the ship on the 28th May to start mobilisation. Flight 
cases with instrumentation were distributed within the lab and chemical 
reagents identified and stored in the respective ship’s hazardous 
chemicals lockers. The two other members (HD and MS) arrived on the 30th 
when instrument installation began. Installation of the AA3 took two full 
days, involving; the fitting of new pump tubing and new cadmium columns, 
tubing connections between sampler-pumps-manifold-detectors, and a 
thorough cleaning with wash solutions as per Seal Analytical protocols. 
Simultaneously, chemical reagents (stock and working solutions) and 
standards (stock solutions and calibrants) were prepared. ‘Stocks’ are 
concentrated solutions from which working reagents/standards are prepared 
as required by solution stability or usage. Working standards were 
prepared in a saline solution (40 g NaCl in 1 L of Milli-Q water, here 
after artificial seawater or ASW), which was also used as a diluent for 
the analysis. Seal Analytical protocols used during JR302 were:

  i. Silicate in seawater method No. G-177-96 Rev 10 (Multitest MT19).
 ii. Phosphate in water and seawater method No. G-175-96 Rev. 13 
     (Multitest MT 18).
iii. Total dissolves phosphorus in seawater method No. MKA-0152-14 Rev. 0.
 iv. Total dissolved nitrogen in seawater method No. G-218-98 Rev. 12 
     (Multitest MT23).
  v. Nitrate and nitrite in seawater method No. G-172-96 Rev. 13 
     (Multitest MT19).
 vi. Nitrite in seawater method No. G-062-92 Rev. 3.
vii. Ammonium in water and seawater No. G-327-05 Rev. 6.


Calibrants

Table 3.3.1 lists compounds used for the preparation of stock standard 
solutions, weight of compound dissolved in 1 L of Milli-Q water and the 
resulting molarity of the solution. Dilutions were then made from stock 
solutions to prepare a set of five standards to calibrate the analysis. 
Table 3.3.2 shows target concentrations -which are concentrations aimed 
for when preparing the standards- and actual concentrations –which have 
been obtained given the molarity of stock solutions and/or that result 
from the combination of related chemical species (e.g., TN, NO3-+NO2-, 
NO2-, NH4+).


Table 3.3.1: Compounds used to prepare stock standard solutions, weight 
             dissolved in 1 L of Milli-Q water and Molarity of the 
             solution.

Compound                         Weight (g)  Molarity 1 L stock solution
———————————————————————————————  ——————————  ———————————————————————————
Ammonium Sulphate                  0.6919             10.0118
Potassium Nitrate                  0.5066              5.0107
Sodium Nitrite                     0.3449              4.9989
Potassium Di-hydrogen Phosphate    0.6811              5.0049
Sodium Metasilicate                1.4219              5.0032

 

Table 3.3.2: Set of calibration standards (Std) used for dissolved 
             inorganic and total dissolved nutrient analysis. 
             Concentration units are mmol L-1. Target concentrations are 
             shown in bold characters. Actual concentrations as 
             calculated from the molarity of the stock solution are shown 
             in normal characters. Note that concentrations for NO3-+NO2- 
             are the sum of NO3-+NO2- and NO2-, and concentrations for TN 
             also include those of NH4+.

        Si(OH)4    PO43-/TP       TN     NO3-+NO2-     NO2-      NH4+
—————  —————————  ——————————  —————————  —————————  —————————  —————————
Std 1   1   1.00  0.25  0.25   1   1.20   1   1.10  0.1  0.10  0.1  0.10
Std 2   5   5.00  0.75  0.75   5   6.51   5   5.51  0.5  0.50  1.0  1.00
Std 3  10  10.01  1.50  1.50  10  13.02  10  11.02  1.0  1.00  2.0  2.00
Std 4  20  20.01  3.00  3.00  20  25.54  20  22.04  2.0  2.00  3.5  3.50
Std 5  30  30.02  5.00  5.00  30  38.07  30  33.06  3.0  3.00  5.0  5.00


Although the range of calibrant concentrations is typically determined by 
minimum and maximum expected nutrient levels at any given location, for 
JR302 the range of calibrants for phosphate and ammonium were set to 5 
mmol L-1 despite the fact that maximum concentrations in the area of 
investigation were not expected to be greater than 1.5 mmol L-1 and ~2 
mmol L-1 for phosphate and ammonium, respectively. In the case of 
phosphate the decision was taken following lab based tests of the TP 
channel (which uses the same calibrants as those for phosphate) and whose 
performance was not acceptable at calibration levels of ≤2.5 mmol L-1. 
Once on board JR302, a top standard level of 5 mmol L-1 was found to 
properly reproduce peak shapes. In the case of ammonium, lab tests showed 
ammonium peak shapes were also not acceptable at ≤2.0 mmol L-1. Poor peak 
shape is observed at low concentrations because the resulting amplified 
instrument gain also amplifies the noise signal, rendering analytical 
results unreliable.

Unfortunately, less than two weeks into the cruise the TP channel stopped 
working. Attempts were made to fix it, but the work load did not allow 
for much time to be spent on this and it was then decided that samples 
from selected stations (upper 150 m of the water column where DOP occurs 
at detectable levels) would be collected and stored frozen for later 
analysis on land. At the same time, the ammonium channel was found to be 
performing well and reliably. Thus, from run 19 the calibrant range for 
phosphate and ammonium was changed as shown in Table 3.3.3. Additionally, 
the silicate range was increased to include the certified values (KANSO 
CRMs) for this variable, which were slightly higher than our original 
adopted range.


Table 3.3.3: Set of calibration standards (Std) used for dissolved 
             inorganic and total dissolved nutrient analysis from 
             run 19 (see text for further information). Concentrations 
             in µmol L-1.

        Si(OH)4    PO43-/TP       TN     NO3-+NO2-     NO2-      NH4+
—————  —————————  ——————————  —————————  —————————  —————————  —————————
Std 1   1   1.00  0.10  0.25   1   1.20   1   1.10  0.1  0.10  0.1  0.10  
Std 2   5   5.00  0.50  0.75   5   6.01   5   5.51  0.5  0.50  0.5  0.50  
Std 3  10  10.01  1.00  1.50  10  12.02  10  11.02  1.0  1.00  1.0  1.00  
Std 4  20  20.01  2.00  3.00  20  24.05  20  22.04  2.0  2.00  2.0  2.00  
Std 5  40  40.03  3.00  5.00  30  36.07  30  33.06  3.0  3.00  3.0  3.01



Quality Controls (QCs)

Organic standards: Total dissolved nitrogen (TDN) and total dissolved 
phosphorus (TDP) are measured as nitrate and phosphate respectively 
following oxidation of the sample by exposure to UV radiation and a wet 
chemical oxidation with potassium persulphate. During JR302 five organic 
compounds containing phosphorus and/or nitrogen were used to test the 
efficiency of the oxidation. Table 3.3.4 lists the compounds used to 
prepare stock solutions and Table 3.3.5 lists the concentration of 
standards prepared, the average concentration measured during the cruise 
for each compound, the standard deviation of all measurements, and the 
percent oxidation efficiency. Time series of the recovery of nitrogen 
from each of the organic compounds used are shown in Figure 3.3.1.


Table 3.3.4: Compounds used to prepare stock organic standard solutions 
             to test oxidation efficiency of TDN and TDP, weight dis-
             solved in 1 L of Milli-Q water and Molarity of the solution.

Compound                       Weight (g)  N molarity 1 L stock solution
—————————————————————————————  ——————————  —————————————————————————————  
Caffeine (Caff)                  0.1203               2.4780    
Urea (Ur)                        0.1547               5.0509    
Adenosine triphosphate (ATP)     0.3030               2.5033   
Guanosine monophosphate (GMP)    0.2065               2.5106    
Adenosine monophosphate (AMP)    0.1895               2.5685  



Table 3.3.5: Set of organic standards used to test the oxidation 
             efficiency of the TDP and TDN channels. This table shows 
             prepared concentration ([ ]), average concentration ([Av]) 
             of total measurements (n) during JR302 and respective 
             standard deviation of measurements, and average percent (%) 
             oxidation efficiency. Concentration units are mmol L-1.

          |             N              |             P
     —————|————————————————————————————|——————————————————————————
          | [  ]  [Av]  Sd    n    %   | [  ]  [Av]   sd   N   %  
     Caff | 4.99  4.24  0.18  54  85.4 | ----          
     Ur   | 5.05  4.09  0.91  54  81.0 | ----          
     ATP  | 2.50  1.77  0.20  54  70.6 | 1.50  0.81  0.02  3  54.1  
     GMP  | 5.02  3.03  0.22  54  60.4 | 1.00  0.73  0.01  3  73.0  
     AMP  | 5.14  3.84  0.14  53  74.7 | 1.03  0.97  0.04  3  93.7  



Certified Reference Materials (CRM) from Hansell’s Lab (University of 
Florida, USA) from deep and surface Atlantic Ocean waters were also used 
to test the oxidation efficiency for TN. These CRMs are designed for the 
measurement of dissolved organic carbon and dissolved organic nitrogen 
via high temperature combustion and are fixed with small amounts of 
hydrochloric acid. In order to measure them with the colorimetric 
techniques employed here, we needed to neutralise their pH of ~3.00 to a 
pH of 7.0 using NaOH (20-50 mL of a 10.2 M solution). Although this 
introduced noise to these measurements, these CRMs provided an additional 
test for the oxidation efficiency of the method (not shown here).

 
Figure 3.3.1a: Time series of the nitrogen recovered (TN autoanalyser 
               channel) from the various organic compounds used to test 
               the oxidation efficiency of the method (concentration 
               plotted against run number; n=54). Error bars show the 
               standard deviation of the global mean. The concentration 
               of nitrogen of each organic compound was 5 mmol L-1, 
               except ATP, which was 2.5 mmol L-1.

 
Figure 3.3.1b: Time series of the nitrogen recovered (TN autoanalyser 
               channel) from the various organic compounds used to test 
               the oxidation efficiency of the method (concentration 
               plotted against run number; n=54). Error bars show the 
               standard deviation of the global mean. The concentration 
               of nitrogen of each organic compound was 5 mmol L-1, 
               except ATP, which was 2.5 mmol L-1.



Inorganic nutrients: 

In order to test the accuracy and precision of the analyses, CRMs from 
The General Environmental Technos Co., Ltd., (KANSO) were measured in all 
but one run. During JR302 KANSO CRMs lot CA and lot BU were used; 
certified concentrations of both are shown in Table 3.3.6. Lot CA is 
water from Suruga Bay, Japan, collected at 270 m depth, 19ºN, 130ºE, 
salinity 34.376 (certified date 19/06/2013, production date 22/02/2013, 
expiry date 22/02/2019). Lot BU is from the Suruga Bay, Japan, collected 
at 397 m depth, 32ºN, 144ºE, salinity 34.538 (certified date 03/08/2012, 
production date 26/04/2011, expiry date 26/04/2017). Average results from 
the measurement of KANSO CRMs are also shown in Table 5. The methods 
employed here are able to reproduce the CRMs values for nitrate+nitrite 
and phosphate within the overall analytical uncertainty. However, our 
methods seem to underestimate nitrite and silicate by 0.017 mmol L-1 (Lot 
CA) and 0.016 mmol L-1 (Lot BU) and by 3.99 mmol L-1 (Lot CA) 2.69 mmol 
L-1 (Lot BU) for nitrite and silicate, respectively (see Table 5). 
Although no certified concentration is reported for TN, measurements of 
KANSO CRMs provided consistent values throughout the cruise (Lot CA 
21.68±1.19 mmol L-1; Lot BU 8.03±0.64 mmol L-1).

 
Table 3.3.6: Certified concentrations (mmol kg-1) of KANSO CRMs used dur-
             ing JR302 and our results for each lot (also in mmol kg-1).


            | Nitrate        Nitrite         Silicate      Phosphate  
————————————|——————————————  ——————————————  ————————————  —————————————
KANSO CA    | 19.56 ± 0.19   0.055 ± 0.0047  36.06 ± 0.30  1.419 ± 0.029  
KANSO BU    |  3.88 ± 0.063  0.068 ± 0.0043  21.01 ± 0.68  0.372 ± 0.010  
————————————|——————————————  ——————————————  ————————————  —————————————
Measured CA | 19.48 ± 054    0.038 ± 0.019   32.07 ± 0.45  1.47 ± 0.03  
Measured BU |  3.94 ± 0.21   0.052 ± 0.021   18.32 ± 0.62  0.36 ± 0.01



Cadmium column reduction efficiency: 

The reduction of the nitrate (NO3-) present in a sample or from the 
oxidation of TN in a sample, to nitrite (NO2-), is achieved by passing 
the sample through a column filled with granular cadmium (cadmium 
column); cadmium is oxidised and nitrate is reduced. With use, the 
capacity of the cadmium column to reduce nitrate diminishes. The 
reduction efficiency was determined in every run by measuring nitrite and 
nitrate standards of similar concentrations (30 mmol L-1). The ratio of 
nitrate to nitrite expressed as a percentage provides an indication of 
the reduction efficiency of the cadmium column.  For the analysis to 
produce reliable results, the oxidation efficiency needs to be >90%. When 
the efficiency is lower, the cadmium column is typically replaced. New 
cadmium columns are conditioned by flushing ammonium chloride through 
them for at least 10 hours; the time it takes to attain stable reduction 
efficiencies.

AA3 Test
Upon installation, the AA3 was tested by carrying out three analytical 
runs. For the first test, only standards (calibrants) were used to 
provide an indication of the linearity of calibration curves. This was 
followed by two runs with a full set of QCs standards and KANSO and 
Hansell’s Lab CRMs to verify the system was working properly. Following 
the tests, every run was set up as shown in Table 3.3.7.

Analyses
Seawater was collected for the analysis of micro-molar concentrations of 
dissolved inorganic and total nutrients. Samples were collected directly 
into 15 mL plastic centrifuge tubes. These were rinsed with sample water 
at least three times before withdrawing the sample. Tubes were stored in 
a fridge at approximately 4°C until sampling for 2 or more stations was 
completed; analyses were thus carried out for typically 2-10 stations at 
a time depending on frequency of sampling and number of samples per cast. 
Analyses of individual CTD casts were thus done from just after sampling 
to within 10 h after sample collection. All unique sampling depths were 
sampled and analysed.

Observations
Prior to the cruise all labware was washed with 10% HCl and rinsed with 
MQ water. Once on board, all labware was rinsed several times before use. 
Following each run, each analytical channel was flushed with wash 
solutions and the autosampler with Milli-Q water following Seal 
Analytical cleaning protocols. At least once per week the system was 
thoroughly cleaned with sodium hydroxide (TP lines), ~10 % hydrochloric 
acid (ammonium), and sodium hypochlorite (nitrite, nitrate, TN, phosphate 
and silicate line). After turning the AA3 on, about 2 hours are required 
before obtain stable baselines are established and a run can be started 
(approximately 30 minutes of flushing the instrument with wash solutions 
(as per Seal Analytical protocols) and 1.5 h flushing channels with their 
respective chemical reagents).

Batches of ASW were prepared about twice per week, and the different 
chemical reagents were prepared from daily, to every 2 or 3 days.

Samples from sections around Cape Farewell affected by sea ice and 
glacier melt with salinity <34 were analysed separately using ASW of 
lower salinity (diluted by using 800 mL of normal ASW topped up to 1000 
mL with Milli-Q water).

Performance of the Analyser
The performance of the autoanalyser was monitored by producing time 
series of standards, QCs, CRMs and cadmium column reduction efficiency, 
plotted against run/analysis number. The precision of the method employed 
by each nutrient channel was determined by monitoring the variations of 
the complete set of standards, QCs and CRMs measured throughout the 
cruise. Accuracy of the analysis was determined via the measurement of 
KANSO CRMs.

Results of the measurement of standards; average concentration, 
analytical uncertainty (sd) and precision of the analysis at the 
different concentration levels, are summarised in Tables 3.3.8 and 3.3.9 
and shown in Figure 3.3.2. Random samples were collected in duplicate in 
every cast to assess reproducibility. The average difference between 
duplicates (n=315) were < 0.03, 0.005, 0.2, 0.05, 0.003, and 0.013 mmol 
L-1 for silicate, phosphate, TP, TN, nitrate+nitrite, nitrite, and 
ammonium, respectively. The limits of detection for the different 
variables, determined as twice the standard deviation of the lowest 
concentration standard were 0.08, 0.02, 0.18, 0.15, 0.04 and 0.07 mmol L-
1 for silicate, phosphate, TP, TN, nitrate+nitrite, nitrite, and 
ammonium, respectively.

Problems
(i) TP channel: this channel stopped working after run 3 and we were not 
able to fix it. This channel has never worked properly since it was first 
installed at NOC back in January 2013. We tested it for three months 
between July-September 2013 following Seal Analytical advice, but were 
not able to make it work. The system was then sent back to Seal 
Analytical headquarters in Germany where it was further tested and the 
method modified and improved. We tested that new method a week before 
packing for JR302, but did not get it to work in the lab. We have been in 
contact with Seal Analytical and they are planning to send an 
engineer/technician to carry out further work on the TP channel once back 
at NOC.

(ii) Ammonium Channel: this channel stopped working from run 19 to 21; 
there was no signal from the channel despite the fact that the 
fluorometer and connections were working properly. Following some tests 
by MS, it was found that some batches of the main fluorescence reagent, 
orthophthalaldehyde (OPA), were most likely degraded and thus the 
reaction for florescent detection of ammonium was not occurring. Due to 
the OPA being a hazardous material that requires storage at less than 
5ºC, this reagent was airfreighted just a few days prior to the team 
joining the ship. Unfortunately, the shipping company re-packed our boxes 
and did not label them properly. As a result, upon delivery to the ship 
there was confusion as to what boxes contained temperature-sensitive 
reagents and thus they were not stored in the fridge for about two days. 
This seems to have affected some of the OPA. Another problem found with 
this channel is that clogs tend to form within the manifold and within 
the fluorometer, possibly due to a combination of heat and reaction of 
residual chemical reagents mixed with washing/cleaning solutions. It was 
observed that clogging could be diminished by cleaning the system after 
switching off the heater and allowing it to cool down to room 
temperature. By station 216 the gain of the ammonium channel had 
increased from 3 or 4 (as initially) to over a hundred, rendering the 
measurements unreliable despite the preparation of several new OPA 
solutions. Thus, we were not able to measure ammonium from CTD cast 216 
onwards.

(iii) Cadmium column on the nitrate+nitrite channel: For reasons we do 
not fully understand, any newly installed cadmium column on this channel 
seems lose its reduction efficiency from the start (see Figure 3.3.3). By 
experience using autoanalysers in previous cruises we know that the life 
span of a new cadmium column is approximately 2 to 3 weeks depending on 
number of samples analysed. However, on the AA3 the efficiency starts to 
decrease from the moment the column is installed. What is most puzzling 
is the fact that once the reduction efficiency decreased below 90%, the 
cadmium column was swapped to the TN channel, where it performed at 100% 
for far longer (1-1.5 weeks); this despite having been used for 3 or 4 
days in the nitrate+nitrite. Also intriguing is the fact that the CRMs 
and QCs continue to produce reliable results. Thus, rather than using the 
nitrate to nitrite ratio of the reduction efficiency standards as a way 
of monitoring the performance of the cadmium column, we decided to 
replace any new column after 3-4 days and then switch it over to the TN 
channel where it performed well.  When we first noticed this problem, CTD 
casts 30 and 31 (run 11), and casts 32 and 33 (run 12) had been affected. 
By measuring CRMs in every run we were able to detect when the reduction 
efficiency of the cadmium column affected the results. We were then able 
to correct affected stations using a correction factor determined from 
the ratio of the average results of KANSO CRMs of non-affected runs 
relative to those affected. By re-evaluating the data, we concluded this 
resulted in nitrate+nitrite (or TN) profiles consistent with neighbouring 
stations which were not affected by the problem. Table 3.3.10 lists 
stations that were affected by low reduction efficiency and correction 
factors employed.


Table 3.3.7: Calibration and QCs analysis template.

ID                         Description                        Comment
—————————————————————————  —————————————————————————————————  ————————————————————————
Primer                     Initial peak identified by         Followed by a 
                           the AA3 software as the start      null (or wash)
                           of a run.

2 Drifts                   Separate standard of constant      Followed by a null
                           concentration used by the soft-   
                           ware in combination with 
                           ‘baseline’ checks to correct 
                           for potential drifts of the 
                           baseline. The first drift is 
                           specified as a null since it 
                           may be affected by carry over 
                           and thus is not taken into 
                           account by the software.
 
3 x STD 1                  The first standard is specified    Followed by a null
                           as a null since it may be affec-   
                           ted by carry over and thus is
                           not taken into account by the 
                           software.
 
3 x STD 2                  As above.                          Followed by a null

3 x STD 3                  As above.                          Followed by a null

3 x STD 4                  As above.                          Followed by a null

3 x STD 5                  As above.                          Followed by a null

2 Drifts                   As for the drifts above.           Followed by 2 nulls

Baseline                   Baseline check                     Followed by 1 null

4 x 30 mmol L-1 NO2- STD   The first is specified as a null   Cadmium column 
                                                              efficiency test

3 x 30 mmol L-1 NO3- STD                                      Cadmium column 
                                                              efficiency test. 
                                                              Followed by a null

2 x GMP                    The first is specified as a null   Followed by a null

2 x Ur                     The first is specified as a null   Followed by a null

2 x AMP                    The first is specified as a null   Followed by a null

2 x ATP                    The first is specified as a null   Followed by a null

2 x Caff                   The first is specified as a null   Followed by a null

2 x Hansell’s Lab CRM      The first is specified as a null   Followed by a null
  surface

2 x Hansell’s Lab CRM      The first is specified as a null   Followed by a null
  deep

2 x KANSO CRM              The first is specified as a null   Followed by a null

2 Drifts                   The first is specified as a null   Followed by 2 nulls

Baseline                   Baseline check                     Followed by a null

Samples                    Ordered from surface to deep       Samples from CTD casts
                           samples to avoid cross contamina-  were separated by Drifts
                           tion and grouped by CTD cast.      and baselines as above.

Pairs of STD 1 to 5        To test consistency with stan-     Followed by Drifts and
                           dards specified as calibrants      baseline check.
                           in the software.

End of run



Table 3.3.8a: Mean and variation of all calibration standards measured 
              for initial standard concentrations (runs 1-18), and 
              precision of the analysis at each concentration (mmol L-1). 
              Note that TP was included in runs 1-3 only.

      |   Si(OH)4  Prec.|   PO43-   Prec.|    TP     Prec.|     TN     Prec. 
————— | ——————————————— | —————————————— | —————————————— | ————————————————
Std 1 |  1.03±0.06  6.3 | 0.24±0.02  7.4 | 0.29±0.01  4.6 |  1.30±0.12  9.0  
Std 2 |  5.07±0.08  1.6 | 0.74±0.01  1.7 | 0.73±0.02  2.7 |  6.52±0.11  1.7  
Std 3 | 10.03±0.21  2.1 | 1.51±0.04  3.1 | 1.41±0.04  3.1 | 12.96±0.25  1.9  
Std 4 | 20.15±0.21  1.0 | 3.09±0.05  1.6 | 2.94±0.01  0.4 | 25.63±0.27  1.0  
Std 5 | 29.90±0.17  0.6 | 4.95±0.04  0.8 | 5.07±0.01  0.2 | 38.03±0.27  0.7  



Table 3.3.8b: Mean and variation of all calibration standards measured 
              for initial standard concentrations (runs 1-18), and 
              precision of the analysis at each concentration (mmol L-1).

          |   NO3+NO2   Prec.|    NO2    Prec.|    NH4     Prec.  
    ————— | ———————————————— | —————————————— | ———————————————
    Std 1 |  0.98±0.10  10.4 | 0.09±0.01  9.7 | 0.08±0.03  32.4  
    Std 2 |  5.69±0.14   2.4 | 0.50±0.01  2.3 | 1.00±0.03   3.2  
    Std 3 | 11.34±0.24   2.1 | 1.00±0.02  1.7 | 2.04±0.05  2.3  
    Std 4 | 22.38±0.14   0.6 | 2.02±0.02  1.0 | 3.56±0.04  1.1  
    Std 5 | 32.69±0.19   0.6 | 2.99±0.02  0.6 | 4.97±0.04  0.8  



Table 3.3.9a: Mean and variation of all calibration standards measured 
              for second standard concentrations (runs 19-54), and 
              precision of the analysis at each concentration (mmol L-1).

      |   Si(OH)4  Prec.|   PO43-   Prec.|   TP  Prec.  |     TN     Prec.  
————— | ——————————————— | —————————————— | ———————————— | ———————————————
Std 1 |  1.00±0.04  3.9 | 0.11±0.01  8.7 | not analysed |  1.37±0.09  6.6  
Std 2 |  5.08±0.03  0.6 | 0.48±0.01  1.9 | not analysed |  5.88±0.14  2.3  
Std 3 | 10.13±0.07  0.7 | 0.98±0.02  1.9 | not analysed | 11.83±0.20  1.4  
Std 4 | 20.10±0.09  0.5 | 1.99±0.02  1.1 | not analysed | 23.89±0.17  0.7  
Std 5 | 39.94±0.12  0.3 | 3.02±0.02  0.7 | not analysed | 36.25±0.23  0.6  



Table 3.3.9b: Mean and variation of all calibration standards measured 
              for second standard concentrations (runs 19-54), and 
              precision of the analysis at each concentration (mmol L-1). 
              Note that NH4 was included in runs 22-52 only.

             |   NO3+NO2  Prec.|    NO2     Prec.|    NH4     Prec.  
       ————— | ——————————————— | ——————————————— | ———————————————
       Std 1 |  1.06±0.08  7.3 | 0.10±0.02  15.8 | 0.12±0.03  28.0  
       Std 2 |  5.52±0.12  2.2 | 0.50±0.01   1.4 | 0.48±0.02   5.0  
       Std 3 | 11.14±0.20  1.8 | 1.00±0.01   1.5 | 0.99±0.02   2.3  
       Std 4 | 22.18±0.14  0.6 | 2.00±0.02   0.8 | 2.04±0.03   1.3  
       Std 5 | 32.93±0.17  0.5 | 3.00±0.01   0.5 | 2.99±0.02   0.6  



Table 3.3.10: Correction factors used to correct data affected by low 
              reduction efficiency of the cadmium column in the 
              nitrate+nitrite channel and TN channel.

             Channel     | Run No  CTD casts   Correction factor  
         ——————————————— | ——————  ——————————  —————————————————
         Nitrate+nitrite |   11     30 to 31         1.067  
         Nitrate+nitrite |   12     32 to 33         1.168  
         Nitrate+nitrite |   47    170 to 180        1.09  
         Nitrate+nitrite |   48    181 to 185        1.14  
         Nitrate+nitrite |   49    186 to 191        1.12  
         Nitrate+nitrite |   51    198 to 208        1.046  
         Nitrate+nitrite |   52    209 to 215        1.043  
         Nitrate+nitrite |   53    216 to 224        1.062  
         TN              |   14     37 to 40         1.089  



Figure 3.3.2a: Time series of standards set up as calibrants for the 
               analysis (black |symbols) and measured as unknowns at the 
               end of each run (blue symbols). Error bars show the 
               standard deviation of the mean of all runs (n=54)

Figure 3.3.2b: Time series of standards set up as calibrants for the 
               analysis (black symbols) and measured as unknowns at the 
               end of each run (blue symbols). Error bars show the 
               standard deviation of the mean of all runs (n=54)

Figure 3.3.3:  The efficiency of the cadmium column in reducing nitrate 
               to nitrite is tested by measuring a nitrite and nitrate 
               standard of similar concentration (~30 mmol L-1). The 
               ratio of nitrate to nitrite expressed as percentage (%) 
               provides an indication of the reduction efficiency. The 
               concentration of both standards may not be exactly the 
               same, resulting in a ratio slightly higher or lower or 
               than 1 (or lower than 100%). Knowing this, the nitrate to 
               nitrite ratio of a newly installed cadmium column is 
               expected to remain relatively constant. 7 new cadmium 
               columns were installed during JR302. It can be seen that 
               any new column installed (open diamonds close to 100% 
               efficiency) in the nitrate+nitrite channel lost its 
               reduction efficiency immediately. This column, when 
               swapped to the TN channel, performed well (slightly above 
               100%, black dots).



3.4  Carbonate system measurements

Eithne Tynan, Rebecca Garley, Alex Griffiths and Claudia Fry


3.4.1  DIC/TA

Sampling protocol
Samples for total alkalinity (TA) and dissolved inorganic carbon (DIC) 
were drawn from the Niskin bottles with a piece of Tygon tubing into 
borosilicate glass bottles following best practices (Dickson et al 2007). 
Most bottles were 250ml but for every cast two 500ml bottles were taken 
at an upper water column and deep water column depth to test instrument 
precision. Additionally, the surface and deepest depths were sampled as 
duplicates in two 250 ml bottles, to test for sampling error. All samples 
were immediately poisoned with 50ul of a saturated mercuric chloride 
solution (100ul for 500ml bottles) after leaving a headspace of 1% of the 
volume in each bottle to allow for thermal expansion. Samples were taped 
and stored in a cool dark place until analysis.


3.4.2 Analysis
Two VINDTA 3C system (Marianda, Kiel) were brought to sea to analyze DIC 
and TA on board. VINDTA #24 was connected to a CM5014 CO2 coulometer 
(UIC, Inc.) and VINDTA #38 was connected to a newer CM5015 CO2 coulometer 
(UIC, Inc.). Both these coulometers have the CM5011 emulation software.

For DIC analysis, samples are warmed in a water bath for at least 30 mins 
before analysis. A set volume of the sample (~20ml) is acidified by 
addition of excess 10% phosphoric acid, which converts all inorganic 
carbon species to CO2. This is carried into the coulometric cell by an 
inert carrier gas (CO2-free N2 that is first passed through a magnesium 
perchlorate and soda lime scrubber), and a coulometric titration deter-
mines the amount of CO2, which is equal to DIC.

For TA determination, small increments of 0.1 M hydrochloric acid are 
added to a set volume of sample (~100ml) while the electromotive force is 
measured by a glass and reference electrode system. The amount of acid 
added to reach the carbonic acid equivalence point is equal to the TA.

Once analysis started and on testing with the same batch of seawater, it 
was noticed that VINDTA #38 had a considerable DIC drift, with values 
decreasing by 10umol every 10-15 samples. When investigating into the 
cause of this, and after switching the coulometers on the two systems, 
the 5015 coulometer was identified as the source of this drift. UIC were 
contacted and after failed attempts to correct this it was decided to 
leave CM5015 and send it back to UIC after the cruise. In order to 
maximize the number of samples analyzed for the rest of the cruise DIC 
was run on VINDTA #24 connected to the CM5014 coulometer and TA was run 
on VINDTA #38. DIC titrations are quicker than TA so samples for TA would 
accumulate during the run. However when changing the coulometric cell for 
DIC was required, the majority of TA samples were run by the time the new 
cell was prepared and settled. This set-up allowed a throughput of 
approximately 50 samples per 24 hours.

On the fourth week of the cruise, the DIC titrations started to be 
extremely noisy with alternating end- points of 0 and ~100. Once again, 
electronic issues with the coulometer were identified but on this 
occasion it was possible to correct them on the ship and mainly consisted 
of adjusting the voltages on some of the coulometer components. The 
CM5014 will need a recalibration after the cruise, but this should not 
affect results as it just produces an offset in the measurements that is 
corrected for by running CRMs.

Regular measurements of both DIC and TA were made from batch 135 and 136 
Certified Reference Material (CRM) from A. G. Dickson (Scripps 
Institution of Oceanography) and used to calibrate the results as 
follows:

DICsample, corrected = DICsample, measured x (DICCRM, certified/DICCRM, measure) 
TAsample, corrected  = TAsample, measured x (TACRM, certified/TACRM, measured)

No difference in correction factors was found between the two batches. To 
obtain the final results in units of µmol kg-1, a correction for density 
(ρ) due to salinity (S) variations was then applied using salinity 
measured from Niskin bottle samples and an equation of the form (Zeebe 
and Wolf-Gladrow 2001):

ρsea water, 25°C = ρpure water, 25°C + AS + BS1.5 + CS2

For DIC, CRMs were run at the beginning, middle and end of each 
coulometer cell. Cell solution was replaced every 12 hours with average 
titration times of 10 minutes (ranged from 8-17 mins). The average value 
of the three CRMs during the cell session was used to calculate the 
correction factor for each cell (shown on Figure 3.4.1). Before cell 
session 40 correction factors were centred around 1.0333, while after it 
they were centred around 1.0343. This shift was due to the adjustment of 
the electronics on the CM5014 coulometer due to the noise described 
previously. While recalibration of the unit will be needed after the 
cruise, the spread of the correction factors appeared to decrease after 
electronic adjustment.

For TA measurements, one 20L batch of 0.1M HCl acid was prepared at the 
beginning of the cruise and stored in a plastic carboy in the fumehood. 
Bottles for the titrino were subsampled from this throughout the cruise. 
VINDTA 24 was only used for TA in the first two weeks of the cruise when 
all TA measurements were switched to VINDTA 38. Figure 3.4.2 shows the 
correction factors for TA obtained from the CRMs run during each of the 
acid bottles. The decrease in the correction factor for VINDTA 38 
throughout the cruise can be attributed to the evaporation of the bulk 
batch of acid in fumehood and not to a drift of the instrument itself. 
Therefore each set of samples run on a particular acid bottle was 
corrected with the average correction factor obtained from that bottle.

For TA determination, small increments of 0.1 M hydrochloric acid are 
added to a set volume of sample (~100ml) while the electromotive force is 
measured by a glass and reference electrode system. The amount of acid 
added to reach the carbonic acid equivalence point is equal to the TA.

Once analysis started and on testing with the same batch of seawater, it 
was noticed that VINDTA #38 had a considerable DIC drift, with values 
decreasing by 10umol every 10-15 samples. When investigating into the 
cause of this, and after switching the coulometers on the two systems, 
the 5015 coulometer was identified as the source of this drift. UIC were 
contacted and after failed attempts to correct this it was decided to 
leave CM5015 and send it back to UIC after the cruise. In order to 
maximize the number of samples analyzed for the rest of the cruise DIC 
was run on VINDTA #24 connected to the CM5014 coulometer and TA was run 
on VINDTA #38. DIC titrations are quicker than TA so samples for TA would 
accumulate during the run. However when changing the coulometric cell for 
DIC was required, the majority of TA samples were run by the time the new 
cell was prepared and settled. This set-up allowed a throughput of 
approximately 50 samples per 24 hours.

On the fourth week of the cruise, the DIC titrations started to be 
extremely noisy with alternating end- points of 0 and ~100. Once again, 
electronic issues with the coulometer were identified but on this 
occasion it was possible to correct them on the ship and mainly consisted 
of adjusting the voltages on some of the coulometer components. The 
CM5014 will need a recalibration after the cruise, but this should not 
affect results as it just produces an offset in the measurements that is 
corrected for by running CRMs.

Regular measurements of both DIC and TA were made from batch 135 and 136 
Certified Reference Material (CRM) from A. G. Dickson (Scripps 
Institution of Oceanography) and used to calibrate the results as 
follows:

DICsample, corrected = DICsample, measured x (DICCRM, certified / DICCRM, 
measure) TAsample, corrected = TAsample, measured x (TACRM, certified / 
TACRM, measured)

No difference in correction factors was found between the two batches. To 
obtain the final results in units of μmol kg-1, a correction for density 
(ρ) due to salinity (S) variations was then applied using salinity 
measured from Niskin bottle samples and an equation of the form (Zeebe 
and Wolf-Gladrow 2001):

ρsea water, 25°C = ρpure water, 25°C + AS + BS1.5 + CS2

For DIC, CRMs were run at the beginning, middle and end of each 
coulometer cell. Cell solution was replaced every 12 hours with average 
titration times of 10 minutes (ranged from 8-17 mins). The average value 
of the three CRMs during the cell session was used to calculate the 
correction factor for each cell (shown on Figure 3.4.1). Before cell 
session 40 correction factors were centred around 1.0333, while after it 
they were centred around 1.0343. This shift was due to the adjustment of 
the electronics on the CM5014 coulometer due to the noise described 
previously. While recalibration of the unit will be needed after the 
cruise, the spread of the correction factors appeared to decrease after 
electronic adjustment.

For TA measurements, one 20L batch of 0.1M HCl acid was prepared at the 
beginning of the cruise and stored in a plastic carboy in the fumehood. 
Bottles for the titrino were subsampled from this throughout the cruise. 
VINDTA 24 was only used for TA in the first two weeks of the cruise when 
all TA measurements were switched to VINDTA 38. Figure 3.4.2 shows the 
correction factors for TA obtained from the CRMs run during each of the 
acid bottles. The decrease in the correction factor for VINDTA 38 
throughout the cruise can be attributed to the evaporation of the bulk 
batch of acid in fumehood and not to a drift of the instrument itself. 
Therefore each set of samples run on a particular acid bottle was 
corrected with the average correction factor obtained from that bottle.

 
Figure 3.4.1: Correction factors per coulometer cell run on VINDTA 24.


Replicate analysis from a 500ml bottle were used to evaluate precision of 
the instruments for both TA and DIC. Duplicate analysis (samples drawn on 
two different 250ml bottles from the same niskin bottle) were used on DIC 
to check for sampling technique, while on TA it was used to check no 
change in concentration occurred between the time the bottle had been run 
for DIC and running on TA. Figure 3.4.3 shows the absolute differences 
between duplicate and replicate measurements. The standard deviation of 
the duplicates was taken as the precision of the measurements for this 
cruise.

In total 2167 samples were collected for DIC/TA on JR302, and 1616 of 
these were analysed on board. 551 samples were taken back to the lab in 
Southampton for analysis there.


Figure 3.4.2: TA correction factors per acid bottle used for the two 
              VINDTAs where TA was run.

 
Table 3.4.1: TA and DIC Duplicate and replicate statistics

                      Replicates       Duplicates    
                   Average  St.Dev.  Average  St.Dev.  
              ———  ————————————————  ————————————————
              TA     1.27    1.07      2.00    1.46  
              DIC    1.60    1.16      2.22    1.64  



Figure 3.4.3: Distribution of absolute difference between duplicate and 
              replicate measurements.



3.4.2: Isotope Samples

Samples for δ13C of DIC and δ18O of H2O were collected during the cruise 
and will be analyzed at the NERC Isotope Geosciences Laboratory (NIGL) in 
East Kilbride.

Samples for δ13C were collected in either 100 ml soda-lime glass bottles 
or 250 ml borosilicate glass bottles. Preparation for storage was as 
recommended by Dickson et al. (2007) for DIC samples: soon after 
collection, a 1% bottle volume headspace was created and 20 μl (for 100ml 
bottles) or 50 μl (250 ml bottles), of saturated mercuric chloride were 
added. The stopper was dried and Apiezon L grease was added to make the 
seal air-tight. Electrical tape was wrapped around the bottle and stopper 
to hold the lid shut. Samples were then stored at 4°C.

Samples for δ18O were collected in 5 ml glass vials. These vials were 
filled completely and closed with the screw cap top. Parafilm was put 
around the top before wrapping with electrical tape. Samples were stored 
at 4° C to avoid evaporation.


References

Dickson, Andrew G., Christopher L. Sabine, and J. R. Christian. (2007). 
    Guide to Best Practices for Ocean CO2 Measurements. PICES Special 
    Publication 3.

Zeebe, Richard E., and D. A. Wolf-Gladrow. (2001). CO2 in Seawater: 
    Equilibrium, Kinetics, Isotopes. Elsevier Oceanography Series 65.



3.5  Chlorofluorocarbons (CFCs) and sulphur hexafluoride (SF6) 
     measurements

Marie-José Messias, Tobia Tudino, Pete Mead, Lilo Henke and Gary Murphy

A series of three halocarbons (dichlorodifluoromethane – CFC-12, 
trichlorofluoromethane - CFC-11, and trichlorotrifluoroethane - CFC-113) 
and sulphur hexafluoride (SF6) were measured on board by a purge-and-trap 
gas chromatographic method. The method combines the Lamont Doherty Earth 
Observatory CFC method [Smethie et al., 2000] and the Plymouth Marine 
Laboratory SF6 method [Law et al. 1994] tied together with a common valve 
for the introduction of gas and water samples. This system has the 
advantage of a simultaneous analysis of SF6 and halocarbons from the same 
water sample with a running time per sample of ~20 minutes when CCl4 is 
not measured. The system was set up in the temperature controlled NMF 
container # 200227 which was installed on the after deck of the JCR.


3.5.1  Sample collection

Water samples were collected from 10 litre bottles as soon as the CTD 
sampling rosette was on board. As per WOCE protocol, they were the first 
samples drawn. The Niskin nitrile 'O' rings were first washed in 
isopropanol and baked in a vacuum oven for 24 hours to remove susceptible 
contamination before installation in individual Niskin bottles. The 
trigger system of the bottles was external stainless steel springs. Water 
samples were collected in 500 ml ground glass stoppered bottles that were 
filled from the bottom using Tygon tubing and overflowed at least 2 times 
to expel all water exposed to the air. Immediately after sampling, the 
glass bottles were immersed in a cool box of clean cold deep seawater and 
stored in the cold room (~5°C) to prevent degassing until their analysis.

For air sampling, ¼” o.d. Dekabon tubing was run from the system to the 
monkey island of the ship. Air was pumped through the line to the 
instrument using a DA1 SE Charles Austen pump, with the line being 
flushed for approximately 30 minutes before beginning analysis.


3.5.2  Analysis technique

Sample analysis was performed on board as soon as possible after 
collection using a coupled SF6 and CFCs system with a common valve for 
the introduction of gas and water samples. Samples were introduced to the 
system by applying nitrogen (N2) pressure to the top of the sample 
bottles, forcing the water to flow through and fill a 27 cm3 calibrated 
volume for CFCs and a 300 cm3 volume for SF6. The measured volumes of 
seawater were then transferred to separate purge and trap systems, before 
being stripped with N2 and trapped at -100°C on a Unibeads 3S trap (for 
CFCs) and at -80 °C on a Porapak Q trap (for SF6) each immerged in the 
headspace of liquid nitrogen. Each purge and trap system was interfaced 
to an Agilent 6890N gas chromatograph with electron capture detector (GC-
ECD). The traps were heated to 100° C for CFCs and 65°C for SF6 and 
injected into the respective gas chromatographs. The SF6 separation was 
achieved using a molecular sieve packed 2 meters main column and 1meter 
buffer column. The CFCs separation was achieved using a 1m Porasil B 
packed pre-column and a 1.5m carbograph AC main column. The carrier gas 
was pure nitrogen, which was cleaned by a series of purity traps.

Liquid nitrogen was used as the cryogenic cooling material for the sample 
traps, and was provided by an on-board liquid nitrogen generator located 
in the deck workshop of the JCR.


3.5.3  Calibrations

The CFCs and SF6 concentrations in air and water were calculated using an 
external gaseous standard. The standards supplied by NOAA (Brad Hall, 
December 2008 and 2009) correspond to clean dry air slightly enriched in 
SF6, CFC-11 and CCl4 in 29L Aculife-treated aluminum cylinders (Table 
3.5.1). The calibration curves were made by multiple injections of 
different volumes (0.1, 0.25, 0.3, 0.5, 1, 2, 3, 5, 8 ml) of standard 
that span the range of tracers measured in the water. Complete 
calibration curves were made at the beginning, middle and end of the 
cruise (Figure 3.5.1). The changes in the sensitivity of the system for 
each compound were tracked by injections of a fixed volume of standard 
gas (Figure 3.5.2) and used to adjust the calibration curves 
respectively.


Figure 3.5.1: Calibration curves for CFC-11, CFC-12, CFC-113 and SF6 at 
              the beginning of the cruise (8th  of June 2014).

 

Table 3.5.1: Concentrations of the used NOAA standards

                  | NOAA2008 AAL-70510 | NOAA2009 AAL-072073
          ————————|————————————————————|————————————————————
                  |   PPT   | STDVE    |    PPT   | STDVE  
          ————————|————————————————————|————————————————————
          SF6     |    7.27 | 0.02     |    10.15 | 0.03  
          CFC-11  | 1010    | 5        |  1003    | 6  
          CFC-12  |  510.6  | 0.8      |   532    | 1.4  
          CFC-113 |   75.2  | 0.28     |    76.9  | 0.2  



Figure 3.5.2: Instrument response as for the analysis of 1ml standard 
              analyses (NOOA 2009 and 2008) for CFC-12, CFC-11, CFC-113 
              and SF6. The time is the number of days from 1rst of 
              January 2014. Abrupt changes noticeable for CFC-12 and CFC-
              113 correspond to instrument interventions. The gradual 
              loss of sensitivity for CFC-11 was due to the deterioration 
              of the Porasil B column changed days 180.



3.5.4  Precision and accuracy

The precision (or reproducibility) for the water samples measurements can 
be determined from replicate samples drawn on the same Niskin. 5% of the 
samples were duplicate samples drawn randomly from the rosette along the 
cruise when possible (time and sampling permitting). This gave 
measurement precisions for SF6 of 1.05 % for surface values & 0.011 
fmol/kg for values < 0.1 fmol/kg, for CFC-12 0.95 % for surface values & 
0.003 pmol/kg for values < 0.1 pmol/kg, for CFC-11 1.1 % for surface 
values & 0.006 pmol/kg for values < 0.1 pmol/kg and for CFC-113 1.5% for 
surface values & 0.001 pmol/kg for values < 0.1 pmol/kg. The 
reproducibility for tracer concentration was also estimated at the test 
station (#34) where all Niskin bottles were fired at the same depth (2700 
dbars) and only one sample was drawn per Niskin (Table 3.5.2).


Table 3.5.2: Results from the test station (#34) for 24 samples, mole/kg.

                     SF6      CFC-12     CFC-11     CFC-113  
           —————  —————————  —————————  —————————  ————————— 
           MEAN   7.084E-16  1.429E-12  2.96E-14   1.347E-13  
           STDEV  1.873E-17  5.491E-15  4.919E-15  2.168E-15  


The blank correction is to compensate for any trace CFCs/SF6 originating 
from the sampling bottles, handling and from the measurements procedure. 
This correction is normally estimated from analysis of either samples 
collected in water that are free of CFCs or water collected after 
sparging all the tracers out of a niskin bottle. System blanks were 
determined through the analysis of water samples that had been purged of 
all dissolved gases.

Sparge efficiencies were investigated through the continual resparge of a 
single sample until results did not change (having reached the system 
blank) at a number of different flow rates. Initial results for general 
lab conditions are reported in Table 3.5.3.


Table 3.5.3: Sparge efficiency

                     Tracer   Sparge efficiency  
                     ———————  —————————————————
                     SF6            97.5 %  
                     CFC-12         98.5 %  
                     CFC-11         99.2 %  
                     CFC-113       100 %  


3.5.5  Preliminary data

137 stations were sampled [1: 10, 12, 14, 16, 18:19, 21, 22, 23, 24, 26, 
27, 28, 30:34, 36:38, 40, 42:50, 52:55, 57, 59:61, 63, 65:66, 68, 71, 73, 
75, 78:79, 82, 84:89, 91:94, 96, 99, 101, 103, 113:115, 117, 119:120, 
124, 126, 128:130, 132:138, 140:142, 144:155,157, 171, 175, 176, 177, 
180:186, 188:196, 202:206, 210:215] and analysed for CFCs and SF6. 
However, some stations were sampled only for the Nordics Seas Overflows 
because analysis time was limited. Initial results for the first transect 
are presented in Fig. 3.5.3. The distributions of the CFCs and SF6 seen 
here are largely consistent with previous studies, showing ventilation in 
the Labrador Sea down to 1800m and the Denmark Strait Overflow Water 
signal in the bottom waters.

 
Figure 3.5.3: Preliminary plots of CFC-12 and SF6 extending from southern 
              Labrador to the southwestern tip of Greenland across the 
              mouth of the Labrador Sea (OSNAP West) in the Labrador Sea 
              in Mole/kg.



3.6  Methane and Nitrous Oxide

Ian Brown

Nitrous oxide and methane are biogenically produced trace gases whose 
atmospheric concentrations are increasing at a rate in the order of 0.7 
ppbv y-1. Both gases are radiatively active, contributing approximately 
6% and 15% of “greenhouse effect” respectively, whilst N2O contributes to 
stratospheric ozone depletion and CH4 limits tropospheric oxidation 
capacity.

The oceans are generally considered to be close to equilibrium relative 
to the atmosphere for both gases, however oceanic source/sink 
distributions are largely influenced by oxygen and nutrient status and 
regulatory processes are complicated and are currently not well 
understood.

The aim for this cruise is to examine spatial variability in methane 
production and Nitrous oxide along the cruise track.

Samples were collected from CTD stations. 1 litre samples were 
equilibrated with compressed air and headspace analysis performed onboard 
using FID-gas chromatography and ECD-gas chromatography for CH4 and N2O 
respectively. Atmospheric concentrations were determined by the same 
methods using a Tedlar bag filled with a hand pump from the bow of the 
ship.



3.7  Surfactants, CDOM and Pigments

Bita Sabbaghzadeh

The aim of this work was to investigate the vertical and horizontal 
distribution of natural surfactants and CDOM in North Atlantic Ocean 
which then will be combined with the next AMT cruise (AMT24) data to 
explore natural surfactants control of air-sea CO2 exchange in regions of 
contrasting primary productivity. Surfactants will be measured by AC 
Voltammetry and in order to provide some preliminary characterisation of 
the organic matter pool of which surfactants are a component CDOM will be 
determined using an ULTRAPATH system.


Methods

During the cruise I targeted specific stations for my analysis. For 
surface samples, I chose the stations which allowed me to assess the 
impact of variability in wind speed and its direction and also primary 
productivity impact on surfactant concentration and their distribution. 
For vertical profile water samples I selected the stations which enabled 
me to compare surfactant distribution between different water masses and 
to investigate the impact of ocean circulation.


Figure 3.7.1: Location surfactant/CDOM and pigment sampling stations


Surface Micro Layer (SML) samples (upper 400um) were collected using in-
house constructed Garrett Screen (60cmx60cm). The screen pre-rinsed 10 
times in sea water that it was about to sample and then it was allowed to 
drain 5s before collection start. The screen was deployed horizontally 
and lift through the SML and the samples were drained along one of its 
corners until most of the adhering water was drawn.

The thickness of the SML also may vary depending on both the 
oceanographic and meteorological conditions at the time the samples are 
taken. So, the thickness of the SML was measured in two ways in every 
sample station; firstly, the Garrett Screen was dipped 10 times in one 
place and the water samples were taken each time. Then the total volume 
of the samples was recorded. Secondly, the screen was dipped 10 times in 
10 different places around the ship and the volume of the sample from 
each place was recorded and then added the volume taken up. In order to 
minimise the disturbance to SML from the ship’s discharges at the 
stations, the ship went to full attention (i.e. no discharge to the sea).

The vertical profile water samples were also collected during daily 
hydrocasts from a 24x10L water- bottle rosette fitted with a CTD probe 
(Sea-Bird Electronics, SBE09). Finally, the underway water samples (~6 
meter depth) were collected.

All the samples were made in two duplicates. Samples for surfactant 
analysis were collected in 15ml centrifuge tubes. For CDOM samples, 200ml 
borosilicate volumetric flasks were used.

All the containers were pre-rinsed with 10% HCL and Milli-Q water 
(Millipore, model ZFSQ240P4) first and then rinsed with some samples 
three times prior to collection. During the sampling Nitrile Powder-Free 
disposable gloves were worn.

One batch of CDOM samples was filtered through 0.22µm Surfactant-Free 
single use syringe filters (MILLEX GP, Millipore). In order to avoid 
contamination during the filtration process, the syringes and all 
containers used during filtration rinsed with 10% HCL and M.Q. three 
times prior to use and between each sample. A small volume of sample 
(~20ml) was used to rinse filters and the filtrate discarded before 
collection.


Surfactant activity (SA) measurement

SA measurements were carried out by 797 VA Computerace Voltammetry 
(Metrohm) with a hanging mercury drop electrode. The calibration was 
conducted by analysing 10ml of 0.55mol l¯¹ NaCl as the blank/reference 
solution and followed by adding and analysing the standard (Triton-X-100) 
to the initial reference solution. The surfactant activity of the sample 
was measured from the decrease of the capacity current over a range of 
potentials after 15 and 60s accumulation of surfactants at the starting 
potential. The potential range was between E=-0.6V at the starting point 
and E=-0.9998V at ending point.

It has been noticed from the capacity current that the ship vibration is 
a potential problem. In order to minimize the vibration effect, the 
instrument was set up in Biology Lab (central line of the ship) and was 
stood on a gimballed table over some foam. However, the later results 
showed that the issue still exists when the winch is in operation at the 
stations and also low current capacity results was due to the Reference 
Electrode (R.E.) malfunction. Therefore, no further measurements were 
carried out at the stations. In this occasion, the samples were stored at 
-80˚C for later analyses.


CDOM determination

CDOM measurements were conducted by high-performance spectrophotometer 
(UltraPath). Absorbance spectra (250-730nm) of filtered (0.2µm) and 
unfiltered for SML, underway and CTD samples were measured using a 50cm 
pathlength, providing greater sensitivity compared to conventional 10cm 
pathlength spectrophotometer.

The single scan mode with an average of 10 numbers of scans was applied 
to record the CDOM spectrums. In order to minimize the refractive index 
effect due to the salinity difference between seawater samples and M.Q. 
water, NaCl solution standards with the same salinity as the samples were 
used. The solutions were prepared using analytical grade NaCl dissolved 
in M.Q. water. To remove any organic contaminants, the salt was baked at 
400˚C in advance. The absorbance of the salt solution was measured at the 
same time as the samples. The integration time was set to maximize the 
signal measured for the applied pathlength while avoiding oversaturation 
of the detector. Between the samples run the UltraPath was flushed with 
M.Q. water. The data were gathered for both filtered and unfiltered 
samples and will be available after calibration.


Chlorophyll a measurements

3 litre water samples were collected from the depth with maximum 
Chlorophyll a during daily hydrocasts from Niskin bottles. Then the 
samples were split into pseudo-replicates of 1L and filtered through 0.22 
µm pore size 25mm diameter nylon membrane filters using the vacuum pump 
(Millipore) at low pressure (4.2 Hg).Then the filters were folded in half 
twice, wrapped in aluminium foil and stored at -20˚C for later analysis.


Table 3.7.1: Chlorophyll analysis: station number, Niskin bottles and the 
             approximate depths.

             Station  Niskin Bottle  Approximate Depth(m)  
             ———————  —————————————  ————————————————————
             CTD007         21                24  
             CTD014         23                 5  
             CTD021         23                20  
             CTD027         22                45  
             CTD031         23                29  
             CTD040         22                37  
             CTD046       23&24                5  
             CTD050       16&17               14  
             CTD059         22                15  
             CTD077         18                32  
             CTD084         24                 7  
             CTD096         18                26  
             CTD110         16                27  
             CTD124         14                31  
             CTD133         22                24  
             CTD145         20                25  
             CTD152         21                24  
             CTD161        7&8                24  
             CTD170       21&22               25  
             CTD180       20&21               15  
             CTD186       13&14               13  
             CTD191       21&22               21  
             CTD198       21&22               27  
             CTD200        9&10               38  
             CTD206       21&22               33  
             CTD216       11&12               17  
             CTD230        7&8                13  
     


3.8  Trace Metals

Stefan Gary

Samples for trace metal analysis were collected at 12 stations along the 
cruise (Table 3.8.1). A total of 90 125 mL polyethylene bottles were 
specially cleaned and completely filled with deionized water to minimize 
contamination during transport and storage before the cruise. Each bottle 
was in a plastic re- sealable bag and only removed from the bag for 
labeling the bottle and taking the seawater sample. After the sample was 
collected, the bottle was put back in the bag. Each sample was 100 mL and 
drawn after all the other samples were taken. For each sample, the bottle 
and lid were rinsed three times with the seawater from the Niskin bottle 
and the fourth time bottle was filled with seawater was the final sample. 
Immediately after sampling was finished, the freshly filled sample 
bottles were carried to the -18°C freezer for storage for the remainder 
of the cruise. Gloves were worn whenever the bottles were handled 
(labeling, sampling, organization in the freezer, and packing).

For each cast, samples were taken on at most 7 depth levels but most 
frequently at 6 levels. The goal was to sample the subsurface chlorophyll 
maximum (if present), waters below the seasonal thermocline (~100 m), an 
intermediate depth (~300 – 500 m), the oxygen minimum zone (~800 m), a 
deeper intermediate level (~1500 m), and the bottom. On shallow stations 
other levels were chosen. Every cast also included at least one duplicate 
sample (usually two) ideally drawn from a second Niskin bottle that was 
fired at the same depth as the duplicated sample's Niskin bottle. This 
was not always possible, so if there was only one Niskin fired at each 
depth, then the duplicated sample was drawn from the same Niskin.

The trace metal samples will be analyzed for transition metals (Ti to Zn) 
and the rare earth elements (La to Lu). The concentrations will be 
measured by the method of combined preconcentration using the SeaFAST 
Pico (Elemental Scientific Inc., Nebraska, USA) and analysis by ICP-MS 
(Thermo XSeries2).






Table 3.8.1: Summary of trace metal samples by zone along the section and 
             station number. Adjacent gray blocks indicate duplicate 
             samples.

Zone       Station  Samples →           1     2     3     4    5    6   7   8  
—————————  ———————  ————————————————  ————  ————  ————  ————  ———  ———  ——  ——
OSNAPWest     12    Depth [m]          246   226   131    76   52   37  12  12
                    Niskin  bottle #    01    04    07    09   11   13  15  16
              24    Depth [m]         3452  3454  2768  1670  469   81  25  25
                    Niskin  bottle #    01    02    05    09   15   20  23  23
              40    Depth [m]         3467  3467  2051   664  330   92  37  -
                    Niskin  bottle #    01    02    09    15   17   20  22  -  

Green-land   107    Depth [m]          496   253   104    24   24   -   -   -
                    Niskin  bottle #    01    04    06    08   09   -   -   -    

OSNAPEast     89    Depth [m]         2835  1750   427   250   87   87  26  -
                    Niskin  bottle #    01    07    13    14   17   18  21  -
             138    Depth [m]         2668  2568  1500   469  470  102  30  -
                    Niskin  bottle #    01    02    08    14   15   19  22  -              

EEL          169    Depth [m]  1206   1006   751   751   345   80   28  29
                    Niskin  bottle #    01    04    05    06   11   17  21  22
             177    Depth [m]         2413  1754   586   586  449  151  26  26
                    Niskin  bottle #    01    06    11    11   12   15  18  18
             192    Depth [m]         1788  1487   713   713  353  104  24  24
                    Niskin  bottle #    01    04    08    08   11   14  16  17
             204    Depth [m]         1789  1251   899   898  451   98  42  42
                    Niskin  bottle #    01    05    06    07   10   17  19  20
             213    Depth [m]         1915  1500   916   916  451  101  23  23
                    Niskin  bottle #    01    05    08    09   12   17  21  22
             225    Depth [m]          208   208   142    98   99   53  28  29
                    Niskin  bottle #    01    02    03    05   06   07  09  10  


 
3.9  Phytoplankton community structure and species identification.

Mark Stinchcombe

Samples for particulate organic carbon (POC), particulate organic 
nitrogen (PON), particulate organic phosphorous (POP), high performance 
liquid chromatography (HPLC), scanning electron microscopy (SEM), 
taxonomy (Lugols) and bacterial composition (Glutaraldehyde) were taken 
from approximately one station per day. In all but one station (CTD006) 
water was drawn from the shallowest Niskin into a 20L plastic jerrycan.

For POC/PON, water was filtered onto a pre-combusted GF/F filter, rinsed 
with 1% HCl and then put into a cryovial. For POP, water was filtered 
onto a GF/F filter that had been pre-combusted, soaked in 10% HCl for 24 
hours, soaked in MilliQ water for 12 hours and finally left in a second 
MilliQ bath until required. The filter was then rinsed with MilliQ and 
placed into a pre-combusted glass tube. For HPLC, water was filtered onto 
a normal GF/F filter, rinsed with MilliQ and placed into a cryovial.   
For SEM water was filtered onto a 0.8µm polycarbonate filter, rinsed with 
MilliQ water that had been adjusted to a pH of 7.5 with ammonia, and then 
placed onto a petri-slide. In all cases 500ml was filtered unless 
otherwise stated in Table 3.9.1. One SEM sample was not taken, from 
CTD022, as there was not enough water. POC/PON, POP and SEM filters were 
dried in an oven at 60°C for approximately 24 hours.  The HPLC sample was 
placed straight into the -80°C freezer.

A sample for taxonomy was taken by filling a 100ml amber glass with water 
and adding 2ml of acidified Lugols solution. These were kept at room 
temperature. For bacterial composition, 45-50ml was put into a 50ml 
centrifuge tube and 250ml glutaraldehyde was added. The lid was then put 
on and sealed with parafilm.  The sample was left for 10-15 minutes 
before being placed in the -80°C freezer.


Table 3.9.1: All the stations sampled for biological parameters, the 
             associated Niskin numbers and the approximate depths the 
             samples were taken from.

                 Approximate 
Station  Niskin  depth from 
                 wire out (m)  POC/PON  POP  HPLC  SEM    Lugols  Glut.     
———————  ——————  ————————————  ———————  ———  ————  —————  ——————  —————
CTD005     24          5          √      √     √     √       √      √     
CTD006     20         29          √      √     √     √       √      √     
CTD011     24          5          √      √     √     √       √      √     
CTD022     24          5          √      √     √     X       √      √     
CTD023     24          5          √      √     √     √       √      √     
CTD028     24          0          √      √     √     √       √      √     
CTD033     24         11          √      √     √     √       √      √     
CTD038     24         10          √      √     √     √       √      √     
CTD042     24         10          √      √     √     √       √      √     
CTD043     24          5          √      √     √     √       √      √     
CTD048     24          2          √      √     √     √       √      √     
CTD049     24          1          √      √     √     √       √      √     
CTD056     24          5          √      √     √     √       √      √     
CTD062     24          5          √      √     √   180ml     √      √     
CTD068     24         10          √      √     √     √       √      √     
CTD071     24          5          √      √     √     √       √      √     
CTD075     24          5          √      √     √     √       √      √     
CTD078     24          0          √      √     √     √       √      √     
CTD088     24          5          √      √     √     √       √      √     
CTD093     24          0          √      √     √     √       √      √     
CTD099     24          0          √      √     √     √       √      √     
CTD104     24          0          √      √     √     √       √      √     
CTD116     24          0          √      √     √     √       √      √     
CTD119     24          0          √      √     √     √       √      √     
CTD128     16          0          √      √     √     √       √      √     
CTD137     19          0          √      √     √     √       √      √     
CTD142     21          5          √      √     √     √       √      √     
CTD148     19          0          √      √     √     √       √      √     
CTD156     19          0          √      √     √     √       √      √     
CTD166     12          0          √      √     √     √       √      √     
CTD177     20         10          √      √     √     √       √      √     
CTD183     19          0          √      √     √     √       √      √     
CTD196     19          0          √      √     √     √       √      √     
CTD202     14          0          √      √     √     √       √      √     
CTD211     19          0          √      √     √     √       √      √     
CTD226     10          5          √      √     √     √       √      √     



3.10  Iodine Isotope Sampling

Mark Stinchcombe

45 samples for 129Iodine were taken along the cruise track. These 
consisted of 5 profiles, 8 depths each, and 5 surface samples taken from 
the shallowest Niskin on the associated cast.  Water was drawn from the 
required depths into 200ml polyethylene bottles and stored at 
approximately 4°C in the dark.

The required stations can be seen in Figure 3.10.1, the closest station 
to these locations were chosen and sampled as per our instructions from 
Dr Maria Villa from the University of Seville. If the required sampling 
depth was not available, the Niskin closest to this depth was chosen 
instead. The samples will be returned the University of Sevilla for 
analysis. The actual stations and depths sampled can be seen in Table 
3.10.1.

 
Figure 3.10.1: Location map of the required sampling stations for 129I 
               including the required depths at these stations.



Table 3.10.1: The actual stations that were sampled for 129I and the 
              associated Niskin and approximate depth of those samples.

                               Approximate
              Station  Niskin  depth from    129Iodine     
                               wire out (m)
              ———————  ——————  ————————————  —————————
              CTD005     24           5          √     
              CTD024      1        3450          √     
              CTD024      8        1920          √     
              CTD024     10        1420          √     
              CTD024     12         920          √     
              CTD024     14         670          √     
              CTD024     16         360          √     
              CTD024     19         120          √     
              CTD024     24           5          √     
              CTD032      1          ?           √     
              CTD032      8          ?           √     
              CTD032     10          ?           √     
              CTD032     12          ?           √     
              CTD032     14          ?           √     
              CTD032     15          ?           √     
              CTD032     19          ?           √     
              CTD032     24          ?           √     
              CTD042      1        3172          √     
              CTD042      7        2055          √     
              CTD042     10        1455          √     
              CTD042     14         891          √     
              CTD042     15         667          √     
              CTD042     16         472          √     
              CTD042     20          92          √     
              CTD042     24          10          √     
              CTD094      1        3087          √     
              CTD094      6        2000          √     
              CTD094      8        1500          √     
              CTD094     10        1000          √     
              CTD094     11         750          √     
              CTD094     12         500          √     
              CTD094     15         100          √     
              CTD094     22           0          √     
              CTD116      1        2650          √     
              CTD116      4        2100          √     
              CTD116      6        1500          √     
              CTD116      8        1000          √     
              CTD116      9         750          √     
              CTD116     10         500          √     
              CTD116     13         100          √     
              CTD116     19           0          √     
              CTD136     19           0          √     
              CTD147     21           0          √     
              CTD156     19           0          √     
              CTD211     18           0          √     





4.  UNDERWAY MEASUREMENTS

Team Physics

4.1  SCS data streams

The SCS data streams (ashtech [nav/ash], ea600 [sim], anemometer 
[met/surfmet], oceanlogger [ocl], emlog-vhw [chf], gyro [nav/gyro], 
seatext-gell [nav/seapos], em122 [em122], seatext-hdt [nav/seahead]) were 
processed on fola during the cruise. Most were processed in 24-hour 
segments, using m_jr302_daily_processing.m, with cleaning and appending 
as required. Winch data were processed by CTD station as part of the 
standard CTD processing.

Daily processing generates a best navigation file, 
data/nav/seapos/bst_jr302_01.nc. 

The final surface meteorological data file is 
data/met/surfmet/met_jr302_truav.nc. 

Other final, cleaned and appended files from the daily processing are:

chf_jr302_01.nc 
ocl_jr302_01_medav_clean_cal_botcompare.nc 
em122_jr302_01.nc 
ocl_jr302_01_medav_clean_cal.nc 
ocl_nav_jr302_01.csv
gyr_jr302_01.nc 
sim_jr302_01_nav_cordep.nc

Notes on the processing stages of these underway data are available in 
the cruise report for JR306 (Firing, 2015).



4.2  VMADCP

4.2.1  Introduction

A 75 kHz RD Instruments Ocean Surveyor (OS75, – model 71A-1029-00, SN 
2088) ADCP was used during this cruise. The OS75 is capable of profiling 
to deeper levels in the water column than the previous 150 kHz ADCP and 
can also be configured to run in either narrowband or broadband modes.


4.2.2  Instrumentation

The OS75 unit is sited in the transducer well in the hull of the JCR. 
This is flooded with a mixture of 90% de-ionised water and 10% 
monopropylene glycol. The OS75 transducer on the JCR is aligned at 
approximately 60 degrees relative to the centre line. The hull depth was 
6.47m. Combined with a value for the distance of the transducer behind 
the seachest window of 100-200mm and a window thickness of 50mm, this 
implies a transducer depth of 6.3m.

The OS75 causes interference with most of the other acoustic instruments 
on JCR, including the EM120 swath bathymetry system. To circumvent this, 
the ADCP pinging can be synchronised with the other acoustic instruments 
using the SSU. The heading feed to the OS75 is the heading from the 
Seapath GPS unit.

 
4.2.3  Configuration

The OS75 was controlled using Version 1.42 of the RDI VmDas software. The 
OS75 ran in narrowband with bottom-tracking on and narrowband with 
bottom-tracking off. The ‘set modes’ configuration files, as described in 
JR195 report, were used during the cruise.

Salinity at the transducer was set to zero, and Beam 3 misalignment was 
set to 60.08 degrees. Data logging was stopped and restarted once a day 
to keep files to a manageable size for processing.


4.2.4  Outputs

The ADCP writes files to a network drive that is samba-mounted from the 
Unix system. The raw data (.ENR and .N1R) are also written to the local 
PC hard drive. For use in the matlab scripts the raw data saved to the PC 
would have to be run through the VMDas software again to create the .ENX 
files. When the Unix system is accessed (via samba) from a separate 
networked PC, this enables post- processing of the data without the need 
to move files.

Output files are of the form JRNNN_XXX_YYYYYY.ZZZ, where XXX increments 
each time the logging is stopped and restarted, and YYYYYY increments 
each time the present filesize exceeds 10 Mb. ZZZ are the filename 
extensions, and are of the form:-

.N1R (NMEA telegram + ADCP timestamp; ASCII)
.ENR (Beam co-ordinate single-ping data; binary). These two are the raw 
      data, saved to both disks
.VMO (VmDas configuration; ASCII)
.NMS (Navigation and attitude; binary)
.ENS (Beam co-ordinate single-ping data + NMEA data; binary)
.LOG (Log of ADCP communication and VmDas error; ASCII)
.ENX (Earth co-ordinate single-ping data; binary). This is read by matlab 
      processing
.STA (Earth co-ordinate short-term averaged data; binary)
.LTA (Earth co-ordinate long-term averaged data; binary).
.N1R  and .ENR files are saved to the secondary file path and can be 
      reprocessed by the software to create the above files.


4.2.5  CODAS/Hawaii processing.

The data were processed using the CODAS software. The processing route 
can be summarised as copying the raw files, converting them into a 
working format, merging navigation data, deriving velocities, quality 
control, and conversion of data to matlab and netcdf files. Calibration 
information can be obtained after several water and bottom-track data 
files have been processed; calibration can be performed at any time 
during the cruise or left until the end.

While the ship is steaming, the main signal that the ADCP instrument 
records is the ship speed. 12 knots (6 m/s) is 1-2 orders of magnitude 
greater than the water velocity. This velocity is removed using GPS 
derived ship velocities but there is clearly the potential for a 
significant error associated with this process as the output data is the 
small difference between two large numbers. To address this, the velocity 
of the bottom can be measured and compared directly to the GPS velocity 
of the ship.  This should give the amplitude error for the ADCP and the 
misalignment with the ship heading. This only works in water where the 
bottom track ping can reach the sea bed – 800m or shallower. In deeper 
water the processing uses changes in the ship velocity to assess what 
proportion of the ship velocity is contaminating the calculated water 
velocity. This calculation necessarily invokes assumptions that the true 
water velocity is relatively constant in space (if slowing down) or time 
(if turning round) and is therefore considered less precise than bottom 
tracking. A large number of water track data were collected, from slowing 
down and speeding up from stations.

Note that this software sometimes outputs a decimal day, calculated from 
time in seconds since the start of the year. Decimal day is 0.5 for noon 
on the 1st January: this contrasts with a jday of 1.5 for noon on the 1st 
January.

Below is a summary of the processing steps.

1) Created once at start of cruise
~/data/vmadcp/jr302_os75
~/data/vmadcp/jr302_os75/rawdata

2) For dataset NNN (eg NNN = 002),
copy raw data files (ENX, N1R, etc) from 
/mnt/data/cruise/jcr/current/adcp into 

/local/users/pstar/jr302/data/vmadcp/jrCCC_os75/rawdata file names like 
OS75_JR302NNN_000000.ENX 
NNN increments each time the ADCP logging is re-started. Data logging was 
stopped and started once every day. The 000000 increments each time a new 
file is started, when the previous one reaches 10 Mb. All raw files are 
automatically transferred to /mnt/data/cruise/jcr/current/adcp (i.e. on 
jrlb)

3) cd ~pstar/jr302/data/vmadcp/jr302_os75

cshell script in /local/users/pstar/cruise/data/exec 
vmadcp_movescript
redistributes raw data from rawdata to rawdataNNN; rawdataNNN is created 
if necessary (may need to edit movescript so that it parses the file 
names correctly).

4) adcptree.py jrCCCNNNnbenx --datatype enx

Note "nb" for narrowband ping, and that the -- datatype has two dash 
characters

5) cd jrCCCNNNnbenx
copy in a q_py.cnt file. Generally, you only need to edit the dbname and 
datadir for each NNN. An example q_py.cnt file is
# q_py.cnt is
## comments follow hash marks; this is a comment line
--yearbase 2011
--dbname jr302001nnx
--datadir /local/users/pstar/cruise/data/vmadcp/jr302_os75/rawdata001
#--datafile_glob "*.LTA"
--datafile_glob *.ENX
--instname os75
--instclass os
--datatype enx
--auto
--rotate_angle 0.0
--pingtype nb
--ducer_depth 5
#--verbose
# end of q_py.cnt
# end of q_py.cnt
At the start of the cruise check yearbase, dbname, os75 or os150 and 
datatype enx (glob ENX). Dbname should be of form jrCCCNNNPTT where P is 
n for narrowband, b for broadband. The instrument should be operated in 
narrow unless there is a good reason to choose broad. TT is “nx” for ENX; 
“ns” for ENS; “nr” for ENR; “lt” for LTA; “st” for STA. Standard 
processing is to process ENX. As far as I can tell, dbname must not 
exceed 11 chars. So if we use 9 for jr195NNNn, there are only two left to 
identify ENX, ENS, LTA, STA

6) still in directory ~data/vmadcp/jr302_os75/jr302001nbenx 

quick_adcp.py --cntfile q_py.cnt
("killed matlab engine" is the normal message received). This takes a 
minute or two per 24 hours of ENX data. Note –cntfile has two dash 
characters


7) To see the BT (bottom track) or WT (water track) calibration, look at 
the ascii output of jr302001nbenx/cal/*/*out (note that a calibration is 
not always achieved, for example if the ship has made no manoeuvres while 
the ADCP is in water tracking mode, so there may be no *out file). Note 
also that additional calibration information maybe saved after flags 
applied after gautoedit process.

8) To access data in Matlab 
matlab &
>> m_setup
>> codaspaths

9) Can manually clean up data by applying flags to suspected bad data 
cycles (this can be done post- cruise, ie omitted, go straight to step 
10). This step can also be a useful first look at the data. Note that the 
uncalibrated files may show a slight bias in u and/or v which will appear 
as stripes that coincide with periods of on-station and steaming. This 
effect will disappear when you correct for the amplitude and phase error 
(step 12).

>> cd data/vmadcp/jr302_os75/jr302001nbenx/edit
>> gautoedit

Clean up data. Select day and step (typically 0.1 or 0.2 days) to view, 
then "show now". "show now" may have to be done twice to get the surface 
velocity plot. "show next" to step through the file. "Del bad times" sets 
"bad" flags for a section of time, or for a whole profile. "rzap" allows 
single bins to be flagged. Note that "list to disk" must be clicked each 
time for the flags to be saved.

Applying edits identified in gautoedit, The gautoedit process in Matlab 
sets flags, but doesn’t change the data. To apply the flags and 
recalculate a calibration, quick_adcp.py –-cntfile q_pyedit.cnt (note two 
dashes before cntfile)
where q_pyedit.cnt contains
# q_pyedit.cnt is
## comments follow hash marks; this is a comment line
--yearbase 2009
--steps2rerun apply_edit:navsteps:calib:matfiles
--instname os75
--auto
# end of q_pyrot.cnt

10) To get data into MSTAR:

>> cd /local/users/pstar/cruise/data/vmadcp/jr302_os75/jr302NNNnbenx
>> mcod_01
produces output file os75_jr302NNNnnx.nc
which has a collection of vars of dimensions Nx1 1xM NxM
>> mcod_02
will calculate water speed and ship speed and get all the vars onto an 
NxM grid. This step makes data available for comparison with LADCP data.


11) Append individual 48-hour files using

>>mcod_mapend
This script will append individual files to create a single cruise file. 
It does seem to depend on the files having the same bin number and bin 
depths which was not the case on JR302.


12) cd /local/users/pstar/cruise/data/vmadcp/jr302_os75/jr302NNNnbenx
In directory apply the final cal ONLY ONCE (adjustments are cumulative, 
so if this step is done   twice, the cal is applied twice) when you have 
done the edits and applied the time-varying heading adjustment. After 
inspecting the cal out files, and deciding what the amplitude and phase 
of the calibration should be:
quick_adcp.py –-cntfile q_pyrot.cnt        (note two dashes before 
cntfile), where q_pyrot.cnt contains:

# q_pyrot.cnt is
## comments follow hash marks; this is a comment line
--yearbase 2011

--rotate_angle -1.0564
--rotate_amp 1.0116
--steps2rerun rotate:navsteps:calib

--auto
# end of q_pyrot.cnt


Final calibration values used were those given by the JR302 Bottom Track 
data.

13) In each directory re-create Matlab files:
>>cd /local/users/pstar/cruise/data/vmadcp/jr302_os75/jr302NNNnbenx

>>mcod_01
>>mcod_02
Then remove and recreate the appended matlab file:
>>cd /local/users/pstar/cruise/data/vmadcp/jr302_os75

>>!/bin/rm os75_jr302nnx_01.nc
>>mcod_mapend



4.3  Pumped seawater: underway carbon

Jennifer Clarke, Alex Griffiths, Becky Garley Eithne Tynan


4.3.1  Introduction

The carbonate system is a key component of the chemical perspective of 
oceanography as it plays an important role in the oceans’ capacity to 
take up atmospheric CO2. Dissolved inorganic carbon (DIC) is present in 
seawater in three forms (CO2(aq), HCO3- and CO3-2) which are in 
equilibrium on timescale longer than a few minutes. In oceanography, the 
carbonate system can be determined by four parameters: DIC, dissolved 
carbon dioxide (pCO2), alkalinity (TA) and pH.

3 instruments were set-up to measure with high resolution from the non-
toxic underway water supply along the entire cruise track. This cruise 
was an opportunity to test the immobilised fluorophore pCO2 sensor JC is 
developing for her PhD, alongside pH and DIC analysers.


4.3.2  Method

pH sensor:
pH is measured by adding a coloured indicator to the seawater sample and 
measuring the colour of the mix. The indicator is 2 mM Thymol Blue for 
the underway system. The spectrophotometric sensor was developed by 
Victoire Rerolle at NOCS sensors group (Rérolle, Floquet et al. 2012).

DIC Sensor:
An Apollo SciTech System has been used. The equipment is divided into two 
sections. The first part allows the conversion of all the inorganic 
species of carbon into CO2 gas by mixing it with 10% vol phosphoric acid 
in a closed cell. The total CO2 gas is then carried out with the help of 
N2 gas (99.9%) to the Li-COR, where- by infrared analysis, the amount of 
CO2 gas produced is analysed. The flow rate of the gas was maintained at 
300ml/min.

The sample volume used was 0.75 ml and a partial calibration was 
undertaken twice daily. The calibration consisted of flushing the 
instrument with air (2 x 1.5ml), followed by deionised water (1 x 1.5 ml) 
before being flushed with the Certified Reference Material provided by 
Professor A. Dickson from Scripps Oceanographic Institute (Batch 136). 
Seven repeats of 3 volumes (0.5, 0.75, and 1 ml) were then run with the 
Certified Reference Material. Furthermore, every 30 samples, the CRM was 
analysed 7 times (0.75 ml) to allow corrections due to the natural drift 
of the LICOR analyser.

The CRM was changed daily, and kept in the glass bottle with a special 
lid and sample tube that once the CRM was opened remained on the bottle 
until changed. The sample tube was always sampling from the bottom of the 
bottle.

Drift in the underway water measurements was corrected using the ratio of 
the measured CRM DIC (umol kg-1) to the certified value for the 
particular CRM.

pCO2 sensor:
The sensor is based on an immobilised indicator entrapped in a polymer 
membrane alongside a fluorescent reference compound. The indicator 
fluorescence altered according to the pCO2 of the seawater. The 
fluorescence intensity was recorded throughout the cruise and analysed 
based on   time-domain dual-luminophore referencing (Liebsch, Klimant et 
al. 2000, Liebsch, Klimant et al. 2001, Stahl, Glud et al. 2006, 
Schroeder, Neurauter et al. 2007) using a PMT (Hamamatsu). The sensing 
spot was purchased from PreSens GmbH, previously attached to a PMMA disc 
using silicon glue provided by PreSens GmbH and soaked in artificial 
seawater for a month prior to use. The PMMA disc/sensing spot was then 
attached to the fibre optic cable head with a glue gun.

Drift in the underway water measurements was corrected using the ratio of 
the measured CRM pCO2 (ppm) to the certified value for the particular 
CRM.

Underway Sampling:
Underway sampling for DIC and TA was undertaken every 6 hours when not at 
a station until the 04/07/14 where it was reduced to one sample per 8 
hours. Samples were collected in 250 ml Schott Duran borosilicate glass 
bottles with glass stoppers that provided an air-tight seal, held shut 
with electrical tape wrapped around the stopper and the bottle. 2.5 ml 
headspace was left in each bottle and 50 µl saturated mercuric chloride 
solution added directly after sampling. Samples were stored in dark, 
insulated boxes. These will be analysed at a later date at the NOC.


4.3.3	Underway measurements

The automated pCO2 and DIC systems were running continuously on the non-
toxic water supply from the 06/06/2014 to 17/07/2012. Measurements were 
only interrupted for system performance checking, maintenance and in the 
ice when the non-toxic water supplied was stopped. The pH system was 
running from 26/06/2014 to the 17/07/2012.

The data will undergo further corrections for temperature and salinity 
changes. The pCO2 sensor will also undergo post cruise calibration and 
testing and further corrections based the results of this.

The consistency of the data will finally be checked thanks to comparison 
between the sensors, 100 underway supply DIC/Alkalinity samples and 
trends and correlation in other parameters such as chlorophyll, 
temperature, salinity and nutrients.


Figure 4.3.1: CRM 136 drift for the DIC analyser

Figure 4.3.2: CRM 135 drift for the DIC analyser:

Figure 4.3.3: Correction factor over the whole cruise

Figure 4.3.4: CRM 136 Drift for the experimental pCO2 sensor.

Figure 4.3.5: CRM 135 Drift for the experimental pCO2 sensor.

Figure 4.3.6: Correction factor for the experimental pCO2 sensor.

Figure 4.3.7: CRM 136 Drift pH sensor 



References

Liebsch, G., I. Klimant, B. Frank, G. Holst and O.S. Wolfbeis (2000). 
    "Luminescence lifetime imaging of oxygen, ph and carbon dioxide 
    distribution using optical sensors." Applied Spectroscopy 54(4): 548-
    559.

Liebsch, G., I. Klimant, C. Krause and O.S. Wolfbeis (2001). "Fluorescent 
    Imaging of pH with Optical Sensors Using Time Domain Dual Lifetime 
    Referencing." Analytical Chemistry 73(17): 4354- 4363.

Rérolle, V.M.C., C.F.A. Floquet, M.C. Mowlem, R. Bellerby, D.P. Connelly 
    and E.P. Achterberg (2012). "Seawater-pH measurements for ocean-
    acidification observations." Trac-Trends in Analytical Chemistry 40: 
    146-157.

Schroeder, C., G. Neurauter and I. Klimant (2007). "Luminescent dual 
    sensor for time-resolved imaging of pCO2 and pO2 in aquatic systems." 
    Microchimica Acta 158: 205-218.

Stahl, H., A. Glud, C. R. Schroder, I. Klimant, A. Tengberg and R. N. 
    Glud (2006). "Time-resolved pH imaging in marine sediments with a 
    luminescent planar optode." Limnology and Oceanography: Methods 4: 
    336-345.



Table 4.3.1: Underway DIC/TA Sampling Log

Sampler  Sample ID     Date      GMT   Notes  
———————  —————————  ——————————  —————  —————————————————————————————
  ET       UW000    16/06/2014  15:40  A lot of bubbles in underway  
  ET       UW001    16/06/2014  16:12    
  ET       UW002    16/06/2014  22:55    
  AG       UW003    17/06/2014  06:10    
  AG       UW004    17/06/2014  10:20    
  JC       UW005    17/06/2014  22:00    
  AG       UW006    17/06/2014  05:10  At station- delayed sample  
  BG       UW007    18/06/2014  10:07    
  JC       UW008    18/06/2014  16:02  Almost at station 53  
  ET       UW009    18/06/2014  23:04    
  AG       UW010    19/06/2014  04:10    
  BG       UW011    19/06/2014  12:34    
  JC       UW012    19/06/2014  16:03    
  JC       UW013    20/06/2014  01:07  bubbly  
  AG       UW014    20/06/2014  05:56  At station 57- delayed sample  
  BG       UW015    20/06/2014  12:53    
  ET       UW016    20/06/2014  21:53    
  AG       UW017    21/06/2014  05:00    
  BG       UW018    21/06/2014  12:19    
  JC       UW019    21/06/2014  16:04  STN BY GREENLAND  
  JC       UW020    21/06/2014  23:07    
  AG       UW021    22/06/2014  07:06  STN 69  
  BG       UW022    22/06/2014  10:21    
  JC       UW023    22/06/2014  16:09    
  JC       UW024    22/06/2014  21:55    
  AG       UW025    23/06/2014  04:11    
  BG       UW026    23/06/2014  10:19  NO SAMPLING TUBE  
  JC       UW027    23/06/2014  16:56  NO SAMPLING TUBE  
  JC       UW028    23/06/2014  23:37    
  AG       UW029    24/06/2014  05:16    
  BG       UW030    24/06/2014  10:26      
  JC       UW031    24/06/2014  16:11      
  JC       UW032    24/06/2014  01:02      
  AG       UW033    25/06/2014  04:54      
  BG       UW034    25/06/2014  10:26      
  JC       UW035    25/06/2014  17:52      
  AG       UW036    26/06/2014  05:42      
  BG       UW037    26/06/2014  10:21      
  JC       UW038    26/06/2014  17:22      
  JC       UW039    26/06/2014  22:04      
  AG       UW040    27/06/2014  06:14      
  BG       UW041    27/06/2014  10:23      
  JC       UW042    27/06/2014  16:05      
  AG       UW043    28/06/2014  06:00      
  BG       UW044    28/06/2014  10:14      
  JC       UW045    28/06/2014  23:51      
  AG       UW046    29/06/2014  08:25      
  BG       UW047    30/06/2014  10:17      
  AG       UW048    01/07/2014  07:27      
  JC       UW049    30/06/2014  17:54      
  JC       UW050    30/06/2014  00:57      
  BG       UW051    01/07/2014  11:20      
  JC       UW052    01/07/2014  21:38      
  BG       UW053    01/07/2014  11:01      
  JC       UW054    02/07/2014  16:11      
  JC       UW055    02/07/2014  23:27      
  AG       UW056    03/07/2014  05:19      
  BG       UW057    03/07/2014  10:18      
  JC       UW058    03/07/2014  17:30      
  JC       UW059    03/07/2014  22:04      
  AG       UW060    04/07/2014  06:15      
  BG       UW061    04/07/2014  11:33      
  JC       UW062    04/07/2014  18:05      
  AG       UW063    05/07/2014  04:10      
  BG       UW064    05/07/2014  09:00      
  JC       UW065    05/07/2014  19:13      
  AG       UW066    06/07/2014  03:23      
  BG       UW067    06/07/2014  09:29      
  JC       UW068    06/07/2014  17:51      
  AG       UW069    07/07/2014  03:42      
  BG       UW070    07/07/2014  10:27      
  JC       UW071    07/07/2014  18:49      
  AG       UW072    08/07/2014  01:31      
  BG       UW073    08/07/2014  09:20      
  AG       UW074    09/07/2014  01:30      
  BG       UW075    09/07/2014  09:25      
  JC       UW076    09/07/2014  18:18      
  AG       UW077    10/07/2014  02:03      
  BG       UW078    10/07/2014  11:11      
  CF       UW079    10/07/2014  19:38      
  AG       UW080    11/07/2014  02:22      
  BG       UW081    11/07/2014  09:11      
  JC       UW082    11/07/2014  17:22      
  AG       UW083    12/07/2014  02:28      
  BG       UW084    12/07/2014  10:08      
  JC       UW085    12/07/2014  17:50      
  AG       UW086    13/07/2014  05:36      
  BG       UW087    13/07/2014  10:04      
  JC       UW088    13/07/2014  17:03      
  AG       UW089    14/07/2014  01:21      
  BG       UW090    14/07/2014  08:33      
  JC       UW091    14/07/2014  17:59      
  AG       UW092    15/07/2014  02:02      
  BG       UW093    15/07/2014  09:08      
  JC       UW094    15/07/2014  16:36      
  AG       UW095    16/07/2014  01:14      
  BG       UW096    16/07/2014  08:11      
  JC       UW097    16/07/2014  17:23      
  AG       UW098    17/07/2014  02:35      
  BG       UW099    17/07/2014  08:23      
  JC       UW100    17/07/2014  16:03  




 
5.  AUTONOMOUS PLATFORMS

5.1  Floats

Eight Met Office Argo floats were deployed during the cruise. All floats 
were checked for functionality before being deployed; they were connected 
to a laptop and a series of pre-deployment checks carried out. After 
disconnection from the laptop they were reset and activated using a 
magnet. Deployment was from the stern starboard quarter with a rope, as 
the ship steamed slowly forwards.


Table 5.1: Float deployments

Float  Reset time  Deployment time  Deployment  Deployment   Associated CTD       
ID                  (year day/UTC)  latitude    longitude    station number
—————  ——————————  ———————————————  ——————————  ———————————  ——————————————
7011   186/0158    186/0350         57.95295    -27.00062    jr302/138      
                   5 July 2014      57 57.18 N   27 0.04 W   

7012   187/2242    187/2352         57.90795    -20.68557    jr302/148      
                   6 July 2014      57 54.48 N   20 41.13 W   

7013   191/0016    191/0144         59.40160    -18.43511    jr302/177   
                   10 July 2014     59 24.10 N   18 26.11 W            

7014   191/0907    191/1108         59.80868    -19.50388    jr302/180 
                   10 July 2014     59 48.52 N   19 30.23 W      

6608   191/1728    191/1855         60.24949    -19.99944   
                   10 July 2014     60 14.97 N   19 59.97 W  jr302/182      

6611   193/1836    193/2005         61.49963    -20.00134  
                   12 July 2014     61 29.98 N   20 0.08 W   jr302/195      

6610   194/0837    194/0955         61.00055    -20.00137
                   13 July 2014     61 0.03 N    20 0.08 W   jr302/198      

6609   196/1720    196/1852         57.29858    -10.38108
                   15 July 2014     57 17.91 N   10 22.86 W  jr302/211      



5.2  Seaglider

Stefan Gary

The iRobot Seaglider Bellatrix (SG532) was recovered on the morning of 13 
July. Bellatrix had been waiting at 61N, 20W, which coincided 
approximately with stations 185 and 198, for several days for an 
appropriate weather window for recovery. On 13 July, conditions were 
ideal: good visibility and low swell. As the JCR approached the 
rendezvous point, Bellatrix was commanded to execute successively 
shallower dives and the positions of each dive were monitored in real 
time via an SSH link to the glider's base station at the Scottish 
Association for Marine Science (SAMS). At 0700GMT, the pilot commanded 
Bellatrix to enter recovery mode.  She was sighted about 10 minutes later 
and the ship pulled alongside at 0736GMT.

After several attempts, at 0748GMT, a line was secured to Bellatrix's 
rudder, the lift point for a Seaglider, using a bowline-in-a-bight taped 
on the end of an approximately 10 m pole. This process was challenging 
since Bellatrix's rudder was almost continuously submerged and the line 
sunk very slowly. After the recovery, it was discovered that the glider 
was floating low because the pilot ommitted to command Bellatrix to pump 
to maximum buoyancy. Future Seaglider recoveries should be easier if this 
command is executed. The ~10 m pole, worked by a minimum of two people, 
was of sufficient length to lasso the glider despite the height of the 
freeboard. With the glider lassoed, she was then lifted aboard with the 
gantry at 0750GMT, placed in her cradle, and the wings, rudder, and 
antenna where disassembled.

Standard post-recovery internal pressure (~8.5 PSIA) and internal 
humidity (~14.00RH) checks were carried out and these values matched the 
safe operating ranges maintained by the glider for the duration of her 
mission. Bellatrix was then commanded to enter travel mode, turned off, 
and then rinsed with freshwater before being packed into the shipping 
crate. The Argos tag on Bellatrix's antenna was also switched into 
standby mode.

Bellatrix was deployed west of the Isle of Coll on the Scottish Shelf on 
April 30th and navigated to the rendezvous point over the course of two 
months (Figure 5.2.1). The raw data collected during this mission were 
posted in real time to http://velocity.sams.ac.uk/gliders/sg532. 
Bellatrix operated with remarkably few errors or other issues for her 
whole mission.  Recovering a glider from a large ship is a challenging 
task and the crew of the JCR did an outstanding job supporting the 
recovery; everyone was very keen to sort out logistical details, open to 
hearing about the special requirements of gliders, and enthusiastic.


Figure 5.2.1: Seaglider Bellatrix (SG532) track from 30th April, 2014 to 
              13th July, 2014 (red line) compared to the Extended Ellet 
              Line (black line). Bathymetry is contoured at 500 m 
              intervals (black lines) and 100 m intervals for depths less 
              than 500 m (gray lines).





6.  OUTREACH

N.P. Holliday

A daily cruise blog was written during JR302 (ukosnap.wordpress.com), 
with the specific ambition of attracting readers who are not marine 
scientists.  The aim was to provide simplified explanations of our 
science and of life onboard the ship and to illustrate this with nice 
photographs. Posts were mainly written by Penny Holliday and featured 
contributions from scientists and ship's staff.

The blog was advertised through Facebook and Twitter (@ukosnap) and word 
of mouth (family and friends). The readership grew steadily throughout 
the cruise, peaking at over 1200 views on one day, and reaching a total 
of over 25,000 views by the end of the cruise.

Video footage was collected throughout the cruise by Penny Holliday, 
Sinhue Torres Valdes and Stefan Gary. We filmed people working, the 
scenery, and the CTD underwater, and interviewed the PS. We also made 
some time lapse movies.  Some were put on the UKOSNAP youtube channel 
during the cruise, and more will be added after the cruise and advertised 
through our websites, twitter and facebook. The clips will be used for 
outreach activities by NOC, PML and SAMS for the RAGNARRoC and OSNAP 
projects.





CCHDO Data Processing Notes


• File Submission Andrew Barna
ar07_74JC20140606_ct1.zip (download) #43b94 
Date: 2015-06-17 
Current Status: merged 
Notes
Test submission of an already existing file


• File Merge CCHDO Staff
ar07_74JC20140606_ct1.zip (download) #43b94 
Date: 2015-05-28 
Current Status: merged


• CTD online, exchange and netcdf formats SEE 
Date: 2015-05-28 
Data Type: CTD 
Action: Website Update 
Note: 
AR07 2014 74JC20140606 processing - CTD online - CTDPRS,CTDTMP,CTDSAL,CTDOXY

2015-05-28

SEE


Submission

filename                          submitted by date       id  
--------------------------------- ------------ ---------- ----
ar07_74JC20140606_ct1.zip         Brian King   2014-07-22 4490

Changes

ar07_74JC20140606_ct1.zip
- for file ar07_74JC20140606_00171_00001_ct1.csv,  changed CTDOXY flags from 2 to 4 between 361 and 
433 dbar.

:Updated parameters: 
CTDPRS,CTDPRS_FLAG_W,CTDTMP,CTDTMP_FLAG_W,CTDSAL,CTDSAL_FLAG_W,CTDTMP,C
TDTMP_FLAG_W

ar07_74JC20140606_ct1.zip opened in JOA with no apparent problems.
ar07_74JC20140606_nc_ctd.zip opened in JOA and ODV with no apparent problems.


• File Submission Brian King
ar07_74JC20140606_ct1.zip (download) #43b94 
Date: 2014-09-08 
Current Status: merged 
Notes
CTD data


• to go online Brian King 
Date: 2014-09-08 
Data Type: CTD 
Action: Submitted 
Note: 
CTD data are final we believe.

Bottle data still need some work.

The Bottle data file is an 'end of cruise' file. CFCs are incomplete. Samples were analysed on board but 
analyses not yet received. Carbon data have a number of stored samples for analysis ashore, signified by 
absent analysis value and flag = 1.

Bottle oxygen have some unexplained station offsets making all bottle oxygen data from those stations 
questionable. However the data are not yet flagged as 3.
					

• Available under 'Files as received' CCHDO Staff 
Date: 2014-09-08 
Data Type: CTD 
Action: Website Update 
Note: 
The following files are now available online under 'Files as received', unprocessed by the CCHDO.

ar07_74JC20140606_ct1.zip
					

• File Submission Brian King
ar07_74JC20140606_ct1.zip (download) #43b94 
Date: 2014-07-22 
Current Status: merged 
Notes
Expocode: 74JC20140606
Ship: James Clark Ross
Woce Line: AR07W/OSNAP-W/AR07E/OSNAP-E/AR28
Note: CTD data are final we believe.

Bottle data still need some work. 

The Bottle data file is an 'end of cruise' file. CFCs are incomplete. Samples were analysed on board but 
analyses not yet received. Carbon data have a number of stored samples for analysis ashore, signified by 
absent analysis value and flag = 1.

Bottle oxygen have some unexplained station offsets making all bottle oxygen data from those stations 
questionable. However the data are not yet flagged as 3.

[...] the CTD data are GO-SHIP and can be considered as fully public.
We believe they are final.

I would like to get confirmation of the preferred line designators eg
AR07W
ONSAP-W
AR07E
OSNAP-E
AR28
so that we can start using them now and avoid switching in the future.

Bottle data contain a variety of data issues remaining to be resolved, so they are not suitable for
public dissemination yet. But the bottle file can be used to compile a list of parameters measured.