    CRUISE REPORT: A16S_2005a
    (Updated 02 NOV 2005)
     
    A.    HIGHLIGHTS
    
    A.1.  CRUISE SUMMARY INFORMATION
    
             WOCE section designation  A16S_2005a
    Expedition designation (ExpoCode)  33RO200501
                  Co-Chief Scientists  Dr. Rik Wanninkhof/NOAA/AMOL
                                       Dr. Scott Doney/WHOI
                                Dates  2005 JAN 11 - 2005 FEB 24
                                 Ship  R/V RONALD H. BROWN
                        Ports of call  Punta Arenas, Chile - Fortaleza, Brazil
                                                    2° 20.01' S
        Station geographic boundaries  36° 22.98' W             24° 59.71' W
                                                    60° 0.94' S
                             Stations  121
         Floats and drifters deployed  12 ARGOS floats, 
                                       11 drifters deployed 
       Moorings deployed or recovered  0
    
                            Dr. Rik Wanninkhof / NOAA / AMOL
                4301 Rickenbacker Causeway • Miami, FL • 33149-1046 • USA
         TEL: 305-361-4379 • FAX: 305-361-4582 • EMAIL: wanninkhof@aoml.noaa.gov
    
          Dr. Scott Doney / WHOI • Dept. of Marine Chemistry and Geochemistry
                       MS #25 • Woods Hole, MA • 02543-1543 • USA
          TEL: +1-508-289-3776 • FAX: +1-508-457-2193 • EMAIL: sdoney@whoi.edu
    
    
    
    
    
                              TABLE OF CONTENTS
    
    SUMMARY
    ACKNOWLEDGMENTS
    INTRODUCTION
    
    DESCRIPTION OF MEASUREMENT TECHNIQUES
    1. CTD/Hydrographic Measurements Program
       1.1. Water Sampling Package
       1.2. Underwater Electronics Packages
       1.3. Navigation and Bathymetry Data Acquisition
       1.4. Real-Time CTD Data Acquisition System
       1.5. Shipboard CTD Data Processing
       1.6. CTD Laboratory Calibration 
       1.7. Shipboard CTD Calibration Procedures
            1.7.1. CTD Pressure
            1.7.2. CTD Temperature
            1.7.3. CTD Conductivity
            1.7.4. CTD Dissolved Oxygen
       1.8. Final CTD Data Processing
       1.9. Final CTD Calibration Procedures
            1.9.1. CTD Pressure
            1.9.2. CTD Temperature
            1.9.3. CTD Conductivity
            1.9.4. CTD Dissolved Oxygen
       1.10. Particulate Optical Sensors on CTD Package
       1.11. Lowered Acoustic-Doppler Current Profiler (LADCP)
    
    2. BOTTLE SAMPLING
       2.1. Bottle Sampling Procedures
       2.2. Bottle Data Processing
       2.3. Sampling and Analyses of Bottle Data
       2.4. Tests Performed on Bullister Bottles to Determine Sample Integrity of CFC, Salts, and O2 
       2.5. Discussion of Bottle Sampling for Samples Preserved for Shore-Side Analysis.
            2.5.1. Helium and Tritium Sampling
            2.5.2. Particulate Sampling
            2.5.3. DOC Sampling 
            2.5.4. C-DOM Sampling 
            2.5.5. 14C Sampling 
            2.5.6. OXYGEN, NITROGEN, AND ARGON (ONAR) SAMPLING
       2.6. Parameters Sampled and Analyzed on the Cruise
            2.6.1. Chlorofluorocarbon (CFC) Measurements
            2.6.2. Dissolved Oxygen Analyses
            2.6.3. Discrete Halocarbon/Alkyl Nitrate Analyses
            2.6.4. Discrete pCO2 Analyses
            2.6.5. Total Dissolved Inorganic Carbon (DIC) Analyses
            2.6.6. Discrete pH Analyses
            2.6.7. Total Alkalinity Analyses
            2.6.8. Salinity Analysis
            2.6.9. Inorganic Nutrients (Phosphate, Nitrate, Nitrite, and Silicate)
       2.7. Underway Measurements
            2.7.1. Shipboard Computing System (SCS)
            2.7.2. Underway pCO2 (fCO2) Measurements
            2.7.3. SAMI Underway pCO2 Measurement System
            2.7.4. Underway Spectrophotometric Measurements of pCO2, TCO2, and pH
       2.8. Aerosol Sampling 
    
    
    LIST OF FIGURES
      FIGURE  1.0.   Sample distribution, stations 1-34
      FIGURE  1.1.   Sample distribution, stations 32-62
      FIGURE  1.2.   Sample distribution, stations 60-92
      FIGURE  1.3.   Sample distribution, stations 88-121
      FIGURE  1.4.   T1-T2 by station, p > 500 db
      FIGURE  1.5.   T1-T2 by pressure, station/casts 5/2-50/1
      FIGURE  1.6.   Uncorrected C1-C2 by station, p > 500 db
      FIGURE  1.7.   Uncorrected bottle C-C1 by station, p > 500 db
      FIGURE  1.8.   Corrected bottle C-C1 by station, all pressures
      FIGURE  1.9.   Corrected bottle C-C1 by pressure, all pressures
      FIGURE  1.10.  Corrected bottle C-C1 by station, p > 500 db
      FIGURE  1.11.  Salinity residual by station, p > 500 db
      FIGURE  1.12.  O2 residuals by station, all pressures
      FIGURE  1.13.  O2 residuals by pressure, all pressures
      FIGURE  1.14.  O2 residuals by station number, p > 500 db
      FIGURE  1.15.  Calibrated CTD-bottle conductivity differences plotted against station number
      FIGURE  1.16.  Calibrated CTD-bottle conductivity differences plotted against pressure
      FIGURE  1.17.  Calibrated CTD-bottle oxygen differences plotted against station number
      FIGURE  1.18.  Calibrated CTD-bottle oxygen differences plotted against pressure
      FIGURE  1.19.  Preliminary observations of (a) zonal velocity, (b) meridional
                     velocity, (c) velocity standard error, and (d) acoustic backscatter
      FIGURE  1.20.  Preliminary shaded estimates of eddy diffusivity and log-scale
                     eddy diffusivity uncertainty from cruise-processed LADCP data
      FIGURE  2.1.   Control plot of the reagent blanks over the cruise
      FIGURE  2.2.   Control plot of thiosulfate concentration changes over the cruise
      FIGURE  2.3.   Difference between photometrically and amperometrically determined
                     oxygen concentration versus photometric oxygen concentration
      FIGURE  2.4.   Schematic of the automated purge and trap GCMS system
      FIGURE  2.5.   Comparison of the results from the two SAMIs and the underway pCO2 system
    
    
    LIST OF TABLES
      TABLE  1.1.   Scientific personnel, A16S 2005
      TABLE  1.2.   Principal programs of A16S 2005
      TABLE  1.3.   A16S 2005 rosette underwater electronics
      TABLE  1.4.   A16S 2005 CTD sensor calibration dates
      TABLE  1.5.   A16S 2005 CTD sensor configurations
      TABLE  1.6.   Final oxygen calibration coefficients 
      TABLE  1.7.   Initial configuration and instrument and command changes
      TABLE  2.1.   Water requirements for the different parameters drawn on the Bullister bottles
      TABLE  2.2.   Results for station 88 storage tests
      TABLE  2.3.   Results for station 102 storage tests
      TABLE  2.4.   Results for station 112 storage tests
      TABLE  2.5.   Changes in concentrations for station 112 storage test
      TABLE  2.6.   Summary of CFC changes for the storage tests
      TABLE  2.7.   Bottle blanks for Bullister bottles
      TABLE  2.8.   Summary of bottle tests for station 121
      TABLE  2.9.   Comparison of oxygen concentrations determined by photometric 
                    and amperometric point detection methods at station 106
      TABLE  2.10.  Calibration standard tanks used for discrete pCO2
      TABLE  2.11.  Duplicate discrete pCO2 samples
      TABLE  2.12.  Test results of different sample bottle sizes for DIC
      TABLE  2.13.  Summary of number of nutrient samples taken and estimated precision
      TABLE  2.14.  Hourly sampling cycle for the underway pCO2 system (version 2.5)
      TABLE  2.15.  Wavelengths used for spectrophotometric determination of inorganic
                    carbon species
    
    
    
    
    SUMMARY
    
    A hydrographic survey consisting of a meridional LADCP/CTD/rosette section in 
    the western South Atlantic was carried out in January-February 2005.  The R/V Ronald 
    H. Brown departed Punta Arenas, Chile on 11 January 2005. A total of 121 
    LADCP/CTD/Rosette stations were occupied, and 12 Argos floats and 11 drifters were 
    deployed from 17 January-21 February. Water samples (up to 36), LADCP, CTD and 
    bio-optical data were collected on each cast to within 20 m of the bottom.  Salinity, 
    dissolved oxygen, and nutrient samples were analyzed from every bottle sampled on 
    the rosette. Other parameters from the bottles were sampled at a lower density. The 
    cruise ended in Fortaleza, Brazil on 24 February 2005. This report describes the 
    participants and details of sampling and analytical methodologies of all projects.  
    Further information, pictures, graphics, and data can be found on the A16S 2005 cruise 
    website at http://sts.ucsd.edu/cruise/a16s/hydro/. The data are also posted at 
    http://ushydro.ucsd.edu/
    
    
    ACKNOWLEDGMENTS
    
    The successful completion of the cruise relied on dedicated assistance from many 
    individuals on shore and on the NOAA ship Ronald H. Brown.  Funded investigators in 
    the project and members of the Repeat Hydrography Oversight Committee, with Lynne 
    Talley and Richard Feely as co-chairs, were instrumental in planning and executing the 
    cruise.  The participants in the cruise showed dedication and camaraderie during their 45 
    days at sea.  Officers and crew of the Ronald H. Brown exhibited a high degree of 
    professionalism and assistance to accomplish the mission and to make us feel at home 
    during the long voyage.
    
    The U.S. CLIVAR/CO2 Repeat Hydrography Program is jointly sponsored by the 
    National Science Foundation's Physical and Chemical Oceanography Programs, and 
    NOAA's Office of Climate Observation, with contributions from the National 
    Aeronautics and Space Administration and the Department of Energy.  In particular, we 
    wish to thank program managers Eric Itsweire (NSF/OCE), Don Rice (NSF/OCE), Mike 
    Johnson (NOAA/OCO), and Kathy Tedesco (NOAA/OGP) for their moral and financial 
    support in the effort.  Editorial assistance in producing this report by Gail Derr of 
    AOML was greatly appreciated.
    
    
    INTRODUCTION
    
    A sea-going science team from 12 oceanographic institutions in the U.S. participated 
    on the cruise.  Several other science programs were supported with no dedicated cruise 
    participant.  The science party and their responsibilities are listed in Tables 1.1 and 1.2.
    
    
                        Table 1.1.  Scientific personnel, A16S_2005.           
    
              ================================================================
              Duties                        Name                Affiliation*
              ----------------------------------------------------------------
              Co-Chief Scientist            Rik Wanninkhof      AOML
              Co-Chief Scientist            Scott Doney         WHOI
              Data Manager                  Frank Delahoyde     SIO
              CTD Processing                Kristy McTaggart    PMEL
              Watch Stander                 Naomi Levine        MIT/WHOI
              Watch Stander                 Carlos Fonseca      CIMAS-U. Miami
              LADCP/Electronics Technician  Doug Anderson       AOML
              LADCP/Electronics Technician  Philip Orton        LDEO
              Salinity                      David Wisegarver    PMEL
              O2                            Chris Langdon       RSMAS-U. Miami
              O2                            George Berberian    CIMAS-U. Miami
              Nutrients                     Charlie Fischer     AOML
              Nutrients                     Calvin Mordy        UW
              CFCs                          Mark Warner         UW
              CFCs                          John Bullister      PMEL
              CFCs                          Eric Wisegarver     PMEL
              Helium/Tritium                Andrew Mutter       LDEO
              HCFCs                         Shari Yvon-Lewis    TAMU
              HCFCs                         Benjamin Kates      AOML
              Alkalinity/pH                 William Hiscock     RSMAS-U. Miami
              Alkalinity/pH                 John Michael Trapp  RSMAS-U. Miami
              Alkalinity/pH                 Mareva Chanson      RSMAS-U. Miami
              Alkalinity/pH                 Taylor Graham       RSMAS-U. Miami
              DIC                           Esa Peltola         AOML
              DIC                           Robert Castle       AOML
              DOM                           Wenhao Chen         RSMAS-U. Miami
              POC/PIC                       Alexandra Thompson  LBNL
              CO2 Development               Zhaohui Aleck Wang  USF
              CO2 Development               Brittany Doupnik    USF
              SAMI/pCO2                     Stacy Smith         U. Montana
              Aerosols                      Matt Lenington      CWU
              ----------------------------------------------------------------
    
    
    AFFILIATIONS:
    
      AOML        NOAA-Atlantic Oceanographic and Meteorological Laboratory
      CIMAS       Cooperative Institute for Marine and Atmospheric Studies
      CWU         Central Washington University
      LBNL        Lawrence-Berkeley National Laboratory
      LDEO        Lamont-Doherty Earth Observatory, Columbia University
      MIT         Massachusetts Institute of Technology
      PMEL        NOAA-Pacific Marine Environmental Laboratory
      RSMAS       Rosenstiel School of Marine and Atmospheric Sciences
      SIO         Scripps Institution of Oceanography, University California, San Diego
      TAMU        Texas A&M University
      U. Hawaii   University of Hawaii
      U. Miami    University of Miami
      U. Montana  University of Montana
      UCSB        University of California at Santa Barbara
      USF         University of South Florida
      UW          University of Washington
      WHOI        Woods Hole Oceanographic Institution
    
    
                          Table 1.2.  Principal programs of A16S 2005.
    
               ==================================================================
               Analysis             Institution     Principal Investigator
               ------------------------------------------------------------------
               CTD                  PMEL/AOML       Greg Johnson/Molly Baringer
               Salinity             PMEL            Greg Johnson
               CFCs                 UW/PMEL         Mark Warner/John Bullister
               HCFCs                TAMU            Shari Yvon-Lewis
               DIC                  AOML/PMEL       Rik Wanninkhof/Dick Feely
               Discrete pCO2        AOML            Rik Wanninkhof
               Dissolved O2         RSMAS-U. Miami  Chris Langdon
               Nutrients            UW/AOML         Calvin Mordy/Jia-Zhong Zhang
               Helium/Tritium       LDEO            Peter Schlosser
               CO2-Alkalinity       RSMAS-U. Miami  Frank Millero
               CO2-pH               RSMAS-U. Miami  Frank Millero
               DOC                  RSMAS-U. Miami  Dennis Hansell
               CDOM                 UCSB            Norm Nelson/Craig Carlson
               Underway pCO2        AOML            Rik Wanninkhof
               13C/14C              WHOI            Ann McNichol
               ADCP/LADCP           U. Hawaii/LDEO  Eric Firing/Andreas Thurnherr
               Aerosols             CWU             Anne Johansen
               SAMI/CO2             U. Montana      Mike DeGrandpre
               CO2 System Develop.  USF             Robert Byrne
               ------------------------------------------------------------------
    
    
    DESCRIPTION OF MEASUREMENT TECHNIQUES
    
    1.  CTD/HYDROGRAPHIC MEASUREMENTS PROGRAM
    
    The basic CTD/hydrographic measurements consisted of salinity, dissolved oxygen, 
    and nutrient measurements made from water samples taken on CTD/rosette casts, plus 
    pressure, temperature, salinity, dissolved oxygen, and transmissometer from CTD 
    profiles.  A total of 125 CTD/rosette casts were made, usually to within 20 m of the 
    bottom.  No major problems were encountered during the operation.  The distribution of 
    samples is illustrated in Figures 1.0-1.3.
    
    
    Figure 1.0.  Sample distribution, stations 1-34.  (see PDF file for figures)
    Figure 1.1.  Sample distribution, stations 32-62.
    Figure 1.2.  Sample distribution, stations 60-92.
    Figure 1.3.  Sample distribution, stations 88-121.
    
    
    1.1.  Water Sampling Package
    
    LADCP/CTD/rosette casts were performed with a package consisting of a 36-place, 
    12-liter rosette frame (PMEL), a 36-place pylon (SBE32) and 36, 12-liter Bullister 
    bottles. This package was deployed on station/casts 5/2-121/1. A smaller 24-place 3-liter 
    foul weather rosette package was deployed on station/casts 1/1-5/1. Underwater 
    electronic components consisted of a Sea-Bird Electronics (SBE) 9 plus CTD with dual 
    pumps and the following sensors: dual temperature (SBE3), dual conductivity (SBE4), 
    dissolved oxygen (SBE43), transmissometer (Wetlabs SeaStar), turbidity (Seapoint 
    Sensors), and PIC (Wetlabs). The other Underwater electronic components consisted of 
    RDI LADCPs, a Simrad or Benthos altimeter, an AM Cells load cell, and a Benthos 
    pinger.
    
    The CTD was mounted vertically in an SBE CTD cage attached to the bottom center 
    of the rosette frame. All SBE4 conductivity and SBE3 temperature sensors and their 
    respective pumps were mounted vertically as recommended by SBE. Pump exhausts were 
    attached to outside corners of the CTD cage and directed downward. The altimeter was 
    mounted on the inside of a support strut adjacent to the bottom frame ring. The 
    transmissometer, turbidity and PIC sensors were mounted horizontally on a fiberglass 
    grid attached off center to the rosette frame adjacent to the CTD.  The LADCPs were 
    vertically mounted inside the bottle rings with one set of transducers pointing down, the 
    other up.
    
    The rosette system was suspended from a UNOLS-standard three-conductor 0.322" 
    electro-mechanical sea cable.
    
    The R/V Brown's forward CTD winch was used with the 24-place 3-liter rosette for 
    station/casts 1/1-5/1.  The aft CTD winch was used with the 36-place 12-liter rosette for 
    the remaining station/casts (5/2-121/2).
    
    A single Sea cable termination for each winch served the entire leg.  Station/cast 5/1 
    was aborted due to problems with the forward winch that required lowering the package 
    back to the bottom (~1000 m) after bottles had been tripped. The decision was made to 
    switch to the aft winch, the 36-place12-liter package and CTD #315 for station/cast 5/2.
    Station/cast 51/1 was aborted when the CTD signal was abruptly lost at 1274 decibars on 
    the down cast.  The problem was later traced to the turbidity sensor, which was shorting 
    out the CTD #315 auxiliary power supply. Station/cast 51/2 was made with CTD #209 
    (installed in the 36-place rosette) which was used for all subsequent casts.
    
    The deck watch prepared the rosette within 40 minutes prior to each cast.  All valves, 
    vents, and lanyards were checked for proper orientation. The bottles were cocked and all 
    hardware and connections rechecked. Once stopped on station, the LADCP was turned on 
    and syringes were removed from the CTD sensor intake ports.  As directed by the deck 
    watch leader, the CTD was powered-up and the data acquisition system started. Two 
    stabilizing taglines were threaded through rings on the rosette frame.  The deck watch 
    leader directed the winch operator to raise the package, the squirt boom and rosette were 
    extended outboard, and the package quickly lowered into the water. The tag lines were 
    removed and the package was lowered to 10 m.  The CTD console operator waited for 
    the CTD sensor pumps to turn on, waited an additional 60 seconds for sensors to 
    stabilize, then directed the winch operator to bring the package close to the surface, pause 
    for typically 10 seconds, and begin the descent.
    
    Descent speeds were 30 m/min to 50m, 45 m/min to 200m, and 60 m/min beyond 
    200m. Each rosette cast was usually lowered to within 20 m of the bottom, using the 
    altimeter and pinger to determine a safe distance.
    
    On the up cast, the winch operator was directed to stop at each bottle trip depth. The 
    CTD console operator waited 30 seconds before tripping a bottle, then an additional 10 
    seconds after receiving the trip confirmation before directing the winch to proceed to the 
    next bottle stop.
    
    Standard sampling depths were used throughout A16S 2005, depending on the 
    overall water depth. The standard depths were staggered every other pair of stations.
    
    Recovering the package at the end of the deployment was essentially the reverse of 
    launching, with the additional use of poles and snap-hooks to attach tag lines for added 
    safety and stability.  The rosette was left on deck for sampling.  The bottles and rosette 
    were examined before samples were taken, and anything unusual noted on the sample 
    log.
    
    Each bottle on the rosette had a unique serial number. This bottle identification was 
    maintained independently of the bottle position on the rosette, which was used for sample 
    identification. Nine bottles were replaced on this leg, and parts of others were replaced or 
    repaired.
    
    Routine CTD maintenance included soaking the conductivity and DO sensors in a 
    solution of Triton-X as recommended by Sea-Bird between casts to maintain sensor 
    stability.  Rosette maintenance was performed on a regular basis.  O-rings were changed 
    as necessary and bottle maintenance was performed each day to insure proper closure and 
    sealing. Valves were inspected for leaks and repaired or replaced as needed.
    
    
    1.2.  UNDERWATER ELECTRONICS PACKAGES
    
    CTD data were collected with SBE9plus CTDs (PMEL #315 and #209).  These 
    instruments provided pressure, dual temperature (SBE3), dual conductivity (SBE4), 
    dissolved oxygen (SBE43), transmissometer (Wetlabs SeaStar), turbidity (Seapoint 
    Sensors), PIC (Wetlabs), load cell (AM Cells), and altimeter (Benthos/Simrad 807) 
    channels (Table 1.3).  The CTDs supplied a standard Sea-Bird format data stream at a 
    data rate of 24 frames/second.
    
    The CTD was outfitted with dual pumps. Primary temperature, conductivity, and 
    dissolved oxygen were plumbed on one pump circuit and secondary temperature and 
    conductivity on the other. The sensors were deployed vertically.  The primary 
    temperature and conductivity sensors (T1 #4193, C1 #2882 sation/casts 1/1-5/1, 51/2-
    120/1; T1 #4341, C1 #2887 station/casts 5/2-51/1; and T1 #4193, C1 #0354 station/casts 
    121/1) were used for reported CTD temperatures and conductivities on all casts.  The 
    secondary temperature and conductivity sensors were used for calibration checks.
    
    The SBE9plus CTD was connected to the SBE32 36-place pylon providing for 
    single-conductor sea cable operation.  Power to the SBE9plus CTD (and sensors), SBE32 
    pylon, auxiliary sensors, and altimeter was provided through the sea cable from the 
    SBE11plus deck unit in the computer lab.
    
    
    1.3.  Navigation and Bathymetry Data Acquisition
    
    Navigation data were acquired by the database workstation at 1-second intervals 
    from the ship's Trimble PCODE GPS receiver beginning January 11.  Although the ship 
    had a Seabeam multibeam system functioning during the cruise and displaying center 
    beam depth, the data were not available to other computers on the ship. The A16S 
    bathymetry data were synthesized from ETOPO2 data along the cruise track and used for 
    preliminary vertical sections, maps and estimated bottom depths.
    
    
                     Table 1.3.  A16S 2005 rosette underwater electronics.
    
    ===========================================================================================
    Item                                           Serial Number (station/cast used)
    -------------------------------------------------------------------------------------------
    Sea-Bird SBE32 36-place Carousel Water Sampler  
    Sea-Bird SBE9plus CTD                          PMEL #315
    Sea-Bird SBE9plus CTD                          PMEL #209
    Paroscientific Digiquartz Pressure Sensor      S/N 53960 (5/2-51/1)
    Paroscientific Digiquartz Pressure Sensor      S/N 53586 (1/1-5/1, 51/2-121/1)
    Sea-Bird SBE3plus Temperature Sensor           S/N 03P-4193 (Primary 1/1-5/1, 51/2-121/1)
    Sea-Bird SBE3plus Temperature Sensor           S/N 03P-4335 (Secondary 1/1-5/1,51/2-121/1)
    Sea-Bird SBE3plus Temperature Sensor           S/N 03P-4341 (Primary 5/2-51/1)
    Sea-Bird SBE3plus Temperature Sensor           S/N 03P-1370 (Secondary 5/2-51/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-2882 (Primary 1/1-5/1, 51/2-120/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-2882 (Secondary 121/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-1434 (Secondary 1/1-5/1, 51/2-58/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-2887 (Primary 5/2-51/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-0354 (Secondary 5/2-51/1, 59/1-120/1)
    Sea-Bird SBE4C Conductivity Sensor             S/N 04-0354 (Primary 121/1)
    Sea-Bird SBE43 DO Sensor                       S/N 43-0312 (1/1-5/1, 51/2-121/1)
    Sea-Bird SBE43 DO Sensor                       S/N 43-0664 (5/2-51/1)
    Wetlabs SeaStar Transmissometer                S/N CST-391DR
    Seapoint Sensors OBS Turbidity Sensor          S/N 10366
    Wetlabs PIC Sensor                             S/N PIC001
    Benthos Altimeter                              S/N 1035
    Simrad 807 Altimeter                           S/N 92010101 (AOML)
    AM Cell (Load Cell)                            S/N 1109
    RDI LADCP                                      S/N 299 (5/1-10/1, 36/1-63/1, 82/1)
    RDI LADCP                                      S/N 149 (10/1-35/1, 64/1-81/1, 83/1-121/1)
    LADCP Battery Pack  
    -------------------------------------------------------------------------------------------
    
    
    1.4.  Real-Time CTD Data Acquisition System
    
    The CTD data acquisition system consisted of an SBE-11plus (V1) deck unit and a 
    networked generic PC workstation running Windows 2000. SBE Seasave software was 
    used for data acquisition and to close bottles on the rosette.
    
    CTD deployments were initiated by the console watch after the ship stopped on 
    station.  The watch maintained a console operations log containing a description of each 
    deployment, a record of every attempt to close a bottle and any pertinent comments.
    
    Once the deck watch had deployed the rosette, the winch operator would lower it to 
    10 m. The CTD sensor pumps were configured with a 60 second startup delay. The 
    console operator checked the CTD data for proper sensor operation, waited an additional 
    60 seconds for sensors to stabilize, then instructed the winch operator to bring the 
    package to the surface, pause for 10 seconds, and descend to a target depth. The profiling 
    rate was no more than 30 m/min to 50 m, no more than 45 m/min to 200 m, and no more 
    than 60 m/min deeper than 200 m depending on sea cable tension and the sea state.
    
    The console watch monitored the progress of the deployment and quality of the CTD 
    data through interactive graphics and operational displays. Additionally, the watch 
    created a sample log for the deployment which would be later used to record the 
    correspondence between rosette bottles and analytical samples taken.  The altimeter 
    channel, CTD pressure, wire-out and bathymetric depth were all monitored to determine 
    the distance of the package from the bottom, usually allowing a safe approach to within 
    20 m.
    
    Bottles were closed on the up cast by operating a "point and click" graphical trip 
    button.  The data acquisition system responded with trip confirmation messages and the 
    corresponding CTD data in a rosette bottle trip window on the display.  All tripping 
    attempts were noted on the console log.  The console watch then directed the winch 
    operator to raise the package up to the next bottle trip location.
    
    After the last bottle was tripped, the console watch directed the deck watch to bring 
    the rosette on deck.  Once on deck, the console watch terminated the data acquisition, 
    turned off the deck unit, and assisted with rosette sampling.
    
    
    1.5.  SHIPBOARD CTD DATA PROCESSING
    
    Shipboard CTD data processing was performed automatically at the end of each 
    deployment using SIO/ODF CTD processing software. The raw CTD data and bottle trips 
    acquired by SBE Seasave on the Windows 2000 workstation were copied onto the Linux 
    database and webserver workstation, then processed to a 0.5 second time series.  Bottle 
    trip values were extracted and a 2-decibar (dbar) down cast pressure series created. This 
    pressure series was used by the web service for interactive plots, sections, and CTD data 
    distribution (the 0.5 second time series was also available for distribution). During and 
    after the deployment the data were redundantly backed up to another Linux workstation 
    and a Windows workstation.
    
    CTD data were examined at the completion of each deployment for clean corrected 
    sensor response and any calibration shifts.  As bottle salinity and oxygen results became 
    available, they were used to refine shipboard conductivity and oxygen sensor 
    calibrations.
    
    A total of 125 casts were made (including 1 test cast and 2 aborted casts). The 24-
    place 3-liter rosette and CTD #209 was used on station/casts 1/1-5/1, the 36-place 12-liter 
    rosette and CTD #315 was used on station/casts 5/2-51/1, and the 36-place 12-liter rosette 
    and CTD #209 was used on station/casts 51/2-121/1.
    
    
    1.6.  CTD LABORATORY CALIBRATION
    
    Laboratory calibrations of the CTD pressure, temperature, and conductivity sensors were 
    all performed at SBE. The calibration dates are listed in Table 1.4.
    
    
                      Table 1.4.  A16S 2005 CTD sensor calibration dates.
    
           =========================================================================
                                                         Pre-Cruise   Post-Cruise
                                               Serial    Calibration  Calibration
           Sensor                              Number      Date         Date
           -------------------------------------------------------------------------
           Paroscientific Digiquartz Pressure  53960     23-Sep-03    25-May-05
           Paroscientific Digiquartz Pressure  53586     17-Aug-00    Not calibrated
           Sea-Bird SBE3plus Temperature       03P-4193  30-Nov-04    13-Apr-05
           Sea-Bird SBE3plus Temperature       03P-4335  30-Nov-04    13-Apr-05
           Sea-Bird SBE3plus Temperature       03P-4341  30-Nov-04    13-Apr-05
           Sea-Bird SBE3 Temperature           03-1370   23-Jul-04    13-Apr-05
           Sea-Bird SBE4C Conductivity         04-2882   15-Dec-04    12-Apr-05
           Sea-Bird SBE4C Conductivity         04-1434   30-Nov-04    Not calibrated
           Sea-Bird SBE4C Conductivity         04-2887   30-Nov-04    12-Apr-05
           Sea-Bird SBE4C Conductivity         04-0354   30-Nov-04    12-Apr-05
           -------------------------------------------------------------------------
      
    
    1.7.  SHIPBOARD CTD CALIBRATION PROCEDURES
    
    Two CTDs (PMEL #315 and #209) were used on this leg, for a total of four distinct 
    pressure, temperature and conductivity sensor configurations (Table 1.5).
    
    
                         Table 1.5.  A16S 2005 sensor configurations.            
                
                ===============================================================
                Configuration  CTD    T1    C1    T2    C2   Station/Cast
                ---------------------------------------------------------------
                      1        0209  4193  2882  4335  1434  1/1-5/1, 51/2-58/1
                      2        0315  4341  2887  1370  0354  5/2-51/1
                      3        0209  4193  2882  4335  0354  59/1-120/1
                      4        0209  4193  0354  4335  2882  121/1
                ---------------------------------------------------------------
    
    
    Each CTD was deployed with all sensors and pumps aligned vertically, as 
    recommended by SBE. CTD #209 was initially configured in the small 24-place 3-liter 
    rosette and was used for the first five stations because of sea conditions. CTD #315 was 
    configured in the 36-place 12-liter rosette and was used on station/casts 5/2-51/1. CTD 
    #209 was installed in the 36-place rosette prior to 51/2 and was used for all subsequent 
    station/casts (51/2-121/1). Secondary temperature and conductivity (T2 and C2) sensors 
    served as calibration checks for the reported primary temperature and conductivity (T1 
    and C1) on all casts.  In-situ salinity and dissolved O2 check samples collected during 
    each cast were used to calibrate the conductivity and dissolved O2 sensors.
    
    
    1.7.1.  CTD PRESSURE
    
    Pressure sensor calibration coefficients derived from the pre-cruise calibrations were 
    applied to raw pressure data during each cast.  Residual pressure offsets (the difference 
    between the first and last submerged pressures) were examined to check for calibration 
    shifts. All were <0.5 db, and both sensors exhibited <0.5 db offset shift over their periods 
    of use. No additional adjustments were made to the calculated pressures.
    
    
    1.7.2.  CTD TEMPERATURE
    
    Temperature sensor calibration coefficients derived from the pre-cruise calibrations 
    were applied to raw primary and secondary temperature data during each cast.
    
    
    Figure 1.4.  T1-T2 BY STATION, p > 500 db.
    
    
    Calibration accuracy was examined by tabulating T1-T2 over a range of pressures 
    (bottle trip locations) for each cast. These comparisons are summarized in Figure 1.4.
    
    CTD configurations 1, 3, and 4 (CTD #209, station/casts 1/1-5/1,51/2-121/1) exhibit 
    a deep relative calibration error of 0.0008°C at station/cast 59/1, drifting to 0.0002°C by 
    station/cast 85/1 and stabilizing. CTD configuration #2 (CTD #315, station/casts 5/2-
    50/1) exhibits a relative error of -0.0008°C at station/cast 20/1 and drifts to +0.0004°C by 
    station/cast 50/1.  Configuration #2 also shows a T1-T2 pressure response of 
    -2.7e-7°C/db as shown in Figure 1.5.
    
    
    Figure 1.5.  T1-T2 by pressure, station/casts 5/2-50/1.
    
    
    It is likely that all three temperature sensors used on A16S 2005 exhibited some 
    calibration drift. Although the mean deep T1-T2 for the leg is close to 0, it should not be 
    interpreted as a reliable metric of temperature calibration accuracy.
    
    
    1.7.3.  CTD CONDUCTIVITY
    
    Conductivity sensor calibration coefficients derived from the pre-cruise calibrations 
    were applied to raw primary and secondary conductivities.
    
    Comparisons between the primary and secondary sensors and between each of the 
    sensors to check sample conductivities (conductivity calculated from bottle salinities) 
    were used to derive conductivity corrections. These corrections were determined for three 
    distinct groupings of station/casts, corresponding to the T1/C1 sensor pair used. Although 
    1/1-5/1 used the same T1/C1 as 51/2-120/1, it was treated as a separate grouping because 
    of the amount of time between 5/1 and 51/2. 121/1 was a 1-cast grouping in which C1 
    and C2 were swapped (T1C2, T2C1) in an attempt to resolve the source of a .0007 
    salinity offset in T1/C1 observed between the down and up casts.
    
    Uncorrected C1-C2 and bottle C-C1 were first examined to identify sensor drift 
    (Figures 1.6 and 1.7).
    
     
    Figure 1.6.  Uncorrected C1-C2 by station, p > 500db.
    Figure 1.7.  Uncorrected bottle C-C1 by station, p > 500db.
    Figure 1.8.  Corrected bottle C-C1 by station, all pressures.
    
    
    C1 offset corrections were determined to account for drift over time. After applying 
    the drift corrections, the residuals were examined to determine conductivity slope and 
    pressure response corrections. Figures 1.8-1.11 show the residuals after applying all 
    corrections.
    
    
    Figure 1.9.  Corrected bottle C-C1 by pressure, all pressures.
    Figure 1.10. Corrected bottle C-C1 by station, p > 500 db.
    Figure 1.11. Salinity residual by station, p > 500 db.
    Figure 1.11. represents an estimate of the salinity accuracy on A16S 2005.  
                 The 95% confidence limit is ±0.0015.
    
    
    1.7.4.  CTD DISSOLVED OXYGEN
    
    Two SBE43 dissolved O2 (DO) sensors were used on this leg; S/N 43-0312 on 
    station/casts 1/1-5/1, 51/2-121/1 and S/N 43-0664 on 5/2-50/1.  Both sensors behaved 
    well, the only problems occurring on station/casts 105/1-107/1 when some particulate 
    material clogged the primary pump circuit relief valve. This problem affected the top 50 
    db of the down casts.
    
    The DO sensors were calibrated to dissolved O2 check samples by matching the up 
    cast bottle trips to down cast CTD data along isopycnal surfaces, calculating CTD 
    dissolved O2, and then minimizing the residuals using a non-linear least-squares fitting 
    procedure. The fitting determined calibration coefficients for the sensor model 
    conversion equation and proceeded in a series of steps. Each sensor was fit in a separate 
    sequence. The first step was to determine the time constants for the exponential terms in 
    the model. These time constants are sensor-specific but applicable to an entire cruise.
    
    Once the time constants had been determined, casts were fit individually to O2 check 
    sample data.  The resulting calibration coefficients were then smoothed and held constant 
    during a refit to determine sensor slope and offset.  The residuals are shown in Figures 
    1.12-1.14.
    
    
    Figure 1.12.  O2 residuals by station, all pressures.
    Figure 1.13.  O2 residuals by pressure, all pressures.
    Figure 1.14.  O2 residuals by station number, p > 500 db.
    
    
    The standard deviations of 1.14 µM/kg for all oxygens and 0.81 µM/kg for deep 
    oxygens are presented as metrics of variability between up cast and down cast dissolved 
    O2.  We make no claims regarding the precision or accuracy of CTD dissolved O2 data.
    
    The general form of the SIO/ODF O2 conversion equation for Clark cells follows 
    Brown and Morrison (1978) Millard (1982), and Owens and Millard (1985).  ODF 
    models membrane and sensor temperatures with lagged CTD temperatures and a lagged 
    thermal gradient.  In-situ pressure and temperature are filtered to match the sensor 
    response. Time-constants for the pressure response, Taup, two temperature responses, 
    TauTs and TauTf, and thermal gradient response, TaudT, are fitting parameters.  The 
    thermal gradient term is derived by low-pass filtering the difference between the fast 
    response (Tf) and slow response (Ts) temperatures. This term is SBE43-specific and 
    corrects a non- linearity introduced by analog thermal compensation in the sensor.  The 
    Oc gradient, dOc/dt, is approximated by low-pass filtering first-order Oc differences.
    
    This gradient term attempts to correct for reduction of species other than O2 at the sensor 
    cathode.  The time-constant for this filter, Tauog, is a fitting parameter.  The dissolved O2 
    concentration is then calculated:
    
          O2 ml/l = [c1*Oc+c2.]*fsat(S,T,P)*e**(c3*Pl+c4*Tf+c5*Ts+c6*dOc/dt(1.7.4.0)
    
    where:
    
       O2 ml/l      = Dissolved O2 concentration in ml/l;
       Oc           = Sensor current (uamps);
       fsat (S,T,P) = O2 saturation concentration at S,T,P (ml/l);
       S            = Salinity at O2 response-time (PSUs);
       T            = Temperature at O2 response-time (°C);
       P            = Pressure at O2 response-time (decibars);
       Pl           = Low-pass filtered pressure (decibars);
       Tf           = Fast low-pass filtered temperature (°C);
       Ts           = Slow low-pass filtered temperature (°C);
       dOc/dt       = Sensor current gradient (uamps/secs);
       dT           = low-pass filtered thermal gradient (Tf - Ts).
    
    
    1.8.  FINAL CTD DATA PROCESSING
    
    The reduction of profile data began with a standard suite of processing modules 
    using Sea-Bird Data Processing Win32 version 5.32 software in the following order:
    
    DATCNV   converts raw data into engineering units and creates a .ROS bottle file.
             Both down and up casts were processed for scan, elapsed time(s), pressure, t0, t1, c0, c1, 
             and oxygen voltage.  Optical sensor data were not carried through the processing stream.
    
    MARKSCAN was used to determine the number of scans acquired on deck and while 
             priming the system to exclude these scans from processing.
    
    ALIGNCTD aligns temperature, conductivity, and oxygen measurements in time 
             relative to pressure to ensure that derived parameters are made using measurements from 
             the same parcel of water.  Primary conductivity is automatically advanced in the deck 
             unit by 0.073 seconds.  No additional alignment was necessary for either of the primary 
             conductivity sensors.  As for the secondary conductivity sensors used during this cruise, 
             s/n 354 associated with CTD 315 was advanced 0.068 seconds in ALIGNCTD, and s/n 
             1434 associated with CTD 209 was advanced 0.056 seconds.  It was not necessary to 
             align temperature or oxygen.
             
    ROSSUM   averages bottle data over an 8-second interval and derives salinity, theta, 
             sigma-theta, and oxygen (µmol/kg).  Averaging began at the bottle confirm bit for casts 
             0011-0251, and from 4 seconds before the confirm bit to 4 seconds after the confirm bit 
             for casts 0261-1211.
             
    WILDEDIT computes the standard deviation of 100 point bins, and then makes two 
             passes through the data.  The first pass flags points that differ from the mean by more 
             than 2 standard deviations.  A new standard deviation is computed excluding the flagged 
             points and the second pass marks bad values greater than 20 standard deviations from the 
             mean.  For this data set, data were kept within a distance of 100 of the mean (i.e., all 
             data).
             
    FILTER   applies a low pass filter to pressure with a time constant of 0.15 seconds.  In 
             order to produce zero phase (no time shift), the filter is first run forward through the file 
             and then run backwards through the file.
             
    CELLTM   uses a recursive filter to remove conductivity cell thermal mass effects 
             from measured conductivity.  In areas with steep temperature gradients the thermal mass 
             correction is on the order of 0.005 PSS-78.  In other areas the correction is negligibl
             The value used for the thermal anomaly amplitude (alpha) was 0.03°C.  The value used 
             for the thermal anomaly time constant (1/beta) was 7.0°C.
             
    LOOPEDIT removes scans associated with pressure slowdowns and reversals.  If the 
             CTD velocity is less than 0.25 m/s or the pressure is not greater than the previous 
             maximum scan, the scan is omitted.
             
    BINAVG   averages the data into 1 dbar bins.  Each bin is centered on an integer 
             pressure value, e.g., the 1 dbar bin averages scans where pressure is between 0.5 dbar and 
             1.5 dbar.  There is no surface bin.  The number of points averaged in each bin is included 
             in the data file.
             
    DERIVE   uses 1 dbar averaged pressure, temperature, and conductivity to compute 
             primary and secondary salinities.
             
    TRANS    converts the binary data file into ASCII format.
    
    Package slowdowns and reversals owing to ship roll can move mixed water in tow to 
    in front of the CTD sensors and create artificial density inversions and other artifacts.  In 
    addition to Seasoft module LOOPEDIT, a PMEL program computes values of density 
    locally referenced between every 1 dbar of pressure to compute N2 and linearly 
    interpolates temperature, conductivity, and oxygen voltage over those records where N2 
    is less than or equal to -1 10-5 per s2.  During this cruise it was noted that 19 profiles 
    failed the criteria in the top 10 meters.  These data were retained but flagged as 
    questionable in the final WOCE formatted files.
    
    Final calibrations are applied to delooped data files.  ITS-90 temperature, salinity, 
    and oxygen are computed, and WOCE quality flags are created.  ASCII files are 
    converted WOCE format for submission to the CLIVAR and Carbon Hydrographic Data 
    Office (CCHDO).
    
    During casts 105/1-107/1, the air-bleed hole in the plumbing of the primary sensors 
    was blocked, resulting in low surface salinities and oxygen spikes as deep as 53 dbar.
    
    Low salinities were flagged as bad and slightly low salinities were flagged as 
    questionable.
    
    
    1.9.  FINAL CTD CALIBRATION PROCEDURES
    
    1.9.1.  CTD PRESSURE
    
    Pressure calibrations for both CTD instruments used during this cruise are pre-cruise.
    
    On deck pressure readings prior to each cast were examined and remained within 1 dbar 
    of calibration.  Differences between first and last submerged pressures for each cast were 
    also examined and the residuals for both sensors shifted <0.5 dbar over their periods of 
    use.  So no additional adjustments were applied.
    
    
    1.9.2.  CTD TEMPERATURE
    
    Using pre- and post-cruise laboratory calibrations, a linearly interpolated drift 
    correction at the midpoint of the cruise was applied to each sensor.  For temperature 
    sensor s/n 4193 used for station/casts 1/1-5/1 and 51/2-120/1, this correction is 
    0.00024°C.  For temperature sensor s/n 4341 used for station/casts 5/2-51/1, this 
    correction is 0.00038°C.  And for temperature sensor s/n 4335 used for cast 121/1, this 
    correction is 0.00032°C.  Also, a uniform correction was applied to all sensors for heating 
    of the thermistor owing to viscous effects.  Thermistors are biased high by this effect and 
    were adjusted down by 0.0006°C.  This adjustment results in errors of no more than 
    ±0.00015°C from this effect for the full range of oceanographic temperature and salinity.
    
    
    1.9.3.  CTD CONDUCTIVITY
    
    CTD conductivity are calibrated against bottle salinity data assuming a constant 
    additive correction (bias), a station-dependent multiplicative correction (slope), and 
    where needed, a linear pressure-dependent term.  PMEL FORTRAN programs combine 
    individual ROSSUM bottle files into one listing for each conductivity sensor.  Sample 
    salinities flagged as "good" are matched to CTD salinities by station/sample number.
    
    MATLAB functions CALCOSn are used to determine the best fit of CTD and bottle data, 
    where n is the order of the station-dependent linear or polynomial fit.  CALCOSn 
    recursively throws out data greater than 2.8 standard deviations.  CALCOSn returns a 
    single conductivity bias and a conductivity slope for each station.  A station-dependent 
    slope coefficient best models the gradual shift in the conductivity sensor with time.
    
    CALCOPn additionally returns a linear pressure term (modified beta) that is multiplied 
    by CTD pressure and added to conductivity.
    
    For conductivity sensor s/n 2882 used for station/casts 1/1-5/1 and 51/2-121/1, the 
    best results are an overall, second-order, station-dependent fit with a linear pressure 
    correction.  About 82% of the 2509 points (2052 points) used in the fit produced a 
    standard deviation of 0.0010 PSS-78.  The bias is 0.0018644 mS/cm, the pressure 
    correction is -3.4731617 10-8 mS/cm/dbar, and the slope coefficients range from 
    1.0000184-1.0002895.  For conductivity sensor s/n 2887 used for station/cast 5/2-051/1, 
    the best results are an overall, linear, station-dependent fit with a linear pressure 
    correction.  About 85% of the 1525 points (1302 points) used in the fit produce a 
    standard deviation of 0.0008 PSS-78.  The bias is 0.0071032 mS/cm, the pressure 
    correction is -3.3595083 10-7 mS/cm/dbar, and the slope coefficients range from 
    0.9998770-1.0000159.
    
    CTD-bottle conductivity differences plotted against station number and pressure 
    (Figures 1.15-1.16) are used to verify the success of the fit parameters.  Matlab routines 
    apply post-cruise calibrations to temperature and conductivity, and compute final salinity 
    values.
    
    
    Figure 1.15.  Calibrated CTD-bottle conductivity differences plotted against station number.
    Figure 1.16.  Calibrated CTD-bottle conductivity differences plotted against pressure.
    
    
    1.9.4.  CTD DISSOLVED OXYGEN
    
    CTD oxygen sensors are modeled following the essential form of Owens and Millard 
    (1985).  Here, the equation 
    
            O2 = (slope*Oc+bias+lag*dOc/dt)*O2sat(S,T)*exp(Tcor*T+Pcor*P)
    
    is used where O2 is the calibrated CTD oxygen value, Oc is the reported oxygen current, 
    dOc/dt is its time derivative (smoothed with a 15-dbar hanning filter), and O2sat is the 
    oxygen saturation (Benson and Krause, 1984).  CTD temperature, pressure, and salinity 
    are used for T, P, and S.  The parameters of slope, bias, lag, Tcor, and Pcor are solved by 
    nonlinear least squares regression of matched bottle oxygen and CTD downcast data, 
    recursively discarding 2.8 standard deviation outliers.
    
    Significant hysteresis between the down and up oxygen profiles at deep stations 
    warrant using the downcast oxygen data for calibration.  PMEL FORTRAN programs 
    combine individual ROSSUM bottle files into one listing for each oxygen sensor.
    
    Sample oxygen flagged as good (2 or 6) are matched to CTD oxygen by station/sample 
    number.  Upcast bottle data are matched to downcast profile data by locally referenced 
    potential densities using MATLAB routine MATCH_SG_N_nnn, where nnn is the 
    oxygen sensor serial number.  If interpolated bottle pressures were more than 50 dbar 
    from matched downcast pressures, then matching was redone using pressure instead of 
    density in MATCH_SG_N_nnn.  Calibration coefficients are determined using function 
    RUN_OXYGEN_CAL_1.  The best results are from a least-squares fit with a linear 
    station-dependent slope (Table 1.6).
    
    
                     Table 1.6.  Final oxygen calibration coefficients.
        
        ============================================================================
        Station   Slope Range     Bias     Lag    Tcor    Pcor  Points Used  Std Dev
        ----------------------------------------------------------------------------
          1-4    0.3477-0.3481  -0.5814  8.2167 -0.0001  0.0001   85  88.2%  0.7401
          5-20   0.4350-0.4375  -0.5047  4.3258  0.0015  0.0001  464  80.17% 0.8677
         21-34   0.4373-0.4426  -0.5016  3.8727  0.0008  0.0001  489  85.5%  1.1244
         35-50   0.4423-0.4434  -0.5036  4.3414  0.0007  0.0001  566  86.4%  0.6828
         51-65   0.3423-0.3440  -0.5718  7.2016  0.0015  0.0001  535  92.0%  0.6009
         66-89   0.3467-0.3499  -0.5787  7.5763  0.0013  0.0001  843  97.0%  0.7276
         90-99   0.3517-0.3521  -0.5841  7.1488  0.0011  0.0001  359  93.6%  0.5822
        100-121  0.3518-0.3521  -0.5777  5.5720  0.0010  0.0001  774  88.4%  0.6449
        ----------------------------------------------------------------------------
    
    
    CTD-bottle oxygen differences plotted against station number and pressure show the 
    stability of the calibrated CTD oxygens relative to the bottle oxygens (Figures 1.17-1.18).
    
    Matlab routines apply oxygen calibration coefficients to profile and bottle data and 
    compute final oxygen values in µmol/kg.
    
    
    Figure 1.17.  Calibrated CTD-bottle oxygen differences plotted against station number.
    Figure 1.18.  Calibrated CTD-bottle oxygen differences plotted against pressure.
    
    
    REFERENCES
    
    Benson, B.B., and D. Krause, 1984: The concentration and isotopic fractionation of 
        oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere.
    
    Limnol. Oceanogr., v. 29, pp. 620-632.
    
    Brown, N.L., and G.K. Morrison, 1978:  WHOI/Brown conductivity, temperature, and 
        depth microprofiler.  Woods Hole Oceanographic Institution, Technical Report 
        No. 78-23.
    
    Joyce, T., and C. Corry (eds.), 1994:  Requirements for WOCE Hydrographic Programme 
        data reporting. WOCE Hydrographic Programme Office, Woods Hole, MA, USA 
        (May 1994, Rev. 2), Report WHPO 90-1, WOCE Report No. 67/91, pp. 52-55.
    
    Millard, R.C., Jr., 1982:  CTD calibration and data processing techniques at WHOI using 
        the practical salinity scale. Proceedings, International STD Conference and 
        Workshop, Marine Technical Society, La Jolla, CA, p. 19.
    
    Owens, W.B., and R.C. Millard, 1985:  A new algorithm for CTD oxygen calibration.
        J. Phys. Oceanogr., v. 15, no. 5, pp. 621-631.
        
    
    
    1.10. PARTICULATE OPTICAL SENSORS ON CTD PACKAGE
    
          Principal Investigator: Jim Bishop, LBNL, JKBishop@lbl.gov
          On board personnel:     Alexandra Thompson, LBNL, alex@nature.berkeley.edu
    
    EQUIPMENT:
    
    1. Seastar transmissometer (Wetlabs SN: CST-391DR): Detects mainly particulate 
       organic carbon
    2. PIC equipped with open flow cell (Wetlabs SN: PIC-001): Detects particulate 
       inorganic carbon
    3. Seapoint (Seapoint): Measures turbidity
    
    DATA COLLECTION:
    
    1. The Seastar collected data every cast apart from:
       • Stations 1-5/1: due to deployment of small CTD
       • Stations 52-57: due to CTD failure and until problem identified
       • Total casts: 112 (including test cast)
       • Seawater data not available for station 101 when deployed with beam blocked for 
         calibration.
    
    2. The PIC collected data every cast apart from:
       • Stations 1-5/1: due to deployment of small CTD
       • Stations 52-57: due to CTD failure and until problem identified
       • Stations 84-104: due to inconsistent calibration caused by faulty filter holder and 
         then because cabling issues delayed its redeployment.
       • Total casts: 91 (including test cast)
       • Seawater data not available for station 111 when deployed with beam blocked, 
         and stations 117 and 121 when deployed with filtered beam (4.3 OD) for 
         calibration.
    
    3. The Seapoint collected data on the following casts:
       • Stations: Test, 4 (up only), 6 - 20, 21 (up only), 22 - 24, 25 (down only).
       • Total casts: 18 (up and down), 3 (up or down)
    
    CALIBRATION:
    
    The Seastar and PIC sensors were calibrated 20 times over the course of the cruise, 
    and the Seapoint 7 times. Calibrations were carried out in air while mounted on the CTD 
    and in the lab using an alternate power supply. The Seastar and Seapoint sensors were 
    calibrated using end points: the signal in air and with a blocked beam. The PIC sensor is 
    calibrated by determining the signal when the beam is subjected to a series of optical 
    density (OD) filters (4.3 OD, 4.6 OD, 4.9 OD, and 5.2 OD, flow cell removed) and when 
    it is completely blocked. The signal through the flow cell in air was also recorded. These 
    calibrations were carried out from 0°C to 25°C.
    
    In order to probe in-situ temperature dependence and response times during casts, the 
    Seastar and PIC were deployed on casts with the beam blocked and, in the case of the 
    PIC, with a 4.3 OD filter in the beam.
    
    PROBLEMS:
    
    1. The Seapoint began to show an erratic behavior on the downcast of station 21 at 
       >3600 db. The signal returned to normal until the upcast of station 25 when again the 
       sensor produced unreasonable signals and continued to do so until failing completely 
       at station 27.  The failure coincides with the first deployments to pressures above 
       ~5000 db. The Seapoint was not removed from the CTD package until the CTD failed 
       at station 52.
       
    2. The flow cell of the PIC at cold temperatures can be subject to torque. Torturing 
       results in increased signals, and due to warming delays, at times significant hysteresis 
       between up and down cast data. This problem was solved by increasing the amount of 
       allowable movement of the flow cell. To determine optimal "give," movement of the 
       cell was probed over the duration of the cruise: i.e., allowing varying amounts of 
       movement in each of three dimensions at the laser or detector end of the cell.
       
       Eventually this thermal hysteresis was removed by filing away the inside of both cell 
       mounts and loosening holding screws/adding others to allow ~2 mm up/down and 
       in/out movement at the detector end, less at the laser end, and no movement back and 
       forth between the laser and detector windows.
       
    3. In order to determine the in-situ temperature dependence of the PIC sensor, a special 
       apparatus was built on the ship to hold three optical density filters in place 
       perpendicular to the beam over the detector window during a cast while the 
       instrument was on the CTD. However, the middle (and unseen) filter was not 
       positioned correctly or robustly, giving inconsistent calibrations and increasingly 
       erratic signals. This resulted in the PIC sensor being removed from the CTD for 21 
       stations (stations 84-104). A second filter holder was made and deployed successfully 
       in stations 117 and 121.
       
    4. In order to redeploy the PIC sensor on the CTD package at station 105, cabling 
       modifications needed to be made because a spare port was not available following the 
       replacement of the altimeter on the CTD package. To have both the PIC sensor and 
       the Seastar on the CTD package simultaneously, a Y-cable was spliced so that both 
       sensor ends were four point (as opposed to one 4 and one 6 point). During the casts at 
       station 105 and 106, the PIC signal dropped out for short periods and recovered.
       
       Before station 107, the cable ends were swapped between the PIC sensor and the 
       Seastar. There were no more dropouts of PIC data. The Seastar had data dropouts on 
       stations 115 and 119-121, indicating that this problem may have been in the Y-cable.
       
    
    1.11. LOWERED ACOUSTIC-DOPPLER CURRENT PROFILER (LADCP)
    
          Principal Investigator: Andreas Thurnherr
                                    Lamont-Doherty Earth Observatory of Columbia
                                    University (LDEO), ant@ldeo.columbia.edu
          Onboard Personnel:      (primary) Philip Orton, LDEO, orton@ldeo.columbia.edu
                                  Douglas Anderson, NOAA-AOML
          Additional Personnel:   Bruce Huber, LDEO
    
    SUMMARY:
    
    Paired upward and downward LADCPs on the CTD rosette frame collected data at 
    every station where the primary CTD rosette frame was used (stations 5-121); no LADCP 
    data was collected stations 1-4, where the smaller 24-bottle weather rosette was used due 
    to high wind/sea-state conditions. Preliminary processing was completed during the 
    cruise, using LDEO-LADCP software. A noteworthy highlight is that strong velocities 
    associated with the Antarctic Circumpolar Current were captured very well by the 
    LADCP system. Velocity uncertainties were low relative to resolved velocities in the 
    southern 40% of the section but increased rapidly afterward due to low backscatter levels; 
    the acoustic measurements of velocity rely on the presence of particles in the water 
    column. Uncertainty levels decreased somewhat over the final ten stations, as we 
    approached the equator. Final processing will likely lead to a slight improvement in the 
    data quality, due primarily to the incorporation of shipboard ADCP data that helps 
    constrain the best-fit velocity profile solution. Additional useful data from the LADCP 
    system includes acoustic backscatter and estimates of eddy diffusivity.
    
    EQUIPMENT:
    
    One Workhorse Monitor broadband 300 kHz RDI Acoustic Doppler Current Profiler 
    (ADCP) was directed upward and one directed downward on the rosette frame. Both 
    instruments were equipped with RDI's LADCP firmware upgrade that expands the list of 
    available user commands. The instruments shared one battery pack, which held a stack of 
    36 alkaline D-cells, and batteries were changed every 5-10 stations. On-deck 
    communication with the ADCPs was facilitated through RS-232 communications with a 
    laptop, via a long cable leading into the main lab. Both instruments were hooked up to a 
    4-port RS-232 to USB converter, feeding into a Dell laptop running Linux.
    
    Communication software written by Andreas Thurnherr (utilizing bbabble and expect 
    scripts) allowed data to be downloaded from both instruments simultaneously at full 
    nominal speed (115 kbps).
    
    Instruments swapouts and command-file changes are summarized in Table 1.7. The 
    first instrument change (station 10) was motivated by perceived failure of a quality 
    control test - the attempted matching of the down-looking instrument only solution with 
    the up-looking instrument only solution. Later, it was discovered that the test was being 
    executed incorrectly, and the instrument was giving comparable data to the 150 kHz 
    shipboard ADCP (SADCP). The next instrument change (station 36) was made due to a 
    "broken beam" warning in the LADCP software (described below), which indicates that 
    power on the beam is low. The beam was still collecting data, and the profile appears to 
    have been of reasonably good quality, however. The station 62 and 64 instrument 
    changes occurred when we tested a high-power LADCP for two stations. The instrument 
    performed poorly on the first cast, and on the second cast reported a broken beam. In this 
    case, the beam collected almost no data, severely reducing the quality of station 63 
    velocity estimates. The final instrument changes occurred at stations 82-83. There, the up 
    looking and down looking ADCPs were switched to test whether the data quality 
    improved. The result was an apparent decrease in performance - a "bad beam" warning 
    on ADCP S/N 299, which is less severe than a broken beam warning. The ADCPs were 
    switched back again for the next station and no further bad beam warnings were received 
    the rest of the cruise.
    
    
                 Table 1.7. Initial configuration (started at station 5) and 
                            instrument and command changes.
    
                 ============================================================
                                                 Transformation to   3-Beam
                 Station   Master  Slave  Nbins  Earth Coordinates  Solutions
                 ------------------------------------------------------------
                 Initial    299     754    25          ADCP           ADCP
                   10       149                                      
                   34               150                              
                   36       299                                      
                   49                      20         Laptop          None*
                   62       5089                                      
                   64       149                                      
                   82       299     149                              
                   83       149                                      
                   101                                 ADCP           ADCP
                 ------------------------------------------------------------
                 *No 3-beam solutions are currently computed by the software. 
                 By including 3-beam solutions, one could increase the number 
                 of samples per depth interval and possibly the data quality.
    
    
    Calibration drift is not a serious problem with ADCPs, and the instruments are 
    generally only serviced (calibrated and tank-tested) when wear and tear causes equipment 
    malfunctions. Three of the five ADCPs utilized were serviced in recent months and the 
    other two were likely serviced about two years ago.
    
    SAMPLING:
    
    Stations have the same numbering system as with the CTD data collection, and 
    progress from 5 (58°S latitude) through 121 (2°20´S). Command files were uploaded to 
    the instruments at each station, ~10 minutes prior to rosette deployment. Sampling 
    parameters included: bin size of 10 m, ambiguity velocity of 250 cm s-1, 0 m blanking 
    distance (but discarding the first bin of data), 1.5 seconds per 1-ping ensemble, and 
    synchronization of the down-looking (master) and up-looking (slave) units. As shown in 
    Table 1.6, the initial configuration called for the transformation from beam coordinates to 
    earth coordinates within the ADCP, with 3-beam solutions enabled. This was changed at 
    station 49, because we were examining the impact of 3-beam solutions on the frequency 
    of warnings of velocities over 3 m s-1. We found that the warnings persisted. At this 
    point, the number of bins was also reduced from 25 to 20 because the range was never 
    over 20 bins. The coordinate transformation and 3-beam solutions was re-enabled at 
    station 101, because there were few scatterers in the water column and it was felt that 3-
    beam solutions might improve the data.
    
    PRELIMINARY PROCESSING:
    
    Data were processed using the LDEO LADCP Software, Version 8b, written in 
    Matlab by Martin Visbeck and modified by Andreas Thurnherr. This software 
    implements an inversion for the best possible velocity profiles estimates (Visbeck, 2002), 
    and enables the user to incorporate two ADCPs, bottom track estimates from water pings, 
    CTD/GPS data, SADCP data, and a frame/cable drag model, if so desired. LADCP 
    profiles for stations 5-45 were processed with 10 m bins, while those thereafter were 
    processed with 20 m bins in an attempt to combat poor data quality resulting from low 
    backscatter levels (data was collected using 10 m bins, however). Although it is possible 
    with the LDEO software, we did not utilize the "small shear" (i.e., low-mode solution) 
    constraint or the drag model.
    
    In the final post-cruise processing, two steps remain that could improve the data 
    quality. First, the ship based ADCP data will be incorporated into the inversion. Second, 
    3-beam solutions are not possible with the software, so were not incorporated for the 
    casts that did not have internal ADCP coordinate transformations (49-100). Code may be 
    written that computes these velocity estimates.
    
    
    DATA QUALITY, UNCERTAINTY AND PRELIMINARY RESULTS:
    
    VELOCITY
    
    Preliminary velocity data are presented in Figures 1.19a-b, with uncertainty 
    estimates in Figure 1.19c. Between 50 and 45°S latitude, we appear to have observed the 
    well-documented Antarctic Circumpolar Current flow along the Sub-Antarctic and Polar 
    Fronts (Rintoul et al., 2001). Maximum currents in both fronts were 50 cm s-1 at 300-
    350 m depth and were at least 15 cm s-1 through most of the water column.
    
    Velocity uncertainty was low in the southern 40% of the section, but increased rapidly 
    afterwards due to low backscatter levels (Figure 1.19d); the acoustic measurements of 
    velocity rely on particles in the water column. Uncertainty decreased somewhat as we 
    approached the equator. The estimated standard error was generally below 5 cm s-1 
    between 57°30´ and 35°S, then 10-30+ cm s-1 between 35 and 7°S, and finally back to 5-15 
    cm s-1 from 7° to 2°20´S. These confidence intervals are conservative; they not only 
    incorporate observed single-ping noise but are also automatically increased when solution 
    consistency checks are not passed. These checks include comparisons of downcast-only 
    versus upcast-only solutions, and shear method versus the inversion solutions. If any of 
    these solutions disagree substantially, the error is amplified.
    
    
    Figure 1.19. Preliminary observations of (a) zonal velocity, (b) meridional velocity, (c) velocity 
                 standard error, and (d) acoustic backscatter. All panels include logarithmically-
                 spaced contours of density anomaly sigma-4 (kg m-3) to identify density structure 
                 and black bathymetry shading interpolated along the ship-track from a satellite-derived 
                 global dataset. Velocity data have been omitted (white) where acoustic backscatter was low,  
                 generally indicating low data quality. For brief discussions of these preliminary data, 
                 their quality, and uncertainty, see the section titled Data Quality, Uncertainty, and 
                 Preliminary Results.
    
    
    A preliminary test of data quality was possible using the SADCP data. The range of 
    the SADCP was from 0-450 m in the first 40% of the cruise, due to good backscatter 
    levels, and about 0-230 m for the remainder of the cruise. Frequent approximate 
    comparisons between the LADCP and SADCP during the cruise generally showed good 
    agreement. The incorporation of SADCP data, as well as 3-beam solutions for stations 
    49-100, will likely improve the data quality somewhat. Apart from a few regions with 
    anomalously high backscatter and strong currents (e.g., bottom boundary layers), it is 
    unlikely that uncertainty levels from stations 63-110 below roughly 1000 m can be 
    reduced to be below velocity estimates.
    
    ACOUSTIC BACKSCATTER
    
    Acoustic backscatter (ABS) data (Figure 1.19d) has not been range-normalized, but 
    it would not be difficult to make this alteration if there is interest in more quantitative 
    analyses. Fortunately, the data collection procedure approximately normalizes ABS, 
    because the LADCPs measure backscatter at a given depth from many distances. Depths 
    a few tens of meters above or below rosette stops are likely to have a bias toward high 
    backscatter (the top few hundred meters and the bottom 50 m), but this bias should be 
    constant from station-to-station throughout the cruise. Acoustic pings at 300 kHz 
    dominantly scatter off particles of sizes above roughly 1 mm, and high backscatter is 
    likely due to zooplankton, marine snow, or higher-density falling detritus. There is a clear 
    diurnal periodic signal in the surface 100 m between stations 44 and 80, with high near-
    surface backscatter at night likely resulting from vertical zooplankton migrations. Also 
    note the elevated backscatter levels at roughly 500 m between stations 50 and 80, 
    particularly in the core of the station 77 eddy.
    
    EDDY DIFFUSIVITY
    
    Philip Orton developed a separate Matlab toolbox during the cruise, for 
    LADCP/CTD ocean mixing research. Of four published methods the toolbox uses for 
    determining eddy diffusivity, the most promising utilizes vertical strain (nonlinearity in 
    d_/dz) and velocity shear, following methods of Polzin et al. (2002) as modified by 
    Naveira Garabato et al. (2004). Preliminary results (Figure 1.20) indicate that typical 
    diffusivities were roughly 10-4 m2 s-1 in the ACC, often higher in the bottom 1000 m, and 
    10-4 to 10-6 m2 s-1 in other regions. Note that uncertainties for this method, when applied 
    to individual profiles, are estimated to be close to plus or minus one order of magnitude 
    (±10x). This could be reduced with spatial averaging, as was done in Naveira-Garabato et 
    al. (2004), but this would require major modifications to the toolbox (e.g., to work with 
    the velocity data from the entire transect instead of profile-by-profile).
    
    FILES AND DIRECTORIES:
    
    The LADCP datasets should contain the following directories, which contain 
    everything that is needed in order to re-process the LADCP data:
    • Raw data, instrument-setup command files, communication logfiles
    • CTD time series and profiles used for LADCP processing
    • Shipboard ADCP data used for LADCP processing
    • Processed data files and processing figures
    
    
    Figure 1.20. Preliminary shaded estimates of (top) eddy diffusivity and (bottom) 
                 log-scale eddy diffusivity uncertainty (± log10 std. err.) from 
                 cruise-processed LADCP data. As with Figure    1, each panel includes 
                 logarithmically-spaced contours of density anomaly sigma-4 (kg m-3) to 
                 identify density structure, and black bathymetry shading interpolated 
                 along the ship-track from a satellite-derived global dataset. Data 
                 have been omitted (white) where the lower error bar on the estimate was 
                 zero.
    
    
    REFERENCES
    
    Naveira Garabato, A.C., K.L. Polzin, B.A. King, K.J. Heywood, and M. Visbeck, 2004: 
        Widespread intense turbulent mixing in the Southern Ocean. Science, v. 303, 
        pp. 210-213.
    
    Polzin, K., E. Kunze, J. Hummon, and E. Firing, 2002: The fine-scale response of 
        lowered ADCP velocity profiles. J. Atmos. Oceanic Tech., v. 19, pp. 205-224.
    
    Rintoul, S.R., C.W. Hughes, and D. Olbers, 2001: The Antarctic Circumpolar Current 
        system. In Ocean Circulation and Climate: Observing and Modeling the Global 
        Ocean, G. Siedler, J. Church, and J. Gould (eds.).  Academic Press, pp. 271-302.
    
    Visbeck, M., 2002: Deep velocity profiling using lowered acoustic Doppler current 
        profilers: Bottom track and inverse solutions. J. Atmos. Oceanic Tech., v. 19, 
        pp. 795-807.
    
    
    
    2.  BOTTLE SAMPLING
    
    2.1.  BOTTLE SAMPLING PROCEDURES
    
    At the end of each rosette deployment, water samples were drawn from the bottles in 
    the following order listed below.  The correspondence between individual sample 
    containers and the rosette bottle from which the sample was drawn was recorded on the 
    sample log for the cast.  This log also included any comments or anomalous conditions 
    noted about the rosette and bottles.  One member of the sampling team was designated 
    the "sample cop," whose responsibility was to maintain this log and insure that sampling 
    progressed in the proper drawing order.
    
    Normal sampling practice included opening the drain valve and then the air vent on 
    the bottle, indicating an air leak if water escaped.  This observation, together with other 
    diagnostic comments (e.g., "lanyard caught in lid," "valve left open") that might later 
    prove useful in determining sample integrity, were routinely noted on the sample log.
    
    Drawing oxygen samples also involved taking the sample draw temperature from the 
    bottle. The temperature was noted on the sample log and was sometimes useful in 
    determining leaking or mis-tripped bottles.
    
    Once individual samples had been drawn and properly prepared, they were 
    distributed for analysis. Oxygen, nutrient, and salinity analyses were performed on 
    computer-assisted (PC) analytical equipment networked to the data processing computer 
    for centralized data management.
    
    
    2.2.  BOTTLE DATA PROCESSING
    
    Water samples collected and properties analyzed shipboard were managed centrally 
    in a relational database (PostgreSQL-7.4.6) run on a Linux workstation. A web service 
    (OpenAcs-5.1.3 and AOL Server-4.0.9) front-end provided ship-wide access to CTD and 
    water sample data through web pages. Web-based facilities included on-demand arbitrary 
    property-property plots and vertical sections, as well as data uploads and downloads.
    
    The sample log (and any diagnostic comments) was entered into the database once 
    sampling was completed. WOCE/CLIVAR quality flags associated with sampled 
    properties were set to indicate that the property had been sampled, and sample container 
    identifications were noted where appropriate (e.g., oxygen flask number).
    
    The results of individual shipboard analyses were then uploaded through the website 
    as results became available.  These results included a quality code associated with each 
    measured value and followed the coding scheme developed for the World Ocean 
    Circulation Experiment (WOCE) Hydrographic Programme (WHP) (Joyce, 1994).
    
    Various consistency checks and detailed examination of the data continued 
    throughout the cruise.
    
    
    2.3.  SAMPLING AND ANALYSES OF BOTTLE DATA
    
    Samples for chlorofluorocarbons (CFCs), helium isotopes (3He), oxygen (O2), 
    hydrochlorofluorocarbon (HCFCs), partial pressure of CO2 (pCO2), dissolved inorganic 
    carbon (DIC), hydrogen ion activities (pH), total alkalinity (TAlk), radiocarbon (DI14C), 
    tritium, dissolved organic carbon (DOC), chromophoric dissolved organic matter 
    (CDOM), particulate inorganic/organic carbon (PIC/POC), salinity, and nutrients were 
    drawn in this sequence from a CTD sampling package containing 36, 12-l Bullister 
    bottles.   Sampling of the 36 bottles on the package took about 1.5 hours.  The samples 
    analyzed for gases were sampled first and usually drawn within an hour.  The deepest 
    bottle was sampled first and bottles were sampled sequentially to the surface bottle.  Care 
    was taken to coordinate the sampling to minimize the time between the initial opening of 
    each bottle and the completion of sample drawing. In most cases, CFCs, 3He, dissolved 
    oxygen, and HCFC samples were collected within several minutes of the initial opening 
    of each bottle.
    
    Oxygen, nutrient, and salinity samples were taken from all bottles.  Oxygen draw 
    temperature readings were commenced after station 25.  For the other parameters, not all 
    stations or all bottles were sampled.  The stations at full degrees of latitude (odd 
    numbered stations) were generally completely sampled for CFCs, DIC, pH, and TAlk, 
    with partial sampling for DOC and CDOM.  The half-degree stations were partially 
    sampled for HCFC, PIC/POC, CFCs, DIC, pH, and TAlk. Discrete pCO2 profiles were 
    obtained at every two degrees.  3He, DI14C, and tritium were sampled at different 
    intervals (primarily at full-latitude stations) as noted below.  For casts where many 
    parameters were sampled, water levels in the Bullister bottles were very low when the 
    salinity and nutrients were drawn.  This was particularly true for the bottom two bottles 
    and top two bottles that were often used for duplicate sampling for parameters with large 
    water requirements such as DIC and TAlk.  Estimated water requirements for the samples 
    are listed in the Table 2.1.
    
    
          Table 2.1. Water requirements (including bottle rinses and sample) for the 
                     different parameters drawn on the Bullister bottles.
    
                     =======================================================
                     Parameter                                    Volume (l)
                     -------------------------------------------------------
                     Chlorofluorocarbons (CFCs)                      0.5
                     Helium isotopes (3He)                           0.5
                     Oxygen (O2)                                     0.5
                     Hydrochlorofluorocarbons (HCFCs)                0.5
                     Partial pressure of CO2 (pCO2)                  1.2
                     Dissolved inorganic carbon (DIC)                1.5
                     Hydrogen ion activities (pH) )                  0.3
                     Total alkalinity (TAlk)                         1.5
                     Radiocarbon (DI14C)                             0.8
                     Tritium                                         1.2
                     Dissolved organic carbon (DOC)                  0.2
                     Chromophoric dissolved organic matter (CDOM)    0.2
                     Particulate inorganic/organic carbon (PIC/POC)  1.5
                     Salinity                                        0.3
                     Nutrients                                       0.3
                     -------------------------------------------------------
    
    
    Most samples were analyzed on board with the exception of 3He, DI14C, tritium, 
    DOC, CDOM, and PIC/POC that were sampled and preserved for shore-based analysis.
    Below are the descriptions of sampling and analysis procedures for each parameter, as 
    well as the relevant statistics on data quantity and quality.
    
    
    2.4. TESTS PERFORMED ON BULLISTER BOTTLES TO DETERMINE SAMPLE INTEGRITY OF CFCS, 
         SALTS, AND O2
    
    Two types of  tests were performed on the 12-liter Bullister bottles ("12-B Bottles") 
    used on A16S cruise:
    
        1. Test Type 1 was designed to estimate the rate of change of dissolved CFCs (CFC-11, 
           CFC-12, CFC-113 and carbon tetrachloride (CCl4)) concentrations in seawater held 
           inside closed bottles.
        2. Test Type 2 was designed to determine the rate of change of dissolved CFCs, CCl4, 
           oxygen, and salinity in seawater remaining inside a bottle after the bottle had been 
           opened and other seawater samples withdrawn.
    
    BACKGROUND:
    
    Once a bottle is closed in the water column during a hydrocast, the concentrations of 
    dissolved CFCs in the water inside may increase slowly due to release of trace amounts 
    of CFCs present in the bottle walls, O-rings, and other materials.  The release of these 
    contaminants contributes to the non-zero CFC concentrations ("bottle blank") typically 
    observed even in regions of the deep ocean thought to be essentially CFC-free.
    
    The extent of this contamination is thought to be a function of:
      • the materials used in constructing the bottles
      • the exposure of these materials to CFCs in the atmosphere prior to the cast
      • the length of time the water remains in the bottle before transfer
      • the temperature
    
    Once a bottle is opened on deck and water withdrawn for sampling, gas exchange 
    between the air in the headspace and water in the bottle begins and can alter the dissolved 
    gas concentrations and salinity in the remaining water.  The unbuffered gases, e.g., He, 
    CFCs, HCFCs and O2, are believed to be most susceptible to these changes.  These 
    changes can be especially significant when large gradients in partial pressures are present 
    between the gases in the water and in the headspace, for example, when a deep sample 
    containing near-zero concentrations of dissolved CFC is exposed to a headspace of 
    marine air.
    
    BOTTLE TESTS:
    
    Test Type 1: Changes in CFC Concentration in Closed 12-B Bottles
    The following tests were performed to estimate the rates at which dissolved CFCs 
    increase in water stored in closed 12-B Bottles.  In each test, replicate sets of bottles were 
    closed at a depth with low CFC concentrations to allow small changes to be more easily 
    detected.  Some replicate deep bottles were allowed to warm on deck before sampling, 
    while others were kept cold in a walk-in refrigerator before sampling.
    
    Bottle temperatures ("O2 Draw Temp") were recorded as each oxygen sample was 
    drawn using a thermistor inserted into the oxygen flask, following the same procedure 
    used for standard oxygen draw temperatures. These tests were performed at stations 88, 
    102, and 112.
    
    Station 88:  five 12-liter bottles (9-13) were closed at ~3100 m depth (Table 2.2):
      • Bottle 9 was sampled normally in sequence (about 32 minutes after arrival on deck); 
      • Bottles 10 and 12 were left closed on the rosette frame and sampled before the next cast;
      • Bottles 11 and 13 were removed from the rosette and placed on a spare frame in the 
        shade on deck to allow for longer storage times.
    
    
                        Table 2.2.  Results for station 88 storage tests.
    
    ==========================================================================================
                                                         CFC-12 CFC-11 CFC-13  CCl4
          CFC    HCFC    O2     O2 Draw   Salt   Sample  (pmol  (pmol  (pmol  (pmol
    Bot Syringe  Flask  Flask  Temp1(°C)  Bot   Time2(Z)  kg-1)  kg-1)  kg-1)  kg-1)  Salinity
    ------------------------------------------------------------------------------------------
     9   5573      4     161      7.3     209    00:30    0.011  0.021    0    0.082  34.9137
     9   7692                                    00:31    0.013  0.024    0    0.089  
    10   5564      4      40     13.2     210    01:40    0.012  0.027    0    0.084  34.9153
    12   7674      4             17.9     212    03:05    0.014  0.022    0    0.088  34.9151
    11   7735      5             23.4     211    07:45    0.017  0.027    0    0.090  34.9148
    13   9888      4      40     26.5     213    15:05    0.024  0.050    0    0.089  34.9155
    ------------------------------------------------------------------------------------------
         Cast on deck 11 Feb 2005 at ~23:58Z.
         1 Initial (potential) temperature for seawater samples was ~2.430°C.
         2 Date: 12 Feb 2005; all times are UTC.
    ------------------------------------------------------------------------------------------
    
    
    Station 102:  five bottles (6-10) closed at ~2950 m (Table 2.3):
      • Bottle 6 was sampled normally (about 32 minutes after arrival on deck);
      • Bottles 6 and 10 were left closed on frame and sampled before the next cast;
      • Bottles 7 and 9 were removed from the rosette frame after about 1 hour on deck and 
        placed in walk in cooler at ~4°C  Substantial warming occurred during the period on 
        deck, and subsequent cooling may have caused air to be drawn into the bottles.
    
    Sounds were detected when bottle 9 was inverted, indicating the presence of an air 
    pocket in this bottle. Consequently, samples from bottle 9 were not drawn, and the 
    data from bottle 7 are considered suspect.
    
    
                        Table 2.3.  Results for station 102 storage tests.
    
    ==========================================================================================
                                                         CFC-12 CFC-11 CFC-13  CCl4
          CFC    HCFC    O2     O2 Draw   Salt   Sample  (pmol  (pmol  (pmol  (pmol
    Bot Syringe  Flask  Flask  Temp1(°C)  Bot   Time2(Z)  kg-1)  kg-1)  kg-1)  kg-1)  Salinity
    ------------------------------------------------------------------------------------------
     6    629      3      6       6.4     606    05:00    0.016  0.030    0    0.100  34.9173
     6   7695A                                   05:01    0.020  0.031    0    0.102  
     8   7638     16             14.7     608    06:10    0.018  0.043    0    0.104  34.9175
    10    367     17             16.9     610    07:10    0.022  0.048  0.005  0.102  34.9189
    73   7701     18              5.5     607    19:10    0.035  0.061    0    0.110  34.9189
    ------------------------------------------------------------------------------------------
        Cast on deck 16 Feb 2005 at ~04:18Z.
        1 Potential temperature for seawater samples was ~2.507°C.
        2 Date: 16 Feb 2005; all times are UTC.
        3 Bottle 7 likely contaminated with air.
    ------------------------------------------------------------------------------------------
    
    
    Station 112:  five bottles (10-14) closed at ~3000 m (Table 2.4):
      • Bottle 10 was sampled normally (about 11 minutes after arrival on deck);
      • Bottles 12 and 14 were left closed on frame and sampled before the next cast;
      • Bottles 11 and 13 were removed immediately after arrival on deck and placed in walk 
        in cooler at ~4°C;
      • No oxygen samples were drawn on bottles 11-14.
    
    
                        Table 2.4.  Results for station 112 storage tests.
    
    ==========================================================================================
                                                         CFC-12 CFC-11 CFC-13  CCl4
          CFC    HCFC    O2     O2 Draw   Salt   Sample  (pmol  (pmol  (pmol  (pmol
    Bot Syringe  Flask  Flask  Temp1(°C)  Bot   Time2(Z)  kg-1)  kg-1)  kg-1)  kg-1)  Salinity
    ------------------------------------------------------------------------------------------
    10   7628      4      10      6.7     110    03:45    0.011  0.022  0.003  0.084  34.9173
    12   5567A     1             13.0     112    05:10    0.018  0.023    0    0.087  34.9179
    14    674     17             18.2     114    06:35    0.017  0.024    0    0.087  34.9170
    11   7674
         7692A  17, 18            5.1     111    19:20    0.019  0.029    0    0.086  34.9181
    13   9833    1, 2             4.4     113    20:403   0.015  0.031    0    0.086  34.9159
    ------------------------------------------------------------------------------------------
         Cast on deck 19 Feb 2005 at ~03:36Z.
         1 Potential temperature for seawater samples was ~2.439°C.
         2 Date:  19 Feb 2005; all times are UTC.
         3 Date:  20 Feb 2005.
    ------------------------------------------------------------------------------------------
    
    
    DISCUSSION OF RESULTS FROM TEST TYPE 1:
    
    During hydrocasts on the A16S cruise, the deep bottles were closed earlier than 
    shallower bottles; however, the deep bottles were sampled first on deck.  Hence, for deep 
    hydrocasts on A16S, the mean time that seawater typically remained inside bottles before 
    opening was roughly the same (about 2 hours) for both deep and shallow bottles.
    
    At high latitudes during the A16S cruise, there was typically little warming of the 
    water on deck before sampling.  In mid and low latitudes, mid-depth and deep water 
    samples underwent warming (as determined by the difference between the potential 
    temperature and oxygen draw temperature) during their transit through the thermocline, 
    mixed layer, and while on deck before sampling. The amount of warming was 
    determined by temperature measurements made during the oxygen sampling process, and 
    was typically several degrees.
    
    The station 112 experiment examined the CFC changes in bottles where seawater 
    was stored inside at cold temperatures (~5oC) for an extended period of time.  The 
    changes in the cold bottles (relative to the initially sampled bottle) are denoted in 
    Table 2.5.
    
                Table 2.5.  Changes in concentrations for station 112 storage test.                 
    
    =================================================================================================
                       O2                                                            
                      Draw  CFC-12                   CFC-11                   CC14   
               Time   Temp  (pmol     dCFC-12/dt     (pmol     dCFC-11/dt     (pmol     dCCl4/dt
    Sta. Bot. (Hours) (°C)  kg-1)  (pmol kg-1 hr-1)  kg-1)  (pmol kg-1 hr-1)  kg-1)  (pmol kg-1 hr-1)
    ---- ---- ------- ----  ------ ----------------  ------ ----------------  -----  ----------------
    112   11   15.58   5.1  0.008      0.00051        0.007     0.00045       0.002      0.00013
    112   13   40.91   4.4  0.004      0.00010        0.009     0.00022       0.002      0.00005
    ---- ---- ------- ----  ------ ----------------  ------ ----------------  -----  ----------------
                               mean =  0.00031          mean =  0.00033          mean =  0.00009
                                sd = ±0.00029             sd = ±0.00016            sd = ±0.00006
    -------------------------------------------------------------------------------------------------
    
    
    The scatter in the derived rates in Table 2.5 is likely due to the fact that the observed 
    concentration changes in Table 2.5 are close to detection limits for these compounds 
    (roughly ~0.002-0.004 pmol kg-1).  These results do indicate that in regions where there 
    is little warming before sampling (e.g., high latitudes) the rate of increase of CFCs in the 
    12-B bottles during the 2 hours between closing and sampling is small.  CFC-113 showed 
    no consistent pattern of increase (see Table 2.4).  CFC-11, CFC-12 and CCl4 showed 
    very small increases (Table 2.5) of <0.001 pmol kg-1  hr-1.
    
    The station 88, 102, and 112 experiments examined the CFC changes in bottles 
    where seawater inside was allowed to warm on deck for various periods of time.  The 
    changes in the bottles (relative to the initially sampled bottle) are listed in Table 2.6.
    
    
                     Table 2.6.  Summary of CFC changes for the storage tests.                   
    
    =============================================================================================
                       O2                                                         
                      Draw CFC-12                  CFC-11                  CC14   
               Time   Temp (pmol     dCFC-12/dt    (pmol     dCFC-11/dt    (pmol     dCCl4/dt
    Sta. Bot. (Hours) (°C) kg-1)  (pmol kg-1 hr-1) kg-1)  (pmol kg-1 hr-1) kg-1)  (pmol kg-1 hr-1)
    ---- ---- ------- ---- ------ ---------------- ------ ---------------- ------ ----------------
     88   12    2.58  17.9 0.002      0.00078      -0.001    -0.00039      0.0026     0.00101
     88   11    7.25  23.4 0.005      0.00069       0.004     0.00062      0.0046     0.00063
     88   13   14.58  26.5 0.012      0.00082       0.027     0.00189      0.0036     0.00025
    102    8    1.17  14.7 0.000      0             0.013     0.01068      0.003      0.00256
    102   10    2.17  16.9 0.004      0.00184       0.018     0.00806      0.001      0.00046
    112   12    1.41  13.0 0.007      0.00496       0.001     0.00071      0.003      0.00213
    112   14    2.83  18.2 0.006      0.00212       0.002     0.00071      0.003      0.00106
    ---------------------- ----------------------- ----------------------- ----------------------
                              mean =  0.00140         mean =  0.00327         mean =  0.00086
                                sd = ±0.00163           sd = ±0.00403           sd = ±0.00116
    ---------------------------------------------------------------------------------------------
    
    
    As in the cold experiment in Table 2.5, since the observed concentration changes 
    were often near the minimum detection limits for the compounds, there is considerable 
    scatter in the rates of CFC increase derived in Table 2.6.
    
    As in the cold tests, CFC-113 showed no consistent pattern of increase (see Tables 
    2.2 and 2.3) in the warming bottles.  CFC-12 and CCl4 showed small mean increases 
    (Table 2.6) of ~0.0014  and ~0.0011 pmol kg-1  hr-1, respectively.  The mean rate of 
    increase in CFC-11 (~0.0033 pmol kg-1  hr-1) was somewhat larger.
    
    The results from Table 2.5 indicate that in cold regions, blanks for seawater stored 
    for 2 hours in the 12-B bottles are <0.001 pmol kg-1 for all four compounds.
    
    An estimate of the deep bottle blanks in warm regions can be made from Table 2.6, 
    assuming that for the typical 2 hours that water is held inside the bottles, significant 
    warming occurs only during the last hour as the bottle passed though the thermocline and 
    were stored on deck.
    
    From Tables 2.5 and 2.6, rough estimates of the bottle blanks are denoted in 
    Table 2.7.
    
                    Table 2.7.  Bottle blanks for Bullister bottles.
    
                          ==================================
                                  Cold Regions  Warm Regions
                                   (pmol kg-1)   (pmol kg-1)
                          ----------------------------------
                          CFC-12        0           0.002     
                          CFC-11        0           0.004     
                          CFC-113       0           0     
                          CC14          0           0.001     
                          ----------------------------------
    
    
    TEST TYPE 2: A16S BOTTLE TIME SERIES
    
    At station 121, three 12-B bottles (19, 20, 21) were closed at the same depth 
    (1000 m) near the oxygen minimum zone and in a region of low CFCs.  This depth was 
    chosen to maximize the gradient in partial pressures of these gases between the water and 
    air present in the bottle headspace once the bottles were opened.  The goal of this test was 
    to determine possible changes in dissolved CFCs, oxygen, and salinity as a function of 
    time and of the volume of water drained from a 12-B bottle after the bottle was initially 
    opened.  Table 2.8 depicts a summary of the bottle tests for station 121.
    
    PROCEDURE:
      • Bottle 20 was sampled normally, approximately 20 minutes after the cast was on deck.
      • Bottle 19 was sampled for salinity, CFCs, and oxygen ~5 minutes after the cast was 
        on deck and then resampled for these parameters as rapidly as possible four additional 
        times.  The total sampling time for the five sets of samples from bottle 19 was 
        ~17 minutes.
      • Bottle 21 was sampled for salinity, CFCs, and oxygen ~6 minutes after the cast came 
        on deck, and then resampled for these parameters four more times at ~30 minute 
        intervals over a period of 2.5 hrs.
    
    Samples in bottles 19 and 21 were drawn in the order: salinity, salinity, CFC, 
    oxygen.  For bottles 19 and 21, a total of about 2 l of water was used to draw each set of 
    samples, so at the completion of the fifth set, about 2 l of water remained in the bottles.
    
    Bottle temperatures ("O2 Draw Temp") were recorded as each oxygen sample was 
    drawn using a thermistor inserted into the oxygen flask, following the same procedure 
    used for standard oxygen draw temperatures.
    
    
                           Table 2.8.  Summary of bottle tests for station 121.
    
    ==================================================================================================
                                            O2    
                                           Draw    CFC-12  CFC-11  CFC-113   CCl4
         Sample   Salt     CFC    Oxygen   Temp2   (pmol   (pmol   (pmol   (pmol    Oxygen3
    Bot  Time1   Bottle  syringe  Flask    (°C)     kg-1)   kg-1)   kg-1)   kg-1)  (µmol l-1) Salinity 
    --------------------------------------------------------------------------------------------------
    20   17:55    820      984     168      9.0     0.030   0.077    0      0.155              34.5782
    19   17:40    1001    7692A     41      6.7     0.036   0.077    0      0.156    165.2     
                  1002                                                                         34.5781
         17:43    1003    9837      42      7.7     0.034   0.077    0      0.147    165.      34.5778
                  1004                                                                         34.5775
         17:48    1005    7701      43      8.4     0.038   0.077    0      0.154    165.4     34.5775
                  1006                                                                         34.5778
         17:52    1007    lost      44      9.5      ---     ---    ---      ---     166.4     34.5779
                  1008                                                                         34.5779
         17:57    1009    9825      45     11.4     0.056   0.118    0      0.183    167.0     34.5777
                  1010                                                                         34.5770
    --------------------------------------------------------------------------------------------------
                                                                               mean salinity = 34.5787
                                                                                          sd =  0.0006
    --------------------------------------------------------------------------------------------------
    21   17:40    1011    18(4)     46      7.0     0.052   0.076    0      0.151    165.3     34.5771
                  1012                                                                         34.5762
         18:10    1013    7674      47     10.2     0.047   0.103    0      0.177    165.9     34.5763
                  1014                                                                         34.5766
         18:40    1015    17(4)     48     13.3     0.074   0.095    0      0.169    166.0     34.5762
                  1016                                                                         34.5756
         19:10    1017    9833      49     16.2     0.054   0.106    0.005  0.178    167.3     34.5769
                  1018                                                                         34.5769
         19:40    1019    7638     167     18.7     0.078   0.148    0.008  0.221    169.9     34.5756
                  1020                                                                         34.5759
    --------------------------------------------------------------------------------------------------
                                                                               mean salinity = 34.5763
                                                                                          sd =  0.0005
    --------------------------------------------------------------------------------------------------
        Cast on deck 21 Feb 2005 ~17:29; all times are UTC.
        (1) 21 Feb 2005.
        (2) Potential temperature for seawater samples was ~4.274°C.
        (3) Oxygen values are preliminary and in µmol l-1.
        (4) Indicates syringe borrowed from HCFC group, CFC values may be suspect.
        
        Notes on Test 2:  Ship was underway during this period--little ship roll. Bottles were in shade, 
                          relative wind ~10 knots; relative humidity, 84%; air temp, 27.6°C.  After 
                          sampling, approximately 2 liters remained of original 12 liters--each 
                          sampling cycle is estimated to have used ~2 liters of water.
    --------------------------------------------------------------------------------------------------
    
    
    DISCUSSION OF TEST TYPE 2:
    
    From the very small data set in this test, changes in dissolved CFC concentrations 
    appear to be functions of the time after the bottle is opened and of the volume of water 
    removed prior to drawing the samples.  For bottle 19, the changes in measured CFCs and 
    dissolved oxygen within the first 8 minutes of sampling (and after two sets of samples 
    have been removed previously) were very small and are within the analytical precision of 
    the analyses.  These results indicate that under some conditions a short delay in sampling 
    for CFC and oxygen after a bottle is opened (and after a few liters of water are 
    withdrawn) may not cause measurable changes in the resulting CFC and oxygen 
    concentration measurements.  It is important to note that these tests were performed using 
    12-liter bottles on a large, stable research vessel under calm conditions.  The rate of 
    change of dissolved CFC and oxygen inside opened bottles may be significantly greater 
    under other conditions.
    
    Significant increases in CFC and oxygen concentrations did occur within 17 minutes 
    in bottle 19, after four sets of samples (~8 liters of water) had been withdrawn.  The rate 
    on change of CFCs and oxygen in bottle 21 during the first hour is slower than the rate in 
    bottle 19 during the first 18 minutes, perhaps because of less water draw down (~4 liters 
    vs. ~8 liters) up to that point.  Changes in Bottle 21 are large at the end of the 2-hour 
    period, where 8 liters of water had been drawn previously.
    
    There was no significant change in salinity during the drawdown tests, although 
    there was substantial warming of the bottles during the sampling period (see Table 2.8).
    Changes in salinity observed in some heavily sampled bottles during the A16S cruise 
    may be due water vapor exchange between the water inside the bottle and the air 
    introduced into the headspace.  Since the vapor pressure of water is strongly dependent 
    on temperature, this effect may be increased when the bottle undergoes warming on deck, 
    and may also depend on the temperature and humidity of air entering the headspace.
    These effects may become more pronounced as the volume of water remaining in the 
    bottle decreases during sampling.
    
    
    2.5.  Discussion of Bottle Sampling for Samples Preserved for Shore-Side Analysis
    
    2.5.1.  Helium and Tritium Sampling
    
            Principal Investigator:  Peter Schlosser, Lamont-Doherty Earth Observatory
                                       Palisades NY 10964
                                       schlosser@ldeo.columbia.edu
            Sampler:                 Andrew Mutter, LDEO, amutter@ldeo.columbia.edu
    
    Sampling of helium isotope (3He) and tritium samples for Peter Schlosser of LDEO 
    was carried out by Andrew Mutter (amutter@ldeo.columbia.edu).  A total of 26 stations 
    were sampled with an average of 20 samples taken per cast, for both 3He and tritium.
    The total number of samples obtained is 508 3He samples and 570 tritium samples.  No 
    duplicates were taken.
    
    Sampling involved separate containers for 3He and tritium.  Seawater for 3He 
    analysis was sampled into re-useable stainless steel tubes of 90-ml in volume.  Tritium 
    was sampled into 1 liter brown glass bottles.  The 3He samples were taken first and care 
    was made to rid the vessel of air bubbles by hitting them with a stick and opening and 
    closing the two valves at each end of the tube.  Tritium was sampled by rinsing the 
    bottles twice and filling with water up to the curve at the top of the bottle to allow room 
    to allow for thermal expansion.
    
    The He extraction was done on ship.  Eight filled tubes were pumped down on a 
    vacuum extraction system supplied by WHOI (W. Jenkins and D. Lott).  The tube was 
    pumped down in two-step processes.  First, by a mechanical pump the pressure was taken 
    down to below 10-3 torr (approximately 10 min).  Second, the pressure was pumped to 
    mid 10-6 to high 10-7 torr pressure by a diffusion pump (approximately 1 hr).  The water 
    was then allowed out of the container and into a lower metal container where it was 
    heated to 90-100°C.  The gas was collected in a glass bulb cooled in ice water.  After 
    10 minutes, the bulbs were flame sealed and stored for on-shore analyses.
    
    One tritium sample was lost (dropped on deck). Two to three 3He samples were lost 
    due to bad seals and one to operator error of the extraction vacuum system, which called 
    for dismantling and cleaning of equipment.
    
    
    2.5.2.  PARTICULATE SAMPLING
    
            Principal Investigator: Jim Bishop, LBNL, JKBishop@lbl.gov
            Onboard Personnel:      Alexandra Thompson, LBNL, alex@nature.berkeley.edu
    
    Particulate matter sampling was performed in support of the optics program on the 
    CTD. ICP-MS phosphorus gives us a cross-check on estimating POC, and ICP-MS 
    calcium gives us a calibration/verification of the PIC sensor.
    
    SAMPLING:
    
    Seawater samples were collected from casts from every even numbered station, 
    excluding stations 60 and 102. From each sampled cast, 7-18 samples were collected 
    from the rosette, chosen with a focus on the first 200 m and either the top 2000 m or 
    bottom 3000 m. The 1-liter samples were collected in plastic bottles and, in most cases, 
    filtering began within 30 minutes. The seawater was filtered under vacuum (0.25-
    0.5 atm) through polycarbonate 0.4 Micron 47mm filters (Osmonics Cat #K04CP04700) 
    in filter holders equipped with PreSep mesh spacers (Osmonics Cat #C32WP04200).
    Filtration was carried out in a flow bench (Airclean 600 PCR Workstation) and took 
    between 10 minutes to 5 hours for each sample. After exposure, each filter was rinsed 
    with 0.5 ml MQ water and the filter transferred to 100 ml Nalgene bottles, capped, and 
    stored at room temperature for transport to LBNL. After use all bottles, caps, and filter 
    holders were rinsed in MQ water.
    
        Total number of samples:  921
        Number of blanks:          39
        Number of repeats:         41
        Number of casts sampled:   59
    
    PROBLEMS:
    
    The only problems encountered were minor and included leaky bottles and occasional air bubbles causing the filtration to stall.
    
    SHORE-SIDE ANALYSIS:
    
    At LBNL, the filters will be analyzed using ICP-MS for 20 elements, including P, C, Ca, Fe, Ba, and Sr.
    
    
    2.5.3.  DOC SAMPLING
    
            Principal Investigator: Dennis Hansell, U. Miami, RSMAS, 4600 Rickenbacker
                                      Causeway, Miami, FL 33149, dhansell@rsmas.miami.edu
            Sampler:                Wenhao Chen, U. Miami, RSMAS
                                      wenchen@rsmas.miami.edu
    
    Seawater samples were taken directly from the Niskin Bottles into the 60 ml 
    precleaned bottles for deeper than 200 m. Samples from the up 200 m were collected by 
    in-line filtration through a GF/F filter. All samples were kept in frozen before analysis.
    
        Total number of samples:    1630
        Total number of duplicates:   12
        Total number of stations:     60
    
    
    2.5.4.  C-DOM SAMPLING
    
            Principal Investigator: Norm Nelson, UCSB
            Sampler:                Wenhao Chen, U. Miami, RSMAS
                                      wenchen@rsmas.miami.edu
    
    Seawater was taken directly from the Niskin bottles into a 120-ml dark glass bottle 
    and then filtered through a 0.2 um Nucleopore filter by vacuum filtration within 2 hours.
    
    Filtrates were collected in  40 ml dark glass vials and kept refrigerated before analysis.
    
        Total number of samples:     540
        Total number of duplicates:    4
        Total number of stations:     36
    
    
    2.5.5.  14C SAMPLING
    
            Principal Investigator:  Ann McNichol, WHOI
            Samplers:                Wenhao Chen, U. Miami, RSMAS
                                       wenchen@rsmas.miami.edu
                                       Matt Lenington, CWU, leningtm@cwu.edu
    
    Seawater was drawn directly from the Niskin bottles into 500-ml glass bottles after 
    about 250 ml overflow of the water. Samples were then poisoned with 100 µl saturated 
    HgCl2 solution and sealed by greased stoppers. Bottles with samples are kept in cases for 
    shipping back to WHOI.
    
    Reference: Measuring 14C in Seawater TCO2 by Accelerator Mass Spectrometry, 
        WHOI in WHP Operation and Methods-July, 2003.
    
        Total number of samples:     496
        Total number of duplicates:   16
        Total number of stations:     29
    
    
    2.5.6.  OXYGEN, NITROGEN, AND ARGON (ONAR) SAMPLING
    
            Principal Investigator:  Steven Emerson, University of Washington
                                       emerson@u.washington.edu
            Samplers:                Mark Warner, University of Washington
                                       warner@u.washington.edu
    
    Samples were collected for analyses of dissolved oxygen, nitrogen, and argon 
    (ONAR) at three stations during the A16S repeat hydrography section. At each station, 
    duplicate samples (~100 ml) from six different depths were collected into evacuated glass 
    flasks for analyses in the laboratory of Dr. Steven Emerson at the University of 
    Washington.  The samples were collected from the 12-l bottle immediately after the 
    dissolved oxygen sample was drawn. In the shipboard laboratory, the headspace in the 
    neck of the flask was flushed with CO2 gas and capped for transport back to the 
    laboratory.
    
    The goal of this ancillary project is to determine the saturations of these gases in 
    water masses formed in the northern (NADW) and southern (AABW, AAIW) high 
    latitudes. The differences in saturation values should provide useful information on the 
    relative importance of bubbles in mediating the gas exchange, thus setting the surface 
    ocean boundary conditions, in the formation regions of these water masses.
    
        Total number of samples:      36          
        Total number of duplicates:   18
        Total number of stations:      3
    
    
    2.6.  PARAMETERS SAMPLED AND ANALYZED ON THE CRUISE
    
    2.6.1.  Chlorofluorocarbon (CFC) Measurements
    
            Principal Investigators: Mark J. Warner, University of Washington
                                       warner@u.washington.edu
                                       John L. Bullister, NOAA-PMEL
                                       John.L.Bullister@noaa.gov
            Samplers and Analysts:   Mark J. Warner, University of Washington
                                       John L. Bullister, NOAA-PMEL
                                       Eric Wisegarver, University of Washington
                                       esw@u.washington.edu
    
    Samples for the analysis of dissolved CFC-11, CFC-12, CFC-113, and carbon 
    tetrachloride (CCl4) were drawn from 2378 of the 4192 water samples collected during 
    the expedition. Specially-designed 12-liter Bullister sample bottles were used on the 
    cruise to reduce CFC contamination.  These bottles have the same outer diameter as 
    standard 10 liter Niskin bottles, but use a modified end-cap design to minimize the 
    contact of the water sample with the end-cap O-rings after closing.  The O-rings used in 
    these water sample bottles were vacuum-baked prior to the first station.  Stainless steel 
    springs covered with a nylon powder coat were substituted for the internal elastic tubing 
    provided with standard Niskin bottles. When taken, water samples for CFC and carbon 
    tetrachloride analysis were the first samples drawn from the 12-liter bottles.  Care was 
    taken to coordinate the sampling of CFCs with other samples to minimize the time 
    between the initial opening of each bottle and the completion of sample drawing. In most 
    cases, dissolved oxygen, 3He, and HCFC samples were collected within several minutes 
    of the initial opening of each bottle.  To minimize contact with air, the CFC samples were 
    drawn directly through the stopcocks of the 12-liter bottles into 100 ml precision glass 
    syringes equipped with two-way metal stopcocks. The syringes were immersed in a 
    holding tank of clean surface seawater until analyzed.
    
    For air sampling, a ~100 m length of 3/8" OD Dekaron tubing was run from the main 
    laboratory to the bow of the ship.  A flow of air was drawn through this line into the main 
    laboratory using a KNF Neuburger pump.  The air was compressed in the pump, with the 
    downstream pressure held at ~1.5 atm. using a backpressure regulator.  A tee allowed a 
    flow (100 ml min-1) of the compressed air to be directed to the gas sample valves of the 
    CFC and HCFC analytical systems, while the bulk flow of the air (>7 l min-1) was vented 
    through the backpressure regulator.  Air samples were only analyzed when the relative 
    wind direction was within 60 degrees of the bow of the ship to reduce the possibility of 
    shipboard contamination.  The pump was run continuously to insure that the air inlet lines 
    and pump were thoroughly flushed. Analysis of bow air was performed at 26 locations 
    along the cruise track. At each location, five measurements were made to increase the 
    precision.
    
    Concentrations of CFC-11 and CFC-12, CFC-113, and carbon tetrachloride in air 
    samples, seawater, and gas standards were measured by shipboard electron capture gas 
    chromatography (EC-GC) using techniques modified from those described by Bullister 
    and Weiss (1988). For seawater analyses, water was transferred from a glass syringe to a 
    fixed volume chamber (~30 ml).  The contents of the chamber were then injected into a 
    glass-sparging chamber.  The dissolved gases in the seawater sample were extracted by 
    passing a supply of CFC-free purge gas through the sparging chamber for a period of 
    4 minutes at 70 ml min-1. Water vapor was removed from the purge gas during passage 
    through an 18 cm long, 3/8" diameter glass tube packed with the desiccant magnesium 
    perchlorate.  The sample gases were concentrated on a cold-trap consisting of a 1/8" OD 
    stainless steel tube with a ~10 cm section packed tightly with Porapak N (60-80 mesh). A 
    vortex cooler, using compressed air at 100 psi, was used to cool the trap, to 
    approximately -20°C.  After 4 minutes of purging, the trap was isolated, and the trap was 
    heated electrically to ~100oC.  The sample gases held in the trap were then injected onto 
    a precolumn (~25 cm of 1/8" O.D. stainless steel tubing packed with 80-100 mesh Porasil 
    C, held at 70°C) for the initial separation of CFC-12, CFC-11, and CFC-113 from carbon 
    tetrachloride. After the CFCs had passed from the pre-column into the main analytical 
    column (~183 cm of 1/8" OD stainless steel tubing packed with Carbograph 1AC, 80-100 
    mesh, held at 70°C) of GC1 (a HP 5890 Series II gas chromatograph with ECD), a valve 
    was used to direct the precolumn flow (and more slowly eluting carbon tetrachloride 
    peak) to a second gas chromatograph (Shimadzu Mini II GC with ECD). For the first 52 
    stations, the chromatographic column in the Shimadzu GC was 1 m of 1/8" OD stainless 
    steel tubing packed with 80/100 mesh Porasil C.
    
    The apparent supersaturation of dissolved CCl4 observed in the near surface waters 
    of these stations was attributed to an unidentified compound present in near surface 
    waters that co-eluted with CCl4. The Porasil C column was replaced with a Carbograph 
    1AC 80-100 mesh column (183 cm of 1/8' OD SS tubing), resulting in the separation of 
    the CCl4 peak from this interfering peak. In both cases the column was maintained at 
    90°C.
    
    Both of the analytical systems were calibrated frequently, with frequency listed 
    below, using a standard gas of known CFC composition.  Gas sample loops of known 
    volume were thoroughly flushed with standard gas and injected into the system. The 
    temperature and pressure was recorded so that the amount of gas injected could be 
    calculated. The procedures used to transfer the standard gas to the trap, precolumn, main 
    chromatographic column, and EC detector were similar to those used for analyzing water 
    samples.  Two sizes of gas sample loops were used.  Multiple injections of these loop 
    volumes could be made to allow the system to be calibrated over a relatively wide range 
    of concentrations. Air samples and system blanks (injections of loops of CFC-free gas) 
    were injected and analyzed in a similar manner.  The typical analysis time for seawater, 
    air, standard or blank samples was ~11 minutes.
    
    Concentrations of the CFCs and CCl4 in air, seawater samples, and gas standards are 
    reported relative to the SIO98 calibration scale (Cunnold et. al., 2000).  Concentrations in 
    air and standard gas are reported in units of mole fraction CFC in dry gas, and are 
    typically in the parts per trillion (ppt) range.  Dissolved CFC and CCl4 concentrations are 
    given in units of picomoles per kilogram seawater (pmol kg-1). CFC and CCl4 
    concentrations in air and seawater samples were determined by fitting their 
    chromatographic peak areas to multi-point calibration curves, generated by injecting 
    multiple sample loops of gas from a working standard (PMEL cylinder 45191 for CFC-
    11, CFC-12, CFC-113, and CCl4) into the analytical instrument.  The response of the 
    detector to the range of moles of CFC passing through the detector remained relatively 
    constant during the cruise. Full-range calibration curves were run at intervals of 14 days 
    during the cruise.  These were supplemented with occasional injections of multiple 
    aliquots of the standard gas at more frequent time intervals. Single injections of a fixed 
    volume of standard gas at one atmosphere were run much more frequently (at intervals of 
    ~90 minutes) to monitor short-term changes in detector sensitivity. The CFC-113 peak 
    was often on a small bump on the baseline, resulting in a large dependence of the peak 
    area on the choice of endpoints for integration. The height of the peak was instead used to 
    provide better precision. The precisions of measurements of the standard gas in the fixed 
    volume (n = 690) were ± 0.67% for CFC-12, 0.59% for CFC-11, 2.6% for CFC-113, and 
    1.8% for CCl4.
    
    Although the CCl4 calibration and precision are of high quality over most of the 
    cruise, there appears to be a problem with the preliminary calibration of the working 
    standard. The calculated atmospheric concentrations, relative to this standard, are 
    approximately 70 part per trillion (ppt). The values reported by the AGAGE network are 
    approximately 20 ppt higher. This would also explain the undersaturations in the surface 
    waters calculated using the AGAGE concentrations.  The working standard will be 
    recalibrated at PMEL when returned at the end of the expedition.
    
    The efficiency of the purging process was evaluated periodically by re-stripping high 
    concentration surface water samples and comparing the residual concentrations to initial 
    values. These re-strip values ranged from approximately 1% for CFC-11 and CFC-12, 
    3% for CFC-113, and 4% for CCl4 in cold waters to values of <1% for all four 
    compounds in warm waters.  A fit of the re-strip efficiency as a function of temperature 
    will be applied to the final data set. The cold-water values have been applied to all values 
    in the preliminary data set.
    
    There were very few measurements of CFC-11 and CFC-12 concentrations less than 
    0.005 pmol kg-1 along this section. CFC-113, on the other hand, was extremely low 
    throughout the section. There were also no measurements of CCl4-free waters.  Several 
    tests of the 12-l sampling bottles were performed to estimate the possible desorption of 
    CFCs and CCl4 from the walls into the seawater sample and the changes in CFCs, CCl4, 
    dissolved oxygen, and salinity in bottles as a function of time after opening. The results 
    are discussed above under the subsection "Bullister Bottle Tests."
    
    On this expedition, based on the analysis of 100 duplicate samples, we estimate 
    precisions (1 standard deviation) of 0.45% or 0.003 pmol kg-1 (whichever is greater) for 
    dissolved CFC-11, 0.78% or 0.004 pmol kg-1 for CFC-12 measurements, 2.6% or 
    0.004 pmol kg-1 for CFC-113, and 1.1% or 0.005 pmol kg-1 for CCl4 measurements.
    
    A very small number of water samples had anomalously high CFC or CCl4 
    concentrations relative to adjacent samples.  These samples occurred sporadically during 
    the cruise and were not clearly associated with other features in the water column (e.g., 
    anomalous dissolved oxygen, salinity, or temperature features).  This suggests that these 
    samples were probably contaminated with CFCs or CCl4 during the sampling or analysis 
    processes.  Measured concentrations for these anomalous samples are included in the 
    preliminary data, but are given a quality flag value of either 3 (questionable 
    measurement) or 4 (bad measurement). A quality flag of 5 was assigned to samples 
    which were drawn from the rosette but never analyzed due to a variety of reasons (e.g., 
    leaking stopcock, plunger jammed in syringe barrel). A total of 13 analyses of CFC-11, 
    16 analyses of CFC-12, 10 analyses of CFC-113, and 145 analyses of CCl4 were assigned 
    a quality flag of 3.  A total of 4 analyses of CFC-11, 6 analyses of CFC-12, 7 analyses of 
    CFC-113, and 6 of CCl4 were assigned a quality flag of 4.  A total of 13 samples were 
    given a flag of 5 (sampled but not analyzed).
    
    
    REFERENCES
    
    Bullister, J.L., and R.F. Weiss, 1988:  Determination of CC13F and CC12F2 seawater and 
        air.  Deep-Sea Res., v. 25, pp. 839-853.
    
    Prinn, R.G., R.F. Weiss, P.J. Fraser, P.G. Simmonds, D.M. Cunnold, F.N. Alyea, S.
        O'Doherty, P. Salameh, B.R. Miller, J. Huang, R.H.J. Wang, D.E. Hartley, C. Harth, 
        L.P. Steele, G. Sturrock, P.M. Midgley, and A. McCulloch, 2000:  A history of 
        chemically and radiatively important gases in air deduced from ALE/GAGE/ 
        AGAGE.  J. Geophys. Res., v. 105, pp. 17,751-17,792.
    
    
    2.6.2.  DISSOLVED OXYGEN ANALYSES
    
            Principal Investigator: Chris Langdon, U. Miami, RSMAS, 4600 Rickenbacker
                                      Causeway, Miami FL 33149
                                      clangdon@rsmas.miami.edu
            Samplers:               Chris Langdon (12 midnight-12 noon)
                                    George Berberian, NOAA-AOML (12 noon-12 midnight)
                                      George.Berberian@noaa.gov
            Analysts:               Chris Langdon (12 midnight-12 noon)
                                    George Berberian (12 noon-12 midnight)
            Data Reduction:         Chris Langdon
                                    Frank Delahoyde, SIO
    
    SAMPLING:
    
    Samples were drawn from 12-l Bullister bottles into calibrated 140 ml iodine 
    titration flasks using Tygon tubing with a Silicone adapters that fit over the petcock to 
    avoid contamination of DOC samples.  Bottles were rinsed twice and filled from the 
    bottom, overflowing three volumes while taking care not to entrain any bubbles.  One-ml 
    of MnCl2 and one-ml of NaOH/NaI were added, the flask stoppered, and shaken.  DIW 
    was added to the neck of each flask to create a water seal.  The flasks were stored in the 
    lab in plastic totes at room temperature for 1-2 hours before analysis.
    
    Thirty-six samples were drawn from most stations (exceptions for shallow stations 
    where fewer bottles tripped or for bottles with visible problems during sampling, e.g., 
    leaking, open vent cap, etc.) for a total of 121 stations.  Two to three duplicates were 
    drawn at each station.  In addition, samples were drawn in duplicate from the underway 
    seawater line at 6-hour intervals between Punta Arenas and the start of the line at 60°S, 
    31°W which are not included in the tally below.
    
        Total number of samples:    4659
        Total number of samples flagged after initial shipboard reduction of quality control:
            Questionable (QC=3):      37
                     Bad (QC=4):       4
            Not reported (QC=5):       3
    
    Sampling for dissolved oxygen began within minutes of the rosette being brought on 
    deck.  Using a Tygon and silicone drawing tube, nominal 125 ml volume-calibrated 
    iodine flasks were rinsed 3 times, then filled and allowed to overflow for at least 3 flask 
    volumes.  From station 33 onward (46.6 ˚S, 31.8 ˚W, 1/25/05) sample draw temperature 
    was measured with a platinum resistance thermometer placed in the flask while the flask 
    was overflowing.  These temperatures were used to calculate µmol kg-1 concentrations 
    and a diagnostic check of bottle integrity.  For station 1-32 the CTD temperature at trip 
    depth was used. Reagents were added to fix the oxygen before stoppering.  The flasks 
    were shaken until thoroughly mixed, once immediately after drawing, and then again 
    after about 20 minutes.  Samples were analyzed within 1-4 hours of collection, and 
    uploaded into the cruise database.
    
    ANALYZER DESCRIPTION:
    
    Dissolved oxygen analyses were performed with a MBARI-designed automated 
    oxygen titrator using photometric end-point detection based on the absorption of 365 nm 
    wavelength ultra-violet light.  The titration of the samples and the data logging were 
    controlled by a 386 PC running the Oxygen program written by Gernot Friedrich 
    (Friederich, 1984).  Thiosulfate was dispensed by a Dosimat 665 fitted with a 5.0 ml 
    burette.  The whole-bottle titration technique of Carpenter (1965) with modifications by 
    Culberson et al. (1991), but with a more dilute solution of thiosulfate (10 g l-1).  The 
    autotitrator and Dosimat generally performed well.
    
    STANDARDIZATION:
    
    Standard curves were run at the beginning and end of each 1-l batch of thiosulfate, 
    typically 2-3 days.  The reagent blank was taken to be the intercept of the standard curve.
    The titrant for the photometric titrator was standardized via the standard curve method 
    where standards are prepared by dispensing 2, 4, 6, 8, and 10 ml of the 0.0100 N KIO3 
    standard solutions. Thiosulfate molarities were calculated from each standard curve and 
    corrected to 20°C.  The 20°C molarities were plotted versus time and were reviewed for 
    possible problems.  Blank volumes and thiosulfate molarities were smoothed (linear fits) 
    at the end of the cruise and the oxygen values recalculated (see Figures 2.1 and 2.2).
    
    Two to three sets of duplicates were drawn at each station for a total of 265 duplicates. 
    The average standard deviation was 0.25 µmol kg-1.
    
    
    Figure 2.1.  Control plot of the reagent blanks over the cruise.
    Figure 2.2.  Control plot of thiosulfate concentration changes over the cruise.
    
    
    COMPARISON OF PHOTOMETRIC AND AMPEROMETRIC END POINT TITRATORS:
    
    A comparison was conducted between the photometric end point titrator and a titrator that 
    detected the end point amperometrically. Standardization of the thiosulfate titrant and 
    determination of the reagent blank for the amperometric titrator were done as described in 
    Culberson et al. (1991).  The oxygen concentration in the seawater sample was calculated as 
    described by Culberson et al. (1991).  Sets of duplicate or quadruplicate flasks were drawn 
    from the same rosette bottle and then analyzed by the two systems.  The systems used different 
    burettes (photometric 5 ml and amperometric 2 ml) and different molarity thiosulfate solutions 
    (photometric 0.040 M and amperometric 0.14 M).  Blanks and standards for both systems were 
    prepared using the same standard solution and the same dispenser.   The reagent blank was 
    assumed to be equal to the intercept of the plot of thiosulfate titer versus ml of standard 
    solution. Standardization of the thiosulfate titrant and determination of the reagent blank 
    for the amperometric titrator were done as described in Culberson et al. (1991).  The oxygen 
    concentration in the seawater sample was calculated as described by Culberson et al. (1991).  
    Data are summarized in Table 2.9.  Each method was found to have a similar precision, i.e., 
    0.11 and 0.14 µmol l-1.  There was a small but significant bias for the amperometric result to 
    be smaller than the photometric result by 0.47 µmol l-1.  This was investigated further by 
    comparing sets of duplicates from station 106 (9°30'S, 25°W) where the oxygen concentration 
    spanned a very wide range (Table 2.9).  It was found that the difference between the two 
    methods was not randomly distributed with respect to oxygen concentration (Figure 2.3).  The 
    cause for the systematic bias requires further investigation back at the shore-based 
    laboratory.
    
    
          Table 2.9:  Comparison of oxygen concentrations determined by photometric and 
                      amperometric point detection methods at station 106.
    
            =======================================================================
                       |     Photometric      |     Amperometric     |
                       |     (µmoles l-1)     |     (µmoles l-1)     |
            -----------|----------------------|----------------------|-------------
            CTD  Niskin|  [O2]   Mean    SD   |  [O2]   Mean    SD   | Photo-Ampero
            -----------|----------------------|----------------------|-------------
            106     8  | 259.50  259.45  0.05 | 259.70  259.65  0.05 |    -0.2
            106     8  | 259.40               | 259.60               |
            106    20  | 175.20  175.20  0.00 | 175.80  175.80  0.00 |    -0.6
            106    20  | 175.20               | 175.80               |
            106    27  |  98.30   98.15  0.15 |  98.90   98.80  0.10 |    -0.7
            106    27  |  98.00               |  98.70               |
            106    27  |                      |  98.80               |
            106    33  | 218.30  218.45  0.15 | 218.70  218.75  0.05 |    -0.3
            106    33  | 218.60               | 218.80               |
            -----------------------------------------------------------------------
    
    
    Figure 2.3.  Difference between photometrically and amperometrically determined oxygen 
                 concentration versus photometric oxygen concentration.
    
    
    VOLUMETRIC CALIBRATION:
    
    Oxygen flask volumes were determined gravimetrically with degassed deionized 
    water to determine flask volumes at AOML.  The Dosimat and Wheaton positive 
    displacement dispenser used for dispensing the KIO3 were calibrated in the same way.
    
    STANDARDS:
    
    Liquid potassium iodate standard solution with a normality of 0.0100 was prepared 
    and bottled at AOML prior to the cruise.  A single batch was used during the cruise.
    
    
    
    REFERENCES
    
    Carpenter, J.H., 1965:  The Chesapeake Bay Institute technique for the Winkler dissolved 
        oxygen method.  Limnol. Oceanogr., v. 10, pp. 141-143.
    
    Culberson, C.H., and S. Huang, 1987: Automated amperometric oxygen titration. Deep-
        Sea Res., v. 34, pp. 875-880.
    
    Culberson, C.H., G. Knapp, M. Stalcup, R.T. Williams, and F. Zemlyak, 1991: A 
        comparison of methods for the determination of dissolved oxygen in seawater.
    
    Friederich, G.E., P. Sherman, and L.A. Codispoti, 1984: A high precision automated 
        Winkler titration system based on a HP-85 computer: A simple colorimeter and an 
        inexpensive electromechanical buret.  Bigelow Lab., Technical Report 42, 24 pp.
    
    
    2.6.3.  DISCRETE HALOCARBON/ALKYL NITRATE ANALYSES
    
            Principal Investigators: Shari Yvon-Lewis, Dept. of Oceanography, Texas A&M
                                       University, 3146 TAMU, College Station, TX 77845
                                       syvon-lewis@ocean.tamu.edu
                                     Eric Saltzman, Earth System Science, 3325 Croul Hall
                                       University of California-Irvine, Irvine, CA 92697
                                       esaltzma@uci.edu
            Samplers:                Ben Kates (12 midnight-12 noon), Ben.Kates@noaa.gov
                                     Shari Yvon-Lewis (12 noon-2 midnight)
            Analysts:                Ben Kates (12 midnight-12 noon)
                                     Shari Yvon-Lewis (12 noon-12 midnight)
            Data Reduction:          Shari Yvon-Lewis
            
    
    SAMPLING:
    
    Samples were drawn from 12-l Bullister bottles into 100 ml ground glass syringes.
    The syringes have nickel-plated Luer tipped stopcocks.  The Luer tips are inserted 
    directly into the petcocks.  The syringes are rinsed twice with full 100 ml volumes of 
    water.  Bubbles are carefully flushed out, and the third fill is the final sample.  The 
    syringes are wrapped with a stiff rubber band to maintain pressure on the plunger and 
    sample reducing the potential for outgassing in the syringes.  Storage of the samples is 
    kept to a minimum (<3 hours).  They are stored vertically in buckets in the climate 
    controlled cold-room (~4oC).  The cold temperature is used to minimize the chemical 
    degradation of some of the species being measured.  Fifteen to 17 samples were drawn 
    from the even numbered stations.  This represents 1o latitude spacing on the half degree 
    for a total of 60 stations.
    
            Total number of samples: 893
    
    Each sample was analyzed for 21 chemical species (HCFC-22, CFC-12, HCFC-
    142b, Halon-1211, CFC-11, HCFC-141b, CFC-113, CH3CCl3, CCl4, C2Cl4 (PCE), 
    CH3Cl, CH3Br, CH3I, CH2Cl2, CH2Br2, CHCl3, CHBr3, CH2ONO2, C2H4ONO2, 
    i-C3H6ONO2, n-C3H6ONO2).  The total number of samples flagged after preliminary 
    shipboard data reduction and quality control, varied by compound:
    
            Questionable (QC=3):      ~3
            Bad (QC=4):              ~21
            Not Reported (QC=5):     ~22
    
    ANALYZER DESCRIPTION:
    
    The halocarbon measurement system was described in Yvon-Lewis et al. (2004).
    There have been a couple of modifications since to facilitate analysis of alkyl nitrates and 
    to improve performance. The measurements were made with a laboratory-built, 
    automated purge and trap system coupled to a gas chromatograph (GC, HP5890 series II) 
    with mass spectrometer (MS, HP5973) (Figure 2.4).  The autosampler allows us to load 
    all of the depth profile samples directly into gas tight glass bulbs (each with a measured 
    volume including tubing of ~70 ml) kept in a temperature-controlled cooler at 
    approximately 5°C.  The entire 100+ ml of seawater in the syringe is flushed through the 
    bulb and tubing.
    
     
    Figure 2.4.  Schematic of the automated purge and trap GCMS system.  There are 16 calibrated 
                 sample bulbs attached to PV2; however, to reduce clutter in the diagram, 
                 only calibrated sample bulb #3 is shown.
    
    
    The computer switches purge valve #2 (PV2), a Valco loop selection valve (VICI 
    Metronics, TX) with 34 ports and 16 positions, from bulb to bulb allowing the humidified 
    helium purge gas stream to push each sample from the bulb into the temperature-
    controlled (50°C) sparger.  The purge gas passes through the bulb on its way to the 
    sparger and will pick up any trace amounts of the gases left in water along the walls and 
    any of the trace gases that may have undergone some degassing while sitting in the bulb 
    prior to sampling.  In this way, we maximize sample recovery and preconcentration on 
    the first cryotrap.  The dried (Nafion PD-100T-24SS, PermaPure Inc.) sparger effluent 
    passes over a Unibeads 1S packed trap (3.175 mm OD, 1.6 mm ID) at -80°C and into a 
    calibrated, evacuated stainless steel flask.  The change in flask pressure and the flask 
    temperature are recorded electronically.  For a calibration run, the pressure in the flask is 
    used to determine the exact volume of the whole air standard that passed over the 
    cryotrap.  GC valve #1 (GCV1) is switched from load to transfer, and the primary trap is 
    then flash heated (200°C, 3 min.).  The sample is focused on a second Unibeads 1S 
    packed trap (1.59 mm OD, 0.5 mm ID) at -80°C.  GC valve #2 (GCV2) is switched from 
    backflush to inject, the focusing trap is flash heated (200°C, 3 min.) and the sample is 
    injected onto the analytical column (0.25 mm ID _ 5m pre- and 55m main, DB-VRX; 
    J&W).  The pre-column is backflushed at 10 min. after injection to prevent accumulation 
    of the heavier compounds on the column between runs.  The GC is temperature 
    programmed to start at 30°C and end at 210°C.
    
    PARAMETERS SAMPLED ON THE CRUISE:
    
    Each sample, blank, and standard is analyzed simultaneously for all of the 
    compounds, HCFC-22, CFC-12, HCFC-142b, CFC-11, HCFC-141b, CFC-113, 
    CH3CCl3, CCl4, PCE, CH3Cl, CH3Br, CH3I, CH2Cl2, CH2Br2, CHCl3, CHBr3, methyl 
    nitrate, ethyl nitrate, isopropyl nitrate, and n-propyl nitrate.  The mass spectrometer is 
    programmed to record signals from specific sets of masses over predetermined intervals 
    (i.e., single ion monitoring, SIM).  In this way, the mass spectrometer is extremely 
    selective and can detect only the compound of interest at any given time, reducing the 
    potential for co-elution contamination of the signal.
    
    CALIBRATION:
    
    Purge valve #1 (PV1) is used to switch between the humidified purge helium and the 
    calibration gas streams before they enter the rest of the purge system.  The calibration 
    gases are from secondary standard cylinders filled with coastal Miami air.  These whole 
    air standards (two dry acculife treated cylinders and one wet electropolished 6-l flask) 
    have been calibrated using NOAA/CMDL halocarbon standards and alkyl nitrate 
    standards from the lab of Dr. Eric Saltzman (University of California, Irvine).  During a 
    calibration run, the calibration gas follows the same path as the humidified purge helium 
    does during a normal sample run; however, PV2 is kept in the position of the last sample, 
    which has already been analyzed so the sample bulb is empty.  The number of moles of 
    gas that pass over the trap is calculated from the known volume of the flask and the 
    recorded temperature and pressure of the flask.  The dry mole fractions of the 
    halocarbons and alkyl nitrates in the calibration gas are used to determine the number of 
    moles of each compound in each calibration run, sample, and blank.  After a calibration 
    run and before the next sample run, the entire flow path is flushed with the humidified 
    helium.  Blanks are run in the same way as calibration runs except that PV1 is in position 
    to allow the humidified helium to flow through the system not the calibration gas.  Every 
    seventh injection is a standard.  This allows for tracking drift in the detector's response 
    for each compound.
    
    DATA PROCESSING:
    
    As mentioned above, every seventh injection is a calibration gas standard.  The three 
    standards were swapped periodically during the cruise.  The standard or reference gases 
    are used to determine the response factors (response per mole of analyte) for the mass 
    spectrometer for each compound.  Any drift or degradation in signal over time is 
    corrected by interpolating the response factors between reference runs.  The interpolated 
    response factor is then used with the observed sample response (blank corrected) to 
    determine the moles of analyte present in that sample.  Blanks are run every seventh 
    injection just prior to the reference run.  The blank response for a specific compound in 
    any given sample is determined by interpolating between blanks.  The three reference gas 
    tanks will be recalibrated after the cruise to determine if there was any drift in their 
    concentrations over time.
    
    ANCILLARY MEASUREMENTS:
    
    Approximately once per day, for a total of 40 samples, a calibration run was 
    substituted with an air sample.  A 3/8" O.D. Decabon line was run from the aft section of 
    the main lab to the jackstaff on the bow of the ship.  A pump (KNF Neuburger with a 
    Viton diaphragm) with a back pressure regulator maintained a 6 l min-1 flow through the 
    Decabon with a back pressure of ~6 psi in sampling line that could be attached to the 
    purge and trap instrument.  When an air sample was collected, the calibration gas line 
    was swapped with the sample line from the air pump, and the air sample was collected 
    and analyzed instead of a calibration gas sample.  The air data will be reported in the final 
    report after post-cruise calibrations are done.
    
    PROBLEMS:
    
    The HCFC-22 concentrations measured in the water samples were excessively high 
    at the beginning of the cruise.  There were leaks in the ship refrigerator compressor, and 
    apparently not too long before this cruise a large amount of HCFC-22 was lost in a leak 
    in the engine room and permeated the entire ship.  Later in the cruise, the HCFC-22 
    background appeared to decrease.  Some of the HCFC-22 data may be recoverable after 
    some post-cruise analysis.  However, at the time of this preliminary data report, all of the 
    HCFC-22 data has been flagged as bad (QC=4).
    
    During the last week of the cruise a possible problem with calibrated volume #1 was 
    observed.  Steps were taken to avoid a loss of data after the possible problem was 
    identified.  There was not enough time left in the cruise to attempt to fix the problem.
    Post-cruise analysis will determine the full extent of the data that may have been 
    compromised.
    
    
    REFERENCES
    
    Yvon-Lewis, S.A., D.B. King, R. Tokarczyk, K.D. Goodwin, E.S. Saltzman, and J.H.
        Butler, 2004:  Methyl bromide and methyl chloride in the Southern Ocean. J.
        Geophys Res., v. 109, C02008, doi:10.1029/2003JC001809.
    
    
    2.6.4.  DISCRETE pCO2 ANALYSES
    
            Principal Investigator:  Rik Wanninkhof, NOAA/AOML, 4301 Rickenbacker 
                                       Causeway Miami Fl 33149
                                       Rik.Wanninkhof@noaa.gov
            Samplers:                Naomi Levine (12 midnight-12 noon), nlevine@whoi.edu
                                     Rik Wanninkhof (12 noon-12 midnight)
            Analysts:                Robert Castle (12 midnight-12 noon)
                                       Robert.Castle@noaa.gov
                                     Rik Wanninkhof (12 noon-12 midnight)
                                     Stacey Smith (day time through station 43)
                                       Stacy.Smith@mso.umt.edu
            Data Reduction:          Robert Castle, Robert.Castle@noaa.gov
    
    
    SAMPLING:
    
    Samples were drawn from 12-l Bullister bottles into 500 ml Pyrex(tm) volumetric 
    flasks using Tygon(tm) tubing with a Silicone adapter that fit over the petcock to avoid 
    contamination of DOM samples.  Bottles were rinsed twice and filled from the bottom, 
    overflowing half a volume while taking care not to entrain any bubbles.  About 5 ml of 
    water was withdrawn by removing the pinched off sampling tube from the neck of the 
    flask to create a small expansion volume.  0.2 ml of saturated mercuric chloride (HgCl2 ) 
    solution was added as a preservative.  The sample bottles were sealed with a screw cap 
    containing a polyethylene liner.  The samples were stored upside down in coolers at room 
    temperature for a maximum of 10 hours.
    
    Thirty samples were drawn every fourth station (@ 2 degree intervals) for a total of 
    29 stations.  In addition, samples were drawn in duplicate from the underway seawater 
    line at 6-hour intervals between Punta Arenas and the start of the line at 60°S, 31°W.
    
    These samples are not included in the tally below.
    
            Total number of samples:     847
            Total number of samples flagged after initial shipboard data reduction of quality control:
              Questionable (QC=3):         9
              Bad (QC=4):                  1
              Not reported (QC=5) (tests): 5
              Duplicates (QC=6):           9
    
    ANALYZER DESCRIPTION:
    
    The discrete pCO2 system is patterned after the setup described in Chipman et al.
    (1993) and is discussed in detail in Wanninkhof and Thoning (1993) and Chen et al.
    (1995).  The major difference between the system of Chipman and ours is that our setup 
    uses a LI-COR(tm) (model 6262) non-dispersive infrared analyzer, while the system of 
    Chipman et al. (1993) utilizes a gas chromatograph with a flame ionization detector and a 
    methanizer that quantitatively converts CO2 into CH4 for analysis.
    
    Samples collected in the 500-ml volumetric flasks are brought to a temperature of 
    20.00 ± 0.02°C by first inserting the flasks upside down in a pre-bath at ≈21°C and 
    subsequently in a Neslab(tm) (model RT-220) controlled temperature bath for equilibration 
    and analysis.  A 60-ml headspace is created in the sample flask by displacing the water 
    using a compressed standard gas with a CO2 mixing ratio close to the anticipated pCO2 of 
    the water.  The headspace is circulated in a closed loop through the infrared analyzer that 
    measures CO2 and water vapor levels in the sample cell.  The headspaces of two flasks 
    are equilibrated simultaneously in two channels. While headspace from the flask in the 
    first channel goes through the IR analyzer, the headspace of the flask in second channel is 
    recirculated in a closed loop.  After the first sample is analyzed, a valve is switched to put 
    the second channel in line with the analyzer.  The samples are equilibrated until the 
    running mean of 20 consecutive 1-second readings from the analyzer differ by less than 
    0.1 ppm (parts per million by volume), which on average takes about 10 minutes.  An 
    expandable volume in the circulation loop near the flasks consisting of a small deflated 
    balloon keeps the content of flasks at room pressure.
    
    STANDARDIZATION:
    
    In order to account for instrument drift and to maintain measurement precision, a set 
    of six gas standards is run through the system before and after every eight seawater 
    samples. The standards were obtained from Scott-Marin and referenced against primary 
    standards purchased from C.D. Keeling in 1991.  The primary standards are on the 
    WMO-78 scale (Table 2.10).
    
    
            Table 2.10.  Calibration standard tanks used for discrete pCO2.
            
              ==========================================================
              Standard sequence  Tank number     CO2 concentration (ppm)
              ----------------------------------------------------------
                      1            CA05989              378.71
                      2            CA05980              792.51
                      3            CA05984              1036.92
                      4            CA05940              1533.7
                      5            CA05988              593.64
                      6            CA05998              205.07
              ----------------------------------------------------------
    
         
    These concentrations bracket the pCO2 at 20°C (pCO2(20)) values observed during the 
    South Atlantic A16S 2005 cruise.
    
    DATA PROCESSING:
    
    The determination of pCO2(20) in water from the headspace measurement involves 
    several steps. The IR detector response for the standards is normalized for temperature.
    The IR analyzer raw output of derived dry mole fraction of CO2 (XCO2) for samples are 
    normalized to 1 atm pressure. The sample values are converted to the true mixing ratio 
    based on a second-order polynomial fit between the instrument XCO2 readout and the 
    values of the three nearest concentrations compressed gas standards.  The mixing ratio in 
    the headspace is converted to a partial pressure assuming 100% humidity and corrected to 
    partial pressure of CO2 in the water sample prior to equilibration by accounting for 
    change in total CO2 in water during the equilibration process (for details see Wanninkhof 
    and Thoning, 1993).  The change in pCO2(20) caused by the change in DIC is calculated 
    using the constraint that TAlk remains constant during exchange of CO2 gas between the 
    headspace and the water.  The calculation is outlined in the appendix of Peng et al. (1987).
    
    Uncertainty based on duplicate sampling of the same Bullister bottle for pCO2 analysis 
    was determined on select stations of the cruise.  The comparisons are presented in Table 2.11.
    
                      Table 2.11.  Duplicate discrete pCO2 samples.
                    =================================================
                    Station  Sample No.  pCO2av   ∆pCO2  % difference
                    -------------------------------------------------
                       5        203      1093.8    3.        0.3
                       5        209      1089      2.3       0.2
                       9        103      1087.3    1.5       0.1
                       9        105      1088.8    2.4       0.2
                       9        109      1081.6    2.7       0.2
                      21        135       572.7    0.4       0.07
                      49        121       838.     0.4       0.05
                      65        121       756.1    5.6       0.7
                      93        124      1040.3    2.3       0.2
                    -------------------------------------------------
                    pCO2av = average of the duplicate samples.
                    ∆pCO2 = absolute difference between the duplicates
                    % difference = ∆pCO2/pCO2av * 100
                    -------------------------------------------------
    
    
    PROBLEMS:
    
    The instrument performed very well during the cruise despite its age and outdated 
    DOS GW Basic instrument control software.  At the start of the cruise it was noticed that 
    the standard values drifted during the 30-second read sequence.  It was determined that 
    diffusion out of the line leading from the IR cell to the internal barometer was the cause.
    The internal barometer was placed in this unit in the spring of 2003. This problem was 
    remedied by placing a capillary tube in the 1/4" OD tube to decrease its internal volume 
    and decrease exchange.  In addition, the read sequence was shortened to 10 readings from 
    the original 30 readings for standards and samples.
    
    One solenoid failed and was replaced without discernable downtime.  Three 
    sampling bottles were broken; two because of thermal expansion of the water without 
    adequate headspace and one was dropped on deck during sampling.
    
    
    REFERENCES
    
    Chen, H., R. Wanninkhof, R.A. Feely, and D. Greeley, 1995:  Measurement of fugacity 
        of carbon dioxide in sub-surface water: An evaluation of a method based on infrared 
        analysis.  NOAA Technical Memorandum, ERL AOML-85, 54 pp.
    
    Chipman, D.W., J. Marra, and T. Takahashi, 1993:  Primary production at 47°N and 
        20°W in the North Atlantic Ocean: A comparison between the 14C incubation 
        method and mixed layer carbon budget observations. Deep-Sea Res., II, v. 40, 
        pp. 151-169.
    
    Peng, T.-H., T. Takahashi, W.S. Broecker, and J. Olafsson, 1987:  Seasonal variability of 
        carbon dioxide, nutrients, and oxygen in the northern North Atlantic surface water:  
        Observations and a model.  Tellus, v. 39B, pp. 439-458.
    
    Wanninkhof, R., and K. Thoning, 1993:  Measurement of fugacity of CO2 in surface 
        water using continuous and discrete sampling methods. Mar. Chem., v. 44, no. 2-4, 
        pp. 189-205.
    
    
    2.6.5.  TOTAL DISSOLVED INORGANIC CARBON (DIC) ANALYSES (updated 7/27/05)
    
            Principal Investigator:  Rik Wanninkhof, NOAA/AOML, 4301 Rickenbacker 
                                       Causeway,  Miami, FL 33149
                                       Rik.Wanninkhof@noaa.gov
            Samplers:                Robert Castle (12 midnight-12 noon)
                                       Robert.Castle@noaa.gov
                                     Esa Peltola (12 noon-12 midnight), Esa.Peltola@noaa.gov
            Analysts:                Robert Castle (12 midnight-12 noon)
                                       Robert.Castle@noaa.gov
                                     Esa Peltola (12 noon-12 midnight), Esa.Peltola@noaa.gov
            Data Reduction:          Robert Castle, Robert.Castle@noaa.gov
                                     Esa Peltola, Esa.Peltola@noaa.gov
    
    SAMPLING:
    
    Samples were drawn according to procedures outlined in the Handbook of Methods 
    for CO2 Analysis (DOE, 1994) from 12-l Bullister bottles into cleaned 540-ml Pyrex 
    bottles using Tygon tubing with a silicone adapter on the petcock to avoid contamination 
    of DOC samples. Bottles were rinsed and filled from the bottom, leaving 5 ml of 
    headspace. Care was taken not to entrain any bubbles. 0.2 ml of saturated HgCl2 solution 
    was added as a preservative. The sample bottles were sealed with glass stoppers lightly 
    covered with Apiezon-L grease and were stored at room temperature for a maximum of 
    12 hours prior to analysis.
    
    DIC samples were collected at every degree from 36 depths with three replicate 
    samples. Some samples were also collected at every half-degree. The replicate seawater 
    samples were taken from the surface, 1000 m, and bottom Bullister bottles and run at 
    different times during the cell.  The first replicate of the bottom water was used at the 
    start of the cell with fresh coulometer solution, the first one of the 1000 m replicates was 
    run in the middle of the cell after about 12 mg of C were titrated. The second one of the 
    bottom replicates was run at the end of the cell after about 25 mg of C were titrated. A 
    new coulometer cell was started with the second one of the 1000 m replicate and the first 
    one of the surface replicate samples. In the middle of this cell the second one of the 
    surface replicates was run and the first one of the surface duplicates of a partial station.
    The second one of the duplicates of the partial station was run at the end of this cell.  No 
    systematic difference between the replicates was observed.  There was no systematic 
    dependency of results with an amount of carbon titrated for a particular cell.
    
            Total number of samples analyzed: 2482
            Total number of samples flagged after initial shipboard data reduction of quality control:
            Good (QC=2):                      2245
            Duplicates (QC=6):                 180
            Questionable (QC=3):                31
            Bad (QC=4):     20
            Not Reported (QC=5):                6
            
    ANALYZER DESCRIPTION:
    
    The DIC analytical equipment was set up in a seagoing laboratory van. The analysis 
    was done by coulometry with two analytical systems (AOML-1 and AOML-2) used 
    simultaneously on the cruise.  Each system consisted of a coulometer (UIC, Inc.) coupled 
    with a SOMMA (Single Operator Multi-parameter Metabolic Analyzer) inlet system 
    developed by Kenneth Johnson (Johnson et al., 1985, 1987, 1993; Johnson, 1992) 
    formerly of Brookhaven National Laboratory (BNL).  In the coulometric analysis of DIC, 
    all carbonate species are converted to CO2 (gas) by addition of excess hydrogen ion 
    (acid) to the seawater sample, and the evolved CO2 gas is swept into the titration cell of 
    the coulometer with pure air or compressed nitrogen, where it reacts quantitatively in 
    with a proprietary reagent based on ethanolamine to generate hydrogen ions. In this 
    process the color changes from blue to colorless, which triggers a current through the cell 
    and causes coulometrical generation of OH- ions at the anode.  The OH- ions react with 
    the H+, and the color of the solution turn back to blue.  A lightbeam shines through the 
    solution and a photometric detector at the opposite side of the cell senses the change in 
    transmission. Once the percent transmission reaches its original value, the coulometric 
    titration is stopped and the amount of CO2 that enters the cell is determined by integrating 
    the total charge during the titration.
    
    STANDARDIZATION:
    
    The coulometers were calibrated by injecting aliquots of pure CO2 (99.995%) by 
    means of an 8-port valve outfitted with two sample loops with known gas volumes 
    (AOML-1: 1.9951 ml @ 25.05°C and 0.9807 ml @ 25.10°C; AOML-2: 2.0018 ml @ 
    25.09°C and 0.9949 ml @ 25.06°C) bracketing the amount of CO2 extracted from the 
    water samples for the two AOML systems.
    
    The stability of each coulometer cell solution was confirmed three different ways: 
    the Certified Reference Material (CRM, Batch 66, supplied by Dr. A. Dickson of Scripps 
    Institution of Oceanography, SIO) was measured at the beginning and the middle, gas 
    loops in the beginning and at the end, and the duplicate samples in the beginning, middle 
    and at the end of each cell solution. The coulometer cell solution was replaced after 
    25 mg of carbon was titrated, typically after 9-12 hours of continuous use.
    
    The pipette volume was determined by taking aliquots at known temperature of 
    distilled water from the volumes. The weights with the appropriate densities were used to 
    determine the volume of the pipettes (AOML1: 28.716 ml @ 20.00°C, AOML2: 
    22.547 ml @ 20.00°C).
    
    DATA PROCESSING:
    
    Calculation of the amount of CO2 injected was according to the Department of 
    Energy (DOE) CO2 handbook (DOE, 1994).  The concentration of CO2 ([CO2]) in the 
    samples was determined according to:
    
                                   (Counts-Blank*Run Time)* K µmol/count
                [CO2]=Cal.factor * -------------------------------------
                                    pipette volume* density of sample
    
    where 
        "Cal. Factor" is the calibration factor, "Counts" is the instrument reading at the 
        end of the analysis, "Blank" is the counts/minute determined from blank runs 
        performed at least once for each cell solution, "Run Time" is the length of 
        coulometric titration (in minutes), and K is the conversion factor from counts to µmol.
    
    The instrument has a salinity sensor, but all DIC values were recalculated to a molar 
    weight (µmol kg-1) using density obtained from the CTD's salinity sensor. The DIC 
    values were corrected for dilution by 0.2 ml of HgCl2 used for sample preservation. The 
    total water volume of the sample bottles was 540 ml. The correction factor used for 
    dilution was 1.00037. A correction was also applied for the offset from the CRM. This 
    correction was applied for each cell using the CRM value obtained in the beginning of 
    the cell. The results underwent initial quality control on the ship using property plots: 
    DIC-Depth, DIC-Potential Temperature, DIC-AOU, DIC-NO3; DIC-SiO3, DIC-PO4, 
    DIC-TAlk, and DIC-pH. Also DIC-LAT-Depth contour plots were used to analyze the 
    quality of the data.
    
    PROBLEMS:
    
    The overall performance of the instruments was good during the cruise. The air 
    purifier supplying carrier and pneumatic gas malfunctioned during station 24.
    Compressed tanks of ultra-high purity nitrogen gas were used thereon. At the same time, 
    soda lime traps used to scrub any CO2 from the carrier gas were removed from the air/N2 
    line, since they developed cracks over time and also they appeared to release CO2 in 
    pulses into the carrier.  A coulometer was replaced during the test cast runs. It did not 
    find an endpoint and did not stop counting. A number of pinch valves failed and they 
    were replaced. Also some cell caps started leaking and leads of electrodes broke. The 
    Orbo tubes (filled with silica gel to absorb possible acid vapors) tended to break and leak 
    and they were not used after station 109 on either system.
    
    TESTS OF DIFFERENT SIZE SAMPLING BOTTLES:
    
    Because of concerns about the large amount of water used for a DIC sample and use 
    of grease on the stoppers that could contaminate samples for DOM, comparison tests 
    were performed with samples drawn in 250 ml borosilicate bottles with ground glass 
    stoppers stored under cold water with the regular sampling procedures outlined above.
    The results are shown in Table 2.12.
    
    
          Table 2.12.  Test results of different sample bottle sizes for DIC.
    
                  ======================================================================
                                                   Bullister  Volume 
                         Type   Bottle  RT    DIC   Bottle     (ml)   Average
                  ----------------------------------------------------------------------
                        CRM      213    14  1971.11            
                        bottle   A9     13  2122.29    9       500   
                        bottle   C9     13  2121.10    9       500   2121.69
                        bottle   S76    10  2119.95    9       250   
                        bottle   S77    12  2120.01    9       250   2119.98
                        bottle   S78    12  2120.28   10       250   
                        bottle   S79    11  2120.89   10       250   2120.58
                        bottle   A10    13  2121.04   10       500   
                        bottle   C10    12  2122.5    10       500   2121.77
                        bottle   A11    12  2121.37   11       500   
                        bottle   C11    14  2123.05   11       500   2122.21
                        CRM      213    15  1972.10               
                        bottle   S80    13  2120.74   11       250   
                        bottle   S81    19  2121.09   11       250   2120.915
                        bottle   S82    11  2120.51   12       250   
                        bottle   S83    17  2121.03   12       250   2120.77
                        bottle   A12    20  2126.01   12       500   
                        bottle   C12    20  2125.5    12       500   
                        bottle   A13    20  2128.34   13       500   
                        bottle   C13    17  2122.12   13       500   2122.12
                        bottle   S84    11  2120.61   13       250   
                        bottle   S85    11  2119.34   13       250   2119.97
                        bottle   S86     9  2119.26   14       250   
                        bottle   S87     9  2119.41   14       250   2119.33
                        bottle   A14     9  2120.74   14       500   
                        bottle   C14     9  2121.61   14       500   2121.17
                  ----------------------------------------------------------------------
                  CRM Certified Value 1969.57.
    
                  Legend:
                    Type:    CRM = certified reference material; bottle = sample bottle.
                    Bottle:  bottles with prefix "S" are the 250 ml bottle, the others 
                             are the 540 ml bottles used during the cruise.
                    RT:      run time of the sample on the coulometer in minutes.
                    DIC:     results of the analyses in µmol kg-1
                    Bullister Bottle:  Bullister bottle number.
                    Volume:  nominal sample bottle volume.
                    Average: Average of duplicate large or duplicate small bottles taken 
                             from a particular Bullister bottle.
                  ----------------------------------------------------------------------              
    
    
    STATISTICS:
                                Large       Small
                  --------------------------------
                  Average:     2121.79     2120.26
                  St. Dev.:       0.37        0.55
    
    These test and more ad-hoc tests at the beginning of the cruise showed a small but 
    systematic difference between the small and large sample bottles.  The cause of the 
    artifact is not clear, but the tests led to our decision to use the 500-ml greased stopper 
    bottles for the entire cruise.
    
    
    REFERENCES
    
    DOE, 1994:  Handbook of methods for the analysis of the various parameters of the 
        carbon dioxide system in sea water. Version 2, A.G. Dickson and C. Goyet (eds.), 
        ORNL/CDIAC-74.
    
    Johnson, K.M., K.D. Wills, D.B. Butler, W.K. Johnson, and C.S. Wong, 1993: 
        Coulometric total carbon dioxide analysis for marine studies: Maximizing the 
        performance of an automated continuous gas extraction system and coulometric 
        detector.  Mar. Chem., v. 44, pp. 167-189.
    
    Johnson, K.M., 1992:  Operator's manual: Single operator multiparameter metabolic 
        analyzer (SOMMA) for total carbon dioxide (CT) with coulometric detection.
        Brookhaven National Laboratory, Brookhaven, NY, 70 pp.
    
    Johnson, K.M., P.J. Williams, L. Brandstrom, and J. McN. Sieburth, 1987: Coulometric 
        total carbon analysis for marine studies: Automation and calibration.  Mar. Chem., 
        v. 21, pp. 117-133.
    
    Johnson, K.M., A.E. King, and J. McN. Sieburth, 1985. Coulometric DIC analyses for 
        marine studies: An introduction.  Mar. Chem., v. 16, pp. 61-82.
    
    
    2.6.6.  DISCRETE pH ANALYSES
    
            Principal Investigators: Frank J. Millero, U. Miami, RSMAS
                                       4600 Rickenbacker Causeway, Miami, FL 33149
                                       fmillero@rsmas.miami.edu
            Samplers:                William T. Hiscock (12 noon-12 midnight)
                                       whiscock@rsmas.miami.edu
                                     John M. Trapp (12 midnight-12 noon)
                                       jtrapp@rsmas.miami.edu
            Analysts:                William T. Hiscock (12 noon-12 midnight)
                                       whiscock@rsmas.miami.edu
                                     John M. Trapp (12 midnight-12 noon)
                                       jtrapp@rsmas.miami.edu
            Data Reduction:          William T. Hiscock, whiscock@rsmas.miami.edu
    
    
    SAMPLING:
    
    Samples were drawn from 12-l Bullister bottles into 50 ml glass syringes using 
    polycarbonate Luer-lock valves that fit in the petcock.  Syringes were rinsed a minimum 
    of three times and filled while taking care not to entrain any bubbles.  A rubber band 
    ensured positive pressure on the barrel of the syringe. The samples were stored at room 
    temperature for a maximum of 7 hours.  Thirty-six samples and three duplicates were 
    drawn on odd numbered stations (at 1 degree intervals) for a total of 60 full stations.  At 
    even number stations, surface water and a duplicate were always taken; in addition, five 
    to 20 other depths were also sampled, for a total of 59 half stations.  Typically, nine 
    depths were sampled with a duplicate at the surface for the half-stations.  Underway 
    samples were drawn in duplicate from the underway seawater line at 6-hour intervals 
    between Punta Arenas, Chile and the start of the line at 60°S, 31°W which are not 
    included in the tally below.
    
         Total number of samples: 2811
         Questionable (QC=3):       44
         Bad (QC=4):                64
         Not Reported (QC=5):       51
    
    ANALYZER DESCRIPTION:
    
    Measurements of the pH of seawater on the total hydrogen ion concentration pH 
    scale (pHt) were made using the multi-wavelength spectrophotometric techniques of 
    Clayton and Byrne (1993).  Determination of the absorbance at several wavelengths 
    eliminates the need to know the concentrations of indicator in the sample.
    Sulphonphthalein indicators such as m-cresol purple (mCP), thymol blue, and cresol red 
    are suitable for the determination of pH.  The system is patterned after the standard 
    operating procedure developed by the U.S. Department of Energy (DOE) (1994) and 
    utilizes mCP.  This fully automated system performs discrete analysis of pH samples 
    approximately every 12 minutes on a sample volume of 25 ml.  A microprocessor 
    controlled syringe and sampling valve aspirates and injects the seawater sample into the 
    10 cm optical cell at a precisely controlled rate.  The syringe rinses and primes the optical 
    cell with 20 ml of sample and the software permits five minutes for temperature 
    stabilization.  A refrigerated circulating temperature bath (Neslab, model RTE-17) 
    regulates the temperature of the sample at 25 ± 0.01°C.  An Agilent 8453 UV/VIS 
    spectrophotometer measures background absorbance of the sample.  The automated 
    syringe and sampling valves aspirates 4.90 ml seawater and 0.008 ml of indicator and 
    injects the mixture into the cell.  After the software permits five minutes for temperature 
    stabilization, a Guildline 9540 digital platinum resistance thermometer measures the 
    temperature and the spectrophotometer acquires the absorbance at 434, 578 and 730 nm.
    
    REAGENTS:
    
    A concentrated solution, 2.0 mM, of mCP (C21H18O3S) dye solution of known 
    pHt = 7.91 and R = 1.625 at 25°C.
    
    STANDARDIZATION:
    
    A precision of better than 0.001 pH units is possible with care, specifically with 
    regard to temperature equilibration and sample handling.  Measurements made on 
    duplicate samples, TRIS buffers and Certified Reference Material, Batch 59 (Dr. Andrew 
    Dickson, Marine Physical Laboratory, La Jolla, California) provide validation of the 
    precision and accuracy.  Duplicate analyses provide additional quality assurance and 
    were taken from same Bullister bottle. The pHsws for the Certified Reference Material 
    was determined by spectrophotometric methods independently in the laboratory at 
    RMSAS, University of Miami:
    
    Batch #59:  pHsws @ 25°C    7.9048 ± 0.0007  (n = 19)
                Salinity       33.316
    
    DATA PROCESSING:
    
    The pHt of the sample is perturbed by the addition of the indicator.  The magnitude 
    of this perturbation is a function of the difference between the seawater and indicator 
    acidity. A correction factor applied for each batch of dye adjusts for this perturbation.
    For a 4.90 ml sample of seawater, 0.008 ml of mCP is added and the absorbance ratio 
    measured.  From a second addition of mCP and a second absorbance ratio measurement, 
    a change in the absorbance ratio per ml of added indicator (DR) is calculated. The value 
    of the absorbance ratio (Rm) measured subsequent to the initial addition of the indicator 
    was used to calculate R from:
    
            R = Rm + (0.00095 - 0.00133 Rm) Vind                          (1)
    
    where Vind is the volume of mCP used.  Clayton and Byrne (1993) calibrated the mCP indicator 
    using TRIS buffers (Ramette et al., 1977) and the equations of Dickson (1993).  These equations 
    are used to calculate pHt, the total scale in units of moles per kilogram of solution.  The 
    conversion of the pHt (mol/kgH2O) to the seawater scale (mol/kgsol) can be made using equations of 
    Dickson and Millero (1987), Dickson and Riley (1979), and Dickson (1990).
    
    CRM
      Total number of Sets:  136
      Number of Sets Used:   124
      CRM Batch #59:         7.9050 ± 0.0024 (pHsws @ 25°C)
    
    TRIS Buffer
      Total number of Sets:   296
      Number of Sets Used:    264
      TRIS Buffer (0.04 m):   8.0935 ± 0.0019 (pHt @ 25°C)
      
    Duplicates
      Total number of Sets:   291
      Number of Sets Used:    214
      Standard Deviation:     ± 0.0019 (pHsws @ 25°C)
      
    NOTE: 
    
    The instrumental software automatically runs a duplicate analysis when the baseline 
    absorbance at 730 nm is beyond a set threshold, thus a large number of omitted 
    duplicate results.Duplicate samples whose difference was three times larger than 
    the standard deviation were omitted from the analyses.  The number omitted is the 
    difference between the total number of sets and the sets used.
    
    PROBLEMS:
    
    At the start of the cruise, the outflow from the optical cell leaked into the 
    thermostated water jacket; this was repaired by replacing the tubing.  Sporadically, 
    samples drawn from the syringe entrained an air bubble because the valve was 
    improperly opened, tubing was pinched, or the syringe plunger was dry and became stuck 
    in the barrel.  Some syringes suffered from fatigue at the metal Luer-lock and resulted in 
    the sample being lost or a failed analysis.  Occasionally the software would lose 
    communication with the microprocessor-controlled syringe pumps and pause analysis; 
    the problem was resolved by following the steps outlined in the software to reestablish 
    communication.
    
    
    REFERENCES
    
    Clayton, T.D., and R.H. Byrne, 1993: Spectrophotometric seawater pH measurements: 
        Total hydrogen ion concentration scale calibration of m-cresol purple and at-sea 
        results.  Deep-Sea Res., v. 40, pp. 2315-2329.
    
    Dickson, A.G., 1990:  Thermodynamics of the dissociation of boric acid in synthetic 
        seawater from 273.15 to 318.15 K.  Deep-Sea Res., Part A, v. 37, no. 5, pp. 755-766.
        
    Dickson, A.G., 1993:  The measurement of seawater.  Mar. Chem., v. 44, no. 2-4, pp.
        131-142.
        
    Dickson, A.G., and F.J. Millero, 1987:  A comparison of the equilibrium constants for the 
        dissociation of carbonic acid in seawater media.  Deep-Sea Res., Part A, v. 34, 
        no. 10, pp. 1733-1743.
    
    Dickson, A.G., and J.P. Riley, 1979:  The estimation of acid dissociation constants in 
        seawater media from potentiometric titration with strong base, 1: The ionic product 
        of water-KSUS-w.  Mar. Chem., v. 7, no. 2, pp. 89-99.
    
    DOE, 1994:  Handbook of methods for the analysis of the various parameters of the 
        carbon dioxide system in sea water. Version 2, A.G. Dickson and C. Goyet (eds.), 
        ORNL/CDIAC-74.
    
    Ramette, R. W., C. H. Culberson, and R. G. Bates,1997: Acid-base properties of 
        Tris(hydroxymethyl)aminomethane (Tris) buffers in seawater from 5 to 40 ˚C.
        Anal. Chem., v. 49, pp.867-870.
    
    
    
    2.6.7.  TOTAL ALKALINITY ANALYSES
    
            Principal Investigator: Frank J. Millero, U. Miami, RSMAS
                                      4600 Rickenbacker Causeway, Miami, FL 33149
                                      fmillero@rsmas.miami.edu
            Samplers:               Taylor B. Graham (12 noon-12 midnight)
                                      tgraham@rsmas.miami.edu
                                    Mareva Chanson (12 midnight-12 noon)
                                      mchanson@rsmas.miami.edu
            Analysts:               Taylor B. Graham (12 noon-12 midnight)
                                      tgraham@rsmas.miami.edu
                                    Mareva Chanson (12 midnight-12 noon)
                                      mchanson@rsmas.miami.edu
            Data Reduction:         William T. Hiscock, whiscock@rsmas.miami.edu
    
    
    SAMPLING:
    
    Samples were drawn from 12-l Bullister bottles into 500 ml borosilicate flasks using 
    Silicone tubing that fit over the petcock to avoid contamination of DOC samples.  Bottles 
    were rinsed a minimum of two times and filled from the bottom, overflowing a quarter of 
    a volume while taking care not to entrain any bubbles.  Approximately 15 ml of water 
    was withdrawn from the flask by arresting the sample flow and removing the sampling 
    tube, thus creating a small expansion volume and a reproducible headspace.  The sample 
    bottles were sealed at a ground glass joint with a glass stopper.  The samples were stored 
    at room temperature for a maximum of 7 hours.   Thirty-six samples and three duplicates 
    were drawn on odd number stations (at 1 degree intervals) for a total of 61 full stations.
    Typically, nine depths were sampled with a duplicate at the surface at the 60 "half 
    stations."  Periodically, multiple duplicate samples were drawn with a specific focus on 
    photic zone and region of high dissolved organic carbon (DOC).  The purpose was to 
    determine the difference in Total Alkalinity after filtration with a 0.45 µm nylon 
    membrane filter.  Additional underway samples were drawn in duplicate from the 
    underway seawater line at 6-hour intervals between Punta Arenas, Chile and the start of 
    the line at 60°S, 31°W, which are not included in the tally below.
    
         Total number of samples:  2784
         Questionable (QC=3):        64
         Bad (QC=4):                 42
         Not Reported (QC=5):        51
    
    ANALYZER DESCRIPTION:
    
    The total alkalinity of seawater (TAlk) was evaluated from the proton balance at the 
    alkalinity equivalence point, pHequiv = 4.5 at 25°C and zero ionic strength in one kilogram 
    of sample.  The method utilizes a multi-point hydrochloric acid titration of seawater 
    according to the definition of total alkalinity (Dickson, 1981).
    
    The titration system used consists of a Metrohm 665 Dosimat titrator, an Orion 
    720A pH meter and a custom designed plastic water-jacketed titration cell (Millero et al., 
    1993b). Both the seawater sample and acid titrant are temperature equilibrated to a 
    constant temperature of 25 ± 0.1°C with a water bath (Neslab, model RTE-17).  The 
    plastic water-jacketed cell is similar to the cells used by Bradshaw and Brewer (1988) 
    except a larger volume (~200 ml) is employed to increase the precision.  Each cell has a 
    fill and drain valve which increases the reproducibility of the volume of sample contained 
    in the cell.  The titration acidified seawater past the carbonic acid endpoint by adding HCl 
    stepwise through an injection tip into the cell.  A typical titration recorded the EMF after 
    the readings became stable (deviation less than 0.09 mV) and then enough acid was 
    added to change the voltage a pre-assigned increment (13 mV).  A full titration 
    (~25 points) takes about 20 minutes.  The electrodes used to measure the EMF of the 
    sample during a titration consisted of a ROSS glass pH electrode (Orion, model 810100) 
    and a double junction Ag, AgCl reference electrode (Orion, model 900200).
    
    REAGENTS:
    
    A single 50-l batch of ~0.25 m HCl acid was prepared in 0.45 m NaCl by dilution of 
    concentrated HCl, AR Select‚ Mallinckrodt, to yield a total ionic strength similar to 
    seawater of salinity 35.0 (I ≈ 0.7 M).  The acid was standardized by a coulometric 
    technique (Marinenko and Taylor, 1968; Taylor and Smith, 1959) and verified with 
    alkalinity titrations on seawater of known alkalinity.  Furthermore, Andrew Dickson's 
    laboratory performed an independent determination of the acid molality on sub-samples.
    The calibrated molality of the acid used was 0.2434 ± 0.0001 m HCl.  The acid was 
    stored in 500-ml glass bottles sealed with Apiezon(r) L grease for use in the field.
    
    STANDARDIZATION:
    
    The volumes of the cells used were determined to ± 0.03 ml in the laboratory by 
    multiple titrations using seawater of known total alkalinity and CRM.  Calibrations of the 
    burette of the Dosimat with water at 25°C indicate that the systems deliver 3.000 ml (the 
    approximate value for a titration of seawater) to a precision of ± 0.0004 ml, resulting in 
    an error of ± 0.3 µmol·kg-1 in TAlk and DIC.  The reproducibility and precision of 
    measurements are checked using low nutrient surface seawater and Certified Reference 
    Material (Dr. Andrew Dickson, Marine Physical Laboratory, La Jolla, California), Batch 
    59 and 66.  CRM were utilized in order to account for instrument drift and to maintain 
    measurement precision.  Duplicate analyses provide additional quality assurance and 
    were taken from same Bullister bottle.
    
    The assigned values of the Certified Reference Material provided by A. Dickson of 
    SIO are:
    
        Batch #59:  Total Alkalinity:  2220.98 ± 0.58 µmol·kg-1  Salinity: 33.316 
        Batch #66:  Total Alkalinity:  2193.27 ± 0.60 µmol·kg-1  Salinity: 32.962
        
    DATA PROCESSING:
    
    An integrated program controls the titration, data collection, and the calculation of 
    the carbonate parameters (TAlk, pH, and DIC ) (Millero et al., 1993a).  The program is 
    patterned after those developed by Dickson (1981), Johansson and Wedborg (1982), and 
    U.S. Department of Energy (DOE) (1994).  The program uses a Levenberg-Marquardt 
    nonlinear least-squares algorithm to calculate the TAlk, DIC, and from the potentiometric 
    titration data.
    
    CRM                      Instrument 1        Instrument 2  
    -------------------     --------------      --------------
    Total number of set          56                  52
    Number of sets used:         48                  46
    Standard deviation:     ±3.5 µmol·kg-1      ±2.7 µmol·kg-1
         
    Duplicates              Between Systems      Instrument 1        Instrument 2   
    -------------------     --------------      --------------      --------------
    Total number of sets:       143                   31                 42
    Number of sets used:        130                   25                 35
    Standard deviation:     ±2.9 µmol·kg-1      ±1.6 µmol·kg-1      ±1.3 µmol.kg-1
    
    
    NOTE:  
    
    Duplicate samples whose difference was three times larger than standard deviation were 
    omitted from the analyses.  The number omitted is the difference between the total 
    number of set and the sets used.
    
    PROBLEMS:
    
    At the start of the cruise a titration cell was swapped out for a spare cell because of a 
    combination of instability in the electrodes and an air bubble consistently being trapped.
    One valve and a proximity switch were replaced without discernible downtime.
    Sporadically, a solenoid valve at the bottom of the titration cell would fail to engage or 
    disengage, resulting in the loss of the sample or a failed titration due to a poor rinse or an 
    air bubble.  The titration cell on system one showed some drift in CRM values on 
    February 4, 2005; the titration cells recalibration values were used to correct this.
    Communication problems between the software and the components of the TAlk system 
    were remedied with replacement of cables and/or components. A  Metrohm 665 Dosimat 
    titrator and Orion 720A pH meter were replaced.  Computer instability resulted in the 
    loss of one sample.
    
    
    REFERENCES
    
    Bradshaw, A.L., and P.G. Brewer, 1988:  High precision measurements of alkalinity and 
        total carbon dioxide in seawater by potentiometric titration, 1: Presence of unknown 
        protolyte(s)?  Mar. Chem., v. 23, pp. 69-86.
    
    Dickson, A.G., 1981: An exact definition of total alkalinity and a procedure for the 
        estimation of alkalinity and total CO2 from titration data. Deep-Sea Res., Part A, v.
        28, pp. 609-623.
    
    DOE, 1994:  Handbook of methods for the analysis of the various parameters of the 
        carbon dioxide system in sea water. Version 2, A.G. Dickson and C. Goyet (eds.), 
        ORNL/CDIAC-74.
    
    Johansson, O., and M. Wedborg, 1982:  On the evaluation of potentiometric titrations of 
        seawater with hydrochloric acid. Oceanologica Acta, v. 5, pp. 209-218.
        
    Marinenko, G., and J.K. Taylor, 1968:  Electrochemical equivalents of benzoic and oxalic 
        acid.  Anal. Chem., v. 40, pp. 1645-1651.
        
    Millero, F.J., R.H. Byrne, R. Wanninkhof, R. Feely, T. Clayton, P. Murphy, and M.F.
        Lamb, 1993a: The internal consistency of CO2 measurements in the equatorial 
        Pacific.  Mar. Chem., v. 44, pp. 269-280.
    
    Millero, F.J., J.-Z. Zhang, K, Lee, and D.M. Campbell, 1993b: Titration alkalinity of 
        seawater.  Mar. Chem., v. 44, pp. 153-165.
        
    Taylor, J.K., and S.W. Smith, 1959: Precise coulometric titration of acids and bases. J.
        Res. Natl. Bur. Stds., v. 63, pp. 153-159.
        
    
    
    2.6.8.  SALINITY ANALYSIS
            Principal Investigators: Gregory C. Johnson, NOAA/PMEL
            Analyst:                 Dave Wisegarver, NOAA/PMEL
            Samplers:                Dave Wisegraver (primary from 4 a.m.-4 p.m.)
                                     Scott Doney, Rik Wanninkhof, Bill Hiscock, Wenhau Chen
    
    Samples were run on a Guildline 8400B Laboratory Salinometer, serial number 
    60843.  The salinometer had been last calibrated at Guildline in January of 2004. IAPSO 
    Standard Seawater was used to standardize the instrument.  The standard water was from 
    batch:
                   P143, 26-Feb-2003, K15 = 0.99989, Salinity 34.996.
    
    The instrument was located in a small temperature controlled room, off the hydro lab.  A 
    recording temperature sensor was placed near the salinometer to monitor the temperature 
    during analyses.  For the most part, the temperature logged by this sensor was 22-24°C; 
    however, there were several deviations, one as high as 25.3°C and one as low as 21.7°C.
    On one occasion, analysis was halted for about half an hour, while the room cooled.
    
    Samples were drawn from the Bullister bottles into 250-ml Kimax borosilicate 
    bottles.  The bottles were rinsed at least three times before filling to approximately 
    220 ml.  A plastic insert and Nalgene cap were used to seal the sample in the bottle. At 
    the conclusion of sampling, the time was noted and samples were placed into the 
    salinometer lab so they could equilibrate to the room temperature.  Samples were 
    analyzed after a period of at least 10 hours and typically not more than 24 hours from the 
    time of sampling.  With the exception of a few shallow casts, an IAPSO standard 
    seawater bottle was analyzed before and after each station.
    
    The software used (ASALW) was developed at Scripps Institution of Oceanography.
    As per the instructions provided in the software, the cell was rinsed at least two times 
    with sample at a relatively fast flow rate; the flow was adjusted to a slower rate for the 
    final fill, and a reading was taken.  The cell was drained and slowly filled for a second 
    reading.  If the two readings agreed within 0.00005, the values were accepted; otherwise, 
    an additional reading was required. PSS-78 salinity (UNESCO, 1981) was calculated.
    Corrections were applied to the data for differences between beginning and ending 
    standards.
    
    A total of 4174 salinity samples were taken, of which 127 were flagged as 
    questionable, 3 as bad, and 2 were lost during analysis. A number of samples could not 
    be drawn during heavily sampled casts, due to a lack of water.  This occurred most 
    frequently when using the small 3-liter bottles in the first few stations.
    
    
    REFERENCES
    
    UNESCO, 1981:  Background papers and supporting data on the practical salinity scale., 
        1978.  UNESCO Technical Papers in Marine Science, No. 37, p. 144.
        
    
    
    2.6.9.  INORGANIC NUTRIENTS (PHOSPHATE, NITRATE, NITRITE AND SILICATE)
    
            Principal Investigators: Dr. Calvin Mordy, NOAA/PMEL
                                     Dr. Jia-Zhong Zhang, NOAA/AOML
            Samplers and Analysts:   Charlie Fischer, NOAA/AOML (12 noon-12 midnight)
                                     Calvin Mordy, UW (12 midnight-12 noon)
            Data Reduction:          Calvin Mordy
            
    
    EQUIPMENT AND TECHNIQUES:
            
    Dissolved nutrients (phosphate, silicic acid, nitrate and nitrite) were measured using 
    automated continuous flow analysis with a segmented flow and colorimetric detection.
    The four-channel autoanalyzer was customized using components from various systems.
    The major components were an Alpkem 301 sampler, two 24 channel Ismatek peristaltic 
    pumps, four ThermoSeparation monochrometers, and custom software for digitally 
    logging and processing the chromatographs.  Glass coils and tubing from the Technicon 
    Autoanalyzer II were used for analysis of phosphate, and micro-coils from Alpkem were 
    used for the other three analyses.
    
    The detailed methods were described by Gordon et al. (1992).  Because pump tubing 
    destined for the cruise was lost in transit, some of the pump tube sizes suggested in the 
    manual had to be modified.  Pump tubes were changed four times during the expedition.
    
    Silicic acid was analyzed using a modification of Armstrong et al. (1967).  An acidic 
    solution of ammonium molybdate was added to a seawater sample to produce 
    silicomolybic acid.  Oxalic acid was added to inhibit a secondary reaction with 
    phosphate.  Finally, the reduction with ascorbic acid formed the blue compound 
    silicomolybdous acid.  The color formation was detected using a 6 mm flowcell at 
    660 nm.  The use of oxalic acid and ascorbic acid (instead of tartaric acid and stannous 
    chloride as suggested by Gordon et al.) was to reduce the toxicity of our waste stream.
    
    Nitrate and nitrite analyses were also modified from Armstrong et al. (1967).  Nitrate 
    was reduced to nitrite in a cadmium column, formed into a red azo dye by complexing 
    nitrite with sulfanilamide and N-1-naphthylethylenediamine, and the color formation was 
    detected using a 6 mm flowcell at 540 nm.  The same technique was used to measure 
    nitrite (excluding the reduction step), but the color formation was detected using a 10 mm 
    flowcell at 540 nm.
    
    Phosphate analysis was based on the technique of Bernhardt and Wilhelms (1967).
    An acidic solution of ammonium molybdate was added to the sample to produce 
    phosphomolybdic acid, and this was reduced to the blue compound phosphomolybdous 
    acid following the addition of hydrazine sulfate.  The reaction was heated to 55°C to 
    bring the reaction to completion, and color formation was detected using a 10 mm 
    flowcell at 815 nm.
    
    SAMPLING AND STANDARDS:
    
    Nutrient samples were drawn in 40 ml HDPE Boston Round sample bottles that had 
    been stored in 10% HCl and rinsed four to five times with sample before filling.  A 
    replicate was always drawn from the deep bottle for analysis on the subsequent station.
    All samples were brought to room temperature prior to analysis.  A separate analytical 
    run was conducted at each station (except for the most shallow stations).  An analytical 
    run consisted of blanks and working standards, old working standard, deep water from 
    the previous station, samples analyzed from deep to surface, replicate analysis of the four 
    deep samples and any problem samples, and finally the working standards and blanks.
    The blanks were deionized water, and the standards were simply a "zero" standard in 
    Low Nutrient Seawater (LNSW), and a high standard.  Linearity of the autoanalyzer was 
    checked every ten days, and corrections for non-linearity will be applied during final data 
    reduction.
    
    The high standard was made from the addition of 1 ml of primary nitrite standard 
    and 20 ml of a secondary mixed standard (containing silicic acid, nitrate, and phosphate) 
    in 500 ml of LNSW.  A new high standard was prepared for each analytical run.
    Calibrated Eppendorf pipettes normally used for dispensing the primary and secondary 
    standards were not delivered to the ship, so a calibrated Rainin electronic digital pipette 
    was used.
    
    Dry standards were pre-weighed at PMEL and dissolved to prepare primary 
    standards at sea.  Silicic acid (Na2SiF6, >98%) and nitrate (KNO3, 99.99%) were from 
    Aldrich, phosphate (KH2PO4, 99.99%), and nitrite (NaNO2, 98.2%) were from Baker.
    The mixed standard was prepared by additions of the nitrate and phosphate primary 
    standards during preparation of the silicic acid primary standard.
    
    After each run, the electronic chromatograph was scrutinized to ensure proper 
    selection of individual peak heights.  The peak information was inserted into Microsoft 
    Excel and the concentrations were calculated after factoring the baseline drift, carryover 
    corrections, refractive index, and standard drift.  Quality control plots were maintained of 
    the baseline, matrix, carryover, standard factor, old standard, and station-to-station 
    variability of the deep water replicate.
    
    Nutrient concentrations were reported to the shipboard data manager in micromole 
    per liter.  The laboratory temperature during analysis was also reported to facilitate unit 
    conversion to a micromole per kg basis.  The nutrient concentration as shown in 
    µmol kg-1 units presented in the bottle data files.
    
    PROBLEMS:
    
    During the cruise, several detectors and a sampler had to be replaced, but no data 
    were compromised due to these equipment failures.  During the first two stations, the 
    phosphate heater was not functioning, and these data were considered suspect.
    
    NUMBER OF SAMPLES, REPLICATES, AND PRECISION:
    
    A replicate sample was almost always drawn from the deepest bottle, and replicate 
    analyses were almost always conducted on the four deepest bottles.  A few replicate 
    analyses were conducted for samples in the upper water, and the precision of nitrate was 
    determined from those samples with concentrations >0.05 µM.  The precision of 
    phosphate, silicic acid and nitrate was within 2% of full scale (Table 2.13).
    
    
      Table 2.13.  Summary of number of nutrient samples taken and estimated precision.
    
          =========================================================================
                                          Phosphate  Silicic Acid  Nitrate  Nitrite
          -------------------------------------------------------------------------
          Number of samples                 4286         4286       4243     4286
          Number of replicates              755          759        680      19*
          Average standard deviation (µM)   0.01         0.4        0.08     0.005
          Percent deviation                 0.8%         1.7%       1.4%     2%
          *Samples with nitrate concentrations higher that 0.05 µM.
          -------------------------------------------------------------------------
    
    
    
    REFERENCES
    
    Armstrong, F.A.J., C.R. Stearns, and J.D.H. Strickland, 1967: The measurement of 
        upwelling and subsequent biological processes by means of the Technicon 
        AutoAnalyzer and associated equipment.  Deep-Sea Res., v. 14, pp. 381-389.
    
    Bernhardt, H., and A. Whihelms, 1967:  The continuous determination of low level iron, 
        soluble phosphate, and total phosphate with the AutoAnalyzer.  Technicon 
        Symposia, I., pp. 385-389.
    
    Gordon, L.I., J.C. Jennings Jr., A.A. Ross, and J.M. Krest, 1993:  A suggested protocol 
        for continuous automated analysis of seawater nutrients (phosphate, nitrate, nitrite, 
        and silicic acid) in the WOCE Hydrographic program and the Joint Global Ocean 
        Fluxes Study, WOCE Operations Manual, Vol. 3: The Observational Programme, 
        Section 3.2: WOCE Hydrographic Programme, Part 3.1.3: WHP Operations and 
        Methods. WHP Office Report WHPO 91-1; WOCE Report No. 68/91. November, 
        1994, Revision 1, Woods Hole, Mass., USA, 52 pp.
    
    
    2.7.  UNDERWAY MEASUREMENTS
    
    Several groups measured carbon system parameters from the uncontaminated 
    seawater line.  All systems but one were located in the hydrolab where the seawater 
    stream was diverted to the different instruments.  A total of about 25 l/min of water was 
    used, while an additional 10-15 l/min was discharged overboard aft of the hydrolab.  This 
    decreased the transit time from the intake at 5-m depth at the bow through the 100-m 2" 
    Teflon lined stainless steel tube. Transit time from the bow to the hydrolab was about 2.5 
    minutes.  An EnviroTech nutrient monitor (NAS-2E) was set up at an outlet in the main 
    lab but did not function properly throughout the cruise.
    
    Underway systems that were used on the cruise included an underway pCO2 system 
    that is installed on a permanent basis from AOML, two SAMI pCO2 systems from the 
    University of Montana, and a multi-inorganic carbon species analyzer from the 
    University of South Florida.  A Seabird thermosalinograph (SBE-45) was situated in the 
    sink of the hydrolab and logged in the datastream from the underway pCO2 system.  In 
    addition, there was an uncalibrated fluorometer in the hydrolab and a thermosalinograph 
    at the bow of the ship approximately 5 m from the intake.  The fluorometer and 
    thermosalinograph data are logged on the shipboard computing system (SCS).
    
    The underway data was not submitted to the data manager while at sea as further 
    quality control of the full data set is to be performed on shore.  The data will be submitted 
    to the data manager, Frank Delahoyd at SIO, and placed on the A16S website. The data 
    will include the appropriate time and location stamps such that the datasets can be 
    compared with each other and surface bottle data from the CTD casts. The bottle data 
    taken from the underway sample line for a surface survey between Punta Arenas and the 
    start of the CTD section at 60°S, 32˚W is provided as a separate file.
    
    
    2.7.1.  SHIPBOARD COMPUTING SYSTEM (SCS)
    
    The shipboard computing system logs all data routinely acquired by the permanent 
    shipboard sensors including TSG, rain, meteorological parameters, and speed and course.
    The data are logged at 30-second intervals and are available from the chief scientist 
    (RW).
    
    
    2.7.2.  UNDERWAY pCO2 (fCO2) MEASUREMENTS
    
            Principal Investigator: Rik Wanninkhof, NOAA/AOML
                                      4301 Rickenbacker Causeway, Miami FL 33149
                                      Rik.Wanninkhof@noaa.gov
            Shipboard Analyst:      Jonathan Shannahoff, Chief Survey Technician
                                      R/V Ronald H. Brown
                                      Jonathan.Shannahoff@noaa.gov
            Data Reduction:         Robert Castle, NOAA/AOML
                                      4301 Rickenbacker Causeway, Miami FL 33149
                                      Robert.Castle@noaa.gov
    
    The shipboard automated underway pCO2 system is situated in the hydrolab.  It runs on an 
    hourly cycle during which three gas standards, eight headspace samples from the 
    equilibrator, and three ambient air samples are analyzed.  The system consists of an 
    equilibrator where surface seawater from the bow intake is equilibrated with headspace, a
    valve box that contains the infrared analyzer, and an electronics box with a computer 
    and interface boards that control valves and log sensors.
    
    The equilibrator, designed by R. Weiss of SIO, is made from a 58 cm H X 23 cm ID 
    cylindrical Plexiglas(tm) chamber.  Surface seawater flows through a showerhead in the top 
    at a rate of 10-13 l/min. The water spray through the 16-l headspace and the turbulence 
    of the water streams impinging on the surface of 8 l of water cause the gases in water 
    and headspace to equilibrate.  Excess water flows through an outlet 20 cm from the bottom 
    of the equilibrator into an over-the-side drain.  Two vents in the top of the 
    equilibrator insure that the headspace remains at the measured laboratory pressure.  
    Headspace gas circulates in a closed loop driven by a KNF pump at 200 ml/min.  From the 
    equilibrator the gas passes through a condensor, a column of magnesium perchlorate, a 
    mass flow meter (MFM), the 12 ml sample cell of a Licor(tm) Model 6251 non-dispersive 
    infrared analyzer (IR), and back into the equilibrator headspace.
    
    A second KNF pump draws marine air from an intake on the bow mast through 100 m of 0.95 
    cm (= 3/8") OD Dekoron(tm) tubing at a rate of 6-8 l/min.  A filter of glass wool at the 
    intake prevents particles from entering the gas stream.  At designated times, the program 
    diverts 250 ml/min of air from this line into the Licor sample cell for analysis.  Excess 
    marine air and the two vent lines from the equilibrator empty through an endcap into an 
    open ended PVC tube.  This means that any air drawn into the equilibrator is marine air 
    rather than lab air with elevated and variable CO2 concentration.
    
    Both sample streams (equilibrator headspace and marine air) are analyzed bone dry.  They 
    pass first through a cold trap (condensor) at 5oC and then through a column of magnesium 
    perchlorate.  Standard gases also run through the magnesium perchlorate.
    
    A custom developed program run under LabView(TM) controls the system and graphically 
    displays air and water XCO2 readings.  The program logs the voltage and temperature of the 
    infrared analyzer, water flow, gas flows, equilibrator temperature, and barometric 
    pressure.  It also logs temperature and salinity from a Seabird MicroTSG' unit connected 
    to the seawater line near the equilibrator.  An RS-422 feed from the shipboard computing 
    system (SCS) provides additional data including time, latitude, longitude, temperature 
    and salinity in the sea chest near the seawater intake, relative and absolute wind speed 
    and direction, and fluorometer readings.  The program writes all of this data to disk at 
    the end of each measurement phase.
    
    The details of instrumental design can be found in Wanninkhof and Thoning (1993), 
    Ho et al. (1995), and Feely et al. (1998).
    
    SAMPLING CYCLE:
    
    The system runs on an hourly cycle during which three standard gases, three marine air 
    samples, and eight surface water samples (from the equilibrator headspace) are analyzed on 
    the schedule listed below (Table 2.14).  A Valco multi-port valve selects the gas to be 
    analyzed.  Each measurement phase starts by flowing either standard (@~50ml/min), 
    equilibrator headspace (@~200ml/min), or marine air (@~250ml/min) through the Licor.  
    Fifteen seconds before the end of each phase, a solenoid valve stops the gas flow.  Ten 
    seconds later, the program logs all sensors and writes the data to disk.
    
    
        Table 2.14.  Hourly sampling cycle for the underway pCO2 system (version 2.5).
    
                 ===========================================================         
                 Minutes after the Hour  Sample
                 -----------------------------------------------------------
                           4             Low standard
                           8             Mid standard
                          12             High standard
                          16.5           Water (= headspace of equilibrator)
                          21             Water
                          25.5           Water
                          30             Water
                          34             Air (marine air from the bow line)
                          38             Air
                          42             Air
                          46.5           Water
                          51             Water
                          55.5           Water
                          60             Water
                 -----------------------------------------------------------
    
    
    The headspace equilibration time, as determined by return to equilibrium after 
    perturbation by adding nitrogen to the headspace, is approximately 2.5 minutes.  The 
    transit time of water from the bow to the equilibrator was determined in 1998 by 
    injecting a slug of dye into the intake and measuring the response on a fluorometer that 
    is located in the hydrolab, close to the equilibrator.  The response time, defined as the 
    time elapsed between peak concentration and the half peak level, t1/2, is 1.45 minutes.  
    This short time suggests little dispersion of the water during transit through the 
    tubing.
    
    STANDARDS:
    
    The unit is standardized every hour with three compressed air standards containing 
    known amounts of CO2 gas in (natural) air. The standard gases are purchased from 
    NOAA/CMDL in Boulder and are directly traceable to the WMO scale.
    
    The standards used on the cruise are:
    
                                        Mole Fraction
                             Tank #   CO2 (ppm) (= XCO2)
                            ----------------------------
                            CC 71588       531.98
                            CA05344       411.42
                            CA05395       315.25
    
    UNITS:
    
    All XCO2 values are reported in parts per million (ppm), and fCO2 values are 
    reported in micro atmospheres (µatm).
    
    DATA PROCESSING:
    
    The mixing ratios of ambient air and equilibrated headspace air are calculated by 
    fitting a second-order polynomial through the hourly-averaged response of the detector 
    versus mixing ratios of the standards preceding and following the air and water samples.
    Mixing ratios of dried equilibrated headspace and air are converted to fugacity of CO2 in 
    surface seawater (fCO2) and water saturated air.  For ambient air (a) and equilibrator 
    headspace (eq), the fCO2a, or fCO2eq, are calculated assuming 100% water vapor content:
    
                     fCO2a/eq = xCO2a/eq(P-pH2O) exp((B11+2d12)P/RT)
    where 
    
        fCO2a/eq is the fugacity in ambient air or equilibrator, pH2O is the water vapor, 
        pressure at the sea surface temperature, P is the atmospheric pressure (in atm), 
        T is the SST or equilibrator temperature (in K), and R is the ideal gas constant 
        (82.057 ml atm deg-1 mol-1). 
    
    The exponential term is the fugacity correction where B11 is the second 
    virial coefficient of pure CO2:
    
                B11 = -1636.75 + 12.0408 T - 0.032795T2 + 3.16528E-5 T3
    and
                                d12 = 57.7 - 0.118 T
    
    where d12 is the correction for an air-CO2 mixture in units of ml mol-1 (Weiss, 1974).
    
    The calculation for the fugacity at SST as measured by the thermosalinograph 
    involves a temperature correction term for the increase of fCO2 due to heating of the 
    water from passing through the pump and through 5 cm ID Teflon sleeved stainless steel 
    tubing within the ship.  The water in the equilibrator is typically 0.2 to 0.3°C warmer than 
    sea surface temperature. At the Southern end of the transect when SST ≈ 2-5 ˚C the 
    difference was as much as 1 ˚C. The empirical temperature correction from equilibrator 
    temperature to SST is outlined in Weiss et al. (1982).
    
            dln(fCO2)=(teq-SST)(0.03107-2.7851 10-4 teq - 1.839 10-3 ln(fCO2eq))
    
    where 
    
        dln(fCO2) is the difference between the natural logarithm of the fugacity at teq and 
        SST, and teq is the equilibrator temperature in ˚C.
    
    The precision of the measurements is estimated at 0.2 ppm based on repetitive measurements 
    of marine air.  The accuracy of the air values is believed to be better than 0.5 ppm based 
    on comparisons with flask samples on tests performed in 1995.Equilibrator headspace values 
    are believed to be accurate to within 2 µatm.  The greater uncertainty is attributed to the 
    equilibration efficiency.  Outside the calibration range of the standards, an accuracy of 5 
    ppm (µatm) is assigned based on laboratory tests where the calibrated IR output is compared 
    with standards of known concentration outside the calibration range.
    
    PROBLEMS:
    
    At the start of the cruise, from 1/14/05 17:04 (UTC) until 1/16/05 15:50 (UTC), Problems with 
    the electrical power caused the program to run out of sync and the equilibrator thermistor to 
    give bad readings.  Connecting the instrument to an uninterruptible power supply (UPS) 
    eliminated the problem.  A similar problem surfaced in the spring of 2004 at the end of a 
    cruise when the USF group removed their equipment. We suspect that some electrical 
    interference is caused by the USF instrumentation, although our system was on the ship's UPS 
    and their water bath was on a different ("dirty power") outlet.
    
    
    REFERENCES
    
    DOE, 1994:  Handbook of methods for the analysis of the various parameters of the 
        carbon dioxide system in sea water. Version 2, A.G. Dickson and C. Goyet (eds.), 
        ORNL/CDIAC-74.
    
    Feely, R.A., R. Wanninkhof, H.B. Milburn, C.E. Cosca, M. Stapp, and P.P. Murphy, 
        1998: A new automated underway system for making high precision pCO2 
        measurements onboard research ships.  Analytica Chim. Acta, v. 377, pp. 185-191.
    
    Ho, D.T., R. Wanninkhof, J. Masters, R.A. Feely, and C.E. Cosca, 1997:  Measurement 
        of underway fCO2 in the eastern equatorial Pacific on NOAA ships Baldrige and 
        Discoverer.  NOAA Data Report, ERL AOML-30, 52 pp.
    
    Masters, J., R. Wanninkhof, D. Ho, M. Steckley, R. Feely, and C. Cosca, 1997: 
        Continuous air and surface seawater measurements of fCO2 on board the NOAA ship 
        Malcolm Baldrige around the world cruise in 1995.  NOAA Data Report, ERL 
        AOML-31, 80 pp.
        
    Wanninkhof, R., and K. Thoning, 1993: Measurement of fugacity of CO2 in surface water 
        using continuous and discrete sampling methods. Mar. Chem., v. 44, no. 2-4, pp.
        189-205.
    
    Weiss, R.F., 1970:  The solubility of nitrogen, oxygen, and argon in water and seawater.
        Deep-Sea Res., v. 17, pp. 721-735.
        
    Weiss, R.F., 1974:  Carbon dioxide in water and seawater: The solubility of a non-ideal 
        gas.  Mar. Chem., v. 2, pp. 203-215.
        
    Weiss, R.F., R.A. Jahnke, and C.D. Keeling, 1982:  Seasonal effects of temperature and 
        salinity on the partial pressure of CO2 in seawater. Nature, v. 300, pp. 511-513.
        
    
    
    2.7.3.   SAMI UNDERWAY pCO2 MEASUREMENT SYSTEM
    
             Principal Investigator: Michael DeGrandpre, Chemistry Department
                                       University of Montana, Missoula, MT  59812
                                       Michael.DeGrandpre@umontana.edu
                                       (NOAA grant NA04OAR4310092)
             Shipboard analyst:      Stacy Smith, Chemistry Department
                                       University of Montana, Missoula, MT  59812
                                       Stacy.Smith@mso.umt.edu
    
    
    EQUIPMENT: SAMI-CO2 SYSTEM (SUBMERSIBLE AUTONOMOUS MOORED INSTRUMENT FOR CO2):
    
    The SAMI is a chemical sensor designed to measure pCO2; the technology is based upon CO2 
    equilibration with a pH sensitive indicator (DeGrandpre et al., 1999, 2000). The instrument 
    is commercially available from Sunburst Sensors (Missoula, MT).  SAMI's components include 
    the indicator, pump, valve, membrane equilibrator, optical cell and detector.
    
    Briefly, 50 µl of the indicator bromothymol blue (BTB) is pumped through a coiled CO2-
    permeable silicone rubber membrane into a custom-made optical cell. A tungsten filament lamp 
    and fiber optic cable direct light into the optical cell, which has a 5 µl volume and path 
    length of 0.75 cm. Another fiber optic cable guides light out of the cell to a 1X3 fiber 
    optic splitter. The splitter ends are each connected to a port in a photodiode detector. Each 
    port is covered with interference filters, one at each of the following wavelengths, 434 nm 
    (acid), 620 nm (base) and 740 nm (reference). The blank solution is deionized water. Data is 
    acquired using the TFX-11 data logger (Onset Computers).
    
    RATIONALE FOR SHIPBOARD ANALYSIS:
    
    The SAMI is usually deployed on ocean moorings at varying depths for time periods of up to 
    one year. Since its inception in the commercial realm, few intensive intercomparisons have 
    been made with the conventionally-used equilibrator-infrared method.  The goal of underway 
    testing is to provide extensive equilibrator-IR data to evaluate the SAMI-CO2's precision, 
    accuracy, time response and temperature coefficient.   Shipboard testing is also being used 
    to evaluate different SAMI designs and to determine the potential for using SAMIs as a 
    shipboard underway system on research vessels and volunteer observing ships.  
    
    For the A16 cruise in 2005, the SAMI-CO2s (2) were fitted with flow-through chambers and 
    connected to the same seawater line as the equilibrator-IR.  The equilibrator-IR was operated 
    by Rik Wanninkhof's group from NOAA AOML.   Two SAMIs were used for this study, an older 
    model SAMI 16 and the newly built SAMI 48. The SAMIs took measurements every 15 minutes. 
    Water blank measurements were taken every three days.
    
    RESULTS:
    
    Data collected from the two SAMIs and equilibrator-IR are shown in Figure 2.5.  One can see 
    from these results that SAMI 48 had ~10 (atm offset until the end of the cruise when the 
    offset approached 20 (atm.  SAMI 16 matched more closely with the equilibrator-IR except 
    during some periods when the pump failed (after Year Day ~12, data not shown) and or did not 
    pump efficiently (Year Day 25-30).  One weakness in the SAMI technology is the Lee solenoid 
    pump.  Factors leading to pump failures are backpressure and general wear on pumps.  As 
    stated above, the SAMI periodically records the transmittance through a blank solution.  If 
    the pump does not flush the indicator from the optical cell, poor blank readings are obtained 
    which subsequently affect all pCO2 measurements after the blank.  Although we are still 
    evaluating the results, poor flushing of the blank appears to be the source of the large 
    offset between YD 25 and 30 (SAMI 16). 
    
    Two other factors may have contributed to the observed pCO2 offsets between the SAMIs and the 
    equilibrator-IR. First, during the south to north cruise transect the temperature increased 
    from ~1 to 27oC.  This large change leads to a large temperature correction from the 
    calibration temperature (18oC).  Small errors in the temperature coefficient could lead to 
    ~5-10 (atm errors in the calculated pCO2, based on our recent calculations.  We are 
    completing a thorough re-evaluation of the SAMI temperature response based on these results.  
    Secondly, we have found a variable offset in our calibration based on intercomparisons with 
    NOAA CMDL standards that we purchased after completion of the A16 cruise.  We are now 
    requantifying the offset to determine the most accurate correction to the A16 data. 
    
    
    Figure 2.5.  Comparison of the results from the two SAMIs and the underway pCO2 system (Licor).  
                 See text for discussion. 
    
    
    REFRENCES
    
    DeGrandpre, M.D., M.M. Baehr, and T.R. Hammar, 1999: Calibration-free optical 
        chemical sensors.  Anal.Chem., v. 71, pp. 1152-1159.
    
    DeGrandpre, M.D., M.M. Baehr, and T.R. Hammar, 2000: Development of an optical 
        chemical sensor for oceanographic applications: The Submersible Autonomous 
        Moored Instrument for Seawater CO2. In Chemical Sensor in Oceanography, M.
    
    Varney (ed.). Gordon and Breach Publ., Amsterdam, pp. 123-141.
    
    
    2.7.4.  UNDERWAY SPECTROPHOTOMETRIC MEASUREMENTS OF pCO2, TCO2, AND pH
     
            Principal Investigator: Robert H. Byrne, College of Marine Science
                                      University of South Florida, 140 7th Avenue South
                                      St. Petersburg, FL 33701
                                      byrne@marine.usf.edu
            Shipboard Analysts:     Zhaohui Aleck Wang, Research Associate
                                      College of Marine Science, University of South Florida
                                      140 7th Avenue South, St. Petersburg, FL 33701
                                      awang@seas.marine.usf.edu
                                    Brittany Doupnik, Graduate Student
                                      College of Marine Science, University of South Florida
                                      140 7th Avenue South, St. Petersburg, FL 33701
                                      bdoupnik@marine.usf.edu
            Data Reduction:         Zhaohui Aleck Wang
    
    
    EQUIPMENT AND ANALYTICAL TECHNIQUES: UNDERWAY CO2 SYSTEM, USF:
    
    As part of the USF instrumental development effort, the USF automated underway CO2 system was 
    tested to simultaneously measure surface sea water pCO2, TCO2, pH, and air XCO2. The 
    resulting data can then be compared to measurements either from the AOML underway LiCOR pCO2 
    system (surface sea water pCO2 and air XCO2) or discrete surface sampling (surface sea water 
    pH and TCO2) to evaluate performance. 
    
    The system consists of three sea water channels (surface sea water pCO2, TCO2, and pH) and an 
    air channel (atmospheric XCO2). All measurements (four channels) are based on the same 
    spectrophotometric principles. The system can operate continuously with a sample period of 
    around 9 minutes.
    
    Spectrophotometric pH measurements are based on the method described in Clayton and Byrne 
    (1993), but use thymol blue as the pH indicator (Yao and Byrne, 2001). Sea water samples are 
    directly injected with thymol blue (1 mM) and changes of absorbances are monitored by a 
    spectrophotometer.
    
    The method for sea water TCO2 measurements is based on Byrne et al. (2002), while sea water 
    pCO2 and air XCO2 measurements are similar to those described in Wang et al. (2003) 
    (significant differences will be reported elsewhere). In these measurements, Teflon AF 2400 
    (DuPont) is used as both a CO2 permeable membrane and a long liquid-core waveguide (LCW). For 
    the pCO2 and XCO2 measurements, phenol red (2 µM) is used as the indicator, while Bromcresol 
    purple (2 µM) is used as the indicator in TCO2 measurements after sea water samples are 
    acidified. During each measurement, the indicator solution in each of three channels is 
    motionless inside the LCW. The sea water or air samples are directed to flow outside the LCW. 
    After CO2 molecules equilibrate through LCW, the internal indicator solution changes its 
    equilibrium pH. At equilibrium, absorbances are recorded by spectrophotometers.
    
    In each of four channels, three wavelengths are chosen for measurement of absorbances. Two 
    wavelengths assess the absorbance peaks of acid and base forms of the indicator, while a 
    third wavelength serves as a reference wavelength. Absorbances vary at the acid and base 
    wavelengths in response to pH changes, but not at the reference wavelength. Absorbance ratios 
    between acid and base wavelengths are calculated, and used to evaluate CO2 system parameters. 
    The wavelengths chosen for the four channels are listed in Table 2.15.
    
    
    Table 2.15.  Wavelengths used for spectrophotometric determination of inorganic carbon 
                 species.
    
      =========================================================================================
      Channel         Indicator          Acid Wavelength  Base Wavelength  Reference Wavelength
      -----------------------------------------------------------------------------------------
      Sea water pCO2  Phenol red             434 nm           558 nm             700 nm
      Air XCO2        Phenol red             434 nm           558 nm             700 nm
      TCO2            Bromcresol purple      432 nm           589 nm             700 nm
      pH              Thymol blue            435 nm           596 nm             730 nm
      -----------------------------------------------------------------------------------------
      
    
    Four Ocean Optic 2000 spectrophotometers are used to detect the light signals of the four 
    channels. Lamps, spectrophotometers, and detecting channels are connected through optic 
    fibers. The light source of each channel is custom-made with blue and IR glass filters in 
    order to balance the signals at the acid and base wavelengths.
    
    Indicator and reference solutions for all measurements are stored in aluminum bags and pumped 
    through separate lines into their respective channels by digital peristaltic pumps. Surface 
    sea water is pumped on board by a shipboard pumping system. It first flows through a Sea Bird 
    CTD that records salinity and temperature. Sea water samples are then pumped through three sea 
    water channels (pCO2, TCO2, and pH). Before entering the TCO2 channel, sea water samples are 
    acidified with ~3 M HCl using another peristaltic pump. The mixing ratio is approximately 
    ~1000 (sea water to HCl). An in-line mixing coil is used to facilitate mixing. Thymol blue is 
    mixed with sea water samples for pH measurement with a mixing ratio of ~800 (sea water to 
    thymol blue). An in-line mixing coil is also used in this case. Air samples are drawn from a 
    shipboard air sample line set up for the LiCOR IR underway pCO2 measurement. The air flow rate 
    is controlled at 20 ~ 30 ml/min using a gas flow controller. Atmospheric pressure is recorded 
    by a barometer.
    
    All channels are thermostated in a Lauda E100 water bath that is set to 25 ± 0.1°C. All 
    samples, reference and indicator solutions are also temperature pre-equilibrated in the water 
    bath to 25°C through glass or copper coils. All measurements, as well as calibrations, are 
    taken at this temperature.
    
    All units of the system are connected to a custom-made electronic motherboard and controlled 
    by a laptop computer. The program run cycles to operate the CO2 system continuously. The time 
    required for each measurement cycle varies depending on the equilibration time (5 to 7 
    minutes) and flushing time for the indicator/reference solution and samples (2 to 3 minutes). 
    The following sequence is taken during a measurement cycle:
    
      1. Flush pH reference (sea water samples without indicator solution).
      2. Flush reference for pCO2, XCO2, and TCO2.
      3. Read and store reference readings.
      4. Flush indicator solutions for pCO2, XCO2, and TCO2, mix thymol blue with 
         sea water samples (pH), and acidify TCO2 samples.
      5. pCO2, XCO2, TCO2 equilibration (5 - 7 minutes).
      6. Read and store measurements.
      7. Repeat step 4-6 four times.
      8. End of one measurement cycle and repeat from the beginning.
    
    During measurements, the sea water and air samples are continuously flowing through the 
    channels.
    
    STANDARDS:
    
    pCO2 and XCO2 are calibrated every few days during the cruise against four standard CO2 
    gases (315.25, 357.18, 380.98, and 411.42 [or 531.98] ppm) provided by AOML. TCO2 is 
    calibrated using a Certified Reference Material (CRM) every few days. pH is internally 
    calibrated in the spectrophotometric method and does not need calibration onboard.
    
    DATA PROCESSING::
    
    The absorbance ratio R for each measurement (all four parameters) is given as:
    
                                     R = (A2-Aref)/(A1-Aref)
    
    where A1 and A2 are the peak absorbance at acid and base wavelengths, respectively; and Aref 
    is the absorbance at the reference wavelength. For all four parameters measured, R is used to 
    calculate pH via the following equation:
    
                                         R-E2(HA)/E1(HA)
                            pH=log(---------------------------)-pKa2
                                   E2(A)/E1(HA)-R•E1(A)/E1(HA)
    
    where E1(HA) and E2(HA) are the molar absorptivities of the acid form (HA-) of indicator at 
    two peak-absorbance wavelengths; (1(A) and (2(A) are the molar absorptivities of the A2- 
    (fully unprotonated) form of indicator at two peak-absorbance wavelengths; and Ka2 is the 
    second dissociation constant of the indicator used. Molar absorptivities and Ka2 for all 
    indicators are determined in the laboratory at 25°C before the cruise. They are treated as 
    constants since we only measure samples at 25°C.
    
    From the above equations, pH can be directly calculated from absorbance ratios and pCO2/XCO2 
    and TCO2 are calculated by referencing R to their respective standards.
    
    Our sea water pCO2 measurement reflects pCO2 at 25°C with 100% water vapor content. It can be 
    corrected for temperature and water vapor to compare with LiCOR underway pCO2 measurement.
    The precisions of all parameters measured, estimated by replicate measurements, are given as follows:
    
                                     pH          ± 0.001
                                     XCO2/pCO2   ± 1 uatm
                                     TCO2        ± 3 µmol/kg
    
    Details on the mathematical treatment and calculation procedure are being prepared for publication.
    
    PROBLEMS:
    
    Due to the huge temperature difference between surface sea water and the water bath, a 10 
    foot pre-heating Tygon tube was added to the sea water sample line and resided in the water 
    bath during the first three weeks of the cruise. Over time, organisms grew inside this tube 
    and contaminated the sea water samples. This problem was identified on February 03, 2005 and 
    measures were taken to prevent contamination thereafter.
    
    The air channel experienced a drift problem throughout the cruise. After each calibration of 
    the air channel, the air XCO2 readings drifted away from the LiCOR air XCO2 readings within a 
    few days of continuous measurement. The drift seemed to stop thereafter, and the difference 
    between the two systems was approximately 10 ppm. Many measures were taken to identify the 
    problem. Unfortunately, we did not resolve the issue during the cruise. 
    
    
    REFERENCES
    
    Byrne, R.H., L. Xuewu, E. Kaltenbacher, and K. Sell, 2002: Spectrophotometric 
        measurement of total inorganic carbon in aqueous solutions using a liquid core 
        waveguide.  Anal. Chim. Acta, v. 451, pp. 221-229.
    
    Clayton, T.D., and R.H. Byrne, 1993: Spectrophotometric seawater pH measurements: 
        Total hydrogen ion concentration scale calibration of m-cresol purple and at-sea 
        results.  Deep-Sea Res., v. 40, pp. 2315-2329.
    
    Wang, Z.A., W. Cai, Y. Wang, and B.L. Upchurch, 2003: A long pathlength liquid-core 
        waveguide sensor for real-time pCO2 measurements at sea. Mar. Chem., v. 84, 
        pp. 73-84.
    
    Yao, W. and R.H. Byrne, 2001: Spectrophotometric determination of freshwater pH 
        using bromocresol purple and phenol red. Environ. Sci. Technol., v. 35, pp. 1197-
        1201.
    
    
    2.8.  AEROSOL SAMPLING 
    
          Principal Investigator: Anne M. Johansen, Central Washington University
                                    Department of Chemistry, 400 East University Way
                                    Ellensburg, WA 98926-7539
                                    Phone:  (509) 963-2164; Fax:  (509) 963-1050
                                    johansea@cwu.edu
          Sampler:                Matt Lenington
                                    Central Washington University
                                    Phone: (509) 963-1086
                                    leningtm@cwu.edu
    
    AEROSOL SAMPLING SETUP:
    
    Atmospheric aerosols and acidic gases were collected with two types of collectors: 1) A high 
    volume cascade impactor (ChemVol Model 2400, Rupprecht and Patashnik) to separate aerosols 
    into four size fractions (large particles (>10 um aerodynamic diameter (AD)), coarse particles 
    (10 to 1 um AD), fine particles (1 to 0.1 um AD), and ultrafine particles (< 0.1 um AD)), and 
    2) Two low volume collectors to collect total suspended particulates (TSP) and acidic gaseous 
    species in a filter pack configuration.  On the first part of the leg, to approximately 30°S, 
    these collectors were located on the O3 deck forward of the captain's cabin to avoid excessive 
    seaspray from reaching the collector.  However, this location turned out to be unsatisfactory 
    due to eddying of the air and once the seas got milder (north of 30°S) the whole setup was 
    moved forward and down to the forward edge of the O2 deck to assure the collection of 
    uncontaminated air.
    
    The vacuum pumps for the collectors were controlled by a datalogger through a series of relay 
    boxes whereby they were automatically shut off when rain was sensed with a rain sensor or when 
    the wind speed and direction were unfavorable as determined by a weather vane; the low limit 
    wind speed cut-off was 0.2 m s-1 and, while the wind direction varied throughout the trip, a 
    guideline of 60 degrees in either direction off the bow was used to set the limits.
    
    Flow rates on the high volume collector were determined by measuring the pressure drop across 
    a critical orifice.  A valve was used to adjust the flowrate to 760+-5% L min-1 to ensure 
    correct size fractionation.  The flow rate for the low volume collectors was fixed with a 
    critical orifice to approximately  12 L min-1 and checked with a flowmeter.  
    
    Although the goal was to collect daily samples, collection periods had to be adjusted due to 
    two factors: low ambient concentrations of particulates in the southern part of the Atlantic 
    Ocean and the reduced collection times due to rain (or heavy fog) and the wind direction being 
    out of sector.  A collection time of 30 hours per set of filters was used as a guideline to 
    collect enough material to ensure analysis above detection limits. Typically, sample change 
    occurred at dawn.
    
    SUBSTRATE HANDLING AND STORAGE:
    
    All sample handling was carried out in a laminar flow hood with HEPA filtration and all 
    substrates had been precleaned in lab following established procedures.  For the high volume 
    collector flat segments of polyurethane foam (PUF) were used for the impaction of particles in 
    the three larger size fractions. These are rings of PUF of varying width, depending on the 
    size fraction.  The outer diameter is approximately 17 cm.  The final collection stage (i.e., 
    for the ultrafine particles) is based on filtration through a multilayer polypropylene filter 
    of approximately 17 cm diameter.  Storage of these substrates required cutting into segments 
    that could be placed in precleaned polystyrene Petri dishes of 15 and 9 cm diameter.  Cutting 
    was performed with ceramic scissors or ceramic exacto knives on a sheet of Teflon.  For the 
    low volume collectors, a 47 mm diameter Teflon membrane filter was used to collect particles 
    followed by two carbonate impregnated paper filters in series to trap acidic gaseous species.  
    These filters were stored in 47 mm polystyrene Petri dishes.  All Petri Dishes were sealed 
    with Teflon tape, doubly bagged and stored in the freezer.  
    
    Samples were sent to the lab overnight on ice in coolers and are stored in a freezer until 
    analysis.  
    
    ANALYSIS:
    
    16 sets of samples were collected.  Since each sample set consists of 4 high volume and 6 low 
    volume substrates, overall there are 16x10 = 160 aerosol samples.  In addition, 5 sets of 
    field blanks were obtained, amounting to a total of 210 samples that will be analyzed with the 
    following procedures.
    
    Chemical analysis on all high volume size fractions will consist of iron speciation with long 
    pathlength UV-Vis, trace metals with ICP-MS, and anions and cations with IC.  The Teflon 
    filters from the low volume collectors will be weighed (they were preweighed in a microbalance 
    before the trip) and analyzed for trace metals and anions and cations.  The carbonate 
    impregnated filters will be analyzed for anions of the corresponding acidic gases. These 
    analyses are expected to be carried out within a year.  Subsequently, data will be analyzed 
    statistically with principal component and linear regression analyses and interpreted in 
    conjunction with air mass trajectories computed with HYSPLIT.
    
    Furthermore, during this cruise, blue agar plates were inoculated with extracts of filter from 
    10 different samples sections in an attempt to look for siderophore producing microorganisms 
    in the remote marine atmosphere.  The blue plates did turn orange for most of the inoculations 
    thus indicating the production of siderophores.  As of now (Aug 05) these organisms have been 
    further cultured and are being characterized.
    
    This study is part of a project (NSF-ATM 0137891) to further elucidate mechanisms that 
    influence iron speciation, and thus iron bioavailability, in aerosol particles over the remote 
    open oceans.  
    
    
    
    CCHDO DATA PROCESSING NOTES

        Date      Contact     Data Type        Data Status  Summary
        --------  ----------  ---------------  ---------------------------------------------------
        07/27/05  Wanninkhof  CTD/BTL/SUM      Submitted preliminary data
                  Most of our data can be found on [our website].  The part that is missing is the 
                  underway data that I will post/link shortly.
                  
                  The data on the website is the data that everyone provided Frank before they 
                  left the ship.  Its needs to undergo final QC and inclusion of metadata.  A 
                  comprehensive cruise report which will serve as the source of metadata for much 
                  of the measurements was, coincidentally, sent to all participants and PIs this 
                  morning.  It will be placed on the website  in the third week of August.
                  
                  As you know, the QC of bottle data is an iterative procedure that works best 
                  when done in an appropriate sequence with frequent updates.  On the ship we 
                  discussed the possibility that this could be done through the database that 
                  Frank Delahoyde created and maintained.  I have not followed up on with Frank 
                  and Jim [Swift] how this would be done and who would do it this but will do so 
                  shortly.
                  
                  We will not be able to provide the final bottle data by the end of August but 
                  feel confident that it will be done by early winter.
                            
        07/28/05  Diggs       Cruise Report    Submitted
                  Here is the most recent cruise report for A16S  2005.
                            
        09/22/05  Kappa       Cruise Report    Converted prelim report to pdf
                  emailed it to DMB to put online
                            
        10/04/05  Anderson    CFCs             Website Updated: CFCs online
                  Merged the final cfc-11, cfc-12, cfc-113, and ccl4 submitted by Mark Warner on 
                  Sept. 27, 2005, into the online file 20050921CCHDOSIODBK.  There were  no 
                  apparent problems.
                            
        10/07/05  Bartolacci  CTD              Website Updated: all data online except CTD NetCDF
                  All but the netCDF CTD files are now up and linked to the web for the a16s 2005 
                  cruise.  PDF cruise doc is up as well and it looks like Sarilee was able to put 
                  the newly merged bottle file(s) online.
                            
        12/08/05  Wanninkhof  Cruise Report    Submitted; downloaded from NOAA website
                  A detailed cruise report can be found at
                  http://www.aoml.noaa.gov/ocd/gcc/a16s/>http://www.aoml.noaa.gov/ocd/gcc/a16s/
                  
        12/08/05  Wanninkhof  CO2  Submitted   DIC, TAlk, pCO2 discrete, pH
                  In the following message (just to Steve and Alex), I'm sending the final carbon 
                  system parameters: DIC, TAlk, pCO2 discrete, and pH bottle data from the repeat 
                  hydrography cruise A16S.
                  This includes the DIC and pCO2 data from AOML(Wanninkhof), and TAlk and pH data 
                  from RSMAS (Millero).  The data has been extensively quality controlled and, in 
                  my view, is the best 4-parameter C-system dataset ever produced at sea.
                  
                  We'll submit the underway pCO2 data to Alex next week.
                  
                  I have attached a summary of status of final data submission. Several groups 
                  have their final bottle data ready but have not submitted it yet. I'll send an 
                  inspirational message to all PI's next week to do so.
                  
        Date      Contact     Data Type        Data Status  Summary
        --------  ----------  ---------------  ---------------------------------------------------
        01/30/06  Bishop      TRANSMISSOMETER  Submitted raw data only
                  A16N_2003 & A16S_2005 wil be completed together  All I can do is work forward on 
                  this. A16N and A16S data will be completed together, after Ocean Sciences. The 
                  raw data are on line at SIO. 
                            
        05/19/06  Kozyr       DOC  Submitted   Data are Final, not online yet
                  On March 15 this year I submitted the final DOC data for repeat sections 
                  P02_2004 and A16S_2005 I received from Dennis Hansell of RSMAS. I don't see 
                  these data have been merged in the hydrographic file at CCHDO for each above 
                  cruise yet. Could you please tell me the DOC data merging status at CCHDO and 
                  let me know as soon as these data will be merged.
                            
        05/22/06  Kozyr       DOC              Submitted
                  I submitted the DOC data from P02_2004 and A16N_2005 using CCHDO submission 
                  page. I received the A20 and A22 DOC data files from you, so I guess you have 
                  these files, but I did not see the DOC numbers for these cruises were merged at 
                  CCHDO yet.
                  
                  Here are attached 3 files for DOC data from P02_2004, A16N_2003, and A16S_2005 
                  cruises. Please, let me know if you received these files OK and when are you 
                  planning to merge these data.
    
        08/15/06  Kappa       Cruise Report    Updated, added text version & these processing notes
    
    
    
