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CRUISE REPORT: P16N_2006
(Updated: 26 JUL 20017)


A.  HIGHLIGHTS 

A.1. WHP CRUISE SUMMARY INFORMATION

             WOCE section designation:  P16N_2006
    Expedition designation (ExpoCode):  325020060213
                Chief Scientist Leg 1:  Christopher L. Sabine/NOAA-PMEL 
                Chief Scientist Leg 2:  Richard A. Feely/NOAA-PMEL 
             Co-Chief Scientist Leg 1:  Erica Key/RSMAS 
             Co-Chief Scientist Leg 2:  Sabine Mecking/UW-APL
                          Dates Leg 1:  13 FEB 2006 -  3 MAR 2006 
                          Dates Leg 2:  10 MAR 2006 - 30 MAR 2006
                                 Ship:  R/V Thomas G. Thompson
                  Ports of call Leg 1:  Papeete, Tahiti - Honolulu, HI USA 
                  Ports of call Leg 2:  Honolulu, HI - Kodiak, AK USA
             Number of stations Leg 1:  43
             Number of stations Leg 2:  41
                                                21°N
Stations' Geographic boundaries Leg 1:  150°W           152°W
                                                17°S

                                                56°17'N
Stations' Geographic boundaries Leg 2:  152°W           153°13'W
                                                22°N
   Floats and drifters deployed Leg 1:  0
   Floats and drifters deployed Leg 2:  8 APEX floats deployed 
       Moorings deployed or recovered:  0
                 Contributing Authors:  none cited



TABLE OF CONTENTS LEG 1
 
SUMMARY           
INTRODUCTION          
DESCRIPTION OF MEASUREMENTS FROM FULL-DEPTH PROFILES   
    1. CTD/Hydrographic Measurements Program      
    2. LADCP                   
    3. Salinity Measurements   
    4. Oxygen Measurements     
    5. Nutrient Measurements   
    6. CFC Measurements        
    7. DIC Measurements        
    8. TAlk Measurements       
    9. pH Discrete Measurements 
   10. Discrete pCO2          
   11. Carbon/Oxygen Isotopes 
   12. Dissolved Organic Carbon/Dissolved Organic Carbon 
   13. CDOM, chlorophyll, bacterial suite                
   14. Helium-tritium          
DESCRIPTION OF MEASUREMENTS FROM TRACE METAL CASTS    
DESCRIPTION OF OPTICAL CASTS        
DESCRIPTION OF UNDERWAY MEASUREMENTS 
    1. Underway DIC/pCO2/pH   
    2. Underway pCO2          
    3. Underway Fluorometer   
    4. Meteorological Measurements 
    5. Aerosol Measurements        
REFERENCES           
APPENDIX: ADDENDUM TO CTD REPORT




                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson




SUMMARY 

The R/V Thomas G. Thompson conducted a hydrographic survey in the Central 
Pacific Ocean, nominally along 151°W between 17°S and 21°N, from 13 February 
to 3 March 2006. Thirty-four scientists from 11 academic institutions and two 
NOAA laboratories participated in the cruise. Full-depth CTD/rosette/LADCP 
casts were collected every 60 nautical miles. Water samples were collected at 
34 depths at each station and analyzed for salinity, nutrients, dissolved 
oxygen, four inorganic carbon parameters, radiocarbon, dissolved organic 
matter, colored dissolved organic carbon, chlorofluorocarbons, helium/tritium, 
oxygen isotopes, chlorophyll, and a suite of bacterial measurements. Trace 
metal casts to 1000m were conducted at approximately every other station. 
Optical profiles were collected once each day. Near surface seawater and 
atmospheric measurements were also made along the cruise track. The last of the 
43 stations were completed on Thursday 2 March, 2006. No major problems were 
encountered on the cruise and all major cruise objectives were achieved.  

INTRODUCTION 

The P16N cruise is a meridional hydrographic section nominally along 151°W in 
the Pacific Ocean. This cruise is part of a decadal series of repeat 
hydrography sections jointly funded by NOAA-OGP and NSF-OCE as part of the 
CLIVAR/CO2 Repeat Hydrography Program <http://ushydro.ucsd.edu/>. The repeat 
hydrography program focuses on the need to monitor inventories of CO2, heat and 
freshwater and their transports in the ocean. Earlier programs under WOCE and 
JGOFS have provided baseline observational fields for these parameters. The new 
measurements will reveal much about the changing patterns on decadal scales. 
The program will serve as a structure for assessing changes in the ocean's 
biogeochemical cycle in response to natural and/or man-induced activity. 

Thirty-four scientists from 11 academic institutions and two NOAA research 
laboratories participated in a cruise covering the central portion of this line 
from Tahiti to Hawaii (Table 1). Leg 2 of this cruise will run from Hawaii to 
Alaska immediately after leg 1. The R/V Thomas G. Thompson departed Papeete, 
Tahiti on 3 March 2006 for the beginning of leg 1. The first station was at 
17°S, 150°W. This station and the next station at 16°S, 150°W were repeats of 
two stations run the previous year as part of P16S. The ship then proceeded 
north conducting a full- depth CTD/rosette/LADCP cast every 60 nautical miles 
to 21°N, 152°W. Station spacing was closed to 30 miles between 2°S and 2°N. 
Thirty-four 12L Niskin type bottles were used to collect water samples from 
throughout the water column at each station. Each Niskin was sub-sampled on 
deck for a variety of analyses. Twenty projects were represented on leg 1 of 
the cruise (see Table 1). A 1000 m trace metal cast was conducted at every 
other station, except between 2°S and 1°N where a profile was collected at 
every station, for a total of 23 trace metal casts. The trace metal casts were 
conducted at approximately the same locations as the primary profiles and were 
either before or after the full-depth casts depending on time of day. One 
optical profile was collected each day on stations that occurred between 10:00 
and 14:00 local time. Near surface seawater (temperature, salinity, pCO2, ADCP) 
and atmospheric measurements (CO2, CFCs, aerosols) were also made along the 
cruise track (Table 1). The last of 43 stations was completed on Thursday 2 
March, 2006. The cruise ended in Honolulu, HI on 3 March, 2006.



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



TABLE 1. Projects and participants on P16N leg 1 
==================================================================================
Reseach Project                PI's                      Leg 1 Participant 
----------------------------------------------------------------------------------
Chief Scientist                                          Christopher Sabine (PMEL) 
Co-chief Scientist                                       Erica Key (RSMAS) 
Student Support                                          Sara Bender (Rutgers) 
   to Chief Scientist                                    Jessica Silver (UW) 
                                                         Jonathan Reum (UW) 
Data Management                Woody Sutherland(UCSD)    Frank Delahoyde (UCSD) 
CTD-Hydrography                Gregory Johnson(PMEL)     Kristy McTaggart (PMEL) 
                               Molly Beringer (AOML)     David Bitterman (AOML) 
                                                         Grant Rawson (CIMAS) 
LADCP                          Jules Hummon (UH)         Kevin Bartlett (UVIC) 
Oxygen Measurements            Chris Langdon(RSMAS)      George Berberian (CIMAS) 
Nutrients                      Calvin Mordy (PMEL)       Calvin Mordy (PMEL) 
                               Jia Zang (AOML)           Charlie Fisher (AOML) 
CFC Measurements               John Bullister (PMEL)     David Wisegarver (PMEL) 
                               Mark Warner (UW)          Eric Wisegarver (JISAO) 
DIC Measurements               Christopher Sabine (PMEL) Bob Castle (AOML) 
                               Rik Wanninkhof(AOML)      Alex Kozyr (ONRL) 
                                                         Richard Feely (PMEL)   
TA Measurements                Frank  Millero (RSMAS)    Ben West (RSMAS) 
                                                         Patrick Gibson (RSMAS) 
pH Discrete Measurements       Frank Millero (RSMAS)     Mike Trapp (RSMAS) 
                                                         Taylor Graham (RSMAS) 
pH Discrete Measurements       Robert Byrne (USF)        Renate Bernstein (USF) 
Discrete pCO2                  Rik Wanninkhof (AOML)     Kevin Sullivan (AOML) 
Underway DIC/pCO2/pH           Robert Byrne (USF)        Dr. Xuewu Liu (USF) 
Underway pCO2 Richard          Feely (PMEL)              David Wisegarver (PMEL) 
Underway fluorometer           Paul Falkowski (Rutgers)  Sara Bender (Rutgers) 
Carbon/Oxygen Isotopes         Ann McNichol (WHOI)       Josh Burton (WHOI) 
                                                         Paul Quay (UW)   
Dissolved Organic Carbon       Dennis Hansell(RSMAS)     Charlie Farmer (RSMAS) 
CDOM, CHLORO, bacterial suite  Dave Siegel (UCSB)        Norm Nelson (UCSB) 
CDOM fluorometer on rosette    Craig Carlson (UCSB)      Dave Menzies (UCSB) 
Helium-tritium                 Bill Jenkins (WHOI)       Kevin Cahill (WHOI) 
Trace Metals (seawater and     Chris Measures (UH)       Bill Landing (FSU) 
              aerosols)        Bill Landing (FSU)        Cliff Buck (FSU) 
                                                         Paul Hansard (FSU) 
                                                         Chris Measures (UH) 
                                                         Bill Hiscock (UH) 
Meteorological Measurements    Peter J. Minnett (RSMAS)  Erica Key (RSMAS) 
Transmissometer on rosette     Wilf Gardner (TAMU)       Dave Menzies (UCSB) 
  


                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



DESCRIPTION OF MEASUREMENTS FROM FULL-DEPTH PROFILES 
 

1.  CTD/HYDROGRAPHIC MEASUREMENTS PROGRAM 

The basic CTD/hydrographic measurements consisted of pressure, temperature, 
salinity, dissolved oxygen, transmissometer and fluorometer from CTD profiles. 
A total of 44 CTD/rosette casts were made (cast 25/1 was aborted) usually to 
within 10m of the bottom prior to cast 37/1, and up to 5200m of wire out 
subsequently. No major problems were encountered during the operation.  


1.1 WATER SAMPLING PACKAGE 

CTD/rosette casts were performed with a package consisting of a 36-bottle 
rosette frame (PMEL), a 36-place pylon (SBE32) and 34 12-liter Bullister 
bottles (PMEL). Two bottle positions on the rosette (2 & 36) were left vacant 
to accommodate the LADCP. Underwater electronic components consisted of a Sea-
Bird Electronics SBE9plus CTD (PMEL #315) with dual pumps, dual temperature 
(SBE3plus), dual conductivity (SBE4), dissolved oxygen (SBE43), transmissometer 
(Wetlabs), fluorometer (Wetlabs), load cell (PMEL), altimeter (Simrad), pinger 
(Benthos) and LADCP (RDI). 

The CTD was mounted vertically in an SBE CTD frame attached to a plate welded 
in the center of the rosette frame, under the pylon. The SBE4 conductivity and 
SBE3plus temperature sensors and their respective pumps were mounted vertically 
as recommended by SBE. Pump exhausts were attached to inside corners of the CTD 
cage and directed downward. The transmissometer was mounted horizontally and 
the fluorometer vertically, attached to a rigid plastic screen that did not 
impede water flow. The altimeter was mounted on the inside of the bottom frame 
ring. The RDI LADCP was mounted vertically on one side of the frame between the 
bottles and the CTD. Its battery pack was located on the opposite side of the 
frame, mounted on the bottom of the frame. 

The CTD also had a WetLabs UV fluorometer, which stimulates and measures 
fluorescence of CDOM. We were evaluating the use of this instrument to 
supplement or enhance bottle CDOM measurements, as bottle samples often do not 
have the depth resolution needed to resolve the observed strong near-surface 
gradients in CDOM concentration, and on cruises such as this we were not able 
to sample CDOM on every station. On four of the casts, the sensors were covered 
to quantify the background "dark" readings for calibration purposes. This 
fluorometer was ganged to a WetLabs C-star 660 nm 0.25m pathlength beam 
transmissometer belonging to Dr. Wilf Gardner, TAMU. 

The rosette system was suspended from a new UNOLS-standard three-conductor 
0.322" electro-mechanical sea cable. A second sea cable retermination was made 
after cast 1/2, and a third retermination after cast 25/1. The R/V Thompson's 
aft starboard-side Markey winch was used for all casts. Wire spooling problems 
developed during the up cast on 37/1 and the package was sent back down to 
correct it. This cast was the deepest to date and it was found that the next 
lower layer of wire on the drum had flat spots. The cause of these flat spots 
is currently being investigated. The rest of the casts on leg 1 were limited to 
a maximum wireout of 5200 m. Cast 25/1 was aborted at 4400m on the up cast due 
to a shorted sea-cable conductor. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



The deck watch prepared the rosette 10-15 minutes prior to each cast. The 
bottles were cocked and all valves, vents and lanyards were checked for proper 
orientation. Once stopped on station, the CTD was powered-up and the data 
acquisition system in the computer lab started when directed by the deck watch 
leader. The rosette was unstrapped from its tiedown location on deck. The 
pinger was activated and syringes were removed from the CTD intake ports. The 
winch operator was directed by the deck watch leader to raise the package, the 
squirt boom and rosette were extended outboard and the package quickly lowered 
into the water. The package was lowered to 10 meters, by which time the sensor 
pumps had turned on. The winch operator was then directed to bring the package 
back to the surface (0 winch wireout) and to begin the descent. 

Each rosette cast up to 37/1 was usually lowered to within 10 meters of the 
bottom, using both the pinger and altimeter to determine distance. Casts 38/1-
43/1 were made to within 10 meters of the bottom, or a maximum wire-out of 
5200m, whichever was less. During the up cast the winch operator was directed 
to stop the winch at each bottle trip depth. The CTD console operator waited 30 
seconds before tripping a bottle to insure the package wake had dissipated and 
the bottles were flushed, then an additional 15 seconds after bottle closure to 
insure that stable CTD comparison data had been acquired. Once a bottle had 
been closed, the deck watch leader was directed to haul in the package to the 
next bottle stop. Standard sampling depths were used throughout CLIVAR P16N. 
These standard depths were staggered every other station. 

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. The rosette was secured on deck under the block 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. No bottles were replaced on 
this cruise, but various parts of bottles were occasionally changed or 
repaired. 

Routine CTD maintenance included soaking the conductivity and DO sensors in 
fresh water between casts to maintain sensor stability and occasionally putting 
dilute Triton-X solution through the conductivity sensors to eliminate any 
accumulating biofilms. Rosette maintenance was performed on a regular basis. O-
rings were changed and lanyards repaired as necessary. 

Bottle maintenance was performed each day to insure proper closure and sealing. 
Valves were inspected for leaks and repaired or replaced as needed. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



1.2 UNDERWATER ELECTRONICS PACKAGES 

CTD data were collected with a SBE9plus CTD (PMEL #315). This instrument 
provided pressure, dual temperature (SBE3), dual conductivity (SBE4), dissolved 
oxygen (SBE43), fluorometer (Wetlabs), transmissometer (Wetlabs), load cell 
(PMEL) and altimeter (Simrad 807) channels. The CTD supplied a standard SBE-
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 into one pump circuit and secondary temperature 
and conductivity into the other. The sensors were deployed vertically. The 
primary temperature and conductivity sensors (T1 #03P-4341 and C1 #04-2887) 
were used for reported CTD temperatures and conductivities on all casts except 
cast 21/2, when the secondaries were used because of bio fouling of C1 on the 
down cast. The secondary temperature and conductivity sensors were used as 
calibration checks. 

The SBE9plus CTD was connected to the SBE32 24-place pylon providing for 
single- conductor sea cable operation. The sea cable armor was used for ground 
(return). Power to the SBE9plus CTD (and sensors), SBE32 pylon and Simrad 807 
altimeter was provided through the sea cable from the SBE11plus deck unit in 
the main lab. 


TABLE 2. P16N leg 1 underwater electronics 
====================================================================================
                                                                     Calibration
Sensor                                   Serial Number.           Date      Facility 
------------------------------------------------------------------------------------
Sea-Bird SBE32 36-place Carousel 
  Water Sampler                          N/A                      N/A        N/A 
Sea-Bird SBE9plus CTD                    PMEL #315                N/A        N/A 
Paroscientific Digiquartz Press. Sensor  S/N 0315                 25-MAY-05  SBE 
Sea-Bird SBE3plus Temp. Sensor           S/N 03P-4341 (Primary)   15-NOV-05  SBE 
Sea-Bird SBE3plus Temp. Sensor           S/N 03P-4335 (Secondary) 15-NOV-05  SBE 
Sea-Bird SBE4C Conductivity Sensor       S/N 04-2887 (Primary)    15-NOV-05  SBE 
Sea-Bird SBE4C Conductivity Sensor       S/N 04-3068 (Secondary)  15-NOV-05  SBE 
Sea-Bird SBE43 DO Sensor                 S/N 43-0664              29-NOV-05  SBE 
Wetlabs Fluorometer                      S/N FLCDRTD-428          N/A        N/A 
Wetlabs CST Transmissometer              S/N CST-327DR            N/A        N/A 
PMEL LoadCell                            S/N 1109                 N/A        N/A 
Simrad 807 Altimeter                     S/N 98110   
Benthos Pinger N/A   
RDI LADCP N/A   



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



1.3 NAVIGATION AND BATHYMETRY DATA ACQUISITION 

Navigation data were acquired at 1-second intervals from the ship's P-Code GPS 
receiver by a Linux system beginning February 13. No Bathymetric data were 
logged although the Ship's 12khz Knudsen echosounder system was run for much of 
the leg.  


1.4 CTD DATA ACQUISITION AND ROSETTE OPERATION 

The CTD data acquisition system consisted of an SBE-11plus (V2) deck unit and a 
networked generic PC workstation running Windows XP. 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 had 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 meters. The CTD sensor pumps were configured with a 30 
second startup delay, and were usually on by this time. The console operator 
checked the CTD data for proper sensor operation, waited an additional 60 
seconds for sensors to stablize, then instructed the winch operator to bring 
the package to the surface, pause for 10 seconds, and descend to a target depth 
(wire-out). The profiling rate was no more than 30m/min to 50m, no more than 
45m/min to 200m and no more than 60m/min deeper than 200m 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, pinger and bathymetric depth 
were all monitored to determine the distance of the package from the bottom, 
usually allowing a safe approach to within 10 meters. Bottles were closed on 
the up cast by operating an on-screen control. Bottles were tripped at least 30 
seconds after stopping at the trip location to allow the rosette wake to 
dissipate and the bottles to flush. The winch operator was instructed to 
proceed to the next bottle stop at least 15 seconds after closing bottles to 
insure that stable CTD data were associated with the trip. After the last 
bottle was closed, the console operator directed the deck watch to bring the 
rosette on deck. Once on deck, the console operator terminated the data 
acquisition, turned off the deck unit and assisted with rosette sampling. 


1.5 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 XP workstation were copied onto 
the Linux database and web server system, then processed to a 0.5 second time 
series. Bottle trip values were extracted and a 2 decibar 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 were also available for distribution). During and after the deployment 
the data were redundantly backed up to another Linux system. 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. T, S and theta-O2 comparisons were made between down and 
up casts as well as between groups of adjacent deployments. Vertical sections 
of measured and derived properties from sensor data were checked for 
consistency. Few CTD acquisition and processing problems were encountered 
during P16N. Reterminations were made after casts 1/2 and 25/1. Down cast noise 
in the primary conductivity channel led to using T2 and C2 sensors for reported 
values on 21/02. Cast 25/1 was aborted at 4400m on the up cast because of a 
seacable short. A total of 44 casts were made (including 1 aborted cast) using 
the 36-place CTD/LADCP rosette. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



1.6 CTD SENSOR LABORATORY AND SHIPBOARD CALIBRATIONS 

Laboratory calibrations of the CTD pressure, temperature, conductivity and 
dissolved oxygen sensors were performed prior to CLIVAR P16N. The calibration 
dates are listed in table 2. 

CTD #315 was used for all P16N casts. The CTD was deployed with all sensors and 
pumps aligned vertically, as recommended by SBE. The primary temperature and 
conductivity sensors (T1 & C1) were used for all reported CTD data on all casts 
except 21/2, the secondary sensors (T2 & C2) serving as calibration checks. In-
situ salinity and dissolved O2 check samples collected during each cast were 
used to calibrate the conductivity and dissolved O2 sensors. 

The Paroscientific Digiquartz pressure transducer (S/N 315) was calibrated in 
May 2005 at SBE. Calibration coefficients derived from the calibration were 
applied to raw pressures during each cast. Residual pressure offsets (the 
difference between the first and last submerged pressures) were examined to 
check for calibration shifts. All were < 0.7dbar, and the sensor exhibited < 
0.2 dbar offset shift over the period of use. No additional adjustments were 
made to the calculated pressures. 

A single primary temperature sensor (SBE 3, S/N 03P-4341) and secondary 
temperature sensor (SBE 3, S/N 03P-4335) served the entire cruise. Calibration 
coefficients derived from the pre-cruise calibrations were applied to raw 
primary and secondary temperatures during each cast. 

Calibration accuracy was monitored by comparing the primary and secondary 
temperatures at each rosette trip. Calibration accuracy was examined by 
tabulating T1-T2 over a range of pressures and temperatures (bottle trip 
locations) for each cast. No significant temperature or pressure slope was 
evident. These comparisons are summarized in figure 1. 

The 95% confidence limit for the mean of the differences is ±0.0068°C. The 
variance is relatively high in spite of the small spatial separation of the 
sensors (<0.5 meters) because of package wake effects. 

A single primary conductivity sensor (SBE 4, S/N 04-2887) and secondary 
conductivity sensor (SBE 4, S/N 04-3068) served the entire leg. 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 (calculated from bottle salinities) were used to derive 
conductivity corrections. To reduce the contamination of the comparisons by 
package wake, differences between primary and secondary temperature sensors 
were used as a metric of variability and used to qualify the comparisons. The 
coherence of this relationship is illustrated in figure 2. 

Neither of the sensors exhibited a secondary pressure response. The uncorrected 
comparison between the primary and secondary sensors is shown in figure 3, and 
between C2 and the bottle salinities in figure 4. Note that the bottle 
salinities were unusable for check sample purposes due to analytical 
temperature problems for casts 1/2-7/1. 

Since C2 showed no significant conductivity slope or offset relative to bottle 
conductivities, and since the comparison to C1 showed only minor (<0.001mS/cm) 
drift and shifts), C1 was calibrated to C2. No correction was made to C2. The 
comparison of the primary and secondary conductivity sensors by cast after 
applying shipboard corrections is summarized in figure 5. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



FIGURE 1. T1-T2 by station, 4σ rejected. 
FIGURE 2. C1-C2 by T1-T2, all points. 
FIGURE 3. Uncorrected C1 and C2 conductivity differences by cast  
          (-0.005°C<=T1-T2<=0.005°C). 
FIGURE 4. Uncorrected C2 residual differences with bottle conductivities by 
          cast (-0.005°C<=T1-T2<=0.005°C). 
FIGURE 5. Corrected C1 and C2 conductivity differences by cast  
          (-0.001°C<=T1-T2<=0.001°C). 


Salinity residuals after applying shipboard T1/C1 corrections are summarized in 
figures 6 and 7. Figures 6 and 7 represent estimates of the salinity accuracy 
on P16N. The 95% confidence limits are ±0.001 PSU relative to C2, and ±0.010 
PSU relative to the bottle salts. 


FIGURE 6. Corrected C1 and C2 salinity differences by cast  
          (-0.005°C<=T1-T2<=0.005°C). 
FIGURE 7. salinity residuals by cast (-0.005°C<=T1-T2<=0.005°C). 


A single SBE43 dissolved O2 (DO) sensor was used during this cruise (S/N 43-
0060). The sensor was plumbed into the primary T1/C1 pump circuit after C1. The 
DO sensors were calibrated to dissolved O2 check samples at bottle stops by 
calculating CTD dissolved O2 then minimizing the residuals using a non-linear 
least-squares fitting procedure. The fitting procedure determined the 
calibration coefficients for the sensor model conversion equation, and was 
accomplished in stages. The timeconstants for the exponential terms in the 
model were first determined for each sensor. These time constants are sensor-
specific but applicable to an entire cruise. Next, casts were fit individually 
to check sample data. 

The resulting calibration coefficients were then smoothed and held constant 
during a refit to determine sensor slope and offset. Standard and blank values 
for bottle oxygen data were smoothed and the bottle oxygen recalculated prior 
to the final fitting of CTD oxygen. The residuals are shown in figures 8-10. 


FIGURE 8   O2 residuals by cast (all points). 
FIGURE 9.  O2 residuals by pressure (all points). 
FIGURE 10. O2 residuals by cast (-0.005°C<=T1-T2<=0.005°C). 


The standard deviations of 3.76 µmol/kg for all oxygens and 1.11 µmol/kg for 
low- gradient oxygens are only presented as general indicators of goodness of 
fit. ODF makes no claims regarding the precision or accuracy OF CTD dissolved 
O2 data. The general form of the ODF O2 conversion equation for Clark cells 
follows Brown and Morrison (1978), Millard (1982) and Owen 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 °C gradient, 
dOc/dt, is approximated by low-pass filtering 1st-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. 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) 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



 where: 
      O2(ml/l)    = Dissolved O2 concentration in ml/l; 
      Oc          = Sensor current (µamps); 
      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 (µamps/secs); 
      dT          = low-pass filtered thermal gradient (Tf - Ts). 


1.7 BOTTLE SAMPLING 

At the end of each rosette deployment water samples were drawn from the bottles 
in the following order: 
      • CFCs 
      • He 
      • O2 
      • Ar and O2 isotopes 
      • pCO2 
      • Dissolved Inorganic Carbon (DIC) 
      • pH 
      • Total Alkalinity 
      • C-13/C-14 
      • Dissolved Organic Carbon (DOC) 
      • CDOM 
      • Bacterial Suite 
      • Nutrients 
      • PIC/POC 
      • Salinity 
      • Tritium 


The correspondence between individual sample containers and the rosette bottle 
position (1-36) 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 sole 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. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



1.8 BOTTLE DATA PROCESSING 

Water samples collected and properties analyzed shipboard were managed 
centrally in a relational database (PostgreSQL-8.0.3) run on a Linux system. A 
web service (OpenAcs-5.2.2 and AOLServer-4.0.10) front-end provided ship-wide 
access to CTD and water sample data.  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. Quality flags associated with sampled 
properties were set to indicate that the property had been sampled, and sample 
container identifications were noted where applicable (e.g., oxygen flask 
number). Analytical results were provided on a regular basis by the various 
analytical groups and incorporated into the database. 

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 and Corry, 1994). Various 
consistency checks and detailed examination of the data continued throughout 
the cruise. 


2. LADCP 

A downward-looking RDI 150-kHz Acoustic Doppler Current Profile (ADCP) was 
attached to the CTD rosette prior to the departure of the R/V Thompson from 
Papeete, Tahiti on cruise T191. This self- contained instrument was activated 
before the start of each CTD cast, so there are lowered-ADCP data for each CTD 
cast, and vice versa. 

Preliminary processing of the data was performed between casts. A lowered ADCP, 
or LADCP, acquires multiple velocity profiles as it is lowered into the ocean. 
Much of the processing of LADCP data consists of combining these overlapping 
profiles into a single profile of absolute velocities for the entire water 
column. Other steps in the preliminary processing are the correction of 
velocity directions for local magnetic variation and range corrections made 
using sound speed profiles calculated from the contemporaneous CTD data. CTD 
data are also used to calculate more accurate depths than can be obtained from 
the ADCP's own pressure sensor. 

LADCP data may be further processed, but the preliminary processing that was 
performed during cruise T191 is sufficient to produce plots of absolute 
velocities as a function of depth. An example is included here, showing 
contours of zonal velocities between 17°S and 17°N (Fig. 11). Shaded areas 
denote westward flow; the contour interval is 10 cm/second. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



3. SALINITY MEASUREMENTS 

A single Guildline Autosal Model 8400A salinometer (S/N 48-266), located in the 
forward analytical lab, was used for all salinity measurements. The salinometer 
was modified by SIO/ODF to contain an interface for computer-aided measurement. 
The water bath temperature was set and maintained at a value near the 
laboratory air temperature (24°C). The salinity analyses were performed after 
samples had equilibrated to laboratory temperature, usually within 6-8 hours 
after collection. The salinometers were standardized for each group of analyses 
(usually 1-2 casts, up to ~40 samples) using at least two fresh vials of 
standard seawater per group. Salinometer measurements were made by computer, 
the analyst prompted by the software to change samples and flush. 


FIGURE 11. Zonal velocities between 17°S and 17° N. Shaded areas denote   
           westward flow; the contour interval is 10 cm/second. 


1692 salinity measurements were made and approximately 100 vials of standard 
water (SSW) were used. Salinity samples were drawn into 200 ml Kimax high-
alumina borosilicate bottles, which were rinsed three times with sample prior 
to filling. The bottles were sealed with custom-made plastic insert thimbles 
and Nalgene screw caps. This assembly provides very low container dissolution 
and sample evaporation. Prior to sample collection, inserts were inspected for 
proper fit and loose inserts replaced to insure an airtight seal. The draw time 
and equilibration time were logged for all casts. Laboratory temperatures were 
logged at the beginning and end of each run. PSS-78 salinity (UNESCO, 1981) was 
calculated for each sample from the measured conductivity ratios. The 
difference (if any) between the initial vial of standard water and the next one 
run as an unknown was applied as a linear function of elapsed run time to the 
data. The corrected salinity data were then incorporated into the cruise 
database. 

The temperature in the salinometer laboratory varied from 21 to 24°C, during 
the cruise.  The air temperature change during any particular run varied from 
-1.2 to +2.2°C. Insufficient sample equilibration times were sometimes a problem 
as was having to collect samples on deck. 

The laboratory air temperature (21°C) was significantly lower than the bath 
temperature (24°C) for the first 7 casts. The estimated accuracy of bottle 
salinities run at sea is usually better than ±0.002 PSU relative to the 
particular standard seawater batch used. The 95% confidence limit for residual 
differences between the bottle salinities and calibrated CTD salinity relative 
to SSW batch P-145 was ±0.010 PSU for all salinities, and ±0.0035 PSU for 
salinities collected in low gradients. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



4. OXYGEN MEASUREMENTS 

Dissolved oxygen analyses were performed with an AOML-designed automated oxygen 
titrator using photometric end-point detection based on the absorption of 365nm 
wavelength ultra-violet light. The titration of the samples and the data 
logging were controlled by PC software. Thiosulfate was dispensed by a Dosimat 
665 buret driver fitted with a 1.0 ml buret. 

AOML used a whole-bottle modified-Winkler titration following the technique of 
Carpenter [1965] with modifications by Culberson et al. [1991]. Pre-made liquid 
potassium iodate standards were run every other day approximately every 4 
stations, unless changes were made to the system or reagents. Reagent/distilled 
water blanks were determined every other day or more often if a change in 
reagents required it to account for presence of oxidizing or reducing agents. 

1442 oxygen measurements were made. Samples were collected for dissolved oxygen 
analyses soon after the rosette was brought on board. Using a Tygon and 
silicone drawing tube, nominal 125ml volume-calibrated iodine flasks were 
rinsed 3 times with minimal agitation, then filled and allowed to overflow for 
at least 3 flask volumes. The sample drawing temperatures were measured with a 
small glass bead thermistor thermometer embedded in the drawing tube. These 
temperatures were used to calculate µmol/kg concentrations, and as a diagnostic 
check of bottle integrity. Reagents were added to fix the oxygen before 
stoppering. The flasks were shaken twice (10-12 inversions) to assure thorough 
dispersion of the precipitate, once immediately after drawing, and then again 
after about 20 minutes. The samples were analyzed within 1-4 hours of 
collection, and the data incorporated into the cruise database. Thiosulfate 
normalities were calculated from each standardization and corrected to 20°C. 
Oxygen flask volumes were determined gravimetrically with degassed deionized 
water at AOML. 


5. NUTRIENT MEASUREMENTS 

Nutrient samples were collected from the Niskin bottles in acid washed 25-ml 
linear polyethylene bottles after three complete seawater rinses and analyzed 
within 1 hour of sample collection. Measurements were made in a temperature-
controlled laboratory (20±2°C). 

Concentrations of nitrite (NO2-), nitrate (NO3-), phosphate (PO43-) and silicic 
acid (H4SiO4) were determined using an Alpkem Flow Solution Auto-Analyzer 
aboard the ship. The following analytical methods were employed:  


5.1 NITRATE AND NITRITE 

Nitrite was determined by diazotizing with sulfanilamide and coupling with N-1 
naphthyl ethylenediamine dihydrochloride to form an azo dye. The color produced 
is measured at 540 nm (Zhang et al., 1997a). Samples for nitrate analysis were 
passed through a home made cadmium column (Zhang et al., 2000), which reduced 
nitrate to nitrite and the resulting nitrite concentration was then determined 
as described above. Nitrate concentrations were determined from the difference 
of nitrate + nitrite and nitrite. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



5.2 PHOSPHATE 

Phosphate in the samples was determined by reacting with molybdenum (VI) and 
antimony (III) in an acidic medium to form an antimonyphosphomolybdate complex 
at room temperature. This complex was subsequently reduced with ascorbic acid 
to form a blue complex and the absorbance was measured at 710 nm (Grasshoff et 
al.,1983).  


5.3 SILICIC ACID 

Silicic acid in the sample was analyzed by reacting the aliquote with molybdate 
in a acidic solution to form molybdosilicic acid . The molybdosilicic acid was 
then reduced by ascorbic acid to form molybdenum blue (Zhang et al., 1997b). 
The absorbance of the molybdenum blue was measured at 660 nm. 


5.4 CALIBRATION AND STANDARDS 

Stock standard solutions were prepared by dissolving high purity standard 
materials (KNO3, NaNO2 , KH2PO4 and Na2SiF6 ) in deionized water. Working 
standards were freshly made at each station by diluting the stock solutions in 
low nutrient seawater. The low nutrient seawater used for the preparation of 
working standards, determination of blank, and wash between samples was 
filtered seawater obtained from the surface of the Gulf Stream. 

Standardizations were performed prior to each sample run with working standard 
solutions. Two or three replicate samples were collected from the Niskin bottle 
sampled at deepest depth at each cast. The relative standard deviation from the 
results of these replicate samples were used to estimate the overall precision 
obtained by the sampling and analytical procedures. The precisions of these 
samples were 0.04 µmol/kg for nitrate, 0.01 µmol/kg for phosphate and 0.1 
µmol/kg for silicic acid. 


6. CFC MEASUREMENTS 

The CFC analysis was based on the work of Bullister and Weiss (1988). CFC 
samples were drawn from the niskin bottles into glass syringes to prevent 
contamination from air. A 30 ml aliquot was injected into a glass fritted 
reservoir, and clean nitrogen bubbled through the water to remove the CFC's 
which were dried over magnesium perchlorate and concentrated on a trap of 
Porapak N at -20°C. The trap was subsequently heated and the gases swept off of 
the trap with nitrogen and injected onto a precolumn of porasil C (70°C). Once 
the gases of interest had passed through the precolumn, the remaining gases 
were vented while the CFCs passed to the main analytical column (carbograph 
1AC, 70°C). The gases were detected by a Hewlett Packard ECD. 

Aproximately 900 samples were drawn and analyzed for CFC during p16N leg 1. In 
addition, 120 samples were analyzed for SF6. The precision of the CFC analysis, 
base on replicate pairs, is estimated to be the greater of 1% or 0.005 pmol/kg.   



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



7. DIC MEASUREMENTS 

The DIC analytical equipment was set up in a seagoing container modified for 
use as a shipboard laboratory. The analysis was done by coulometry with two 
analytical systems (PMEL- 1 and PMEL-2) operated simultaneously on the cruise 
by Bob Castle (AOML) and Alex Kozyr (CDIAC). Each system consisted of a 
coulometer (UIC, Inc.) coupled with a SOMMA (Single Operator Multiparameter 
Metabolic Analyzer) inlet system developed by Ken Johnson (Johnson et al., 
1985,1987,1993; Johnson, 1992) of Brookhaven National Laboratory (BNL). In the 
coulometric analysis of DIC, all carbonate species are converted to CO2 (gas) 
by addition of excess hydrogen to the seawater sample, and the evolved CO2 gas 
is carried into the titration cell of the coulometer, where it reacts 
quantitatively with a proprietary reagent based on ethanolamine to generate 
hydrogen ions. These are subsequently titrated with coulometrically generated 
OH-. CO2 is thus measured by integrating the total change required to achieve 
this. 

The coulometers were each calibrated by injecting aliquots of pure CO2 
(99.995%) by means of an 8-port valve outfitted with two sample loops (Wilke et 
al., 1993). The instruments were calibrated at the beginning of each station 
with a set of the gas loop injections. Subsequent calibrations were run either 
in the middle or end of the cast if replicate samples collected from the same 
Niskin, which were analyzed at different stages of analysis, were different by 
more than 2 µmol/kg-1. 

Secondary standards were run throughout the cruise on each analytical system; 
these standards are Certified Reference Materials (CRMs) consisting of 
poisoned, filtered, and UV irradiated seawater supplied by Dr. A. Dickson of 
Scripps Institution of Oceanography (SIO), and their accuracy is determined 
shoreside manometrically. On this cruise, the overall accuracy for the CRMs on 
both instruments combined was 0.8 µmol/kg (n=66). Preliminary DIC data reported 
to the database have not yet been corrected to the Batch 73 CRM value, but a 
more careful quality assurance to be completed shoreside will have final data 
corrected to the secondary standard on a per instrument basis. 

Samples were drawn from the Niskin-type bottles into cleaned, precombusted 300-
mL Pyrex bottles using silicone tubing. Bottles were rinsed three times and 
filled from the bottom, overflowing half a volume, and care was taken not to 
entrain any bubbles. The tube was pinched off and withdrawn, creating a 3-mL 
headspace, and 0.2 mL of 50% 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 24 hours prior to analysis. 

DIC values were reported for 1324 samples or approximately 80% of the tripped 
bottles on this cruise. Full profiles were completed at stations on whole 
degrees, with replicate samples taken from the surface, oxygen minimum, and 
bottom depths. Duplicate samples were drawn from 121 bottles and interspersed 
throughout the station analysis for quality assurance of the coulometer cell 
solution integrity. The average of the absolute value of the difference between 
duplicates was 1 µmol kg-1 for both systems. No systematic differences between 
the replicates were observed. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



8. TA MEASUREMENTS 

Total alkalinity (TA) measurements were made potentiometrically using closed 
cell systems consisting of: a ROSS 8101 glass and Orion 90-92 double junction 
Ag/AgCl reference electrode monitored by an Orion 720A pH meter, Metrohm 665 
Dosimat titrator that adds our 0.7m acid (0.25n HCl and 0.45m NaCl) and a 
system of solenoid valves that controls the rinsing and filling of the cell. 
The titration systems are controlled programmatically using National 
Instrument's Labwindows/CVI environment (developed by Dr. Pierrot). A typical 
titration (including rinse and fill) takes about 20 minutes, using two systems 
a typical 34 bottle cast requires about seven hours. 

During the first leg of the P16N cruise, about 1439 TA samples were run between 
the two systems, with Dickson certified reference material (CRM) run between 
each station to monitor the accuracy of the instruments. If the CRM run was 
outside of the standard error of our systems (3 µmol/kg) a correction factor 
was applied to the reported TA (ratio of measured TA to certified TA) with the 
systems generally giving ±2 µmol/kg. Duplicate (same samples run on each 
system) and replicate (same samples run on the same system) samples were taken 
to asses the precision of the instruments, with duplicates giving a standard 
deviation of ±2 µmol/kg and replicate on System A giving a standard deviation 
of ±1.5 µmol/kg and System B giving ±1.4 µmol/kg.  


9. pH DISCRETE MEASUREMENTS 

9.1 UM pH 

pH measurement were made using the spectrophotometric techniques of Clayton and 
Byrne (1993) with m-cresol purple (mCP) indicator determined from:    pH = 
pKind + log[(R- 0.0069)/(2.222 - 0.133R)]   (2)  where Kind is the dissociation 
constant for the indicator and R (A578/A434) is the ration of the absorbance of 
the acidic and basic forms of the indicator corrected for baseline at 730 nm. 
The samples are drawn from 50cc glass syringes using a Kloehn 50300 syringe 
pump and injected into the 10cm optical cell. The syringe rinses and primes the 
optical cell with 20 cm3 of sample and the software permits three minutes of 
temperature stabilization before a blank is measured. 

The automated syringe then draws 0.008 cm3 of indicator and 4.90 cm3 of sample 
and allows for five minutes of temperature stabilization. A typical pH 
measurement takes about 15 minutes to run, with a 34 bottle cast taking about 
six plus hours. Values are reported with temperature to allow the user the 
greatest quality in interpretation and calculation with the data, but were made 
near 25°C reported in the seawater scale (SWS). During the first leg of the 
P16N cruise, about 1439 pH samples were run on the pH system. Measurements of 
Tris were made to insure the precision and accuracy of the instrument with a 
standard deviation of 0.003. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



9.2 USF pH 

USF personnel measured seawater pH using the procedures outlined in SOP 7 of 
DOE Handbook (Dickson and Goyet, 1996, Clayton and Byrne, 1993). Samples were 
drawn from Niskin bottles into 10 cm glass cells using a 20cm long silicon 
tube. The samples were thermostated to 25°C. After a blank was taken per 
sample, an aliquot of 10 µl of m-cresol purple indicator dye at a concentration 
of 10mM was added using a Gilmont pipet. The absorbance ratio, R, of A578/A434 
was then measured. The pHT on the total scale is calculated using following 
equation:

pHT = 1245.69/T +3.8275-0.00211(35-S) + log((R-0.00691)/(2.222-0.1331R))    (3)  

Twenty eight stations were sampled during the leg 1 of the P16N cruise. The 
overall precision based on the duplicate analyses is better than 0.001 pH unit. 


10. DISCRETE pCO2 

Samples were drawn from Niskin bottles into 500 ml volumetric flasks using 
Tygon(c) tubing with a Silicone adapter that fit over the petcock to avoid 
contamination of DOM samples.  Bottles were rinsed while inverted and filled 
from the bottom, overflowing half a volume while taking care not to entrain any 
bubbles. About 5 ml of water was withdrawn to allow for expansion of the water 
as it warms and to provide space for the stopper, tubing, and frit of the 
analytical system. Saturated mercuric chloride solution (0.2 ml) was added as a 
preservative.  The sample bottles were sealed with a screw cap containing a 
polyethylene liner. The samples were stored in coolers at room temperature 
generally for no more than 5 hours. 

On previous cruises with this instrument the analyses were done at 20°C. Due to 
the anticipated high pCO2 results for analyses at 20°C of intermediate waters 
in the north Pacific, two water baths were used for analyses at 20°C and 12°C. 
There were two secondary baths to get the samples close to the analytical 
temperatures prior to analyses. As soon as space was available in the secondary 
and then primary baths, the sample flasks were moved into the more controlled 
temperature bath. No flask was analyzed without spending at least 2.5 hours in 
a bath close to the analytical temperature. 

Generally when samples were taken, flasks were drawn on all the Niskins 
including four duplicates. Two of the duplicates were analyzed at different 
temperatures. Five hundred forty- nine samples were collected at sixteen 
stations. The fifty-seven pairs of duplicates include thirty-one pairs run at 
different temperatures. Most of the duplicates had relative standard deviations 
less than 0.5%. 

The discrete pCO2 system is patterned after the instrument 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 two systems is that 
Wanninkhof instrument uses a LI-COR(c) (model 6262) non-dispersive infrared 
analyzer, while the Chipman instrument utilizes a gas chromatograph with a 
flame ionization detector.  

Once the samples reach the analytical temperature, a 50-ml headspace is created 
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 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). This equilibration takes about 10 minutes.  
An expandable volume in the circulation loop near the flask consisting of a 
small, deflated balloon keeps the headspace of the flask at room pressure. 

In order to maintain analytical accuracy, a set of six gas standards (ranging 
from 206 to 1534 ppm) is run through the analyzer before and after every ten 
seawater samples. The standards were obtained from Scott-Marin and referenced 
against primary standards purchased from C.D. Keeling in 1991, which are on the 
WMO-78 scale. 

The calculation of pCO2 in water from the headspace measurement involves 
several steps. The CO2 concentrations in the headspace are determined via a 
second-degree polynomial fit using the nearest three standard concentrations. 
Corrections for the water vapor concentration, the barometric pressure, and the 
changes induced in the carbonate equilibrium by the headspace-water mass 
transfer are made. The corrected results are reported at the analytical 
temperature and at a reference temperature of 20°C. 

No instrumental problems occurred during the cruise. The relatively time-
consuming analyses and the presence of only one analyst limited the spatial 
coverage. Sampling and analyses focused on precision and accuracy rather than 
high throughput. 


11. CARBON/OXYGEN ISOTOPES 

Samples for C-14/C-13 analysis were collected in 500 ml borosilicate bottles 
with ground stoppers. The samples were preserved with 100 µl of saturated 
mercuric chloride solution. The stoppers were greased with Apezion grease and 
held in place with rubber bands. Samples were collected from 32 Niskins on 
stations 1, 6, 11, 18, 20, 24, 29, 33, 36 and 43. Short casts of 16 bottles 
(Niskins 19 to 35, skipping bottle 34) were collected in stations 8, 13, 15, 
16, 22, 25, 27, 31, 38 and 41. Samples will be returned to the WHOI NOSAMS 
facility for analysis. 

Samples for oxygen isotopes and oxygen:argon ratio were collected from the 15m 
Niskin at 18 stations. Another 5 stations had 5 samples collected in the upper 
175m. Samples were collected in 500 ml evacuated glass sampling bottles and 
preserved with mercuric chloride. 

Samples will be returned to the University of Washington for analysis. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



12. Dissolved Organic Carbon/ Dissolved Organic Nitrogen 

Samples for DOC/DON were collected in 60 ml high density polyethylene (HDPE) 
bottles from every cast (1412 samples total). The samples were frozen in -80°C 
Freezer and returned to RSMAS for analysis. 


13. CDOM, CHLOROPHYLL, BACTERIAL SUITE 

Samples were collected from the rosette for absorption spectroscopy on one deep 
ocean cast each day. CDOM is typically quantified as the absorption coefficient 
at a particular wavelength or wavelength range (we are using 325 nm). CDOM was 
determined at sea by measuring absorption spectra (280-730 nm) of 0.2um 
filtrates using a liquid waveguide spectrophotometer with a 200cm cell. Samples 
were concurrently collected for bacterial abundance and carbohydrates to 
compare the distribution of these quantities to that of CDOM. In surface waters 
(< 300m) bacterial productivity of field samples was estimated by measuring the 
uptake of bromo-deoxyuridine (BrdU), a non-radioactive alternative to the 
standard bacterial productivity technique using tritiated thymidine. Because of 
the connections to light availability and remote sensing, samples were 
collected for chlorophyll, carotenoid, and mycosporine-like amino acid pigment 
analysis (HPLC), chlorophyll a (fluorometric), and particulate absorption 
(spectrophotometric). Large volume (ca. 2L) samples were sporadically collected 
for CDOM photolysis experiments back at UCSB, and occasionally large volume 
samples were collected for POC analysis by Dr. Gardner's lab to compare with 
transmissometer data. CDOM and chlorophyll a samples were analyzed at sea. The 
rest of the samples were prepared for later analysis. 


14. HELIUM-TRITIUM 

Helium samples were collected in stainless steel containers with pneumatic 
valves ("bunnies"). 

To draw a sample, two pieces of tubing are attached to the ends of the 
container, and one end is attached to the spigot on the Niskin bottle. The 
sample is held vertically above the water level in the Niskin bottle, the valve 
is opened to establish flow, and the sample is lowered over a ten- to twenty-
second period to establish gravity flow. The relatively slow entry of the water 
into the container minimizes trapped air and bubble formation. The amount of 
water flushed through the tube is about six volumes. During the flush period, 
the container is tapped to remove bubbles. 

The pneumatic valves are closed and the sample is stored until it can be 
further processed. 

After all samples were collected, the helium samples were degassed and 
extracted into glass vials for analysis in the shore-based laboratory. In 
general, the extraction and degassing procedures were executed with several 
(~8) samples in parallel, with extraction or degassing sections coupled to a 
common vacuum manifold. 

Tritium samples were collected in 1 liter flint glass bottles, sealed with caps 
fitted with high density polyethylene cones to minimize water vapor 
transpiration. To achieve a minimum contamination, the bottles were pretreated 
to remove adsorbed water. The bottles are sealed with argon inside. After the 
tritium samples were collected they are sealed and retuned to the shore- based 
laboratory for analysis.  



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



DESCRIPTION OF MEASUREMENTS FROM TRACE METAL CASTS 

Hydrographic sampling for the trace elements Al and Fe was conducted during leg 
1 of P16N. Samples were collected using a specially designed rosette system 
which consists of 12 x 12L Go-Flo bottles mounted on a powder-coated rosette 
frame. The package is equipped with a SeaBird SBE 911 CTD that also has an SBE 
43 oxygen sensor and a Wet Labs FL1 flourometer.  The package is lowered using 
a Kevlar conducting cable and bottles were tripped at pre- determined depths 
from the ship using a deck box. Water samples were collected in the upper 1000 
m at a total of 21 stations spaced at 2° intervals. Near the equator (between 
2°S and 1°N) more frequent sampling was undertaken at 0.5° intervals to 
provide high resolution of the Equatorial Undercurrent. 

The purpose of the dissolved Fe(II) sampling program (W. Landing, FSU) is to 
study the effects of photochemical reduction and biological remineralization on 
the redox chemistry of iron in seawater. Filtered samples (0.2 µm) are 
collected from the Trace Metal Go-Flo bottles immediately upon recovery into 
polyethylene bottles that have been pre-charged with a small amount of 
ultrapure 6M HCl to drop the pH to 6.0-6.2. This stabilizes the existing Fe(II) 
from rapid oxidation, but is not low enough to trigger thermochemical Fe(III) 
reduction. The samples are quickly analyzed for dissolved Fe(II) using the 
FeLume chemiluminescent method. Samples for dissolved Fe(II) analysis have been 
collected from each depth on every Trace Metal cast. 

Dissolved Al was determined on Go-Flo samples using shipboard FIA (C.I. 
Measures, University of Hawaii). Additional experiments being conducted on the 
ship include laboratory photochemical exposure experiments to study the 
wavelength dependence of Fe(II) photoproduction and to quantify the maximum 
extent to which photochemical Fe reduction might occur in surface waters. We 
are also measuring H2O2 on selected profiles since H2O2 is known to enhance the 
chemiluminescent response of the Fe(II) measurement. A correction to the Fe(II) 
concentrations must therefore be applied, and we are conducting Fe(II) and H2O2 
spike experiments to quantify the effect. 

We are also collecting approximately 200 filtered seawater samples for 
dissolved Ga and Sc analysis by Alan M. Shiller (University of Southern 
Mississippi). These samples will be shipped back to USM for later shore-based 
analysis. 


DESCRIPTION OF OPTICAL CASTS 

Once each day we are casting a hand-deployed free-fall Satlantic MicroPro II 
multichannel UV/Visible spectroradiometer. This instrument has 14 upwelling 
radiance sensors and 14 downwelling irradiance sensors in wavelength bands 
ranging from 305 to 683 nm. The package also mounts a WetLabs chlorophyll 
fluorometer and scattering meter, plus ancillary sensors including X-Y tilt, 
internal and external temperatures. The instrument is allowed to trail away 
behind the port quarter, then free-falls to 150m and is hand-recovered. We are 
using the radiometric data to study the effects of CDOM on the underwater light 
environment, to validate satellite ocean radiance sensor data, and to develop 
new algorithms employing satellite and in situ optical sensor data to retrieve 
ocean properties such as CDOM light absorbance, chlorophyll concentration, and 
particulate backscattering. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



DESCRIPTION OF UNDERWAY MEASUREMENTS   

1. UNDERWAY DIC/pCO2/pH 

An automated CO2 system analyzer was set up on board to measure underway 
surface seawater CO2 parameters, including total CO2 (CT), pH, air and seawater 
pCO2 at 25oC and at a rate of about 7 samples per hour. CT was measured by 
equilibrating acidified seawater across a liquid waveguide membrane with a 
known alkalinity standard solution (Byrne et al., 2002). pCO2 was analyzed by 
equilibrating seawater or air across a liquid waveguide membrane with a known 
alkalinity standard solution. The pH at equilibration was measured and CT and 
pCO2 was calculated. The assessed precisions are 2 µm for CT, 2 ppm for pCO2 
and 0.001 for pH. 


2. UNDERWAY pCO2 

The NOAA/PMEL underway surface pCO2 system was started shortly after leaving 
Papeete, Tahiti. The semi-autonomous system analyzes surface water collected 
from the ship's uncontaminated seawater supply and marine air from the ship's 
bow on a repeating hourly cycle. 

The first quarter of each hour is devoted to calibration with four CO2 
standards (Feely et al., 1998). A second order polynomial calibration curve is 
calculated for the LiCor 6262 infrared detector. The remaining time in each 
hour is used to measure equilibrator air (15 min), bow air (15 min), and 
equilibrator air once again (15 min). The analytical precision of the system is 
estimated to be approximately 0.3-0.4 ppm for seawater and for air. 

The underway system experienced some problems the first week of the cruise 
first with low water flow rate, then air contamination in the equilibrator. 
These problems were resolved and the data from the last two weeks of the cruise 
appear to be good. 


3. UNDERWAY FLUOROMETER 

The fast-repetition-rate fluorometry (FRRF) technology permits quantitative 
evaluation of the quantum efficiency of photochemistry (ΦPSII), the effective 
absorption cross-section of PSII (σPSII) and rates of photosynthetic 
electron transport (Falkowski and Kolber, 1995). FRRF can serve as a rapid 
diagnostic tool to detect Fe deficiency. 

The technique relies on active stimulation and highly resolved detection of the 
induction and subsequent relaxation of chlorophyll fluorescence yields on 
micro- and millisecond time scales. 

To accommodate efficient excitation of diverse functional groups within 
phytoplankton communities including a variety of cyanobacteria, the system uses 
a multicolor excitation source. 

A computer-controlled LED driver circuitry generates pulses with the duration 
varied from 0.5µs to 50 ms. Each LED generate up to 1 W/cm2 of peak optical 
power density in the sample chamber to ensure fast saturation of PSII within 
the single photosynthetic turnover (less than 50µs). The fluorescence signal is 
isolated by red (680 nm or 730 nm, each with 20 nm bandwidth, for Chl-a 
fluorescence) or infra-red (880 nm with 50 nm bandwidth, for BChl-a 
fluorescence) interference filters and detected by a sensitive avalanche 
photodiode module. A small portion of the excitation light is recorded by a PIN 
photodiode as a reference signal. Both the fluorescence and reference signals 
are amplified and digitized by 12-bit analog-to-digital converters at 1 MHz 
sampling rate by a custom-designed data acquisition board. To accommodate a 
wide range of Chl-a concentrations (0.01 to 100 mg/m3) in natural 
phytoplankton, the gain of the detector unit is automatically adjusted over the 
range of three orders of magnitudes. An embedded low-power Pentium-based board 
controls the excitation protocols and data acquisition and performs the real- 
time data analysis using a custom analysis toolbox. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



4. METEOROLOGICAL MEASUREMENTS 

Nineteen days of continuous meteorological, radiative, and cloud data were 
collected by Dr. Erica Key during the length of the P16N transect, Papeete to 
Honolulu. A basic meteorological suite, including relative humidity, barometric 
pressure, air temperature, winds and wind gusts was collected at one minute 
intervals by a Coastal Environmental Systems' Weatherpak, located on the O3 
deck forward. Eppley radiometers were sited near to the Weatherpak to provide 
continuous, 24-hour measurement of downwelling short- and longwave radiation, 
also at 1-minute intervals. Gimballing these radiation sensors reduced the 
effect of ship's motion on the tilt of the pyrgeometer and pyranometer domes, 
and their siting away from the ship's superstructure minimized shadowing and 
promoted ventilation of each radiometer.  Along the port railing of the O3 deck 
forward was installed an all-sky imager that collected 2π hemispheric snapshots 
of sky cover every 30 seconds during daylit hours. Three gel filters were used 
to reduce glare and promote clear images for later analysis by a meteorologist 
at RSMAS.  The cloud time series will be reviewed for determination of cloud 
amount (in oktas), cloud level, cloud type, weather events, and obscuration of 
the sun by cloud over 10-minute intervals.  Combining this cloud information 
with the meteorological measurements will provide the necessary information for 
calculating incident cloud radiative forcing, as defined by Ramanathan et al. 
(1989).   


5. AEROSOL MEASUREMENTS 

The purpose of the FSU aerosol sampling program is primarily to measure the 
concentration of total aerosol Fe, and to quantify the aerosol Fe fractions 
that are soluble in natural surface seawater and in ultra-pure deionized water. 
Additional analyses are conducted on the samples in an effort to understand the 
atmospheric processes that yield differences in the aerosol Fe solubility. The 
aerosol sampling equipment consists of four replicate filter holders deployed 
on a 20' fold-down aerosol tower mounted on the forward, starboard corner of 
the 03 deck of the ship. One of the replicate filters (0.4 µm Nuclepore 
polycarbonate track-etched) is used for total aerosol measurements (see below); 
one replicate filter (0.45 µm polypropylene) is used to quantify the seawater-
soluble fraction; one replicate filter (0.45 µm polypropylene) is used to 
quantify the ultra-pure deionized water soluble fraction; and one replicate 
filter (0.45 µm polypropylene) is used for precision (QA) tests or stored as a 
backup sample. Size-fractionated aerosols are also collected for 48 hour 
intervals starting every 3rd day using a MOUDI cascade impactor (>3.2 µm, 1.0 
µm, 0.56 µm, 0.056 µm). 

Air is pulled through the filters using two high-capacity vacuum pumps. The 
sampling is controlled by a Campbell Scientific CR10 datalogger that 
immediately shuts off the flow when the wind might blow stack exhaust forward 
towards the sampling tower, or when the wind drops below 0.5 m/s. Air flow is 
measured using Sierra mass-flow meters. We have collected 24-hour integrated 
aerosol samples each day for the entire leg for the following analyses: Total 
aerosol Si, Al, Fe (to be analyzed using Energy Dispersive X-Ray Fluorescence 
by Dr. Joe Resing at NOAA/PMEL); Seawater-soluble aerosol Al and Fe (to be run 
back at FSU); Ultra- pure water soluble Si, Al, Ti, Fe, chloride, sulfate, 
nitrate, sodium (to be run back at FSU). The MOUDI size-fractionated aerosol 
filters are also leached with ultra-pure water for these same analytes. 



                                                 P16N_2006 • Leg 1 • Sabine/Feely • R/V Thomas G. Thompson



REFERENCES 

Brown, N. L. and G.K. Morrison. 1978. WHOI/Brown conductivity, temperature and 
    depth microprofiler, Technical Report No. 78-23, Woods Hole Oceanographic 
    Institution. 

Bullister, J.L. and R.F. Weiss. 1988. Determination of CCl3F and CCl2F2 in 
    seawater and air. Deep-Sea Res., 35, 839-853. 

Byrne, R.H., Liu, X., Kaltenbacher, E., and Sell, K. 2002. Spectrophotometric 
    Measurement of Total Inorganic Carbon In Aqueous Solutions Using a Liquid 
    Core Waveguide, Analytica Chimica Acta, 451: 221-229. 

Carpenter, J. H., 1965. The Chesapeake Bay Institute technique for the Winkler 
    dissolved oxygen method, Limnology and Oceanography, 10, 141-143. 

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. 

Clayton, T.D., R.H. Byrne. 1993. Spectrophotometric seawater pH measurements:
    Total Hydrogen Ion Concentration Scale Calibration of m-cresol purple and 
    At-Sea Results. Deep-Sea Research 40:2115-2129. 

Culberson, C. H., Knapp, G., Stalcup, M., Williams, R. T., and Zemlyak, F.,
    Aug. 1991. A comparison of methods for the determination of dissolved
    oxygen in seawater, Report WHPO 91-2, WOCE Hydrographic Programme Office. 

DOE Handbook. 1996. SOP 7: Determination of the pH of seawater using the
    indicator dye m- cresol purple. In Handbook of Methods for the Analysis of 
    the Various Parameters of the Carbon Dioxide System in Sea Water, eds 
    Andrew G. Dickson and Catherine Goyet. 

Falkowski, P. G., Kolber, Z., 1995. Variations in chlorophyll fluorescence 
    yields in phytoplankton in the world oceans. Aust. J. Plant Physiol. 22, 
    341-355. 

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 aboard research ships. Anal. Chim. Acta, 377, 185-191. 

Johnson, K.M., A.E. King, and J. McN. Sieburth. 1985 Coulometric DIC analyses 
    for marine studies: An introduction. Mar. Chem., 16, 61-82. 

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., 21, 117- 133. 

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, N.Y., 70 pp. 

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., 44, 167-189. 

Joyce, T., ed. and Corry, C., ed., May 1994, Rev. 2. Requirements for WOCE 
    Hydrographic Programme Data Reporting, Report WHPO 90-1, WOCE Report No. 
    67/91, 52-55, WOCE Hydrographic Programme Office, Woods Hole, MA, USA. 
    UNPUBLISHED MANUSCRIPT. 

Millard, R. C., Jr., 1982. CTD calibration and data processing techniques at 
    WHOI using the practical salinity scale, Proc. Int. STD Conference and 
    Workshop, p. 19, Mar. Tech. Soc., La Jolla, Ca. 

Owens, W. B. and Millard, R. C., Jr., 1985. A new algorithm for CTD oxygen 
    calibration, Journ. of Am. Meteorological Soc., 15, p. 621. 

Ramanathan, V., R. D. Cess, E. F. Harrison, P. Minnis, B. R. Barkstrom, E. 
    Ahmad, and D. Hartmann, 1989. Cloud radiative forcing and climate: Results 
    from the Earth Radiation Budget Experiment. Science, 243, 57-63. 

UNESCO, 1981. Background papers and supporting data on the Practical Salinity 
    Scale, 1978, UNESCO Technical Papers in Marine Science, No. 37, p. 144. 

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. 

Wilke, R.J., D.W.R. Wallace, and K.M. Johnson. 1993. Water-based gravimetric 
    method for the determination of gas loop volume. Anal. Chem. 65, 2403-2406. 

Zhang, J-Z., Fischer C., and Ortner, P. B., 2000. Comparison of open tubular 
    cadmium reactor and packed cadmium column in automated gas-segmented 
    continuous flow nitrate analysis. International Journal of Environmental 
    Analytical Chemistry, 76(2):99-113. 

Zhang, J-Z., Ortner P. B., and Fischer, C., 1997a. Determination of nitrite and 
    nitrate in estuarine and coastal waters by gas segmented continuous flow 
    colorimetric analysis. EPA's manual, Methods for the determination of 
    Chemical Substances in Marine and Estuarine Environmental Matrices - 2 nd 
    Edition. EPA/600/R- 97/072. 

Zhang, J-Z., and Berberian, G. A., 1997b. Determination of dissolved silicate 
    in estuarine and coastal waters by gas segmented continuous flow 
    colorimetric analysis. EPA's manual, Methods for the determination of 
    Chemical Substances in Marine and Estuarine Environmental Matrices - 2 nd 
    Edition. EPA/600/R- 97/072. 





__________________________________________________________________________________________________________
__________________________________________________________________________________________________________
                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson


TABLE OF CONTENTS LEG 2

1.0  SUMMARY
2.0  INTRODUCTION
3.0  DESCRIPTION OF MEASUREMENTS FROM VERTICAL PROFILES
     3.1   CTD/Hydrographic Measurements Program
     3.2   LADCP
     3.3   Salinity Measurements
     3.4   Oxygen Measurements
     3.5   Nutrient Measurements
     3.6   CFC Measurements
     3.7   DIC Measurements
     3.8   TA Measurements
     3.9   pH Discrete Measurements
     3.10  Discrete pCO2
     3.11  Carbon/Oxygen Isotopes
     3.12  Dissolved Organic Carbon/Dissolved Organic Nutrients 
     3.13  CDOM, chlorophyll, bacterial suite
     3.14  Helium-tritium
     3.15  Trace Metals
     3.16  Optical Casts
     
4.0  UNDERWAY MEASUREMENTS
     4.1   USF Underway DIC/pCO2/pH
     4.2   NOAA/PMEL Underway pCO2
     4.3   UM Underway pH

5.0  OTHER MEASUREMENTS
     5.1   Net tows/Pteropods 
     5.2   Floats 
      
6.0  ACKNOWLEDGEMENTS
7.0  REFERENCES
APPENDIX: ADDENDUM TO CTD REPORT


1.0  SUMMARY

The R/V Thomas G. Thompson completed the second half of a hydrographic survey 
in the North Pacific Ocean, nominally along 152°W between 22°S and 55°N, from 
10 - 30 March 2006. Thirty-five scientists from 11 academic institutions and 
two NOAA laboratories participated in the cruise. Full-depth CTD/rosette/LADCP 
casts were collected every 60 nautical miles. Water samples were collected from 
the 36-bottle rosette at each station and analyzed for salinity, nutrients, 
dissolved oxygen, four inorganic carbon parameters, radiocarbon, dissolved 
organic matter, colored dissolved organic matter, chlorofluorocarbons, 
helium/tritium, oxygen isotopes, chlorophyll, and a suite of bacterial 
measurements. Trace metal casts to 1000m were conducted at approximately every 
other station. Optical profiles were collected once each day. Plankton tows 
were conducted at about 10 stations at night. Argo floats were deployed at 8 
locations. Near surface seawater and atmospheric measurements were also made 
along the cruise track. No major problems were encountered on the cruise and 
all major cruise objectives were achieved.




                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson




2.0 INTRODUCTION

The P16N Leg 2 cruise is the second half of a meridional hydrographic section 
nominally along 152°W in the Pacific Ocean. This cruise is part of a decadal 
series of repeat hydrography sections jointly funded by the NOAA Office of 
Global Programs (now the Climate Program Office) and the National Science 
Foundation Division of Ocean Sciences as part of the Climate Variability and 
Predictability Study (CLIVAR) CO2 Repeat Hydrography Program 
(http://ushydro.ucsd.edu). The repeat hydrography program focuses on the need 
to monitor inventories of CO2, heat and freshwater and their transports in the 
ocean. Earlier programs under WOCE and JGOFS have provided baseline 
observational fields for these parameters. The new measurements will reveal 
much about the changing patterns on decadal scales. The program will serve as a 
structure for assessing changes in the ocean's biogeochemical cycle in response 
to natural and/or man-induced activity. 

Thirty-five scientists from 11 academic institutions and two NOAA research 
laboratories participated in leg 2 (Table 1) covering the northern portion of 
the P16N line from Honolulu, HI to Kodiak, AK. The R/V Thomas G. Thompson 
departed Honolulu, HI on 10 March 2006 for the start of leg 2. Leg 1 of P16N 
from Papeete, Tahiti to Honolulu, HI was conducted just prior to leg 2 from 14 
February - 3 March 2006. The first station of leg 2 was at 22°N, 152°W. The 
ship then proceeded north while we conducted a full-depth CTD/rosette/LADCP 
cast every 60 nautical miles to 55°N, 152°W, where we conducted a series of 8 
closely-spaced stations normal to the Alaskan coast. Thirty-six 12L Niskin-type 
bottles were used to collect water samples from throughout the water column at 
each station. Each Niskin was sub-sampled on deck for a variety of analyses.  
Twenty projects were represented on Leg 2 of the cruise (see Table 1). A 1000 m 
trace metal cast was conducted approximately every other station for a total of 
17 trace metal casts. The trace metal casts were conducted at approximately the 
same locations as the primary profiles and were either before or after the 
full- depth casts depending on time of day. One optical profile was collected 
each day on stations that occurred between 10:00 and 14:00 local time. A total 
of 41 stations were occupied on leg 2 (Table 2). In addition, net tows were 
conducted at night at about 10 stations either while steaming into a station or 
upon departure. As part of the Argo program, floats were deployed at about 8 
locations usually upon departure from a station. Underway measurements of 
surface seawater properties (temperature, salinity, pCO2, ADCP) and atmospheric 
concentrations of CO2, CFCs, and aerosols were also made along the cruise 
track.  The last station was completed on Wednesday, 29 March, 2006. The cruise 
ended in Kodiak, AK on 30 March, 2006.


TABLE 1. Projects and participants on P16N leg 2
=================================================================================================================
RESEARCH PROJECT             PI                         LEG 2 PARTICIPANT           PARTICIPANT E-MAIL
-----------------------------------------------------------------------------------------------------------------
Chief Scientist                                         Richard Feely (PMEL)        richard.a.feely@noaa.gov
Co-chief Scientist                                      Sabine Mecking (APL/UW)     smecking@apl.washington.edu
Student Support to           David Archer (UChi)        Samantha Deringer (UChi)    siedlesa@uchicago.edu
  Chief Scientists           Victoria Fabry (CSUSM)     David Faber (CSUSM)         dfaber@csusm.edu
Data Management              Woody Sutherland (UCSD)    Frank Delahoyde (UCSD)      fdelahoyde@ucsd.edu
CTD-Hydrography              Gregory Johnson (PMEL)     Kristy McTaggart (PMEL)     kristene.e.mctaggart@noaa.gov
                             Molly Baringer (AOML)      David Bitterman (AOML)      david.bitterman@noaa.gov
                                                        Grant Rawson (CIMAS/UM)     grant.rawson@noaa.gov
Argo Floats                  Howard Freeland (IOS)      Kristy McTaggart (PMEL)     kristene.e.mctaggart@noaa.gov
LADCP                        Andreas Thurnherr (LDEO)   Debra Tillinger (LDEO)      debrat@ldeo.columbia.edu
Oxygen Measurements          Chris Langdon (RSMAS/UM)   Chris Langdon (RSMAS/UM)    clangdon@rsmas.miami.edu
Nutrients                    Calvin Mordy (PMEL)        Peter Proctor (PMEL)        peter.proctor@noaa.gov
                             Jia Zhang (AOML)           Charlie Fisher (AOML)       charles.fischer@noaa.gov
CFC Measurements             John Bullister (PMEL)      Mark Warner (UW)            mwarner@ocean.washingon.edu
                             Mark Warner (UW)           Wendy Ruef (UW)             wruef@u.washington.edu
DIC Measurements             Christopher Sabine (PMEL)  Dana Greeley (PMEL)         dana.greeley@noaa.gov
                             Rik Wanninkhof(AOML)       Dave Wisegarver (PMEL)      david.wisegarver@noaa.gov
                             Richard Feely (PMEL)       
TA Measurements/pH Discrete  Frank  Millero (RSMAS/UM)  Taylor Graham (RSMAS/UM)    tgraham@rsmas.miami.edu
Measurements (secondary)/Un-                            Ben West (RSMAS/UM)         sharkey585@yahoo.com
  derway pH                                             Mareva Chanson (RSMAS/UM)   mchanson@rsmas.miami.edu
pH Discrete Measurements     Robert Byrne (USF)         Robert Byrne (USF)          byrne@marine.usf.edu
  (primary)                                             Zhaohui 'Aleck' Wang (USF)  awang@marine.usf.edu
                                                        Johan Schijf (USF)          schijf@marine.usf.edu
                                                        Ryan Bell (USF)             rbell@marine.usf.edu
Discrete pCO2                Rik Wanninkhof (AOML)      Bob Castle (AOML)           robert.castle@noaa.gov
Underway DIC/pCO2/pH         Robert Byrne (USF)         Zhaohui 'Aleck' Wang (USF)  awang@marine.usf.edu
Underway pCO2                Richard Feely (PMEL)       David Wisegarver (PMEL)     david.wisegarver@noaa.gov
Biologist/Net Tows           Victoria Fabry (CSUSM)     Victoria Fabry (CSUSM)      fabry@csusm.edu
Carbon Isotopes              Ann McNichol (WHOI)        Laurie Juranek (UW)         juranek@ocean.washington.edu
                             Paul Quay (UW)        
Dissolved Organic Carbon     Dennis Hansell (RSMAS/UM)  Wenhao Chen (RSMAS/UM)      wenchen@rsmas.miami.edu
CDOM, CHLORO, bacteria,      Dave Siegel (UCSB)         Chantal Swan (UCSB)         swan@icess.ucsb.edu
CDOM fluorometer on rosette  Craig Carlson (UCSB)       Elisa Wallner (UCSB)        wallner@lifesci.ucsb.edu
Helium-tritium               Peter Schlosser (LDEO)     Anthony Dachille (LDEO)     dachille@ldeo.columbia.edu
Trace Metals (seawater and   Chris Measures (UH)        Bill Landing (FSU)          wlanding@fsu.edu
 aerosols)                   Bill Landing (FSU)         Cliff Buck (FSU)            cbuck@ocean.fsu.edu
                                                        Paul Hansard (FSU)          hansard@ocean.fsu.edu
                                                        Bill Hiscock (UH)           hiscock@hawaii.edu
                                                        Lyle Leonard (UH)           lylel@hawaii.edu
Oxygen/Argon Measurements    Paul Quay (UW)             Laurie Juranek (UW)         juranek@ocean.washington.edu
Transmissometer on rosette   Wilf Gardner (TAMU)        Chantal Swan (UCSB)         swan@icess.ucsb.edu




                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson




3.0  DESCRIPTION OF MEASUREMENTS FROM VERTICAL PROFILES

3.1  CTD/HYDROGRAPHIC MEASUREMENTS PROGRAM

The basic CTD/hydrographic measurements consisted of salinity, dissolved oxygen 
and nutrient measurements made from water samples taken on LADCP/CTD/rosette 
casts, plus pressure, temperature, salinity, dissolved oxygen, transmissometer 
and fluorometer from CTD profiles. A total of 43 casts (78/1 and 83/1 were 
aborted) were conducted on leg 2, usually to within 10-20m of the bottom (Table 
2). Figure 1 shows the sample locations of the discrete water samples. No major 
problems were encountered during the operation; however, one station was lost 
due to bad weather conditions.


3.1.1 WATER SAMPLING PACKAGE

CTD/rosette casts were performed with a package consisting of a 36-bottle 
rosette frame (PMEL), a 36-place pylon (SBE32) and 36 12-liter Niskin type 
Bullister bottles (PMEL). Underwater electronic components consisted of a Sea- 
Bird Electronics SBE9plus CTD with dual pumps, dual temperature sensors 
(SBE3plus), dual conductivity sensors (SBE4), a dissolved oxygen sensor 
(SBE43),transmissometer (Wetlabs), fluorometer (Wetlabs), load cell (PMEL), 
altimeter (Simrad), pinger (Benthos) and upward and downward looking LADCPs 
(RDI) (see table 3).

The CTD was mounted vertically in an SBE CTD frame attached to a plate welded 
in the center of the rosette frame, under the pylon. The SBE4 conductivity and 
SBE3plus temperature sensors and their respective pumps were mounted vertically 
as recommended by SBE. Pump exhausts were attached to inside corners of the CTD 
cage and directed downward. The transmissometer was mounted horizontally and 
the fluorometer vertically, attached to a rigid plastic screen that did not 
impede water flow. The altimeter was mounted on the inside of the bottom frame 
ring. The RDI LADCPs were mounted vertically on the top and bottom frame rings.  
The LADCP battery pack was mounted on the bottom of the frame.

The WetLabs UV fluorometer was designed to stimulate and measure fluorescence 
of CDOM. We were evaluating the use of this instrument to supplement or enhance 
bottle CDOM measurements, as bottle samples often do not have the depth 
resolution needed to resolve the observed strong near-surface gradients in CDOM 
concentration, and on cruises such as this we were not able to sample CDOM on 
every station. On  three of the stations, the fluorometer was covered with duct 
tape to quantify the background "dark" readings for calibration purposes.  This 
fluorometer was ganged to a WetLabs C-star 660 nm 0.25m pathlength beam 
transmissometer belonging to Dr. Wilf Gardner, TAMU. The transmissometer 
developed troubles on the upcast of station 56. The instrument remained on on 
the CTD, but the data beyond this station may not be correctable.

The rosette system was suspended from a UNOLS-standard three-conductor (0.322") 
electro-mechanical sea cable using the R/V Thompson's forward winch on the aft 
starboard side. This cable replaced the 0.322" cable used on leg 1 (spooled on 
the aft winch) since it was found that the aft cable had flat spots in the 
lower layers on the drum which limited the maximum wireout to 5200m. Despite 
initial concerns that the weight of the 36 bottle rosette would put an 
extensive amount of stress on the older replacement wire, especially at deep 
stations and under rough seas, no significant winch or wire problems were 
encountered on leg 2.    



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



TABLE 2. P16N leg 2 CTD rosette station locations 
============================================================================
Sta    Date     UTC      Latitude     Longitude   Depth1  Hab2   Wire3  Pmax4  
----------------------------------------------------------------------------
 44  12 Mar 06  1330    22  0.02 N   152  0.02 W   5156    10    5188   5252      
 45  13 Mar 06  0058    23  0.00 N   152  0.00 W   5397     9    5546   5547     
 46  13 Mar 06  1347    24  0.00 N   152  0.01 W   5526    10    5628   5700    
 47  13 Mar 06  2350    24 59.97 N   152  0.01 W   5361     8    5417   5486  
 48  14 Mar 06  1131    26  0.01 N   152  0.02 W   5292    10    5381   5448    
 49  14 Mar 06  2114    27  0.00 N   152  0.00 W   5347     9    5396   5463 
 50  15 Mar 06  0828    28  0.01 N   152  0.01 W   5467    11    5547   5617
 51  15 Mar 06  2012    29  0.00 N   152  0.00 W   5508    10    5655   5730
 52  16 Mar 06  0708    30  0.00 N   152  0.00 W   5326    10    5417   5480
 53  16 Mar 06  1644    30 59.98 N   152  0.02 W   5301    10    5578   5446      
 54  17 Mar 06  0327    31 59.99 N   152  0.02 W   5194     9    5288   5354     
 55  17 Mar 06  1342    32 59.98 N   152  0.00 W   5373    10    5451   5522    
 56  18 Mar 06  0002    33 59.98 N   152  0.03 W   5507    10    5643   5619   
 57  18 Mar 06  1040    35  0.00 N   152  0.00 W   5652    16    5739   5809  
 58  18 Mar 06  2107    36  0.00 N   152  0.01 W   5510    14    5575   5662 
 59  19 Mar 06  1048    36 59.99 N   152  0.00 W   5530    20    5603   5682   
 60  19 Mar 06  2302    37 59.98 N   152  0.03 W   4930    19    4988   5051  
 61  20 Mar 06  0953    39  0.00 N   152  0.00 W   5782    13    5862   5948 
 62  20 Mar 06  2018    40  0.00 N   152  0.00 W   5177   n/a     n/a   5324
 63  21 Mar 06  0837    41  0.00 N   152  0.00 W   4995    20    5054   5120    
 64  21 Mar 06  2008    41 59.98 N   151 59.92 W   5035    21    5099   5166   
 65  23 Mar 06  0952    44  0.01 N   151 59.97 W   5497    22    5632   5716  
 66  23 Mar 06  2116    44 59.99 N   151 59.98 W   5282    19    5354   5428 
 67  24 Mar 06  1006    46  0.00 N   152  0.01 W   5230    20    5343   5416     
 68  24 Mar 06  1938    47  0.00 N   152  0.01 W   5073    15    5143   5218    
 69  25 Mar 06  0612    48  0.10 N   151 59.92 W   4896    22    4885   4950   
 70  25 Mar 06  1628    49  0.01 N   151 59.96 W   4980    10    5043   5110  
 71  26 Mar 06  0248    50  0.00 N   151 59.97 W   4908    21    4963   5031 
 72  26 Mar 06  1159    50 59.99 N   151 59.99 W   4951     9    5011   5081    
 73  26 Mar 06  2238    51 59.99 N   151 59.93 W   5087    12    5130   5201   
 74  27 Mar 06  1007    53  0.00 N   152  0.00 W   4446    11    4483   4541  
 75  27 Mar 06  2018    54  0.00 N   152 13.21 W   4393    19    4450   4508     
 76  28 Mar 06  0637    55  0.00 N   152 39.58 W   4199    19    4122   4266    
 77  28 Mar 06  1429    55 30.00 N   152 52.82 W   5352    19    5404   5482   
 78  29 Mar 06  0105    55 40.20 N   152 57.00 W   4954    16    5035   5106  
 79  29 Mar 06  0713    55 46.19 N   153  0.02 W   3920    13    4048   4095     
 80  29 Mar 06  1203    55 51.01 N   153  1.81 W   3429    20    3292   3324    
 81  29 Mar 06  1645    55 55.18 N   153  3.59 W   2422    10    2361   2380   
 82  29 Mar 06  2147    56  0.60 N   153  5.98 W   1832    20    1795   1809  
 83  30 Mar 06  0313    56 13.19 N   153 11.38 W   1084    20    1125   1134 
 84  30 Mar 06  0711    56 16.81 N   153 13.21 W    399     9    391    395
----------------------------------------------------------------------------
  1 Depth [m] is uncorrected bottom depth from shipboard Knudsen echosounder
  2 Height above bottom [m] at maximum pressure from Simrad altimeter
  3 Wire out [m] of winch cable at maximum pressure
  4 Maximum pressure [db] of CTD package     



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



The deck watch prepared the rosette 10-15 minutes prior to each cast. The 
bottles were cocked and all valves, vents and lanyards were checked for proper 
orientation. The CTD was powered up about 10 minutes prior to station. Once 
stopped on station, the data acquisition system in the computer lab was started 
when directed by the deck watch leader. The rosette was unstrapped from its 
tiedown location on deck. The pinger was activated and syringes were removed 
from the CTD intake ports. The winch operator was directed by the deck watch 
leader to raise the package, the squirt boom and rosette were extended outboard 
and the package quickly lowered into the water. The package was lowered to at 
least 10 meters and held there for 1 minute after the sensor pumps had turned 
on. The winch operator was then directed to bring the package back to the 
surface (0 winch wireout) and to begin the descent.

At each station the CTD rosette was lowered to within 10-20 meters of the 
bottom (Table 2) depending on weather conditions and bottom slope, using both 
the pinger and altimeter to determine the height above bottom. During the 
upcast the winch operator was directed to stop the winch at each bottle trip 
depth. The CTD console operator waited 30 seconds before tripping a bottle to 
insure the package wake had dissipated and the bottles were flushed, then an 
additional 10 seconds after bottle closure to insure that stable CTD comparison 
data had been acquired. Once a bottle had been closed, the console operator 
directed the winch operator to haul in the package to the next bottle stop. 
Standard sampling depths that were staggered at every other station were used 
throughout the cruise (Figure 1). 

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. The rosette was secured on deck under the block 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. No bottles were replaced on 
this cruise, but various parts of bottles were occasionally changed or 
repaired.

Routine CTD maintenance included soaking the conductivity and DO sensors in 
dilute Triton-X solution between casts to maintain sensor stability by 
eliminating any accumulating biofilms. Rosette maintenance was performed on a 
regular basis. O-rings were changed and lanyards repaired as necessary. Bottle 
maintenance was performed each day to insure proper closure and sealing. Valves 
were inspected for leaks and repaired or replaced as needed.

The SBE32 carousel frequently didn't release properly causing mistripped 
bottles. This continual problem worsened toward the end of the cruise, in spite 
of several repair attempts.

Two rosette casts (78/1 and 83/1) were aborted because of a sudden loss of 
shipboard power. The casts were brought back on deck and the ship repositioned 
before deploying the rosette again.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.1.2 UNDERWATER ELECTRONICS PACKAGES

CTD data were collected with a SBE9plus CTD (Table 3). This instrument provided 
pressure, dual temperature (SBE3), dual conductivity (SBE4), dissolved oxygen 
(SBE43), fluorometer (Wetlabs), transmissometer (Wetlabs), load cell (PMEL) and 
altimeter (Simrad 807) channels. The CTD supplied a standard SBE-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 into one pump circuit and secondary temperature 
and conductivity into the other. The sensors were deployed vertically. The 
primary temperature and conductivity sensors (Table 3) were used for reported 
CTD temperatures and conductivities on all casts except cast 81/1 where 
biofouling occurred on the sensors. The secondary temperature and conductivity 
sensors were used in this case as well as for calibration checks otherwise.

The SBE9plus CTD was connected to the SBE32 36-place pylon providing for 
single- conductor sea cable operation. The sea cable armor was used for ground 
(return). Power to the SBE9plus CTD (and sensors), SBE32 pylon and Simrad 807 
altimeter was provided through the sea cable from the SBE11plus deck unit in 
the main lab.


3.1.3  NAVIGATION AND BATHYMETRY DATA ACQUISITION

Navigation data were acquired at 1-second intervals from the ship's P-Code GPS 
receiver by a Linux system that provided a web-page with continuous updates to 
the ship's position and to the arrival times for upcoming stations throughout 
the cruise.  Bathymetric data were collected using the Ship's 12khz Knudsen 
echosounder system. These data were logged using the R/V Thompson's DAS system 
as well as a direct connection to the above Linux system about half-way through 
leg 2. Interruptions to the acquisition of the bathymetric data occurred when 
the Knudsen system was switched to receive the frequency of the pinger to track 
the distance between the CTD rosette package and the bottom starting at about a 
1000m above the bottom.


TABLE 3. P16N leg 2 underwater electronics
=====================================================================================
                                                                     Calibration
Sensor                                  Serial Number             Date       Facility
-------------------------------------------------------------------------------------
Sea-Bird SBE32 36-place Carousel        S/N 3229650-0431          N/A        N/A
    Water Sampler
Sea-Bird SBE9plus CTD                   S/N 09P8431-0315          N/A        N/A
Paroscientific Digiquartz Pres. Sensor  S/N 53960                 25-MAY-05  SBE
Sea-Bird SBE3plus Temp. Sensor          S/N 03P-4341 (Primary)    15-NOV-05  SBE
Sea-Bird SBE3plus Temp. Sensor          S/N 03P-4335 (Secondary)  15-NOV-05  SBE
Sea-Bird SBE4C Conductivity Sensor      S/N 04-2887 (Primary)     15-NOV-05  SBE
Sea-Bird SBE4C Conductivity Sensor      S/N 04-3068 (Secondary)   15-NOV-05  SBE
Sea-Bird SBE43 DO Sensor                S/N 43-0664               29-NOV-05  SBE
Sea-Bird SBE43 DO Sensor                S/N 43-0313               03-DEC-05  SBE
Wetlabs CDOM Fluorometer                S/N FLCDRTD-428           09-DEC-05  Wetlabs
Wetlabs CST Transmissometer             S/N CST-327DR             26-JAN-06  Wetlabs
PMEL LoadCell                           S/N 1109                  N/A        N/A
Simrad 807 Altimeter                    S/N 98110                 N/A        N/A
Benthos Pinger                          S/N 1134                  N/A        N/A
RDI WH300 Workhorse LADCP               LDEO #299 (Upward)        N/A        N/A
RDI WH300 Workhorse LADCP               LDEO #149 (Downward)      N/A        N/A



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.1.4  CTD DATA ACQUISITION AND ROSETTE OPERATION

The CTD data acquisition system consisted of an SBE-11plus (V2) deck unit and a 
networked generic PC workstation running Windows XP. 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 had 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 meters. The CTD sensor pumps were configured with a 60 
second startup delay, and were usually on by this time. 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 
(wire-out). The profiling rate was no more than 30m/min to 50m, no more than 
45m/min to 200m and no more than 60m/min deeper than 200m varying with 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, pinger and bathymetric depth 
were all monitored to determine the distance of the package from the bottom, 
usually allowing a safe approach to within 10 meters. Bottles were closed on 
the up cast by operating an on-screen control. Bottles were tripped 30 seconds 
after stopping at the trip location to allow the rosette wake to dissipate and 
the bottles to flush. The winch operator was instructed to proceed to the next 
bottle stop 10 seconds after closing bottles to insure that stable CTD data 
were associated with the trip. After the last bottle was closed, the console 
operator directed the deck watch to bring the rosette on deck. Once out of the 
water, the console operator terminated the data acquisition, turned off the 
deck unit and assisted with rosette sampling.


3.1.5 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 XP workstation were copied onto 
the Linux database and web server system, then processed to a 0.5 second time 
series. Bottle trip values were extracted and a 2 decibar 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 were also available for distribution). During and after the deployment 
the data were redundantly backed up to another Linux system. 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. T, S and theta-O2 comparisons were made between down and 
up casts as well as between groups of adjacent deployments. Vertical sections 
of measured and derived properties from sensor data were checked for 
consistency. Few CTD acquisition and processing problems were encountered 
during P16N. A clogged bleeder valve in the primary pump circuit led to using 
the upcasts of 50/1 and 51/1. DO sensor offsets appearing on the downcasts 
during unscheduled winch stops on 60/2 and 64/1 led to replacement of the DO 
sensor prior to 67/1, and filtering-out the offsets. Cast 78/1 and 83/1 were 
aborted due to shipwide power failures. Biofouling of the primary sensors on 
81/1 led to using T2 and C2 sensors for reported T and C data, and filtering 
the downcast O2 data. A total of 43 casts were made (including 2 aborted casts) 
using the 36-place CTD/LADCP rosette. 



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.1.6 CTD SENSOR LABORATORY AND SHIPBOARD CALIBRATIONS

Laboratory calibrations of the CTD pressure, temperature, conductivity and 
dissolved oxygen sensors were performed prior to P16N. Serial numbers and 
calibration dates are listed in table 3. In-situ salinity and dissolved O2 
samples collected during each cast were used in addition to calibrate the 
conductivity and dissolved O2 sensors.

Calibration coefficients derived from the calibration of the Paroscientific 
Digiquartz pressure transducer were applied to raw pressures during each cast.  
Residual pressure offsets (the difference between the first and last submerged 
pressures) were examined to check for calibration shifts. All were < 0.7dbar, 
and the sensor exhibited < 0.2 dbar offset shift over the period of use. No 
additional adjustments were made to the calculated pressures.


3.1.7 CTD SHIPBOARD CALIBRATION PROCEDURES 

CTD 09P8431-0315 was used for all P16N casts (Table 3). The CTD was deployed 
with all sensors and pumps aligned vertically, as recommended by SBE. The 
primary temperature and conductivity sensors (T1 & C1) were used for all 
reported CTD data on all casts except 81/1, the secondary sensors (T2 & C2) 
serving as calibration checks. In-situ salinity and dissolved O2 check samples 
collected during each cast were used to calibrate the conductivity and 
dissolved O2 sensors. 


3.1.8 CTD PRESSURE 

The Paroscientiﬁc Digiquartz pressure transducer (S/N 53960) was calibrated in 
May2005 at SBE (Table 3). Calibration coefﬁcients derived from the calibration 
were applied to raw pressures during each cast. Residual pressure offsets (the 
difference between the ﬁrst and last submerged pressures) were examined to 
check for calibration shifts. All were < 0.7db, and the sensor exhibited < 0.2 
db offset shift over the period of use. No additional adjustments were made to 
the calculated pressures. 


3.1.9 CTD TEMPERATURE 

A single primary temperature sensor (SBE 3, S/N 03P-4341) and secondary 
temperature sensor (SBE 3, S/N 03P-4335) served the entire cruise (Table 3).  
Calibration coefficients derived from the pre-cruise calibrations were applied 
to raw primary and secondary temperatures during each cast. Calibration 
accuracy was monitored by comparing the primary and secondary temperatures at 
each rosette trip. Calibration accuracy was examined by tabulating T1-T2 over a 
range of pressures and temperatures (bottle trip locations) for each cast. No 
significant temperature or pressure slope was evident. These comparisons are 
summarized in Figure 2 for all stations from legs 1 and 2. Since the primary 
and secondary conductivity sensors had been stable, analysis of the differences 
between salinity calculated from sensor pairs with bottle salinities identified 
the drifting temperature as T2.

The 95% confidence limit for the mean of the differences is ±0.0073°C. The 
variance is relatively high in spite of the small spatial separation of the 
sensors (<0.5 meters) because of package wake effects.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.1.10 CTD CONDUCTIVITY

A single primary conductivity sensor (SBE 4, S/N 04-2887) and secondary 
conductivity sensor (SBE 4, S/N 04-3068) served the entire leg (Table 3).  
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 (calculated from bottle salinities) were 
used to derive conductivity corrections. To reduce the contamination of the 
comparisons by package wake, differences between primary and secondary 
temperature sensors were used as a metric of variability and used to qualify 
the comparisons. The coherence of this relationship is illustrated in Figure 3.

Neither of the sensors exhibited a secondary pressure response. The uncorrected 
comparison between the primary and secondary sensors is shown in Figure 4, and 
between C2 and the bottle salinities in Figure 5 for legs 1 and 2. Note that 
the bottle salinities were unusable for check sample purposes due to analytical 
temperature problems for casts 1/2-7/1.

Since C2 showed no significant conductivity slope or offset relative to bottle 
conductivities, and since the comparison to C1 showed only minor (<0.001mS/cm) 
drift and shifts), C1 was calibrated to C2. No correction was made to C2. The 
comparison of the primary and secondary conductivity sensors by cast after 
applying shipboard corrections is summarized in Figure 6.

C1 was calibrated against C2 on the previous leg, and the sensors continued to 
track to within ±0.74 mS/cm over both legs. No changes in conductivity slopes 
or secondary responses were noted during leg 2. The bottle salinities are 
problematic after cast 71/1. The salinometer dial setting was changed from 525 
to 545 and standard drift rates increased sharply for subsequent runs. It 
appears that the lab temperature was fluctuating, and the standard dial setting 
was changed to attempt to compensate for the fluctuation. C1-C2 differences 
indicate that these check samples have a mean offset of +0.002. Salinities are 
reported using the Practical Salinity Scale of 1978 (PSS-78). Salinity 
residuals after applying shipboard T1/C1 corrections are summarized in Figures 
7 and 8.  Figures 7 and 8 represent estimates of the salinity accuracy on P16N. 

A single SBE43 dissolved O2 (DO) sensor was used for most of leg 2 (S/N 43- 
0663). The sensor was plumbed into the primary T1/C1 pump circuit after C1. The 
sensor was replaced prior to cast 67/1 against a different SBE43 DO sensor (S/N 
43-0313) because of offsets that began to appear after unscheduled winch stops 
on the downcasts of 60/2 and 64/1. The DO sensors were calibrated to dissolved 
O2 check samples at bottle stops by calculating CTD dissolved O2 then 
minimizing the residuals using a non-linear least-squares fitting procedure. 
The fitting procedure determined the calibration coefficients for the sensor 
model conversion equation, and was accomplished in stages. The time constants 
for the exponential terms in the model were first determined for each sensor. 
These time constants are sensor-specific but applicable to an entire cruise. 
Next, casts were fit individually to check sample data. The resulting 
calibration coefficients were then smoothed and held constant during a refit to 
determine sensor slope and offset. Standard and blank values for bottle oxygen 
data were smoothed and the bottle oxygen recalculated prior to the final 
fitting of CTD oxygen. The residuals are shown in Figures 9-11.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



The standard deviations of 5.63 uM/kg for all oxygens and 1.29 uM/kg for low- 
gradient oxygens are only presented as general indicators of goodness of ﬁt.  
ODF makes no claims regarding the precision or accuracy of CTD dissolved O2 
data. 

The general form of the ODF O2 conversion equation for Clark cells follows 
Brown and Morrison (1978), Millard (1982) and Owen 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 1st-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. 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/d       (1)
where:
     O2(ml/l)    = Dissolved O2 concentration in ml/l;
     Oc          = Sensor current (µamps);
     fsat(S,T,P) = O2 saturation concentration at S,T,P (ml/l);
     S           = Salinity at O2 response-time;
     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 (µamps/secs);
     dT          = low-pass filtered thermal gradient (Tf - Ts).


3.1.11 BOTTLE SAMPLING

At the end of each rosette deployment water samples were drawn from the bottles 
in the following order:
     • CFCs
     • He
     • O2
     • Ar and O2 isotopes
     • pCO2
     • Dissolved Inorganic Carbon (DIC)
     • pH
     • Total Alkalinity
     • C-13/C-14
     • Dissolved Organic Carbon (DOC)
     • CDOM
     • Bacterial Suite
     • Salinity
     • Nutrients
     • Tritium
     • PIC/POC



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



Water samples for analyses of dissolved SF6 and pteropods were collected at a 
few stations throughout the cruise. These samples were collected to support 
laboratory experiments onboard the ship. 

The correspondence between individual sample containers and the rosette bottle 
position (1-36) 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 sole 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.


3.1.12 BOTTLE DATA PROCESSING

Water samples collected and properties analyzed shipboard were managed 
centrally in a relational database (PostgreSQL-8.0.3) run on a Linux system. A 
web service (OpenAcs-5.2.2 and AOLServer-4.0.10) front-end provided ship-wide 
access to CTD and water sample data. 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. Quality flags associated with sampled 
properties were set to indicate that the property had been sampled, and sample 
container identifications were noted where applicable (e.g., oxygen flask 
number). Analytical results were provided on a regular basis by the various 
analytical groups and incorporated into the database. 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 and Corry, 1994). Various consistency checks and 
detailed examination of the data continued throughout the cruise.


3.2 LADCP

Two RDI 300-kHz Acoustic Doppler Current Profilers (ADCPs) were mounted on the 
CTD frame with one transducer pointing downward and the other pointing upward. 
They were powered by a "DeepSea Power and Light"rechargeable sealed lead-acid 
battery pack. The battery was charged and the instruments activated before each 
cast. While on deck, the ADCPs were connected to a Macintosh computer that 
handled both instrument setup and data processing. Both ADCPs were set up to 
record single-ping beam-coordinate velocity ensembles in 10m bins. Between 
casts, the data from the ADCPs were downloaded and processed using the LDEO 
(Columbia University) processing software (Thurnherr, 2006). The processing 
combined CTD, GPS, and shipboard ADCP data with the data from the lowered ADCPs 
to produce both shear and inverse solutions of absolute velocities. The results 
showed weak currents in most areas, with a strong eastward surface current at 
station 49 (Figure 12). The strongest flow was recorded in the Alaska current, 
which reached a westward velocitity maximum of 60 cm/s at station 80. This 
current was noticeable in the data from stations 78 through 82 (Figure 12).



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.3 SALINITY MEASUREMENTS

A single Guildline Autosal Model 8400A salinometer (S/N 48-266), located in a 
container lab on the aft deck , was used for all salinity measurements. The 
salinometer was modified by SIO/ODF to contain an interface for computer-aided 
measurement. The water bath temperature was set and maintained at a value near 
the laboratory air temperature (24°C). The salinity analyses were performed 
after samples had equilibrated to laboratory temperature, usually within 6-8 
hours after collection. The salinometers were standardized for each group of 
analyses (usually 1-2 casts, up to ~40 samples) using at least two fresh vials 
of standard seawater per group. Salinometer measurements were made by computer, 
the analyst prompted by the software to change samples and flush.

3250 salinity measurements were made and approximately 200 vials of standard 
water (SSW) were used. Salinity samples were drawn into 200 ml Kimax high- 
alumina borosilicate bottles, which were rinsed three times with sample prior 
to filling. The bottles were sealed with custom-made plastic insert thimbles 
and Nalgene screw caps. This assembly provides very low container dissolution 
and sample evaporation. Prior to sample collection, inserts were inspected for 
proper fit and loose inserts replaced to insure an airtight seal. The draw time 
and equilibration time were logged for all casts. Laboratory temperatures were 
logged at the beginning and end of each run. PSS-78 salinity (UNESCO, 1981) was 
calculated for each sample from the measured conductivity ratios. The 
difference (if any) between the initial vial of standard water and the next one 
run as an unknown was applied as a linear function of elapsed run time to the 
data. The corrected salinity data were then incorporated into the cruise 
database.

The temperature in the salinometer laboratory varied from 21 to 24°C, during 
the cruise. The air temperature change during any particular run varied from -
1.2 to +2.2°C. Insufficient sample equilibration times were sometimes a problem 
as was having to collect samples on deck. The salinometer standard dial setting 
which had been constant for most of the cruise was changed from 525 to 545 
after cast 71/1 and the standard drift rates increased sharply for subsequent 
runs. 

These runs show a mean offset of +0.002 relative to calibrated CTD 
conductivity. 

The estimated accuracy of bottle salinities run at sea is usually better than 
±0.002 relative to the particular standard seawater batch used. The 95% 
confidence limit for residual differences between the bottle salinities and 
calibrated CTD salinity relative to SSW batch P-145 was ±0.010 for all 
salinities, and ±0.0035 for salinities collected in low gradients. IAPSO 
Standard Seawater Batch P-145 was used to standardize all casts.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.4 OXYGEN MEASUREMENTS

Samples were drawn from Niskin bottles into calibrated 140 ml iodine titration 
flasks using Tygon tubing with a Silicone adapted that fit over the petcock to 
avoid contamination of DOM samples. Bottles were rinsed twice and filled from 
the bottom, overflowing three volumes while taking care not to entrain any 
bubbles. The draw temperature was taken using a digital thermometer with a 
flexible thermistor probe that was inserted into the flask while the sample was 
being drawn. These temperatures were used to calculate µmol/kg-1 
concentrations, and a diagnostic check of bottle integrity. One-ml of MnCl2 and 
one-ml of NaOH/NaI were added using a Repipetor, 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 plus 1-2 duplicates were drawn from 
each station except the shallow coastal stations where only 15-28 samples were 
drawn. Total number of samples collected was 1536; total number of samples 
flagged after initial shipboard reduction of quality control: Questionable 
(QC=3): Bad (QC=4): Not reported (QC=5).

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. Thiosulfate was dispensed by a Dosimat 665 fitted with a 5.0 
ml buret. The whole-bottle titration technique of Carpenter (1965) with 
modifications by Culberson et al. (1991) was used, but with a more dilute 
solution of thiosulfate (10 g L-1). Standard curves were run each day. The 
reagent blank was taken to be the intercept of the standard curve and compared 
to the reagent blank determined by the convention two titration method. The 
autotitrator and Dosimat generally performed well. Endpoints were noted to be 
noisy during periods of particularly bad weather. Thiosulfate molarities were 
calculated from titration of the standard iodate solution dispensed using a 
calibrated Wheaton bottle top dispensor and corrected to 20ºC. The 20ºC 
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 recalculate. Oxygen flask volumes were 
determined gravimetrically with degassed deionized water to determine flask 
volumes at AOML and corrected for the buoyancy factor. The Dosimat and Wheaton 
positive displacement dispenser used for dispensing the KIO3 were calibrated in 
the same way. 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.

In addition to the photometric end-point technique, samples from several 
stations during leg 2 were analyzed using an amperometric detection method 
(Culberson and Huang, 1987) for comparison. This was done to test amperometric 
detection method for future standard use. The difference between the two 
techniques was on average <1 µmol/kg-1.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.5 NUTRIENT MEASUREMENTS

Nutrient samples were collected from the Niskin bottles in acid washed 25-ml 
linear polyethylene bottles after three complete seawater rinses and analyzed 
within 1 hour of sample collection. Measurements were made in a temperature- 
controlled laboratory (20±2°C). Concentrations of nitrite (NO2-), nitrate 
(NO3-), phosphate (PO43-) and silicic acid (H4SiO4) were determined using an 
Alpkem Flow Solution Auto-Analyzer aboard the ship. During this cruise 
approximately 3000 samples were analyzed along with their standards and 
baseline samples. The following analytical methods were employed:


3.5.1 NITRATE AND NITRITE 

Nitrite was determined by diazotizing with sulfanilamide and coupling with N-1 
naphthyl ethylenediamine dihydrochloride to form an azo dye. The color produced 
is measured at 540 nm (Zhang et al., 1997). Samples for nitrate analysis were 
passed through a home made cadmium column (Zhang et al., 2000), which reduced 
nitrate to nitrite and the resulting nitrite concentration was then determined 
as described above. Nitrate concentrations were determined from the difference 
of nitrate + nitrite and nitrite.


3.5.2 PHOSPHATE

Phosphate in the samples was determined by reacting with molybdenum (VI) and 
antimony (III) in an acidic medium to form an antimonyphosphomolybdate complex 
a temperature of 55(C. This complex was subsequently reduced with hydrazine to 
form a blue complex and the absorbance was measured at 815 nm (Zhang et al., 
2001). 


3.5.3 SILICIC ACID

Silicic acid in the sample was analyzed by reacting the aliquote with molybdate 
in a acidic solution to form molybdosilicic acid. The molybdosilicic acid was 
then reduced by SnCl2 to form molybdenum blue (Gordon et al., 1995). The 
absorbance of the molybdenum blue was measured at 660 nm.


3.5.4 CALIBRATION AND STANDARDS

Stock standard solutions were prepared by dissolving high purity standard 
materials (KNO3, NaNO2, KH2PO4 and Na2SiF6 ) in deionized water. Working 
standards were freshly made at each station by diluting the stock solutions in 
low nutrient seawater. The low nutrient seawater used for the preparation of 
working standards, determination of blank, and wash between samples was 
filtered seawater obtained from low-nutrient Pacific surface waters. 
Standardizations were performed prior to each sample run with working standard 
solutions.  Replicates were usually collected at the deepest Niskin bottle from 
each cast.  The relative standard deviation from the results of these replicate 
samples was used to estimate the overall precision obtained by the sampling and 
analytical procedures. The precisions of these samples were 0.04 µmol/kg for 
nitrate, 0.01 µmol/kg for phosphate and 0.1 µmol/kg for silicic acid.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.6 CFC MEASUREMENTS

Samples for the analysis of dissolved CFC-11, CFC-12, and CFC-113 were drawn 
from 960 of the 1300 water samples collected during the expedition. Specially 
designed 12 liter water 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 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, helium-3, dissolved oxygen, 
alkalinity and pH 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 3-way plastic stopcocks. The syringes 
were immersed in a holding bath of freshwater until analyzed.

For air sampling, a ~100 meter 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 CFC van using an Air Cadet pump. The air was compressed in 
the pump, with the downstream pressure held at ~1.5 atm. using a back-pressure 
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 SF6 analytical systems, while 
the bulk flow of the air (>7 l min-1) was vented through the back pressure 
regulator. Air samples were generally analyzed when the ship was on station and 
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 for 
approximately 45 minutes prior to analysis to insure that the air inlet lines 
and pump were thoroughly flushed. The average atmospheric concentrations 
determined during the cruise (from a set of 5 measurements analyzed 
approximately once per day, n=23) were 252.9 ±4.4 parts per trillion (ppt) 
for CFC-11, 547.2 ±5.0 ppt for CFC-12, and 76.3 ±1.9 ppt for CFC-113.

Concentrations of CFC-11 and CFC-12, and CFC-113 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 95 psi, was used to cool the trap, to approximately -
20°C. After 4 minutes of purging, the trap was isolated, and the trap was 



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



heated electrically to ~100°C. 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 other compounds. 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), the flow through the pre-column was 
reversed to backflush slower eluting compounds. Both of the analytical systems 
were calibrated frequently 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 ~10.5 minutes.

Concentrations of the CFCs in air, seawater samples and gas standards are 
reported relative to the SIO98 calibration scale (Prinn 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 concentrations are given in units of picomoles per kilogram 
seawater (pmol kg-1). CFC 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 (UW cylinder 45191 for CFC-11: 386.94 ppt, CFC-12: 200.92 ppt, 
and CFC-113: 105.4 ppt) into the analytical instrument. The response of the 
detector to the range of moles of CFC-12 and CFC-113 passing through the 
detector remained relatively constant during the cruise. A thorough baking of 
the column and trap after a power outage during trapping of a seawater sample 
introduced an unknown contaminant into the column changed the response of the 
detector to CFC-11. Full-range calibration curves were run at intervals of 10 
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=395) were ± 0.44% for CFC-12, 0.56% for CFC-11, and 3.0% for 
CFC-113.

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 were approximately <1% 
for all 3 compounds. A fit of the re-strip efficiency as a function of 
temperature will be applied to the final data set. No correction has been 
applied to the preliminary data set. The determination of a blank due to 
sampling and analysis of CFC-free waters was hampered by a contamination peak 
that co-eluted with CFC-11 and varied greatly in size during this leg. The size 
of the peak decreased exponentially with time, but jumped to very high values 
(0.05 pmol kg-1) after each of the four power outages encountered during leg 2. 



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



Further investigation needs to be done to understand the origin of this 
contamination. CFC-113 and CFC-12 sampling blanks were less than 0.005 pmol/kg-1.
No sampling blank corrections have been made to this preliminary data set.

On this expedition, based on the analysis of 38 duplicate samples, we estimate 
precisions (1 standard deviation) of 0.45% or 0.004 pmol kg-1 (whichever is 
greater) for dissolved CFC-11, 0.36% or 0.003 pmol kg-1 for CFC-12 
measurements, and 0.004 pmol kg-1 for CFC-113.

A very small number of water samples had anomalously high CFC 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 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 that were drawn from the rosette but never 
analyzed due to a variety of reasons (e.g. power outage during analysis). 


3.7 DIC MEASUREMENTS

The DIC analytical equipment was set up in a seagoing container modified for 
use as a shipboard laboratory. The analysis was done by coulometry with two 
analytical systems (PMEL-1 and PMEL-2) operated simultaneously on the cruise by 
Dana Greeley and David Wisegarver of PMEL. Each system consisted of a 
coulometer (UIC, Inc.) coupled with a SOMMA (Single Operator Multiparameter 
Metabolic Analyzer) inlet system developed by Ken Johnson (Johnson et al., 
1985,1987,1993; Johnson, 1992) of Brookhaven National Laboratory (BNL). In the 
coulometric analysis of DIC, all carbonate species are converted to CO2 (gas) 
by addition of excess hydrogen to the seawater sample, and the evolved CO2 gas 
is carried into the titration cell of the coulometer, where it reacts 
quantitatively with a proprietary reagent based on ethanolamine to generate 
hydrogen ions. These are subsequently titrated with coulometrically generated 
OH-. CO2 is thus measured by integrating the total change required to achieve 
this.

The coulometers were each calibrated by injecting aliquots of pure CO2 (99.99%) 
by means of an 8-port valve outfitted with two sample loops (Wilke et al., 
1993). The instruments were calibrated at the beginning of each station with a 
set of the gas loop injections. Subsequent calibrations were run either in the 
middle or end of the cast if replicate samples collected from the same Niskin, 
which were analyzed at different stages of analysis, were different by more 
than 2 µmol/kg-1. Secondary standards were run throughout the cruise on each 
analytical system; these standards are Certified Reference Materials (CRMs) 
consisting of poisoned, filtered, and UV irradiated seawater supplied by Dr. A. 

Dickson of Scripps Institution of Oceanography (SIO), and their accuracy is 
determined shoreside manometrically. On this cruise, the overall accuracy for 
the CRMs on both instruments combined was 0.8 µmol/kg (n=66). Preliminary DIC 



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



data reported to the database have not yet been corrected to the Batch 73 CRM 
value, but a more careful quality assurance to be completed shoreside will have 
final data corrected to the secondary standard on a per instrument basis.

Samples were drawn from the Niskin-type bottles into cleaned, precombusted 300- 
mL Pyrex bottles using silicone tubing. Bottles were rinsed three times and 
filled from the bottom, overflowing half a volume, and care was taken not to 
entrain any bubbles. The tube was pinched off and withdrawn, creating a 6-mL 
headspace, and then 0.2 mL of 50% saturated HgCl2 solution was added as a 
preservative. The sample bottles were sealed with glass stoppers lightly 
covered with Apiezon-L grease.

DIC values were reported for 1324 samples or approximately 80% of the tripped 
bottles on this cruise (92% of the non-trace metal bottles). Full profiles were 
completed at stations on whole degrees, with replicate samples taken from the 
surface, oxygen minimum, and bottom depths. Duplicate samples were drawn from 
72 bottles and interspersed throughout the station analysis for quality 
assurance of the coulometer cell solution integrity. The average of the 
absolute value of the difference between duplicates was 1.0 µmol/kg-1 for both 
systems. No systematic differences between the replicates were observed.


3.8 TA MEASUREMENTS

Total alkalinity (TA) measurements were made potentiometrically using closed 
cell systems consisting of: a ROSS 8101 glass and Orion 90-92 double junction 
Ag/AgCl reference electrode monitored by an Orion 720A pH meter, Metrohm 665 
Dosimat titrator that adds our 0.7m acid (0.25n HCl and 0.45m NaCl) and a 
system of solenoid valves that controls the rinsing and filling of the cell. 
The titration cell was thermostated to 25°C using a Neslab RTE 17 constant 
temperature bath. The titration systems are controlled programmatically using 
National Instrument's Labwindows/CVI environment (developed by Dr. Pierrot). A 
typical titration (including rinse and fill) takes about 15 minutes, using two 
systems a typical 36 bottle cast requires about six hours. 

During the second leg of the P16N cruise, about 1444 TA samples were run 
between the two systems, with Dickson certified reference material (CRM) run 
between each station to monitor the accuracy of the instruments. If the CRM run 
was outside of the standard error of our systems (3 µmol/kg) a correction 
factor was applied to the reported TA (ratio of measured TA to certified TA) 
with the systems generally giving ±2 µmol/kg. Duplicate (same samples run on 
each system) and replicate (same samples run on the same system) samples were 
taken to assess the precision of the instruments, with duplicates giving a 
standard deviation of ±2.3 µmol/kg and replicate on System A giving a standard 
deviation of ±1.2 µmol/kg and System B giving ±1.0 µmol/kg. 



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.9 pH DISCRETE MEASUREMENTS

3.9.1 UM pH

pH measurement were made using the spectrophotometric techniques of Clayton and 
Byrne (1993) with m-cresol purple (mCP) indicator determined from:

     pH = pKind + log[(R- 0.0069)/(2.222 - 0.133R)]             (2)

where Kind is the dissociation constant for the indicator and R (A578/A434) is 
the ration of the absorbance of the acidic and basic forms of the indicator 
corrected for baseline at 730 nm. The samples are drawn from 50cc glass 
syringes using a Kloehn 50300 syringe pump and injected into the 10cm optical 
cell. The syringe rinses and primes the optical cell with 20 cm3 of sample and 
the software permits three minutes of temperature stabilization before a blank 
is measured. The automated syringe then draws 0.008 cm3 of indicator and 4.90 
cm3 of sample and allows for five minutes of temperature stabilization. A 
typical pH measurement takes about 15 minutes to run, with a 36 bottle cast 
taking about six plus hours. Values are reported with temperature to allow the 
user the greatest quality in interpretation and calculation with the data, but 
were made near 25°C reported in the seawater scale (SWS). 

During leg 2 of P16N, the pH system was converted to a flowing mode. This 
entailed circulating the optical cell with underway seawater for insitu pH 
measurements. Discrete pH samples were taken, for comparison sake, on 8 
stations (about 280 samples) throughout the course of the second leg. These 
runs were measured at the insitu surface temperature relative to the ship's 
position, and reported with the temperature of the measurement. A normalization 
of theses pH measurement will be made once on shore to a temperature of 25°C to 
be consistent with the measurements made on the first leg.


3.9.2 USF pH

USF pH measurements were the primary pH measurements on leg 2. Discrete USF pH 
measurements were made on all water samples for which discrete DIC measurements 
were obtained by NOAA personnel. Measurements of discrete pH were precise, and 
highly effective at prompt identification of mistrips. Comparison with pH 
measurements obtained 15 years earlier, using nearly identical procedures, 
revealed substantial decreases in pH down to approximately 500 meters along the 
entire transect. The observed decreases generally correlated well with observed 
15-year DIC differences along the transect. USF personnel measured seawater pH 
using the procedures outlined in SOP 7 of DOE Handbook (1996) and in Clayton 
and Byrne (1993). Samples were drawn from the Niskin bottles into 10 cm glass 
cells using a 20cm long silicon tube. The samples were thermostated to 25°C. 
After a blank was taken for each sample, an aliquot of 10 µL (early in the 
transect) to 20 µL (late in the transect) of m-cresol purple indicator dye 
(concentration ~ 10mM) was added using a Gilmont pipette. The absorbance ratio, 
R, of A578/A434 was then measured. The pHT on the total scale is calculated 
using the following equation:

      pHT = 1245.69/T +3.8275-0.00211(35-S) + log((R-0.00691)/(2.222-0.1331R))

where T is the measurement temperature (T = 273.15 + t) and S is salinity. The 
overall precision of pH measurements from duplicate samples was better than 
0.001 pH units.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.10 DISCRETE pCO2

Samples were drawn from the Niskin bottles into 500 ml volumetric flasks using 
Tygon(c) tubing with a Silicone adapter that fit over the petcock to avoid 
contamination of DOM samples. Bottles were rinsed while inverted and filled 
from the bottom, overflowing half a volume while taking care not to entrain any 
bubbles. About 5 ml of water was withdrawn to allow for expansion of the water 
as it warms and to provide space for the stopper, tubing, and frit of the 
analytical system. Saturated mercuric chloride solution (0.2 ml) was added as a 
preservative. The sample bottles were sealed with a screw cap containing a 
polyethylene liner. The samples were stored in coolers at room temperature 
generally for no more than 5 hours.

On previous cruises with this instrument the analyses were done at 20°C. Due to 
the anticipated high pCO2 results for analyses at 20°C of intermediate waters 
in the North Pacific, two water baths were used for analyses at 20°C and 12°C.  
There were two secondary baths to get the samples close to the analytical 
temperatures prior to analyses. As soon as space was available in the secondary 
and then primary baths, the sample flasks were moved into the more controlled 
temperature bath. No flask was analyzed without spending at least 2.5 hours in 
a bath close to the analytical temperature. The pCO2 in the intermediate water 
in the North Pacific reaches the highest values in the world's oceans and even 
with samples run at 12°C some analyses would exceed the working range of the 
detector of about 2000 ppm. The depth interval where very high pCO2 
concentrations are encountered gets progressively greater going northward. 

Therefore no pCO2 samples were taken between 700 and 1200 db at station 53 and 
the range progressively increased to 175 to 1500 db at station 77.

Generally when samples were taken, flasks were drawn on all the Niskins 
including four duplicates. Two of the duplicates were analyzed at different 
temperatures. Four hundred sixteen samples were collected at fourteen stations 
(stations 44, 47, 56, 53, 56, 59, 62, 65, 68, 70, 73, 75, 77, 80). The data 
from eighteen of these samples was lost due to power failures.  The fifty-four 
pairs of duplicates include twenty-six pairs run at different temperatures. The 
breakdown and precision of replicates are:


Duplicates @ 12°C:           0.23 + -0.15%  N = 15
Duplicates @ 20°C:           0.17 + -0.15%  N = 12, one duplicate omitted 
                                                    (bad analysis)
Duplicates @ 12°C and 20°C*: 0.64 + -0.60%  N = 25, one duplicate omitted 
                                                    (bad analysis)

*for comparison of the duplicates run at 12° and 20°C the 12°C results were 
 normalized to 20°C using the procedures and constants listed in the Appendix 
 of Peng et al. (1987) as incorporated in the GW BASIC data reduction 
 program. 


The discrete pCO2 system is patterned after the instrument 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 two systems is that 
Wanninkhof instrument uses a LI-COR(c) (model 6262) non-dispersive infrared 
analyzer, while the Chipman instrument utilizes a gas chromatograph with a 
flame ionization detector.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



Once the samples reach the analyses temperature, a 50-ml headspace is created 
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 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).  This equilibration takes about 10 minutes. 
An expandable volume in the circulation loop near the flask consisting of a 
small, deflated balloon keeps the headspace of the flask at room pressure.

In order to maintain analytical accuracy, a set of six gas standards is run 
through the analyzer before and after every ten seawater samples. The cylinder 
serial numbers and mole fractions of CO2 with balance artificial air are: 

                           CA5998   205.1 ppm 
                           CA5989   378.7 ppm 
                           CA5988   593.6 ppm 
                           CA5980   792.5 ppm 
                           CA5984  1037.0 ppm 
                           CA5940  1533.7 ppm 
 
The standards were obtained from Scott-Marin and referenced against primary 
standards purchased from C.D. Keeling in 1991, which are on the WMO-78 scale.

The calculation of pCO2 in water from the headspace measurement involves 
several steps. The CO2 concentrations in the headspace are determined via a 
second- degree polynomial fit using the nearest three standard concentrations.  
Corrections for the water vapor concentration, the barometric pressure, and the 
changes induced in the carbonate equilibrium by the headspace-water mass 
transfer are made. The corrected results are reported at the analytical 
temperature and at a reference temperature of 20°C.

No instrumental problems occurred during the cruise. The relatively time- 
consuming analyses and the presence of only one analyst limited the spatial 
coverage. Sampling and analyses focused on precision and accuracy rather than 
high throughput.


3.11 CARBON/OXYGEN ISOTOPES

Samples for C-14/C-13 analysis were collected in 500 ml borosilicate bottles 
with ground stoppers. The samples were preserved with 100 µl of saturated 
mercuric chloride solution. The stoppers were greased with Apezion grease and 
held in place with rubber bands. Samples were collected from 32 Niskin bottles 
on stations 46, 50, 54, 58, 64, 68, 72, 76. Short casts of 16 bottles were 
collected at stations 44, 48, 52, 56, 60, 62, 66, 70, 74, 77, 80, 83. Samples 
will be returned to the WHOI NOSAMS facility for analysis.

Samples for oxygen isotopes and oxygen:argon ratio were collected from a near- 
surface (15-25 m) Niskin at all stations. Another 11 stations had 5 samples 
collected in the upper 300m. Samples were collected in 500 ml evacuated glass 
sampling bottles and preserved with mercuric chloride. Samples will be returned 
to the University of Washington for analysis.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.12 DISSOLVED ORGANIC CARBON/ DISSOLVED ORGANIC NITROGEN

Water for DOC/DON analyses were collected into 60 ml high density polyethylene 
(HDPE) bottles from every cast (2818 samples total). Samples from the upper 250 
m were passed through GF/F filters using in-line filtration from the Niskin 
bottles; at greater depths the samples were whole (unfiltered) water. The 
samples then were frozen in a -20°C freezer room and returned to RSMAS for 
analysis..


3.13 CDOM, CHLOROPHYLL, BACTERIAL SUITE

Samples were collected from the rosette for absorption spectroscopy on one deep 
ocean cast each day. CDOM is typically quantified as the absorption coefficient 
at a particular wavelength or wavelength range (we are using 325 nm). CDOM was 
determined at sea by measuring absorption spectra (280-730 nm) of 0.2um 
filtrates using a liquid waveguide spectrophotometer with a 200cm cell. Samples 
were concurrently collected for bacterial abundance and carbohydrates to 
compare the distribution of these quantities to that of CDOM. In surface waters 
(< 300m) bacterial productivity of field samples was estimated by measuring the 
uptake of bromo-deoxyuridine (BrdU), a non-radioactive alternative to the 
standard bacterial productivity technique using tritiated thymidine. Because of 
the connections to light availability and remote sensing, samples were 
collected for chlorophyll, carotenoid, and mycosporine-like amino acid pigment 
analysis (HPLC), chlorophyll a (fluorometric), and particulate absorption 
(spectrophotometric). Large volume (ca. 2L) samples were sporadically collected 
for CDOM photolysis experiments back at UCSB, and occasionally large volume 
samples were collected for POC analysis by Dr. Gardner's lab to compare with 
transmissometer data. CDOM and chlorophyll a samples were analyzed at sea. The 
rest of the samples were prepared for later analysis.


3.14 HELIUM-TRITIUM

Helium samples were collected in stainless steel containers with pneumatic 
valves ("bunnies"). To draw a sample, two pieces of tubing are attached to the 
ends of the container, and one end is attached to the spigot on the Niskin 
bottle. The sample is held vertically above the water level in the Niskin 
bottle, the valve is opened to establish flow, and the sample is lowered over a 
ten- to twenty-second period to establish gravity flow. The relatively slow 
entry of the water into the container minimizes trapped air and bubble 
formation. The amount of water flushed through the tube is about six volumes.  
During the flush period, the container is tapped to remove bubbles. The 
pneumatic valves are closed and the sample is stored until it can be further 
processed.

After all samples were collected, the helium samples were degassed and 
extracted into glass vials for analysis in the shore-based laboratory. In 
general, the extraction and degassing procedures were executed with several 
(~8) samples in parallel, with extraction or degassing sections coupled to a 
common vacuum manifold. 

Tritium samples were collected in 1 liter flint glass bottles, sealed with caps 
fitted with high density polyethylene cones to minimize water vapor 
transpiration.  To achieve a minimum contamination, the bottles were pretreated 
to remove adsorbed water. The bottles are sealed with argon inside. After the 
tritium samples were collected they are sealed and retuned to the shore-based 
laboratory for analysis.


3.15 TRACE METALS

Hydrographic sampling for the trace elements Al and Fe was conducted during leg 
2 of P16N. Samples were collected using a specially designed rosette system 
which consists of 12 x 12L Go-Flo bottles mounted on a powder-coated rosette 
frame. The package is equipped with a SeaBird SBE 911 CTD that also has an SBE 
43 oxygen sensor and a Wet Labs FL1 flourometer. The package is lowered using a 
Kevlar conducting cable and bottles were tripped at pre-determined depths from 
the ship using a deck box. Water samples were collected in the upper 1000 m at 
a total at 17 stations, collecting roughly 200 samples. Bad weather (high winds 
and rough seas) prevented us deploying at only one station (station 64, 43N).  
Subsamples were taken from each GoFlo bottle for at-sea analysis of salinity, 
nutrients, dissolved total Fe and Al (Bill Hiscock of the Measures Group), and 
dissolved Fe(II). 


3.15.1 AEROSOL SAMPLING 

Aeolian transport and deposition of soluble aerosol Fe is believed to influence 
phytoplankton primary productivity in the majority of the open ocean (far from 
Fe inputs from rivers and coastal sediments). The purpose of the FSU aerosol 
sampling program is primarily to measure the concentration of total aerosol Fe, 
and to quantify the aerosol Fe fractions that are soluble in natural surface 
seawater and in ultra-pure deionized water. Additional analyses are conducted 
on the samples in an effort to understand the atmospheric processes that yield 
differences in the aerosol Fe solubility. 

The aerosol sampling equipment consists of four replicate filter holders 
deployed on a 20' fold-down aerosol tower mounted on the forward, starboard 
corner of the 03 deck of the ship. One of the replicate filters (0.4 (m 
Nuclepore polycarbonate track-etched) is used for total aerosol measurements 
(see below); one replicate filter (0.45 (m polypropylene) is used to quantify 
the seawater-soluble fraction; one replicate filter (0.45 (m polypropylene) is 
used to quantify the ultra-pure deionized water soluble fraction; and one 
replicate filter (0.45 (m polypropylene) is used for precision (QA) tests or 
stored as a backup sample. Size-fractionated aerosols are also collected for 48 
hour intervals starting every 3rd day using a MOUDI cascade impactor (>3.2 (m, 
1.0 (m, 0.56 (m, 0.056 (m). Air is pulled through the filters using two high- 
capacity vacuum pumps. The sampling is controlled by a Campbell Scientific CR10 
datalogger that immediately shuts off the flow when the wind might blow stack 
exhaust forward towards the sampling tower, or when the wind drops below 0.5 
m/s. Air flow is measured using Sierra mass-flow meters. 

We have collected 24-hour integrated aerosol samples each day for the entire 
leg (24 days of sampling) for the following analyses:

 1. Total aerosol Si, Al, Fe (to be analyzed using Energy Dispersive X-Ray 
    Fluorescence by Dr. Joe Resing at NOAA/PMEL). 
 2. Seawater-soluble aerosol Al and Fe (to be run back at FSU).
 3. Ultra-pure water soluble Si, Al, Ti, Fe, chloride, sulfate, nitrate, 
    sodium (to be run back at FSU).  The MOUDI size-fractionated aerosol 
    filters are also leached with ultra-pure water for these same analyses.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



3.15.2  DISSOLVED Fe(II) 

The purpose of the dissolved Fe(II) sampling program is to study the effects of 
photochemical reduction and biological remineralization on the redox chemistry 
of iron in seawater. Filtered samples (0.2 (m) are collected from the Trace 
Metal Go-Flo bottles immediately upon recovery into polyethylene bottles that 
have been pre-charged with a small amount of ultrapure 6M HCl to drop the pH to 
6.0-6.2. This stabilizes the existing Fe(II) from rapid oxidation, but is not 
low enough to trigger thermochemical Fe(III) reduction. The samples are quickly 
analyzed for dissolved Fe(II) using the FeLume chemiluminescent method. Samples 
for dissolved Fe(II) analysis have been collected from each depth on every 
Trace Metal cast (17 stations, approx. 200 samples).

Additional experiments being conducted on the ship include laboratory 
photochemical exposure experiments to study the wavelength dependence of Fe(II) 
photoproduction and to quantify the maximum extent to which photochemical Fe 
reduction might occur in surface waters. We are also measuring H2O2 on selected 
profiles since H2O2 is known to enhance the chemiluminescent response of the 
Fe(II) measurement.  A correction to the Fe(II) concentrations must therefore 
be applied, and we conducted Fe(II) and H2O2 spike experiments to quantify the 
effect. 


3.15.3 OTHER SAMPLING

We collected archived samples from each trace metal cast (17 stations, approx. 
200 samples) for FSU shore-based analysis of dissolved Fe, Ni, Cu, Zn, Cd, and 
Pb using isotope dilution ICPMS.

The Total Suspended Matter (TSM) from each trace metal cast was collected on 47 
mm 0.4 um Nuclepore filters for EDXRF analysis of total particulate Si, Mn, Fe, 
and Al (Joe Resing, NOAA/PMEL). 

We collected approximately 200 filtered seawater samples for dissolved Mn, Ga 
and Sc analysis by Alan M. Shiller (University of Southern Mississippi). These 
samples will be shipped back to USM for later shore-based analysis.

We collected approximately 100 samples for Dave Krabbenhoft (USGS, Madison) for 
dissolved total mercury and methyl mercury analyses. Human exposure to 
environmental mercury is mainly through consumption of marine fish containing 
methyl mercury, so these samples will help us understand the marine mercury 
cycle and the production of methyl mercury.


3.16 OPTICAL CASTS

Once each day, an optical cast with a hand-deployed free-fall Satlantic 
MicroPro II multichannel UV/Visible spectroradiometer was conducted. This 
instrument has 14 upwelling radiance sensors and 14 downwelling irradiance 
sensors in wavelength bands ranging from 305 to 683 nm. The package also mounts 
a WetLabs chlorophyll fluorometer and scattering meter, plus ancillary sensors 
including X-Y tilt, internal and external temperatures. The instrument is 
allowed to trail away behind the port quarter, then free-falls to 150m and is 
hand- recovered. The radiometric data will be used to study the effects of CDOM 
on the underwater light environment, to validate satellite ocean radiance 
sensor data, and to develop new algorithms employing satellite and in situ 
optical sensor data to retrieve ocean properties such as CDOM light absorbance, 
chlorophyll concentration, and particulate backscattering.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



4.0 UNDERWAY MEASUREMENTS

4.1 USF UNDERWAY DIC/pCO2/pH

An automated CO2 system analyzer was set up on board to measure underway 
surface seawater CO2 parameters (7 samples per hour), including total CO2 
(DIC), pH, air and seawater pCO2 at 25°C. DIC was measured by equilibrating 
acidified seawater across a liquid-core waveguide membrane with a known 
alkalinity standard solution (Byrne et al., 2002). pCO2 was analyzed by 
equilibrating seawater or air across a liquid-core waveguide membrane with a 
known alkalinity standard solution. The equilibrium pH was measured, and DIC 
and pCO2 were calculated.  The assessed precisions are 2 µM for DIC, 2 ppm for 
pCO2 and 0.001 for pH.

Underway measurements of surface pH, DIC and pCO2 along the transect generally 
went smoothly and correlated well with discrete measurements. Underway surface 
pH measurements were in excellent agreement with discrete measurements, even 
though the procedures for the measurements had distinct differences. Underway 
and discrete DIC measurements were in very good agreement with the exception of 
one short segment of stations over an approximately two to three day period. 
Comparisons of USF and NOAA underway pCO2 measurements were somewhat 
compromised by the limited flow of seawater to the PMEL underway system. 
Comparisons with AOML discrete measurements should eventually shed light on 
underway pCO2 measurement issues.


4.2 NOAA/PMEL UNDERWAY pCO2

The NOAA/PMEL underway surface pCO2 system was started shortly after leaving 
Honululu, HI. The semi-autonomous system analyzes surface water collected from 
the ship's uncontaminated seawater supply and marine air from the ship's bow on 
a repeating hourly cycle. The first quarter of each hour is devoted to 
calibration with four CO2 standards (Feely et al., 1998). A second order 
polynomial calibration curve is calculated for the LiCor 6262 infrared 
detector. 

The remaining time in each hour is used to measure equilibrator air (15 min), 
bow air (15 min), and equilibrator air once again (15 min). The analytical 
precision of the system is estimated to be approximately 0.3-0.4 ppm for 
seawater and for air.

The underway system experienced some problems throughout cruise because of low 
water flow rate and air contamination in the equilibrator.


4.3 UM UNDERWAY pH

pH measurement were made using the spectrophotometric techniques of Clayton and 
Byrne (1993) with m-cresol purple (mCP) indicator determined from:

           pH = pKind + log[(R- 0.0069)/(2.222 - 0.133R)]             (2)



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



where Kind is the dissociation constant for the indicator and R (A578/A434) is 
the ration of the absorbance of the acidic and basic forms of the indicator 
corrected for baseline at 730 nm. The samples are drawn from a SBE 45, which 
measured the temperature and salinity, using a Kloehn 50300 syringe pump and 
injected into the 10cm optical cell. The syringe rinses and primes the optical 
cell with 20 cm3 of sample and the software permits three minutes of 
temperature stabilization before a blank is measured. The automated syringe 
then draws 0.008 cm3 of indicator and 4.90 cm3 of sample and allows for five 
minutes of temperature stabilization. The program was set to measure an 
underway sample every ten minutes and reported with a timestamp (the GPS line 
provided by the ship was not compatible the software) that will have to be 
matched with the ship's GPS position. The system was stopped while on station, 
and restarted during the transit between stations, this yielded about 1480 
samples. The values reported are with the measured temperature and are in terms 
of the sea water scale.


5.0 OTHER MEASUREMENTS

5.1 NET TOWS/PTEROPOD

In an add-on project funded by the NSF Chemical Oceanography Program, V. Fabry 
(CSUSM), R. Byrne (USF), and J. Schijf (USF) worked on the dissolution of 
freshly collected pteropod shells. At about 10 stations, plankton tows were 
conducted in the upper 25 m at night. Pteropod shells were quickly sorted and 
used in dissolution experiments employing a high precision, spectrophotometric 
method to measure pH. The main objective of this cruise work was to test a 
newly constructed experimental cell. We conducted dissolution experiments at 25 
stations between Honolulu and Kodiak. In addition, we conducted preliminary 
experiments on live pteropods at 8 stations. Samples were shipped back to CSUSM 
for laboratory analysis.


5.2 FLOATS

Eight Web Research Corporation APEX floats were launched for Howard Freeland of 
the Institute of Ocean Sciences in British Columbia. These floats are part of 
the Canadian Argo project and were deployed at the northern end of the P16N 
section to better populate this area. Floats were deployed after the completion 
of all station work at 31˚N, 34˚N, 37˚N, 40˚N, 44˚N, 47˚N, 50˚N, and 55˚N. Each 
deployment required 30 minutes of startup time to unpack, inspect, and test the 
float. All floats passed their self-check routines and were launched 
successfully. Immediately following deployment, an email was sent to Dr. 
Freeland to report the exact time and position of the float. Return emails from 
Dr. Freeland confirmed that all floats were working properly.


6.0 ACKNOWLEDGEMENTS. 

The scientific party of the P16N cruise would like to express sincere thanks to 
Captain Al McClenaghan and all of the crew of the R/V Thompson for their 
outstanding work in support of our cruise despite some very difficult 
wintertime weather conditions in the North Pacific Ocean.



                                                 P16N_2006 • Leg 2 • Sabine/Feely • R/V Thomas G. Thompson



7.0  REFERENCES

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    depth microprofiler, Technical Report No. 78-23, Woods Hole Oceanographic 
    Institution.

Bullister, J.L. and R.F. Weiss. 1988. Determination of CCl3F and CCl2F2 in 
    seawater and air. Deep-Sea Res., 35, 839-853.
    
Byrne, R.H., Liu, X., Kaltenbacher, E., and Sell, K. 2002. Spectrophotometric 
    Measurement of Total Inorganic Carbon In Aqueous Solutions Using a Liquid 
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Carpenter JH (1965) The Chesapeake Bay Institute technique for the Winkler 
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Chen, H., R. Wanninkhof, R.A. Feely, and D. Greeley, 1995. Measurement of 
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Chipman, D.W., J. Marra, and T. Takahashi, 1993. Primary production at 47°N and 
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Clayton, T.D., R.H. Byrne. 1993. Spectrophotometric seawater pH measurements: 
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Culberson C.H., and Huang S (1987). Automated amperometric oxygen titration. 
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Culberson, C. H., Knapp, G., Stalcup, M., Williams, R. T., and Zemlyak, F., 
    Aug. 1991. A comparison of methods for the determination of dissolved 
    oxygen in seawater, Report WHPO 91-2, WOCE Hydrographic Programme Office.

DOE Handbook, 1996. SOP 7: Determination of the pH of seawater using the 
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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 aboard research ships. Anal. Chim. Acta, 377, 185-191.

Gordon, L.I., Joe C. Jennings, Jr., Andrew A. Ross, and James M. Krest. 1995. A 
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    nutrients (Phosphate, Nitrate, Nitrite and Silicic Acid) in the WOCE 
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    Oc. Descr. Chem. Oc. Grp. Tech. Rpt. 93-1.

Johnson, K.M., A.E. King, and J. McN. Sieburth. 1985 Coulometric DIC analyses 
    for marine studies: An introduction. Mar. Chem., 16, 61-82.
    
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., 21, 117-133.

Johnson, K.M. 1992. Operator's manual: Single operator multiparameter metabolic 
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    Brookhaven National Laboratory, Brookhaven, N.Y., 70 pp.

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 
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Joyce, T., ed. and Corry, C., ed., May 1994, Rev. 2. Requirements for WOCE 
    Hydrographic Programme Data Reporting, Report WHPO 90-1, WOCE Report No. 
    67/91, 52-55, WOCE Hydrographic Programme Office, Woods Hole, MA, USA. 
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    Workshop, p. 19, Mar. Tech. Soc., La Jolla, Ca.

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    calibration, Journ. of Am. Meteorological Soc., 15, p. 621.
    
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    F.N., O'Doherty, S., Salameh, P., Miller, B.R., Huang, J., Wang, R.H.J., 
    Hartley, D.E., Harth, C., Steele, L.P., Sturrock, G., Midgley,  P.M., 
    McCulloch, A., 2000.  A history of chemically and radiatively important 
    gases in air deduced from ALE/GAGE/AGAGE.  Journal of Geophysical  
    Research, 105, 17,751-17,792.
    
Peng, T.-H., Takahashi, T., Broecker, W. S., and Olafsson, J., 1987. Seasonal 
    variability of carbon dioxide, nutrients and oxygen in the northern North 
    Atlantic surface water:  observations and a model. Tellus, v. 39B, p. 439-
    458.

Thurnherr, A.M., 2006: How To Process LADCP Data With the LDEO Software 
    (Draft). Lamont-Doherty Earth Observatory. Thurnherr, A.M. and B. Huber, 
    2006. Setup and Operation of the LDEOLowered ADCP System. Lamont-Doherty 
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UNESCO, 1981. Background papers and supporting data on the Practical Salinity 
    Scale, 1978, UNESCO Technical Papers in Marine Science, No. 37, p. 144.
    
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.

Wilke, R.J., D.W.R. Wallace, and K.M. Johnson. 1993. Water-based gravimetric 
    method for the determination of gas loop volume. Anal. Chem. 65, 2403-2406.
    
Zhang, J-Z., Fischer C., and Ortner, P. B., 2000. Comparison of open tubular 
    cadmium reactor and packed cadmium column in automated gas-segmented 
    continuous flow nitrate analysis. International Journal of Environmental 
    Analytical Chemistry, 76(2):99-113.
    
Zhang, J-Z., Ortner P. B., and Fischer, C., 1997. Determination of nitrite and 
    nitrate in estuarine and coastal waters by gas segmented continuous flow 
    colorimetric analysis. EPA's manual, Methods for the determination of 
    Chemical Substances in Marine and Estuarine Environmental Matrices - 2nd 
    Edition.  EPA/600/R- 97/072.

Zhang, J.-Z., C. Fischer and P. B. Ortner, 2001. Continuous flow analysis of 
    phosphate in natural waters using hydrazine as a reductant. International 
    Journal of Environmental Analytical Chemistry, 80(1), 61-73.





__________________________________________________________________________________________________________
__________________________________________________________________________________________________________

                                                         P16N_2006 • Sabine/Feely • R/V Thomas G. Thompson



                         APPENDIX: ADDENDUM TO CTD REPORT
                                   (12 OCT 2006)


Data Manager:               Frank Delahoyde
Marine Technicians:         Bill Martin, Tony Burke
CTD Watchstanders (leg 1):  Sara Bender, John Reum, Jessica Silver, Josh Burton 
                  (leg 2):  Samantha Deringer, Dave Faber 
CTD Electronics Technician: Dave Bitterman
Quality Control/Processing: Kristy McTaggart
Sample Salinity Analyst:    Grant Rawson
Sample Oxygen Analyst:      George Berberian (leg 1), Chris Langdon (leg 2)


ACQUISITION

During this cruise, 84 stations were occupied in the central and north Pacific 
from 17°S, 150°W to 56.3°S, 153.2°W at nominally 60-nm spacing, but closer 
crossing the equator and between the Aleutian Trench and the continental shelf 
just south of Kodiak Island, Alaska. A total of 87 CTD/O2 profiles were 
collected. At station 25, the first cast was aborted during the up-cast and a 
second complete profile was collected after the sea cable was re-terminated. At 
stations 78 and 83, the first casts were aborted during the downcast because of 
a ship-wide power outage and a second complete profile was collected after power 
was restored. All casts were deep profiles, the majority to within 20m of the 
bottom, with bottom depths determined from echo-sounding ranging from 399 m to 
5784 m uncorrected for deviations from a nominal 1500 m s-1 sound speed. No 
water samples were collected from aborted casts 0251, 0781, and 0831.

All CTD/O2 profiles were collected using Sea-Bird instrumentation mounted in a 
36- position stainless steel frame with 34 (leg 1) to 36 (leg 2) 12-liter Niskin 
bottles and 36- position carousel s/n 431. Sea-Bird sensors included 9plus CTD 
s/n 315, primary TC s/n 03P-4341 and 04C-2887, secondary TC s/n 03P-4335 and 
04C-3068, and oxygen s/n 43- 0664 (stations 1-66) and 43-0313 (stations 67-84). 
Also mounted on the underwater package, were an LACDP and battery pack, 
fluorometer, transmissometer, altimeter, load cell, and pinger.

Data were acquired at full 24 Hz resolution through the ship's Sea-Bird 11plus 
V2 deck unit onto the ship's dedicated PC using Sea-Bird Seasave Win32 version 
5.27c acquisition software. Real-time digital data were backed up onto Scripps 
and PMEL networked PCs. No real-time data were lost.

TERMINATION PROBLEMS

The initial termination of the sea cable failed during the test cast at station 
1, likely because all three positive conducting wires were included in the 
solder joint. Modulo errors began on deployment and reached a total of 1956 by 
the end of the cast. Water samples were collected as planned, however, and the 
sea cable was successfully re- terminated before station 2 using only one 
conducting wire.

At station 25, the sea cable fuse in the deck unit blew repeatedly at about 
5000m during the up-cast. The cast was aborted. It was determined that a dead 
short existed somewhere in the red conducting wire used in the termination. The 
cable was successfully re-terminated using one of the remaining white wires and 
a second full profile was collected at this station.



                                       P16N_2006 • CTD Addendum • Sabine/Feely • R/V Thomas G. Thompson



PROCESSING

The reduction of profile data began with a standard suite of processing modules 
(process.bat) using Sea-Bird Data Processing Win32 version 5.37b 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 skip 
       over scans acquired on deck and while priming the system under water. 
       MARKSCAN values were entered at the DATCNV menu prompt. 

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. Both conductivities are 
       automatically advanced in the V2 deck unit by 0.073 seconds. No 
       additional alignment was necessary for primary conductivity sensor s/n 
       2887. An additional alignment of .030 seconds was made to secondary 
       conductivity sensor s/n 3068 for a net advance of .043 seconds. It was 
       not necessary to align temperature or oxygen.

BOTTLESUM averages burst data over an 8-second interval (±4 seconds of the 
       confirm bit) and derives both primary and secondary salinity, primary 
       potential temperature (Θ), primary potential density anomaly 
       (∑σ), and oxygen (in µmol/kg). 

WILDEDIT makes two passes through the data in 100 scan bins. The first pass 
       flags points greater than 2 standard deviations; the second pass removes 
       points greater than 20 standard deviations from the mean with the flagged 
       points excluded. Data were kept within 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 negligible.  The value used for the thermal anomaly 
       amplitude (α) was 0.03. The value used for the thermal anomaly time 
       constant (ß-1) was 7.0 s.  LOOPEDIT removes scans associated with 
       pressure slowdowns and reversals. If the CTD velocity is less than 0.25 m 
       s-1 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 salinity.

TRANS converts the binary data file to ASCII format.



                                       P16N_2006 • CTD Addendum • Sabine/Feely • R/V Thomas G. Thompson



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, program deloop.m 
computes values of density locally referenced between every 1 dbar of pressure 
to compute the square of the buoyancy frequency, N2, and linearly interpolates 
temperature, conductivity, and oxygen voltage over those records where N2 is 
less than or equal to -1 x 10-5 s-2. Twelve profiles failed this criteria in the 
top 10 meters. These data were retained by program deloop_post.m and flagged as 
questionable in the final WOCE formatted files.

Program calctd.m reads the delooped data files and applies final calibrations to 
primary temperature and conductivity, and computes salinity and calibrated 
oxygen. Program cnv_eps.f computes ITS-90 temperature, potential temperature 
(Θ), density anomalies σt and σθ, and dynamic height; creates 
WOCE quality flags, and converts the ASCII calibrated data files into NetCDF 
format for PMEL's database. Program wocelst.f converts the ASCII calibrated data 
files into ASCII WOCE format for submission to the WHPO.

PRESSURE CALIBRATION

Pressure calibrations for the CTD instrument used during this cruise were pre-
cruise. No additional adjustments were applied. On deck pressure readings prior 
to each cast were examined and remained within 0.5 dbar of calibration. 
Differences between first and last submerged pressures for each cast were also 
examined and the residual pressure offsets were <0.7 dbar.

TEMPERATURE CALIBRATION

In addition to a viscous heating correction of -0.0006°C, a linearly 
interpolated temperature sensor drift correction using pre and post-cruise 
calibration data for the midpoint of the cruise was determined. For primary 
temperature sensor s/n 4341 used for all casts, the drift correction was 
0.000475°C. Viscous and drift corrections were applied to profile data using 
program calctd.m, and to burst data using calclo.m.

CONDUCTIVITY CALIBRATION

Seasoft module BOTTLESUM creates a sample file for each cast. These files were 
appended using program sbecal1.f. Program addsal.f matched sample salinities 
flagged as good to CTD salinities by station/sample number. Primary sensor s/n 
2887 was selected for calibration and program calcos0.m produced the best 
results for an overall linear fit of sample data from stations 8-71. 

                   number of points used    1797
                   total number of points   2057
                   % of points used in fit    87.36
                   fit standard deviation      0.001389             
                   fit bias                   -0.00093990233
                   fit slope                   0.99997966



                                       P16N_2006 • CTD Addendum • Sabine/Feely • R/V Thomas G. Thompson



Note that bottle sample salinities were poor for stations 1-7, 25, and 72-84. 
These data   were not used in the fit above. Temperature stability problems 
during the salinity analysis for stations 1-7 resulted in poor data. Samples 
from station 25 were run with a bad standardization. After station 71, the 
autosalinometer standard dial was substantially adjusted in an attempt to 
compensate for fluctuating lab temperatures and standard drift rates increased 
sharply for subsequent runs, again resulting in poor quality bottle salinity 
data. Conductivity calibrations were applied to profile data using program 
calctd.m, and to burst data using calclo.m.

Primary sensor CTD - bottle conductivity differences plotted against station 
number (Figure 1) and pressure (Figure 2) are used to allow a visual assessment 
of the success of the fit. Note that although data from stations 72-84 are 
plotted here, they were not used in the fit.

During the cruise, the primary and secondary cells were stable and tracked each 
other very well. The primary cell was salty of the secondary cell by about 0.002 
PSS-78 during the entire cruise. However, there was no drift in the calibration 
of either cell with time during the cruise discernible through comparisons 
between the sensor pairs and with bottle salinity data deemed good. Post-cruise 
calibrations suggested no discernible calibration shift in the primary cell and 
a 0.002 PSS-78 shift fresh in the secondary cell.  Putting all this information 
together suggests that the fresh offset was in the secondary cell and occurred 
after the pre-cruise calibrations but prior to the cruise. Calibrating each 
sensor to sample salinities resulted in the primary cell being abut 0.003 PSS-78 
fresh of its pre- and post-cruise calibrations and the secondary cell being more 
than 0.002 PSS-78 fresh of its post-cruise calibration. So both conductivity 
sensors were adjusted to be fresh of their pre and post-cruise calibrations on 
the basis of the bottle salts, and agree within 0.001 PSS-78 after this 
adjustment.

In spite of this fresh adjustment, final P16 2006 CTD/O2 salinity data are 
noticeably salty of historical data from previous occupations of this line. 
Comparisons with previous cruises (WOCE P16C in 1991, WOCE P16N in 1990, and 
Marathon II in 1984) along a deep potential isotherm (θ=1.2°C), even after 
correcting for standard seawater batch differences following the recommendations 
of Kawano et al. (in press), suggest that the calibrated CTD salinities are on 
average 0.0022 (±0.0005) PSS-78 saltier than previous cruise data. This 
discrepancy is unresolved, and the CTD O2 salinity data have not been adjusted 
beyond the calibration described above.


OXYGEN CALIBRATION 

Program addoxy.f matched bottle sample oxygen values flagged as good (2 or 6) to 
CTD oxygen values by station/sample number. Because of sensor hysteresis, 
programs match_sg2_664.m (stations 1-66) and match_sg2_313.m (stations 67-84) 
were used to match up-cast oxygen data to downcast oxygen data by potential 
density anomalies referenced to the closest 1000-m interval. A least-squares 
station-dependent fit was determined for groups of stations using program 
run_oxygen_cal_1.m: 



                                       P16N_2006 • CTD Addendum • Sabine/Feely • R/V Thomas G. Thompson



Station  Slope Range     Bias    Lag     Tcor    Pcor  Points Used  StdDev
------- -------------  -------  ------  ------  ------ -----------  -------
  1- 4  0.3309-0.3399  -0.4972  3.0197  0.0029  0.0001  100 98.0%   0.4481 
  5-20  0.3511-0.3645  -0.5119  3.1121  0.0023  0.0001  528 90.5%   0.7684
 21-22  0.3731-0.3731  -0.5271  3.7915  0.0016  0.0001   68 88.2%   0.6854
 23-43  0.3620-0.3693  -0.5059  3.3016  0.0023  0.0001  628 89.6%   0.8648
 44-66  0.3756-0.3820  -0.5145  7.3144  0.0017  0.0001  783 89.8%   0.8288
 67-67  0.3612-0.3612  -0.4606  3.7839  0.0102  0.0002   29 96.6%   0.6001
 68-84  0.4244-0.4359  -0.4600  6.7851 -0.0056  0.0001  524 82.1%   0.7518


Oxygen calibration coefficients were applied to profile data using program 
calctd.m, and to burst data using calclo.m.

Primary sensor CTD - bottle oxygen differences plotted against station number 
(Figure 3) and pressure (Figure 4) are used to allow a visual assessment of the 
success of the fits.

FINAL PROCESSING NOTES ON ANOMALOUS DATA

The initial termination of the sea cable failed during the test cast at station 
1, likely because all three positive conducting wires were included in the 
solder joint. Modulo errors began on deployment and reached a total of 1956 by 
the end of the cast. Program cleaner.m was used to clean up raw 24-Hz pressure, 
temperature, conductivity, and oxygen voltage data. Program cleaner.m uses a 
positive real number (either 2 or 3) that is the tolerance of the mean absolute 
value of the second difference, tested in runs of 3, and an integer number that 
tells roughly how many offset but smooth data points to interpolate over (1 
would be for spikes and 2 or 3 for longer glitches). Then a 13-point median 
filter was used to identify bad data deeper than 500 dbar and greater than 
0.002°C in temperature and 0.002 mS/cm in conductivity. Bad data were replaced 
with interpolated values and the profile was processed as usual. 

During casts 0501 and 0511, the air-bleed in the y-fitting of the primary sensor 
plumbing was blocked resulting in slightly low surface salinities within 10 dbar 
of the surface, and oxygen spikes as deep as 53 dbar. Temperature was 
unaffected. Low salinities were flagged as questionable by wocelst.f for WOCE 
data files. Conductivities were copied back to the surface from the first good 
value and salinities recomputed by cnv_eps.f for PMEL data files. Bad CTD 
oxygens were flagged by wocelst.f for WOCE data files, and copied back as 225.0 
µmol kg-1 (in agreement with surrounding profiles and sample oxygens) by 
cnv_eps.f for PMEL data files. Copied back values were flagged 8 in PMEL data 
files.

A fouling event occurred near depth in the primary sensors at station 81. TCO 
data deeper than 2348 dbar were flagged as bad by wocelst.f for WOCE data files, 
and the profile truncated by cnv_eps.f for the PMEL data file.

Quality flags for bottle sample salinities were amended by viewing plots of 
calibrated CTD/O2 and bottle salinity data generated by program plot_th_sa.m. 
Similarly, recommendations for bottle sample oxygens were forwarded to the 
bottle oxygen PI after viewing plots of calibrated CTD/O2 and bottom oxygen data 
with plot_pr_ox.m. Final CTD/O2 bottle data, p16n_allf.flg, was submitted to 
WHPO to incorporate into the master data file. For PMEL's database, individual 
bottle files for each cast were created in NetCDF format using clb_eps.f. Since 
PMEL EPIC programs do not recognize WOCE flags, those sample data flagged as bad 
were changed to 1e35. 



__________________________________________________________________________________________________________
__________________________________________________________________________________________________________

                                                         P16N_2006 • Sabine/Feely • R/V Thomas G. Thompson



CCHDO DATA PROCESSING NOTES

Date      Contact    Data Type      Data Status Summary  

01/27/06  Sabine     Cruise ID      Preliminary cruise info.  
          You can find the cruise web site at the following address:
                     http://www.pmel.noaa.gov/co2/p16n/
          However, I don't think you will find the information you are looking 
          for yet. The cruise track that is shown at the site is not the final 
          track. The final track is not set yet because we are still 
          negotiating with the ship to determine whether we are doing a port 
          stop in Hilo or Honolulu. The cruise personnel are not finalized 
          either. We are told that there are 35 berths and at the moment we 
          have 37 people that want to go on each leg. We are negotiating with 
          the groups to get this number down. We just designated the student 
          participants last Friday. I think we will have a much better idea 
          next week if you can wait that long. I will let you know once we have 
          these things better nailed down.
                    
03/23/06  Sabine     Cruise Report  Submitted Preliminary report  
          As you know, I recently returned from the first leg of the 
          P16N cruise on the Thomas G. Thompson. The cruise went very well. 
          Attached, please find a copy of my preliminary cruise report. Please 
          let me know if you have any questions or concerns with this report. 
          Frank Delahoyde provided me with a DVD of the shipboard data. I 
          presume he will deliver the data to Scripps.

03/23/06  Sabine     BTL/SUM           Submitted Exchange format, CTD to follow 
          I have attached the SEA, SUM, and WOCE EXCHANGE format data from the 
          cruise.  I can also send you the CTD data, but that is a bit large to 
          send over email. Hopefully this is enough to get the site started, 
          then when Frank returns in a couple of weeks he can give you the 
          larger files. 
                    
05/01/06  Feely      Cruise Report  Submitted leg 2 report
          Attached please find a copy of our cruise report for P16N Leg 2 on 
          the Thomas G. Thompson.  Please post this cruise report on the cruise 
          website.  I will have Dana Greeley post it on the PMEL cruise website 
          as well.  Let me know if there are any other places that we should 
          send it to.
                    
05/06/06  Diggs      CTD/BTL/SUM    Website Updated: Data Online  
          The preliminary data for P16N from 2006 (3250200602) are now available 
          on the CCHDO website:
          http://cchdo.ucsd.edu/data/co2clivar/pacific/p16/p16n_2006a/index.htm
          (WOCE-SUM, BTL & CTD in Exchange format as well as pdf documentation)
          
          These data are also available through the website through the normal 
          means of discovery.  For now, the cruise report on reflects the 
          events pertaining to Leg 1, though I believe that the information for 
          Leg 2 is available.
          
          NetCDF files will be available later next week. 
                    
05/07/06  Diggs      BTL            Website Updated: BTL data taken Offline  
          As of Sunday morning (9:00am PDT) I have removed all links to the 
          bottle data for P16n as you have requested.  Only the SUM, CTD and DOC 
          links remain.  Also, I've updated the contact information regarding 
          Chief Scientists to include both of your names and contact informa-  
          tion.  My apologies, that link wasn't made active, but it was there.
          
          This brings up an interesting dilemma pertaining to the de facto 
          bylaws for the US Repeat Hydrography Program.  I think that there was 
          a deadline for getting these data to the data center by a certain 
          date, but nothing that says the the files need to be >available< to 
          the public.
          
          For now, please check the website and determine if you are all 
          comfortable with the data that are available and the accuracy of the 
          information provided on the webpage.  If there are any additional 
          changes or updates, please feel free to let us know.

05/07/06  Feely      CTD/BTL/SUM    Data are NOT Public  Too preliminary  
          Please call me before you place any of the P16N bottle data on the 
          CCHDO website. I am certain that most the PIs, including myself, feel
          that this data is much too preliminary to be put on a public website 
          at this time. In most cases, the data must be further corrected for 
          standards, temperature corrections, etc, before we want the data on 
          the website. I would prefer that you remove it immediately until we 
          resolve this issue.
          
          Also you should correct the website to have Sabine/Feely as co-chief 
          scientists for the P16N cruise.  There were two legs of this cruise 
          and each of us was responsible for one of the legs.  Chris and I have 
          sent Jim copies of the individual cruise reports and they should be 
          included in the documentation as pdf files.
                    
05/08/06  Kozyr      PCO2           Data are Final  Ready to merge into hyd file  
          I have received the final discrete pCO2 measurements from Rik 
          Wanninkhof for P16N_2006  cruise (the World record for the final data 
          submission).  Could you please send me the preliminary bottle data 
          files (both WOCE and Exchange format if it is possible), so I could 
          merge the pCO2 data and other carbon-related data before I submit 
          these data to CCHDO?
                    
05/09/06  Diggs      PCO2           Ready to merge into hyd file; csv only 
          Here you go!  Let me know if there are any problems.  I only have the  
          data in WHP-Exchange (csv) format.  
                    
05/11/06  Kappa      Cruise Report  Ready to go online     
          I just put pdf and text docs for the p16n_2006a cruises (both legs) in 
          my directory.  Please put them online when possible.

05/11/06  Sara       BTL            Submitted; Preliminary  
          Chris Sabine instructed me to send my preliminary data from the P16N 
          cruise to you. This data was collected by myself, Sara Bender. It will 
          be used by Paul Falkowski (Rutgers University). Chris said the data is 
          classified as "level 3 measurements." I have attached an excel file as 
          well as a brief description of what these measurements will be used for. 
                    
05/22/06  Feely      CTD/BTL        Data are Public; except DIC and pH
          You have made an excellent suggestion. Let's go forward with that 
          approach.  Unfortunately, I do not have someone in my group to 
          reformat that particular file format. Dan Greeley from my group is 
          actively working on the DIC data this week and I will contact Frank 
          Millero to see where he stands with the pH data.
          
          Susan Piercy wrote:
          Hi Dick,
          
          From the recent email you sent to Lynne, it sounds like all bottle 
          data except DIC and pH data should go online. Just want to make sure 
          about this and ask for your formal permission.
          
          If we have your permission to link all data except for these two 
          parameters, can someone in your group reformat the file?
                    
05/26/06  Feely      ALKALI         Not public  Reply to Frank Millero   
          I knew there were some issues with the pH data, I wasn't aware that you 
          had concerns over the TALK data as well.  By copy of this e-mail I 
          will ask Susan not to post the TALK and pH data on the website until 
          she hears back from you.
                    
06/15/06  Millero    ALKALI/DIC/pH  DQE Complete; will send data & report next week  
          All of our quality control of the data is finished and we have 
          complete our data report on the cruise. I am off on a trip tomorrow 
          for a week and will have my group send you our final results next 
          week.

06/15/06  Diggs      BTL            Website Updated: BTL data online (no ALK/DIC)
          We've finally removed the offending parameters from the bottle file.  
          Actually, just 'parameter', since PH from the two institutions was all 
          that needed removing. TALK and DIC were not in this version of the 
          Exchange bottle file
          
          The webpage reflects this change:
          
          <http://cchdo.ucsd.edu/data/co2clivar/pacific/p16/p16n_2006a/>http:/
                /cchdo.ucsd.edu/data/co2clivar/pacific/p16/p16n_2006a/
          
          Please let me know if the are questions, comments or concerns.  Once 
          we receive the sanctioned versions of TALK,PH and DIC, we will merge 
          them into the online bottle file and replace the one currently 
          online.
          
06/15/06  Greeley    DIC            Submitted  as csv files  
          I've just uploaded final DIC data and QC Flags to the web site: 
          http://cchdo.ucsd.edu/.  I did this for Dr's Feely and Sabine.  They 
          were uploaded as separate csv files.  Please let me know if there are 
          problems and/or questions.
                    
08/01/06  Kozyr      CO2            Submitted TCO2, TALK, pCO2, and pH  
          Here is attached the final carbon data (TCO2, TALK, pCO2, and pH) and 
          quality flags for Repeat hydrography cruise P16N_2006, EXPOCODE  
          3250200602.  The data are in the  exchange formatted file. Please 
          merge these data into the final hydrography file. Could you please let 
          me know when the data will be merged.
                    
08/02/06  Kozyr      TCARBN         Submitted; Data Update  
          We made some corrections to the data files I've sent you yesterday 
          (P16N_2006 and P16S_2005). The new files are attached. Please, discard 
          both yesterday's files.
                    
08/15/06  Diggs      ALKALI/DIC/pH  Data received  
          I did receive these files via email and they will be merged within the  
          week.    
                    
09/19/06  Kozyr      CO2            Data are Final  Submitted 8/2/06  
          The August 2nd files are the final ones. After I sent the data to CCHDO 
          on Aug. 1, Bob Key from Princeton, who is my collaborator on QA-QC 
          independent work sent me some additional quality flags which I 
          incorporated in the final data files. All PIs have "finalized" the 
          carbon data (pH, TALK, TCO2 and pCO2 parameters for P16N_2006 and 
          TCO2 only for P16S_2005). The final data for P16N_2006 are open 
          through CDIAC web page now and you could extract these parameters 
          from the file to avoid any confusion. You can copy the final files 
          at: http://cdiac.ornl.gov/oceans/RepeatSections/clivar_p16n.html and 
          click on "Data files". 
                    
09/25/06  Warner     CFCs           Data submission eta   
          I do anticipate a final update to the CFC data. I suspect it will be 
          completed in mid-October.
                    
09/26/06  Kozyr      DOC            Data submission ETA 2+ weeks  
          I have talked to Dennis yesterday. The DOC measurements are performed 
          onshore and it takes longer time to finalize these data than other 
          measurements made at sea. Dennis is in UK at this time, he will be 
          back in two weeks. The data will be submitted to CDIAC shortly after 
          his return.
                    
10/10/06  McTaggart  CTDOXY/report  Submitted  Data are Final
          File:      p16n_allf.flg  Type: ASCII CTDO discrete data Status: Public
          Name:      McTaggart, Kristy 
          Institute: NOAA PMEL 
          Country:   USA
          Expo:      33TT200601 Line: P16N
          Date:      02/2006
          Action:    Merge Data,Place Data Online,Updated Parameters
          Notes:
          • Calibrated CTDO bottle data with ammended sample salinity flags.
          • 87 profiles in ASCII format
          • 1 file of calibrated discrete CTDO data and ammended sample 
            salinity flags
          • 1 documentation file and 4 .pdf figures
                    
11/09/06  Kappa      Cruise report  Update; added leg 2 & new CTD reports, dpns
          • Added new CTD data report from Kristy McTaggart (10/10/06) to text
            and pdf files
          • Added report for leg 2 to text and pdf files
          • Added these Data Processing Notes to text and pdf files
          


