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CRUISE REPORT: A22_2003  
(updated: 2009 OCT 07)

A.  HIGHLIGHTS 

                            CRUISE SUMMARY INFORMATION

                     Section designation  A22
       Expedition designation (ExpoCode)  316N200310
 Chief Scientists and their affiliations  Dr. Terrence M. Joyce/WHOI*
                                          Dr. William M. Smethie Jr./LDEO**
                                   Dates  2003 OCT 23 to 2003 NOV 13
                                    Ship  R/V Knorr
                           Ports of call  Port of Spain, Trinidad - 
                                          Woods Hole, Ma.
                      Number of stations  82
                                                    40° 0.63'N
         Stations' Geographic boundaries  70° 0.45'W          64° 9.37'W
                                                    11° 0.02'N

            Floats and drifters deployed  3 ARGO floats deployed (one failed)
          Moorings deployed or recovered  0
                    Contributing Authors  T. Joyce
                                          F. Delahoyde
-------------------------------------------------------------------------------
                   *Dr. Terrence M. Joyce • Senior Scientist
                      Woods Hole Oceanographic Institution
                        360 Woods Hole Rd., Mail Stop 21
                           Woods Hole  MA  02543 USA
        Phone: 508-289-2530 • Fax: 508-457-2181 • E-mail: tjoyce@whoi.edu

                          **Dr. William M. Smethie Jr.
              Lamont-Doherty Earth Observatory • Columbia University
                 Route 9W PO Box 1000 • Palisades  NY  10964-8000
   Phone: 914-365-8566 • Fax: 914-365-8155 • E-mail: bsmeth@ldeo.columbia.edu


 
                         
                           PRELIMINARY CRUISE REPORT
                             mod. 13 November 2003
                               Data Submitted by:
                          Oceanographic Data Facility
                      Scripps Institution of Oceanography
                            La Jolla, Ca. 92093-0214


SUMMARY

A hydrographic survey consisting of LADCP/CTD/rosette sections and float 
deployments in the western North Atlantic was carried out October to November 
2003. The R/V Knorr departed Port of Spain, Trinidad on 23 October 2003. A 
total of 82 LADCP/CTD/Rosette stations were occupied, and 3 profiling ARGO 
floats were deployed from 23 October - 13 November.  Water samples (up to 36), 
LADCP and CTD data were collected in most cases to within 10 meters of the 
bottom. Salinity, dissolved oxygen and nutrient samples were analyzed from 
every bottle sampled on the rosette.  The cruise ended in Woods Hole, Ma. on 13 
November 2003.


PRINCIPAL INVESTIGATORS:

PARAMETER/PROGRAM    NAME             Inst       EMAIL ADDRESS
-----------------    ----             ----       ------------------------
Chief Scientist      Terrence Joyce   WHOI       tjoyce@whoi.edu
Co-Chief Scientist   William Smethie  LDEO       bsmeth@ldeo.columbia.edu
CTDO/S/O2/Nutrients  James Swift      SIO        jswift@ucsd.edu
DIC                  Richard Feely    PMEL       Richard.A.Feely@noaa.gov
                     Chris Sabine     PMEL       Chris.Sabine@noaa.gov
CFC                  William Smethie  LDEO       bsmeth@ldeo.columbia.edu
                     Rana Fine        UofMiami   rfine@rsmas.miami.edu
TALK                 Frank Millero    UofMiami   fmillero@rsmas.miami.edu
CDOM, DOC, DON       Craig Carlson    UCSB       carlson@lifesci.ucsb.edu
He/Tr                William Jenkins  WHOI       wjenkins@whoi.edu
Surface C14          Ann McNichol     WHOI       amcnichol@whoi.edu
                     Robert Key       Princeton  rkey@princeton.edu
C13 profiles         Paul Quay        UofWash    pdquay@u.washington.ed


INTRODUCTION

A sea-going science team gathered from ten oceanographic institutions around 
the U.S. participated on the cruise.  Several other science programs were 
supported with no dedicated cruise participant. The science party and their 
responsibilities are listed below: 


SCIENTIFIC PERSONNEL: 

NAME                 AFFILIATION  DUTIES              E-MAIL
-------------------  -----------  ------------------  -------------------------------
Terrence Joyce       WHOI         Chief Scientist     tjoyce@whoi.edu
William Smethie      LDEO         Co-Chief Scientist  bsmeth@ldeo.columbia.edu

Jane Dunworth-Baker  WHOI         BTL                 jdunworth@whoi.edu

David Cooper         Miami        CFC                 fleece@eritter.net
Ryan Ghan            LDEO         CFC                 rng14@columbia.edu
Fred Menzia          Miami        CFC                 menzia@pmel.noaa.gov
Rick Wilke           Miami        CFC                 wilke@bnl.gov

Timothy Newberger    LDEO         LADCP               tnewberg@ldeo.columbia.edu

Dana Greeley         NOAA         DIC                 greeley@pmel.noaa.gov
Chris Sabine         NOAA         DIC                 sabine@pmel.noaa.gov

Mareva Chanson       RSMAS        TALK
Vanessa Koeler       RSMAS        TALK                vkoeler@rsmas.miami.edu

Peter Landry         WHOI         Helium/Tritium      plandry@whoi.edu

Susan Becker         SIO          Nutrients           sbecker@ucsd.edu
John Calderwood      SIO          Deck/O2             jcalderwood@ucsd.edu
Cambria Colt         SIO          Deck/Salts          restech@sdsioa.ucsd.edu
Frank Delahoyde      SIO          CTD/DP              fdelahoyde@ucsd.edu
Scott Hiller         SIO          ET/Deck/Salts       shiller@ucsd.edu
Dan Schuller         SIO          Nutrients           dschuller@ucsd.edu
Tina Sohst           SIO          Deck/O2

Craig Carlson        UCSB         CDOM                carlson@lifesci.ucsb.edu
Stu Goldberg         UCSB         CDOM                s_goldbe@lifesci.ucsb.edu
Jon Klamberg         UCSB         CDOM                jon@icess.ucsb.edu

Kate Boyle (GRA)     SIO          watchstander        kaboyle@ucsd.edu
Monica Byrne (GRA)   WHOI/MIT     watchstander        mcbyrne@mit.edu

Dr Julian Castaneda  Venezuela    observer            julianc@cumana.sucre.udo.edu.ve


OTHER SCIENCE PROGRAMS:

Eric Firing          U. Hawaii    Shipboard ADCP
Jules Hummon         U. Hawaii    Shipboard ADCP
Ann McNichol         WHOI         Surface C14
Robert Key           Princeton    Surface C14
Paul Quay            UW           C13 profiles
Allyn Clarke         BIO          Profiling ARGO floats
Wilf Gardnert        AMU, Canada  Transmissometer profiles




B.  CRUISE NARRATIVE
    (T. Joyce/WHOI)

B.1  FRESHWATER FRONT IN CARIBBEAN

A selection of data obtained with the thermosalinograph in the bow 
intake of the Knorr shows a strong SSS front near 12°40'N, which is 
between CTD stations 8 & 9. This is the same location of a similar 
feature found during the cruise in 1997 along this transect, and could 
be a signature of the Orinoco river plume in the Caribbean. The 
latitude extent of the fresh water layer is larger and the near surface 
salinity lower in the present section, with a return to higher salinity 
surface water just to the south of 16 oN, whereas this low salinity 
layer terminated just to the north of 14 oN in 1997. This fresh layer is 
very thin, limited to the upper 20-30m. In the 1997 section, a strong 
surface velocity jet was associated with the front. While SADCP data on 
ship suggested this as present, we were unable to produce processed 
SADCP data at sea & this will be investigated later.


FIGURE B.1.1: Preliminary TSG data from the A22 section on KN173/2 using 
              constant salinity offset based on surface Rosette samples 
              from CTD stations.
	

We have been able to download a Seawiffs composite image from 24-31 
October showing ocean color for the Caribbean and the north coast of 
Brazil. This figure follows and shows a clear Orinoco signal which is 
likly to be the cause of the low salinity water seen on the TSG series 
above as well as the high CDOM signal in the surface waters of the 
Caribbean. The plume from the Amazon is clearly not going into the 
Caribbean, but is being diverted into the interior of the tropical 
Atlantic by the North Equatorial Counter Current.


FIGURE B.1.2: Seawifs image of ocean color for  24-31 October 2003 
              obtained with the help of Mike Caruso (WHOI)  from MODIS 
              data available from a NASA website.



B.2  DEEP WATER VENTILATION OF THE CARIBBEAN

The deepest sill into the Caribbean is the Jungfern sill with a depth 
of 1824m. This sill separates the Caribbean from the Virgin Island 
Basin, in which station 24 was taken. The sill is about 35 nm directly 
eastward of our section. As the deep flow is westward at 66W at the 
northern margin of the Caribbean, the overflow water from the N. 
Atlantic will be swept downstream across our section. Moored current 
meter observations together with hydrography done previously has 
indicated that occasional dense, high velocity pulses of overflow water 
are capable of reaching the bottom of the Caribbean after mixing and 
entraining ambient water. As the vertical "fall" from the sill to the 
bottom is over 2 km, the resulting water, though high in oxygen 
initially, is highly attenuated by mixing. We have observed this newly 
ventilated water to be higher in salinity with a small positive 
temperature anomaly. Compare stations 14 & 15 in the central Caribbean 
with stations 17 & 18 near the northern boundary in the westward flow. 
Water depths for stations 17 & 18 are 4500 & 3350m, respectively, and 
high oxygen/ salinity anomalies of this deep ventilation appear in the 
lower part of the water column as revealed in the following figure, 
where we have plotted CTD data at 10 dbar resolution with preliminary 
calibrations from the water samples. Note the large anomaly at theta = 
4.0°C and again at the bottom. Silica samples collected in these anomalies 
confirm that high oxygen/low silica is a characteristic of the ventilation, 
which should also appear in the other tracers such as CFCs. 


FIGURE B.2.1: Deep Caribbean properties from CTD data on KN173/2. Stations 
              are identified by different colors & symbols.


The High oxygen signal theta = 4.0 °C on station 18 is slightly shallower 
than the sill depth and could have entered the basin without mixing. 
However, the deeper signal on that station and is found at 3300 m 
depth. The bottom depth on station 17 is 4570m, where there is an 
oxygen signal (and silica) near the bottom and 600 m above the bottom 
(see following figure)


FIGURE B.2.2: Salinity and oxygen profiles relative to depth above bottom 
              for the stations selected in the previous figure.



B.3  CHANGES IN LABRADOR SEA WATER TO THE NORTH OF PUERTO RICO

Comparing the properties of the water column in 2003 with those 
measured in WOCE in 1997 on A22 reveals substantial change in the 
properties of the classical Labrador Sea Water. This layer, occupies a 
depth interval of approximately 2000-2500m. We show examples of this 
difference using neutral density as the 'vertical' coordinate, thus 
removing any signature of vertical heaving from the differences. In the 
first case, we plot salinity differences over much of the water column 
and for a close-up of the LSW. This is followed by similar plots 
showing differences in dissolved oxygen. Similar changes can be seen in 
the nutrients, CFCs, and TCO2 for the classical LSW but will not be 
presented here.


FIGURE B.3: Comparison of bottle measurements of salinity and oxygen from the 
            region north of Puerto in the DWBC between 18 & 20N. Top panels for 
            salinity and bottom for oxygen: left panels are overall & right are 
            blowups of LSW layer. 



B.4  STRATIFICATION CHANGES IN THE SARGASSO SEA

It is apparent that properties of the SubTropical Mode Water (eighteen 
degree water - EDW) have changed between 1997 and the present. This can 
be seen in the oxygen, nutrients and other tracers with a clear 
signature of lower ventilation of the density associated with the EDW. 
Here we show a comparison of the potential vorticity (related to the 
inverse of the thickness between density layers) for the EDW in the 
northern Sargasso Sea. We show the vertical profile of PV against both 
pressure and neutral density using mean CTD data between 31 and 33N. 
Because of our extra stations in 2003 around Bermuda, there are 7 
stations in this latitude band in 2003 compared with 5 in 1997. We have 
used the station and pressure-averaged mean CTD data in the figure 
below.


FIGURE B.4: Potential vorticity for the northern Sargass Sea in 1997 and 
            2003 from A22. Note how the PV in '97 was about half that at 
            present and much more concentrated in a 'mode' with a density 
            near 26.47gamma-n. 



B.5  ARGO FLOAT RELEASES

Allyn Clarke provided three Argo floats to be deployed on the section 
in the Northern Sargasso, Gulf Stream, and Slope Water. One of the 
three floats refused to initiate its pre-launch sequence when the 
magnet was removed, despite it responding to some rudimentary 
communication tests with a computer connection in the lab on Knorr. The 
launch sites for the two other floats are given in the table.


Float number  ARGOS ID  Latitude   Longitude     Day/time    Station #
------------  --------  ---------  ---------  -------------  ---------
   M-106       30175    34 43.38N  66 34.20W   8 Nov. 1948Z     61
  MT-115       30237    37 24.16N  68 10.02W  10 Nov. 1854Z     68



B.6  CARBON ISOTOPE SAMPLING

Surface 14C samples and three complete vertical profiles of 13C were 
taken on the cruise for later analysis ashore at the following 
stations: 

14C surface samples on stations: 1, 4, 11, 31, 36, 41, 49, 61, 64, 68, 72, 75, 79
13C full profiles on stations:   42, 56, 75



B.7  SUMMARY

In all, 82 stations were taken, 2 more than originally planned. One 
station was added to the NE of Bermuda and a second was added to the 
DWBC crossing SE of Cape Cod. With excellent support by ship personnel, 
the seagoing scientific groups, and the weather, this cruise was both 
enjoyable and successful.




C.  DESCRIPTION OF MEASUREMENT TECHNIQUES
    (F. Delahoyde/SIO)

C.1.  CTD/HYDROGRAPHIC MEASUREMENTS PROGRAM

The basic CTD/hydrography program consisted of salinity, dissolved oxygen and 
nutrient measurements made from bottles taken on CTD/rosette casts, plus 
pressure, temperature, salinity, dissolved oxygen and transmissometer from CTD 
profiles.  A total of 88 CTD/rosette casts were made, usually to within 10 
meters of the bottom. No major problems were encountered during the operation. 
The distribution of samples is illustrated in FIGURES C.1.0-C.1.3.


FIGURE C.1.0:  Sample distribution, stations  1-27.
FIGURE C.1.1:  Sample distribution, stations 27-38.
FIGURE C.1.2:  Sample distribution, stations 38-52.
FIGURE C.1.3:  Sample distribution, stations 52-88.



C.2.  WATER SAMPLING PACKAGE

LADCP/CTD/rosette casts were performed with a package consisting of a 36-bottle 
rosette frame (ODF), a 36-place pylon (SBE32) and 36 10-liter Bullister bottles 
(ODF). Underwater electronic components consisted of a Sea-Bird Electronics 
(SBE) 9plus CTD (ODF #474) with dual pumps, dual temperature (SBE3), dual 
conductivity (SBE4), dissolved oxygen (SBE43), transmissometer (Wetlabs C-Star) 
and fluorometer (Seapoint Sensors); an SBE35RT Digital Reversing Thermometer, 
RDI LADCPs (Workhorse 300khz/Broadband 150khz) and a Simrad 1007 altimeter.

The CTD was mounted horizontally along one side of the bottom center of the 
rosette frame for casts 1/1-61/1, and vertically in an SBE CTD frame attached 
to the same rosette location for casts 62/1-82/1. The SBE sensors and pumps 
were deployed along the CTD pressure case for both horizontal and vertical 
mountings.  The transmissometer, fluorometer and SBE35RT temperature sensor 
were mounted horizontally along the rosette frame adjacent to the CTD.  The 
LADCP battery pack was mounted alongside and outboard from the CTD.  The LADCPs 
were vertically mounted inside the bottle rings on the opposite side of the 
frame from the CTD and LADCP battery pack, with one set of transducers pointing 
down, the other up.  The altimeter was mounted on the inside of support strut 
outboard from the LADCP battery pack.

The rosette system was suspended from a UNOLS-standard three-conductor 0.322" 
electro-mechanical sea cable.  The R/V Knorr's starboard-side CTD winch was 
used on all casts except 58/1, where the port-side winch was used. A broken sea 
cable conductor resulting in signal loss resulted in the premature termination 
of cast 57/1 (renamed 57/2) at 4600 decibars after tripping 3 bottles.  One 
other cast (51/1, renamed 51/3) was repeated due to all bottle vents having 
been left open and no usable samples taken. No other casts were aborted and no 
other reterminations were performed on the sea cable.

The deck watch prepared the rosette 10-20 minutes prior to each cast. All 
valves, vents and lanyards were checked for proper orientation. The bottles 
were cocked and all hardware and connections rechecked. Once stopped on 
station, the LADCP was turned on and the rosette moved into position under the 
starboard boom via an air-powered cart and tracks.  As directed by the deck 
watch leader, the CTD was powered-up and the data acquisition system started. 
Two stabilizing tag lines were threaded through rings on the rosette frame, and 
syringes were removed from the CTD sensor intake ports.  The deck watch leader 
directed the winch operator to raise the package, the boom and rosette were 
extended outboard and the package quickly lowered into the water. The tag lines 
were removed and the package was lowered to 10 meters. The CTD console operator 
then directed the winch operator to bring the package close to the surface, 
pause for typically 30 seconds and begin the descent.

Each rosette cast was lowered to within 10-20 meters of the bottom (with the 
exception of 3 shallow incubation casts).

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 changed or 
replaced on this leg, although parts of a few of them were replaced or 
repaired.

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 air 
tugger-powered tag lines for added safety and stability.  The rosette was moved 
into the CTD hangar for sampling. The bottles and rosette were examined before 
samples were taken, and anything unusual noted on the sample log.

Routine CTD maintenance included soaking the conductivity and CTD DO sensors in 
distilled water between casts to maintain sensor stability, and cleaning the 
transmissometer windows.  Rosette maintenance was performed on a regular basis.  
O-rings were changed as necessary and bottle maintenance was performed each day 
to insure proper closure and sealing. Valves were inspected for leaks and 
repaired or replaced as needed.



C.3.  UNDERWATER ELECTRONICS PACKAGES

CTD data were collected with a SBE9plus CTD (ODF #474). This instrument 
provided pressure, dual temperature (SBE3), dual conductivity (SBE4), dissolved 
oxygen (SBE43), transmissometer (Wetlabs C-Star), fluorometer (Seapoint 
Sensors) and altimeter (Simrad 1007) channels.  CTD #474 supplied a standard 
Sea-Bird format data stream at a data rate of 24 frames/second (fps).


TABLE 1.3.0:  A22 Rosette Underwater Electronics.

Sea-Bird SBE32 36-place Carousel Water Sampler  S/N 0187

Sea-Bird SBE35RT Digital Reversing Thermometer  S/N 0035
Sea-Bird SBE9plus CTD                           S/N09P9852-0474
Paroscientific Digiquartz Pressure Sensor       S/N 69008
Sea-Bird SBE3plus Temperature Sensor            S/N 03P-4138 (Primary)
Sea-Bird SBE3plus Temperature Sensor            S/N 03P-2359 (Secondary)
Sea-Bird SBE4C Conductivity Sensor              S/N 04-2419 (Primary)
Sea-Bird SBE4C Conductivity Sensor              S/N 04-2319 (Secondary)
Sea-Bird SBE43 DO Sensor                        S/N 43-0255 (casts 2/1-37/1)
Sea-Bird SBE43 DO Sensor                        S/N 43-0199 (casts 38/1-82/1)
Wetlabs C-Star transmissometer                  S/N 507DR
Seapoint Sensors Fluorometer                    S/N 2273
Simrad 1007 Altimeter                           S/N 0201075
RDI Workhorse 300khz LADCP                      S/N 3898-XR
RDI Workhorse 300khz LADCP                      S/N 3898-VXR
RDI Workhorse 300khz LADCP                      S/N 149
RDI Workhorse 300khz LADCP                      S/N 150
RDI Workhorse 300khz LADCP                      S/N 754
RDI Broadband 150khz LADCP                      S/N 1546
LADCP Battery Pack


The CTD was outfitted with dual pumps.  Primary temperature, conductivity and 
dissolved oxygen were plumbed on one pump circuit and secondary temperature and 
conductivity on the other.  The sensors were deployed horizontally for casts 
2/1-61/1, and vertically for casts 62/1-82/1. The secondary temperature and 
conductivity sensors (T2 #2359 and C2 #2319) were used for reported CTD 
temperatures and conductivities on all casts, due to a down/upcast conductivity 
offset observed in the primary channel. The primary temperature and 
conductivity sensors (T1 #4138 and C1 #2419) were used for calibration checks.

The SBE9 CTD and the SBE35RT Digital Reversing Thermometer were both connected 
to the SBE32 36-place pylon providing for single-conductor sea cable operation. 
All 3 sea cable conductors were connected together to improve reliability.  
Power to the SBE9 CTD,SBE32 pylon, and SBE35RT was provided through the sea 
cable from the SBE11plus deck unit in the main lab.  The Simrad altimeter and 
LADCP were powered by battery packs.



C.4.  NAVIGATION AND BATHYMETRY DATA ACQUISITION

Navigation data were acquired (at 1-second intervals) from the ship's Seanav 
GPS receiver by one of the Linux workstations beginning October 23. Data from 
the ship's Knudsen 320B/R Echosounder (12 KHz transducer) were also acquired, 
corrected using Carter tables [Cart80] and merged with the navigation. The 
Knudsen bathymetry data were noisy and subject to washing out on station when 
the bow thrusters were engaged.

Bathymetric data from the ship's multibeam (SeaBeam) echosounder system were 
also logged by the R/V Knorr's underway system.



C.5  LOWERED ACOUSTIC DOPPLER CURRENT PROFILER

Velocity profiles were obtained during the standard hydrographic casts of the 
Knorr A20 cruise using self contained ADCPs (Acoustic Doppler Current 

Profilers) attached to the CTD rosette.  Dual WH300 ADCPs (RDI Instruments 
Inc.) were used for Stations 1 through 37 and the test station 999. A single 
broadband 150 khz ADCP (RDI Instruments Inc.) was used for stations 38 through 
84. Lowered ADCP data for stations 85 through 88 was not collected given that 
these stations were too shallow to obtain meaningful information. An 
experimental high power version of the WH300 ADCP was used on casts 1-11 and 
initially exhibited promising (higher range) results.  Unfortunately a failed 
transducer on that instrument required that it be replaced with a standard 
WH300 ADCP for subsequent casts.

Based on the instrument range and the magnitude of the error associated with 
the velocity estimates, the dual WH300 ADCPs performed well in the high back-
scatter region on the northern portion of the transect. The range of these 
instruments declined steadily and the velocity error increased as the ship 
proceeded south into lower back-scatter waters, requiring the switch to the 
higher powered broadband 150 khz instrument after station 37. While the 
performance of the broadband 150 khz instrument was adequate in the low back-
scatter waters of the main gyre, the range and velocity error steadily improved 
as the ship made progress south. Poor velocity estimates in the upper 200 
meters of the water column is common when profiling with a single ADCP and is 
not entirely understood. This proved to be the case when the single BB150 ADCP 
was used during this cruise.  The hull mounted ADCP data will be used to fill 
in for the poor surface data that was obtained while using the single BB150 
ADCP.  Additional post processing will be done to optimize the threshold 
settings that will allow our bottom tracking routines to decrease the error in 
the velocity estimates when the paired WH300 ADCPs were used. However, 
preliminary examination of the velocity profiles indicates good correlation 
with the geostrophic velocities computed from the temperature and salinity 
data.


C.6.  REAL-TIME CTD DATA ACQUISITION SYSTEM

CTD data acquisition system consisted of an SBE-11plus deck unit and four 
networked generic PC workstations running RedHat 9 Linux. Each PC workstation 
was configured with a color graphics display, keyboard, trackball, 60 GB disk, 
CD-R and CDRW drives. Two of the four systems also had 8 additional RS-232 
ports via a Rocketport PCI serial controller.  The systems were networked 
through 2 100BaseTX ether net switches which were also connected to the ship's 
network. These systems were available for real-time operational and CTD data 
displays, as well as providing for CTD and hydrographic data management and 
backup.  Hardcopy capability was provided by a networked HP 1600CM color 
printer.

One of the workstations was designated the CTD console and was connected to the 
CTD deck unit via RS-232. The CTD console provided an interface for controlling 
CTD deployments as well as real-time operational displays for CTD and rosette 
trip data, GPS navigation, bathymetry and the CTD winch.

CTD deployments were initiated by the console watch once the ship was stopped 
on station. A console operations log was maintained by the watch containing a 
description of each deployment, a record of every attempt to close a bottle and 
any pertinent comments.  The deployment software presented the operator with a 
short dialog instructing them to turn on the deck unit, examine the on screen 
raw data display for stable CTD data and to notify the deck watch that this was 
accomplished. When the deck watch was ready to put the rosette over the side, 
the console watch was notified and the CTD data acquisition started. Time, GPS 
position and bottom depth were automatically logged at 1 second resolution. 
Both raw and processed (2 Hz time-series) CTD data were automatically backed up 
by one of the other workstations via ethernet. The deployment software display 
changed to indicate that a cast was in progress.  A processed data display 
appeared, as did a rosette bottle trip display and control for closing bottles.  
Various real-time plots were then initiated to display the progress of the 
deployment.

Once the deck watch had deployed the rosette, the winch operator would 
immediately lower it to 10 meters.  The CTD pumps were configured with an 8 
second startup delay, and would be on by this time. The console operator would 
check the CTD data for proper operation, then instruct the winch operator to 
bring the package to the surface and then descend to a target depth (wire-out). 
The lowering rate was normally 60 meters/minute for this package, depending on 
sea cable tension and 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 decided where to trip bottles on the up cast, noting this on the 
console log. The altimeter channel, CTD depth, wire-out and bathymetric depth 
were monitored to determine the distance of the package from the bottom. The 
on-screen winch and altimeter displays allowed the watch to refine the target 
wire-out relayed to the winch operator and safely approach to within 10-20 
meters of the bottom.

Bottles were closed on the up cast by operating a "point and click" graphical 
trip control button. The data acquisition system responded with trip 
confirmation messages and the corresponding CTD data in a rosette bottle trip 
window on the display. All tripping attempts were noted on the console log. The 
console watch then directed the winch operator to raise the package up to the 
next bottle trip location. The console watch was also responsible for creating 
a sample log for the deployment which was used to record the correspondence 
between rosette bottles and analytical samples taken.

After the last bottle was tripped, the console watch directed the deck watch to 
bring the rosette on deck. Once on deck, the console watch terminated the data 
acquisition, turned off the deck unit and assisted with rosette sampling.



C.7.  CTD DATA PROCESSING

ODF CTD processing software consists of over 30 programs running in a Unix run-
time environment. The initial CTD processing program (ctdrtd/ctdba) is used 
either in real-time or with existing raw CTD data to:

  • Convert raw CTD scans into scaled engineering units, and assign the data to 
    logical channels
  • Filter various channels according to specified criteria
  • Apply sensor- or instrument-specific response-correction models
  • Decimate the channels according to specified criteria
  • Store the output time-series in a CTD-independent format

Once the CTD data are reduced to a standard format time-series, they can be 
manipulated in various ways.  Channels can be additionally filtered. The time-
series can be split up into shorter time-series or pasted together to form 
longer time-series.  A time-series can be transformed into a pressure-series, 
or into a larger-interval time-series.  The pressure, temperature and 
conductivity laboratory calibration coefficients are applied during the 
creation of the initial time-series.  Oxygen conversion equation coefficients 
and any adjustments to pressure, temperature or conductivity are maintained in 
separate files and are applied whenever the data are accessed.

The CTD data acquisition software acquired and processed the data in real-time, 
providing calibrated, processed data for interactive plotting and reporting 
during a cast. The 24 Hz data from the CTD were filtered, response-corrected 
and decimated to a 2.0 Hz time-series.  Sensor correction and calibration 
models were applied to pressure, temperature, conductivity and O2 .Rosette trip 
data were extracted from this time-series in response to trip initiation and 
confirmation signals.  The calibrated 2.0 Hz time-series data, as well as the 
24 Hz raw data, were stored on disk and were backed up via ethernet to a second 
system. At the end of the cast, various consistency and calibration checks were 
performed, and a 2-db pressure-series of the down cast was generated and 
subsequently used for reports and plots.

CTD data were examined graphically at the completion of deployment for 
potential problems.  The two CTD temperature sensors were compared, 
intercompared with the SBE35RT Digital Reversing Thermometer and checked for 
sensor drift. CTD conductivity sensors were compared and monitored by examining 
differences between CTD values and check-sample conductivities.  Additionally, 
deep theta-salinity comparisons were made between down and up casts as well as 
adjacent deployments.  The CTD O2 sensor data were calibrated to bottle check-
sample data.

The minor sea cable noise problems on this cruise did not significantly affect 
the CTD data, being filtered out during the data acquisition. No additional 
filtering was done on any of the CTD data.

The initial 10 M yo in each deployment resulting from lowering then raising the 
package to the surface to start the pumps was removed during the generation of 
the 2.0 db pressure-series.

Density inversions can be induced in high-gradient regions by ship-generated 
vertical motion of the rosette.  Detailed examination of the raw data shows 
significant mixing can occur in these areas because of "ship roll". To minimize 
density inversions, a "ship-roll" filter which disallowed pressure reversals 
was applied during the generation of all 2.0 db pressure-series down-cast data.



C.8.  CTD LABORATORY CALIBRATION PROCEDURES

Laboratory calibrations of the CTD pressure, temperature and conductivity 
sensors were used to generate Sea-Bird conversion equation coefficients applied 
by the data acquisition software at sea.

Pressure calibrations were last performed on CTD #474 at the ODF Calibration 
Facility (La Jolla) 26 August 2003, immediately prior to A22_2003a.

The Paroscientific Digiquartz pressure transducer (S/N 69008) was calibrated in 
a temperature-controlled water bath to a Ruska Model 2400 Piston Gauge Pressure 
Reference.  Calibration curves were measured at 4 temperatures from -1.38 to 
29.30°C to two maximum loading pressures (1191 and 6081 decibars).

The SBE3plus temperature sensors (primary S/N 03-4138, secondary S/N 03-2359) 
were calibrated at SBE on 08 August 2003.

The SBE4 conductivity sensors (primary S/N 04-2419, secondaries S/Ns 04-1908, 
04-2572 and 04-2319) were calibrated on 08 August 2003, 08 August 2003, 08 
August 2003 and 03 May 2003 at SBE respectively..

The SBE35RT Digital Reversing Thermometer (S/N 0035) was calibrated on 27 June 
2003 at SIO/ODF. Laboratory pressure, temperature and conductivity calibrations 
will be repeated post-cruise.



C.9.  CTD SHIPBOARD CALIBRATION PROCEDURES

CTD #474 was used for all A22_2003a casts, and had been used for the previous 
leg (A20-2003a, kn173-1) as well. The CTD was deployed with sensors and pumps 
aligned horizontally for casts 1/1-61/1, the same configuration as on the 
previous leg. The sensors and pumps were aligned vertically for casts 62/1-
88/1. Primary temperature and conductivity sensors served as calibration checks 
for the secondary temperature and conductivity.  The primary sensors were not 
used for reported data because of a conductivity offset between down and up 
casts that was discovered on the previous leg. This offset was attributed to 
pump flow rate, a conjecture that was substantiated on this leg. The SBE35RT 
Digital Reversing Thermometer served as an independent temperature calibration 
check. In-situ salinity and dissolved O2 check samples collected during each 
rosette cast were used to calibrate CTD conductivity and dissolved O2 .


C.9.1.  CTD PRESSURE

Pressure sensor conversion equation coefficients derived from the pre-cruise 
pressure calibration were applied to raw pressures during each cast. No 
additional adjustments were made to the calculated pressures, but a change in 
the on-deck pressure offset was observed when the CTD was reoriented vertically 
prior to cast 62/1. The offset changed from +0.1 db to +1.0 db.

Residual offsets at the beginning and end of each cast (the difference between 
the first/last pressures in-water and 0) were monitored during the cruise to 
check for shifts in the pressure calibration. All residual differences were 0.5 
decibar or less prior to cast 62/1 and 1.0 decibar or less thereafter.

There was no apparent shift in pressure calibration during the cruise.  This 
will be verified by a post-cruise laboratory pressure calibration.


C.9.2.  CTD TEMPERATURE

Temperature sensor calibration coefficients were derived from the pre-cruise 
calibrations and applied to raw primary and secondary temperatures.

Two independent metrics of calibration accuracy were examined. The primary and 
secondary temperatures were compared at each rosette trip, and the SBE35RT and 
secondary temperatures were compared at each rosette trip.  These comparisons 
are summarized in FIGURES C.9.2.0 and C.9.2.1.


FIGURE C.9.2.0:  Primary and secondary temperature comparison, p>1000db.


The comparison between primary and secondary temperatures shows a small 
(0.00011 °C) mean calibration offset, well within the reported accuracy of the 
SBE temperature calibrations.


FIGURE C.9.2.1:  Primary and SBE35RT temperature comparison, p>1000db.


The comparison between SBE35RT and T2 temperatures shows a constant offset of 
-0.00027°C prior to cast 62/1 and less distinct differences thereafter.  This 
change corresponds to the change in sensor orientation and an increase in 
distance from the T2 pump intake to the SBE35 (from -0.5 meters to -0.8 
meters).


C.9.3.  CTD CONDUCTIVITY

Conductivity sensor conversion equation coefficients were derived from the pre-
cruise calibrations and applied to raw primary and secondary conductivities.

A single pair of conductivity sensors were used on A22: #2419 (primary) and 
#2319 (secondary). Both conductivity sensors were stable and noise-free.  The 
primary conductivity sensor exhibited a 0.0007 mS/cm offset between down and up 
cast on the previous leg that was attributed to pump flow rate (and horizontal 
sensor alignment) and so was not used for reported CTD data on A22. This offset 
disappeared (cast 62/1) when the CTD was reconfigured for vertical sensor 
alignment. No offset was apparent in the secondary conductivity data, perhaps 
due to the absence of the SBE43 DO sensor in the P2 sensor circuit. Comparisons 
to bottle salinities to the secondary conductivity sensor showed a mean 
conductivity correction slope of 0.000 mS/cm and a constant offset of 0.000212 
mS/cm.

The comparison of the primary and secondary conductivity sensors by station is 
summarized in FIGURE C.9.3.0.


FIGURE C.9.3.0:  C1 and C2 conductivity differences by pressure, p>500db.


The salinity residuals after applying the shipboard calibration are summarized 
in figures C.9.3.1 and C.9.3.2.


FIGURE C.9.3.1:  C2 salinity residuals, p>500db.
FIGURE C.9.3.2:  C2 salinity residuals by station, p>2000db.


Excluding thermocline and gradient values (early and late stations were shallow 
and also excluded), FIGURE C.8.3.3 represents an estimate of the salinity 
accuracy of CTD #474. The 95% confidence limit is ±0.0015 PSU, in agreement 
with the generally accepted limit of repeatability for bottle salinities 
(±0.002PSU).


C.9.4.  CTD DISSOLVED OXYGEN

Two SBE43 dissolved O2 (DO) sensors were used for this cruise (#43-0225 casts 
1/1-37/1, #43-0199 casts 38/1-82/1). Sensor #43-0225 was replaced to determine 
if non-linear pressure response and hysteresis were sensor-dependent (they 
weren't). The sensor was plumbed into the P1/T1/C1 intake line in a horizontal 
configuration after C1 and before P1 (per SBE spec). This was changed to a 
vertical configuration prior to cast 62/1.

One characteristic of this type of sensor (membrane-covered polarigraphic 
oxygen detector or MPOD) is a flow dependence.  Non-pumped sensors of this type 
exhibit a significantly decreased response at bottle  stops.  The pumped 
SBE43 reduces but does not eliminate this problem, perhaps due to pump or flow 
rate variations in the primary sensor circuit. DO sensor calibration to check 
samples is somewhat problematic as sensor data from the bottle stop does not 
provide a representative comparison.

The DO sensor calibration method used for this cruise was to match down-cast 
CTD DO data to up-cast bottle trips along isopycnal surfaces, then to minimize 
the residual differences between the in-situ check sample values and CTD O2 
using a non-linear least-squares fitting procedure.  Since this technique only 
calibrates the down-cast, only the 2.0 pressure series downcast data contain 
calibrated CTD O2 .

A small (<0.02 ml/l) but significant non-linearity apparent in the O2 residuals 
as a function of pressure was corrected with an additional empirical 5th-order 
polynomial pressure correction. The explanation for this non-linearity requires 
further investigation.

FIGURES C.9.4.0, C.9.4.1 and C.9.4.2 show the residual differences between 
bottle and calibrated CTD O2 for all points excluding the thermocline and 
surface gradients.  FIGURE C.9.4.3 shows the residual differences for pressures 
> 1000 db.


FIGURE C.9.4.0:  O2 residuals by station number.
FIGURE C.9.4.1:  O2 residuals by pressure.
FIGURE C.9.4.2:  O2 residuals by temperature.
FIGURE C.9.4.3:  O2 residuals by station number, p>1000db.


The standard deviations of 0.033 ml/l for all oxygens and 0.014 ml/l for deep 
oxygens are only intended as indicators of how well the up-cast bottle O2 and 
down-cast CTD O2 match. ODF makes no claims regarding the precision or accuracy 
of CTD dissolved O2 data.

The general for m of the ODF O2 conversion equation follows Brown and Morrison 
[Brow78] and Millard [Mill82], [Owen85]. ODF models membrane and sensor 
temperatures with lagged CTD temperatures. In-situ pressure and temperature are 
filtered to match the sensor response.  Time-constants for the pressure 
response tp, and two temperature responses tTs and tTf are fitting parameters.  
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, tog, 
is a fitting parameter.  Oxygen partial-pressure is then calculated:

Opp = [c1 Oc + c2 ] ∑ f sat (S, T , P) ∑ e (c3 Pl +c4 Tf +c5 Ts +c6 dOc dt)      (1.8.4.0)

where:

      Opp            = Dissolved O2 partial-pressure in atmospheres (atm);
      Oc             = Sensor current (mamps);
      fsat (S, T, P) = O2 saturation partial-pressure at S,T,P (atm);
      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
      ---            = Sensor current gradient (mamps/secs).
      dt 



C.10.  BOTTLE SAMPLING

At the end of each rosette deployment water samples were drawn from the bottles 
in the following order:

      • CFCs
      • He3
      • O2
      • DIC/Total Alkalinity
      • DOC/DON/DCNS/CDOM
      • Tritium
      • I129
      • C13 and C14
      • Nutrients
      • Salinity

The correspondence between individual sample containers and the rosette bottle 
from which the sample was drawn was recorded on the sample log for the cast. 
This log also included any comments or anomalous conditions noted about the 
rosette and bottles.  One member of the sampling team was designated the sample 
cop, whose 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 analysis.



C.11.  BOTTLE DATA PROCESSING

Bottle data processing began with water sample drawing and continued 
iteratively until the data were considered to be problem-free.  A sample log 
was made for each cast and was filled out during sample drawing, serving both 
as a sample inventory and as a resource for the technicians performing their 
analyses.  Any problems observed with the rosette before or during the sample 
drawing were noted on this for m, including indications of bottle leaks, 
incorrect bottle tripping and out-of-order sample drawing. Additional 
information regarding bottle tripping or leak problems were reported back as 
water samples were analyzed.

Reported water sample values were associated with rosette bottles using cast 
and bottle number to make the association. Bottle integrity and tripping issues 
were usually resolved at this stage, sometimes resulting in changes to the CTD 
properties assigned to the bottle.

A quality code was associated with every reported value (as well as with every 
bottle and associated CTD property). The quality coding followed the coding 
scheme developed for the World Ocean Circulation Experiment (WOCE) Hydrographic 
Programme (WHP) [Joyc94]. Diagnostic comments from the sample log, and notes 
from analysts and data processors were also associated with sample values as 
part of the quality control procedure.  Sample values and quality codes were 
continuously reviewed and revised to best reflect the reliability of the 
measurements.  This included intercomparison of bottle properties, comparison 
to CTD profile data and comparison of properties at adjacent stations.


WHP water bottle quality code assignments were made as defined in the WOCE 
    Operations Manual [Joyc94] with the following additional interpretations:

2 | No problems noted.
3 | Leaking. An air leak large enough to produce an observable effect on a sample 
  | is identified by a code of 3 on the bottle and a code of 4 on the oxygen. 
  | (Small air leaks may have no observable effect, or may only affect gas 
  | samples.)
4 | Did not trip correctly. Bottles tripped at other than the intended depth were 
  | assigned a code of 4. There may be no problems with the associated water 

  | sample data.
5 | Not reported. No water sample data reported. This is a representative level   
  | derived from the CTD data for reporting purposes.  The sample number should 
  | be in the range of 80-99.
9 | The samples were not drawn from this bottle.


WHP water sample quality flags were assigned using the following criteria:

1 | The sample for this measurement was drawn from the water bottle, but the  
  | results of the analysis were not (yet) received.
2 | Acceptable measurement.
3 | Questionable measurement. The data did not fit the station profile or   
  | adjacent station comparisons (or possibly CTD data comparisons). No notes 
  | from the analyst indicated a problem. The data could be acceptable, but are 
  | open to interpretation.
4 | Bad measurement. The data did not fit the station profile, adjacent stations 
  | or CTD data. There were analytical notes indicating a problem, but data 
  | values were reported. Sampling and analytical errors were also coded as 4.
5 | Not reported. There should always be a reason associated with a code of 5, 
  | usually that the sample was lost, contaminated or rendered unusable.
9 | The sample for this measurement was not drawn.


WHP water sample quality flags were assigned to the CTDSAL (CTD salinity) 
    parameter as follows:

2 | Acceptable measurement.
3 | Questionable measurement. The data did not fit the bottle data, or there was  
  | a CTD conductivity calibration shift during the up-cast.
4 | Bad measurement. The CTD up-cast data were determined to be unusable for 
  | calculating a salinity.
7 | Despiked. The CTD data have been filtered to eliminate a spike or offset.


WHP water sample quality flags were assigned to the CTDOXY (CTD O2 )parameter 
    as follows:

1 | Not calibrated. Data are uncalibrated.
2 | Acceptable measurement.
3 | Questionable measurement.
4 | Bad measurement. The CTD data were determined to be unusable for calculating 
  | a dissolved oxygen concentration.
5 | Not reported. The CTD data could not be reported, typically when CTD salinity 
  | is coded 3 or 4.
7 | Despiked. The CTD data have been filtered to eliminate a spike or offset.
9 | Not sampled. No operational CTD O2 sensor was present on this cast.


Note that CTDOXY values were derived from up-cast rosette trip values matched 
to the down-cast CTD pressure-series data along isopycnal surfaces.  Since this 
property depends on CTD salinity, it is not reported if the CTD salinity is 
quality coded as bad or questionable.



C.12.  SALINITY ANALYSIS

Equipment and Techniques 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 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.  It was set to 24°C for the 
entire leg.

The salinity analyses were performed after samples had equilibrated to 
laboratory temperature, usually within 16-36 hours after collection. A 
temperature-controlled waterbath was used to assist sample equilibration. The 
salinometer was standardized for each group of analyses (1-4 casts, up to ~50 
samples) using at least one fresh vial of standard seawater per group.  A 
computer (PC) prompted the analyst for control functions such as changing 
sample, flushing, or switching to "read" mode.  The salinometer cell was 
flushed and results were logged by the computer until two successive 
measurements met software criteria for consistency.  These values were then 
averaged for a final result.


SAMPLING AND DATA PROCESSING

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 collecting each sample, inserts were inspected for proper 
fit and loose inserts were 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 [UNES81] was calculated for each sample from the measured 
conductivity ratios.  The difference (if any) between the initial vial of 
standard water and one run at the end as an unknown was applied linearly to the 
data to account for any drift. The data were incorporated into the cruise 
database. 2493 salinity measurements were made and approximately 60 vials of 
standard water were used. Temperature control was somewhat problematic and 
several runs were rendered unusable for calibration purposes because of a lack 
of temperature stability.  The estimated accuracy of bottle salinities run at 
sea is usually better than ±0.002 PSU relative to the particular standard 
seawater batch used.


LABORATORY TEMPERATURE

The temperature in the salinometer laboratory varied from 20.9 to 25.8°C, 
during the cruise.  The air temperature change during any single run of samples 
was less than ±3.0°C.


STANDARDS

IAPSO Standard Seawater (SSW) Batches P-140 and P-141 were used to standardize 
all salinity measurements.



C.13.  OXYGEN ANALYSIS

EQUIPMENT AND TECHNIQUES

Dissolved oxygen analyses were performed with an ODF-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. ODF used a whole-bottle modified-
Winkler titration following the technique of Carpenter [Carp65] with 
modifications by Culberson et al. [Culb91], but with higher concentrations of 
potassium iodate standard (~0.012N) and thiosulfate solution (~65 gm/l). Pre-
made liquid potassium iodate standards were run at the beginning of each 
session of analyses, which typically included from 1 to 3 stations.  
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. The auto-titrator generally performed well.


SAMPLING AND DATA PROCESSING

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 
draw temperature was measured with a small platinum resistance thermometer 
embedded in the drawing tube.  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 1-6 hours of collection, then the data were 
incorporated into the cruise database.

Thiosulfate normalities were calculated from each standardization and corrected 
to 20°C.  The 20°C normalities and the blanks were plotted versus time and 
were reviewed for possible problems.

As samples warmed up to room temperature they would occasionally degas which 
would cause a noisy endpoint due to gas bubbles in the light path. 2487 oxygen 
measurements were made.

The blank volumes and thiosulfate normalities were smoothed (linear fits) at 
the end of the cruise and the oxygen values recalculated.


VOLUMETRIC CALIBRATION

Oxygen flask volumes were determined gravimetrically with degassed deionized 
water to determine flask volumes at ODF's chemistry laboratory.  This is done 
once before using flasks for the first time and periodically thereafter when a 
suspect bottle volume is detected. The volumetric flasks used in preparing 
standards were volume-calibrated by the same method, as was the 10 ml Dosimat 
buret used to dispense standard iodate solution.


STANDARDS

Liquid potassium iodate standards were prepared and bottled in ODF's chemistry 
laboratory prior to the cruise.  The normality of the liquid standard was 
determined at ODF by calculation from weight. A single standard batch was used 
during A22_2003a. Potassium iodate was obtained from Acros Chemical Co. and was 
reported by the supplier to be >99.4% pure.  All other reagents were "reagent 
grade" and were tested for levels of oxidizing and reducing impurities prior to 
use.



C.14.  NUTRIENT ANALYSIS

EQUIPMENT AND TECHNIQUES

Nutrient analyses (phosphate, silicate, nitrate and nitrite) were performed on 
an ODF-modified 4-channel Technicon AutoAnalyzer II, generally within one hour 
after sample collection. Occasionally samples were refrigerated up to 4 hours 
at ~4°C.  All samples were brought to room temperature prior to analysis.

The methods used are described by Gordon et al. [Gord92]. The analog outputs 
from each of the four colorimeter channels were digitized and logged 
automatically by computer (PC) at 2-second intervals.

Silicate was analyzed using the technique of Armstrong et al. [Arms67]. An 
acidic solution of ammonium molybdate was added to a seawater sample to produce 
silicomolybdic acid which was then reduced to silicomolybdous acid (a blue 
compound) following the addition of stannous chloride.  Tartaric acid was also 
added to impede PO4 color development. The sample was passed through a 15mm 
flowcell and the absorbance measured at 660nm.

A modification of the Armstrong et al. [Arms67] procedure was used for the 
analysis of nitrate and nitrite. For the nitrate analysis, the seawater sample 
was passed through a cadmium reduction column where nitrate was quantitatively 
reduced to nitrite.  Sulfanilamide was introduced to the sample stream followed 
by N-(1-naphthyl)ethylenediamine dihydrochloride which coupled to form a red 
azo dye. The stream was then passed through a 15mm flowcell and the absorbance 
measured at 540nm. The same technique was employed for nitrite analysis, except 
the cadmium column was bypassed, and a 50mm flowcell was used for measurement.

Phosphate was analyzed using a modification of the Bernhardt and Wilhelms 
[Bern67] technique.  An acidic solution of ammonium molybdate was added to the 
sample to produce phosphomolybdic acid, then reduced to phosphomolybdous acid 
(a blue compound) following the addition of dihydrazine sulfate.  The reaction 
product was heated to ~55°C to enhance color development, then passed through a 
50mm flowcell and the absorbance measured at 820nm.


SAMPLING AND DATA PROCESSING

Nutrient samples were drawn into 45 ml polypropylene, screw-capped "oak-ridge 
type" centrifuge tubes. The tubes were cleaned with 10% HCl and rinsed with 
sample 2-3 times before filling. Standardizations were performed at the 
beginning and end of each group of analyses (typically one cast, up to 36 
samples) with an intermediate concentration mixed nutrient standard prepared 
prior to each run from a secondary standard in a low-nutrient seawater matrix. 
The secondary standards were prepared aboard ship by dilution from primary 
standard solutions.  Dry standards were pre-weighed at the laboratory at ODF, 
and transported to the vessel for dilution to the primary standard. Sets of 6-7 
different standard concentrations were analyzed periodically to determine any 
deviation from linearity as a function of concentration for each nutrient 
analysis.  A correction for non-linearity was applied to the final nutrient 
concentrations when necessary.

After each group of samples was analyzed, the raw data file was processed to 
produce another file of response factors, baseline values, and absorbances.  
Computer-produced absorbance readings were checked for accuracy against values 
taken from a strip chart recording. The data were then added to the cruise 
database.

Nutrients, reported in micromoles per kilogram, were converted from micromoles 
per liter by dividing by sample density calculated at 1 atm pressure (0 db), in 
situ salinity, and an assumed laboratory temperature of 25°C.

2497 nutrient samples were analyzed. The pump tubing was changed 2 times.


STANDARDS

Primary standards for silicate (Na2 SiF6 )and nitrite (NaNO2 )were obtained 
from Johnson Matthey Chemical Co.; the supplier reported purities of >98% and 
97%, respectively.  Primary standards for nitrate (KNO3 )and phosphate (KH2 PO4) 

were obtained from Fisher Chemical Co.; the supplier reported purities of 
99.999% and 99.999%, respectively.  The efficiency of the cadmium column used 
for nitrate was monitored throughout the cruise and ranged from 99-100%.

No major problems were encountered with the measurements.  The temperature of 
the laboratory used for the analyses ranged from 20.9°C to 25.5°C, but was 
relatively constant during any one station (±1.5°C).



REFERENCES

Arms67.
  Armstrong, F. A.J., Stearns, C.R., and Strickland, J.D.H., "The measurement 
  of upwelling and subsequent biological processes by means of the Technicon 
  Autoanalyzer and associated equipment," Deep-Sea Research, 14, pp.381-389 
  (1967).

Bern67.
  Bernhardt, H. and Wilhelms, A., "The continuous determination of low level 
  iron, soluble phosphate and total phosphate with the AutoAnalyzer," 
  Technicon Symposia, I, pp.385-389 (1967).

Brow78.
  Brown, N. L. and Morrison, G. K., "WHOI/Brown conductivity, temperature and 
  depth microprofiler," Technical Report No. 78-23, Woods Hole Oceanographic 
  Institution (1978).

Car p65.
  Carpenter, J.H., "The Chesapeake Bay Institute technique for the Winkler 
  dissolved oxygen method," Limnology and Oceanography, 10, pp.141-143 (1965).

Cart80.
  Carter, D.J.T., "Computerised Version of Echo-sounding Correction Tables 
  (Third Edition), "Marine Information and Advisory Service, Institute of 
  Oceanographic Sciences, Wormley, Godalming, Surrey. GU8 5UB.U.K. (1980).

Culb91.
  Culberson, C.H., Knapp, G., Stalcup, M., Williams, R.T., and Zemlyak, F., "A 
  comparison of methods for the determination of dissolved oxygen in seawater,"
  Report WHPO 91-2, WOCE Hydrographic Programme Office (Aug 1991).

Gord92.
  Gordon, L. I., Jennings, J.C., Jr., Ross, A.A., and Krest, J.M., "A suggested 
  Protocol for Continuous Flow Automated Analysis of Seawater Nutrients in the 
  WOCE Hydrographic Program and the Joint Global Ocean Fluxes Study," Grp. 
  Tech Rpt 92-1, OSU College of Oceanography Descr. Chem Oc. (1992).

Joyc94.
  Joyce, T., ed. and Corry, C., ed., "Requirements for WOCE Hydrographic 
  Programme Data Reporting," Report WHPO 90-1, WOCE Report No. 67/91, pp.52-55, 
  WOCE Hydrographic Programme Office, Woods Hole, MA, USA (May 1994, Rev. 2). 
  UNPUBLISHED MANUSCRIPT.

Mill82.
  Millard, R. C., Jr., "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. (1982).

Owen85.
  Owens, W.B. and Millard, R. C., Jr., "A new algorithm for CTD oxygen 
  calibration," Jour n. of Am. Meteorological Soc., 15, p.621 (1985).

UNES81.
  UNESCO, "Background papers and supporting data on the Practical Salinity 
  Scale, 1978," UNESCO Technical Papers in Marine Science, No. 37, p.144 
  (1981).



C.15  CFC-11, CFC-12, CFC-113, and CCl4
Analysts A22: David Cooper and Rick Wilke (RSMAS)
              Fred Menzia and Ryan Ghan (Lamont) 


Sample Collection

All samples were collected from depth using 10 liter Niskin bottles. None of the 
Niskin bottles used showed a CFC contamination throughout the cruise. All 
bottles in use remained inside the CTD hanger between casts.  

Both the LDEO and RSMAS analytical instruments were on board so each group 
sampled and analyzed every other station. Each system was capable of analyzing 
CFC-11, CFC-12, and CFC-113. The RSMAS system was also capable of analyzing 
CCl4. CFC sampling was conducted first at each station, according to WOCE 
protocol. This avoids contamination by air introduced at the top of the Niskin 
bottle as water was being removed. A water sample was collected directly from 
the Niskin bottle petcock using a 100 ml ground glass syringe which was fitted 
with a three-way stopcock that allowed flushing without removing the syringe 
from the petcock.  Syringes were flushed several times and great care was taken 
to avoid contamination by air bubbles. Two duplicate samples were taken on most 
stations from random Niskin bottles, one duplicate was for same analytical 
system analysis, to calculate precision and the other was for cross analytical 
system comparison.  Air samples, pumped into the system using an Air Cadet pump 
from a Dekoron air intake hose mounted high on the foremast were run when time 
permitted.


RSMAS Equipment and Technique

The RSMAS system analyzed 42 complete stations out of 82 for a total of 1298 
samples on A22.  Halocarbon analyses were performed on a gas chromatograph (GC) 
equipped with an electron capture detector (ECD). Samples were introduced into 
the GC-ECD via a purge and dual trap system. The samples were purged with 
nitrogen and the compounds of interest were trapped on a main Porapack N trap 
held at ~ -15°C with a Vortec Tube cooler. After the sample had been purged and 
trapped for several minutes at high flow, the gas stream was stripped of any 
water vapor via a magnesium perchlorate trap prior to transfer to the main trap. 
The main trap was isolated and heated by direct resistance to 140°C. The 
desorbed contents of the main trap were back-flushed and transferred, with 
helium gas, over a short period of time, to a small volume focus trap in order 
to improve chromatographic peak shape. The focus trap was also Porapak N and is 
held at ~ -15 °C with a Vortec Tube cooler. The focus trap was flash heated by 
direct resistance to 155 °C to release the compounds of interest onto the 
analytical pre-column.  The pre-column was the first 5 meters of a 60 m Gaspro 
capillary column with the main column consisting of the remaining 55 meters. The 
analytical pre-column was held in-line with the main analytical column for the 
first 2 minutes of the chromatographic run. After 2 minutes, all of the 
compounds of interest were on the main column and the pre-column was switched 
out of line and back-flushed with a relatively high flow of nitrogen gas. This 
prevented later eluting compounds from building up on the analytical column, 
eventually eluting and causing the detector baseline signal to increase. 

The syringes were stored in a flow-through seawater bath and analyzed within 8 -
12 hours after collection.   Bath temperature was recorded every time a sample 
was analyzed for use in calculating the mass of water analyzed.  Every 12 to 18 
measurements were followed by a purge blank and a standard. The surface sample 
was held after the initial measurement and was sent through the process again in 
order to "restrip" it to determine the efficiency of the purging process. 

A gas phase standard, ALM35078, was used for calibration. The concentrations of 
the CFCs in this standard are reported on the SIO 1998 absolute calibration 
scale. Multiple calibration curves were run over the course of the cruise on 
each analytical system. Estimated accuracy is +/- 2%. Precision for CFC-12, CFC-
11, CFC-113 and CCl4 was less than 1%. Estimated limit of detection is 0.010 
pM/kg for CFC-12 and CFC-113, and 0.005 pM/kg for CFC-11 and CCl4. 


LDEO Equipment and Technique

Water was transferred from the syringe into a purge and trap system interfaced 
to a Hewlett Packard 5890 gas chromatograph with an electron capture detector.  
A 30 ml aliquot of the sample was stripped with ultra pure nitrogen and trapped 
on a unibeads 2s trap at -78°C after passing through a column of magnesium 
perchlorate to remove water vapor.  The trap was heated to 100°C to release the 
trapped gases, which were injected directly into the gas chromatograph. The gas 
chromatography was carried out using a 40 inch x 1/8 inch diameter pre-column of 
porasil B, a 60 inch x 1/8 inch diameter main column of carbograph-1AC and a 4 
inch x 1/8 inch diameter post column of molecular sieve 5A.  The molecular sieve 
5A column separated CFC-12 from nitrous oxide and was valved out of the gas 
stream before CFC-11 eluted from the main column.  The combination of the pre-
column and main column provided excellent separation of CFCs 11, 12 and 113 as 
well as separation of CFC-113 from methyl iodide.  The gas chromatograph was 
calibrated against a known gas standard and concentrations are reported on the 
SIO98 scale.  The precision of this technique was the larger of 1% or 0.01 pmol 
kg-1. 


Technical Problems

In large part, sample collection and measurement were very successful. The 
integration of the computer software with the GC-ECD system hardware made the 
procedure almost completely automated. There were no incidents that caused 
significant instrument down time.

For A22 the Lamont CFC-11 and CFC-12 data were higher than the Miami data and 
were believed to be in error because most of the surface water samples measured 
by the Lamont system were supersaturated by about 10% and the Miami data were 
close to 100% saturation.  A correction was applied to the Lamont data to bring 
it in line with the Miami data.  There were two parts to the correction: 1) a 
correction for a small leak that apparently developed in the Lamont system for 
stations 38-82 was applied and 2) all of the Lamont data was then reduced by 
5.5%.  These corrections were also applied to the CFC-113 data. Comparison of 
the duplicates run on the Lamont and Miami systems after the corrections yielded 
an error of the larger of 0.01 pmol kg-1 or 1.7 % for CFC-11 and CFC-12.  For 
CFC-113 there was a systematic difference of ~10% after the correction, with the 
Miami data being lower than the Lamont data.


Processing of External Duplicates

External duplicates are defined as samples where RSMAS and Lamont both sampled 
the same station/bottle. The Lamont and Miami systems were compared throughout 
the A22 leg by running duplicate samples from stations on both systems.

Following the offset correction made by Lamont on their data, the CFC-11 and 
CFC-12 values were averaged if both RSMAS and Lamont samples had QB=2.  If one 
of the lab's samples had a questionable (QB=3) or bad (QB=4) quality 
designation, then the other lab's sample was used for that CFC value for that 
particular station/bottle.

For CFC-113, since there was a ~10% difference between the RSMAS and Lamont 
values, the external duplicates were not averaged.  The CFC-113 sample from the 
lab that sampled the remainder of the station was used instead.

RSMAS sampled CCl4.  Lamont did not analyze water samples for CCl4.



C.16  Dissolved Organic Carbon Analyses 
      (Craig A. Carlson)

Collection:
All samples were collected directly from the Niskin Bottles.  Because 
particulate organic carbon (POC) concentrations in the surface waters can  be 
elevated all sampltes collected from the upper 500 m were filtered.  Water was 
filtered through a combusted GF/F housed in an acid washed polycarbonate filter 
cartridge attached directly the Niskin bottle spigot.  Water below 500 m was not 
filtered because greater than 98% or the total organic carbon is DOC.  All 
samples were collected directly into an acid washed and Nanopure flushed high 
density polyethylene (HDPE) bottles (60ml).  Samples were immediately placed 
upright in a -20°C freezer and samples were shipped to shore laboratory packed 
in dry ice.  All samples were kept frozen at -20°C in an organic (volatile) free 
environment. 

Analysis:
All DOC samples were analyzed via high temperature combustion using  Shimadzu 
TOC-V in shore based laboratory at the University of California, Santa Barbara. 
The operating conditions of the Shimadzu TOC-V were slightly modified from the 
manufacturer's model system.  The condensation coil was removed and the head 
space of an internal water trap was reduced to minimize the system's dead space.  
The combustion tube contained 0.5 cm Pt pillows placed on top of Pt alumina 
beads to improve peak shape and to reduce alteration of combustion matrix 
throughout the run.  CO2 free carrier gas was produced with a Whatman(r) gas 
generator (Carlson et al. 2004).  Samples were drawn into 5 ml injection syringe 
and acidified with 2M HCL (1.5%) and sparged for 1.5 minutes with CO2 free gas. 
Three to five replicate 100 µl of sample were injected into combustion tube 
heated to 680° C.  The resulting gas stream was passed though a several water 
and halide traps, the CO2 in the carrier gas was analyzed with a non-dispersive 
infrared detector and the resulting peak area was integrated with Shimadzu 
chromatographic software. Injections continued until the at least three 
injection meet the system specified range of a SD of 0.1 area counts, CV ≤2% or 
best 3 of 5 injections.  

Extensive conditioning of the combustion tube with repeated injections of low 
carbon water (LCW) and deep seawater was essential to minimize the machine 
blanks. After conditioning, the system blank was assessed with UV oxidized low 
carbon water. The system response was standardized with a four-point calibration 
curve of  potassium hydrogen phthalate solution in LCW. All samples were 
systematically referenced against low carbon water, deep Sargasso Sea reference 
waters (2600 m) and surface Sargasso Sea water every 6 - 8  analyses (Hansell 
and Carlson 1998).  The standard deviation of the deep and surface references 
analyzed throughout a run generally have a coefficient of variation ranging 
between 1-3% over the 3-7 independent analyses (number of references depends on 
size of the run) (see Hansell 2005) .  Daily reference waters were calibrated 
with DOC CRM provided by D. Hansell (University of Miami).  The UCSB DOC 
laboratory exchanges references and samples with the Hansell DOC laboratory to 
ensure similar performance of DOC systems and comparability of data.

DOC calculation
µMC  =  (average sample area - average machine blank area) / (slope of std 
curve)


References: 

Carlson, C.A., S.J. Giovannoni, D.A. Hansell, S.J. Goldberg, R. Parsons, and K. 
    Vergin. 2004. Interactions between DOC, microbial processes, and community 
    structure in the mesopelagic zone of the northwestern Sargasso Sea. 
    Limnology and Oceanography 49: 1073-1083.

Hansell, D.A. 2005.  Dissolved organic carbon reference material program.  EOS, 
    Transactions, American Geophysical Union 86: 318-319.

Hansell, D.A. and C.A. Carlson. 2001a. Biogeochemistry of total organic carbon 
    and nitrogen in the Sargasso Sea: Control by convective overturn. Deep Sea 
    Research II  48 (8-9): 1649-1667.



C.17.  DISSOLVED ORGANIC MATTER (DOM) PROJECTS

CRUISE PARTICIPANTS: 

Craig A. Carlson  Associate Professor, University of California Santa Barbara 
Stuart Goldberg   Graduate Student,    University of California Santa Barbara 
Jon Klamberg      Graduate Student,    University of California Santa Barbara



PROJECTS 

PROJECT 1

PROJECT TITLE: BIOGEOCHEMISTRY OF DISSOLVED ORGANIC MATTER (DOM) 
PIs:           D. Hansell, University of Miami 
               C. Carlson, University of California, Santa Barbara
SUPPORT:       NSF


PROJECT GOALS

Our goal is to evaluate dissolved organic carbon and nitrogen concentrations 
over a variety of spatial sections of the repeat hydrography program. Funds 
were only available to have samples collected on the various repeat hydrography 
cruises.  Subsequent analyses will take place back at UCSB and University of 
Miami laboratories.  During the A22 cruise, A type casts were specifically 
targeted in order to overlap with the TCO2 sampling program. Surface DOM 
samples were also drawn on a number of B stations. Samples were drawn at higher 
depth resolution for B station located at the beginning of the Sargasso Sea 
line and in the box around Bermuda.

Depending on the station depth, 24 - 36 Niskin bottles were sampled following 
directly behind the TCO2 sample draw.  Dissolved organic carbon (DOC) and 
dissolved organic nitrogen (DON) samples were passed through an inline filter 
holding a combusted GF/F filter attached directly to the Niskin for samples in 
the top 1000 m of each cast. This was done to eliminated particles > than 0.7 
µm from the sample. Previous work has demonstrated that there is no resolvable 
difference between filtered and unfiltered sample in waters below 1000m at the 
µmol kg-1 resolution. The samples are stored frozen at -20°C until analyses.  
All samples will be analyzed via the high temperature combustion technique on a 
Shimadzu TOC-V analyzer.  DOC data is expected to be complete within 
approximately 6 months of their return to the laboratory.  Additional time may 
be required to complete DON samples.


PROJECT 2  

PROJECT TITLE: CHROMOPHORIC DOM: AN IGNORED PHOTOACTIVE TRACER OF GEOCHEMICAL 
               PROCESSES
PIs:           D. Siegel,  University of California, Santa Barbara
               N. Nelson,  University of California, Santa Barbara 
               C. Carlson, University of California, Santa Barbara
SUPPORT:       NSF (2/3) and NASA


PROJECT GOALS 

Our goals are to determine chromophoric dissolved matter (CDOM) distributions 
over a range of oceanic regimes on meridional sections of the CO2/CLIVAR Repeat 
Hydrography survey, and: to quantify and parameterize CDOM production and 
destruction processes with the goal of mathematically constraining the cycling 
of CDOM. CDOM is a poorly characterized organic matter pool that interacts with 
sunlight, leading to the production of climate-relevant trace gases, 
attenuation of solar ultraviolet radiation in the water column, and an impact 
upon ocean color that can be quantified using satellite imagery. We believe 
that the global distribution of CDOM in the open ocean is controlled by 
microbial production and solar bleaching in the upper water column. We are 
testing these hypotheses by a combination of field observation and controlled 
experiments. We are also interested in the deep-sea reservoir of CDOM and its 
origin and connection to surface waters and are making the first large-scale 
survey of the abundance of CDOM in the deep ocean.

Activities on A22: We collected samples of seawater for absorption spectroscopy 
on one deep ocean cast (24 depths) each day. CDOM is typically quantified as 
the absorption coefficient at a particular wavelength or wavelength range (we 
are using 325 nm). We deter mined CDOM at sea by measuring absorption spectra 
(280-730 nm) of 0.2um filtrates using a liquid waveguide spectrophotometer with 
a 200cm cell. We concurrently collected samples for prokaryotic abundance and 
production rates, and carbohydrates to compare the distribution of these 
quantities to that of DOM (see above)and CDOM. In surface waters (< 300m) we 
are also estimating bacterial productivity of field samples by measuring the 
uptake of bromo-deoxyuridine (BrdU) a non radiotracer assay. On selected 
stations (stations 8, 18, 36, 46, 54, and 68) DNA was collected for further 
molecular analyses to identify community structure. This in situ prokaryotic 
community structure will be compared to that which developed in incubation 
experiments used to assess CDOM production (see below).

Because of the connections to light availability and remote sensing, we 
collected samples for pigment analysis (HPLC), chlorophyll a (fluorometric), 
and particulate absorption (spectrophotometric) when possible (ca daily). We 
also deployed a Satlantic free-fall profiling spectroradiometer (SPMR) to 
quantify the underwater light field, and we have a Satlantic surface irradiance 
meter continuously logging the solar spectrum during daylight hours. SPMR casts 
were launched from the fantail as close to local noon as possible. Details of 
casts times and locations are presented in table 1. Due to overcast skies SPMR 
casts were halted on November 9th. Fluorometric chlorophyll analysis were done 
at sea after 48 hour extractions.


TABLE D.1.  Dates, times and locations of SPMR profiles.

            Date      Time GMT  Station #           # of Casts 
            --------  --------  ------------------  ----------
            10/25/03  16:07     A22S8                   3 
            10/26/03  16:45     A22S12                  2 
            10/27/03  16:45     Between A22S15 &16      1 
            10/28/03  16:51     A22S21                  2 
            10/29/03  17:07     A22S25                  1 
            10/30/03  17:41     A22S33                  1
            11/02/03  18:18     A22S43                  2 
            11/03/03  17:22     A22S46                  2 
            11/05/03  16:25     A22S52                  1 
            11/06/03  17:41     A22S55                  1
            11/07/03  17:14     A22S57                  1


Process Experiments: At selected stations (subtropical, and tropical stations) 
we collected extra seawater for a)microbial culture experiments and b) solar 
bleaching experiments. Water was collected from short casts within the surface 
250 m from stations 14, 41, and 54. In these experiments we will examine the 
rate of CDOM production relative to microbial productivity in culture, and 
quantify the rate of solar bleaching of CDOM near the surface. Microbial Growth 
experiments: Three microbial cultures were conducted over the course of the 
cruise with water collected from 3 special shallow casts to 250 m. Experiments 
were conducted with water collected from stations 14, 41 and 54. Each 
experiment comprised of 2 to 4 different treatments of varying organic matter 
mixture and incubated at in situ temperatures over the course of 5 - 7 days. 
The objective was to monitor microbial biomass production, DOM consumption, 
shifts in the microbial community and temporal variability of CDOM throughout 
the microbial growth curves. Culture activity was monitored by microscopic 
direct counts. Preliminary results indicate that all treatments except the 
unamended control cultures showed significant growth. Further analyses of CDOM, 
DOM, molecular composition of the prokaryotic community will be conducted at 
UCSB. Bleaching Experiments: Two bleaching experiments were conducted at with 
water collected at  station 14 and 54. Water was collected from surface and 
250m at station14 and 100 m and 250 m at station 54. The water was then passed 
through an inline 0.2 µm filter. The filtrates were then placed into 24 200 ml 
quartz tubes and exposed with several solar spectra controlled with various 
screens. These time series incubations were sampled 6 times over an 8 day 
period. CDOM scans were completed at sea and will be further processed by N.B. 
Nelson back at UCSB.


TOTAL DISSOLVED INORGANIC CARBON (DIC)

Dissolved Inorganic Carbon (DIC) 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) used 
simultaneously on the cruise. 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. The instruments were calibrated at 
the beginning and end of each station with a set of the gas loop injections. 
Secondary standards were run throughout the cruise on each analytical system. 
These Certified Reference Materials (CRMs) are poisoned, filtered, and UV 
irradiated seawater supplied by Dr. A. Dickson of Scripps Institution of 
Oceanography (SIO), which have been certified in their shore-based facility to 
have a known concentration of DIC. Although there were numerous small equipment 
problems, particularly during the first third of the cruise, the overall 
accuracy and precision of the at-sea analyses of the CRMs on both instruments 
was -0.14±0.74 µmol/kg (n=35) and 0.09±1.06 µmol/kg (n=37) for systems 1 and 2, 
respectively. Preliminary DIC data reported to the database have not yet been 
corrected to the Batch 61 CRM value, but a more careful quality assurance to be 
completed shore-side will evaluate the results on a per instrument basis. 
Samples were drawn from the Niskin-type bottles into cleaned, pre-combusted 
500-mL Pyrex bottles using Tygon tubing. Bottles were rinsed once 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 5-mL headspace, 
and 0.2 mL of saturated HgCl2 solution was added as a preservative. The sample 
bottles were sealed with glass stoppers lightly covered with Apiezon-L grease, 
and were stored at room temperature for a maximum of 12 hours prior to 
analysis. Approximately 1640 samples were analyzed for DIC; full profiles were 
completed on the 'A' (even numbered) stations, with replicate samples taken 
from the surface, oxygen minimum, and bottom Niskin-type bottles. At a minimum, 
replicate surface samples were taken at every 'B' (odd numbered) station, and 
when time permitted, additional depths were sampled. Approximately 120 
replicates were collected in total. The replicate samples were run at different 
times during the station analysis for quality assurance of the integrity of the 
coulometer cell solutions. No systematic differences between the replicates 
were observed and the standard deviation of the differences was approximately 
1.2 µmol/kg on both systems.



REFERENCES 

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.

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. 



C.18.  BROMODEOXYURIDINE INCORPORATION RATES AS A PROXY FOR PROKARYOTIC PRODUCTION.
       Standard Operating Procedure
       Carlson Lab, UCSB


Prepping and quantifying BrdU standards:

For each cruise, BrdU standards are prepped and quantified 1-2 months before 
departure.  These standards consist of raw seawater from the Santa Barbara 
channel incubated for 8-12 hours with 20nmol L-1 BrdU.  Incubations are done 
in parallel with three reagents: radiolabeled BrdU, radiolabeled TdR, and 
cold BrdU.  Every 2-3 hours subsamples from quadruplicate incubations are 
frozen to halt incorporation.  Radiolabeled incubations are extracted in 
parallel using both centrifugation (Smith and Azam 1992) and filtration 
(Nelson and Carlson 2005) techniques.  Filtered radiolabeled samples are cut 
into single-well rectangles and placed into centrifuge tubes filled with 
scintillation cocktail for quantification in parallel with centrifuged 
samples.  Time-course relationships are developed for each substrate to 
ensure linear substrate uptake rates and estimate differential substrate 
uptake rates.  Dilution series for the final timepoint are measured to ensure 
linearity of calculated concentrations. Final concentration of the non-
radioactive standards for use on cruise immunoblots is measured as the mean 
final calculated fmol mL-1 concentration of the filtered, radiolabeled BrdU 
samples. 

Ancillary data associated with every standard prep consists of the following: 
1) Rate of uptake of radiolabeled BrdU and TdR as measured by centrifugation 
   and filtration extraction procedures, 
2) Linearity of serial dilution of radiolabeled BrdU using filter extraction; to 
   be compared with linearity of chemiluminescence of serial dilution of Cold 
   BrdU by comparing identical Hot and Cold filters, 
3) Loss of BrdU substrate during filtration process by comparing timepoints  
   between filter and centrifuge extraction methods, 
4) Quantification in fmol mL-1 of final BrdU standard with variance quantified 
   by comparing 11 separate filtrations of undiluted 12hr. radiolabeled 
   standard.

Preparation of Cruise Sampling Blots:

Water from each sampling point is aliquoted into quadruplicate 2mL 
incubations in microcentrifuge tubes and amended with BrdU to a final 
concentration of 20nM.  Tubes are incubated at in situ temperatures for 8-12h 
followed by rapid freezing to halt incubation.  Tubes are thawed within 1 
month and the full 2mL is filtered onto charged Nylon blotting paper using a 
slot blotter.  Typically each blot is prepped with quadruplicate samples from 
8 depths at a single lat/long station, along with parallel duplicate serial 
dilutions of two separate standards on the same blot.  Immediately after 
filtration blots are taken through a series of treatments designed to lyse 
cells and bind DNA to the charged nylon membrane (Nelson and Carlson 2005). 
Briefly, each blot is placed face down momentarily on filter paper soaked 
with a strongly basic Lysis Buffer, then incubated face up on the soaked 
filter paper for ten minutes.  This process is repeated using a 
Nuetralization Buffer, then again on a nucleic acid fixative called FixDenat 
(Roche Molecular Products).  Finally, the blot is baked at 85°C for 1 hour 
and stored in a sealed plastic bag.

Development of Chemiluminescent Immunoblots:

Upon return to laboratory, baked immunoblots are stored up to 9 months at 
room temperature or refrigerated in plastic bags.  Blots are developed 
according to the HRP-chemiluminescence protocols outlined in Nelson and 
Carlson (2005).  Briefly, each blot is placed into a polystyrene tray and 
incubated shaking at 60rpm for 1hr in blocking buffer, 3hrs in antibody 
buffer, two times five minutes wash buffer, and two times five minutes Maleic 
Acid Buffer. Blots are then removed from liquid and placed on the lid of the 
incubation tray.  1mL each of the two Pierce Supersignal Femto reagents are 
mixed and the 2mL final reagent is immediately pipetted onto the blot to 
cover all available surfaces.  The blot is incubated exactly 2min before a 
paper towel is placed over the surface to absorb the development reagent.  
After development the blot will remain chemiluminescent for about 30min, but 
is strongest in the first 5-10 min after developing. The blot is immediately 
photographed and quantified as follows using a BioRad Versadoc or similar 
chemiluminescent dark CCD-imager. Using 60s exposures, maximum aperture size, 
and "Chemiluminescent Hi-Sensitivity", the blot is photographed repeatedly 
until all wells are squarely within the viewfinder (this makes quantification 
more straightforward).  Using the Transform Fuction, adjusting the High 
slider will permit visualization of low-concentration wells.  When blot is 
correctly centered, a 300s exposure is taken and used to quantify the 
concentration of BrdU in each well. 

Analysis of Chemiluminescent Immunoblot Images:

Quantity One software is used to analyze all immunblots.  Standardized 
rectangular grids are drawn around filtration points on the blotting membrane 
and chemiluminescence is quantified as intensity per well.  Duplicate serial 
dilutions of standards on each blot are used to develop a linear regression 
relating chemiluminescent intensity to concentration of BrdU.  Quadruplicate 
incubations of seawater with BrdU are analyzed for each sample as described 
above, and wells which present a BrdU concentration >1 standard deviation 
above the mean of the four incubations are removed from the analysis.  BrdU 
incorporation rates are calculated as concentration divided by incubation 
duration for each sample, and may be related to rates of TdR incorporation 
using the regression detailed in Nelson and Carlson (2005). 


Reference:

Nelson, C. E., & Carlson, C. A. (2005). A nonradioactive assay of bacterial 
    productivity optimized for oligotrophic pelagic environments. Limnology and 
    Oceanography-Methods, 3, 211-220.




C.19.  DISSOLVED COMBINED NEUTRAL SUGAR SAMPLES
       Standard Operating Procedure
       Carlson Lab UCSB

Cleaning procedures: Glassware, Glass Fiber Filters (G/FF), and collection 
vials  

All glassware and G/FFs used were combusted at 450°C and 400°C 
respectively for 3 hours. High density polyethylene collection bottles (HDPE) 
were cleaned with 5-10 % hydrochloric acid (HCl) and nanopure water 
(Barnstead Thermoline). Polycarbonate tubes used for neutralization were pre-
cleaned with MeOH, 5% HCl, 0.5 M NaOH, nanopure water and dried prior to 
usage. 

Sample collection and storage

Samples were filtered through combusted 47 mm G/FFs and collected in 60 mL 
high density polyethylene (HDPE) bottles. All sample bottles were rinsed 3x 
with sample filtrate before filling. Samples were stored at - 20°C shipboard 
prior to being shipped to UCSB for further storage then analysis. 

Hydrolysis, Neutralization and Desalting 

Extraction of DCNS samples followed the methodology of Borch and Kirchman 
(1997), with slight modification of hydrolysis time and neutralization. Prior 
to hydrolysis, 4 mL of sample water was aliquoted into combusted 5 mL glass 
ampules (Wheaton) Ampules were then flame sealed and samples were hydrolyzed 
(0.85 M H2SO4) at 100°C for 21 hours. 

Samples were cooled to room temperature and neutralized in 30 mL 
polycarbonate tubes filled with 0.427 g of combusted (450°C for 3 hours) 
CaCO3. A series of vortexing and mixing followed to bring pH levels to ~ 6. 
Tubes were vortexed 1 minute, placed on a shaker table for 15 minutes 
(vigorous shaking), and vortexed again for 30 seconds. Samples were then 
placed in an ultracentrifuge for  30 minutes at 14000 RPM's. The supernatant 
was pipetted into combusted 7 mL glass scintillation vials equipped with 
teflon lined caps. Samples were refridgerated (4°C no longer than 2-3 days) 
in the dark until desalting.

Helium gas was used to flush/collect during all desalting steps. Samples were 
desalted in 20 mL HDPE columns (BioRad) that were cleaned with full bed 
volumes of NaOH (0.5 M), HCl (5-10%), and nanopure water. Columns were loaded 
with 7 mL of mixed anion (AG 2-X8) and cation (AG 50W-X8) exchange resin 
(BioRad) then flushed 3x with two bed volumes of nanopure water. Resin was 
primed 3x (and immediately flushed) with 400 uL of sample before 900 uL of 
sample was added to the resin for 7 minutes. Desalted samples were then 
collected in combusted 20 mL scintillation vials. All samples were 
refridgerated (4°C no longer than 2-3 days) in the dark until HPLC analysis.

Analysis of DCNS using HPLC-PAD

DCNS were analyzed using a Dionex Bio-LC 600 equipped with a GS-50 pump, ED-
50 detector, and AS-50 autosampler. Peaknet 6 integration software was used 
for data collection. Sugars were isocratically eluted at 18mM NaOH (50% w/w, 
Fisher), and separated with a CarboPac PA-10 analytical and guard columns. 
The electrochemical detector was equipped with an Au working electrode and a 
pH reference electrode. A 200 mM NaOH post wash was used to minimize CaCO3 
buildup on the columns. 

System Performance and Sample Standardization

System performance was monitored with a known Dionex mono-standard of 6 
sugars every 8th sample. A mono-standard mix of 7 sugars (Absolute Standards, 
Inc.) was used to calculate unknown sample sugar concentrations. Standards 
were run in duplicate and subjected to the same extraction procedure above. A 
4-point standard curve was used to calculate unkowns (10, 75, 125, 250 nM). 
Deep and surface reference seawater samples from the Santa Barbara Channel 
were extracted (reps of 3 each) each run to monitor the efficiency of the 
hydrolysis, neutralization, and desalting steps. 

Various terms on spreadsheet:

DCNS:   is the sum of all individual sugars and refers to dissolved combined 
        neutral sugars after hydrolyses.
FUC:    concentration of fucose after hydrolyses.
RHAM:   concetration of rhamnose after hydrolysis
ARAB:   concentration of arabanose after hydrolysis
GAL:    concetration of galactose after hydrolysis
GLU:    concentration of glucose after hydrolysis
MAN:    concentration of mannose after hydrolysis


Reference:

Borch, N. H. and D. L. Kirchman (1997). "Concentration and composition of 
    dissolved combined neutral sugars (polysaccharides) in seawater 
    determined by HPLC-PAD." Marine Chemistry 57: 85-95.




C.20.  ENUMERATING VARIOUS MICROBIAL CONCENTRATION VIA FLOW CYTOMETRY
       Standard Operating Procedure
       Carlson UCSB

Seawater samples were collected in the field from Niskin bottles into sterile 
cryovials and immediately preserved with fresh Paraformaldehdye stock at a 
0.2% final concentration. Samples were left to fix 10 minutes at room 
temperature, then for long-term storage were placed immediately into liquid 
nitrogen to preserve fluorescence. 

Samples were analyzed via the method of Campbell (2001) using a Becton 
Dickinson FACSCalibur flow cytometer. Internal calibration of the FCM system 
is carried out using commercially available fluorescent polystyrene beads of 
uniform size.  Initial conditions are established by running sheath fluid 
consisting of particle free seawater, prepared by double filtering seawater 
through 0.22um disposable filters.  For analysis of autotrophic picoplankton 
5ul of calibration beads are added to 0.5ml of sample volume. For non-
autofluorescent populations, the nucleic acid stain SYBR Green was added to 
samples to distinguish populations of heterotrophic bacteria cells.  
Oligotrophic ocean samples are run on high flow rate (60ul/min) for 2-4 
minutes and 10 000 events collected per population. Blanks consisting of 
filtered seawater are also run at the standard settings used for analysis.

Flow cytometric listmode data is processed and analyzed using software to 
quantify the abundance and optical properties of individual populations of 
picoplankton.  Cell abundance for each population (N) in a field sample is 
calculated in cells/ml from the equation:

                        N = C / (T x R) x CF x 1000ul/ml

where C is the number of events acquired for a specified population, T is the 
duration of analysis in minutes, R is the sample delivery rate in ul/min, and 
CF is a correction factor accounting for dilution of sample.

Various terms on spreadsheet:

BACT:   refers to concentration (cell /L) of non pigmented "heterotrophic 
        bacterioplankton" 
PRO:    refers to concentration (cell /L) of prochlorophytes
PEUK:   refers to concentration (cell /L) of pigmented picoeukaryotes
SYN:    refers to concentration (cell /L) of Synechococcus species


Reference:

Campbell, Lisa 2001.  Flow Cytometric Analysis of Autotrophic Picoplankton.  
    Methods in Microbiology, Vol. 30: 317-343.





CCHDO DATA PROCESSING NOTES

Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
01/28/04  Delahoyde   ctd/sea/sum     Submitted (note from s.diggs)
          Frank,
          Thanks for the A20/A22 2003 data along with the PDF documentation and 
          the CTD 2 decibar downcast data.  You may put the files in the 
          following location:
             /usr/export/html-public/data/co2clivar/atlantic/a20/a20_2003a
          Please let me know once all files have been copied into that 
          directory. -SCD

02/04/04  Delahoyde   Cruise Report   Submitted  ODF report data report
          Located chief scientist's narrative and forwarded it to J Kappa


02/09/04  Delahoyde   CTD             Submitted  WHP format
          They're (A20 & A22 ctd data) now in WHP format on whpo:
          /usr/export/html-
            public/data/co2clivar/atlantic/a22/a22_2003a/original/a22-CTD/
                and
          /usr/export/html-
            public/data/co2clivar/atlantic/a20/a20_2003a/original/a20-CTD/

02/12/04  Diggs       DOC             Submitted: PI list
          These data were provided by:
          PARAMETER/PROGRAM    NAME             Inst       EMAIL ADDRESS
          -----------------    ----             ----       ------------------------
          Chief Scientist      Terrence Joyce   WHOI       tjoyce@whoi.edu
          Co-Chief Scientist   William Smethie  LDEO       bsmeth@ldeo.columbia.edu
          CTDO/S/O2/Nutrients  James Swift      SIO        jswift@ucsd.edu
          DIC                  Richard Feely    PMEL       Richard.A.Feely@noaa.gov
                               Chris Sabine     PMEL       Chris.Sabine@noaa.gov
          CFC                  William Smethie  LDEO       bsmeth@ldeo.columbia.edu
                               Rana Fine        UofMiami   rfine@rsmas.miami.edu
          TALK                 Frank Millero    UofMiami   fmillero@rsmas.miami.edu
          CDOM, DOC, DON       Craig Carlson    UCSB       carlson@lifesci.ucsb.edu
          He/Tr                William Jenkins  WHOI       wjenkins@whoi.edu
          Surface C14          Ann McNichol     WHOI       amcnichol@whoi.edu
                               Robert Key       Princeton  rkey@princeton.edu
          C13 profiles         Paul Quay        UofWash    pdquay@u.washington.ed

          The data included in these files are preliminary, and are
          subject to final calibration and processing. They have been
          made available for public access as soon as possible following
          their collection.  Users should maintain caution in their
          interpretation and use. Following American Geophysical Union
          recommendations, the data should be cited as: "data
          provider(s), cruise name or cruise ID, data file name(s),
          CLIVAR and Carbon Hydrographic Data Office, La Jolla, CA,
          USA, and data file date." For further information, please
          contact one of the parties listed above or whpo@ucsd.edu.
          Users are also requested to acknowledge the NSF/NOAA-funded
          U.S. Repeat Hydrography Program in publications resulting
          from their use.

02/13/04  Delahoyde   Cruise Report   Updated figs for ODF ctd report

02/17/04  Kappa       Cruise Report   PDF & ASCII Versions Ready to go online
          Combined ODF CTD report with Chief Scientist's Cruise Narrative.  
          Produced PDF and TEXT versions.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
02/20/04  Diggs       CTD             Website Updated:  Data OnLine
          The CTD data for A22 (2003) are now available on-line through all 
          links from the whpo.ucsd.edu webpage.  In addition, ted and I have 
          fixed all of the normal links so that both the A20 and A22 cruises 
          (both versions of each) are accessible from all of the normal links on 
          the WHPO website.


02/21/04  Kozyr       TCARBN          Submitted; QC'd
          The data disposition is:
             Public  
          The bottle file has the following parameters:
             TCO2
          The file format is:
             Plain Text (ASCII) 
          The archive type is:
             NONE - Individual File 
          The data type(s) is:
             Bottle Data (hyd)
          The file contains these water sample identifiers:
             Cast Number (CASTNO)
             Station Number (STATNO)
             Bottle Number (BTLNBR)
             Sample Number (SAMPNO)
          KOZYR, ALEX would like the following action(s) taken on the data:
             Merge Data
          Any additional notes are:
             This is a file with the corrected TCO2 values for the A22 section

03/18/04  Diggs       BTL             Website Updated: Data OnLine

05/24/04  Roberts     TCARBN/Report   Submitted; Data Recalculated
          I have submitted my final A20/A22 data to  WHP, and have included 
          revised documentation with it.  The documentation includes discussion 
          of the final data processing, including recalculation of the TCARBN 
          files using bottle salinities, as well as our secondary standards 
          (CRMs) corrections.  Please notify me if you see any problems with the 
          files.


06/10/04  Kozyr       TCARBN          QC begun; Adjusted for CRM measurements 
          I received the DIC measurements for Repeat Sections A20 and A22 from 
          Marilyn Roberts, PMEL. These measurement were adjusted for CRM 
          measurements and went through preliminary quality control at PMEL. I 
          will have done our routine quality evaluation for these data and will 
          send you new data as soon as I finish.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
06/21/04  Kozyr       TCARBN/ALKALI   Submitted; Corrected TCO2 values, flags
          I have submitted 2 files to WHPO with the corrected TCO2 values for 
          merging to the master file. I hope you like the format of the files. 
          The quality flags changed a bit too, so please merge the flags as 
          well. However, I have a few questions to the TCO2 PI regrading some 
          quality flags, so they might change in a future. TALK corrected values 
          will be sent to CDIAC in a few weeks by Andrew Dickson per our 
          conversation today. 
          The data disposition is:
             Public  
          The bottle file has the following parameters:
              TCO2
          The file format is:
            WOCE Format (ASCII) 
          The archive type is:
            NONE - Individual File 
          The data type(s) is:
            Bottle Data (hyd)
          The file contains these water sample identifiers:
            Cast Number (CASTNO)
            Station Number (STATNO)
            Bottle Number (BTLNBR)
            Sample Number (SAMPNO)
          KOZYR, ALEX would like the following action(s) taken on the data:
            Merge Data
          Any additional notes are:
            This is a file with corrected parameters of TCO2 for section A20. 
            A22 is comming soon.


08/17/04  Davis       Cruise Report   PDF & TXT versions of cruise report online

08/25/04  Bartolacci  CTD/TCARBN      Exchange & netCDF files online
          I have merged the new DIC values sent by Alex Kozyr, into the 
          A20_2003a bottle file.  No other edits were made to the bottle file.  
          Data merged with no errors.  File was format checked with wocecvt and 
          moved to parent directory.  Old file was renamed and moved to original 
          directory.

          It should be noted, however that station 51/1 contains greater than 36 
          bottle/samples.  In the cruise documentation this was explained by the 
          fact that station 51 cast 1 was discarded and renamed 51 cast 3, 
          however the data (CTD) for casts 1 and 3 are not identical as one 
          would expect.  I have begun looking into this issue with ODF, however 
          it is not resolved at this time.  No errors in formatting were 
          produced other than a warning that station 51 cast 1 contains too many 
          samples.

          Exchange and netCDF files were generated with no errors and placed 
          online.


Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
08/26/04  Bartolocci  CTD             Exchange & netCDF files online
          I have converted the CTD files for a22_2003a (316N200310)
          to exchange and netCDF files and place them online.  No
          errors in conversion were found.

10/28/04  Kozyr       TCARBN          Submitted: Final Data from Marilyn Roberts to Kozyr
          A20 and A22:

          I have the final TCO2 (DIC) data from Marilyn Roberts, I merged these 
          data into WHPO format, made our QA-QC work, added some quality flags 
          to the data and sent the data to CCHDO on June 22, I have automatic 
          confirmation on receiving these data. I've checked CCHDO web site for 
          A20 A22 and noticed that the new and final TCO2 data were incorporated 
          to the bottle data files.  However I did not find any mention of this 
          change in the history link.

          Andrew Dickson is still working on his Total Alkalinity (TALK) data 
          for A20/A22 sections. I've talked to him last week during the PICES 
          meeting and he said he will send the TALK final measurements to CDIAC 
          soon (?). So, the TALK numbers in CCHDO bottle data file are 
          preliminary and will be adjusted as soon as I get the data and work on 
          merging and QC.

12/17/04  Kozyr       TCARBN/ALKALI   TCARBN: Final; ALKALI: Preliminary
          A20 and A22 (2003):

          I have the final TCO2 data from Marilyn Roberts, I merged these data 
          into WHPO format, made our QA-QC work, and sent the data to CCHDO on 
          June 22, I have automatic confirmation on receiving these data. I've 
          checked CCHDO web site for A20/A22 and noticed that the final TCO2 
          data were incorporated to the bottle data files. 
          
          Andrew Dickson is still working on his Total Alkalinity data for 
          A20/A22 sections. I've sent Andrew a message a few days ago with 
          question about a status of his TALK data, but did not have a reply 
          yet. The TALK numbers in CCHDO bottle data file are preliminary and 
          will be adjusted as soon as I get the data from Andrew and work on 
          merging and QC.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
01/12/05  Kozyr       ALKALI          Submitted; Ready to go online
          The data disposition is:
               Public  
          The bottle file has the following parameters:
               ALKALI
          The file format is:
               WOCE Format (ASCII) 
          The archive type is:
               NONE - Individual File 
          The data type(s) is:
               Bottle Data (hyd)
          The file contains these water sample identifiers:
               Cast Number (CASTNO)
               Station Number (STATNO)
               Bottle Number (BTLNBR)
               Sample Number (SAMPNO)
          KOZYR, ALEX would like the following action(s) taken on the data:
               Merge Data
          Any additional notes are:
               Please merge these Alkalinities data into the main file for the  
          A22_2003 cruise. TCARBN data have been sent earlied and is correct in 
               the main file.  Thank you,  Alex.

01/13/05  Anderson    ALKALI          WOCE, Exchange and NetCDF files online
          Merged final ALKALI data sent by A. KOZYR into online file.  Made new     
          exchange and netcdf files.

01/21/05  Kozyr       CO2             Data are Public: On CDIAC Webpage
          The attached .doc file is the table for CLIVAR Repeat Section data 
          status summary. As you can see from the table, we have opened the data 
          from A22_2003, A16N_2003, and P17N_2001 for public through CDIAC 
          CLIVAR web page:
            http://cdiac.ornl.gov/oceans/RepeatSections/repeat_map.html
          and these data are also available through Ocean Data Mercury:
            http://mercury.ornl.gov/ocean/


02/02/05  Anderson    CFCs            Website Updated: new cfc data online
          Merged the CFC11, CFC12, CFC113, and CCL4 submitted by D. Willey on 
          Feb. 2, 2005 into the online file.  There were 8 samples that were not 
          merged.  Station 23, cast 1 bottles 28-35 were in the file that Debbie 
          submitted, but the online file did not have these bottle numbers for 
          station 23. 

          Also, the submitted file had -999.000 for missing values for CCL4.  
          The exchange program did not like this value, so I changed it to -
          9.000.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
02/02/05  Willey      CFCs            Submitted: new cfc data, including CCL4 
          The data disposition is:
              Public  
          The bottle file has the following parameters:
               CFC-11, CFC-12, CFC-113, CCL4
          The file format is:
               WHP Exchange 
          The archive type is:
               NONE - Individual File 
          The data type(s) is:
               Bottle Data (hyd)
          The file contains these water sample identifiers:
               Cast Number (CASTNO)
               Station Number (STATNO)
               Bottle Number (BTLNBR)
          WILLEY, DEBRA would like the following action(s) taken on the data:
               Merge Data
              Place Data Online


03/21/05  Kozyr       TCARBN          Update Needed: Qual Flags
          Could you please apply some quality flags changes in your *hy.txt and 
          hy1.csv files for the A22_2003 cruise TCO2 data as follows:
            sta-cast-bot flag
            1-1-3 hi vs P flag 3
            10-1-20 hi vs P flag 3
            14-1-16 low vs P and alkf=4, flag all 3
            16-1-8 flier flag 4
            41-1-28 hi vs P flag 3
            41-1-29 hi vs P flag 3
            42-1-13 hi vs P flag 3


04/20/05  Nelson      CDOM            Submitted: Final CDOM Data
          The data disposition is:
               Public  
          The file format is:
               Plain Text (ASCII) 
          The archive type is:
               NONE - Individual File 
          The data type(s) is:
               Other: Bottle Data (other)
          The file contains these water sample identifiers:
               Cast Number (CASTNO)
               Station Number (STATNO)
               Bottle Number (BTLNBR)
               Sample Number (SAMPNO)
          NELSON, NORMAN would like the following action(s) taken on the data:
               Place Data Online


Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
05/23/05  Anderson    TCARBN          Website Updated: flags corrected 
          Made the changes to the TCO2 flags per Kozyr.  Made new exchange and 
          netcdf files. 


10/25/05  Carlson     Cruise Report   Submitted: DOC collection and analyses
          Here is the documentation for DOC collection and analyses.  Let me 
          know if you need any other info.


10/25/05  Carlson     DOC             Submitted: final data w/ Qual flags
          The DOC data for A20 and A22 are finally complete.  The long delay was 
          largely due to the fact that for a long stretch our machines were down  
          but all the problems have been resolved and all the samples were run 
          when the machines were stable and performing well.  Attached are final 
          DOC data and the quality flags for the A20 and A22 lines.  For a while 
          we have been trying to submit via the web but have not been able 
          through the submit page so I thought I would forward the files 
          directly to you.  Because this page is not working I am not sure if 
          you need any other info associated with this data...so if you need mor 
          info please let me know.

          The final DOC data in these files are reported as µmol/L.  I 
          assigned quality flags according to the WHP codes.  There were a few 
          samples from each line that were misplaced or missing so I have 
          entered a 5 as a quality flag for those sample.


02/07/06  Jenkins     HELIUM          Analysis completed, Data processing pending
          We have also completed the helium analyses for the A20 and A22 
          cruises, and I hope to submit those results shortly. I had hoped to 
          complete the data processing prior to the Ocean Sciences meeting, but 
          may have to do it afterward.


02/14/06  Dunworth     C13/C14        Submitted by email
          We recently got an 'overdue' notice from NSF...they wanted C13/C14 and 
          Tritium/helium from A20_03 and A22_03. I didn't see it on your 
          website. Turns out that it was sent to the state dept in dec 2004. I 
          have a copy of the c13/c14 data...do you want it??  jenkins is still 
          processing the tritium, and hasn't begun the helium.


05/22/06  Carlson     Cruise Report   Submitted: DOC report
          Here is the documentation for DOC collection and analyses.  Let me 
          know if you need any other info


05/31/06  Anderson    DOC             Data online; Exchange file pending
          Merged the DOC sent by C. Carlson on Oct. 25, 2005 into the online 
          file.  Cast 2 for stas. 14, 41, 54, and 57 had no DOC values and no Q 
          flags.  I set the values to -9.0 and the flags to 9.

          The WOCE to EXCHANGE STILL needs to have DOC added, so I DID NOT MAKE 
          A NEW EXCHANGE file.  



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
11/09/06  Carlson     BACT            Submitted; Data are Final
          Here are several additional ancillary data that accompany the core 
          CDOM data (already submitted) for A20 and A22.  They include 
          concentrations of microbes in the upper 250 m, bromodioxyuridine 
          incorporation rates (proxy for microbial production) and 
          concentrations of dissolved combined neutral sugars for A20.  I have 
          also included brief standard operating procedures for each parameter. 
          Again these are level III ancillary data to the bigger CDOM data set. 
          These data analyses are extremely labor intensive to generate and were 
          just recently completed, QC'd and finalized. I am not sure how they 
          are to be incorporated into the larger data sets but wanted to make 
          sure data center received these final data.


11/15/06  Kozyr       CO2             Submitted: TCARBN/ALK OK, DOC Incomplete
          Here are the latest update on the Carbon Data status at CCHDO and CDIAC.
          A22_2003:
          TCO2 - OK;
          TALK - OK;
          DOC - wrong data in the .hy file at CCHDO, no data merged in the 
                exchange file (final DOC sent to CCHDO on 10/26/2005).


11/25/06  Carlson     BACT            Submitted: Microbial abundance data
          File:       A22_BACT_11-20-06.txt  Type: txt Status: Public
          Name:       Carlson, Craig 
          Institute:  University of California Santa Barbara 
          Country:    USA
          Expo:       316N200310 Line: A22
          Date:       11/2003
          Action:     Place Data Online
          Notes:      Microbial abundance data ancillary to core CDOM data


11/25/06  Carlson     BrdU            Submitted: Bacterial production data
          File:       A22_BrdU_11-20-06.txt  Type: txt Status: Public
          Name:       Carlson, Craig 
          Institute:  University of California Santa Barbara 
          Country:    USA
          Expo:       316N200310 Line: A22
          Date:       11/2003
          Action:     Place Data Online
          Notes:      Bacterial production data for A22.  This is ancillary data 
                      to the core CDOM data set



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
12/13/06  Jenkins     He/Tr/Neon      Submitted  Ready to go online
          Please find attached a spreadsheet containing the helium isotope, 
          helium and neon analytical results for A20_2003, A22_2003, and 
          P02_2004. Hopefully the tables are self-explanatory, but please let me 
          know if there are any questions. I will be working on and sending the 
          accompanying tritium data in the near future, and will then work on 
          sending you the A20_1997 and A22_1997 data.
          File:       RH3 Tritium Submission.csv  Type: CSV Status: Public
          Name:       Jenkins, William 
          Institute:  WHOI 
          Country:    USA
          Expo:       316N200310 Line: A22
          Date:       10/2003
          Action:     Place Data Online

01/10/07  Jenkins     TRITUM          Update Needed: computational errors
          We have just discovered a computational error in about 2 dozen of the 
          tritium analysis results I submitted for A20/22. The changes are quite 
          significant and should be corrected. How would I go about doing this?

10/01/07  Kozyr       DOC             submitted; Qual flags updated
          I've just submitted the latest DOC numbers for A22_2003 cruise (we 
          found some problems with flags). As you did not merge previously 
          submitted DOC numbers yet, please replace them with this latest one.

11/19/07  Jenkins     HELIUM          submitted; Ready to go online
          Helium Submission.csv Type:  Status: public
          Name: Jenkins, William J
          Institute:  WHOI
          Country:    USA
          Expo:       316N200310 Line: A22
          Date:       2003-10-23 
          Action:     Place Online

12/19/07  Carlson     TDN             Submitted; upper 300 m
          300m TDN submitted.txt Type:  Status: public
          Name:       Carlson, Craig
          Institute:  UCSB
          Country:    USA
          Expo:       316N200310 Line: A22
          Date:       2003-10-01 
          Action:     Merge Data
          Notes:      Attached are total dissolved nitrogen data determined for 
                      the upper 300 m.   These data are used in combination with 
                      nitrate and nitrite to calculate DON.  TDN is reported 
                      because that's the parameter actually measured.  These are 
                      ancillary data to the larger DOC data sets already 
                      submitted.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
02/02/08  Kozyr       DOC/TDN         Submitted  Resubmitted
          Status:     public
          Name:       Kozyr, Alex
          Institute:  CDIAC/ORNL
          Country:    USA
          Expo:       316N200310 Line: A22_2003
          Date:       2003-10-23 
          Action:     Merge Data, Place Online
          Notes:      Here are the DOC and TDN data. I've submitted DOC 
                      measurements before for this cruise but do not see these 
                      numbers mearged yet, so I send them again.


04/07/08  Key         C13/14          Submitted; Ready to go online
          I resubmitted the data to you guys today (2 files) via the web site. 
          Format of these may be easier for your guys to merge and the data now 
          has the QC flags.

04/16/08  Lee         CFCs            Submitted: CFC11/12/113
          Attached are the cfc data finalized in Lamont.


04/18/08  Johnson     CTD             Update Needed  various errors
          Errors found by ODF in CTDO data submitted 2003/2004 for CLIVAR A20/A22:
          • CTDTEMP data reported were IPTS68, but labeled as ITS90
          • CTDOXY data did not have corrections applied properly, likely due to 
            a scripting error.  The top 10-20db are very skewed for most 
            stations, and deep data are occasionally affected as well.
          • Transmissometer data were not included with the CTD data originally, 
          • Fluorometer data were not block-averaged and are not reported.

          Corrected CTDO data files were submitted by ODF to CCHDO on 3/18/2008.
          Uncalibrated transmissometer data are also included, pending updatesby 
          Wilf Gardner (TAMU).  Fluorometer data were collected with the CTD, 
          but not block-averaged; they are not reported.



Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
05/20/08  Bartolocci  BTL             Website Updated; Several params added
          A22_2003a (316N200310) merging notes
          4.10.2008  DBK
          Files are from:
          CFC11,12,113- emailed from Steve Diggs from Vienna on 04/14/2008.   
          These values are from Bill Smethie.
          C13/14- submitted by Bob Key to cchdo website on 04/07/2008 and 
            supersede Dunworth's.
          BrdU - submitted by Carlson on 11.25.2006 THESE VALUES HAVE NOT YET 
            BEEN MERGED.
          BACT - submitted by Carlson on 11.25.2006 THESE VALUES HAVE NOT YET 
            BEEN MERGED.
          DCNS - submitted by Carlson on 11.25.2006 THESE VALUES HAVE NOT YET 
            BEEN MERGED.
          Helium - submitted by Bill Jenkins on 11.19.2007
          Tritium - submitted by Bill Jenkins on 11.19.2007
          Helium 3 - submitted by Bill Jenkins on 11.19.2007
          Neon - submitted by Bill Jenkins on 11.19.2007
          TDN - upper 300m data submitted by Carlson on 12.19.2007
          TDN - resubmission of TDN by Alex on 2.18.2008
          DOC - resubmission of DOC by Alex on 2.18.2008

          NOTES:
          ------
          TCO2- Changed header mnemonic to read WOCE convention TCARBN.
          TDN- values < 300m were sent by Carlson.  Needed reformatting before 
            merging.  Merged values with no apparant errors (none reported by 
            mrgsea).  Ran wocecvt with no errors.
          Helium, it's error and quality flag, delta helium 3, it's error and 
            quality flag and neon,error and quality flag values were merged into 
            the a22_2003a bottle file with no apparent errors (none reported by 
            mrgsea).  Ran wocecvt afterward with no errors.  15 stations in the 
            original file were not merged into the woce-formatted bottle file.  
            These stations (found in the files named: helium_unmerged.txt, 
            helier_unmerged.txt delhelium_unmerged.txt, delherr_unmerged.txt 
            respectively) are missing station/cast/bottle combinations in the 
            woce-formatted bottle file and are not thought to be an error in 
            merging.
          Tritium and it's erro and quality flag values were merged into the 
            a22_2003a bottle file with no apparant errors (none reported by 
            mrgsea).  Ran wocecvt with no errors.
          CFC 11, CFC 12 and CFC 113 and their associated quality values were 
            merged into the a22_2003a bottle file with no apparant errors (none 
            reported by mrgsea).  Ran wocecvt with no errors.
          C13 and C14 sent by Key were first refromatted, then merged into the 
            a22_2003a bottle file using mrgsea with no errors.
          TDN and DOC sent by Alex were extracted, reformatted and merged into 
            the a22_2003a bottle file using mrgsea with no errors.  Ran wocecvt 
            with no errors.
          BACT, DCNS and BrdU have not been merged at this time.  Current files 
            need refromatting before merging can be completed.
          Final WOCE formatted bottle file has been checked for formatting 
          errors with wocecvt.  No errors were found.  Exchange bottle file was 
          created using the merged WOCE bottle file.  TDN values were not 
          included in the exchange file because this parameter was not 
          recognized by the conversion code.  Netcdf files were generated with 
          no errors.  It has been noticed however that the column for HELIER is 
          offset by one character/byte.  This in turn effects the last 3 columns 
          (error values for tritium, C14, and delhe3).  This occurs only in the 
          exchange file, and will be discussed with the office for possible 
          solutions.  It appears to be a problem with the exchange conversion 
          code although no errors were produced.

          All merged files were placed online and previous version moved to the 
          original directory and renamed to include the date of their transfer.


Date      Contact     Data Type       Event Summary
--------  ----------  --------------  ------------------------------------------
06/26/08  Fine        CFCs            Data Update: Data at CCHDO NOT FINAL
          This is to let you that the A22 file you have is NOT yet final.


07/09/08  Field       Cruise Report   Website Updated  New reports online
          On Mon, Jul 7, 2008 at 3:01 PM, Jerry Kappa wrote:
          I just updated the pdf report for a22_2003a, put it into the 
          appropriate directory, and moved the previously online pdf to the 
          original directory. The old pdf cruise report had an incorrect cruise 
          track.  This has been corrected in the new pdf.

11/24/08  Lee         CFCs            Submitted; Ready to go online
          Attached are the finalized CFCs file of A22_2003 cruise and the report 
          for the A22_2003 CFCS data.


12/02/08  Kozyr       CFCs            Update Needed: Final Data & report avail
          We do have a report on CFC measurements for A20 and A22. And i think 
          we have the final data as well in the data file. i need to compare 
          with your CFC data though.

          You can find the report in NDP-089:          
            http://cdiac.ornl.gov/oceans/ndp_089/ndp089.html and click on 
          Chlorofluorocarbon Measurements, or download the NDP-089 in PDF 
          format.


12/04/08  Hoyle       CFCs            Submitted; Ready to go online
          Action: Merge Data, Place Online, Updated Parameters
          Notes:  (Steve Diggs submitting for Hoyle Lee)
           from: Hoyle Lee <hoyle@ldeo.columbia.edu>
           date: Thu, Dec 4, 2008 at 8:15 AM
          I'd like to submit CFCs data for A22_2003. Attached are the CFCs file 
          and the report, where 
            sys = the GC system used, 
            1 = Lamont System,
            3= Miami System, 
            2 = averaged out the two system (2 = (1+3)/2))
          Thanks,  Hoyle.
          ---
          Additional notes from S. Diggs:  I tarballed the submission and 
          included a base-64 decoded version of the attached documentation, 
          along with a current SUM file from our website.  I also included the 
          original submission from Hoyle Lee which had a headerless data file.
            -sd (2008.12.05)


04/08/09  Kappa       Cruise Report   Submitted; new sections added
          Reports added to this document include:
          • Dissolved Organic Carbon Analyses 
          • Bromodeoxyuridine incorporation rates as a proxy for prokaryotic production
          • Dissolved Combined Neutral Sugar Samples
          • enumerating various microbial concentration via Flow Cytometry
          Expanded these Data Processing Notes
          Converted Cruise Report to PDF and Text formats 


08/18/09  Berys       CFCs            Website Update, data online 
          TCO2 changed to TCARBN in original exchange file header 
          Submission file was converted from WOCE format to CSV
          The following lines were labeled differently than the original file 
            and were omitted - they contained no data 
          Stn 14 cast 2 bottle 1 through  4 labeled as cast 1 bottle 101 through 104
          Stn 41 cast 2 bottle 1 through  4 labeled as cast 1 bottle 101 through 104
          Stn 51 lines labeled cast 1 bottle 51 through 55 omitted
          Stn 51 cast 2 bottle 1 through 34 labeled as cast 1 bottle 101 through 134
          Stn 51 cast 3 bottle 1 through  9 labeled as cast 1 bottle 101 through 109
          Stn 54 cast 2 bottle 1 through  9 labeled as cast 1 bottle 101 through 109
          Stn 57 cast 2 bottle 1 through  9 labeled as cast 1 bottle 101 through 109

          File was merged using merge_exchange_bot.rb (jfields)

          Content-Type: text/plain; name="00_README.txt"
          Content-Description: 00_README.txt
          Content-Disposition: attachment; filename="00_README.txt"; size=1529;
          creation-date="Tue, 18 Aug 2009 11:22:49 GMT";
          modification-date="Tue, 18 Aug 2009 11:22:49 GMT" 

10/07/09  Kappa       Cruise Report   Website Update, new reports online
          PDF and Text cruise reports Updated 04/08/09 now oline
