CRUISE REPORT: AAIW06
(Updated FEB 2009)



HIGHLIGHTS

                           Cruise Summary Information

               Section designation  AAIW06
Expedition designation (ExpoCodes)  316N20060130
                  Chief Scientists  Dr. Bernadette Sloyan / CSIRO, CMAR
                                    Dr. Lynne Talley / SIO, UCSD
                             Dates  30 January 2006 - 14 March 2006
                              Ship  R/V KNORR
                     Ports of call  Puenta Arenas, Chile - Valpariso, Chile
                                               45°19.07'S
             Geographic boundaries  103°4.34'W            72°41.08'W
                                               62°0.67'S
                          Stations  105
      Floats and drifters deployed  3 APEX floats deployed
    Moorings deployed or recovered  0

                               Chief Scientists:
         Dr. Bernadette Sloyan • CSIRO Marine and Atmospheric Research
                  GPO Box 1538 • Hobart, TAS 7001 • AUSTRALIA
        Tel:  +61-3-6232-5109 • Fax:  Email:  Bernadette.Sloyan@csiro.au

             Dr. Lynne Talley • Scripps Institution of Oceanography
                      University of California, San Diego
                 9500 Gilman Dr. • MS 0230 • La Jolla CA • 92093
                  Tel: 858-534-6610 • Email: ltalley@ucsd.edu





                                   AAIW 2006
                             R/V KNORR, KN182-1130
                         January 2006 - 14 March 2006
                     Puenta Arenas,Chile - Valpariso,Chile
                    Chief Scientist: Dr. Bernadette Sloyan
                                  CSIRO, CMAR
                                   Australia



                               Data Submitted by: 
            Shipboard Technical Support/Oceanographic Data Facility
             Kristin M. Sanborn, Mary C. Johnson, Parisa Nahavandi, 
                          Dan G. Schuller, Erik Quiroz 
            Shipboard Technical Support/Shipboard Electronics Group 
                          John Calderwood, Scott Hiller 
                       Scripps Institution of Oceanography 
                             La Jolla, Ca. 92093-0214



Summary 
(Bernadette Sloyan, CSIRO, CMAR) 

A hydrographic survey consisting of CTD/LADCP/rosette sections, underway 
shipboard ADCP, XCTD profiling, and float deployments in the southeast Pacific 
was carried out between January and March 2006. The R/V Knorr departed Punta 
Arenas, Chile on 30 January 2006. A total of 105 LADCP/CTD/rosette stations 
were occupied, 356 XCTDs were launched, and 3 APEX floats with oxygen sensors 
were deployed from 1 February - 11 March 2006. The ODF 36 bottle rosette was 
used successfully during the entire survey. Water samples for nutrient and 
oxygen analysis, LADCP, and CTD data were collected on each cast in most cases 
to within 10 meters of the bottom. Daily samples of pigments and DNA were 
collected on stations nearest local noon. Underway surface pCO2, N2O, 
temperature, conductivity, oxygen, and meteorological measurements were 
collected during the cruise. The cruise ended in Valparaiso, Chile on 14 March 
2006. 


Introduction 

Antarctic Intermediate Water (AAIW) is a low salinity water mass that is formed 
in the southeast Pacific Ocean on the equatorward side on the Subantarctic 
Front (SAF). AAIW is subducted into the Atlantic, Indian and Pacific 
subtropical gyres at about 800 to 1000m depth. AAIW is thought to be the 
densest variety of Subantarctic Mode Waters (SAMW). This cruise (KN 182-11) is 
a followon from the late austral winter cruise that occupied a similar area of 
the southeast Pacific between August-October 2005. The goal of the austral 
winter and summer cruises is to characterize the formation processes and 
restratification of AAIW and SAMW in its formation region. 

The science personnel and their responsibilities are listed below. 


Personnel 


Scientific Personnel AAIW 2006

Duties               Name               Affiliation    email 
-------------------  -----------------  -------------  --------------------------
Chief Scientist      Bernadette Sloyan  CSIRO, CMAR    Bernadette.Sloyan@csiro.au 
Data/O2/TIC          Kristin Sanborn    UCSD/SIO/STS   ksanborn@ucsd.edu 
ET/Deck/Salinity/O2  Scott Hiller       UCSD/SIO/STS   shiller@odf.ucsd.edu 
ET/Deck/O2           John Calderwood    UCSD/SIO/STS   jcalderwood@ucsd.edu 
CTD Data Mary        Johnson            UCSD/SIO/STS   mcjohnson@ucsd.edu 
Deck/Salinity        Lucian Parry       UCSD/SIO/STS   loparry@ucsd.edu 
Nutrients/Deck       Erik Quiroz        UCSD/SIO/STS   equiroz@usm.edu 
Nutrients/Data/Deck  Dan Schuller       UCSD/SIO/STS   dschuller@ucsd.edu 
Data/CTD             Parisa Nahavandi   UCSD/SIO/STS   pnahavandi@ucsd.edu 
CTD/LADCP/XCTD       Sharon Escher      UCSD/SIO       sescher@ucsd.edu 
CTD/ADCP/XCTD        James Holte        UCSD/SIO       jholte@ucsd.edu 
CTD/ADCP/XCTD        Yvonne Firing      UCSD/SIO       firing@hawaii.edu 
PCO2, N2O, PHYTO     Heather Bouman     U. Concepcion  heather@profc.udec.cl 
PCO2, N2O/Deck       David Donoso       U. Concepcion  josedonoso@udec.cl 
PCO2, N2O/Deck       Luis Bravo         U. Concepcion  lbravo@copas.udec.cl 
SSSG Tech            Robert Laird       WHOI           sssg@knorr.whoi.edu 
SSSG Tech            Amy Simoneau       WHOI           sssg@knorr.whoi.edu 



Principal Programs 

Principal Programs of AAIW 2006 

Analysis             Institution  Principal Investigator 
-------------------  -----------  ---------------------------------------------
CTDO/S/O2/Nutrients  UCSD/SIO     Lynne Talley       ltalley@ucsd.edu 
                                  Bernadette Sloyan  Bernadette.Sloyan@csiro.au 
                                  James H. Swift     jswift@ucsd.edu 
ADCP/LADCP           UCSD/SIO     Teresa Chereskin   tchereskin@ucsd.edu 
APEX Floats          UCSD/SIO     Lynne Talley       ltalley@ucsd.edu 
XCTD                 UCSD/SIO     Lynne Talley       ltalley@ucsd.edu 
Underway pCO2        UDEC         Osvaldo Ulloa      oulloa@profc.udec.cl 
                     UDEC         Laura Farias       lfarias@profc.udec.clk 
                     UDEC         Samuel Hormazabal  sam@profc.udec.cl 



Cruise Narrative 

The RV Knorr departed Punta Arenas, Chile on Monday 30th January 2006 at 1300 
local. Our original departure date and time (Sunday 29th January 0900 local) 
was delayed by 28 hours as we waited in port for the arrival of a critical box 
of chemicals that had failed to arrive on time. We left port as soon as 
possible after the delivery of the chemicals, two other chemical boxes that 
were delayed even longer were replaced with chemicals held in Raytheon's Office 
for Polar Programs storeroom in Punta Arenas. Two new winch wires were 
installed on the RV Knorr prior to our cruise. We used the starboard winch on 
which all three conducting cables were functioning to specification. The 36 
bottle rosette with CTD and LADCP mounted in the center was used for the entire 
cruise, apart from 3 stations were only the CTD was deployed. A test station, 
to 200m, was performed in the Straits of Magellan. CTD station and XCTD profile 
numbering was continued from the end of the 2005 Austral winter cruise, i.e. 
first CTD station of the summer 2006 cruise was Station 137, and XCTD 407. 

Many discussions were held between the Chief Scientist, Master of the RV Knorr, 
the SIO/STS/ODF Technician-in-Charge and the STS Electronic Technician (ET) 
about the use of the 36-place rosette. WHOI had a tension meter designed that 
they asked be placed just above the rosette. Scripps ODF designed a system to 
enable this tension information to be feed real time to the ship with the CTD 
data. This information was stored for each cast using the RV Knorr SEASAVE 
program and graphically displayed real-time with the wire tension at the sheave 
as the wire is feed to the boom. Normal wire speed (30m/min in upper 200m and 
60m/min below 200m) with standard wire tension was achieved for a large 
percentage of the 105 stations occupied. However, as with any CTD/rosette 
operation in the Southern Ocean, winds, sea-state and multiple swell directions 
dictated much slower wire speed on some stations - 20-25 m/min to ~2000m and 60 
m/min between ~2000m and bottom. At these stations the CTD and winch operators 
carefully monitored wire tension and adjusted wire speed to minimize the 
occurrence of low wire tension. During the cruise two complete re-terminations 
were performed. The conducting cables of the starboard wire were tested after 
the completion of the CTD/rosette program. All conductors were in the same 
order as when they we first tested in Punta Arenas. 

During the 30 hour steam from Punta Arenas to our first station science 
personnel finished tying down their equipment in the Knorr's main science 
laboratory. Numerous problems were encountered with ODF CTD acquisition and 
database software during the first week of the cruise. As a result the first 
two CTD stations of the cruise were undertaken using the RV Knorr's Seabird 
(SEASAVE) data acquisition software. By CTD station 139 the ODF CTD acquisition 
software was running, and over the next few days the ODF database and website 
became operational. 

CTD station spacing was roughly 50km for much of the southern portion of the 
survey region. In this region the SAF was crossed 6 times and the Polar Front 
(PF) once. Two intensive surveys, centered on the SAF were occupied during the 
cruise. These surveys were centered on Station 149 and Station 187. At each of 
these sites a diamond patterned was steamed with CTD stations occupied on the 
northern, southern, western and eastern corners. XCTDs were deployed along the 
diamond track with a spacing of approximately 8km. 

Our delay in leaving Punta Arenas, weather and technical problems resulted in 
time losses that eventually required us to drop a large number of CTD stations 
in the northern portion of the survey region. Only 105 stations were completed 
of the planned 161 stations. Weather conditions deteriorated during the transit 
between Stations 140 and 141. Arriving at Station 141 the average wind speed 
was 35-45 knots and a short, steep sea had developed. We hove-to for 18 hours 
before conditions abated allowing for the resumption of CTD/rosette operations. 
At Station 177 the pump on the CTD unit failed and the cast was aborted so that 
the pump could be changed. Technical problems at station 183, data spikes, a 
large number of modulo error counts and freezing of the acquisition software 
resulted in this cast being brought directly to the surface from 2000m during 
the upcast. The technical problems were investigated during the transit to 
Station 184, and a possible cause for the problem isolated. However, problems 
continued on Station 184 and the initial cast was aborted. After each 
unsuccessful cast attempt further changes were made to the CTD setup and wire. 
These included: removal of WHOI load cell; new sliprings; new CTD cables; new 
cable between main laboratory and winch and connecting only one conductor to 
the CTD. Three attempts were made to complete Station 184 before the station 
was successfully completed using one conductor wire. A 12 hour delay resulted 
from these technical problems. Further investigations by the STS ET concluded 
that the data spike problem before and at station 184 was due to wire ringing. 
During the remainder of the cruise we successfully rotated CTD operations 
between the three conducting cables. 

Slow station transits due to strong winds and rough seas on our leg from 89W to 
103W resulted in further loss of time. As a result of time delays stations 
spacing was increased on the west-east legs at approximately 55S, on the 
northern portion of the 89W line and final leg into the coast at approximately 
47S. The 54S east-west line from the Chilean coast to 89W was not occupied. 
However, station resolution was maintained at the eastern boundary in order to 
properly sample the complex coastal boundary currents. A deep low pressure 
system passed south of our position on our long west-east section from 103W to 
the Chilean coast. We began Station 224 but wire tension was not stable and the 
cast was stopped at 1500m. Bottles were tripped on the upcast. The weather 
deteriorated over the next 10 hours and three stations in the middle of the 
basin east of 89W were replaced with XCTD profiles. CTD/rosette operation 
resumed at the eastern edge of the basin. While transiting from the Chilean 
coast to 89W to resume the north-south section another low passed south of our 
position resulting in gale force winds and large seas. These conditions slowed 
our transit to 3-4 knots during 5-6 March. Although winds had weakened somewhat 
when we arrived at 89W the sea-state still prohibited the deployment of the 36-
place rosette. At this point with limited time remaining on the cruise and the 
need to get full depth CTD data resolution we decided to re-configure 
rosette/CTD operations and deploy only the CTD with altimeter. In this mode we 
did not get any LADCP or bottle data. This configuration was used on stations 
230, 231 and 232. We reverted back to the 36-place rosette with complete suite 
of measurements at station 233. 

Three hundred and fifty-six XCTD were deployed during the cruise. In the 
southern part of the cruise track 3 XCTDs were deployed between each station 
with a resolution of 10-15 km. In the northern part of the XCTDs were used to 
fill gaps between stations that were eliminated due to time constraints. The 
resolution of the XCTDs in this region varied from 20 to 30km. Three APEX 
floats with temperature, salinity, pressure and oxygen sensors were deployed 
during the cruise west of 89W and north of the SAF. 

Science operations halted at 08:30 local time on 11 March 2006 to begin the 72 
hour steam to Valparaiso. The science party and the officers and crew of the RV 
Knorr are commended for their hard work during the cruise. A CDROM of 
preliminary data obtained within the Chilean EEZ was produced and given to the 
Chilean observer/participating scientist, Luis Bravo. 


DESCRIPTION OF CTD/HYDROGRAPHIC MEASUREMENT TECHNIQUES 
 Shipboard Technical Support/Oceanographic Data Facility 
 Shipboard Technical Support/Shipboard Electronics Group 


1. CTD/Hydrographic Measurements Program 

The basic CTD/hydrographic measurements consisted of salinity, dissolved oxygen 
and nutrient measurements made from water samples taken on CTD/rosette casts, 
plus pressure, temperature, salinity, and dissolved oxygen from CTD profiles. A 
total of 105 CTD/rosette stations were made usually to within 10 meters of the 
bottom. Prior to Station 184, "ringing" occurred in the CTD telemetry signal 
causing intermittent interference resulting in loss of CTD signal. SeaBird is 
aware of this but has no specific recommendation on conductor configuration 
other than to advise that the total loop resistance to below 350 ohms and in no 
case should it be greater than 400 ohms. Both single and 3-parallel wires meet 
this criterion. After 3 diagnostic casts on Station 184, this event was 
discovered and resolved by reterminating using a single conductor instead of 3 
conductors. During the course of the next few stations, each conductor was used 
separately to verify that there was no problem with any one of the 3 
conductors. The distribution of samples is illustrated in figure 1.0 - 1.6. 


Figure 1.0: Sample distribution, stations 137-155. 
Figure 1.1: Sample distribution, stations 155-167.
Figure 1.2: Sample distribution, stations 167-178. 
Figure 1.3: Sample distribution, stations 178-198.
Figure 1.4: Sample distribution, stations 198-207. 
Figure 1.5: Sample distribution, stations 207-213.
Figure 1.6: Sample distribution, stations 213-229. 
Figure 1.7: Sample distribution, stations 230-241. 


1.1. 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 #796, Stations 137-209, #401, Stations 210-241 with dual 
pumps, dual temperature (SBE3plus), dual conductivity (SBE4), dissolved oxygen 
(SBE43); and an SBE35RT Digital Reversing Thermometer, an RDI LADCP (Broadband 
150khz) and a Simrad altimeter and 3PS, model LP-5k-2008, load pin force 
sensor. 

The CTD was mounted vertically in an SBE CTD frame attached to the bottom 
center of the rosette frame. The SBE4 conductivity and SBE3plus temperature 
sensors and their respective pumps were mounted vertically as recommended by 
SBE. Pump exhausts were attached to inside corners of the CTD cage and directed 
downward. The entire cage assembly was then mounted on the bottom ring of the 
rosette frame, offset from center to accommodate the pylon, and also secured to 
frame struts at the top. THE SBE35RT sensor was mounted horizontally, next to 
the intake of temperature sensor 2. The 3PS load pin force sensor owned by 
Woods Hole Oceanographic Institution (WHOI) was attached to the top of the 
rosette to measure loads at the package. The altimeter was mounted to the 
outside of the bottom frame ring. The LADCP was vertically mounted inside the 
bottle rings on the opposite side of the frame from the CTD. 

The rosette system was suspended from a UNOLS-standard three-conductor 0.322" 
electro-mechanical sea cable. The R/V Knorr's starboard-side Markey winch was 
used for all casts. Sea cable reterminations were made prior to casts 171/1, 
184/3 and 230/1. Station 184 casts 1, 2 and 3 were aborted because of 
electronics malfunctions, source was determined to be a "ringing" in the 
telemetry signal. 

The deck watch prepared the rosette 10-20 minutes prior to each cast. The 
bottles were cocked and all valves, vents and lanyards were checked for proper 
orientation. Once stopped on station, the LADCP was turned on and the rosette 
moved into position under the starboard-side squirt boom using an air powered 
cart and tracks. The CTD was powered-up and the data acquisition system in the 
main lab started when directed by the deck watch leader. Tag lines were 
threaded through the rosette frame, and syringes were removed from the CTD 
intake ports. The winch operator was directed by the deck watch leader 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, by which time the sensor pumps had turned on. The winch 
operator was then directed to bring the package back to the surface (0 winch 
wireout) and to begin descent. Each rosette cast was usually lowered to within 
10 meters of the bottom, using the altimeter to determine a safe distance. 

On the up cast the winch operator was directed to stop at each bottle trip 
depth. The CTD console operator waited 30 seconds before tripping a bottle to 
insure the package wake had dissipated and the bottles were flushed, then an 
additional 10 seconds after receiving the trip confirmation to allow the 
SBE35RT temperature sensor time to make a measurement. The winch operator was 
then directed to proceed to the next bottle stop. 

Sea conditions were sufficiently poor toward the end of several casts that no 
stops were made shallower than 200m. In these cases, the rosette was hauled at 
a constant rate (20m/min) and the remaining bottles closed "on-the-fly". These 
bottles have a quality code of "4" (did not trip correctly) associated with 
them and are well-documented. 

Standard sampling depths were used throughout AAIW 2006 depending on the 
overall water depth (table 1.1.0). These standard depths were staggered every 
three stations. 

Recovering the package at the end of the deployment was essentially the reverse 
of launching, with the additional use of poles and snap-hooks to attach tag 
lines, and air-taggers on the tag lines for added safety and stability. The 
rosette was moved into the forward hangar for sampling. The bottles and rosette 
were examined before samples were taken, and anything unusual noted on the 
sample log. 

Each bottle on the rosette had a unique serial number. This bottle 
identification was maintained independently of the bottle position on the 
rosette, which was used for sample identification. One bottle was replaced on 
this cruise, and various parts of bottles were occasionally changed or 
repaired. Routine CTD maintenance included soaking the conductivity and DO 
sensors in fresh water between casts to maintain sensor stability. 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.


Table 1.1.0 AAIW 2006 water sampling guidelines. 

(1) top bottle within sight of the surface 
(2) bottom bottle within 10 meters of bottom 
(3) 0-about 500 meters: spacing no greater than 50-60 meters 
(4) 500-2000 meters: spacing no greater than 100 meters 
(5) 2000-bottom: spacing no greater than 500 meters 
(6) bottom of SAMW: resolve the property break with one bottle above and one 
    below if the layer is obvious (within 50 meters of break) 
(7) AAIW if obvious salinity minimum (north of SAF): try to sample the minimum. 
    (General) Stagger the sampling so that sample depths are not exactly the 
    same from one to the next. Three different scenarios were mapped and rotated 
    from one station to the next to accomplish this. 



1.2. Underwater Electronics Packages 

CTD data were collected with a SBE9plus CTD. This instrument provided pressure, 
dual temperature (SBE3), dual conductivity (SBE4), dissolved oxygen (SBE43) and 
altimeter (Simrad 807) channels. Additionally, a load pin for sensor, attached 
to the top of the rosette, provided load readings at the package for comparison 
with loads at the winch. The CTD supplied a standard SBE-format data stream at 
a data rate of 24 frames/second (fps). 


Table 1.2.0 AAIW 2006 Rosette Underwater Electronics. 

Sea-Bird SBE32 36-place Carousel Water Sampler  S/N 3216715-0187 
Sea-Bird SBE35RT Digital Reversing Thermometer  S/N 35-0011 (137-183,192-229) 
Sea-Bird SBE9plusCTD                            S/N09P39801-0796 (137-209) 
Sea-Bird SBE9plusCTD                            S/N09P11599-0401 (210-241) 
Paroscientific Digiquartz Pressure Sensor       S/N 98627 (137-209) 
Paroscientific Digiquartz Pressure Sensor       S/N 59916 (210-241) 
Sea-Bird SBE3plus Temperature Sensor            S/N 03P-4486 (Primary) 
Sea-Bird SBE3plus Temperature Sensor            S/N 03P-2165 (Secondary) 
Sea-Bird SBE4C Conductivity Sensor              S/N 04-2112 (Primary, 137-208) 
Sea-Bird SBE4C Conductivity Sensor              S/N 04-2659 (Primary, 209-241) 
Sea-Bird SBE4C Conductivity Sensor              S/N 04-3058 (Secondary) 
Sea-Bird SBE43 Dissolved Oxygen Sensor          S/N 43-0255 (137-241) 
Sea-Bird SBE5T Pump                             S/N 05-4128 (Primary/137-176) 
Sea-Bird SBE5T Pump                             S/N 05-4131 (Primary/177-
183,208-241) 
Sea-Bird SBE5T Pump                             S/N 05-4132 (Primary/184-207) 
Sea-Bird SBE5T Pump                             S/N 05-4160 (Secondary) 
Simrad 807 Altimeter                            S/N 9711090 
RDI Broadband 150khz LADCP                      S/N 1394 
LADCP Battery Pack 
3PS LP-5K-2008 Force Sensor                     A0512124 (137-183,202-241) 
SBE11plus-v.2 Deck Unit                         S/N11P21561-0518 (Shipboard) 


The CTD was outfitted with dual pumps. Primary temperature, conductivity and 
dissolved oxygen were plumbed on one pump circuit and secondary temperature and 
conductivity on the other. The sensors were deployed vertically. 

The SBE9plus CTD and SBE35RT temperature sensor were both connected to the 
SBE32 36-place pylon providing for single-conductor sea cable operation. The 
sea cable armor was used for ground (return). Power to the SBE9plus CTD was 
provide through the sea cable from the SBE11 deck unit in the main lab. All 
sensors, dual temperature and conductivity, oxygen, SBE32 carousel, SBE35RT and 
Simrad altimeter, received power from the CTD. 


1.3. Navigation and Bathymetry Data Acquisition 

Navigation data were acquired at 1-second intervals from the ship's C-Nav GPS 
receiver by one of the Linux workstations beginning January 31. Data from the 
ship's Knudsen 320B/R Echosounder (12 KHz transducer) were also acquired and 
merged with the navigation. The Knudsen bathymetry data were noisy and subject 
to washing out when the seas were choppy or the ship's bow thruster engaged. 

Bathymetric data from the ship's multibeam echosounder system (Seabeam 2000) 
were also logged and archived independently. 


1.4. CTD Data Acquisition and Rosette Operation 

The CTD data acquisition system consisted of an SBE-11plus (V2) deck unit and 
three networked generic PC workstations running Fedora Core Linux. Each PC 
workstation was configured with a color graphics display, keyboard, trackball 
and DVD+RW drives. One of the three systems also had 8 additional RS-232 ports 
via a Comtrol Rocketport PCI serial controller. The systems were connected 
through a 100BaseTX ethernet switch, which was also connected to the ship's 
network. These systems were available for realtime operational and CTD data 
displays, and provided for CTD and hydrographic data management and backup. 

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 and operational 
displays for controlling and monitoring a CTD deployment and closing bottles on 
the rosette. 

CTD deployments were initiated by the console watch after the ship had stopped 
on station. The watch maintained a console operations log containing a 
description of each deployment, a record of every attempt to close a bottle and 
any pertinent comments. The deployment and acquisition software presented a 
short dialog instructing the operator to turn on the deck unit, examine the on 
screen CTD data displays and to notify the deck watch that this was 
accomplished. 

Once the deck watch had deployed the rosette, the winch operator would begin 
the descent. When permitted by sea conditions, the rosette was lowered to 10 
meters, raised back to the surface then lowered for the descent. This procedure 
was adopted to allow the immersion-activated sensor pumps time to start and 
flush the sensors. 

Profiling rates were frequently dictated by sea conditions, but never exceeded 
60m/minute on the stations with the rosette package. The stations that employed 
only the CTD, Stations 230-232, were brought up at 75m/minute. 

The progress of the deployment and CTD data quality were monitored through 
interactive graphics and operational displays. Bottle trip locations were 
decided and transcribed onto the console and sample logs. The sample log would 
later be used as an inventory of samples drawn from bottles. 

The combination of altimeter distance, CTD depth, winch wire-out and echo-
sounder depth provided reliable, precise control of package distance from the 
bottom and allowed routine approaches to within 10 meters. 

Bottles were closed on the up cast by operating an on-screen control. The winch 
operator was given a target wire-out for the bottle stop, proceeded to that 
depth and stopped. Bottles were tripped at least 30 seconds after stopping to 
allow the rosette wake to dissipate and the bottles to flush. The winch 
operator was instructed to proceed to the next bottle stop at least 10 seconds 
after closing bottles to allow the SBE35RT calibration temperature sensor time 
to make a measurement. 

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. 

The ship's CTD computer ran the SeaBird SeaSave software simultaneously with 
the STS/ODF acquisition system. This allowed the data from the load cell to be 
fed into the STS/ODF MET system for graphical display of wire tension at the 
winch and load tension at the rosette.


1.5. CTD Data Processing 

The shipboard CTD data acquisition was the first stage in shipboard processing. 
The raw CTD data were converted to engineering units, filtered, response-
corrected, calibrated and decimated to a more manageable 0.5 second time-
series. The laboratory calibrations for pressure, temperature and conductivity 
were applied at this time. The 0.5 second time-series data were used for real-
time graphics during deployments, and were the source for CTD pressure, 
temperature and conductivity associated with each rosette bottle. Both the raw 
24hz data and the 0.5 second time-series were stored for subsequent processing 
steps. 

At the completion of a deployment, a series of processing steps were performed 
automatically. The 0.5 second time-series data were checked for consistency, 
clean sensor response and calibration shifts. A 2 decibar pressure-series was 
generated from the down cast data whenever possible, where the CTD sensors saw 
the water before the rosette disturbed it. Only two casts had surface data 
extrapolated more than 8 decibars due to sea conditions and not being able to 
yoyo back to the surface after sensors stabilized. Both the 2 decibar pressure-
series and 0.5 second time-series data were made available for downloading, 
plotting and reporting on the shipboard cruise website. 

CTD data were routinely examined for sensor problems, calibration shifts and 
deployment or operational problems. The primary and secondary temperature 
sensors (SBE3plus) were compared to each other and to the SBE35RT temperature 
sensor. CTD conductivity sensors (SBE4C) were compared with each other and with 
check-sample conductivity values to determine if any corrections were 
warranted. The CTD dissolved oxygen sensor (SBE43) data were calibrated to 
check-sample data. Additional deep theta-S and theta-O2 comparisons were made 
between down and up casts as well as with adjacent deployments. 

CTD data were collected successfully at all 105 stations occupied. A software 
update caused the serial ports to mentally "disappear" from the main 
acquisition computer just before the first station. The problem was fixed 
before station 139. Stations 137-138 data were collected with SBE software, and 
the SeaSave raw data were later imported into the usual STS processing 
software. The acquisition froze during stations 147 and 173 when a CTD signal 
spike killed the RawCTD display window. The raw data from the SeaSave simul-
casts were imported post-cast to provide a more continuous data stream for 
these two stations. The cast at station 183 was stopped after 11 trips, when 
the acquisition window froze for a seventh time. The acquisition software was 
replaced with a 2-month older version (using the same underlying block-
averaging program) after this cast, and never froze up again. Post-cast 
processing was performed on all casts with the same software. 

The signal spiking problem (random spikes in random channels) was investigated 
prior to station 184, and water was found inside a damaged cable between the 
load cell and CTD. The load cell was removed prior to cast 1, which was aborted 
at 1230m after the signal spiked a second time during the down cast. 
Retermination and new slip rings did not resolve the spiking problem for cast 
2, which was aborted at 1300m on the down cast. All cables between the CTD and 
sensors were replaced and the SBE35RT removed prior to cast 3; it was aborted 
at 680db on the down cast for excessive noise. New cable was installed between 
the lab and winch, a new primary pump was installed, and the wire terminated to 
use one conductor prior to cast 4, which was completed without spiking. A test 
of the conductors in the wire was run during the cast, and the remaining two 
cables had short-circuited at some point. Ultimately, the problem was traced to 
excessive attenuation of the Rochester sea cable due to the tri-conductor 
configuration of the wires. Reterminating the sea cable to the one-conductor 
configuration resolved the problem. 

Two up casts were used for pressure-series instead of down casts (Stations 176 
and 205) because the down casts were not usable. The pump for the primary 
sensors did not turn on until ~100db on the down cast of station 176, and the 
secondary conductivity sensor offset during the same cast. The problem was 
isolated at the start of station 177; the cast was aborted in the top 30m, and 
the primary pump was replaced before cast 2. The secondary sensors on the up 
cast were used for station 205 pressure-series data due to excessive noise in 
primary data after the sensors were fouled starting at 700db down, also causing 
a large ctd oxygen offset. The secondary sensors on the down cast were used for 
station 196 as well, due to fouling/offset of the primary sensors from ~800-
1720db; its down cast oxygen (plumbed to the primary sensors) seemed to be 
unaffected.

Station 196 also began a series of casts with deep (2800+db), large 
spikes/cutouts affecting the primary conductivity (C1) sensor, but also causing 
smaller spikes in secondary conductivity (C2) and oxygen (O2) sensors. The 
problem happened once or twice on stations 196 and 197, then not again until a 
single, brief "blip" on station 201, only in C1. The problem then affected each 
cast (down, up or both) except station 203, with C1 spiking and small C2 
inversions lasting 6-60db, then O2 returning to normal 30-40db later. An 
investigation of the raw data isolated the problem to C1: the signal from that 
one sensor apparently cut out, then both pumps turned off almost immediately 
because of the low conductivity signal (thinking they were out of water). About 
5 seconds after C1 returned to normal, the pumps turned back on; O2 fully 
recovered about 25 seconds later, due to its longer time constant. Since the 
cables between the CTD and its sensors were new and unlikely to be the problem, 
the C1 sensor was changed out before station 209 (from 04-2112 to 04-2659). The 
C1 signal cut out at 2245db on the down cast of station 209 and never returned; 
the cast was aborted at 3528db, since primary and secondary pumps were both 
off. The source was isolated to the C1 bulkhead connector on the CTD (#796). 
The backup CTD (#401) was installed before station 210, using the same 
temperature, conductivity and oxygen sensors as station 209. No more signal 
problems were encountered for the remainder of the cruise. Extreme weather 
conditions and time constraints forced the use only the CTD in its cage with 
weights attached, minus rosette and extraneous instruments other than the 
altimeter, at Stations 230-232. 


1.6. CTD Sensor Laboratory Calibrations 

Laboratory calibrations of the SBE pressure, temperature, conductivity, 
dissolved oxygen and digital Reversing Thermometer sensors were performed prior 
to AAIW 2006 . The calibration dates are listed in table 1.6.0. 


Table 1.6.0 AAIW 2006 CTD sensor laboratory calibrations. 

                                                 Calibration    Calibration
Sensor                                 S/N       Date           Facility 
-------------------------------------  --------  -----------    -----------
Paroscientific Digiquartz Pressure     98627      7-Jul-2005      SIO/STS 
Paroscientific Digiquartz Pressure     59916     16-May-2005      SIO/STS 
Sea-Bird SBE3plus T1 Temperature       03P-4486  12-Dec-2005      SIO/STS 
Sea-Bird SBE3plus T2 Temperature       03P-2165  12-Dec-2005      SIO/STS 
Sea-Bird SBE4C C1 Conductivity         04-2112   13-Dec-2005      SBE 
Sea-Bird SBE4C C1 Conductivity         04-2659   10-Dec-2005      SBE 
Sea-Bird SBE4C C2 Conductivity         04-3058   10-Dec-2005      SBE 
Sea-Bird SBE43 Dissolved Oxygen        43-0255  (23-Dec-2005-N/A) SBE 
Sea-Bird SBE35RT Dig.Reversing Therm.  35-0011   15-Dec-2005      SIO/STS 


1.7. CTD Shipboard Calibration Procedures 

CTD #796 was used for Stations 137-209 and CTD #401 was used on stations 210-
241 on AAIW 2006. The CTD was deployed with all sensors and pumps aligned 
vertically, as recommended by SBE. The primary temperature and conductivity 
sensors (T1 and C1) were used for CTD data reported for all but two casts. The 
secondary temperature and conductivity sensors (T2 and C2) were used for 
stations 196 and 205 reported CTD data, but typically served only as 
calibration checks for the primary sensors. The SBE35RT Digital Reversing 
Thermometer (S/N 35-0011) served as an independent calibration check for 
temperature. In-situ salinity and dissolved O2 check samples collected during 
each cast were used to calibrate the conductivity and dissolved O2 sensors. 


1.7.1. CTD Pressure 

The Paroscientific Digiquartz pressure transducers (CTD796-Pressure S/N 98627 
and CTD401-Pressure S/N 59916) were calibrated in July and May 2005 at the 
SIO/STS Calibration Facility. Coefficients derived from the calibration were 
applied to convert raw pressure frequencies to corrected pressures during each 
cast. Residual pressure offsets (the CTD pressures just before submersion and 
just after coming out of the water) were examined to check for calibration 
shifts. Offsets varied between 0.4-0.9db for the first sensor, and 0.0-0.4db 
for the second pressure sensor. An offset of -0.7db was applied to calculated 
pressures for stations 137-176, then reduced to -0.5db until the CTD/pressure 
sensor were changed before station 210. No adjustments were made to the 
calculated pressures for the replacement sensor. All final corrected residual 
pressure offsets were between -0.3 and +0.5db. 


1.7.2. CTD Temperature 

The same SBE3plus primary and secondary temperature sensors (T1-S/N 03P-4486 
and T2-S/N 03P-2165) served for the entire cruise. Calibration coefficients 
derived from the pre-cruise calibrations in December 2005 were applied to raw 
primary and secondary temperature data during each cast. 

The SBE35RT Digital Reversing Thermometer is an internally recording 
temperature sensor that operates independently of the CTD. It is triggered by 
the SBE32 pylon in response to a bottle trip. According to the Manufacturer's 
specifications the typical stability is 0.001°C/year. The SBE35RT used on AAIW 
2006 (S/N 35-0011) was calibrated in December 2005, at which time its 
correction was reported to have drifted at most by -0.0010°C over the entire 
temperature range (-2 to 30°C) since May 2000. 

The SBE35RT was not on the rosette for stations 184-191, and its internal 
battery died (thereby erasing its memory) while trying to upload data for 
stations 224-229. It was not used after station 229. Occasionally the SBE35RT's 
memory filled between uploads, preventing it from storing more data. 

Two independent metrics of calibration accuracy were examined. T1 and T2 were 
compared, and the SBE35RT temperatures were compared to both T1 and T2 at each 
rosette trip. 

Calibration accuracy was first examined by tabulating T1-T2 over a range of 
pressures (at bottle trip locations) for stations 137-108. The differences 
appeared to have a small drift with station number (time) at the start of the 
cruise. An examination of the SBE35RT-T1 differences showed that T1 drifted -
0.00029°C over the first 35 casts, then stabilized for the rest of the leg. 
SBE35RT-T2 differences indicated T2 did not drift. The T1 drift was corrected 
by applying a smoothly changing offset over the first 35 casts to match T2, 
based on data below 1500db. Then a simple offset was applied to T1 data 
starting at station 171. 

The normalized T1-T2 differences showed an approximate 0.001°C slope from 
surface to deep pressures. A comparison with SBE35RT data indicated that T1 was 
0.002°C high at deep pressures (5500db), while T2 was 0.001°C high. T1 matched 
the SBE35RT at surface pressures, and T2 was offset +0.00027°C. Historical 
calibrations showed that the SBE35RT was more stable over time than the 
SBE3plus sensors. However, the response of either sensor type to large 
pressures has not been documented. Since the two SBE3plus sensors showed a 
relative slope, an offset was applied to T2 data to match the SBE35RT at 
surface pressures, and then a 2nd-order polynomial fit of T2-T1 differences as 
a function of CTD Pressure was generated to correct T1. This compromise brought 
both SBE3plus sensors within 0.001°C of each other and the SBE35RT at all 
pressures. 

Temperature differences were rechecked for stations 210-241 using the 
corrections determined above. The sparse SBE35RT data for these casts did not 
show any notable differences. The overall drift between T1 and T2 from stations 
171-241 was less than 0.0003°C, half of the shift in temperature routinely 
observed when the CTD changes direction during a cast. No further adjustments 
to temperature corrections were warranted. 

The residual differences for all temperatures are summarized in figures 1.7.2.0 
through 1.7.2.4.


Figure 1.7.2.0: T1-T2 vs pressure, all pressures. 
Figure 1.7.2.1: T1-T2 vs station, p>1500db. 
Figure 1.7.2.2: SBE35RT-T1 vs pressure, all pressures. -15- 
Figure 1.7.2.3: SBE35RT-T1 vs station, p>1500db. 
Figure 1.7.2.4: SBE35RT-T2 vs station, p>1500db. 


The 95% confidence limit for the mean deep differences is ±0.0004°C for T1-T2, 
and ±0.0006°C for SBE35RT-T1. 


1.7.3. CTD Conductivity 
 
Two primary SBE4C conductivity sensors (C1A-S/N 04-2112 for stations 137-208, 
C1B-S/N 04-2659 for stations 209-241) and one secondary SBE4C conductivity 
sensor (C2-S/N 04-3058 for all casts) served for the entire cruise. 
Conductivity sensor calibration coefficients derived from the pre-cruise 
calibrations were applied to raw primary and secondary conductivities. 

Comparisons between the primary and secondary sensors, and between each sensor 
vs check sample conductivities calculated from bottle salinities, were used to 
derive conductivity corrections. C1A-C2 differences showed a pressure slope of 
about -0.0005mS/cm from 0 to 5500db, with an average deep difference of 
+0.0004mS/cm. Bottle differences were more scattered, but indicated C1A was 
high and C2 was more nearly correct. A first-order pressure slope was applied 
to C1A, based on a fit of C2-C1A differences above 50db or below 1200db. C1B-C2 
differences did not show any significant slope with pressure. 

The first few stations displayed a greater change in offset with time, then the 
offsets stabilized. The C2 offsets started shifting slowly upward with time, 
with the shifting becoming a little more rapid after the sensors were moved to 
the second CTD before station 210. C1A, C1B and C2 offsets were adjusted in 
groups of stations based on observed shifts of one sensor vs the other in deep 
theta-salinity overlays of nearby stations for each sensor pair. Stations near 
crossover points in the track were also compared to ensure consistency.

Deep primary and secondary conductivity differences by station, after applying 
shipboard corrections, are summarized in figure 1.7.3.0. 


Figure 1.7.3.0: C1-C2 vs station, p>1500db. 


Bottle minus CTD salinity residuals, after applying shipboard T1/C1 and T2/C2 
corrections, are summarized in figures 1.7.3.1 through 1.7.3.3. 


Figure 1.7.3.1: Salinity residuals vs pressure, all pressures.
Figure 1.7.3.2: Salinity residuals vs station, all pressures. 
Figure 1.7.3.3: Salinity residuals vs station, p>1500db. 


Figure 1.7.3.3 represents an estimate of the deep salinity accuracy on AAIW 
2006. The 95% confidence limit is ±0.0022 PSU relative to the bottle salts. 


1.7.4.  CTD Dissolved Oxygen 

One SBE43 dissolved O2 sensor (DO-S/N 43-0255) was used during this cruise. The 
sensor was plumbed into the primary T1/C1 pump circuit after C1. Down cast data 
were used for all but two casts. The DO sensor calibration method used for this 
cruise matched down cast pressure-series CTD O2 data to up cast bottle trips 
along isopycnal surfaces. Residual differences between the in-situ check sample 
values and CTD O2 were minimized using a non-linear least-squares fitting 
procedure. 

The fitting procedure determined the calibration coefficients for the sensor 
model conversion equation, and was accomplished in stages. The time constants 
for the exponential terms in the model were first determined for the sensor. 
These time constants are sensor-specific but applicable to an entire cruise. 
Next, casts were fit individually to check sample oxygen data. CTD data were 
refit if bottle oxygen data changed by 0.005ml/l or more after bottle data were 
recalculated with smoothed standards/blanks. Deep theta-O2 overlays of nearby 
stations were compared to ensure data consistency. Down and up cast differences 
were also considered when bottle data in shallower areas disagreed. CTD O2 data 
were converted from ml/l to µmol/kg units after fitting. 

Two up casts were processed instead of down casts, because of various problems 
with offsets in down cast salinity and/or oxygen data. These up cast time-
series data were fit to bottle oxygens using the same time constants used on 
the down cast fits. The time-dependent corrections were updated before 
pressure-sequencing the data. 

Four casts were acquired without bottle data at stations 209 and 230-232. A 
fifth cast at station 183 had no bottles shallower than 1748db. Bottle data 
from nearby casts were used to approximate the fits for stations 183, 209 and 
230. The correction coefficients for station 233 were used for stations 231-
232, since there were no nearby casts with similar features to use. CTD O2 data 
for these stations may be acceptable, but are coded as "uncalibrated" because 
the bottle data were sparse or missing for such large sections. 

Bottom bottle O2 data were occasionally missing or coded "questionable" due to 
tripping, sampling or analytical problems. Deep theta-O2 comparisons were used 
to estimate a bottom value for fitting where possible, typically helping to 
optimize the fit through other deep bottles. However, deep CTD O2 data for 
stations 140-141 were coded questionable below their last "acceptable" deep 
bottles because it was unclear what value should be used to fit the bottom 
data. 

Figures 1.7.4.0-1.7.4.2 show the residual differences between bottle and 
calibrated CTD O2 where both CTD and bottle oxygen data are coded "acceptable". 


Figure 1.7.4.0: O2 residuals vs pressure, all pressures. 
Figure 1.7.4.1: O2 residuals vs station, all pressures.
Figure 1.7.4.2: O2 residuals vs station, p>1500db . 


The standard deviations of 2.78 µmol/kg for all oxygens and 0.585 µmol/kg for 
deep oxygens are only presented as general indicators of goodness of fit. STS 
makes no claims regarding the precision or accuracy of CTD dissolved O2 data. 

The general form of the STS O2 conversion equation for Clark cells follows 
Brown and Morrison [Brow78] and Millard [Mill82], [Owen85]. STS models membrane 
and sensor temperatures with lagged CTD temperatures and a lagged thermal 
gradient. In-situ pressure and temperature are filtered to match the sensor 
response. Time-constants for the pressure response t p, two temperature 
responses t Ts and t Tf , and thermal gradient response t dT are fitting 
parameters. The thermal gradient term is derived by lowpass filtering the 
difference between the fast response (Tf) and slow response (Ts) temperatures. 
This term is SBE43-specific and corrects a non-linearity introduced by analog 
thermal compensation in the sensor. The Oc gradient, dOc /dt, is approximated 
by low-pass filtering 1st-order Oc differences. This gradient term attempts to 
correct for reduction of species other than O2 at the sensor cathode. The time 
constant for this filter, t(og), is a fitting parameter. Dissolved O2 
concentration is then calculated: 


                                                            dOc 
                                        (c3Pl+c4Tf +c5Ts+c6 --- + c7dT) 
O(2ml/l) = [c1Oc + c2] • fsat(S,T,P) • e                     dt         (1.7.4.0)

where: 
    O(2ml/l)     = Dissolved O2 concentration in ml/l; 
    Oc           = Sensor current (m amps); 
    fsat(S,T ,P) = O2 saturation concentration at S,T,P (ml/l); 
    S            = Salinity at O2 response-time (PSUs); 
    T            = Temperature at O2 response-time (°C); 
    P            = Pressure at O2 response-time (decibars); 
    Pl           = Low-pass filtered pressure (decibars); 
    Tf           = Fast low-pass filtered temperature (°C); 
    Ts           = Slow low-pass filtered temperature (°C); 

    dOc 
    ---          = Sensor current gradient (m amps/secs);
    dt 

    dT           = low-pass filtered thermal gradient (Tf - Ts ).
    
    
1.8. Bottle Sampling 

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

    • O2 
    • Nutrients 
    • Salinity 
    • Phytopigments 
    • DNA 

The 36-place 10-liter rosette was used on most casts. The latch which releases 
the lanyard and subsequently tripping the bottle in position 21 on the carousel 
malfunctioned early in the expedition. By Station 150, it was deemed unusable 
despite efforts to repair it. On Station 161, bottle 7 was replaced by bottle 
37 until it could be properly serviced; bottle 7 was back on the rosette again 
by Station 162. Station 183 was aborted after 11 bottle trips after spiking in 
the CTD signal resulted in a seventh restart of the acquisition; there are no 
bottles shallower than 1748 db. No samples were collected during Station 209: 
the cast was discontinued during the down cast due to CTD problems. The CTD was 
deployed without the rosette or bottles at Stations 230-232. 

The correspondence between individual sample containers and the rosette bottle 
position (1-36) from which the sample was drawn was recorded on the sample log 
for the cast. This log also included any comments or anomalous conditions noted 
about the rosette and bottles. One member of the sampling team was designated 
the sample cop, whose sole responsibility was to maintain this log and insure 
that sampling progressed in the proper drawing order. 

Normal sampling practice included opening the drain valve and then the air vent 
on the bottle, indicating an air leak if water escaped. This observation 
together with other diagnostic comments (e.g., "lanyard caught in lid", "valve 
left open") that might later prove useful in determining sample integrity were 
routinely noted on the sample log. Drawing oxygen samples also involved taking 
the sample draw temperature from the bottle. The temperature was noted on the 
sample log and was sometimes useful in determining leaking or mis-tripped 
bottles. On two stations, 156 and 157, the oxygen draw temperature probe 
failed. In-situ temperatures are therefore used in the conversion of ml/l to 
uM/kg. 

Once individual samples had been drawn and properly prepared, they were 
distributed for analysis. Oxygen, nutrient and salinity analyses were performed 
on computer-assisted (PC) analytical equipment networked to the data processing 
computer for centralized data management. 


1.9.  Bottle Data Processing 

Water samples collected and properties analyzed shipboard were managed 
centrally in a relational database (PostgreSQL-8.0.3) run on one of the Linux 
workstations. A web service (OpenAcs-5.1.5 and AOLSer ver-4.0.10) front-end 
provided ship-wide access to CTD and water sample data. Web-based facilities 
included on-demand arbitrary property-property plots and vertical sections as 
well as data uploads and downloads. 

The Sample Log (and any diagnostic comments) was entered into the database once 
sampling was completed. Quality flags associated with sampled properties were 
set to indicate that the property had been sampled, and sample container 
identifications were noted where applicable (e.g., oxygen flask number). Each 
Sample Log was also scanned and made available as a JPEG file on the website. 
Analytical results were provided on a regular basis by the analytical groups 
and incorporated into the database. These results included a quality code 
associated with each measured value and followed the coding scheme developed 
for the World Ocean Circulation Experiment (WOCE) Hydrographic Programme (WHP) 
[Joyc94]. 

Sea conditions were sufficiently poor at the end of a few deployments that no 
bottle stops were made shallower than 50m. In these cases, the rosette was 
hauled at a constant rate (20m/min) and the remaining bottles closed "on-the-
fly". These bottles have a quality code of "4" (did not trip correctly) 
associated with them and are well-documented.

Various consistency checks and detailed examination of the data continued 
throughout the cruise. 


1.10.  Salinity Analysis 

Equipment and Techniques 

Two Guildline Autosal Model 8400A salinometers (S/N 57-526 & S/N 53-503), 
located in the analytical lab, were used for all salinity measurements. 
Salinometer 53-503 was employed beginning with Station 190 when salinometer 57-
527 was taken out of service due to unusual offsets in the Standard dial 
readings. The salinometers were modified by ODF to contain an interface for 
computer-aided measurement. The water bath temperature was set at 24°C for the 
entire cruise and lab temperature was maintained at a value near 24°C +/- 2°C. 

The salinity analyses were performed after samples had equilibrated to 
laboratory temperature, usually within 8-54 hours after collection. The 
salinometers were standardized for each group of analyses (usually 1-2 casts, 
up to ~48 samples) using at least two fresh vials of standard seawater per 
group. Salinometer measurements were made by computer, where the analyst was 
prompted by software to change samples and flush. 

Sampling and Data Processing 

1911 salinity measurements were made and approximately 130 vials of standard 
water (SSW) were used. Salinity data was used as an additional calibration 
check for the CTD. After the initial comparison with the conductivity sensors, 
salinity was drawn from a few of the surface and bottom bottles. 

Salinity samples were drawn into 200 ml Kimax high-alumina borosilicate 
bottles, which were rinsed three times with sample prior to filling. The 
bottles were sealed with custom-made plastic insert thimbles and Nalgene screw 
caps. This assembly provides very low container dissolution and sample 
evaporation. Prior to sample collection, inserts were inspected for proper fit 
and loose inserts replaced to insure an air tight 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 the next one run as an unknown was applied as a linear 
function of elapsed run time to the data. The corrected salinity data were then 
incorporated into the cruise database. The STD dial issue on salinometer 57-526 
was problematic and a few runs were rendered unusable for calibration purposes. 
A new Chopper/conductivity printed circuit card was placed in this salinometer 
prior to the start of the cruise. It is suspected that the components 
deteriorated on this card and that is the cause of the drift. Salinometer 53-
503 also had problems, but with the Standby/Read switch: it introduced noise in 
the data and was replaced after Station 219. Diagnostics indicated that 
Stations 214-218 may have been affected from the switch problem and were deemed 
questionable with Station 218 unusable. 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 of the laboratory used for the analyses ranged from 21.6°C to 
25.8°C. The air temperature during any particular run varied from -2.1 to 
+1.8°C. Most salinity runs had no or little lab temperature change. 

Standards 

IAPSO Standard Seawater (SSW) Batch P-146 was used to standardize Stations 138-
189 and Batch P145 for stations 190-241.


1.11. 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 LabView 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 (~55 gm/l). Pre-
made liquid potassium iodate standards were run once a day approximately every 
4 stations, unless changes were made to system or reagents. Reagent/distilled 
water blanks were determined every day or more often if a change in reagents 
required it to account for presence of oxidizing or reducing agents. The auto-
titrator performed well. 

Sampling and Data Processing 

3195 oxygen measurements were made. Samples were collected for dissolved oxygen 
analyses soon after the rosette was brought on board. Using a Tygon and 
silicone drawing tube, nominal 125ml volume calibrated iodine flasks were 
rinsed 3 times with minimal agitation, then filled and allowed to overflow for 
at least 3 flask volumes. The sample drawing temperatures were measured with a 
small platinum resistance thermometer embedded in the drawing tube. These 
temperatures were used to calculate uM/kg concentrations, and as a diagnostic 
check of bottle integrity. Reagents were added to fix the oxygen before 
stoppering. The flasks were shaken twice (10-12 inversions) to assure thorough 
dispersion of the precipitate, once immediately after drawing, and then again 
after about 20 minutes. 

The samples were analyzed within 1-2 hours of collection, and the data 
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. 

The blanks and thiosulfate normalities for each batch of thiosulfate were 
smoothed (linear fits) and the oxygen values recalculated. 

A noisy endpoint was occasionally acquired during the analyses, usually due to 
small waterbath contaminations. These endpoints were checked and recalculated 
using STS/ODF designed software. 

Volumetric Calibration 

Oxygen flask volumes were determined gravimetrically with degassed deionized 
water to determine flask volumes at STS/ODF's chemistry laboratory. This is 
done once before using flasks for the first time and periodically thereafter 
when a suspect 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 in 6 liter batches and bottled 
in sterile glass bottles at STS/ODF's chemistry laboratory prior to the 
expedition. The normality of the liquid standard was determined at ODF by 
calculation from weight. Two standard batches were used during AAIW 2006 . 

Potassium iodate was obtained from Acros Chemical Co. and was reported by the 
supplier to be 98% pure. The second standard was supplied by Alfa Aesar and has 
a reported purity of 99.4-100.4%. Tests at ODF indicate no difference between 
these 2 batches. All other reagents were "reagent grade" and were tested for 
levels of oxidizing and reducing impurities prior to use.


1.12. 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 to 
two 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. 

Explicit corrections for carryover in nutrient analyses are not made. In a 
typical AutoAnalyzer system, sample to sample carryover is ~1-2% of the 
concentration difference between samples. This effect is minimized by running 
samples in order of increasing depth such that concentration differences 
between samples are minimized. The initial surface samples could be run twice 
or a low nutrient sea water sample run ahead of the surface sample since these 
samples generally follow standard peaks. 


Sampling and Data Processing 

3211 nutrient samples were analyzed. 

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 7 
different standard concentrations were analyzed periodically to determine any 
deviation from linearity as a function of absorbance for each nutrient 
analysis. A correction for non-linearity was applied to the final nutrient 
concentrations when necessary. A correction for the difference in refractive 
indices of pure distilled water and seawater was periodically determined and 
applied where necessary. In addition, a "deep seawater" high nutrient 
concentration check sample was run with each station as an additional check on 
data quality. The pump tubing was changed 3 times. 

After each group of samples was analyzed, the raw data file was processed to 
produce another file of response factors, baseline values, and absorbencies. 
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 a per-analysis measured laboratory temperature. 

Standards 

Primary standards for silicate (Na2SiF6) 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 (KH2PO4) 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 21.6°C to 25.8°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). 
Carp65. 
    Carpenter, J. H., "The Chesapeake Bay Institute technique for the Winkler 
    dissolved oxygen method," Limnology and Oceanography, 10, pp. 141-143 
    (1965). 
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," Journ. 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).



XCTD Operations 

During the Antarctic Intermediate Water (AAIW) 2006 summer cruise, underway 
profiling of upper ocean temperature and salinity was carried out with 
expendable conductivity-temperature-depth probes (XCTDs). The sampling at 10 to 
50 km spacing supplemented the full-depth CTD stations that were spaced at 
approximately 50-200 km. Generally, 3 XCTDs were launched between CTD stations 
for the southern portion of the survey region, with 2-5 XCTDs for the northern 
survey area where CTD station spacing was generally greater than 70 km. 
Additionally, two intensive surveys were carried out near the Subantarctic 
Front (SAF), steaming a diamond pattern centered on the main AAIW track, with 
dense XCTD sampling throughout and CTD stations at the corners. The first 
intensive survey was centered on CTD station 149 and ended with station 152 
(Stations 148,150,151, and 152 are the corners). The second intensive survey 
was centered on CTD station 187 and ended with station 190 (Stations 186, 188, 
189, and 190 are the corners). 

Instrumentation 

The XCTDs were digital TSK probes purchased from Sippican (Sippican, Inc.) and 
manufactured by TSK (The Tsurumi-Seiki Co.). The science party supplied 
computer, deck unit, and launcher were used throughout the cruise, while the 
standard ship's equipment was a backup to our system. The deck unit was the 
Sippican MK-21 model. 

Data acquisition 

Data acquisition was on a pc computer with the Windows 2000 Professional 
operating system. Two copies of the data files were made: one on the pc hard 
disk; and the second on a backup directory on the pc. The Sippican software 
version was WinMK21 SURFACE. The hand launcher and XCTDs were kept in the aft 
hangar, and the launches were staged from the hanger. 

Launch Procedure 

XCTD launching was a two person effort because the weather deck on the Knorr 
was secured while underway during most of the cruise, thus requiring two 
persons on deck and radio communication to the bridge. XCTD launch times were 
determined from the ETA range to station from the main ODF AAIW webpage. The 
bridge was notified via radio. One person opened the "New Launch" window of the 
MK-21 software while the second person went aft to load a new probe in the hand 
launcher. The software cycles through "Testing Probe", "Prepare to Launch", and 
"Launch Probe". If it is successful in reading the probe's EPROM, it will 
usually get through to the "Launch Probe" window. At this point both persons, 
in work vests and equipped with a handheld radio, would go out to launch the 
probe. There were two launch locations, and the choice was dictated by wind and 
seas. Permanent launch tube was located on the port side, just aft of the 
hangar and on the starboard side rail of the fantail. The fall rate is 
approximately 200 m/min, and a cast typically took 5 mins. Once the probe was 
launched using the tube, both persons would come back inside and monitor the 
launch on the computer. The spent canister was retrieved after the launch. The 
data file was inspected and serial number (SN), time, latitude, and longitude 
were recorded to log sheets and reported to the bridge. 

Data processing and quality 

The Sippican automated processing was the only processing that was applied to 
the profiles. Two files exist for each cast: RDF (binary, raw); and EDF (ascii, 
edited by the Sippican auto processing). Three hundred and fifty-six (356) XCTD 
probes were launched during the cruise. The statistics of probe launches were: 
346 completely successful (cast depth greater than 800m); 6 good data but 
limited depth (profile depth between 800m and 100m); 4 failed (profile depth < 
100 m or failed outright). 

Problems 

During the cruise the ships deck crew cleaned and painted the aft hanger. 
During rough seas on the 8th of February planks on scaffolding in the hanger 
fell onto the XCTD launchers bending the metal yoke. XCTDs would not fit into 
the yoke once it was bent. The Knorr SSSG replaced the metal yoke with the same 
part from the Knorr launcher. The Knorr has ordered a replacement part for our 
equipment and will send the new part to Scripps. 

APEX FLOATS 

Three APEX floats were deployed during the cruise. The floats were equipped 
with a SEABIRD 41 temperature, conductivity and pressure sensor and an Aanderaa 
Oxygen Optone 3830 sensor. The APEX floats were shipped directly to Punta 
Arenas from Webb Research, Falmouth MA. All floats passed the final test 
procedure prior to our departure from Punta Arenas. 

The floats were launched at the end of a CTD stations. Launch location and time 
were: 

                 Float  Date/Time (UTC)  Latitude  Longitude 
                 -----  ---------------  --------  ---------
                 2604    21 Feb 22:17    53 1.49S  91 55.59W 
                 2605    22 Feb 20:28    53 43.8S  95 51.0W 
                 2606    01 Mar 06:15    55 47.2S  91 28.90W 


Each float was functioning and reporting temperature, salinity, pressure and 
oxygen profiles via ARGOS at the end of the cruise 

Problems 

Upon inspection of the shipping crates it was noted that the shockwatch warning 
device of the box housing float 2606 was red. The float passed the final test 
procedure that was undertaken before leaving port. Upon reset for actual 
deployment it gave only one ARGOS transmission, but all other reset functions 
worked as per the manual. ARGOS transmissions were received every 45 seconds 
for the period in which the air pump was operating during the reset. The float 
was deemed to be in working order and deployed as planned. 

Underway PCOs/NO2 

Underway PCO2/NO2 measurements were taken during the cruise by Osvaldo Ulloa 
and Laura Ferrias from the University of Concepcion, Chile. The system was 
monitored by Heather Bouman during the cruise. 

Problems 

The system was turned off due to low flow rate at different times during the 
cruise. 


ADCP/LADCP 
(Teresa Chereskin)

Introduction 

During the Antarctic Intermediate Water (AAIW) summer cruise, direct velocity 
measurements were made by the Chereskin lab group of Scripps Institution of 
Oceanography (SIO) from hull mounted shipboard acoustic Doppler current 
profilers (SADCPs) and from a Lowered Acoustic Doppler Current Profiler 
(LADCP). 


Shipboard ADCPs 

Instrumentation 

Data were recorded from two shipboard ADCPs: an Ocean Surveyor 75 kHz phased 
array (OS75) and an RD Instruments 150 kHz narrowband ADCP (NB150). 

The OS75 is standard ship's equipment on R/V Knorr. The OS75 ADCP transducer 
was mounted in an instrument well located near the center line of the ship and 
below the laundry room. The well is open to the sea, and the transducer is 
located at approximately 5 m depth, with beam 3 oriented 45 deg to starboard. 
The NB150 is an obsolete instrument, no longer supported by the manufacturer, 
that was installed by WHOI on request from the PI specifically for the AAIW 
cruises in order to profile currents at higher resolution and at shallower 
depths than is possible with the OS75. The NB150 ADCP transducer was mounted in 
an instrument well located below the lower laboratory at frame 85, about 8 feet 
starboard of the center line. The well is open to the sea, and the transducer 
is located at approximately 5 m depth, with beam 3 oriented 45 deg to 
starboard. The NB150 that was installed in Miami prior to the AAIW 2005 austral 
late winter/spring cruise. However it failed prior to the ship's arrival in 
Punta Arenas, Chile. A second complete system was sent via air freight. 
Although the system had checked out satisfactorily at WHOI, it reported error 
messages after installation on Knorr. In actual use, the problem was very low 
signal on beam 2 (unsuitable for a 4beam velocity solution). We collected NB150 
data with the intention of implementing a 3beam solution. 

Data acquisition 

Single ping ADCP data from both instruments and ancillary navigation streams 
(GPS, gyrocompass, and POS/MV) were collected on a Dell 1U rackmounted server 
running the Linux operating system (Mandrake 10.2) using UHDAS, a data 
acquisition and processing software suite written by Eric Firing and Jules 
Hummon, University of Hawaii. The data were processed in realtime on the Linux 
server (currents.knorr.whoi.edu) and were recorded in duplicate on a pair of 
internal, mirrored hard disks. Data were copied to Mac G4 laptops via a network 
(Samba) exported file system for further processing. The primary heading source 
was the ship's gyrocompass, and heading corrections were made using the POS/MV. 
After applying the heading corrections, the overall additional calibration was 
an amplitude of 1.0 and a phase of 0.0 degrees. This calibration will be 
refined in post processing. 

Sampling parameters 

The NB150 operating parameters used during AAIW were 50 depth bins and an 8 m 
blank, range bin, and pulse length. The OS75 ADCP was configured to collect 
data in narrowband mode. The OS75 operating parameters were 70 depth bins and a 
16 m blank, range bin, and pulse length. 

Data processing 

Overall, the quality of the OS75 ADCP and navigation data acquired during AAIW 
was excellent. High precision GPS was available throughout the cruise, with an 
estimated single position fix accuracy of 1 m. The estimated accuracy of the 
POS/MV heading corrections is 0.1o (King and Cooper, 1992). The overall error 
in absolute currents is estimated at 12 cm s-1 (Chereskin and Harris, 1997). 
The main problems encountered were bubble sweepdown when the bow thruster was 
used to maintain station and during rough weather and heavy seas. The maximum 
profiling range of the OS75 was about 850 m, but this depth range was 
drastically curtailed when bubbles were severe. 

The NB150 data were processed using a 3beam solution. Where the data overlap 
with the OS75, they are of higher resolution. Unlike the OS75, the NB150 was 
not affected by bubbles from the bow thruster. It was negatively affected by 
bubble sweepdown during rough weather and heavy seas. The maximum range was 
about 225 m; typical range was 180 m. 


Lowered ADCP 

Instrumentation 

The lowered ADCP was Chereskin's 150 kHz RDI Phase 3 broadband ADCP, serial 
number 1394, firmware versions 1.16 (XDC), 5.52 (CPU), 3.22 (RCDR), and C5d3 
(PWRTIM). The LADCP has custom 30o beam angles. It was mounted on the interior 
edge of the CTD rosette, about 1 inch above the bottom of the frame. A 
rechargeable lead acid gel cell battery in an oil filled plastic case 
(SeaBattery, Ocean Innovations, La Jolla, CA) was mounted in a steel box that 
was hoseclamped to the bottom of the rosette frame. 

Data acquisition 

A Mac G4 laptop computer running OSX (Panther 10.3.9) was used to upload an 
LADCP command set prior to each cast, using serial communication and a python 
terminal emulator (rditerm.py). Data acquired during the cast were stored 
internally on a 20 MB EPROM recorder. Data recovery used the terminal emulator, 
a public domain ymodem program (lrb). LADCP data were not collected on stations 
230, 231 and 232 when only the CTD was deployed. 

Sampling protocol 

Commands were uploaded from a file for deployment. The profiler was instructed 
to sample in a 2 ping burst every 2.6 seconds, with 0 s between pings and 1 s 
between (single ping) ensembles, resulting in a staggered ping cycle of [1 s, 
1.6 s]. Other relevant setup parameters were 16x16 m bins, 16 m blank, 16 m 
pulse, bandwidth parameter WB1, water mode 1, and an ambiguity velocity of 330 
cm s-1. Data were collected in beam coordinates. 

The battery pack was recharged after every cast, using an AmRel linear 
programmable power supply. The power supply was set to 57.31 V constant voltage 
and 1.8 A maximum current. Typically, at the end of a cast, the power supply 
was current limited at the maximum current. The power supply switched within 
about 10 min to constant voltage as the current level dropped. Charging was 
stopped nominally at 0.6 A in order to minimize the chance of overcharging, 
although the power supply resorts to trickle charging as the battery approaches 
full charge. Since lead acid gel cells outgas small amounts of hydrogen gas 
when overcharged/discharging, it is necessary to vent the pressure case. The 
pressure case was vented every few casts. There was a small but noticeable 
amount of outgassing. 

Data processing 

The LADCP provides a full depth profile of ocean current from a self contained 
ADCP mounted on the CTD rosette. Using the conventional "shear method" for 
processing (e.g., Fischer and Visbeck, 1993), overlapping profiles of vertical 
shear of horizontal velocity are averaged and gridded, to form a full depth 
shear profile. The shear profile is integrated vertically to obtain the 

baroclinic velocity and the resulting unknown integration constant is the depth 
averaged or barotropic velocity. This barotropic component is then computed as 
the sum of the time averaged, measured velocity and the ship drift (minus a 
small correction, less than 1 cm s-1, to account for a nonconstant fall rate) 
(Fischer and Visbeck, 1993; Firing, 1998). Errors in the baroclinic profile 
accumulate as 1/ (N) where N is the number of samples (Firing and Gordon, 
1990). This error translates to the lowest baroclinic mode and, for a cast of 
2500 m depth it is about 2.4 cm s-1 (Beal and Bryden, 1999). The barotropic 
component is inherently more accurate, because the errors result from 
navigational inaccuracies alone. These are quite small with Pcode GPS, about 1 
cms-1 (2 to 4 cm s-1 without). Comparisons with Pegasus suggest that the LADCP 
can measure the depth-averaged velocity to within 1 cm s-1 (Hacker et al., 
1996). The rms difference between Pegasus and LADCP absolute profiles are 
within the expected oceanic variability, 35 cm s-1 (Send, 1994), due primarily 
to high frequency internal waves. 

In previous experiments the interference layer, which results from the previous 
ping reflecting off the bottom, has caused a large data gap in the LADCP 
profile, causing an uncertain velocity offset (several cm s-1) between the 
parts of the profile on either side of the gap. For this experiment bottom 
velocities were greatly improved by using Chereskin's instrument which pings 
asynchronously, thereby avoiding complete data loss in the interference layer. 
A second problem with data loss arises at the bottom of a CTD/LADCP cast, when 
the package is held 10 m above the sea bed for bottle sampling. At this 
distance the instrument is 'blind' since the blank after transmit is order 20 
m, and a time gap in the data stream will result in an uncertainty in the 
absolute velocity. We attempted to minimize the stop at the bottom of the cast 
to keep this gap to a minimum. 

Initial processing was done with the University of Hawaii CODAS software. The 
method is the traditional shear method outlined in Fischer and Visbeck (1993) 
as implemented by Eric Firing in the UH CODAS LADCP software. CTD time series 
data were available immediately following the cast which provided more accurate 
depth than from integrating LADCP vertical velocity as well as calculated sound 
speed at the transducer. Typically LADCP casts were analyzed through to 
absolute velocity, including CTD data, prior to the next station. 

During the cruise, the casts were also processed with Martin Visbeck's LADCP 
Matlab processing routines, versions 8a and 9a. The method (Visbeck, 2002) 
differs from the shear method in that an inverse technique is used which 
includes two additional constraints, the bottom velocity estimate and the 
average shipboard ADCP profile during the cast. In principle, the Firing shear 
and Visbeck inverse methods should agree when no additional constraints are 
included in the inverse, but at the moment the methods have shown unexplained 
differences on some data sets (Brian King, pers. comm.) Qualitatively, the 
absolute currents computed between the 2 methods agreed reasonably well. 
Detailed comparisons will be made in post processing. Preliminary comparisons 
of shipboard and lowered ADCP data also showed fairly good agreement and 
suggest that the shipboard data will be a useful constraint in the inverse 
method utilized by Visbeck 



Acknowledgements 

Thanks are due to the SIO Oceanographic Data Facility for their outstanding 
support on this cruise. Thanks also to Sharon Escher and Yvonne Firing for 
their diligent watch standing and processing efforts. 



References 

Beal, L. M., and H. L. Bryden, The velocity and vorticity structure of the 
    Agulhas Current at 32•• S, J. of Geophys. Res., 104, 51515176, 1999. 
Chereskin, T. K., and C. L. Harris, Shipboard Acoustic Doppler Current 
    Profiling during the WOCE Indian Ocean Expedition: I10, Scripps Institution 
    of Oceanography Reference Series, SIO9714, 137 pp, 1997. 
Firing, E. F. and R. Gordon, Deep ocean acoustic Doppler current profiling, 
    Proceedings of the IEEE Fourth International Working Conference on Current 
    Measurements, Clinton, MD, Current Measurement Technology Committee of the 
    Ocean Engineering Society, 192201, 1990. 
Firing, E., Lowered ADCP development and use in WOCE, It. WOCE Newsletter, 30, 
    1014, 1998. Firing, E., Erratum, Intl. WOCE Newsletter, 31, 20, 1998. 
Fischer, J. and M. Visbeck, Deep velocity profiling with self-contained ADCPs, 
    J. Atmos. and Oceanic Tech., 10, 764773, 1993. 
Hacker, P., E. Firing, W. D. Wilson, and R. Molinari, Direct observations of 
    the current structure east of the Bahamas, Geophys. Res. Let., 23, 
    11271130, 1996. 
King, B. A. and E. B. Cooper, Comparison of ship's heading determined from an 
    array of GPS antennas with heading from conventional gyrocompass 
    measurements, DeepSea Res., 40, 22072216, 1993. 
Send, U., The accuracy of current profile measurements effect of tropical and 
    midlatitude internal waves, J. Geophys. Res., 99, 1622916236, 1994. 
Visbeck, M., Deep velocity profiling using lowered acoustic Doppler current 
    profilers: bottom track and inverse solution, J. Atmos. and Oceanic Tech., 
    19, 795807, 2002. 


Figure 1: LADCP section across the Subantarctic Front, stations 145 to 154. 
          Upper panel is eastward current (cm/s). Lower panel is northward 
          current (cm/s). Red line on station map indicates location of 
          section. 


Phytoplankton 
(Heather Bouman/University of Concepcion, Chile) 

To assess phytoplankton community structure during the Antarctic Intermediate 
Water (AAIW) 2006 summer cruise, seawater was collected daily to assess pigment 
composition, cell abundance and DNA. In addition, samples were collected to 
assess the population structure of cyanobacteria using Fluorescence In Situ 
Hybridization (FISH). Samples were collected daily at the sea surface for 
validation of remotelysensed estimates of pigment concentration, and 
occasionally at multiple depths within the top 100m of the water column to 
assess vertical variability in phytoplankton community structure. 

High Performance Liquid Chromatography Analysis (HPLC) 

Between 0.5 and 1.5 liters of seawater were filter through a 25 mm GF/F filter. 
Filters were then placed in liquid nitrogen and then transferred to a -80ºC 
freezer. Samples will be processed in the laboratory. Concentrations of 
chlorophyll-a and accessory pigments will be used to assess the relative 
abundance of phytoplankton taxa. 

Flow Cytometry 

At each station 1.35 ml of seawater was placed in a 2 ml cryovial and preserved 
with 0.15 ml of 1% gluteraldehyde solution. Samples were then placed in liquid 
nitrogen and transferred to a -80ºC freezer for later analysis. Phytoplankton 
and bacteria cells will be enumerated based on their scattering and 
fluorescence properties using a FACSCalibur Flow Cytometer (Bection Dickinson, 
San Jose, CA). 

DNA 

Between 5 and 8 liters of seawater was filtered sequentially onto 3.0 and 0.20 
um filters and placed into 5 ml cryotubes containing 1.5 ml lysis buffer. 
Samples were then immediately placed in liquid nitrogen and transferred to a -
80°C freezer. DNA extraction and amplification will be conducted at the 
University of Concepcion. Amplified DNA will be used to examine the genetic 
composition of the cyanobacteria community. 

Fluorescence In Situ Hybridization (FISH) 

Between 100 and 150 ml of seawater was filtered onto a 0.2 um GTTP filter. 
Filters were then air-dried and placed in 1% paraformaldehyde solution for 2 
hours at room temperature. Filters were then sequentially transferred into 50, 
80 and 100 % ethanol for approximately 5 minutes. Filters were then dried and 
stored at -80°C in plastic petrislides for later analysis in the laboratory. 
Fluorescent probes specific for various genotypes of cyanobacteria will be used 
to assess the genetic structure of natural populations. 

Particulate Absorption 

Between 0.3 and 1.5 liters of seawater was filtered through a 25 mm GF/F 
filter. Samples were placed immediately into liquid nitrogen and then stored at 
80°C for later analysis. Absorption of total particulate and phytoplankton will 
be determined using a Shimadzu spectrophotometer with integrating sphere 
according to the method of Kishino et al. (1985). These data will be entered 
into a bio-optical database used to develop ocean color algorithms for open 
ocean waters off Chile. 

Particulate Organic Carbon 

Between 1 and 1.5 liters were filtered onto 25 mm precombusted GF/F filters. 
Samples were then dried and stored for later analysis using a HCN analyzer. 

Problems 

On March 7 and 8 seawater was obtained using the vessel's flow through system, 
since bottles were removed from the CTD rosette




CCHDO DATA PROCESSING NOTES

Date      Contact     Data Type     Event summary
--------  ----------  ------------  -------------------------------------------
10/24/08  Diggs       CTD/BTL/SUM   Exchange & NetCDF files Online
          The AAIW 2006 cruise (316N20060130) was obtained directly from Lynne
          Talley who made a custom website for the data files.
          The old expocode () was changed to the standard format for CCHDO
          expocodes, and the alias field retains all old names and expocodes.
          SUM, SEA, and CTD WOCE formatted files all had their expocodes
          updated.

          Exchange files for Bottle and CTD were made as well as the NetCDF
          versions of these data files. All files checked with Java OceanAtlas
          5.0, and main parameters were examined via property-property and
          vertical section contours.

          The PDF documentation is in "as received" condition.

10/27/08  Key         OXY/NUTs      Possible Qual flag errors
          Recently posted EXCHANGE format file:
          1. Number of oxygen values with flag 0. I haven't checked all
             carefully, but many of these seem bad (flag 4). Try scatter plot
             against silicate. Listing of the worst offenders below - mostly 
             single point fliers.
          2. 2 phosphate samples are well out of envelop. Flag 3?
          3. 2 nitrate results are a bit strange, but perhaps not enough to flag

          Please let me know if All oxygen zero (0) flags should be 3/4.

          Quick QC
          Oxygen
          aaiwdata_qc("aaiw","silicate","oxygen",cuton=c("sf","of"))
          aaiwdata_qc("aaiw","pressure","oxygen",cuton=c("of"))
          140-1-1 mark 4
          144-1-14 mark 4
          163-1-29 mark 4
          167-1-1 mark 4
          167-1-2 mark 4
          174-1-26 hi vs Si,Z mark 4
          180-1-18 mark 4
          186-1-10 mark 4
          222-1-1 mark 4
          
          Nitrate
          aaiwdata_qc("aaiw","pressure","nitrate",cuton=c("no3f"))
          aaiwdata_qc("aaiw","silicate","nitrate",cuton=c("sif","no3f"))
          192-1-18 lo vs si
          192-1-19 lo vs si
          
          Phosphate
          aaiwdata_qc("aaiw","pressure","phosphate",cuton=c("po4f"))
          aaiwdata_qc("aaiw","nitrate","phosphate",cuton=c("po4f","no3f"))
          137-1-1 lo vs P, no3 mark 3
          137-1-2 lo vs P, no3 mark 3

