CRUISE REPORT: I06S
(Updated JUN 2019)









Highlights



                        Cruise Summary Information

               Section Designation  I06S
Expedition designation (ExpoCodes)  325020190403
                  Chief Scientists  Alejandro Orsi / TAMU
                             Dates  2019 APR 03 - 2019 MAY 14
                              Ship  r/v Thomas G. Thompson
                     Ports of call  Cape Town

                                               33°14'3" S
             Geographic Boundaries  28°5'43" E             31°32'4" E
                                               68°21'14" S

                          Stations  55
      Floats and drifters deployed  2 surface drifters, 
                                    4 ARGO floats, 2 SOCCOM floats
    Moorings deployed or recovered  0

                              Contact Information:

                                 Alejandro Orsi
              Texas A&M University O&M Building • Room 616 MS 3146 
                          College Station, Texas 77843
        Ph: (979) 845-4014 • Fax: (979) 847-8879 • Email: aorsi@tamu.edu







                    Report assembled by Jerry Kappa, UCSD/SIO







Cruise Report for the 2019 Reoccupation of I06
**********************************************





1.  GO-SHIP I06 2019 HYDROGRAPHIC PROGRAM


Fig. 1: Cruise track and CTD station locations (red dots) during GO-SHIP 
        I6S 2019. White triangles, circles and squares indicate 
        deployment locations of ARGO and SOCCOM floats and surface 
        drifters. 



1.1  Cruise Scientific Objectives

Alejandro Orsi

Complex oceanic responses to climate change are poorly characterized
due to a general lack of repeat high-quality shipboard measurements of
climate-relevant ocean properties. GO-SHIP repeat transoceanic surveys
(www.go-ship.org) provide full water column hydrographic observations
with temporal and spatial resolutions adequate to resolve decadal
variability in oceanic storage of heat, freshwater, carbon, oxygen,
nutrients and transient tracers. Repeat hydrographic physical-
biogeochemical measurements along 30°E in the southern Indian Ocean
enables scientists to better tackle important unresolved aspects of
Southern Ocean adjustment to atmospheric global warming. The U.S. GO-
SHIP I6S 2019 hydrographic section revisited this intercontinental
line after its first occupation in 2008, itself a repeat of the
original 1996 WOCE transect by France. Temperature, salinity, and
velocity measurements from I6S 2019 reveal how the heat content of
deep and bottom waters in the Enderby Basin have changed while their
parent waters over the Antarctic continental shelves have not, but
freshened instead. I6S 2019 measurements of oxygen, nutrients,
tracers, and dissolved inorganic carbon allow quantifying the
anthropogenic component in the total inventory changes of surface and
deep waters. Combined carbon and current measurements from the repeat
I6S line are used to determine rates of regional carbon accumulation
and exchange with adjacent circulations. The overarching achievement
of GO-SHIP I6S 2019 measurements was the reoccupation of 55 full-depth
CTD stations and the collection of water samples at different levels
with 36 Niskin bottles. Measured temperature, salinity, pressure,
oxygen, fluorometry, shear and micro-scale temperature, and the major
nutrients, oxygen, salinity, CFC and carbon components were discretely
analyzed on board. Argo and SOCCOM floats and surface drifter
deployments were usually carried out after leaving CTD stations or
during slow transits.



1.2  Programs and Principal Investigators


Program                  | Affiliation        | Principal         | Email                    
                         |                    | Investigator      |
—————————————————————————|————————————————————|———————————————————|————————————————————————————
CTDO Data, Salinity,     | UCSD, SIO          | Susan Becker,     | sbecker@ucsd.edu,        
Nutrients, Dissolved O_2 |                    | Jim Swift         | jswift@ucsd.edu          
-------------------------+--------------------+-------------------+----------------------------
Total CO_2 (DIC)         | AOML, PMEL,        | Dana Greely,      | dana.greeley@noaa.gov,   
                         | NOAA               | Rik Wanninkhof    | Rik.Wanninkhof@noaa.gov  
-------------------------+--------------------+-------------------+----------------------------
Underway Temperature,    | PMEL, NOAA         | Dana Greely       | dana.greeley@noaa.gov    
Salinity, and pCO_2      |                    |                   |                          
-------------------------+--------------------+-------------------+----------------------------
Total Alkalinity, pH     | UCSD, SIO          | Andrew Dickson    | adickson@ucsd.edu        
-------------------------+--------------------+-------------------+----------------------------
SADCP                    | UH                 | Eric Firing       | efiring@soest.hawaii.edu 
-------------------------+--------------------+-------------------+----------------------------
LADCP                    | LDEO               | Andreas Thurnherr | ant@ldeo.columbia.edu    
-------------------------+--------------------+-------------------+----------------------------
CFCs, SF6, N20           | UT                 | Dong-Ha Min       | dongha@mail.utexas.edu   
-------------------------+--------------------+-------------------+----------------------------
DOC, TDN, TOC, TN        | RSMAS              | Dennis Hansell    | dhansell@rsmas.miami.edu 
-------------------------+--------------------+-------------------+----------------------------
C13 & C14                | WHOI, Princeton    | Ann McNichol,     | amcnichol@whoi.edu,      
                         |                    | Robert Key        | key@princeton.edu        
-------------------------+--------------------+-------------------+----------------------------
Transmissometry          | TAMU               | Wilf Gardner      | wgardner@ocean.tamu.edu  
-------------------------+--------------------+-------------------+----------------------------
Fluorescence and         | U Maine            | Emmanuel Boss     | emmanuel.boss@maine.edu  
Backscatter (SOCCOM)     |                    |                   |                          
-------------------------+--------------------+-------------------+----------------------------
Chipod                   | OSU                | Jonathan Nash     | nash@coas.oregonstate.edu
-------------------------+--------------------+-------------------+----------------------------
d18O                     | BAS                | Mike Meredith     | mmm@bas.ac.uk            
-------------------------+--------------------+-------------------+----------------------------
CSIRO Argo Floats        | CSIRO              | Rebecca Cowley    | rebecca.cowley@csiro.au  
-------------------------+--------------------+-------------------+----------------------------
NOAA/PMEL Argo Floats    | PMEL, NOAA         | NOAA/PMEL         | elizabeth.steffen@noaa.gov 
-------------------------+--------------------+-------------------+----------------------------
SOCCOM Floats            | UW, UCSD, SIO      | Steve Riser,      | riser@ocean.washington.edu, 
                         |                    | Lynne Talley      | ltalley@ucsd.edu     
                         |                    | Ken Johnson       |
-------------------------+--------------------+-------------------+----------------------------
Surface Drifters         | NOAA, AOML         | Shaun Dolk        | Shaun.dolk@noaa.gov      
-------------------------+--------------------+-------------------+----------------------------
GPS data/bathymetry      | UCSD               | David Sandwell    | dsandwell@ucsd.edu       
-------------------------+--------------------+-------------------+----------------------------
UVP                      | U Alaska Fairbanks | Andrew McDonnell  | amcdonnell@alaska.edu    
-------------------------+--------------------+-------------------+----------------------------
Gliders                  | Caltech            | Andrew Thompson   | andrewt@caltech.edu      



1.3  Science Team and Responsibilities


Duty                      | Name                  | Affiliation       | Email Address           
——————————————————————————|———————————————————————|———————————————————|—————————————————————————
Chief Scientist           | Alejandro Orsi        | TAMU              | aorsi@tamu.edu          
--------------------------+-----------------------+-------------------+-------------------------
Co-Chief Scientist,       | Isabella Rosso        | UCSD              | irosso@ucsd.edu         
floats and drifters       |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander, Gliders | Giuliana Viglione     | Caltech           | gviglion@caltech.edu    
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander, Gliders | Maximilian Kotz       | Caltech           | maxkotz17@hotmail.co.uk 
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander, Chipods | Michael Kovatch       | UCSD              | mkovatch@ucsd.edu       
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander, Chipods | Daniela Faggiani-Dias | UCSD              | dfaggian@ucsd.edu       
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander          | Loicka Baille         | TAMU              | loickabaille@tamu.edu   
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander          | Kay McMonigal         | U Miami           | kmcmonigal@rsmas.miami  
                          |                       |                   | .edu                    
--------------------------+-----------------------+-------------------+-------------------------
CTD Watchstander, LADCP   | Benjamin Musci        | Georgia Tech      | bmusci3@gatech.edu      
--------------------------+-----------------------+-------------------+-------------------------
Nutrients, ODF            | Susan Becker          | UCSD ODF          | sbecker@ucsd.edu        
supervisor, SOCCOM        |                       |                   |                         
floats                    |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
Nutrients, Database       | Melissa Miller        | UCSD ODF          | mhite@ucsd.edu          
Support                   |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
CTDO Processing           | Kenneth Jackson       | UCSD ODF          | kjackson@ucsd.edu       
--------------------------+-----------------------+-------------------+-------------------------
Salts, ET, CTD/Rosette    | John Calderwood       | UCSD SEG          | jcalderwood@ucsd.edu    
Maintenance               |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
Salts, CTD/Rosette        | Joseph Gum            | UCSD ODF          | jgum@ucsd.edu           
Maintenance               |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
Dissolved O_2, Database   | Andrew Barna          | UCSD ODF          | abarna@ucsd.edu         
Management                |                       |                   |                         
--------------------------+-----------------------+-------------------+-------------------------
Dissolved O_2             | Zachary Anderson      | Bermuda Institute | zac.anderson@bios.edu   
                          |                       | of Ocean Science  |                         
--------------------------+-----------------------+-------------------+-------------------------
UVP                       | Jessica Pretty        | U ALASKA          | jlpretty@alaska.edu     
--------------------------+-----------------------+-------------------+-------------------------
DIC, underway pCO2        | Andrew Collins        | UW                | patrick.mears@noaa.gov  
--------------------------+-----------------------+-------------------+-------------------------
DIC                       | Patrick Mears         | U Miami           | andrew.collins@noaa.gov 
--------------------------+-----------------------+-------------------+-------------------------
CFCs, SF6                 | David Cooper          | UT                | davidcooper59@gmail.com 
--------------------------+-----------------------+-------------------+-------------------------
CFCs, SF6                 | Mark Lopez            | UT                | malopez_2014@utexas.edu 
--------------------------+-----------------------+-------------------+-------------------------
CFCs, SF6 student         | Garrett Walsh         | TAMU              | gxwalsh@tamu.edu        
--------------------------+-----------------------+-------------------+-------------------------
Total Alkalinity          | Manuel Belmonte       | UCSD              | mbelmont@ucsd.edu       
--------------------------+-----------------------+-------------------+-------------------------
Total Alkalinity          | Wiley Wolfe           | UCSD              | wwolfe@ucsd.edu         
--------------------------+-----------------------+-------------------+-------------------------
pH                        | Kayleen Fulton        | UCSD              | kcfulton@ucsd.edu       
--------------------------+-----------------------+-------------------+-------------------------
DOC, TDN, Radio           | Chelsi Lopez          | U Miami           | chelsi.lopez@rsmas.miami
Carbon                    |                       |                   | .edu                    
--------------------------+-----------------------+-------------------+-------------------------
Indep/Nurse               | Rachel Campbell       | Other             | n/a                     
--------------------------+-----------------------+-------------------+-------------------------
Marine Technician, Lead   | Jen Nomura            | UW                | jnomura@uw.edu          
--------------------------+-----------------------+-------------------+-------------------------
Marine Technician         | Croy Carlin           | UW                | croyc@uw.edu            





2.  CRUISE NARRATIVE


Alejandro Orsi

Before starting our journey South the entire team safely made it to
Cape Town, where for a few balmy days we savored the majestic scenery
of Table Mountain, the region’s vibrant music and its culinary
delights. Waiting for us docked at berth A was our ship, the research
vessel Thomas G. Thompson. We were greeted by the Captain and an
impressive crew eager to facilitate our smooth transition to living
and working on the ship. A couple of days before departure the
Thompson was refueled and fully loaded with palettes of fresh goods to
keep everybody well-nourished during the next 40 days (or so). Since
no science party had to move out of the ship, we were able to board
and begin loading right away the numerous pieces of equipment from our
different groups. The ODF container arrived early on, as did the DIC
van later secured on the back deck, whereas ODF’s was transferred to
the forward 02 deck. Just watching everybody work together so
efficiently during the set-up days gave the privileged assurance of
having an excellent team to face the likely upcoming challenges on
this cruise. Most impressive is the overall collegiate, respectful and
friendly atmosphere surrounding the Thompson since we started our
journey.

A blessing in disguise, perhaps, resulted in a delayed departure by a
few hours. Before setting sail around 4 PM on April 3, 2019 a
scorching smell emanated from loose light bulbs in a switchboard
panel; it had to be repaired with the help of a local electrician. We
then enjoyed the magnificent, albeit brief, sailing experience of
leaving the city and the Cape of Good Hope behind us, in a sunny
afternoon of calm seas. But the test to our seaworthiness came up
earlier than expected. Rough seas and strong gusty winds took a heavy
toll on our progress to the south. Rolls during the storm left one of
the main engines inoperable. After almost 26 hours of transit the
Captain and I decided to turn around and pursue the purchasing of
replacement parts. We were back to an area off Cape Town late in the
afternoon of April 6. The needed pump was not available in South
Africa. One was purchased from Caterpillar and scheduled to be hand-
carried from Seattle to Cape Town. Meanwhile Meegan Corcoran, our
benefactress Port Captain on her way back to the U.S., managed to
locate, purchase and FedEx another spare part during a layover in
Amsterdam! An arrival date for either of these parts was unknown,
considering ongoing strikes in South Africa. We could only wait. But
we also took advantage of the temporary impasse to conduct our test
cast, originally planned to take place at a location farther to the
south. With some minor hiccups for which we had plenty of time to iron
out, all instruments and data acquisition protocols were successfully
tested. Then we could only wait, and wait more, for the engine’s
parts. Fortunately, both items cleared customs and were available to
our agent at about the same time. They were delivered to the boat
around 8 PM on April 8, 2019.

With the affected engine fixed while underway, and a spare part in
stock, we were ready to face our second southward crossing of the
Agulhas Current Retroflection. This time Mother Nature was more
merciful, allowing us to steam at an average speed of 12.5 knots.
Against all odds, favorable cruising conditions prevailed for another
8 days, and counting! We crossed the Antarctic Circle paying due
respect to king Neptune and celebrating the new Red Noses aboard.
Shortly after, in the morning of April 16, we woke up to a smooth sea
covered with grease ice, that rapidly turned into a patchy field of
small-sized pancake ice. The Thompson’s Captain and Mates very
skillfully navigated towards the target 536-m isobath off Riiser Land
near 31°E. At one point, still at water depths of about 700 m, we
hesitated about continuing straight further south because patches of
older sea ice ahead of us were moving fast to the southwest. Again, we
were fortunate to find a long lead oriented almost across the local
isobaths and only a little off the intended track. We followed it
slowly at 2 knots for about two hours and stopped over the 530-m
isobath to occupy our first station.

All things considered, our petition of compensatory ship time loss (5
days) due to engine problems was followed by an empathetic 2-day
extension of our cruise. This is entirely the result of the prompt
intervention and collaboration between University of Washington, GO-
SHIP Program and National Science Foundation managers. In addition,
our swift steam to the Antarctic shelf resulted in about 1-day gain.
Therefore, with Station 1 we started I06S measurements at 8:47 UCT on
April 16, 2019 with a net ship time deficit of about two days.

A punishing sampling pace was kept, as expected, along the planned
short (39 nm) northwestward segment of nine closely-spaced stations (1
nm to 10 nm) across the Antarctic slope. These extenuating
circumstances resulted in the general backlog of different samples, to
be processed at a later time during the longer transits between
stations 30 nm apart. Less than 24 hours after starting Station 1, we
completed station 9 at a water depth of 3776 m and changed course to
continue due north along 30°E.

By April 20 we had already surveyed the southernmost 330 nm of the
long (1,980 nm) meridional segment of I06S, occupying 10 more stations
in about 41 hours. In addition, our trained students have also
assisted in the overboard deployment of two surface drifters, four
ARGO floats and two SOCCOM floats. We have been occasionally visited
by humpback whales and Antarctic petrels, as well as cruised by large
distant icebergs and enjoyed spectacular views of Aurora Borealis,
sunsets, and bioluminescence. Eerie or not, weather and seas have been
extremely sympathetic to us since we left Cape Town for the second
time.

On April 30 the successful ~4-hr deployment of one glider was carried
out from a zodiac, with the joyful assistance and training of a
graduate student and the Co-Chief Scientist. A second glider was more
spectacularly launched with the Thompson’s crane. Trained students
assisted in the overboard deployment of more surface drifters, ARGO
and SOCCOM floats. By May 1, in one way or another, we had worked
progressively along the main I6S meridional line. However, we had also
been halted extensively, and forced to prematurely terminate the first
cast of Sta. 44, waiting for the recommended working conditions of
swells smaller than 3-5 m – atypical in the Southern Ocean. Almost 3
full days (25-28 April) of work were lost to bad weather during the
passage of a large cyclone.

During workable periods of time we managed to maintain a commendable
pace. A total of 27 stations (Sta. 16-43) were occupied in the Enderby
Abyssal Plain, all located at water depths greater than 5000 m, at an
average time of 3.9 hours per station. All of the 30-nm transits
between stations were done at ship speeds exceeding 11 knots.


Fig. 1: Dodging attempt as a large low-pressure passed through our cruise 
        track during 25-27 April. The final science delay was of about 
        three full days. 

Fig. 2: A relatively weaker storm interrupts science work on May 1st, for 
        1.15 days. 


A 51.6-hr delay in CTD work between April 30 and May 2 was caused by
another large storm. We managed to occupy Stas. 44 and 45 before the
next mega storm got in our way, this timewe valiantly battled it for
42.7 hours during May 2-4. Combining these last two bad weather-
related delays to those suffered in April 24 (9.8 hours), April 25-28
(71.6 hours), plus 7 hours here and there, it adds up to 7.6 days or
18.7% of the cruise duration.

The most unfortunate event in our cruise was the medical evacuation of
a graduate student, while we were coping a storm on May 4 near 30°E,
50°S. The rapid transit to Port Elizabeth (yet **10.7%** of the cruise
duration) resulted in the successful evacuation and provision of
appropriate health care to the student in land. Nonetheless, the
**4.3-day** transit back to the planned location of Sta. 46 could not
be accomplished in the amount of time left.

About 130 nm northeast of Port Elizabeth we occupied a relocated Sta.
46 at water depth of about 550 m. Stations 47 to 51 (30°E, 35°S) were
located farther to the southeast with progressively larger spacing in
between (10 to 35 nm). The last four stations were intended to be 1°
latitude reoccupations along 30°E, but interference from a chines
fishing vessel resulted in the slight relocation of Sta. 54. Strict
implementation of the 23:00 May 11 deadline to our brief and final 69
hours of work time placed Sta. 55 at 30°E, 38.5°S. Near 23:00 local on
May 11, 2019 we had finished Sta. 55 at 30°E, 38.5°S, ending the sixth
calendar week since departing Cape Town at 16:00 local on April 3,
2019.

All in all, accounting for the time spent on transit between and at
stations, the total of work time was **14.8 days**, only **36.3%** of
the 40.7-day cruise. Our expert and relentless teams of hard- working
scientists defied punishing weather, mechanical and medical failures
to accomplish, on average four deep CTD stations per work day.


Fig. 3: GO-SHIP I6S 2019 cruise timeline. 


2.1  Main Result

**2019 occupation of the GO-SHIP I6S Hydrographic Section:** overall
accomplishment of the original hydrographic plan was around 60%, or 55
out of 91 CTD stations.

**How did this happen?** Unfavorable seas, sea-ice and weather are all
well-known and unavoidable conditions that make working in the
Southern Ocean so uniquely unpredictable. The sole remoteness of the
I6S line required long steaming times: 7.5 days to the first station,
and 2.4 days from the last station to Cape Town. That is, 24.3% of the
cruise time was spent on steaming back and for to do CTD work.

Engine problems resulted in the loss of 5.1 days, but they happened at
the very beginning of our cruise, and it was partially ameliorated
with two additional days.

**What ifs?** It’s understandable that sometimes we contemplate
alternative scenarios to less than desirable story endings. Consider,
for instance, how efficient our science teams performed throughout the
working time on this cruise. At the established working pace and 30-nm
spacing a happy ending would have needed:

1. 6.3 more work days to fill in the 11.5° gap now left unsampled
   along 30°E; or

2. only 1.3 days of bad weather out of 41 days in the Southern
   Ocean; or

3. a more reasonable 3.3 bad weather days and no engine failures;
   or,

4. even with all the experienced bad weather but sparing
   preventable mechanical and health failures.

It is hoped that, in addition to acquiring new hydrographic
measurements with the highest quality standards, our I6S 2019
experience will also better prepare the next generations for the many
challenges of working in the Southern Ocean.



2.2  Summary

The quality of the data collected is very high, particularly from the
chemistry teams who have delivered an excellent and very high-
resolution data set. We are confident that this occupation of I6S has
uncovered clear and ongoing changes in the deep ocean heat and carbon
content, and chemistry. The mixing information taken via the shear
measured by the LADCP, sADCP and fine and microscale properties via
the chi-pods and CTD will also be very insightful and unprecedented
along this line.




3.  CTD AND ROSETTE SETUP


For I06S-2019 the new STS 36 place yellow rosette and bottles, built
in 2017, were used. These rosette and bottles was built before P06
2017, making this the third time this package has been deployed. The
bottles were made with new PVC, with new non-baked o-rings and
electro-polished steel springs. This represents a change from the
past, where on GO-SHIP cruises using ODF equipment before P06 2017
o-rings were baked for 3 days at 100°C at 1-3 Torr in a sweeper gas of
hydrogen. Springs used to be painted and Tygon tubing added to the
ends to prevent paint wearing away from bottle firing. As on P06 2017
no sample contamination has been noticed by the change in o-rings and
springs. The package used on I06S-2019 weighs roughly 1500 lbs in air
without water, and 2350 lbs in air with water. The package used on
I06S-2019 weighs roughly 950 lbs in water. In addition to the standard
CTDO package on GO-SHIP cruises three chipods, two LADCPs, and one UVP
were mounted on the rosette. During the cruise we encountered numerous
problems, most notably modulo errors through the cruise resulting in
multiple re-terminations. We describe all of the above in more detail
in the sections below.



3.1  Underwater Sampling Package

CTDO/rosette/LADCP/chipod casts were performed with a package
consisting of a 36 bottle rosette frame, a 36-place carousel and 36
Bullister style Niskin bottles with an absolute volume of 10.6L.
Underwater electronic components primarily consisted of a SeaBird
Electronics housing unit with Paroscientific pressure sensor with dual
plumbed lines where each line has a pump, temperature sensor,
conductivity sensor, and exhaust line. A SeaBird Electronics membrane
oxygen sensor was mounted on the “primary” line. A reference
thermometer, transmissometer, chlorophyll-a fluorometer and
backscatter meter, and altimeter were also mounted on the rosette.
Chipod, LADCP, and UVP instruments were deployed with the CTD/rosette
package and their use is outlined in sections of this document
specific to their titled analysis.

CTD and cage were horizontally mounted at the bottom of the rosette
frame, located below the carousel for all stations. The temperature,
conductivity, dissolved oxygen, respective pumps and exhaust tubing
was mounted to the CTD and cage housing as recommended by SBE. The
reference temperature sensor was mounted between the primary and
secondary temperature sensors at the same level as the intake tubes
for the exhaust lines. The transmissometer was mounted horizontally on
the lower LADCP brace with hose clamps around both of its ends,
avoiding shiny metal or black tape inside that would introduce noise
in the signal. The fluorometer and backscatter meter and altimeters
were mounted vertically inside the bottom ring of the rosette frames,
with nothing obstructing their line of sight. The 150 KHz bi-
directional Broadband LADCP (RDI) unit was mounted vertically on the
bottom side of the frame. The 150 Khz LADCP was later replaced with a
300 Khz LADCP during the cruise in the same position. The 300 KHz bi-
directional Broadband LADCP (RDI) unit was mounted vertically on the
top side of the frame. The LADCP battery pack was also mounted on the
bottom of the frame. The LADCP and LADCP battery pack were mounted
next to each other at the beginning of the cruise. If we imagine the
LADCP being north on the rosette, the LADCP battery was mounted east,
the CTD mounted west, and the UVP mounted south.


Equipment        | Model            | S/N           | Cal Date     | Stations | Responsible
                 |                  |               |              |          | Party      
—————————————————|——————————————————|———————————————|——————————————|——————————|————————————
Rosette          | 36-place         | Yellow        | _            | 1-55     | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
CTD              | SBE9+            | 0830          | _            | 1-18     | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
CTD              | SBE9+            | 0914          | _            | 19       | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
CTD              | SBE9+            | 0057          | _            | 20-55    | *UW*       
-----------------+------------------+---------------+--------------+----------+------------
Pressure Sensor  | Digiquartz       | 99676         | Jan 10, 2019 | 1-18     | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
Pressure Sensor  | Digiquartz       | 110547        | Jan 10, 2019 | 19       | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
Pressure Sensor  | Digiquartz       | 34901         | Oct 25, 2017 | 20-55    | *UW*       
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE3+            | 32380         | Feb 12, 2019 | 1-55     | *STS*/*ODF*
Temperature      |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE4C            | 44545         | Feb 27, 2019 | 1-5      | *STS*/*ODF*
Conductivity     |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE4C            | 42659         | Feb 27, 2019 | 5-6      | *STS*/*ODF*
Conductivity     |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE4C            | 42319         | Feb 27, 2019 | 6-55     | *STS*/*ODF*
Conductivity     |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary Pump     | SBE5             | 51892         | _            | 1-9      | *UCSD*     
-----------------+------------------+---------------+--------------+----------+------------
Primary Pump     | SBE5             | 51549         | _            | 10-55    | *UCSD*     
-----------------+------------------+---------------+--------------+----------+------------
Secondary        | SBE3+            | 35844         | Feb 11, 2019 | 1-55     | *STS*/*ODF*
Temperature      |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Secondary        | SBE4C            | 42818         | Feb 27, 2019 | 1-55     | *STS*/*ODF*
Conductivity     |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Secondary Pump   | SBE5             | 54890         | _            | 1-55     | *UCSD*     
-----------------+------------------+---------------+--------------+----------+------------
Transmissometer  | Cstar            | CST-1803DR    | Sep 16, 2016 | 1-32     | *TAMU*     
-----------------+------------------+---------------+--------------+----------+------------
Transmissometer  | Cstar            | CST-1636DR    | Sep 16, 2016 | 33-55    | *TAMU*     
-----------------+------------------+---------------+--------------+----------+------------
Fluorometer      | WetLabs          | FLBBRTD-3698  | Sep 23, 2014 | 1-55     | *U Maine*  
Chlorophyll and  |                  |               |              |          |            
Backscatter      |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE43            | 433521        | Feb 22, 2019 | 1-7      | *ODF*      
Dissolved Oxygen |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE43            | 430197        | Feb 2, 2019  | 8-11     | *ODF*      
Dissolved Oxygen |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Primary          | SBE43            | 430255        | Jun 28, 2018 | 11-55    | *UW*       
Dissolved Oxygen |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Reference        | SBE35            | 0105          | Feb 01, 2018 | 1-55     | *STS*/*ODF*
Temperature      |                  |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Carousel         | SBE32            | 1178          | _            | 1-55     | *STS*/*ODF*
-----------------+------------------+---------------+--------------+----------+------------
Altimeter        | Valeport 500     | 62488         | _            | 1-20     | *UCSD*     
-----------------+------------------+---------------+--------------+----------+------------
Altimeter        | Valeport 500     | 59116         | _            | 21-55    | *UCSD*     
-----------------+------------------+---------------+--------------+----------+------------
Underwater       | Underwater       |               | _            | 1-55     | *U Alaska* 
Vision Profiler  | Vision Profiler  |               |              |          | Fairbanks  
5 HD (UVP)       | 5 HD             |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
DL *LADCP*       | 150 kHz Teledyne |               | _            | 1-34     | *LDEO*     
                 | RDI WHM150       |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
DL *LADCP*       | 300 kHz Teledyne |               | _            | 35-55    | *LDEO*     
                 | RDI WHM300       |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
UL *LADCP*       | 300 kHz Teledyne |               | _            | 1-55     | *LDEO*     
                 | RDI WHM300       |               |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Chipods          | Chipod           | Logger        | 1-55         | *OSU*    |            
                 |                  | 2008/Pressure |              |          |            
                 |                  | Case Ti 44-5  |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Chipods          | Chipod           | Logger        | 1-55         | *OSU*    |            
                 |                  | 2027/Pressure |              |          |            
                 |                  | Case Ti 44-3  |              |          |            
-----------------+------------------+---------------+--------------+----------+------------
Chipods          | Chipod           | Logger        | 1-55         | *OSU*    |            
                 |                  | 2030/Pressure |              |          |            
                 |                  | Case Ti 44-11 |              |          |            


Fig. 1: Package sensor looking into the rosette from the south, with
        UVP directly in front of the camera.

Fig. 2: Package sensor setup with top as southeast, to show in order
        from top clockwards CTD, downward LADCP, LADCP battery, and UVP.

Fig. 3: Package sensor setup from left to right, LADCP battery,
        LADCP, transmissometer, chipod, CTD in back right.

Fig. 4: Top chipod was already removed from post on right, but it is
        positioned with one inch of overlap between the chipod sensor
        holder and pole.

Fig. 5: Package setup from west, with CTD in foreground.



3.2  Winch and Deployment

The forward DESH5 winch deployment system was used for all but the
last three stations. After the wire on the forward DESH5 winch had a
strand of outer armor wire peel off and form a birdcage with roughly
100 meters of wire, the rosette was reterminated with the aft DESH5
winch. The rosette system was suspended from a UNOLS-standard three-
conductor 0.322” electro-mechanical sea cable. The sea cable was
terminated at the beginning of I06S-2019, and multiple times
afterwards.

The deck watch prepared the rosette 10-30 minutes prior to each cast.
The bottles were cocked and all valves, vents and lanyards were
checked for proper orientation. Any biofouling noted was cleaned off
the outsides of the rosette before the next cast, and the insides of
the bottles were checked for biofouling and sprayed down. LADCP
technician would check for LADCP battery charge, prepare instrument
for data acquisition and disconnect cables. The UVP battery was
monitored for charge and connectors were checked for fouling and
connectivity. Once stopped on station, the Marine Technician would
check the sea state prior to cast and decide if conditions were
acceptable for deployment. Recovering the package at the end of the
deployment was the reverse of launching. The Marine Technician would
perform a quick check of the rosette before allowing samplers to
sample. The rosette would be rinsed off after every cast.



3.3  Maintenance and Calibrations

During I06S-2019 routine maintenance was done to the rosette to ensure
quality of the science done. Actions taken included rinsing all
electrical instruments on the rosette down with fresh water after each
cast. Care was taken not to rinse the spigots and other parts of the
bottle that might be touched by samplers in order to not contaminate
the samples. After each cast salt water filled syringes were connected
to the plumbed lines to rinse the sensors between casts while in
freezing conditions. Salt water was used instead of fresh water due to
the lower freezing point to prevent it from freezing when exposed to
the outside air. Overhead heaters recently installed on the Thompson
were run while in freezing or near freezing conditions. The rosette
was routinely examined for valves and o-ring leaks, which were
maintained as needed. SBE35RT temperature data was routinely
downloaded each day.

Every 20 stations, the transmissometer windows were cleaned and an on
deck blocked and un-blocked voltage readings were recorded prior to
the cast. The transmissometer was also calibrated before and after the
start and end science operations. The same calibration was performed
at the of the cruise during transit to Cape Town. Black tape was put
on the outside of the FLBB sensors to do a calibration “dark cast”.
Dark casts were done at the beginning and end of the cruise to measure
pressure effects on the sensor. A dark cast was performed on a cast
where depths reached at least 2000 meters, preferably average full
ocean depth for the cruise, and where previous profiles showed little
FLBB activity. The post cruise dark cast was performed in a bucket due
to running out of time.



3.4  Logs

In port: Preparation of the CTD and rosette took all but the first day
allocated in port, which was used for unloading the container and
setting up the labs. The large amount of time used for CTD and rosette
can be attributed to the lack of support personnel flown out to assist
with setup, and instead using ODF personnel and experience to help the
following programs: LADCP, UVP, chipods, transmissometry, SOCCOM. On
various previous cruises LADCP, UVP, and chipods have all sent out an
additional person to help install and familiarize cruise participants
with their instruments, for various reasons on this cruise no one from
these groups were available to fly out to Cape Town to help setup.
This led to a large time crunch as all groups want to get their
equipment mounted for testing, yet the students designated as cruise
participants have very little experience with setup requiring the use
of ODF technicians to work long days and nights in port to prepare the
rosette for transit. Additional integrity checks on the rosette, such
as checking lanyard angles, o-ring and lanyard replacement, and spigot
movement waited until being underway to be checked as lower priority
tasks.

We are using a new mounting system for the downward looking LADCP
which has the LADCP clamped facing inward instead of outward, which
will cause problems if we need to change that LADCP in rough weather.

April 6, 2019 – Test cast #1

90001 – Test cast aborted due to deck box complaining upon entering
the water, deck box LEDs displaying 0001. Upon recovery the CTD was
inspected, and the Y cable from fish to water sampler to SBE 35 showed
signs of water leakage into the cable in the form of a greenish,
copper patina on the cable. Cable was replaced with a second Y cable.

April 7, 2019 – Test cast #2

90101 – Test cast occurred with minimal beeping in upper 100 meters of
water column. As the beeping quickly went away, the cast continued to
the bottom and back without any further problems.

90201 – Third test cast done to 100 meters to check for deck box
beeping in the upper water column while still waiting for the pumps to
arrive in Cape Town. No beeping or other signs of error showed up
during the test cast.

April 16, 2019 – First stations, teething issues.

00101 – Bottles fired on fly from 7 to 18. 00201 – RS-232
communication timeout during the cast, 35-10 m above seafloor. On
recovery fired bottles on the fly from 6 to 21. 00301 – Hydroboom
issues during cast, held at surface for 15 minutes while
troubleshooting. 00401 – Slight delay before rosette deployment due to
troubleshooting Hydroboom. Issue resolved – wire came undone inside
box above hydroboom, was reattached. 00501 – Staging bay was around or
below -2C during sampling of 00401. Primary and secondary lines were
frozen without notice, deployment of rosette into water with pumps not
coming on immediately. Attempted to defrost lines by soaking at 300m
in 1C water, eventually gave up and came to surface to defrost on deck
with lukewarm water and heaters. Cast recording for roughly 40-60
minutes total. 00502 – Deployed after defrosting sensors with primary
conductivity problems. Changed primary conductivity from 4545 to 2659
post cast.

April 17, 2019 Sensors (Unknown bulkhead connectors) day

00601 – Primary conductivity sensor should’ve been 2569 as noted on
the CI, instead 2659 was brought. Conductivity was okay after entering
proper calibration, then failed at depth, swapped to 2319 post cast.
00701 – Data acquisition started in water, no deck reading.
Conductivity seems okay. 00801 – Pre cast switched oxygen sensor from
3521 to 0197 to attempt to fix spiky oxygen trace. 00901 – Oxygen
profile still noisy, nothing changed. 01001 – Oxygen profile still
noisy. Changed primary pump from 1892 to 1549.

April 18, 2019 – Deck pressures day

01101 – Oxygen profile still noisy, changed oxygen sensor from 0197 to
TGT SN: 0542. 01201 – Fired bottles on the fly. Niskin 24 top cap
apparently grazed UVP cable (not sure power or data) and trapped it in
top of bottle, ripping the cable out of the bulkhead connector of UVP.
Due to unknown depth at which the cable was ripped out, UVP was
removed as precautionary measure until it could be triaged with remote
assistance. 01301 – Fired bottles on the fly. Noticed that pre and
post deck pressure is fluctuating largely, slightly under 2 decibar,
watching pressures. 01401 – Niskin 14 spigot leaking, reasons unknown.
Rosette slimed, possibly on this cast.

April 19, 2019 – UVP day

01501 – FLBB dark cast for SOCCOM. 01601 – Noisy altimeter at bottom,
not fully dropped out 20 meters from bottom. 01701 – Attached UVP
prior to cast, causing delay of ~20-30 minutes on station. This was
done ad hoc and is secured with one metal cylinder bracket on top and
one large hose clamp with rubber for spacing and padding on bottom.
Noisy altimeter, complete dropout 20 meters from bottom. 01801 – Tag
line still attached on cast, brought back out. Altimeter very jumpy on
bottom approach, dropped out at 20 m.

April 20, 2019 – Fishes day

01901 – Changed fish from 0830 to 0914 prior to cast. Noisy oxygen,
altimeter still dropped out 20 meters from bottom. 02001 – Modulo
error count: 10. Changed fish from ODF SN: 0914 to UW SN: 0057 prior
to cast. Did transmissometer calibration post cast. 02101 – Modulo
error count: 9. Changed altimeter from 62488 to 59116 prior to cast.
New altimeter works fine for bottom approach.

April 21, 2019 – Modulo errors/Electrical retermination day

02201 – Modulo error count: 20. 02301 – Modulo error count: 55. Bottle
19 lanyard caught on spigot of bottle 18 when closing, bottom cap did
not close. Inspected electrical termination post cast, no apparent
water leakage. Replaced Y-cable from fish to sea cable with third and
last cable brought. 02401 – Modulo error count: 110. Replaced
electrical termination post cast with TGT pigtails and Y-cable. UW
marine tech Croy Carlin did the electrical termination.

April 22, 2019

The request was received to swap the downward looking WH150 ADCP with
the WH300 ADCP. Weather is being evaluated for best chance of doing so
without damaging the ADCPs or the rosette.

02501 – Modulo error count: 30.

02601 – Modulo error count: 81. Removed CTD ASAP upon recovery of
cast for cable inspection. After thorough inspection of cables on CTD,
water was discovered leaking from third Y-cable between CTD, water
sampler, and SBE 35. This cable was replaced with the second Y-cable
with the splice. Oxygen sensor cable had suspicious bubbles near the
connector, and so cable was replaced. Normal levels of abrasion and
wear and tear were seen on the other cables, and so were reconnected.
During inspection cable pins and bulkhead connectors were cleaned with
contact cleaner, lubricated, and reconnected.

02701 – Modulo error count: 26.

April 23, 2019

02801 – Modulo error count: 63.

02901 – Modulo error count: 16. Bottle 7 did not trip, cleaned and
worked latch prior to cast.

03001 – Modulo error count: 8. Swapped on straight cable from CTD to
carousel, no SBE 35 for this cast. Cable removed was the second
Y-cable tried with the old splice c. 2008. Bottle 7 did not trip
again.

April 24, 2019

03101 – Modulo error count: 28. Straight cable from CTD to carousel
still on, no SBE 35 for this cast. Swapped on straight ECO cable
before cast to troubleshoot if spliced FLBB cable was cause of modulo
errors. Modulo errors still occurred starting at ~2800 meters. FL
signal dropped from background noise (0.05V) to 0V at multiple points
on cast, cable is suspect. Put original spliced FLBB cable on after
cast. Bottle 7 was moved upwards to adjust angle for lanyard pull, and
so bottle 7 did trip on this cast.

03201 – Modulo error count: 32. Before cast marine techs megged
connection loop from lab to CTD, reading 410 megaohms at 500 V.
Inspection of winch and slip ring showed equipment in good state.

Sharp offset in transmissometer reading at ~1250 meters on downcast
with no adjustment back on upcast at same pressure. Transmissometers
switched from CST-1803DR to CST-1636DR post cast. While on recovery
inspection of the sensor showed no fouling, and deck readings showed
no errors, transmissometers were changed as a precautionary effort.
Attempting to change cables lead to a search of ODF cables, of which
all remaining cables looked to be in worse shape, attempting to use UW
cables showed a different pinout that did not supply power to the
instrument once a deck test was run.

03301 – Modulo error count: 19. Bottle 16 spigot was broken on
recovery.

April 25, 2019

03401 – Modulo error count: 40. Did comprehensive bottle maintenance
on rosette, checked guide rings and spigots – no major adjustments of
note.

Weather delay. When the decision was made to steam south for calmer
weather ODF SBE 9 SN: 0830 was swapped back onto the rosette to test
if the UW SBE 9 was cause of modulo errors, with current configuration
as is on rosette. Test cast was started at the end of April 25 and
ended on April 26.

WH150 (big, downward looking ADCP) was swapped with WH300 during
weather delay. Preliminary data from dual WH300 configuration looks
good.

ODF SBE 9 SN:0914 pressure port was put in its cage with pressure port
facing the flat end, an empty tape container put underneath it, and
port removed to allow oil to drip out from below into the empty tape
container. Very little oil or seawater dripped into the container,
leading to likely large air bubbles forming in pressure port.

April 26, 2019

Weather delay.

90301 - Pulled test cast up after 2 modulo errors at roughly 3000
meters. Conclusion is that barring a full rebuild of CTD with
intensive inspection of each sensor and cable as we swap back to UW
SBE 9 SN: 0057, potential cause of modulo errors might not be found. A
test cast would then be required to see if problem is fixed, which is
not feasible in this weather.  Modulo error issue is concluded for now
barring major failure during cast.

ODF SBE 9 SN: 0914 pressure sensor port was filled with vegetable oil
as a substitute for DC-200 silicone oil. One of the primary
ingredients of vegetable oil is canola oil, also known as rapeseed
oil, which used to be the preferred oil of choice for lubricating
things entering water. Canola oil may still be used on ships for
spraying on winch drums between casts. Or is it linseed oil?
Unfortunately without a test cast, we will not see if said oil serves
as a decent substitute in case oil disappearance.

April 27, 2019

Weather delay. UW SBE 9 SN: 0057 was swapped back onto the rosette.
SBE 35 is cabled up and will remain so for the remainder of the
cruise. Y-cable used for SBE 35 is the original cable on rosette,
which was re-spliced at sea. Second Y-cable, which had the older
splice presumably c. 2008, was left off.

Third Y-cable was cut apart at problem area and insulation showed
green patina on inside of insulation, signs of water intrusion and
corrosion. Thorough inspection remains to be done of the length of the
cable and possibly the other two legs of the cable.

LADCP battery has not been charging while losing power. The battery
was switched to the second battery, which has been tested and is
working.

April 28, 2019

03501 – Modulo error count: 112. First cast in the water after 55
hours without station work. During swap of fish voltage channels were
accidentally switched, V3 for altimeter and V4 for UVP. UVP did not
soak long enough to come on due to this mixup.

03601 – Modulo error count: ???. Removed Y-cable on V2/V3 prior to
cast. UVP is now pulled from CTD, transmissometer is on straight cable
to V2, altimeter on straight cable to V4. No noticeable change made.

Inner lanyard on top cap of bottle 2 was noticed to only be on spring
by one line instead of two. The lanyard was adjusted to have both
lines attached, fraying should be monitored for the rest of the
cruise.

April 29, 2019

03701 – Modulo error count: 28. Put Y-cable back on V2/V3 connector,
UVP hooked up again. UVP signal was on the rails (0 or 5 volts) for
most of the cast, not showing a typical profile for UVP. Post cast UVP
power cable was noticed to have corrosion on pins, person in charge of
UVP will now be rinsing and cleaning pins after unplugging each time.

During recovery it was snowing, leading to the pallet being wet and
slippery. While bringing the rosette in rosette slipped off of the
pallet by 2/3rds. Wooden blocks to stop sliding were installed on the
pallet in addition to straps that were used in adverse conditions.

03801 – Modulo error count: 10. On recovery a tagging hook slipped off
the horizontal rung and grabbed a vertical stanchion with chipod cable
on it, causing damage to cable. Cable was replaced after sampling.
Chipod connected to damaged cable was upward looking SN: 7.

Bottle 7 was noticed to have an anomalous oxygen draw temperature,
suspected mistrip. Bottle will be adjusted post sampling.

03901 – Modulo error count: 6. Bottles 3, 7, 13, 18, 19 had guide
rings adjusted to prevent bottle caps closing too early prior to cast.
The sea cable was found stuck between a horizontal bar and a tab on
its run down from the shackle down to the CTD. The sea cable was freed
from being stuck there on the hypothesis that at pressure and in
sudden tension loads or movement might be enough to cause a slight
pinch in the cable or other deformation leading to modulo errors.
There are some spikes in the data that look like they could be modulo
errors, yet without a modulo error attached to them.

April 30, 2019

04001 – No modulo errors.

04101 – No modulo errors.

04201 – No modulo errors. Rosette kissed the side of the ship during
deployment due to swell and ship motion.

04301 – No modulo errors.

At this point the modulo error problem is believed to be resolved. Any
new problems related to modulo errors will be believed to be due to a
new problem.

May 1, 2019

04401 – No modulo errors. Cast was canceled at 1800 meters downcast
due to incoming weather.

May 2, 2019

04402 – Modulo error count: 18. Due to heavy weather ship was drifting
a lot, altimeter did not kick in at expected depth due to wire angle.
Multiple stops and slow descents to allow angle to settle out before
eventually locking in bottom depth with altimeter.

04501 – No modulo errors. Descended in heavy weather, slowed down
early in order to allow angle to settle out.

May 3, 2019

No stations or issues addressed.

May 4, 2019

No stations or issues addressed.

May 5, 2019

No stations or issues addressed.

May 6, 2019

No stations or issues addressed.

May 7, 2019

No stations or issues addressed.

May 8, 2019

No stations or issues addressed.

May 9, 2019

04601 – An air vent screw was noticed broken on bottle 33 prior to the
cast, and replaced.

04701 – No problems noted.

04801 – Air vent screws on bottles 15 and 17 were noticed opened prior
to sampling.

04901 – No problems noted.

May 10, 2019

05001 – No problems noted.

05101 – One strand of the outer armor on the wire started birdcaging
on upcast around 3700 meters at point where level wind takes in wire
from block. Operations were stopped as the birdcage was cleared from
the wire, during which a Yale grip was put in place on the wire
downstream of the birdcage in case anything happened. 52 to 54 wraps
of wire on the winch appear to have been stripped of a single armor
wire, roughly equivalent to 100 meters of wire. Once safe to bring
aboard the rosette came up at normal speeds, 60 meters per minute
below 100 meters of water depth and 30 meters per minute above 100
meters of water depth.


Fig. 6: Birdcage of approximately 100 meters of wire forming outside
        of the level wind intake being freed by RV Thompson marine
        technician Jen Nomura.

Fig. 7: 52 to 54 wraps of wire showing a single missing strand of
        outer armor wire, estimated at 1.5 - 2 meters of wire per wrap.


Post recovery the termination was cut and the aft DESH-5 winch was
used for deployment, necessitating mechanical and electrical
retermination. It was noted that on previous cruises the winch had
electrical signal problems leading to 300+ modulo errors, and so
ground was doubly connected to both the armor and the red wire, while
signal was connected to the white wire. Deck tests showed no problems
before deployment.

Bottles 8 through 34 were fired on the fly. Bottles 35 and 36 were
fired while stopped at the surface while waiting for conditions to
recover.

05201 – No problems noted during cast. Bottle 12 was open on recovery,
status unknown. The bottle was adjusted upwards between 0.5 to 1 inch
post sampling.

May 11, 2019

05301 – No problems noted during cast.

05401 – Modulo error count: 7. A Chinese fishing vessel was occupying
station, causing a diversion to the west of several nautical miles.

05501 – Modulo error count: 14.

May 12, 2019

During disassembly of the rosette and CTD, nothing out of place was
noticed. The SOCCOM FLBB dark cast was done on deck, with files named
“FLBB_postcruise_deck_readings”. The final transmissometer deck
calibration was done with files named “tx_deckcal_1636_20190512”.


Fig. 8: FLBB readings taken on deck post last station. FL average
        reading was 0.050 volts, BB average reading was 0.070 volts.



3.5  Major Problems (Triage, Care, Analysis):

Deckbox beeping: One of the more common errors that points to bad
cabling, most likely water intrusion. Upon recovery and inspection we
found the damaged cable, replaced it, and everything worked well
afterwards.

Drifting pre and post pressure points on deck: The first sign of a
failing pressure sensor is instability of a deck pressure readings.
This can be monitored by deck pressure readings pre and post cast,
where the CTD is on before deployment into the water and after
recovery. This can also be tested by leaving a CTD powered on for
15-30 minutes and plotting the pressure on deck. If the pressure on
deck drifts by more than 0.1-0.2 decibar over this time consider
looking for problems. Remember 0.1 decibar is equal to 10 milibar –
unless a large storm system is passing over you very quickly, a drift
of 1 decibar during a deck test is equivalent to a change of 100
milibar in the atmosphere.

The current hypothesis for lack of oil in the sensor is thermal
expansion of the oil causing the fluid to leak out of the nylon
tubing. The CTDs were filled with oil in San Diego in January, roughly
at 20 C/high 60s F. The CTDs were then shipped to South Africa by sea,
where they sat in their shipping container in the African summer for
weeks/months, which caused the oil to slowly leak out of CTDs onto the
porous wooden crate, which would have absorbed the oil, leaving no
trace of what had happened.

After seeing a 2 decibar change between pre and post cast readings the
decision was made to swap CTDs. Unfortunately the second ODF CTD was
shipped in the same manner and so had the same pressure problem to
greater effect, where the pressure sensor thought it was at 5 decibar
when it was out of the water. This can be explained by water being
trapped in the pressure port and not leaving the port fast enough. The
second ODF CTD was then quickly replaced with a UW CTD after
attempting to find a substitute to fill the pressure ports with oil.

The problem was solved by switching to the ship’s CTD. The CTD’s most
recent calibration is late 2017, which is within Seabird’s schedule.
In the future mineral oil used for refilling the LADCP battery housing
could also be used to fill the pressure port, an option we had not
thought of at the time.


Fig. 9: Tiny amount of oil dripped out from the pressure port due to
        gravity. No free oil was visible to the eye in the sensor.


Oxygen sensor spikiness: The SBE 43 oxygen sensor showed
uncharacteristic spikiness sharper than usually seen with membrane
issues. The spikes occurred after the plumbed lines for the CTD froze
over on deck while in negative Celcius weather, leading to initial
thoughts of it being a frozen or damaged membrane. However after
swapping the sensors the signal was still spiky. A third swap was done
to a UW SBE 43 in order to preserve the final ODF SBE 43 unused sensor
as a spare. When the third SBE 43 also had the same spiky trace,
electrical problems were suspected and a spare cable was swapped in,
with no change. Finally the cabled connector position was swapped
where the SBE 43 was moved from its own voltage channel (V6) to
another voltage channel (UVP, V3), which showed a cleaned signal.

Altimeter spikiness: The altimeter signal was spiky on approach of the
bottom after working well for the start of the cruise. The signal was
very spiky within 100 meters, and then would drop out ~20 meters from
the seafloor, requiring watchstanders to manually stop the winch
operator without telemetry to guide. The altimeter was swapped out for
the backup altimeter, which solved the issue.

Modulo errors: Modulo errors have dominated the cruise so far. While
worrying more for their potential problem of continuous bad signal,
the total modulo errors to date represent less than 1% of all scans
per cast at worst, usually less than 0.1% of all scans. Attempts to
solve the modulo error issue have been inconclusive at best,
attempting fish swaps, cable swaps, and inspections of all parts of
the entire CTD system from lab to deployment to rosette. While we have
found cables that need to be repaired and replaced, no conclusive
smoking gun has been found to date.

Modulo errors represent transmission problems, where a known function
on the CTD produces a value for the deck box/computer to verify. If
this value is not correct, you have a modulo error, where a scan may
or may not be affected. Only the check value could be altered, or only
the metadata and so no scientific data is affected, or the data could
have erroneous values. In very small amounts the data will be binned
and dealt with, leading to little to no impact on the data. Problems
would occur as more and more modulo errors occur, leading to
unreliable communication with the CTD. If the issue is inside the
transmission loop between the CTD and the deck box communications to
the CTD could be affected, leading to bottles not being fired when
told to, or not being reported as fired. If the modulo error rate
approaches 25-50% of data, the CTD signal may be unsalvageable for
high quality data.

After switching to the aft DESH-5 winch modulo errors started again,
this time known about from previous cruises. These modulo errors seem
to be caused by something in the winch/wire setup, and so the cable
was double grounded to the armor and the red wire. The spread of
modulo errors was much greater, with errors starting higher in the
water column and also sometimes occurring mostly on the upcast.



3.6  Cruise Lessons

Have repair kits for all conditions, no matter how unlikely: After the
recent discussion on the RVTEC mailing list about a SBE 9 with
drifting pressure and most likely loss of oil in the pressure port, it
seems fitting that the first headscratcher once station work started
is the same problem.

Ad hoc oil refill procedure: Stick thin wire down pressure port, to be
used as displacer. We used 22 gauge solid wire, which fits in both the
nylon tubing and the pressure port channel. Fill pressure port well
with oil. Pull wire partially out, which causes oil to be sucked down
into the channel. Repeat process, refilling well with more oil and
continue to pull wire out section by section until wire is fully
removed and oil well is filled.

Use known good equipment, including ancillaries: ODF did not bring its
usual set of equipment out to sea for I06S. While sensors were checked
and found in good order before shipping, the cables shipped out for
use were found to have problems. Roughly a half dozen cables were
swapped on and off of the CTD in the process of testing, and of those
more than half of them were already spliced or had water damage after
the cast. Two of the three Y-cables connecting the CTD, water sampler,
and SBE 35 had extended water damage, with metal sheathing inside the
insulation being corroded away for a foot or more. Additional cables
that were evaluated to be put on the CTD were found to be damaged,
with visible gaps in the insulation through which the inner wires
could be seen. A thorough check of all equipment sent especially when
they have an unknown service or use history would have cut down on
problems and overtime over the cruise.

Trust your experience: Issues were encountered that could have been
avoided had different choices been made. Inexperienced cruise
participants with equipment on the rosette made decisions that ended
up costing time and willpower in the long run, wearing down personnel
on the cruise. Instead of listening to the instrument expert, who may
have field tested the equipment a couple of cruises previously, allow
the cruise experts with decades of experience to have final say on how
equipment is mounted and prepared for deployment.

Have enough support on the ship: The amount of science achieved would
not have been possible without the Thompson’s marine technicians on
the ship supporting the ODF technicians in troubleshooting the CTD and
rosette issues. Both Croy Carlin and Jen Nomura were invaluable in
helping keeping the CTD running and stations moving, and while ODF
tries to bring enough experience and hands to deal with any encounter
at sea, having another set of experienced hands to step in and do the
work when issues have you doubting yourself allowed the cruise to
accomplish more stations that would have without them available. This
cruise may be an outlier in problems encountered along the way, but
having four experienced technicians with CTD work made the workload
manageable, which would have crushed two experienced technicians with
24-hour work.





4.  CTDO AND HYDROGRAPHIC ANALYSIS


PIs
   * Susan Becker

   * James Swift

Technicians
   * Kenneth Jackson



4.1  CTDO and Bottle Data Acquisition

The CTD data acquisition system consisted of an SBE-11+ (V2) deck unit
and a networked generic PC workstation running Windows 7. SBE SeaSave7
v.7.26.1.8 software was used for data acquisition and to close bottles
on the rosette.

CTD deployments were initiated by the console watch operators (CWO)
after the ship had stopped on station. The watch maintained a CTD Cast
logs for each attempted cast containing a description of each
deployment event.

Once the deck watch had deployed the rosette, the winch operator would
lower it to 20 meters. The CTD sensor pumps were configured to start
10 seconds after the primary conductivity cell reports salt water in
the cell. The CWO checked the CTD data for proper sensor operation,
waited for sensors to stabilize, and instructed the winch operator to
bring the package to the surface in good weather or no more than 5
meters in high seas. The winch was then instructed to lower the
package to the initial target wire-out at no more than 30m/min to 100m
and no more than 60m/min after 100m depending on sea-cable tension and
the sea state.

The CWO monitored the progress of the deployment and quality of the
CTD data through interactive graphics and operational displays. The
altimeter channel, CTD pressure, wire-out and center multi-beam depth
were all monitored to determine the distance of the package from the
bottom. The winch was directed to slow decent rate to 40m/min 100m
from the bottom and 20m/min 30m from the bottom. The bottom of the CTD
cast was usually to within 10-20 meters of the bottom determined by
altimeter data. For each up-cast, the winch operator was directed to
stop the winch at up to 36 predetermined sampling pressures. These
standard depths were staggered every station using 3 sampling schemes.
The CTD CWO waited 30 seconds prior to tripping sample bottles, to
ensure package shed wake had dissipated. An additional 15 seconds
elapsed before moving to the next consecutive trip depth, which
allowed for the SBE35RT to record bottle trip temperature averaged
from 14 samples.

After the last bottle was closed, the CWO directed winch to recover
the rosette. Once the rosette was out of the water and on deck, the
CWO terminated the data acquisition, turned off the deck unit and
assisted with rosette sampling.

Additionally, the watch created a sample log for the deployment which
would be later used to record the depths bottles were tripped and
correspondence between rosette bottles and analytical samples drawn.

Normally the CTD sensors were rinsed after each station using a fresh
water tap connected to Tygon tubing. The tubing was left on the CTD
between casts, with the temperature and conductivity sensors immersed
in fresh or salt water depending on ambient air temperatures.

Each bottle on the rosette had a unique serial number, independent of
the bottle position on the rosette. Sampling for specific programs
were outlined on sample log sheets prior to cast recovery or at the
time of collection. The bottles and rosette were examined before
samples were drawn. Any abnormalities were noted on the sample log,
stored in the cruise database and reported in the APPENDIX.



4.2  CTDO Data Processing

Shipboard CTD data processing was performed after deployment using
SIO/ODF python CTD processing software v. 0.1. CTD acquisition data
were copied onto an OS X system, and then processed. CTD data at bottle
trips were extracted, and a 2-decibar down-cast pressure series
created. The pressure series data set was submitted for CTD data
distribution after corrections outlined in the following sections were
applied.

A total of 55 CTD stations were occupied including one test station. A
total of 150 CTDO/rosette/LADCP/chipod casts were completed.

CTD data were examined at the completion of each deployment for clean
corrected sensor response and any calibration shifts. As bottle
salinity and oxygen results became available, they were used to refine
shipboard conductivity and oxygen sensor calibrations.

Temperature, salinity and dissolved O_2 comparisons were made between
down and up casts as well as between groups of adjacent deployments.
Vertical sections of measured and derived properties from sensor data
were checked for consistency.

A number of issues were encountered during I06S-2019 that directly
impacted CTD analysis. Issues that directly impacted bottle closures,
such as slipping guide rings, were detailed in the Underwater Sampling
Package section of this report. Temperature, conductivity and oxygen
analytical sensor issues are detailed in the following respective
sections.



4.3  Sensor Problems

Throughout the cruise, there were many problems with the CTDO sensors,
leading to CTD downcast data to be flagged questionable. SBE43 oxygen
sensors were slightly noisy for most of the cruise, however there were
a few notable casts that contained extremely noisy data. Stations 7
and 34 are shown as examples.


Fig. 1: Station 7

Fig. 2: Station 34

Several stations also had a combination of the conductivity,
temperature, and oxygen sensors producing spikes and questionable
voltages. Station 24 is shown as an example below.


Fig. 3: Station 24


Stations 29 and 32 (not shown) are other examples of stations with
large sections of the profile flagged as questionable.



4.4  Pressure Analysis

Laboratory calibrations of CTD pressure sensors were performed prior
to the cruise. Dates of laboratory calibration are recorded on the
underway sampling package table and calibration documents are provided
in the APPENDIX.

The lab calibration coefficients provided on the calibration report
were used to convert frequencies to pressure. Initially SIO pressure
lab calibration slope and offsets coefficients were applied to cast
data. A shipboard calibration offset was applied to the converted
pressures during each cast. These offsets were determined by the pre
and post-cast on-deck pressure offsets. The pressure offsets were
applied per configuration cast sets.


CTD #0830 (Stations: 1-18):

                          | Start P (dbar) | End P (dbar) 
           ———————————————|————————————————|—————————————
           Min            | -2.2           | -1.3        
           ---------------+----------------+-------------
           Max            | 0.01           | -0.3        
           ---------------+----------------+-------------
           Average        | -0.86          | -0.64       
           ---------------+----------------+-------------
           Applied Offset |                | -0.216      


On-deck pressure reading for varied from -2.2 to 0.01 dbar before the
casts, and -1.3 to 0.3 dbar after the casts. Before and after average
difference was -0.86 and -0.64 dbar respectively. The overall average
offset before and after cast was -0.216 dbar.


CTD #0914 (Stations: 19):

                          | Start P (dbar) | End P (dbar)
           ———————————————|————————————————|—————————————
           Min            | -0.2           | 3.9         
           ---------------+----------------+-------------
           Max            | -0.2           | 3.9         
           ---------------+----------------+-------------
           Average        | -0.2           | 3.9         
           ---------------+----------------+-------------
           Applied Offset |                | 4.102       


On-deck pressure reading for  varied from -0.2 to -0.2 dbar before the
casts, and 3.9 to 3.9 dbar after the casts. Before and after average
difference was -0.2 and 3.9 dbar respectively. The overall average
offset before and after cast was 4.102 dbar.


CTD #0057 (Stations: 20-55):

                          | Start P (dbar) | End P (dbar)
           ———————————————|————————————————|—————————————
           Min            | -0.44          | -0.42       
           ---------------+----------------+-------------
           Max            |  0.21          |  0.31        
           ---------------+----------------+-------------
           Average        | -0.09          | -0.16       
           ---------------+----------------+-------------
           Applied Offset |                | -0.0709     


On-deck pressure reading for varied from -0.44 to 0.21 dbar before
the casts, and -0.42 to 0.31 dbar after the casts. Before and after
average difference was -0.09 and -0.16 dbar respectively. The overall
average offset before and after cast was -0.0709 dbar.


4.5  Temperature Analysis

Laboratory calibrations of temperature sensors were performed prior to
the cruise at the SIO Calibration Facility. Dates of laboratory
calibration are recorded on the underway sampling package table and
calibration documents are provided in the APPENDIX.

The pre-cruise laboratory calibration coefficients were used to
convert SBE3plus frequencies to ITS-90 temperature. Additional
shipboard calibrations were performed to correct sensor bias. Two
independent metrics of calibration accuracy were used to determine
sensor bias. At each bottle closure, the primary and secondary
temperature were compared with each other and with a SBE35RT reference
temperature sensor.

The SBE35RT Digital Reversing Thermometer is an internally-recording
temperature sensor that operates independently of the CTD. The SBE35RT
was located equidistant between the two SBE3plus temperature sensors.
The SBE35RT is triggered by the SBE32 carousel in response to a bottle
closure. According to the manufacturer’s specifications, the typical
stability is 0.001°C/year. The SBE35RT was set to internally average
over a 15 second period.

A functioning SBE3plus sensor typically exhibit a consistent
predictable well modeled response. The response model is second order
with respect to pressure, a first order with respect to temperature
and a first order with respect to time. The functions used to apply
shipboard calibrations are as follows.


     T_{cor} = T + D_1 P_2 + D_2 P + D_3 T_2 + D_4 T + \text{Offset}

                        T_{90} = T + tp_1 P + t_0

          T_{90} = T + a P_2 + b P + c T_2 + d T + \text{Offset}


Corrected temperature differences are shown in the following figures.


Fig. 4: SBE35RT-T1 by station.

Fig. 5: Deep SBE35RT-T1 by station (Pressure ≥ 2000dbar).

Fig. 6: SBE35RT-T2 by station.

Fig. 7: Deep SBE35RT-T2 by station (Pressure ≥ 2000dbar).

Fig. 8: T1-T2 by station.

Fig. 9: Deep T1-T2 by station (Pressure ≥ 2000dbar).

Fig. 10: SBE35RT-T1 by pressure.

Fig. 11: SBE35RT-T2 by pressure.

Fig. 12: T1-T2 by pressure.


The 95% confidence limits for the mean low-gradient (values -0.002°C
≤ T1-T2 ≤ 0.002°C) differences are ±0.0068°C for SBE35RT-T1,±0.0067°C 
for SBE35RT-T2 and ±0.0052°C for T1-T2. The 95% confidence limits for 
the deep temperature residuals (where pressure ≥ 2000dbar) are ±0.00096°C 
for SBE35RT-T1, ±0.0020°C for SBE35RT-T2 and ±0.0018°C for T1-T2.

Minor complications impacted the temperature sensor data used for the
I06S cruise.

   * The SBE35RT sensor data was not available for stations 30 to 34
     due to the SBE35RT not being installed.

   * The SBE35RT sensor memory was partially full, and there are
     partial data reported for cast on station 9.

   * Early stations and station with bad weather had bottles fired
     on the fly, leading to some SBE35RT averaging periods outside of
     the intended depth.

The resulting affected sections of data have been coded and documented
in the quality code APPENDIX.



4.6  Conductivity Analysis

Laboratory calibrations of conductivity sensors were performed prior
to the cruise at the SeaBird Calibration Facility. Dates of laboratory
calibration are recorded on the underway sampling package table and
calibration documents are provided in the APPENDIX.

The pre-cruise laboratory calibration coefficients were used to
convert SBE4C frequencies to mS/cm conductivity values. Additional
ship-board calibrations were performed to correct sensor bias.
Corrections for both pressure and temperature sensors were finalized
before analyzing conductivity differences. Two independent metrics of
calibration accuracy were examined. At each bottle closure, the
primary and secondary conductivity were compared with each other. Each
sensor was also compared to conductivity calculated from check sample
salinities using CTD pressure and temperature.

The differences between primary and secondary temperature sensors were
used as filtering criteria to reduce the contamination of conductivity
comparisons by package wake. The coherence of this relationship is
shown in the following figure.


Fig. 13: Coherence of conductivity differences as a function of
         temperature differences.


Uncorrected conductivity comparisons are shown in figures Uncorrected
CBottle - C1 by station. through Uncorrected C1-C2 by station.


Fig. 14: Uncorrected C_Bottle - C1 by station.

Fig. 15: Uncorrected C_Bottle - C2 by station.

Fig. 16: Uncorrected C1-C2 by station.

Fig. 17: Corrected C_Bottle - C1 by station.

Fig. 18: Deep Corrected C_Bottle - C1 by station (Pressure >= 2000dbar).

Fig. 19: Corrected C_Bottle - C2 by station.

Fig. 20: Deep Corrected C_Bottle - C2 by station (Pressure >= 2000dbar).

Fig. 21: Corrected C1-C2 by station.

Fig. 22: Deep Corrected C1-C2 by station (Pressure >= 2000dbar).

Fig. 23: Corrected C_Bottle - C1 by pressure.

Fig. 24: Corrected C_Bottle - C2 by pressure.

Fig. 25: Corrected C1-C2 by pressure.


A functioning SBE4C sensor typically exhibit a predictable modeled
response. Offsets for each C sensor were determined using C_Bottle -
C_CTD differences in a deeper pressure range (500 or more dbars).
After conductivity offsets were applied to all casts, response to
pressure, temperature and conductivity were examined for each
conductivity sensor. The response model is second order with respect
to pressure, second order with respect to temperature, second order
with respect to conductivity and a first order with respect to time.
The functions used to apply shipboard calibrations are as follows.

Corrections made to all conductivity sensors are of the form:

   C_{cor} = C + cp_2 P^2 + cp_1 P + ct_2 T^2 + ct_1 T + cc_2 C^2 +
   cc_1 C + \text{Offset}

Salinity residuals after applying shipboard P/T/C corrections are
summarized in the following figures. Only CTD and bottle salinity data
with “acceptable” quality codes are included in the differences.
Quality codes and comments are published in the APPENDIX of this
report.


Fig. 26: Salinity residuals by station.

Fig. 27: Salinity residuals by pressure.

Fig. 28: Deep Salinity residuals by station (Pressure >= 2000dbar).


The 95% confidence limits for the mean low-gradient (values -0.002
mPSU ≤ T1-T2 ≤ 0.002 mPSU) differences are ±0.0538 mPSU for
salinity-C1SAL. The 95% confidence limits for the deep salinity
residuals (where pressure ≥ 2000dbar) are ±0.0317 mPSU for
salinity-C1SAL.

A number of issues affected conductivity and calculated CTD salinities
during this cruise.

   * Primary conductivity sensor (S/N: 2569) failed shortly after
     the bottom of cast 116/01. Inspection after recovery showed goo
     inside the cell.

   * Bottle salinity analysis was complicated due to problems with
     the two Autosals, leading to knock-on problems when attempting to
     calibrate conductivity against bottle salinity.

   * Salinity lab temperatures were unstable during the time of
     analysis for stations 134-142. Further details on lab temperature
     complications are outlined in the Salinity section of this
     report.

   * Early stations and station with bad weather had bottles fired
     on the fly.

The resulting affected sections of data have been coded and documented
in the quality code APPENDIX.



4.7  CTD Dissolved Oxygen

Laboratory calibrations of the dissolved oxygen sensors were performed
prior to the cruise at the SBE calibration facility. Dates of
laboratory calibration are recorded on the underway sampling package
table and calibration documents are provided in the APPENDIX.

The pre-cruise laboratory calibration coefficients were used to
convert SBE43 frequencies to µmol/kg oxygen values for acquisition
only. Additional shipboard fitting were performed to correct for the
sensors non-linear response. Corrections for pressure, temperature and
conductivity sensors were finalized before analyzing dissolved oxygen
data. The SBE43 sensor data were compared to dissolved O_2 check
samples taken at bottle stops by matching the down cast CTD data to
the up cast trip locations along isopycnal surfaces. CTD dissolved O_2
was then calculated using Clark Cell MPOD O_2 sensor response model
for Beckman/SensorMedics and SBE43 dissolved O_2 sensors. The residual
differences of bottle check value versus CTD dissolved O_2 values are
minimized by optimizing the SIO DO sensor response model coefficients
with a Levenberg-Marquardt non-linear least-squares fitting procedure.

The general form of the SIO DO sensor response model equation for
Clark cells follows Brown and Morrison [Mill82] and Owens [Owen85] SIO
models DO sensor secondary responses with lagged CTD data. In-situ
pressure and temperature are filtered to match the sensor responses.
Time constants for the pressure response (τ_p), a slow τ_{Tf}
and fast τ_{Ts} thermal response, package velocity τ_{dP},
thermal diffusion τ_{dT} and pressure hysteresis τ_h are fitting
parameters. Once determined for a given sensor, these time constants
typically remain constant for a cruise. The thermal diffusion term is
derived by low-pass filtering the difference between the fast response
T_s and slow response T_l temperatures. This term is intended to
correct non-linearity in sensor response introduced by inappropriate
analog thermal compensation. Package velocity is approximated by low-
pass filtering 1st-order pressure differences, and is intended to
correct flow-dependent response. Dissolved O_2 concentration is then
calculated:


              -                   P_h       -
             |               C_2 ————        |
O_2 {ml/l} = | C_1 • V_DO • e    5000  + C_3 | • ƒ_sat(T,P) •
             |                               |
              -                             -

                                                dO_c        dP
             (C_4 t_l + C_5 t_s + C_7 P_l + C_6 ———— + C_8 ———— + C_9 dT)
            e                                    dT         dTt


Where:

* O_2 ml/l Dissolved O_2 concentration in ml/l

* V_DO  Raw sensor output

* C_1 Sensor slope

* C_2 Hysteresis ronse coefficient

* C_3 Sensor offset

* f_sat ( T , P )|O2| saturation at T,P (ml/l)

* T In-situ temperature (°C)

* P In-situ pressure (decibars)

* P_h Low-pass filtered hysteresis pressure (decibars)

* T_l Long-ronse low-pass filtered temperature (°C)

* T_s Short-ronse low-pass filtered temperature (°C)

* P_l Low-pass filtered pressure (decibars)

* dO_c / dt Sensor current gradient (µamps/sec)

* dP/dt Filtered package velocity (db/sec)

* dT Low-pass filtered thermal diffusion estimate (T_s - T_l)

* C_4 - C_9 Ronse coefficients

CTD dissolved O_2 residuals are shown in the following figures O2
residuals by station. through Deep O2 residuals by station (Pressure
>= 2000dbar).


Fig. 29: O_2 residuals by station.

Fig. 30: O_2 residuals by pressure.

Fig. 31: Deep O_2 residuals by station (Pressure >= 2000dbar).


The standard deviations of 4.78 (µmol/kg) for all dissolved oxygen
bottle data values and 2.12 (µmol/kg) for deep dissolved oxygen values
are only presented as general indicators of the goodness of fit.
CLIVAR GO-SHIP standards for CTD dissolved oxygen data are < 1%
accuracy against on board Winkler titrated dissolved O_2 lab
measurements.

A number of complications arose with the acquisition and processing of
CTD dissolved oxygen data.

   * All SBE43 sensors used exhibited unusual amounts of noise and
     spikes throughout the cruise due to electrical problems

All compromised data signals were recorded and coded in the data
files. The bottle trip levels affected by the signals were coded and
are included in the bottle data comments section of the APPENDIX.

[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).




5.  SALINITY


PIs
   * Susan Becker

   * James Swift

Technicians
   * John Calderwood

   * Joseph Gum



5.1  Equipment and Techniques

Two Guildline Autosals located in salinity analysis room, an 8400B
(S/N 69-180) and an 8400A (S/N 57-526), were used for all salinity
measurements. The salinity analysis room for I06S was located in the
Climate Controlled Chamber, a refrigerator port and amidships between
the Computer Lab and Bioanalytical Lab. Both were serviced prior to
TGT366/I06S in San Diego and sent with other equipment in January. The
salinometer readings were logged on a computer using a LabView program
developed by Carl Mattson. The Autosal water bath temperature was set
to 21°C. The laboratory’s temperature was set and maintained to 20°C.
This is to ensure stabilize reading values and improve accuracy.
Salinity analyses were performed after samples had equilibrated to
laboratory temperature range of 20-21°C, usually 8 hours after
collection. The salinometer was standardized for each group of samples
analyzed (1 or 2 casts, up to 72 samples) using two bottles of
standard seawater: one at the beginning and end of each set of
measurements. The salinometer output was logged to a computer file.
The software prompted the analyst to flush the instrument’s cell and
change samples when appropriate. Between runs the water from the last
standard was left in the cell. For each calibration standard, the
salinometer cell was initially flushed 2 times before a set of
conductivity ratio reading was taken. For each sample, the salinometer
cell was initially flushed at least 2 times before a set of
conductivity ratio readings were taken.

IAPSO Standard Seawater Batch P-162 was used to standardize all casts.

   [image]



5.2  Sampling and Data Processing

The salinity samples were collected in 200 ml Kimax high-alumina
borosilicate bottles that had been rinsed at least three times with
sample water prior to filling. The bottles were sealed with custom-
made plastic insert thimbles and Nalgene screw caps. This assembly
provides very low container dissolution and sample evaporation. Prior
to sample collection, inserts were inspected for proper fit and loose
inserts replaced to insure an airtight seal. Laboratory temperature
was also monitored electronically throughout the cruise. PSS-78
salinity [UNESCO1981] was calculated for each sample from the measured
conductivity ratios. The offset between the initial standard seawater
value and its reference value was applied to each sample. Then the
difference (if any) between the initial and final vials of standard
seawater was applied to each sample as a linear function of elapsed
run time. The corrected salinity data was then incorporated into the
cruise database.



5.3  Narrative

Autosal 69-180 was used to process samples from the test cast,
underway, and the first two stations. Communication errors between
Labview and Autosal 69-180 occurred during processing of samples,
causing the Labview software to lose connection with the Autosal. The
issue was tracked down to the serial-to-USB converter, which had its
buffer settings set lower than expected. Once the buffer value was
fixed, the problem appeared to disappear. A red fleck was found in the
cell before the running of samples from station 3. The fleck is
suspected to be from red paint, or from the red rubber stopper used to
fill the top of the bottle. Autosals were subsequently switched from
69-180 to 57-526. Autosal 57-526 was used from station 3 to 55, with
its most notable problem being water being stuck in the manifold,
causing problems of sections of the cell not filling with water. This
water had to be cleared out multiple times during the cruise. At one
point after clearing the manifold of water the standard number drifted
by 40 units. After much head scratching and waiting it went back to
the previous standard range a few hours later. Autosal 57-526, being a
model 8400A, appeared to be more unstable with its standard numbers
between runs.

1882 salinity samples were taken. 1 sample was lost during measurement
due to sampler error. One bottle was broken during sampling.

[UNESCO1981] UNESCO 1981. Background papers and
             supporting data on the Practical Salinity Scale, 1978.
             UNESCO Technical Papers in Marine Science, No. 37 144.




6.  NUTRIENTS

PIs
   * Susan Becker

   * James Swift

Technicians
   * Susan Becker

   * Melissa Miller


6.1  Summary of Analysis

* 1888 samples from 55 CTD stations, plus 73 from the underway
  system

* The cruise started with new pump tubes and they were changed 2
  times, before stations 19 and 44.

* 3 sets of Primary/Secondary standards were made up over the course
  of the cruise.

* The cadmium column efficiency was checked periodically and ranged
  between 91%-100%.  The column was replaced if/when the efficiency
  dropped below 96%.



6.2  Equipment and Techniques

Nutrient analyses (phosphate, silicate, nitrate+nitrite, and nitrite)
were performed on a Seal Analytical continuous-flow AutoAnalyzer 3
(AA3). The methods used are described by Gordon et al [Gordon1992]
Hager et al. [Hager1972], and Atlas et al. [Atlas1971]. Details of
modification of analytical methods used in this cruise are also
compatible with the methods described in the nutrient section of the
updated GO-SHIP repeat hydrography manual (Becker et al., 2019, in
prep) [Becker 2019].



6.3  Nitrate/Nitrite Analysis

A modification of the Armstrong et al. (1967) [Armstrong1967]
procedure was used for the analysis of nitrate and nitrite. For
nitrate analysis, a seawater sample was passed through a cadmium
column where the nitrate was reduced to nitrite. This nitrite was then
diazotized with sulfanilamide and coupled with
N-(1-naphthyl)-ethylenediamine to form a red dye. The sample was then
passed through a 10mm flowcell and absorbance measured at 520nm. The
procedure was the same for the nitrite analysis but without the
cadmium column.

**REAGENTS**

Sulfanilamide
   Dissolve 10g sulfamilamide in 1.2N HCl and bring to 1 liter volume.
   Add 2 drops of 40% surfynol 465/485 surfactant. Store at room
   temperature in a dark poly bottle.

   Note: 40% Surfynol 465/485 is 20% 465 plus 20% 485 in DIW.

N-(1-Naphthyl)-ethylenediamine dihydrochloride (N-1-N)
   Dissolve 1g N-1-N in DIW, bring to 1 liter volume. Add 2 drops 40%
   surfynol 465/485 surfactant. Store at room temperature in a dark
   poly bottle. Discard if the solution turns dark reddish brown.

Imidazole Buffer
   Dissolve 13.6g imidazole in ~3.8 liters DIW. Stir for at least 30
   minutes to completely dissolve. Add 60 ml of CuSO4 + NH4Cl mix (see
   below). Add 4 drops 40% Surfynol 465/485 surfactant. Let sit
   overnight before proceeding. Using a calibrated pH meter, adjust to
   pH of 7.83-7.85 with 10% (1.2N) HCl (about 10 ml of acid, depending
   on exact strength). Bring final solution to 4L with DIW. Store at
   room temperature.

NH4Cl + CuSO4 mix
   Dissolve 2g cupric sulfate in DIW, bring to 100 m1 volume (2%).
   Dissolve 250g ammonium chloride in DIW, bring to 1l liter volume.
   Add 5ml of 2% CuSO4 solution to this NH4Cl stock. This should last
   many months.



6.4  Phosphate Analysis

Ortho-Phosphate was analyzed using a modification of the Bernhardt and
Wilhelms (1967) [Bernhardt1967] method. Acidified ammonium molybdate
was added to a seawater sample to produce phosphomolybdic acid, which
was then reduced to phosphomolybdous acid (a blue compound) following
the addition of dihydrazine sulfate. The sample was passed through a
10mm flowcell and absorbance measured at 820nm.

**REAGENTS**

Ammonium Molybdate H2SO4 sol’n
   Pour 420 ml of DIW into a 2 liter Ehrlenmeyer flask or beaker,
   place this flask or beaker into an ice bath. SLOWLY add 330 ml of
   conc H2SO4. This solution gets VERY HOT!! Cool in the ice bath.
   Make up as much as necessary in the above proportions.

   Dissolve 27g ammonium molybdate in 250ml of DIW. Bring to 1 liter
   volume with the cooled sulfuric acid sol’n. Add 3 drops of 15% DDS
   surfactant. Store in a dark poly bottle.

Dihydrazine Sulfate
   Dissolve 6.4g dihydazine sulfate in DIW, bring to 1 liter volume
   and refrigerate.



6.5  Silicate Analysis

Silicate was analyzed using the basic method of Armstrong et al.
(1967). Acidified 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.
The sample was passed through a 10mm flowcell and measured at 660nm.

**REAGENTS**

Tartaric Acid
   Dissolve 200g tartaric acid in DW and bring to 1 liter volume.
   Store at room temperature in a poly bottle.

Ammonium Molybdate
   Dissolve 10.8g Ammonium Molybdate Tetrahydrate in 1000ml dilute
   H2SO4. (Dilute H2SO4 = 2.8ml conc H2SO4 or 6.4ml of H2SO4 diluted
   for PO4 moly per liter DW) (dissolve powder, then add H2SO4) Add
   3-5 drops 15% SDS surfactant per liter of solution.

Stannous Chloride
   stock: (as needed)

   Dissolve 40g of stannous chloride in 100 ml 5N HCl. Refrigerate in
   a poly bottle.

   NOTE: Minimize oxygen introduction by swirling rather than shaking
   the solution. Discard if a white solution (oxychloride) forms.

   working: (every 24 hours) Bring 5 ml of stannous chloride stock to
   200 ml final volume with 1.2N HCl. Make up daily - refrigerate when
   not in use in a dark poly bottle.



6.6  Sampling

Nutrient samples were drawn into 30 ml polypropylene screw-capped
centrifuge tubes. The tubes and caps were cleaned with 10% HCl and
rinsed 2-3 times with sample before filling. Samples were analyzed
within 1-3 hours after sample collection, allowing sufficient time for
all samples to reach room temperature. The centrifuge tubes fit
directly onto the sampler.



6.8  Data Collection and Processing

Data collection and processing was done with the software (ACCE ver
7.04) provided with the instrument from Seal Analytical. After each
run, the charts were reviewed for any problems during the run, any
blank was subtracted, and final concentrations (micro moles/liter)
were calculated, based on a linear curve fit. Once the run was
reviewed and concentrations calculated a text file was created. That
text file was reviewed for possible problems and then converted to
another text file with only sample identifiers and nutrient
concentrations that was merged with other bottle data.



6.8  Standards and Glassware Calibration

Primary standards for silicate (Na2SiF6), nitrate (KNO3), nitrite
(NaNO2), and phosphate (KH2PO4) were obtained from Johnson Matthey
Chemical Co. and/or Fisher Scientific. The supplier reports purities
of >98%, 99.999%, 97%, and 99.999 respectively.

All glass volumetric flasks and pipettes were gravimetrically
calibrated prior to the cruise. The primary standards were dried and
weighed out to 0.1mg prior to the cruise. The exact weight was noted
for future reference. When primary standards were made, the flask
volume at 20C, the weight of the powder, and the temperature of the
solution were used to buoyancy-correct the weight, calculate the exact
concentration of the solution, and determine how much of the primary
was needed for the desired concentrations of secondary standard.
Primary and secondary standards were made up every 7-10days. The new
standards were compared to the old before use.

All the reagent solutions, primary and secondary standards were made
with fresh distilled deionized water (DIW).

Standardizations were performed at the beginning of each group of
analyses with working standards prepared every 10-12 hours from a
secondary. Working standards were made up in low nutrient seawater
(LNSW). One batch of LNSW was used on the cruise. LNSW was treated in
the lab. The water was first filtered through a 0.45 micron filter
then re-circulated for ~8 hours through a 0.2 micron filter, passed a
UV lamp and through a second 0.2 micron filter. The actual
concentration of nutrients in this water was empirically determined
during the standardization calculations.

The concentrations in micro-moles per liter of the working standards
used were:


                 - | N+N   | PO_4  | SIL  | NO_2
                   | (uM)  | (uM)  | (uM) | (uM)
                ———|———————|———————|——————|—————
                 0 | 0.0   | 0.0   | 0.0  | 0.0 
                ---+-------+-------+------+-----
                 3 | 15.50 | 1.2   | 60   | 0.50
                ---+-------+-------+------+-----
                 5 | 31.00 | 2.4   | 120  | 1.00
                ---+-------+-------+------+-----
                 7 | 46.50 | 3.6   | 180  | 1.50



6.9  Quality Control

All final data was reported in micro-moles/kg. NO^3, PO_4, and NO_2
were reported to two decimals places and SIL to one. Accuracy is based
on the quality of the standards the levels are:


               NO^3  | 0.05 µM (micro moles/Liter)
              -------+----------------------------
               PO_4  | 0.004 µM                   
              -------+----------------------------
               SIL   | 2-4 µM                     
              -------+----------------------------
               NO_2  | 0.05 µM                    
              

As is standard ODF practice, a deep calibration “check” sample was run
with each set of samples to estimate precision within the cruise. The
data are tabulated below.


            Parameter | Concentration (µM) | stddev 
           ———————————|————————————————————|————————
            NO^3      | 24.60              | 0.30   
           -----------+--------------------+--------
            PO_4      | 1.67               | 0.01   
           -----------+--------------------+--------
            SIL       | 51.1               | 0.3    


Reference materials for nutrients in seawater (RMNS) were also used as
a check sample run once a day. The RMNS preparation, verification, and
suggested protocol for use of the material are described by
[Aoyama2006] [Aoyama2007], [Aoyama2008], Sato [Sato2010] and Becker et
al. [Becker 2019]. RMNS batch CG was used on this cruise, with each
bottle being used once or twice before being discarded and a new one
opened. Data are tabulated below.


        Parameter | Concentration | stddev  | assigned conc 
        -         | (µmol/kg)     | -       | (µmol/kg)     
       ———————————|———————————————|—————————|———————————————
        NO^3      | 23.69         | 0.11    | 23.7          
       -----------+---------------+---------+---------------
        PO_4      | 1.70          | 0.007   | 1.70          
       -----------+---------------+---------+---------------
        Sil       | 56.3          | 0.2     | 56.4          
       -----------+---------------+---------+---------------
        NO_2      | 0.06          | 0.006   | 0.06          



6.10  Analytical Problems

No major analytical problems.

[Armstrong1967] Armstrong, F.A.J., Stearns, C.A., 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).

[Atlas1971] Atlas, E.L., Hager, S.W., Gordon, L.I., and
            Park, P.K., “A Practical Manual for Use of the Technicon
            AutoAnalyzer in Seawater Nutrient Analyses Revised,”
            Technical Report 215, Reference 71-22, p.49, Oregon State
            University, Department of Oceanography (1971).

[Aoyama2006] Aoyama, M., 2006: 2003 Intercomparison
             Exercise for Reference Material for Nutrients in Seawater
             in a Seawater Matrix, Technical Reports of the
             Meteorological Research Institute No.50, 91pp, Tsukuba,
             Japan.

[Aoyama2007] Aoyama, M., Susan B., Minhan, D., Hideshi,
             D., Louis, I. G., Kasai, H., Roger, K., Nurit, K., Doug,
             M., Murata, A., Nagai, N., Ogawa, H., Ota, H., Saito, H.,
             Saito, K., Shimizu, T., Takano, H., Tsuda, A., Yokouchi,
             K., and Agnes, Y. 2007. Recent Comparability of
             Oceanographic Nutrients Data: Results of a 2003
             Intercomparison Exercise Using Reference Materials.
             Analytical Sciences, 23: 1151-1154.

[Aoyama2008] Aoyama M., J. Barwell-Clarke, S. Becker, M.
             Blum, Braga E. S., S. C. Coverly,E. Czobik, I. Dahllof,
             M. H. Dai, G. O. Donnell, C. Engelke, G. C. Gong, Gi-Hoon
             Hong, D. J. Hydes, M. M. Jin, H. Kasai, R. Kerouel, Y.
             Kiyomono, M. Knockaert, N. Kress, K. A. Krogslund, M.
             Kumagai, S. Leterme, Yarong Li, S. Masuda, T. Miyao, T.
             Moutin, A. Murata, N. Nagai, G.Nausch, M. K. Ngirchechol,
             A. Nybakk, H. Ogawa, J. van Ooijen, H. Ota, J. M. Pan, C.
             Payne, O. Pierre-Duplessix, M. Pujo-Pay, T. Raabe, K.
             Saito, K. Sato, C. Schmidt, M. Schuett, T. M. Shammon, J.
             Sun, T. Tanhua, L. White, E.M.S. Woodward, P. Worsfold,
             P. Yeats, T. Yoshimura, A.Youenou, J. Z. Zhang, 2008:
             2006 Intercomparison Exercise for Reference Material for
             Nutrients in Seawater in a Seawater Matrix, Technical
             Reports of the Meteorological Research Institute No. 58,
             104pp.

[Bernhardt1967] 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).

[Gordon1992] Gordon, L.I., Jennings, J.C., Ross, A.A.,
             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).

[Hager1972] Hager, S.W.,  Atlas, E.L., Gordon L.I.,
            Mantyla, A.W., and Park, P.K., ” A comparison at sea of
            manual and autoanalyzer analyses of phosphate, nitrate,
            and silicate ,” Limnology and Oceanography, 17,pp.931-937
            (1972).

[Kerouel1997] Kerouel, R., Aminot, A., “Fluorometric
              determination of ammonia in sea and estuarine waters by
              direct segmented flow analysis.” Marine Chemistry, vol
              57, no. 3-4, pp. 265-275, July 1997.

[Sato2010] Sato, K., Aoyama, M., Becker, S., 2010. RMNS as
           Calibration Standard Solution to Keep Comparability for
           Several Cruises in the World Ocean in 2000s. In: Aoyama,
           M., Dickson, A.G., Hydes, D.J., Murata, A., Oh, J.R.,
           Roose, P., Woodward, E.M.S., (Eds.), Comparability of
           nutrients in the world’s ocean. Tsukuba, JAPAN: MOTHER
           TANK, pp 43-56.




7.  OXYGEN ANALYSIS

PIs
   * Susan Becker

   * James Swift

Technicians
   * Andrew Barna

   * Zac Anderson



7.1  Equipment and Techniques

Dissolved oxygen analyses were performed with an SIO/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 burette.

ODF used a whole-bottle modified-Winkler titration following the
technique of Carpenter [Carpenter1965] with modifications by
[Culberson1991] but with higher concentrations of potassium iodate
standard (~0.012 N), and thiosulfate solution (~55 g/L).

Pre-made liquid potassium iodate standards and reagent/distilled water
blanks were run every day (approximately every 3-4 stations), with
samples analysed within 24 hours of the last standard.



7.2  Sampling and Data Processing

A total of 1952 oxygen measurements were made, of which 1880 were
niskin samples and 72 were underway samples. Niskin samples were
collected soon after the rosette was secured on deck, either from
fresh niskins or immediately following CFC sampling.

Nominal 125 mL volume-calibrated biological oxygen demand (BOD) flasks
were rinsed 3 times with minimal agitation using a silicone draw tube,
then filled and allowed to overflow for at least 3 flask volumes,
ensuring no bubbles remained. Pickling reagents MnCl2 and NaI/NaOH (1
mL of each) were added via bottle-top dispensers to fix samples before
stoppering. Flasks were shaken twice (10-12 inversions) to assure
thorough dispersion of the precipitate - once immediately after
drawing and then again after 30-60 minutes.

Sample draw temperatures, measured with an electronic resistance
temperature detector (RTD) embedded in the draw tube, were used to
calculate umol/kg concentrations, and as a diagnostic check of bottle
integrity.

Niskin samples were analysed within 2-12 hours of collection, and the
data incorporated into the cruise database. Underway samples were
analysed within 96 hours of collection.

Thiosulfate normalities were calculated for each standardisation and
corrected to 20°C. The 20°C thiosulfate normalities and blanks were
plotted versus time and were reviewed for possible problems, and were
subsequently determined to be stable enough that no smoothing was
required.



7.3  Volumetric Calibration

Oxygen flask volumes were determined gravimetrically with degassed
deionised 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 volume is detected. The 10
mL Dosimat buret used to dispense standard iodate solution was
calibrated using the same method.



7.4  Standards

Liquid potassium iodate standards were prepared in 6 L batches and
bottled in sterile glass bottles at ODF’s chemistry laboratory prior
to the expedition. The normality of the liquid standard was determined
by calculation from weight. The standard was supplied by Alfa Aesar
and has a reported purity of 99.4-100.4%. All other reagents were
“reagent grade” and were tested for levels of oxidising and reducing
impurities prior to use.



7.5  Narrative

Cruise setup began on March 28th 2019 in Cape Town, South Africa.

The initial thiosulfate batch was discarded due to flaky material in
the solution that would not dissolve. The problem was pinpointed as an
improperly cleaned 4 L reagent jug. Subsequent thiosulfate batches
were made independently as needed throughout the cruise in a clean 1 L
reagent bottle.

During setup, it was discovered that many ODF oxygen standard bottles
were leaking slightly from around the sealed cap when opened, an
egregious standard was not used, but others were used as normal
throughout the cruise. No differences were noted in Thiosulfate
normality when any ODF standard was changed. Otherwise, setup ran
smoothly and the analysis rig was running, secured, and standardised
before leaving port on April 3rd.

Following a 5-day delay caused by a failed engine water pump, underway
samples were collected every 4 hours during the 8-day transit to the
first station.

Some slight stepping was seen during titration endpoints, usually
beginning after halfway through a sample run. This was caused by
fluctuation in UV lamp voltage and solved by power cycling the UV lamp
power supply. The power supply was temporarily swapped out with an
older spare. However, this was found to have the same issue but more
persistently, so the original power supply was reinstalled. This issue
had no impact on sample analysis quality.

Science was temporarily halted after station 45 for a medical
evacuation to Port Elizabeth, during which underway samples were
collected every 4 hours, and then again following a successful drop-
off until station 46 was reached and normal science activities
resumed.

An OSIL oxygen standard was run against the usual ODF oxygen standard
during the last standardisation of the cruise. The OSIL standard
resulted in thiosulfate normality within specification of the ODF
oxygen standard, which confirmed the leaking standard caps discovered
at the beginning of the cruise did not adversely impact the integrity
of the standards. The OSIL standardisation followed the same procedure
as normal with the exception of using an Eppendorf pipette to dispense
the standard.

The need for smoothing thiosulfate normality was considered separately
for each thiosulfate batch (3 in total). There was no drift or trend
observed in any of the batches, so no smoothing procedure was
performed.

[Carpenter1965] Carpenter, J. H., “The Chesapeake Bay
                Institute technique for the Winkler dissolved oxygen
                method,” Limnology and Oceanography, 10, pp. 141-143
                (1965).

[Culberson1991] Culberson, C. H., Knapp, G., Stalcup,
                M., Williams, R. T., and Zemlyak, F., “A comparison of
                methods for the deter mination of dissolved oxygen in
                seawater,” Repor t WHPO 91-2, WOCE Hydrographic
                Programme Office (Aug 1991).




8.  TOTAL ALKALINITY

PI
   * Andrew G. Dickson – Scripps Institution of Oceanography

Technicians
   * Manuel Belmonte

   * Wiley Wolfe



8.1  Total Alkalinity

The total alkalinity of a sea water sample is defined as the number of
moles of hydrogen ion equivalent to the excess of proton acceptors
(bases formed from weak acids with a dissociation constant K ≤10–4.5 at 
25°C and zero ionic strength) over proton donors (acids with K > 10–4.5) 
in 1 kilogram of sample.



8.2  Total Alkalinity Measurement System

Samples are dispensed using a Sample Delivery System (SDS) consisting
of a volumetric pipette, various relay valves, and two air pumps
controlled by LabVIEW 2012. Before filling the jacketed cell with a
new sample for analysis, the volumetric pipette is cleared of any
residual from the previous sample with the aforementioned air pumps.
The pipette is then rinsed with new sample and filled, allowing for
overflow and time for the sample temperature to equilibrate. The
sample bottle temperature is measured using a DirecTemp thermistor
probe inserted into the sample bottle and the volumetric pipette
temperature is measured using a DirecTemp surface probe placed
directly on the pipette. These temperature measurements are used to
convert the sample volume to mass for analysis.

Samples are analyzed using an open cell titration procedure using two
250 mL jacketed cells. One sample is undergoing titration while the
second is being prepared and equilibrating to 20°C for analysis. After
an initial aliquot of approximately 2.3-2.4 mL of standardized
hydrochloric acid (~0.1M HCl in ~0.6M NaCl solution), the sample is
stirred for 5 minutes while air is bubbled into it at a rate of 200
scc/m to remove any liberated carbon dioxide gas. A Metrohm 876
Dosimat Plus is used for all standardized hydrochloric acid additions.
After equilibration, ~19 aliquots of 0.035 ml are added. Between the
pH range of 3.5 to 3.0, the progress of the titration is monitored
using a pH glass electrode/reference electrode cell, and the total
alkalinity is computed from the titrant volume and e.m.f. measurements
using a non-linear least-squares approach ([Dickson2007]). An Agilent
34970A Data Acquisition/Switch Unit with a 34901A multiplexer is used
to read the voltage measurements from the electrode and monitor the
temperatures from the sample, acid, and room. The calculations for
this procedure are performed automatically using LabVIEW 2012.



8.3  Sample Collection

Samples for total alkalinity measurements were taken at all I06S
Stations (1-55). Three or four Niskin bottles at each station were
sampled twice for duplicate measurements except for stations where 24
or less Niskin bottles were sampled. Stations at which 24 or less
Niskin bottles were sample two or three Niskin bottles were sampled
twice for duplicate measurements Using silicone tubing, the total
alkalinity samples were drawn from Niskin bottles into 250 mL Pyrex
bottles, making sure to rinse the bottles and Teflon sleeved glass
stoppers at least twice before the final filling. A headspace of
approximately 3 mL was removed and 0.05 mL of saturated mercuric
chloride solution was added to each sample for preservation. After
sampling was completed, each sample’s temperature was equilibrated to
approximately 20°C using a Thermo Scientific Isotemp water bath.



8.4  Problems and Troubleshooting

On two occasions, during bad weather days, we shut down our total
alkalinity system and upon restarting the Alkalinity 2.9j program it
could not locate the running file to load the appropriate system
configurations or locate the running data file for I06S and log
subsequent data. Somehow the cruise file identifier was corrupted upon
shutdown or restart so the program could not load the appropriate
configurations. Luckily, the corrupted file identifier was noticed by
the lead operator and corrected to solve this issue. The second time the
source of this issue was not the corrupted file identifier and the actual
culprit was not found. This issue reverted the program to its default
configuration, but luckily the program was able to locate the data
file.  The operator was told to input all of the appropriate
configurations and was able to continue work as usual.

Throughout the cruise, glitches from the Sample Delivery System were
experienced at random. The Sample Delivery System program would freeze
drawing sample in Deliver Sample or Prepare Pipette mode and caused a
few sample bottles to be emptied. This resulted in 3 lost samples.
Also, during station 39 a shift in the Sample Delivery System’s
delivery volume was noticed causing smaller samples sizes to be
dispensed. No further samples were run until a calibration using a
manual pipette was performed to correct this issue.



8.5  Quality Control

Dickson laboratory Certified Reference Material (CRM) Batch 178 and
180 were used to determine the accuracy of the total alkalinity
analyses. The total alkalinity certified value for these batches are:

* Batch 178 2216.53 ± 0.61 μmol/kg (32;16)

* Batch 180 2224.47 ± 0.56 μmol/kg (30;15)

The cited uncertainties represent the standard deviation. Figures in
parentheses are the number of analyses made (total number of analyses;
number of separate bottles analyzed).

At least one reference material was analyzed at every I06S stations
resulting in 240 reference material analyses. On I09N, the measured
total alkalinity value for each batch is:

* Batch 178 2216.53± 2.25 μmol kg-1 (83) [mean ± std. dev. (n)]

* Batch 180 2224.00± 1.56 μmol kg-1 (157) [mean ± std. dev. (n)]

If greater than 24 Niskin bottles were sampled at a station, three or
four Niskin bottles on that station were sampled twice to conduct
duplicate analyses. If 24 or less Niskin bottles were sampled at a
station, two or three Niskins on that station were sampled twice for
duplicate analyses. The standard deviation for the duplicates measured
on I06S is:

Duplicate Standard Deviation ± 1.55 µmol kg–1 (143) [± std. dev. (n)]

The total alkalinity measurements for each I06S stations have been
compared to measurements taken from the neighboring I06S 2019
stations.

1209 total alkalinity values were submitted for I06S. Further volume
and dilution corrections need to be applied to this data and will not
be applied until onshore, therefore this data is to be considered
preliminary.




9.  DISSOLVED INORGANIC CARBON (DIC)

PI’s
   * Rik Wanninkhof (NOAA/AOML)

   * Richard A. Feely (NOAA/PMEL)

Technicians
   * 14. Patrick Mears (NOAA/AOML)


   * Andrew Collins (NOAA/PMEL)



9.1  Sample collection

Samples for DIC measurements were drawn (according to procedures
outlined in the PICES Publication, *Guide to Best Practices for Ocean
CO2 Measurements* [Dickson2007]) from Niskin bottles into 294 ml
borosilicate glass bottles using silicone tubing. The flasks were
rinsed once and filled from the bottom with care not to entrain any
bubbles, overflowing by at least one-half volume. The sample tube was
pinched off and withdrawn, creating a 6 ml headspace, followed by 0.16
ml of saturated HgCl_2 solution which was added as a preservative. The
sample bottles were then sealed with glass stoppers lightly covered
with Apiezon-L grease and were stored at room temperature for a
maximum of 12 hours.



9.2  Equipment

The analysis was done by coulometry with two analytical systems (AOML
3 and AOML 4) used simultaneously on the cruise. Each system consisted
of a coulometer (CM5015 UIC Inc) coupled with a Dissolved Inorganic
Carbon Extractor (DICE). The DICE system was developed by Esa Peltola
and Denis Pierrot of NOAA/AOML and Dana Greeley of NOAA/PMEL to
modernize a carbon extractor called SOMMA ([Johnson1985],
[Johnson1987], [Johnson1993], [Johnson1992], [Johnson1999]).

The two DICE systems (AOML 3 and AOML 4) were set up in a seagoing
container modified for use as a shipboard laboratory on the aft main
working deck of the R/V Thomas G Thompson.



9.3  DIC Analysis

In coulometric analysis of DIC, all carbonate species are converted to
CO_2 (gas) by addition of excess hydrogen ion (acid) to the seawater
sample, and the evolved CO_2 gas is swept into the titration cell of
the coulometer with pure air or compressed nitrogen, where it reacts
quantitatively with a proprietary reagent based on ethanolamine to
generate hydrogen ions. In this process, the solution changes from
blue to colorless, triggering a current through the cell and causing
coulometrical generation of OH^- ions at the anode. The OH^- ions
react with the H^+ and the solution turns blue again. A beam of light
is shone through the solution, and a photometric detector at the
opposite side of the cell senses the change in transmission. Once the
percent transmission reaches its original value, the coulometric
titration is stopped, and the amount of CO_2 that enters the cell is
determined by integrating the total change during the titration.



9.4  DIC Calculation

Calculation of the amount of CO2 injected was according to the CO2
handbook [DOE1994]. The concentration of CO2 ([CO2]) in the samples
was determined according to:


                        (Counts - Blank * Run Time) * K µmol/count
[CO_2] = Cal. Factor} * ——————————————————————————————————————————
                            pipette volume * density of sample


where Cal. Factor is the calibration factor, Counts is the instrument
reading at the end of the analysis, Blank is the counts/minute
determined from blank runs performed at least once for each cell
solution, Run Time is the length of coulometric titration (in
minutes), and K is the conversion factor from counts to micromoles.

The instrument has a salinity sensor, but all DIC values were
recalculated to a molar weight (µmol/kg) using density obtained from
the CTD's salinity. The DIC values were corrected for dilution due
to the addition of 0.12 ml of saturated HgCl_2 used for sample
preservation. The total water volume of the sample bottles was 305.55
ml (calibrated by Dana Greeley, AOML). The correction factor used for
dilution was 1.0004. A correction was also applied for the offset from
the CRM. This additive correction was applied for each cell using the
CRM value obtained at the beginning of the cell. The average (± SD)
correction was 5.5 ±1.21 µmol/kg for AOML 3 and 1.3 ± 1.53 µmol/kg
for AOML 4

The coulometer cell solution was replaced after 25 - 28 mg of carbon
was titrated, typically after 9 - 12 hours of continuous use. The
blanks ranged from 12-28.



9.5  Calibration, Accuracy, and Precision

The stability of each coulometer cell solution was confirmed three
different ways.

1. Gas loops were run at the beginning of each cell

2. CRM’s supplied by Dr. A. Dickson of SIO, were measured near the
   beginning; middle and end of each cell

3. Duplicate samples from the same niskin were run throughout the
   life of the cell solution.

Each coulometer was calibrated by injecting aliquots of pure CO2
(99.999%) by means of an 8-port valve [Wilke1993] outfitted with two
calibrated sample loops of different sizes (~1ml and ~2ml). The
instruments were each separately calibrated at the beginning of each
cell with a minimum of two sets of these gas loop injections.

The accuracy of the DICE measurement is determined with the use of
standards (Certified Reference Materials (CRMs), consisting of
filtered and UV irradiated seawater) supplied by Dr. A. Dickson of
Scripps Institution of Oceanography (SIO). The CRM accuracy is
determined manometrically on land in San Diego and the DIC data
reported to the data base have been corrected to this batch 178 CRM
value. The CRM certified value for this batch is 1952.62 µmol/kg.

The precision of the two DICE systems can be demonstrated via the
replicate samples. Approximately 11.3% of the niskins sampled were
duplicates taken as a check of our precision. These replicate samples
were interspersed throughout the station analysis for quality
assurance and integrity of the coulometer cell solutions. The average
difference for these duplicates on AOML 3 and 4 respectively are 1.45
µmol/kg and 1.45 µmol/kg - No major systematic differences between
the replicates were observed.

The pipette volume was determined by taking aliquots of distilled
water from volumes at known temperatures. The weights with the
appropriate densities were used to determine the volume of the
pipettes.

Calibration data during this cruise:


 UNIT  | L Loop   | S Loop   | Pipette    | Ave CRM1       | Std Dev | Dupes 
———————|——————————|——————————|————————————|————————————————|—————————|———————
 AOML3 | 1.002012 | 1.002196 | 28.003 ml  | 1946.80, N= 41 | 1.21    | 1.45  
-------+----------+----------+------------+----------------+---------+-------
 AOML4 | 1.00442  | 1.00420  | 29.3888 ml | 1952.36, N= 35 | 1.53    | 1.45  



9.7  Underway DIC Samples

Underway samples were collected from the flow thru system in the Hydro
Lab during transit. Discrete DIC samples were collected approximately
every 4 hours with duplicates every fourth sample. A total of 89
discrete DIC samples including duplicates were collected while
underway. The average difference for replicates of underway DIC
samples was 1.18 µmol/kg and the average standard deviation was 0.91.



9.7  Summary

The overall performance of the analytical equipment was good during
the cruise. On two occasions the air supply was unexpectedly reduced
to the van.  Steps were taken to prevent any issues with samples being
run.    During the running of samples for station 8, an unknown issue
prevented the pipette from fully filling during several bottle runs.
It is unknown as to what caused this to occur however, it passed
without discovering the cause.

Including the duplicates, 1,561 samples were analyzed from 55 CTD
casts for dissolved inorganic carbon (DIC) which means that there is a
DIC value for approximately 82% of the niskins tripped. The DIC data
reported to the database directly from the ship are to be considered
preliminary until a more thorough quality assurance can be completed
shore side.

[DOE1994] DOE (U.S. Department of Energy). (1994). *Handbook
          of Methods for the Analysis of the Various Parameters of the
          Carbon Dioxide System in Seawater*. Version 2.0.
          ORNL/CDIAC-74. Ed. A. G. Dickson and C. Goyet. Carbon
          Dioxide Information Analysis Center, Oak Ridge National
          Laboratory, Oak Ridge, Tenn.

[Dickson2007] Dickson, A.G., Sabine, C.L. and Christian,
              J.R. (Eds.), (2007): *Guide to Best Practices for Ocean
              CO2 Measurements*. PICES Special Publication 3, 191 pp.

[Feely1998] Feely, R.A., R. Wanninkhof, H.B. Milburn, C.E.
            Cosca, M. Stapp, and P.P. Murphy (1998): *“A new automated
            underway system for making high precision pCO2
            measurements aboard research ships.”* Anal. Chim. Acta,
            377, 185-191.

[Johnson1985] Johnson, K.M., A.E. King, and J. McN.
              Sieburth (1985): *“Coulometric DIC analyses for marine
              studies: An introduction.”* Mar. Chem., 16, 61-82.

[Johnson1987] 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.

[Johnson1992] 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.

[Johnson1993] 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.

[Johnson1999] Johnson, K.M., Körtzinger, A.; Mintrop,
              L.; Duinker, J.C.; and Wallace, D.W.R. (1999).
              *Coulometric total carbon dioxide analysis for marine
              studies: Measurement and interna consistency of underway
              surface TCO2 concentrations.* Marine Chemistry
              67:123–44.

[Lewis1998] Lewis, E. and D. W. R. Wallace (1998) Program
            developed for CO2 system calculations. Oak Ridge, Oak
            Ridge National Laboratory.
            http://cdiac.ornl.gov/oceans/co2rprt.html

[Wilke1993] 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




10.  DISCRETE PH ANALYSES (TOTAL SCALE)

PI
   * Dr. Andrew Dickson

Technicians
   * Manuel Belmonte

   * Kayleen Fulton



10.1  Sampling

Samples were collected in 250 mL Pyrex glass bottles and sealed using
grey butyl rubber stoppers held in place by aluminum-crimped caps.
Each bottle was rinsed two times and allowed to overflow by one half
additional bottle volume. Prior to sealing, each sample was given a 1%
headspace and poisoned with 0.02% of the sample volume of saturated
mercuric chloride (HgCl_2). Samples were collected only from Niskin
bottles that were also being sampled for both total alkalinity and
dissolved inorganic carbon in order to completely characterize the
carbon system. Additionally, duplicate samples were collected from all
stations for quality control purposes.



10.2  Analysis

pH was measured spectrophotometrically on the total hydrogen scale
using an Agilent 8453 spectrophotometer and in accordance with the
methods outlined by Carter et al., 2013. [Carter2013]. A Kloehn V6
syringe pump was used to autonomously fill, mix, and dispense sample
through the custom 10cm flow-through jacketed cell. A Thermo Fisher
Isotemp recirculating water bath was used to maintain the cell
temperature at 25.0°C during analyses, and a YSI 4600 precision
thermometer and probe were used to monitor and record the temperature
of each sample during the spectrophotometric measurements. Purified
meta-cresol purple (mCP) was the indicator used to measure the
absorbance of light measured at two different wavelengths (434 nm, 578
nm) corresponding to the maximum absorbance peaks for the acidic and
basic forms of the indicator dye. A baseline absorbance was also
measured and subtracted from these wavelengths. The baseline
absorbance was determined by averaging the absorbances from 725-735nm.
The ratio of the absorbances was then used to calculate pH on the
total scale using the equations outlined in Liu et al., 2011
[Liu2011]. The salinity data used was obtained from the salinity
analysis conducted on board.



10.3  Reagents

The mCP indicator dye was made up to a concentration of approximately
2.0mM and a total ionic strength of 0.7 M. A total of two batches were
used during I06S. The pHs of these batches were adjusted with 0.1 mol
kg^-1 solutions of HCl and NaOH (in 0.6 mol kg^-1 NaCl background) to
approximately 7.7, measured with a pH meter calibrated with NBS
buffers. The indicator was obtained from Dr. Robert Byrne at the
University of Southern Florida and was purified using the flash
chromatography technique described by Patsavas et al., 2013.
[Patsavas2013].



10.4  Data Processing

An indicator dye is itself an acid-base system that can change the pH
of the seawater to which it is added. Therefore, it is important to
estimate and correct for this perturbation to the seawater’s pH for
each batch of dye used during the cruise. To determine this
correction, multiple bottles from each station were measured twice,
once with a single addition of indicator dye and once with a double
addition of indicator dye. The measured absorbance ratio (R) and an
isosbestic absorbance (A_{\text{iso}}) were determined for each
measurement, where:


                           A_578 - A_base
                       R = ——————————————
                           A_434 - A_base

and

                     A_iso = A_488 - A_base


The change in R for a given change in A_iso, ∆R/∆A_iso, was then 
plotted against the measured R-value for the normal amount of dye 
and fitted with a linear regression. From this fit the slope and y-
intercept (b and a respectively) are determined by:

                      ∆R/∆A_iso} = bR + a

From this the corrected ratio (R') corresponding to the measured
absorbance ratio if no indicator dye were present can be determined
by:

                     R' = R - A_iso(bR + a)



10.5  Problems and Troubleshooting

Throughout the course of the cruise the pH spectrophotometric system
performed optimally. After a bad weather break and upon start up of
the system the operator noticed the system’s inability to yield
repeatable values for the same sea water source. The lead technician
was able to diagnose that the tungsten and deutrium bulbs in the
Agilent 8453 spectophotometer had burned out and a quick replacement
of these bulbs solved this issue without affecting any sample
measurements.



10.6  Standardization/Results

The precision of the data was assessed from measurements of duplicate
analyses, replicate analyses (two successive measurements on one
bottle), and certified reference material (CRM) Batch 180 (provided by
Dr. Andrew Dickson, UCSD). Three or four duplicates and one or two
replicate measurements were performed on every station when at least
twenty-four Niskins were sampled. If less than twenty-four Niskins
were sampled, only two or three duplicates and one replicate
measurement were performed. CRMs were measured at the beginning and
ending of each day.

The precision statistics for I06S are:


            Duplicate precision   | ± 0.0099 (n=97)       
            ----------------------+-----------------------
            Replicate precision   | ± 0.0005 (n=49)       
            ----------------------+-----------------------
            B180                  | 7.8828 ± 0.0017 (n=56)
            ----------------------+-----------------------
            B180 within-bottle SD | ± 0.0007 (n=56)       


1449 pH values were submitted for I06S. Additional corrections will
need to be performed and these data should be considered preliminary
until a more thorough analysis of the data can take place on shore.

[Carter2013] Carter, B.R., Radich, J.A., Doyle, H.L., and
             Dickson, A.G., “An Automated Spectrometric System for
             Discrete and Underway Seawater pH Measurements,”
             Limnology and Oceanography: Methods, 2013.

[Liu2011] Liu, X., Patsavas, M.C., Byrne R.H., “Purification
          and Characterization of meta Cresol Purple for
          Spectrophotometric Seawater pH Measurements,” Environmental
          Science and Technology, 2011.

[Patsavas2013] Patsavas, M.C., Byrne, R.H.,  and Liu X.
               “Purification of meta-cresol purple and cresol red by
               flash chromatography: Procedures for ensuring accurate
               spectrophotometric seawater pH measurements,” Marine
               Chemistry, 2013.




11.  CFC-11, CFC-12, CFC-113, and SF_6

PIs
   * Dong-Ha Min (University of Texas (Austin))

Analysts
   * David Cooper

   * Mark Lopez

   * Garrett Walsh


Samples for the analyses of the dissolved chlorofluorocarbons (CFCs,
freons) F11 and F12, sulfur hexafluoride (SF6) and nitrous oxide (N2O)
were collected and analyzed during TN366. Seawater samples were taken
from all casts, with full profiles generally taken from alternating
casts and strategically determined bottles sampled from the remaining
casts. These measurements are complemented by periodic measurements of
air samples. Seawater samples were drawn from 10 liter Niskin bottles.
Samples for CFC and SF6 were the first samples drawn, taking care to
check the integrity of the sample and coordinate the sampling analysts
to minimize any time between the initial opening of each bottle and
the completion of sample drawing. To minimize contact with air, the
CFC samples were drawn directly through the stopcocks of the Niskin
bottles into 250 ml precision glass syringes. Syringes were rinsed and
filled via three-way plastic stopcocks. The syringes were subsequently
held at 0-5 degrees C until 30 minutes before being analyzed.  At that
time, the syringe was placed in a bath of surface seawater heated at
approximately 30 degrees C. For atmospheric sampling, a ~90 m length
of 3/8” OD Dekaron tubing was run from the main lab to the bow of the
ship. A flow of air was drawn through this line into the main
laboratory using an air-cadet pump. The air was compressed in the
pump, with the downstream pressure held at ~1.5 atm. using a
backpressure regulator. A tee allowed a flow (100 ml min-1) of the
compressed air to be directed to the gas sample valves of the CFC
analytical systems, while the bulk flow of the air (>7 l min-1) was
vented through the backpressure regulator.  Analysis of bow air was
performed at several locations along the cruise track. Approximately
five measurements were made at each location to increase the
precision. Atmospheric data were not submitted to the database, but
were found to be in excellent agreement with current global databases.

Concentrations of CFC-1l, CFC-12, SF6 and N2O in air samples, seawater
samples and gas standards were measured by shipboard electron capture
gas chromatography (ECD-GC) using techniques described by Bullister
and Wisegarver (2008). This method has been modified with the addition
of an extra ECD to accommodate N2O analysis.  For seawater analyses,
water was transferred from a glass syringe to a glass-sparging chamber
(~200 ml). The dissolved gases in the seawater sample were extracted
by passing a supply of CFC-free purge gas through the sparging chamber
for a period of 6 minutes at 120 - 140 ml/min. Water vapor was removed
from the purge gas by passage through a Nafion drier, backed up by a
18 cm long, 3/8” diameter glass tube packed with the desiccant
magnesium perchlorate. The sample gases were concentrated on a cold-
trap consisting of a 1/16” OD stainless steel tube with a ~5 cm
section packed tightly with Porapak Q (60-80 mesh), a 22 cm section
packed with Carboxen 1004 and a 2.5 cm section packed with molecular
sieve MS5A. A neslab cryocool was used to cool the trap, to below
-50°C.  After 6 minutes of purging, the trap was isolated, and it was
heated electrically to ~150°C. The sample gases held in the trap were
then injected onto a precolumn (~60 cm of 1/8” O.D. stainless steel
tubing packed with 80-100 mesh Porasil B, held at 80°C) for the
initial separation of CFC-12 and CFC-11 from later eluting peaks.
After the F12 had passed from the pre-column through the second pre-
column (22 cm of 1/8” O.D. Stainless steel tubing packed with
Molecular Sieve 5A, 100/120 mesh) and into the analytical column #1
(~170 cm of 1/8” OD stainless steel tubing packed with MS5A and held
at 80°C) the outflow from the first precolumn was diverted to the
second analytical column (~150 cm 1/8” OD stainless steel tubing
packed with Carbograph 1AC, 80-100 mesh, held at 80°C). After F11 had
passed through the first precolumn, the flow was diverted to a third
analytical column (1/8” stainless steel tube with 30cm Molecular Sieve
5A, 60/80 mesh) for N2O analysis. The first pre-column was then
backflushed and vented. The first two analytical columns and precolumn
1 were held isothermal at 80 degrees C in an Agilent (HP) 6890N gas
chromatograph with two electron capture detectors (250°C). The third
analytical column and second pre-column were held at 160C in a
Shimadzu GC-8A gas chromatogram. The ECD in the Shimadzu was held at
250C.

The analytical system was calibrated using a blended standard gas
(seawater ratio, PMEL 464568), with further reference to a second
atmospheric ratio standard (PMEL 72615). Gas sample loops of known
volume were thoroughly flushed with standard gas and injected into the
system. The temperature and pressure was recorded so that the amount
of gas injected could be calculated. The procedures used to transfer
the standard gas to the trap, precolumn, main chromatographic column,
and EC detector were similar to those used for analyzing water
samples. Four sizes of gas sample loops were used. Multiple injections
of these loop volumes could be made to allow the system to be
calibrated over a relatively wide range of concentrations. Air samples
and system blanks (injections of loops of CFC-free gas) were injected
and analyzed in a similar manner. The typical analysis time for
seawater, air, standard or blank samples was ~12 minutes.
Concentrations of the CFCs in air, seawater samples, and gas standards
are reported relative to the SIO98 calibration scale (e.g. Bullister
and Tanhua, 2010). Concentrations in air and standard gas are reported
in units of mole fraction CFC in dry gas, and are typically in the
parts per trillion (ppt) range. Dissolved CFC concentrations are given
in units of picomoles per kilogram seawater (pmol kg-1). CFC
concentrations in air and seawater samples were determined by fitting
their chromatographic peak areas to multi-point calibration curves,
generated by injecting multiple sample loops of gas from a working
standard (PMEL cylinder 464568) into the analytical instrument. The
response of the detector to the range of moles of CFC passing through
the detector remained relatively constant during the cruise. Full-and
partial-range calibration curves were run several times during the
cruise. Single injections of a fixed volume of standard gas at one
atmosphere were run much more frequently (at intervals of ~90 minutes)
to monitor short-term changes in detector sensitivity.

The purging efficiency of the stripper was estimated by re-purging a
high-concentration water sample and measuring this residual signal. At
a flow rate of 120 cc min -1 for 6 minutes, the purging efficiency for
SF6 and F12 was greater than 99%, the efficiency for F11 was about
99%. The purging efficiency for N2O was about 95%, but subject to some
degree of variability due to changes in flow rate and purging
temperature. Although correction is made for this variability, N2O
data from stations 1-22 were rather more compromised than subsequent
data.

Results of 1461 seawater samples are reported from 55 stations, with
data for SF6, F12 and F11. Additional data for N2O will likely be
submitted after further post-cruise quality control. Duplicates were
taken from 32 stations to estimate precision and run variability
tests. Low-level samples were selected from deep casts and higher
level (surface) samples were mostly taken from the ship’s underway
sampling system. From the surface samples, we calculate the average
deviation to be less than 0.5% from the mean of the pairs for F12, F11
and N2O measurements, and 1.6% from the mean for SF6 measurements.
Deviation from the mean of pairs from deeper samples averaged less
than 2% (or 0.01 pM) from the mean for F12 and F11 and approximately
0.04 fM for SF6. Due to the exceedingly low levels of SF6 present in
deeper water, accurate estimates of precision are not possible. A very
small number of additional water samples had anomalous SF6 or CFC
concentrations relative to adjacent samples. These samples occurred
sporadically during the cruise and were not clearly associated with
other features in the water column (e.g., anomalous dissolved oxygen,
salinity, or temperature features).


References 

Bullister, J.L. and T. Tanhua. 2010. Sampling and Measurement of 
    Chlorofluorocarbons and Sulfur Hexafluoride in Seawater. In: The 
    GO-SHIP Repeat Hydrography Manual: A Collection of Expert Reports 
    and Guidelines. IOCCP Report No. 14, ICPO Publication series No. 
    134, Version 1. Bullister, J.L. and D.P. Wisegarver. 2008. The 
    shipboard analysis of trace levels of sulfur hexafluoride, 
    chlorofluorocarbon-11 and chlorofluorocarbon-12 in seawater. 
    Deep-Sea Res. I, v. 55, pp. 1063-1074.




12.  DISSOLVED ORGANIC CARBON, TOTAL ORGANIC CARBON, DISSOLVED NITROGEN 
     AND TOTAL NITROGEN

PI
   * Dennis Hansell (UM)

Technician
   * Chelsi Lopez

Analysts
   * Lillian Custals

   * Chelsi Lopez

Support
   NSF


12.1  Project Goals

The goal of the DOM project is to evaluate dissolved organic carbon
(DOC), total organic carbon (TOC), total nitrogen (TN) and total
dissolved nitrogen (TDN) concentrations along the I06S zonal transect.


12.2  Sampling

DOC profiles were taken from approximately every two out of three
stations from 24 of 36 niskin bottles ranging the full depth of the
water column (32 of 54 stations; ~768 DOC/TN samples). DOC samples
were passed through an inline filter holding a combusted GF/F filter
attached directly to the Niskin for all depths collected. This was
done to eliminated particles larger than 0.7 µm from the sample. To
reduce contamination by the filter or filter holder, a new filter and
holder was used after 12 samples were collected through it. Total
organic carbon (TOC) samples were collected from 19 of 36 depths per
station, approximately at all depths deeper than 250 meters (32 of 54
stations; ~608 TOC/TDN samples). Though previous work has suggested
that DOC at depth is equivalent to TOC (or whole water samples taken
from the niskin, without the need for inline filtration), we aimed to
ensure that this assumption is valid by collecting both whole water
(TOC) and filtered water (DOC) during this cruise. All samples were
rinsed 3 times with about 5 mL of seawater and collected into
combusted 40 mL glass EPA vials. Samples were fixed with 100 µL of 4N
Hydrochloric acid and stored at room temperature on board. Samples
were shipped back to University of Miami for analysis via high
temperature combustion on Shimadzu TOC-V or TOC L analyzers.

Sample Vials were prepared before the cruise by combustion at 450°C
for 12 hours to remove any organic matter.
   Vial caps were cleaned by soaking in DI water overnight, followed
   by a 3 times rinse with DI water and left out to dry.

Sampling goals for this cruise were to continue high resolution, long
term monitoring of DOC distribution throughout the water column, in
order to help better understand biogeochemical cycling in global
oceans.



12.3  Standard Operating Procedure for DOC Analyses- Hansell Lab UM

DOC samples will be analyzed via high temperature combustion using a
Shimadzu TOC-V or Shimadzu TOC-L at an in shore based laboratory at
the University of California, Santa Barbara. The operating conditions
of the Shimadzu TOC-V have been slightly modified from the
manufacturer’s model system. The condensation coil has been removed
and the headspace of an internal water trap was reduced to minimize
the system’s dead space. The combustion tube contains 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. CO_2 free
carrier gas is produced with a Whatman® gas generator [Carlson2010].
Samples are drawn into a 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 are injected into a combustion tube heated
to 680°C. The resulting gas stream is passed though several water and
halide traps, including an added magnesium perchlorate trap. The CO2
in the carrier gas is analyzed with a non-dispersive infrared detector
and the resulting peak area is integrated with Shimadzu
chromatographic software. Injections continue until the at least three
injections meet the 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 is essential to minimize
the machine blanks. After conditioning, the system blank is assessed
with UV oxidized low carbon water. The system response is standardized
daily with a four-point calibration curve of potassium hydrogen
phthalate solution in LCW. All samples are systematically referenced
against low carbon water and deep Sargasso Sea (2600 m) or Santa
Barbara Channel (400 m) reference waters and surface Sargasso Sea or
Santa Barbara Channel sea water every 6 – 8 analyses [Hansell1998].
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). Daily reference waters were calibrated
with DOC CRM provided by D. Hansell (University of Miami;
[Hansell2005]).



12.4  DOC calculation

             average sample area - average machine blank area
       µMC = ————————————————————————————————————————————————
                          slope of std curve



12.5  Standard Operating Procedure for TN/TDN analyses- Hansell Lab UM

TN/TDN samples were analyzed via high temperature combustion using a
Shimadzu TOC-V with attached Shimadzu TNM1 unit at an 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 headspace 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. Carrier gas was
produced with a Whatman® gas generator [Carlson2010] and ozone was
generated by the TNM1 unit at 0.5L/min flow rate. Three to five
replicate 100 µl of sample were injected at 130mL/min flow rate into
the combustion tube heated to 680°C, where the TN in the sample was
converted to nitric oxide (NO). The resulting gas stream was passed
through an electronic dehumidifier. The dried NO gas then reacted with
ozone producing an excited chemiluminescence NO_2 species [Walsh1989]
and the fluorescence signal was detected with a Shimadzu TNMI
chemiluminescence detector. The resulting peak area was integrated
with Shimadzu chromatographic software. Injections continue until at
least three injections meet the 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 nitrogen water and deep seawater was essential to minimize the
machine blanks. After conditioning, the system blank was assessed with
UV oxidized low nitrogen water. The system response was standardized
daily with a four-point calibration curve of potassium nitrate
solution in blank water. All samples were systematically referenced
against low nitrogen water and deep Sargasso Sea reference waters
(2600 m) and surface Sargasso Sea water every 6 – 8 analyses
[Hansell1998]. Daily reference waters were calibrated with deep CRM
provided by D. Hansell (University of Miami; [Hansell2005]).

Dissolved organic nitrogen (DON) concentrations are calculated as the
difference between TDN and DIN. Samples with less than 10 µmol/kg DIN
are most reliable estimates of DON.


              average sample area - average machine blank area
        µMN = ————————————————————————————————————————————————
                           slope of std curve


[Carlson2010] Carlson, C. A., D. A. Hansell, N. B.
              Nelson, D. A. Siegel, W. M. Smethie, S. Khatiwala, M. M.
              Meyers and E. Halewood 2010. Dissolved organic carbon
              export and subsequent remineralization in the
              mesopelagic and bathypelagic realms of the North
              Atlantic basin. Deep Sea Research II, 57: 1433-1445.

[Hansell1998] Hansell, D.A. and C.A. Carlson 1998. Deep
              ocean gradients in the concentration of dissolved
              organic carbon. Nature, 395: 263-266.

[Hansell2005] Hansell, D.A. 2005  Dissolved Organic
              Carbon Reference Material Program.  EOS, 35:318-319.

[Walsh1989] Walsh, T.W., 1989.  Total dissolved nitrogen
            in seawater: a new high-temperature combustion method and
            a comparison with photo-oxidation. Mar. Chem., 26:295-311.




13.  CARBON ISOTOPES IN SEAWATER (14/13C)

PI
   * Ann McNichol (WHOI)

Technician
   * Chelsi Lopez

A total of 432 samples were collected from stations collected along
the I06S transect. 32 samples each were taken from 17 of 54 stations,
approximately every fourth station. Samples were collected in 500 mL
airtight glass bottles. Using silicone tubing, the flasks were rinsed
3 times with seawater from the surface niskin. While keeping the
tubing at the bottom of the flask, the flask was filled and flushed by
allowing it to overflow 1.5 times its volume. Once the sample was
taken, about 10 mL of water was removed to create a headspace and 100
µL of saturated mercuric chloride solution was added to the sample. To
avoid contamination, gloves were used when handling all sampling
equipment and plastic bags were used to cover any surface where
sampling or processing occurred.

After each sample was taken, the glass stoppers and ground glass joint
were dried and Apiezon-M grease was applied to ensure an airtight
seal. Stoppers were secured with a large rubber band wrapped around
the entire bottle. Samples were stored in AMS crates in the ship’s dry
laboratory. Samples were shipped to WHOI for analysis.

The radiocarbon/DIC content of the seawater (DI14C) is measured by
extracting the inorganic carbon as CO2 gas, converting the gas to
graphite and then counting the number of 14C atoms in the sample
directly using an accelerated mass spectrometer (AMS).

Radiocarbon values will be reported as 14C using established
procedures modified for AMS applications. The 13C/12C of the CO2
extracted from seawater is measured relative to the 13C/12C of a CO2
gas standard calibrated to the PDB standard using and isotope radio
mass spectrometer (IRMS) at NOSAMS.




14.  LADCP

PI
   * Dr. Andreas Thurnherr

Cruise Participant
   * Benjamin Musci


LADCP was collected during full depth CTD casts at all stations by
Benjamin Musci. Quality control, preliminary processing, and post-
processing for horizontal and vertical velocity was made on board by
Benjamin Musci. Approximately every 3 casts data was sent to Andreas
Thurnherr for further QC.



14.1  LADCP system configuration

An upward-looking (UL) and a downward-looking (DL) ADCP, and a
rechargeable battery, were affixed to the rosette using custom
brackets (Figure 1 and 2). The UL instrument was positioned ~5 inches
over the top rosette ring while the DL instrument was positioned
between Niskin bottles 4 and 6 and affixed through the brackets to one
of the rosette bottom cross bars. The transducers on the DL were about
5 inches above the bottom ring of the rosette.

An external magnetometer/accelerometer package (independent
measurement package; IMP) was installed inside the Teledyne RDI WHM300
UL ADCP (SN: 12734) to collect additional pitch, roll and heading
data. A star cable was used to connect both UL and DL ADCPs to the
battery and deck/connection cables.

While on deck, two communications and one power cable ran from the aft
wet lab to the staging bay where the CTD package rested on a pallet
while in transit between stations. One of the power cables connected
the battery to a battery charger while the second power cable
connected the ADCPs through the star cable to a power supply. The
communications cable connected the ADCPS to a MAC computer via a USB
serial adapter which was used for communications to the instrument and
data download. The LADCP acquisitions computer clock was synced to the
master clock via the ship network system and set to UTC.

Three different ADCP instruments were used during the course of the
cruise, two of which were always deployed on the Rosette. The initial
set-up consisted of the Teledyne RDI WHM150 (S/N:24544) as DL and a
Teledyne RDI WHM300 (S/N:12734) as the UL. An alternative UL, another
Teledyne RDI WHM300 (S/N:24477), was also provided and would be used
heavily. Two battery packages were used during the course of the
cruise, a Deepsea Power and Light SB 48 V/16 A (S/N: 01283) and
another Deepsea Power and Light SB 48 V/16 A (S/N: N/A). All
instruments were set up to record velocity data with 8 m bins and zero
blanking distance. Staggered pinging was used to avoid previous ping
interference.



14.2  Problems/Setup changes

Several issues arose during the course of the cruise, with some
compromising data quality, although data is available for all casts on
the cruise. Independent issues concerning the CTD also occurred, which
negatively affected LADCP data quality for numerous casts.

* Station 1: Due to DL vertical velocity data issues during the test
  cast, the primary UL (SN:12734) was swapped with the alternative UL
  (SN: 24477). The vertical velocity residuals in the DL were
  correlated with distance from the instrument, and DC-DC converter in
  the Ras-Pi in the UL was thought to be the culprit.

No IMP for stations 1-9.

* Station 2: The CTD lost power at some point during the bottom
  portion of the downcast. It was restarted during the cast, so 2 CTD
  (.cnv) files were created, which must be stitched together manually
  for processing.

* Station 5: “Long-ish gap” (on the order of 10’s of seconds)
  warnings became more frequent on stations 1-4, so UL was switched to
  master role, with DL as slave. CTD froze during initial cast, so
  cast was aborted and restarted. CTD cast number is 00502.

* Station 5-7: Master and slave ADCP roles were switched, but not
  the file naming format. Thus for casts 005-00 master was still saved
  as DL, despite it being UL data. I.e. files such as 005DL000.000 are
  actually 005UL000.000, and vice versa.

* Station 8: Master and slave roles swapped back to original
  configuration.

* Station 10: Vertical velocity quality issues in DL continuing.
  Rules out that problem is caused by UL, so switched back to primary
  UL with IMP/ras-pi for this cast. UL is still slave. Note,
  fortunately it appears that because the scattering environment for
  1-9 is good, satisfactory vertical velocity data can be produced
  from the UL only.

* Station 15: Data download/endladcp2 command failed. Each ADCP lost
  power momentarily during different parts of the cast, which caused
  data download issues. No data was lost, but data files with actual
  data are 015UL001.000 and 015DL000.000.

* Station 16: Master slave roles switched in attempt to remedy
  donwload issues in 015. Master is UL.

* Station 017: Swapped out faulty deck cable. No data lost.

* Station 018: CTD pressure readings became erroneous during cast,
  particularly near the surface. CTD transmission issues as well cause
  issues in vertical velocity processing.

* Station 019: Swapped CTDs prior to this cast (from fish 0830 to
  0914). Pressure readings are still wrong near the surface,
  particularly at beginning and end of cast. May not be able to trust
  fidelity of pressure data for casts up until this point (1-19).
  Particularly stations 001, 002, 004, 005, 009, 010, 011, 014, 018,
  019 show pressure problems at surface. Note that pressure surface
  anomalies should not greatly affect ADCP data quality because of
  LADCP surface detection problems near the surface anyway (due to
  sidelobe and vessel interference). The main effect of these pressure
  anomalies to this point seems to cause gaps in the vertical velocity
  profiles. Although the following stations may show anomalies for
  pressure at depth 006, 007, 008, 012, 013, 015, 016, 017.

* Station 20-27: Swapped to third CTD (from ODF 0914 to UW 0057) due
  to continued pressure and data transmission problems. Pressure data
  seems ok, but data transmission problems cause time lag issues in
  the vertical velocity processing. Particularly for the downcast.

* Station 20-39: CTD transmission problems continue. They do not
  seem to contaminate the horizontal velocity data, but they cause
  significant time lag editing issues in vertical velocity and make
  some data potentially unusable.

* Station 25: Changed CTD termination, transmission problems remain.

* Station 28: LADCPs momentarily lost power before cast, so data is
  in >>*<<001.000 files and not >>*<<000.000 files. No data lost.
  Large inversion residuals for the DL, but solution may be usable.

* Station 29: DL continues to produce poor data. DL seems to have to
  performed especially poorly in this station, as evidenced by the
  inversion residuals. DL data in this run may be unusable. LADCPs
  momentarily lost power before cast, so data is in >>*<<001.000 files
  and not >>*<<000.000 files. No data lost.

* Station 31: Excessive CTD transmission problems on this casts
  cause LEDO_IX processing to fail, as it cannot solve for time lag.
  No velocity profile could be generated. Not clear if this data will
  be usable. LADCPs momentarily power before cast, so data is in
  >>*<<001.000 files and not >>*<<000.000 files.

* Station 32-33: LADCPs lost power during cast, so data is in
  >>*<<001.000 files and not >>*<<000.000 files. Data was not
  collected until ~700m into donwcast for both 032 and 033. 033 seems
  to have only momentarily lost power. Additionally, CTD transmission
  problems here likely causing time lag offsets in horizontal
  velocity. Likely the cause of failed time lag in 031 as well.

* Station Test Cast2 - 903: Because of continued issues with the
  vertical velocity from the DL (high error and depth correlated
  residuals, stations 001-034) the WHM150 (S/N:24544) DL was swapped
  with the WHM300 (S/N:24477) and the new WHM300 was set as the
  master. This immediately solved the vertical velocity DL data
  issues. Would have been switched sooner but weather and CTD
  troubleshooting prevented it. Although, LADCPs momentarily lost
  power before cast, so data is in >>*<<001.000 files and not 000.000
  files. No data lost. This test cast was completed after station 034
  to test CTD troubleshooting. Prior to cast CTD was switched from
  0057 to 0830. Transmission problems remain.

* Station 35: CTD swapped back to UW 0057 from 0830, and this
  configuration remained for rest of cruise. Swapped to back up
  battery Deepsea Power and Light SB 48 V/16 A (S/N: 01283), as had
  determined that battery on the rosette was causing the data
  partitioning problems in stations 033,032,031,028, and 027.

* Station 36-37: CTD transmission problems cause vertical vel time
  lag editing to remove large number of samples.

* Station 40: CTD transmission problems resolved before this cast.
  Sea cable was being pinched under impulsive loads, causing
  transmission problems.

* Station 42: Large towing velocities near the surface due to
  weather and strong currents cause disagreements in velocity data in
  the upper 800m or so.

* Station 44: Large towing velocities near the surface due to
  weather and strong currents cause some disagreement in velocity
  data. CTD transmission issues returned as well.

* Station 51: Winch wire began to fray during upcast. Took 2-2.5
  hours to repair and so CTD was stationary at about 3000m during that
  process. Then for remainder of upcast, rosette was not stopped and
  bottles fired on the fly.

DCP programming and data acquisition were carried out by Benjamin
Musci using the LDEO Acquire software running on a MAC computer. Prior
to each cast, the corresponding command files were sent to both the UL
and DL ADCPs, the ADCPS were switched to battery power, communications
were then terminated, deck cables disconnected and all connections
were secured and sealed with dummy plugs. After the rosette was
brought back up on desk following a cast, the communication and power
cables were connected to the MAC computer. Data acquisition were
terminated and files were downloaded with the corresponding command
using the Acquire software. The battery was disconnected from the star
cable and connected to a charger via a deck cable running from the
staging bay to the wet lab. The battery remained connected to the
charger between stations. The battery pack was periodically vented
manually to prevent pressure build up. The second battery (S/N: 01283)
was vented more frequently as the gas build up during charging caused
large bubbles. Log files were kept for each cast with LADCP and CTD
information to ensure all steps were made properly.



14.3  Data Processing and Quality Control

The ADCP data was processed daily by B. Musci using the Matlab-based
LDEO LADCP processing software version IX (1). Processing warnings and
figures created through the software were reviewed for signs of
anomalies such as rosette rotation and tilt, biased shear, agreement
between LADCP and SADCP velocities, beam strength and range and ADCP
distance to the sea bottom. Data was sent to Andreas Thurnherr every 3
stations or when questionable profiles were observed.

Figures 1, 2, 3, and 4 show the preliminary results of zonal and
meridional velocities for all the available stations. The stations of
the cruise were split up into a North and South portion, due to the
medical evacuation that caused the abandonment of the planned science
program at 50S. After evacuation a portion of the planned Northern
stations were completed. 45 stations were completed in the Southern
portion of the cruise and the final 10 in the Northern portion. The
resolution of the Northern portion was compromised because of this.
Maximum values reach up ~65 cm/s in the upper ~1000m during the
southern portion, and ~120 cm/s in the upper ~200m during the northern
portion. There is a relatively strong upper ocean current at ~57 S,
and an equally strong current at depth around ~59 S in the southern
portion. In the northern portion there is an extremely strong current
at ~33 S. Further QC and post-processing of horizontal and vertical
velocities at all available stations will be done by Andreas Thurnherr
at LDEO post-cruise.

   [image]

   [image]

   [image]

   [image]




15.  Underwater Vision Profiler 5 HD (UVP)

PI
   * Andrew McDonnell

Cruise Participant
   * Jessica Pretty (Technician)



15.1  System Configuration and Sampling

The Underwater Vision Profiler 5 (UVP5) HD serial number 207 was
programmed, mounted on the rosette, and charged. The UVP5 is outfitted
with a High Definition 4 Mp camera with an acquisition frequency of up
to 20 Hz. This optical imaging device obtains in situ concentrations
and images of marine particles and plankton throughout the water
column, capturing objects sized ~100 μm to several cm in diameter. The
camera of the UVP5 HD is different from the previous non-HD version,
but the operations are identical for both. The instrument and data
processing are described in Picheral et al., 2010 [Picheral2010].
Across the Antarctic shelf, particle abundance (#/L) showed a
subsurface maxima up to 150 particles per liter between 50-100m. A
second maxima, usually smaller than the shallower, was seen a few
hundred meters above the seafloor. Mean size, ranging between 0.1 and
0.6 mm across the Antarctic shelf tended to increase until a few
hundred meters above the seafloor, usually in the same depth range as
particle abundance minima. As particles became more abundant, mean
size decreased. Through the open ocean transect, maximum particle
abundances were lower overall, usually less than 50 particles per
liter. Increases in particle abundance were also seen 100-200m above
the seafloor. Open ocean mean sizes tended to range between 0.1 and
0.4mm. Patterns in particle abundance were notably different across
the East African shelf than the Antarctic shelf, with maximum particle
abundances shown in shallower water.

Some image sorting was performed during the cruise using an offline
version of the Ecotaxa database. Total image count gathered during the
cruise was over 800,000 images; just over 146,000 were sorted and
validated using a combination of machine learning and manual
validation. Categories sorted into included various zooplankton taxa
and detrital categories. Zooplankton categories included crustacea
(including copepods and krill), gelatinous (larvacean, jellyfish,
salps), and rhizaria. Detrital images were sorted into general
detritus as well as ‘dark and fluffy’ as well as ‘light and fluffy’.
Examples of these images are shown in figures 2 to 11.



15.2  Figures

Figure 1: Typical Open Ocean Profile from Station 034 of Particle 
          Abundance (#/L), Mean Size (mm), and Greyscale (a proxy
          for how opaque the images tended to be)

Figures 2 to 11: Examples of particle and plankton images captured by 
                 the UVP5HD and processed by custom software. The scale
                 bar indicates 2 millimeters. Station number, image 
                 number for that cast, and depth at which the image was 
                 captured are also given in the image.



15.3  Problems

The CTD rosette was dragged from inside the staging by onto the deck
resulting in damage to the UVP 25 meter data cable as well as a 1
meter pigtail. The data cable was respliced and repaired, but the area
where the damage occurred on the 1m power pigtail made it necessary to
replace the cable. A cable was borrowed from the R/V Thompson for the
duration of the cruise.

Stations 12 to 16 are missing as UVP cables were snagged by a closing
niskin bottle and pulled from the bulkhead at depth. The UVP was
removed from the rosette and the manufacturer of the UVP5, Hydroptic,
was consulted for assistance with troubleshooting. The UVP was
inspected and tested for water intrusion damage; after it was
determined safe to do so (no damage) the UVP was reassembled and UVP
was re-mounted onto the rosette frame before station 17 with new
hardware as the mounts previously used needed to be replaced.

Stations 22, 32, 35, & 36 are missing due to unknown sampling error -
the UVP appeared to be functioning properly but no file was created.
Power shunt pins were cleaned and tested for functionality - appeared
to be in working order (no resistance between pins 1 & 3), but after
cleaning casts are successful. Station 38 data is not usable as a
cable within the rosette came loose and obstructed the view of the
camera during part of the cast. Station 39 is missing due to user
error: the UVP was deployed with the dummy plug instead of power
shunt. Station 41 data contains an artifact throughout the cast,
thought to be a small fiber that adhered to the inside of the camera
lens. The artifact is easily identified and removed, but it is unknown
whether this corrupts the data or can be accounted for.



15.4  Reference

[Picheral2010] Picheral, M., Guidi, L., Stemmann, L.,
               Karl, D.M., Iddaoud, G., Gorsky, G., 2010. The
               Underwater Vision Profiler 5: An advanced instrument
               for high spatial resolution studies of particle size
               spectra and zooplankton. Limnol. Ocean. Methods 8,
               462–473.




16.  CHIPODS

PI
   * Jonathan Nash

Cruise Participants
   * Michael Kovatch

   * Daniela Faggiani Dias



16.1  Overview

Chipods are instrument packages that measure turbulence and mixing in
the ocean. Specifically, they are used to compute turbulent
diffusivity of heat (Κ) which is inferred from measuring dissipation
rate of temperature variance (χ) from a shipboard CTD. Chipods are
self-contained, robust and record temperature and derivative signals
from FP07 thermistors at 100 Hz; they also record sensor motion at the
same sampling rate. Details of the measurement and our methods for
processing chi can be found in Moum and Nash [2009] (Moum, J., and J.
Nash, Mixing Measurements on an Equatorial Ocean Mooring, Journal of
Atmospheric and Oceanic Technology, 26(2), 317–336, 2009). In an
effort to expand our global coverage of deep ocean turbulence
measurements, the ocean mixing group at Oregon State University has
supported chipod measurements on all of the major global repeat
hydrography cruises since Dec 2013.



16.2  System Configuration and Sampling

Three chipods were mounted on the rosette to measure temperature (T),
its time derivative (dT/dt), and x and z (horizontal and vertical)
accelerations at a sampling rate of 100 Hz. Two chipods were oriented
such that their sensors pointed upward. The third one was pointed
downward.

The up-looking sensors were positioned higher than the Niskin bottles
on the rosette in order to avoid measuring turbulence generated by
flow around the rosette and/or its wake while its profiling speed
oscillates as a result of swell-induced ship-heave. The down-looking
sensors were positioned as far from the frame as possible and as close
to the leading edge of the rosette during descent as possible to avoid
measuring turbulence generated by the rosette frame and lowered ADCP.


    Logger Board SN | Pressure Case SN | Up/Down Looker | Cast Used
   —————————————————|——————————————————|————————————————|———————————
    2008            | Ti 44-5          | Up             | 1-55     
   -----------------+------------------+----------------+----------
    2027            | Ti 44-3          | Up             | 1-55     
   -----------------+------------------+----------------+----------
    2025            | Ti 44-7          | Down           | 0        
   -----------------+------------------+----------------+----------
    2030            | Ti 44-11         | Down           | 1-55     


Fig 1: Upward-looking chipod sensor attached to the rosette
 
Fig 2: Highly sensitive temperature probe, which is sampled at 100Hz



16.3  Data

The chipods were turned on by connecting the sensors to the pressure
case at the beginning of the cruise. They continuously recorded data
until the end of the leg. Data was uploaded onto the computer a few
times to ensure proper functioning and data collection.

SN2025 was replaced by SN2030 on 04/05 since we were unable to
communicate with it. SN2008 had sensor cable pulled off during CTD
recovery on 04/29 ~12:30.


Fig 3: A typical plot of chipod raw data




17.  UNDERWAY pCO2

PIs
   * Rik Wanninkhof (NOAA/AOML)

Analysts
   * Andrew Collins (NOAA/PMEL)

The partial pressure of CO2 (pCO2) in the surface ocean was measured
throughout the duration of this expedition with a General Oceanics
8050 underway system. Uncontaminated seawater was continuously passed
(~2.8 l/min) through a chamber where the seawater concentration of
dissolved CO2 was equilibrated with an overlying headspace gas. The
CO2 mole fraction of this headspace gas (xCO2) was measured
approximately every three minutes via a non-dispersive infrared
analyzer (Licor 7000). Roughly every three hours, the system measured
four gas standards with known CO2 concentrations certified by the NOAA
Earth Science Research Laboratory in Boulder, CO ranging from ~300 –
900 ppm CO2. Additionally, a tank of 99.9995% ultra-high purity
nitrogen gas was measured as a baseline 0% CO2 standard. Following
measurements of standard gases, six measurements of atmospheric pCO2
were made of air supplied through tubing fastened to the ships
starboard jackstaff. Twice a day, the infrared analyzer was calibrated
via a zero and span routine using the nitrogen gas and the highest
concentration (872.6 ppm) CO2 standard. In addition to measurements of
seawater xCO2, atmospheric xCO2, and standard gases, several variables
were monitored to evaluate system performance (e.g. gas and water flow
rates, pump speeds, etc). For more detail on the general design of
this underway pCO2 system, see Pierrot et. al (2009). A Seabird (SBE)
38 temperature sensor located at the ship’s seawater intake provided
measurements of in situ seawater temperature, while a SBE 45
thermosalinograph monitored temperature and salinity in the bow of the
ship before the seawater reached the pCO2 system. An Aanderaa 4330
optode plumbed in line with the pCO2 system water supply measured
dissolved oxygen (DO) continuously. Additionally, a modified SeaFET
system was also plumbed in line which measured pH throughout the
duration of the cruise.

During the transit from Cape Town to the continental shelf of
Antarctica and the excursion to Port Elizabeth, discrete samples
(n=73) for measurements of dissolved inorganic carbon, total
alkalinity, pH, DO, nutrients (nitrate, nitrate, silica, phosphate),
and salinity were drawn from the ships uncontaminated seawater supply
every four hours. These were analyzed onboard and will be used for
comparison to measurements collected by the underway system. A
preliminary round of processing was performed on this dataset using
Matlab routines developed by Denis Pierrot of the Atlantic Oceanic and
Meteorological Lab in Miami, FL. pH was calculated from recorded
voltages using the Matlab scripts provided as supplementary material
in Bresnahan et. al (2014). Of 15,744 measurements, 627 were assigned
a WOCE quality flag of 4 (bad measurement), while 72 were assigned a
quality flag of 3 (questionable measurement). Measurements of gas
standards were within 1% of their certified value throughout the
duration of the expedition (Figure 1).

Preliminary review of collected data suggest that the main control on
the surface seawater carbonate system was temperature (Figure 2).
Excursions from thermodynamic controls on pCO2, pH and DO were
measured during the brief times spent on the continental shelf near
the coast of South Africa, where higher rates of organic matter
remineralization may have been contributed to increases in pCO2 and
decreases in pH and DO. However, further evaluation of these data and
the supplementary suite of discrete measurements that were collected
is needed before the controls on pCO2, pH and DO can be fully
elucidated. In two brief instances, the underway system was stopped
due to problems with seawater supply that were encountered on account
of extremely rough weather. This dataset should be considered
preliminary; additional quality control and quality assurance is
needed before these data can be considered final.


Fig 1: Difference between measurements made by the non-dispersive
       infrared analyzer (Licor 7000) of gas standards and the known
       certified value of those standards (in ppm CO2).

Fig 2: Spatial distribution of the relevant parameters (sea surface
       temperature [SST, oC], sea surface salinity [PSU], fCO2 [ppm], pH,
       and DO [M]) measured by the underway pCO2 system during the 2019
       GO-SHIP I06S research expedition.


Literature cited:

   * Pierrot, D., Neill, C., Sullivan, K., Castle, R., Wanninkof,
     R.W., Lüger, H., Johannessen, T., Olsen, A., Feely, R.A., Cosca,
     C.E.; 2009. Recommendations for autonomous underway pCO2
     measuring systems and data-reduction routines. Deep-Sea Research
     II 56 (2009) 512–522

   * Bresnahan, P.J., Martz, T.R., Takeshita, Y., Johnson, K.S.,
     LaShomb, M.; 2014 Best practices for autonomous measurement of
     seawater pH with the Honeywell Durafet. Methods in Oceanography 9
     (2014) 44-60




18.  FLOAT DEPLOYMENTS

A total of 18 profiling Argo floats were deployed during the GO-SHIP
I06S 2019 cruise: 2 NOAA/PMEL and 9 CSIRO core Argo float, and 7
biogeochemical Argo of the SOCCOM program. Isa Rosso (postdoc at SIO
and SOCCOM personnel) was responsible for all the deployments and kept
the communication with the various PIs of the programs. The assistance
from the UW marine technicians was necessary for all deployments. In
addition, the watch stander students were trained to provide
assistance with the deployment.

Each deployment occurred with the use of a line strung to the float,
with one end of the line tied to a cleat and the other held by the
marine technician. Deployments were always done on departure from a
CTD station while the ship was steaming at 1-3 knots, except for
SOCCOM BGC float UW ID #12882 that was deployed during the medical
evacuation, on the way to Port Elizabeth (see Narrative).

The floats have a 10-day cycle, except for SOCCOM float #12888 which
was set with a 5-day cycle for the first 2 months, as its measurements
will be combined with the 2 Caltech sea gliders that were deployed
during the cruise. After an initial test dive, the floats descend to a
parking depth of 1000 m, and then drift for 10 days with the ocean
currents; after the 10-day drift, the floats dive to 2000 m and then
ascend to the surface, during which data are measured and saved. The
2000 m-surface data profiles are then sent to shore via Iridium
Satellite communication, using an antenna located at the top of the
float. Measurements comprehend temperature, salinity, pressure and
additional biogeochemical measurements for the SOCCOM type.

As the sea ice will grow in the colder months and potentially cap the
floats underneath, ice avoidance software on the floats will allow
them to survive beneath it, keeping the cycle and just storing the
collected measurements until they can get free from the ice and send
data to the satellite communication. Each of these floats was self-
activating, so no initial operations where required before their
deployment to activate them.

Argo data is used in various applications, from operational use (to
monitor local environmental conditions and alert significant
temperature and salinity changes, and forecasts) to research (ocean
circulation, water mass properties/formation, air-sea fluxes, ocean
dynamics, seasonal-interannual variability, state estimates). In
addition, with the new BGC floats measuring oxygen, nutrients,
chlorophyll, backscatter and pH, we can now quantify and understand
the seasonal cycles of the biogeochemical and physical processes, as
we are dramatically expanding the in situ winter biogeochemical
observations.

Each float program is discussed in the following sections.



18.1  SOCCOM floats

PIs
   * Steven Riser (UW)

   * Kenneth Johnson (MBARI)

   * Lynne Talley (SIO)

7 biogeochemical floats have been deployed, as part of the “Southern
Ocean Carbon and Climate Observations and Modeling” project (SOCCOM).
SOCCOM is a U.S. project sponsored by NSF that focuses on carbon and
climate in the Southern Ocean. Its goal is to deepen our knowledge of
the processes that regulate the carbon export in the Southern Ocean.
At present, SOCCOM has 130 active floats, and the data are available
to the public at http://soccom.princeton.edu/content/float-data.

5 of the floats deployed during I06S were UW-modified Teledyne Webb
Apex floats and 2 (UW ID #0888 and #0889) were built by Seabird Navis.
The floats are equipped with CTD, oxygen, nitrate, FLBB bio-optical
and pH sensors. Data acquisition is made available through Iridium
Satellite communication and GPS.

Andrew Meyer (UW) tested each float at the beginning of the voyage
during the port call in Cape Town, South Africa. All were tested
“good”.

Before the deployment of each float, the fluorometer/backscatter and
the nitrate sensors were carefully cleaned using lens wipes, DI water
and lens paper. Isa Rosso, SOCCOM personnel responsible for the floats
deployment during this voyage, together with the UW marine technicians
Jennifer Nomura and Croy Carlin, were in charge of all the SOCCOM
float deployments. Additional assistance was received by watch-stander
Maximilian Kotz and ODF/SIO technician Melissa Miller. The procedure
required the use of a line strung through the deployment collar of the
float. Each deployment occurred on the port side, stern, while the
ship was steaming at about 1-2.5 knots. No issues were encountered
during the deployments, except for the Navis #0888: the deployment
line got tangled, and it was decided to cut the line, rather than try
to recover the float. Recovering the float, attached only on one end
of the line, would have probably resulted in the float dropping (if
the line suddenly got free) or in the float hitting the side of the
ship and compromise the sensors. Cutting the line in situations like
these is normal procedure, but of course is far from being ideal: the
rope could tangle around the sensors and/or change the ballasting
during the course of its life.

The deployments occurred after the completion of the CTD station that
was chosen to be the closest to the planned deployment location and
had a bottom depth greater than 2500 m, except for the float #12882,
which was deployed during the medical evacuation steaming to Port
Elizabeth. For this float, only surface samples (nutrients, salinity,
POC/HPLC, DIC, pH, Alk) were collected from the uncontaminated
seawater intake line. For the deployment, the ship slowed down to 2.5
knots, and the whole operation took approximately 10 minutes.

For all the other deployments, samples of nutrients, salinity,
POC/HPLC, DIC, pH and Alkalinity were taken at each depth, at least
down to 2000 m. The HPLC and POC samples were taken from the Niskin
bottles tripped as duplicates, at the surface and at the chlorophyll
maximum depths (DCM), or the base of the mixed layer if the DCM was
not present. The samples were filtered by SIO/ODF team (Susan Becker
and Melissa Miller), and will be sent frozen to the U.S. for analysis
(NASA for HPLC and UCSB for POC). Full-depth (with at least higher
resolution in the top 2000 m) samples of salts, pH, alkalinity,
dissolved inorganic carbon, nitrate and oxygen were collected and
analysed on board, for future validate the floats’ sensors. Data from
a FLBB sensor mounted on the CTD rosette, provided by Emmanuel Boss,
will also be used for the validation of the sensor on the float. To
calibrate the FLBB, a dark cast was taken at station #15: a black
electrical tape was placed on the sensor, in order to get the
background value. The tape was carefully removed after the cast and
the sensor cleaned using ethanol and DIW. pH samples were collected
and analysed by personnel from SIO, part of A. Dickson’s lab;
dissolved inorganic carbon samples by personnel from AOML and PMEL;
oxygen, nitrate and salinity samples by the ODF group at SIO.

The floats were adopted by different schools in the US and one school
in Sydney (Australia), as part of the outreach program
“Adopt-a-float”. Each class named the float and received the details
(and pictures) of their deployment from Isa Rosso, via SOCCOM
personnel onshore George Matsumoto (MBARI). Together with their
teachers, the students will follow the data of the float, which can be
easily downloaded and plotted at the website www.mbari.org/science
/upper-ocean-systems/chemical-sensor-group/soccomviz. As part of this
outreach program, a blog post was written on the I06S blog http
://usgoship-i06s2019.blogspot.com, either by Isa Rosso, Giuliana
Viglione, Melissa Miller or Maximilian Kotz.

Each float has reported its first profiles and it looks like the
sensors are all working well, except for pH on the float #12888: the
SOCCOM team communicated that it looked like there is a “controller-
related issue affecting the pH sensor”, which results in a very few pH
measurements returned throughout the profile (with higher resolution
in the top 200 m). The float is under monitor, and it might start
working properly at some point.

The location and date of the float deployments are indicated in the
table below, with UW ID numbers, list of parameters measured by the
floats and the CTD cast (if any) at the location of deployment.


Table 1: summary of the deployment details of the SOCCOM floats

 UW ID      | Longitude | Latitude | Date and     | Depth | Parameters   | CTD Sta-  | Deployers    
            | (°E)      | (°S)      | Time (UTC)   |  (m)  |              | tion #    |              
————————————|———————————|——————————|——————————————|———————|——————————————|———————————|——————————————
 Apex 12878 | 29.9958   | 65.4993  | 4/18/19      | 4710  | CTD, oxygen, | 14        | Jennifer     
            |           |          | 23:19        |       | nitrate, pH, |           | Nomura and   
            |           |          |              |       | fluorescence |           | Isa Rosso    
            |           |          |              |       | and backsca  |           |              
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Apex 12892 | 29.9997   | 62.998   | 4/20/19 8:50 | 5165  | CTD, oxygen, | 19        | Jennifer     
            |           |          |              |       | nitrate, pH, |           | Nomura and   
            |           |          |              |       | fluorescence |           | Isa Rosso    
            |           |          |              |       | and backsca  |           |              
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Apex 12885 | 29.9896   | 56.0031  | 4/25/19 4:15 | 5463  | CTD, oxygen, | 33        | Jennifer     
            |           |          |              |       | nitrate, pH, |           | Nomura and   
            |           |          |              |       | fluorescence |           | Maximilian   
            |           |          |              |       | and backsca  |           | Kotz         
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Apex 12888 | 29.9915   | 51.4879  | 4/30/19      | 4257  | CTD, oxygen, | 42        | Croy Carlin  
            |           |          | 19:20        |       | nitrate, pH, |           | and Melissa  
            |           |          |              |       | fluorescence |           | Miller       
            |           |          |              |       | and backsca  |           |              
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Apex 12882 | 29.0112   | 44.9717  | 5/6/19 0:28  | 5804  | CTD, oxygen, | On the    | Jennifer     
            |           |          |              |       | nitrate, pH, | way to    | Nomura and   
            |           |          |              |       | fluorescence | Port      | Isa Rosso    
            |           |          |              |       | and backsca  | Elizabeth |              
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Navis 0888 | 28.55     | 33.6965  | 5/9/19 17:48 | 5747  | CTD, oxygen, | 48        | Croy Carlin  
            |           |          |              |       | nitrate, pH, |           | and Melissa  
            |           |          |              |       | fluorescence |           | Miller       
            |           |          |              |       | and backsca  |           |              
            |           |          |              |       | ttering      |           |              
------------+-----------+----------+--------------+-------+--------------+-----------+--------------
 Navis 0889 | 30.0002   | 35.0034  | 5/10/19      | 4448  | CTD, oxygen, | 15        | Croy Carlin, 
            |           |          | 11:55        |       | nitrate, pH, |           | Isa Rosso    
            |           |          |              |       | fluorescence |           | and Melissa  
            |           |          |              |       | and backsca  |           | Miller       
            |           |          |              |       | ttering      |           |              


The figure below shows an example of profiles for the float #12878,
the first SOCCOM float to be deployed on this cruise.


Figure 1: Example of float’s profile: pH, chlorophyll, oxygen, 
          temperature, salinity and nitrate depth profiles for 
          float Apex UW ID #12878



18.2  CSIRO floats

PIs
   * Rebecca Cowley

9 CSIRO core Argo floats were deployed during the cruise. We have
received confirmation that all the floats have reported correctly. The
floats were checked and prepared in port in Cape Town by Craig
Hanstein (CSIRO).

The floats were deployed in their original bio-degradable cardboard
boxes, as requested, in order to prevent any damage. Four straps were
attached around the box, connected to a water release mechanism (a
metal cylinder) at the bottom and with four trailing loops on the top.
The deployment line was slipped through the trailing loops, and then
secured on the other end to a cleat.

However, the water release mechanism on the first float never opened
up: we waited about 5 minutes and by that time the box was
disintegrating at the bottom, which made it impossible for us to
recover the whole box. The MT shook the harnesses around, releasing
the box. The surface temperature was about -0.5 C. We decided to open
the boxes before deploying the floats, based on this, for waters below
0°C.

Other than this initial hiccup, the deployments went smooth, thanks to
the very skilled MTs onboard.

The details were recorded by either Isa Rosso or the watch-stander
students, and sent to the CSIRO team by I. Rosso. The location and
date of the CSIRO float deployments are indicated in the table below,
with serial numbers, CTD cast at the location of deployment and name
of the personnel who deployed the floats.


Table 2: summary of the deployment details of the 9 CSIRO Argo floats

 ID   | Date and time | Longitude | Latitude | Depth | CTD Sta- | Deployers     
      | (UTC)         |   (°E)    |   (°S)    |  (m)  | tion #   |               
——————|———————————————|———————————|——————————|———————|——————————|———————————————
 8446 | 4/18/19 17:50 | 29.9933   | 66.0014  | 4773  | 13       | Croy Carlin,  
      |               |           |          |       |          | Isa Rosso     
------+---------------+-----------+----------+-------+----------+---------------
 8447 | 4/19/19 6:00  | 29.9919   | 65.002   | 4869  | 15       | Jennifer      
      |               |           |          |       |          | Nomura, Isa   
      |               |           |          |       |          | Rosso         
------+---------------+-----------+----------+-------+----------+---------------
 8438 | 4/19/19 19:40 | 29.9973   | 64.005   | 5097  | 17       | Croy Carlin,  
      |               |           |          |       |          | Kay McMonigal 
------+---------------+-----------+----------+-------+----------+---------------
 8439 | 4/20/19 2:15  | 30.0093   | 63.4985  | 5128  | 18       | Jennifer      
      |               |           |          |       |          | Nomura,       
      |               |           |          |       |          | Michael       
      |               |           |          |       |          | Kovatch       
------+---------------+-----------+----------+-------+----------+---------------
 8440 | 4/20/19 23:40 | 29.9953   | 61.9969  | 5186  | 21       | Jennifer      
      |               |           |          |       |          | Nomura,       
      |               |           |          |       |          | Daniela       
      |               |           |          |       |          | Faggiani-Dias 
------+---------------+-----------+----------+-------+----------+---------------
 8455 | 4/23/19 13:44 | 30.002    | 58.0091  | 5433  | 29       | Croy Carlin,  
      |               |           |          |       |          | Kay McMonigal 
------+---------------+-----------+----------+-------+----------+---------------
 8456 | 4/25/19 4:00  | 29.9896   | 56.0031  | 5463  | 33       | Jennifer      
      |               |           |          |       |          | Nomura,       
      |               |           |          |       |          | Maximilian    
      |               |           |          |       |          | Kotz          
------+---------------+-----------+----------+-------+----------+---------------
 8457 | 4/29/19 5:13  | 30.0015   | 53.997   | 5198  | 37       | Jennifer      
      |               |           |          |       |          | Nomura,       
      |               |           |          |       |          | Michael       
      |               |           |          |       |          | Kovatch       
------+---------------+-----------+----------+-------+----------+---------------
 8458 | 5/2/19 23:13  | 29.9698   | 49.9945  | 3475  | 45       | Croy Carlin,  
      |               |           |          |       |          | Maximilian    
      |               |           |          |       |          | Kotz          



18.3  NOAA/PMEL floats

PI
   * Elizabeth Steffen

2 NOAA/PMEL Seabird Navis core Argo floats have been deployed during
I06S, as part of the global Argo array. The floats were all
successfully deployed, with no issues. After the deployment, the
details were recorded by I. Rosso and sent to the PI. Date, time,
location of the deployment, CTD cast associated with the deployments
and the name of the deployers are reported in the Table below.


Table 3: summary of the deployment details of the 2 NOAA/PMEL floats

 ID  | Date and Time | Longitude | Latitude | Depth | CTD Sta- | Deployers     
     | (UTC)         |   (°E)    |   (°S)    |  (m)  | tion #   |               
—————|———————————————|———————————|——————————|———————|——————————|———————————————
 946 | 4/22/19 6:53  | 30.0135   | 60.0155  | 5181  | 25       | Jennifer      
     |               |           |          |       |          | Nomura,       
     |               |           |          |       |          | Daniela       
     |               |           |          |       |          | Faggiani-Dias 
-----+---------------+-----------+----------+-------+----------+---------------
 947 | 4/22/19 22:48 | 30.0027   | 59.0159  | 5427  | 27       | Croy Carlin,  
     |               |           |          |       |          | Michael       
     |               |           |          |       |          | Kovatch       




19.  δ18O

PIs
   * Michael Meredith (BAS)

   * Melanie Leng (BAS)

Technicians
   * Isa Rosso

   * Mike Kovatch

   * Daniela Faggiani-Dias

   * Maximilian Kotz

   * Loicka Baille

   * Guiliana Viglione

   * Kay McMonigal


19.1  Equipment and Techniques

A total of 1302 high density polyethylene (HDPE) wide-mouth 30-ml
vials were used to collect δ18O samples at all I06S CTD station,
following the protocol and sampling strategy provided by the PIs, as
described below.

Watch standers and leaders from each shift drew δ18O samples last,
after all other programs had finished with theirs. Collection was
straightforward. It required filling the vial in half and shaking;
filling to the top and leaving only minimal air; closing tight; drying
with kimpwipes or paper towels; placing vinyl electrical tape around
the neck of the vial and the bottom of the cap to seal the sample.

A maximum of 24 samples per station were distributed with higher
resolution within the surface, intermediate and bottom layers, whereas
with lower resolution within deep waters. Paper and electronic logs of
all the δ18O samples include station (location), Niskin Bottle
(depth), and sample numbers, which were also recorded on the vials.

Once back to port, the samples were shipped back to UK, for analysis.




20.  DRIFTER DEPLOYMENTS

PI
   * Shaun Dolk (*AOML*)

16 drifters (8 SVP and 8 SVP-barometer) were deployed on the I06S line
as part of the Global Drifter Program. Only the plastic wrap was
removed before their deployment. In the case of the two deployments
occurring at the same location (at 60° S), the drifters were released
with 30 seconds of distance between each other, in order to avoid any
entanglement amongst the drifters’ drogues. After collecting the
release details (see table below) by either the watch stander students
or Isa Rosso, the data (see the table below) were communicated to the
CSIRO by I. Rosso.

2 of the drifters were adopted as part of the outreach
“Adopt-a-drifter” program, by schools in Colorado and in Ukraine: ID
#300234066615940 and #300234066338770. Teacher and students will
follow the drifters’ journey and their data, which is public available
at https://www.adp.noaa.gov. As outreach activity, 2 blog posts were
written including the details of the adopted drifters.


Table 1: Table of deployments

 ID       | Date and | Longitude | Latitude | Deployed   | Ship  | Height | Deployers    
          | Time     | (°E)      | (°S)      | from       | speed | above  |              
          | (UTC)    |           |          |            | (kn)  | sea    |              
          |          |           |          |            |       | level  |
          |          |           |          |            |       | (m)    |
——————————|——————————|———————————|——————————|————————————|———————|————————|——————————————
 66615940 | 4/18/19  | 29.9962   | 66.0008  | Port stern | 1     | 3      | Loicka       
          | 17:42    |           |          |            |       |        | Baille and   
          |          |           |          |            |       |        | Giuliana     
          |          |           |          |            |       |        | Viglione     
----------+----------+-----------+----------+------------+-------+--------+--------------
 66615920 | 4/19/19  | 29.9973   | 64.0003  | Port stern | 3     | 3      | Daniela      
          | 19:40    |           |          |            |       |        | Faggiani-    
          |          |           |          |            |       |        | Dias and Isa 
          |          |           |          |            |       |        | Rosso        
----------+----------+-----------+----------+------------+-------+--------+--------------
 66615970 | 4/20/19  | 29.998    | 61.9996  | Port stern | 3     | 3      | Kay          
          | 23:36    |           |          |            |       |        | McMonigal    
          |          |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66338770 | 4/22/19  | 30.0128   | 60.0159  | Port stern | 3     | 3      | Daniela      
          | 6:54     |           |          |            |       |        | Faggiani-    
          |          |           |          |            |       |        | Dias and     
          |          |           |          |            |       |        | Maximilian   
          |          |           |          |            |       |        | Kotz         
----------+----------+-----------+----------+------------+-------+--------+--------------
 66615930 | 4/22/19  | 30.0126   | 60.016   | Port stern | 3     | 3      | Daniela      
          | 6:54     |           |          |            |       |        | Faggiani-    
          |          |           |          |            |       |        | Dias and     
          |          |           |          |            |       |        | Maximilian   
          |          |           |          |            |       |        | Kotz         
----------+----------+-----------+----------+------------+-------+--------+--------------
 66339760 | 4/23/19  | 30        | 58       | Port stern | 1.5   | 3      | Giuliana     
          | 13:44    |           |          |            |       |        | Viglione and 
          |          |           |          |            |       |        | Croy Carlin  
----------+----------+-----------+----------+------------+-------+--------+--------------
 66338830 | 4/28/19  | 30        | 54.99    | Port stern | 3     | 3      | Kay          
          | 15:40    |           |          |            |       |        | McMonigal    
          |          |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66339780 | 0429/2019| 30.0013   | 52.999   | Port stern | 1.2   | 3      | Kay          
          | 19:25    |           |          |            |       |        | McMonigal    
          |          |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66337840 | 5/4/19   | 29.1918   | 49.187   | Port stern | 12    | 3      | Isa Rosso    
          | 23:42    |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66616940 | 5/5/19   | 29.0417   | 45.1769  | Port stern | 10.5  | 3      | Isa Rosso    
          | 23:05    |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66338790 | 5/6/19   | 28.5789   | 43.0193  | Port stern | 12    | 3      | Isa Rosso    
          | 11:05    |           |          |            |       |        | and Croy     
          |          |           |          |            |       |        | Carlin       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66338810 | 5/7/19   | 27.5775   | 40.032   | Port stern | 11.4  | 3      | Daniela      
          | 2:24     |           |          |            |       |        | Faggiani-    
          |          |           |          |            |       |        | Dias and     
          |          |           |          |            |       |        | Michael      
          |          |           |          |            |       |        | Kovatch      
----------+----------+-----------+----------+------------+-------+--------+--------------
 66338990 | 5/7/19   | 26.9881   | 38.0151  | Port stern | 12.9  | 3      | Croy Carlin  
          | 13:38    |           |          |            |       |        |              
----------+----------+-----------+----------+------------+-------+--------+--------------
 66616830 | 5/8/19   | 26.3272   | 36.0271  | Port stern | 12    | 3      | Isa Rosso    
          | 0:00     |           |          |            |       |        | and Jennifer 
          |          |           |          |            |       |        | Nomura       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66616920 | 5/9/19   | 28.0963   | 33.2332  | Starboard  | 4     | 3      | Daniela      
          | 3:00     |           |          | stern      |       |        | Faggiani-    
          |          |           |          |            |       |        | Dias and     
          |          |           |          |            |       |        | Jennifer     
          |          |           |          |            |       |        | Nomura       
----------+----------+-----------+----------+------------+-------+--------+--------------
 66616950 | 5/9/19   | 28.87     | 34.66    | Port stern | 11.4  | 3      | Croy Carlin  
          | 17:58    |           |          |            |       |        | and Benjamin 
          |          |           |          |            |       |        | Mushi        




21.  GLIDER DEPLOYMENTS

PIs
   * Andrew Thompson

   * Alison Gray

Technicians
   * Giuliana Viglione

   * Maximilian Kotz

Two ocean gliders were deployed along the GO-SHIP IO6S section at
51.5S. The deployment was part of a collaborative proposal between
Andrew Thompson, Caltech, and Curtis Deutsch & Alison Gray, U.
Washington, to quantify submesoscale dynamical contributions to carbon
flux in the southern ocean, by tracking a bio-geochemical SOCCOM float
with the two gliders. The gliders were equipped with a Seabird SBE3
temperature and SBE4 conductivity sensor, an Aanderaa 4831 Oxygen
optode, and a WETLabs ECO Puck BB2FL fluorometer.


Fig. 1: Glider deployment location (red) on IO6S line (blue).


21.1  Preparation

On the 02/04/2019, while in port at Cape Town, Giuliana Viglione and
Maximilian Kotz (Caltech Graduate Students) ran the two gliders
through self-tests and simulation-dives to check their communications
and mechanical capabilities.

These tests required the gliders to be carried to the back deck by 4
personnel and then ratchet strapped to the railing so that their
antennae were angled at least 50 degrees from horizontal. During the
course of the cruise, the personnel responsible for moving the gliders
between the back-deck and main-lab were the two Caltech graduate
students; two additional volunteers were regularly recruited from the
science party or crew.

An issue was discovered with SG 660, the bladder of which was not
pumping to its full capacity. While in transit, this glider was taken
out again and given specific instructions to pump to full; it was
found to be able to do so and the issue was considered resolved.

On the 23rd of April, the software on the glider base station was
updated by Kongsberg, the manufacturers. Self-tests and simulation-
dives were required again to check that the gliders were compatible
with the update. Unfortunately, it was discovered that both gliders
were unable to log in to the base station via their Iridium satellite
communication.

Over the following days, further tests were run to troubleshoot the
issue. On the 29th of April the problem was resolved by coordinated
tests by Giuliana, Max and the Kongsberg and Caltech personnel.


Fig. 2: Self-tests and simulation-dives were run with the gliders
        ratchet strapped to the back deck, in port in Cape Town 
        (Giuliana Viglione).

Fig. 3: Self-tests and simulation-dives were run with the gliders
        ratchet strapped to the back deck, tests run on the gliders 
        during a CTD cast (Giuliana Viglione)



21.2  Deployments

On the 30th of April the two gliders were deployed at 51.5S before
casting the CTD. The weather was good enough for the captain to agree
to deploy via zodiac. At 10:30 (UTC) The two gliders were transported
to the O2 deck via the outside stairs. Their wings and rudder were
attached and they were strapped to the railing and  set to launch
mode.

The cap of the fluorometer became detached during this procedure and
some grease was smeared across the sensor. This was fixed by Joseph
Gum (ODF/SIO technician) who reattached the casing and cleaned the
sensor.

*SG 660*

At approximately 11:30 (UTC) the first glider, SG 660, was carried
into the zodiac in its cradle and was ratchet strapped at both top and
bottom to the zodiac to prevent it from slipping. The zodiac was
driven by Todd Schwartz (third mate); Bernadette Castner (A.B.) and
Isa Rosso (co-chief scientist) also came aboard to assist Max with the
deployment. The zodiac was lowered over the edge of the ship and
driven 500m from the ship.

Bernadette attached a line to SG 660 by looping it around the notches
at the base of the rudder; this provided security while Max and Isa
Rosso lowered it over the edge and held it still in the water until it
achieved neutral buoyancy. The glider was held for approximately 10
minutes until only its rudder and antenna were above the waterline - a
criteria which was hard to judge amongst the waves. From the ship
Giuliana then gave the instruction to dive and the line was released.
The glider was watched for approximately 15 minutes until it dived out
of sight. The zodiac returned to the ship and was raised out of the
water.


Fig. 4: zodiac lowered over side of ship with SG 660 ratchet
        strapped to the centre in its cradle. (Andrew Collins)

Fig. 5: SG 660 is set to launch mode on the 02 deck of the RV.
        Thomas G. Thompson. (Andrew Collins)

Fig. 6: SG 660 is held in the water until the rudder and antenna are
        above the water line. (Isa Rosso)


*SG 659*

The second glider, SG 659, was strapped to the zodiac and the process
repeated. Unfortunately, the zodiac engine overheated while driving
away from the boat. The decision was made to return slowly to the ship
and to deploy SG 659 via crane.

A line was attached to the glider via the notches at the base of its
rudder, this was then connected to the crane with a second line and
quick release pin. The winch was operated by Frank Leo Spetla (A.B.).
The glider was raised from its cradle, and guided by hand as the crane
raised it over the side of the ship. Without any suitable places to
attach tag lines, the gliders motion became unstable and it swung
close to the ship. Twice it narrowly avoided the hull before the crane
was able to lower and release it, approximately 5 metres from the
ship. The glider fully submerged and came up at a safe distance from
the ship. The command to dive was given and the glider was watched
until its antenna disappeared beneath the waves. **In future it would
be strongly advised to avoid using the crane without tag lines for
deployment.**

SOCCOM float 12888 was deployed shortly after the CTD cast at the same
latitude and longitude. The two gliders will continue to track it over
the coming four months; the data from their first dives has come back
and shows they are working correctly.




STUDENT STATEMENTS



Daniela Faggiani Dias

GO-SHIP has provided me with an invaluable experience by giving me the
opportunity to sail with the RV Thompson for the I06S line. My work at
SIO focuses on identifying predictable patterns in the ocean and the
atmosphere on time scales longer than seasonal. I use a suite of long
time series of observational data and modelling experiments to
identify such patterns and to better understand the mechanisms that
give rise to those predictable scales. The data that I use for this
project usually comes in the format of a final product: data from many
years, collected in many ways, compiled, processed, and interpolated.
Numbers on the screen of my computer. However, being at sea and
helping to collect data for many projects has helped me immensely to
understand the complexity involved in generating such datasets. As my
grandmother says, “It is good to know where your food comes from.”

My main role during the cruise was as CTD watch stander. The job
consists in preparing the Rosette before each cast, overseeing the CTD
cast once the Rosette is in the water and triggering the bottles to
collect water at different depths. In addition to this, I was helping
to collect water samples for salinity and alkalinity and helping with
the deployment of drifters and ARGO floats. I was also responsible of
download the data and troubleshooting the Chi-pods (those are
instruments that measure the acceleration and temperature derivatives
to estimate the turbulent mixing). All those tasks helped me to
appreciate the behind the scenes of all the effort that is put to
perform every CTD cast, to collect and to run every water sample, to
process the data and to make sure that all the equipment is working
well with the minimal error possible. It also helped me to better
understand all the limitations that we have when working with
observational oceanography and the colossal effort that is required to
make everything run smoothly. And, even with all the care that the
scientists and the crew put when organizing the cruise, unfortunate
and unexpected events may happen and sometimes not everything can be
accounted for. In this cruise, we had many of those unfortunate
events: engine problems, weather days, medical emergency evacuation,
flooding inside the ship and many problems with the CTD “fish”, that
had to be replaced a few times. It is great to be able to see that,
despite all those unfortunate events, we are building a great and
reliable database to better understand different aspects of the ocean
and how it has been changing.

Besides the professional aspects of the cruise, there is something
else that cannot be forgotten: personal growth. During the six weeks
of the cruise, you have to share small spaces with the same few
people. There are not many distractions. Time has a different pace.
There is plenty of time to talk to your colleagues without the
distraction of our everyday life. Because of that, the rush that we
are used to in our lives does not play a role here and we are more
able to make real and deep human connections.

As the cruise comes to an end, I will miss being at sea. I will miss
the feeling of the ship dancing with the waves in a perfect synchrony.
I will miss walking upstairs to the bridge and, for hours, staring at
the ocean. In the rough days, staring at the 50 feet waves, staring at
the ship navigating throughout those seas. I will miss the turquoise
color of the ocean when those waves break, a moment of such delicacy
that contrasts with the roughness of the environment that surround us.
I will also miss the few moments we had of quiet and glassy seas, the
very few sunny days when we could sit outside in the back deck and the
beautiful skies in the night, when we could see and try to guess the
constellations in the Southern Hemisphere. I will miss being at sea.

I truly appreciate the opportunity that was given by the Go SHIP
program.

Maximilian Kotz

As an incoming graduate student, I felt very lucky to take part in the
2019 GO-SHIP IO6S cruise before actually starting grad school. While
primarily on the cruise to deploy two sea gliders for my PI, I had
also volunteered to participate in the CTD watch with the other 5
graduate students on board. My offer to do so could not have been
better rewarded. After 6 weeks of over-seeing CTD casts, taking water
samples for a variety of properties and deploying numerous SOCCOM
floats and drifters as well as the two sea gliders, I feel I have been
thoroughly initiated into the world of oceanography.

Learning first-hand about measurement and deployment techniques has
given me a respect and understanding for the data that beforehand I
had downloaded and analysed with little appreciation. Plotting
underway data as we transit and discussing CTD data as we cast has
helped me to learn about the structure of the southern ocean. Seeing
the beauty of the oceans we study has deepened my desire to learn
about them. But perhaps most importantly, working alongside such
skilled, dedicated technicians and scientists has been an absolute
pleasure. The atmosphere of the sampling bay was equal parts
professionalism and hilarity; and the guidance of co-chief scientist
Isa Rosso with all things scientific and personal was nothing short of
exceptional.

I am grateful to GO-SHIP for the opportunity to be part of this cruise
and I hope to have the opportunity to do so again in the future. I
look forward to piloting the gliders over the coming months and to
using their and SOCCOM’s data over the coming years in my PhD.



Michael Kovatch

I applied to the GO-SHIP I06S cruise in order to experience being out
in the field on a large research vessel, work with oceanographic data
collection, and to sample in a new part of the ocean. Field work is
one of my favorite aspects of oceanography, but all of my previous
work has been shorter, closer to shore, and on smaller vessels and
boats. Previously working only in the Gulf of Mexico and off of
central California, the opportunity to travel to the Southern
Hemisphere and spend time in the Indian and Southern Oceans was an
exciting prospect.

My duties at sea were varied and interesting, so no point of the
cruise ever felt boring. My primary role was being a CTD watchstander,
which involved monitoring the live data outputs of temperature,
salinity, density, oxygen, fluorescence, and more as the rosette was
lowered to 10 meters above the ocean bottom. This also meant
communicating with the winch operator to ensure the wire tension was
kept in an acceptable range and firing Niskin bottles on the upcasts
to collect water samples which would subsequently be analyzed at the
surface. Once the rosette was recovered, I assisted in sampling
alkalinity, salts, and dO18. The other watchstanders and I also took
turns being ‘sample cop’, which meant keeping track of and policing
the order in which people were allowed to sample from the Niskin
bottles to ensure high-quality samples of CFCs, oxygen, carbon, and
pH.

In addition to watchstander responsibilities, I was one of the
students trained to work with the chipods, which are high-frequency
temperature sensors that are used to infer small-scale mixing. This
required beginning data acquisition and monitoring that the values of
temperature, etc. made sense. Lastly, I assisted with deployments of
Argo floats and surface drifters.

Overall, this cruise has been an excellent experience. I met so many
interesting people who were able to provide further insight into the
diversity of oceanographic research and careers. It was helpful in
reaffirming my passion for being in the field and collecting data. The
cruise was a great environment to work in, with endless camaraderie,
stories, and deep discussions. I am very grateful for the time I got
to spend on the R/V Thompson with the rest of the crew, both science
and ship. I hope to be able to participate in future cruises!



Loicka Baille

As an undergraduate student, being able to join a cruise so early in
my career has been a rare and incredibly opportunity. I’m very
thankful for my advisor, Alejandro Orsi for this chance. I was part of
the CTD watch-stander team which was in charge of preparing the
rosette, firing bottles, and collecting salinity samples. I also
volunteered to help collect alkalinity and oxygen 18 samples. This
cruise allowed me to work with world class instruments and scientists,
and see first-hand how science is being done, and how data is
collected. Being around so many graduate students, I am much better
informed on what graduate school consists of, what criteria to look
for when applying and what different tracks might be out there.

Being an undergraduate student leaving to go on a cruise mid-semester,
I had to take the remaining of my classes online. Taking 7 classes
while working 12 hours shifts and having limited internet connection
was definitely one of the most challenging part of this cruise. I’m
grateful to my teammates, work technicians and professors for
supporting and helping me getting my classes done. Aside from science
and classes, there was some free time left. It was filled with card
games, board games, ping-pong tournaments, and jaw-dropping pranks
among the science team.

I’m extremely thankful for having the chance to work with wonderful
people that made this experience incredibly enjoyable while
instructive. I’m grateful to the GO-SHIP program for providing me with
this wonderful opportunity and hope to continue to participate and
contribute to future cruises as well.




CCHDO DATA PROCESSING NOTES


• File Merge Carolina Berys
I06.pdf (download) #6ccdc
Date: 2019-06-12
Current Status: merged


• File Merge Jerry Kappa
325020190403_do.pdf (download) #b8c67
Date: 2019-06-12
Current Status: dataset


• File Submission Jerry Kappa
325020190403_do.pdf (download) #b8c67
Date: 2019-06-12
Current Status: dataset
Notes
The pdf version of I06S_2019's cruise report is ready for the CCHDO 
Dataset.  It includes all of the PI-provided data reports, CCHDO summary 
pages and CCHDO data processing notes.


• File Online Carolina Berys
325020190403_ct1.zip (download) #49e1b
Date: 2019-06-05
Current Status: unprocessed


• File Online Carolina Berys
325020190403_hy1.csv (download) #8d912
Date: 2019-06-05
Current Status: unprocessed


• File Online Carolina Berys
I06.pdf (download) #6ccdc
Date: 2019-06-05
Current Status: merged


• File Submission Kenneth Jackson
I06.pdf (download) #6ccdc
Date: 2019-06-05
Current Status: unprocessed
Notes
I06S end of cruise data and report


• File Submission Kenneth Jackson
325020190403_hy1.csv (download) #8d912
Date: 2019-06-05
Current Status: unprocessed
Notes
I06S end of cruise data and report


• File Submission Kenneth Jackson
325020190403_ct1.zip (download) #49e1b
Date: 2019-06-05
Current Status: unprocessed
Notes
I06S end of cruise data and report