CRUISE REPORT: I09N
(Updated APR 2020)









Highlights


                             Cruise Summary Information

                Section Designation  I09N
 Expedition designation (ExpoCodes)  33RR20160321
                    Chief Scientist  Leticia Barbero
                              Dates  2016 MAR 21 – 2016 APR 28
                               Ship  R/V Roger Revelle
                      Ports of call  Fremantle, Australia - Phuket, Thailand.

                                                     17°53’N
              Geographic Boundaries  84°45'9.72" E              95°0'2.5"E
                                                   28°18'46.8"S

                           Stations  113
       Floats and drifters deployed  8 Argo floats deployed
     Moorings deployed or recovered  0

                                Contact Information:

                           Dr. Leticia Barbero 
                    Ocean Chemistry and Ecosystems Division CIMAS
            NOAA's Atlantic Oceanographic and Meteorological Laboratory
                    4301 Rickenbacker Causeway • Miami, FL 33149
phone: 305-361-4453 • fax: 305-361-4393 • email: Leticia.Barbero@noaa.gov













                   Final Report Assembly by Jerry Kappa, SIO/UCSD










CRUISE REPORT FOR THE 2016 REOCCUPATION OF I09N


1 GO-SHIP I09N 2016 Hydrographic Program 
  1.1 Programs and Principal Investigators 
  1.2 Science Team and Responsibilities
  1.3 Underwater Sampling Package

2 Cruise Narrative.
  2.1 Summary
  2.2 Issues / Goals not Achieved
  2.3 Acknowledgements 

3 CTDO and Hydrographic Analysis 
  3.1 CTDO and Bottle Data Acquisition 
  3.2 CTDO Data Processing 
  3.3 Pressure Analysis
  3.4 Temperature Analysis 
  3.5 Conductivity Analysis
  3.6 CTD Dissolved Oxygen 

4 Salinity 
  4.1 Equipment and Techniques 
  4.2 Sampling and Data Processing 

5 Nutrients
  5.1 Summary of Analysis
  5.2 Equipment and Techniques 
  5.3 Nitrate/Nitrite Analysis 
  5.4 Phosphate Analysis 
  5.5 Silicate Analysis
  5.6 Ammonium Analysis
  5.7 Sampling 
  5.8 Data collection and processing 
  5.9 Standards and Glassware calibration
  5.10 Quality Control 
  5.11 Analytical problems 

6 Oxygen Analysis
  6.1 Equipment and Techniques 
  6.2 Sampling and Data Processing 
  6.3 Volumetric Calibration 
  6.4 Standards
  6.5 Narrative

7 Total Alkalinity 
  7.1 Total Alkalinity 
  7.2 Total Alkalinity Measurement System
  7.3 Sample Collection
  7.4 Problems and Troubleshooting 
  7.5 Quality Control

8 Dissolved Inorganic Carbon (DIC) 
  8.1 Sample collection
  8.2 Equipment
  8.3 DIC Analysis 
  8.4 DIC Calculation
  8.5 Calibration, Accuracy, and Precision 
  8.6 Underway DIC Samples 
  8.7 Summary

9 Discrete pH Analyses.
  9.1 Sampling 
  9.2 Analysis 
  9.3 Reagents 
  9.4 Data Processing
  9.5 Problems and Troubleshooting 
  9.6 Standardization/Results

10 CFC-11, CFC-12, CFC-113, and SF6
   10.1 Sample Collection
   10.2 Equipment and Technique
   10.3 System performance 
   10.4 Calibration

11 Underway pCO2 Analysis

12 Isotopic composition of nitrogen species
   12.1 Dissolved N gases (N2O and N2) 
   12.2 Nitrate and Nitrite
   12.3 Ammonium 
   12.4 Suspended particulate organic matter (POM)

13 ∆18O𝑂 Sampling.

14 CDOM 
   14.1 Chromophoric Dissolved Organic Matter (CDOM) 
   14.2 Chlorophyll a
   14.3 CDOM Rosette Fluorometer 
   14.4 Spectroradiometer casts
   14.5 Underway optics system 
   14.6 POC sampling 
   14.7 Phytoplankton Pigments and Particulate Absorption

15 Dissolved Organic Carbon

16 Carbon Isotopes in seawater (14/13C)

17 Phytoplankton, 15N/13C and Trace Metals 

18 Plankton Genomic Analysis 

19 LADCP.

20 Chipods
   20.1 Overview .
   20.2 System Configuration and Sampling.
   20.3 Data .
   20.4 Chipod issues: Mini-logger freezing when downloading data

21 ARGO FLOAT DEPLOYMENTS
   21.1 Overview 

22 Student Statements
   22.1 Chawalit Charoenpong 
   22.2 Amanda Fay 
   22.3 Karina Khazmutdinova 
   22.4 Patrick Mears

CCHDO Data Processing Notes
















1  GO-SHIP I09N 2016 Hydrographic Program


Fig. 1.1: Cruise track of I09N


The Indian Ocean I09N repeat hydrographic line was reoccupied for the
US Global Ocean Carbon and Repeat Hydrography Program. Reoccupation of
the I09N transect occurred on the R/V Roger Revelle from March 21st,
2016 to April 28th, 2016. The survey of I09N consisted of *CTDO*,
rosette, *LADCP*, chipod, water samples and underway measurements. The
ship departed from the port of Fremantle, Western Australia and
completed the cruise in the port of Cape Panwa on the island of
Phuket, Thailand.

A total of 113 stations were occupied with one CTDO/rosette/LADCP/ 
chipod package. 1 repeat station from the previous section leg I08S 
station number 83 was the I09N initial station 84. 113 stations 117 
CTDO/rosette/LADCP/chipod casts including 1 test cast performed, for 
the most part, a reoccupation of I09N-2007 and detailed in the following 
sections. 8 Argo/O2 floats were deployed on I09N and detailed in the 
Argo section of the cruise report. 3 trace metal casts were complete 
from the aft A-frame and detailed in the "Phytoplankton, 15N/13C and 
Trace Metals" section of the cruise report. 26 successful spectroradio-
meter (optics) casts were performed through the cruise, also detailed 
in the "CDOM, Chlorophyll A and Spectroradiometer” section of the cruise 
report.


Fig. 1.2: Bottle depth distribution


CTDO data and water samples were collected on each CTDO, rosette,
LADCP and chipod cast, usually within 10 meters of the bottom. Water
samples were measured on board for salinity, dissolved oxygen,
nutrients, *DIC*, pH, total alkalinity and *CFCs*/*SF6*. Additional
water samples were collected and stored for shore analyses of δO^18,
δN15 and δO18 in NO3, *DOC*/*TDN*, 13C/14C, *CDOM*, phytoplankton
pigments, *POC*, *HPLC*, *AP*, DNA, dPOC/dPON, d NO3/NO3, d NO2(^-)/
NO2, NH4(^+), cell counts, urea and bacterial abundance.

A sea-going science team assembled from 17 different institutions 
participated in the collection and analysis of this data set. The
programs, principal investigators, science team, responsibilities,
instrumentation, analysis and analytical methods are outlined in the
following cruise document.











1.1  Programs and Principal Investigators

Program                 | Affiliation| Principal         | Email                    
                        |            | Investigator      | 
=====================================================================================
CTDO Data, Salinity,    | UCSD, SIO  | Susan Becker      | sbecker@ucsd.edu        
Nutrients, Dissolved O2 |            | Jim Swift         | jswift@ucsd.edu          
------------------------+------------+-------------------+---------------------------
Total CO2 (DIC),        | AOML, NOAA | Rik Wanninkhof    | Rik.Wanninkhof@noaa.gov  
Underway pCO2           |            |                   |                          
------------------------+------------+-------------------+---------------------------
Total Alkalinity, pH    | UCSD, SIO  | Andrew Dickson    | adickson@ucsd.edu        
------------------------+------------+-------------------+---------------------------
ADCP                    | UH         | Jules Hummon      | Hummon@hawaii.edu        
                        |            | Eric Firing       | efiring@hawaii.edu
------------------------+------------+-------------------+---------------------------
LADCP                   | LDEO       | Andreas Thurnherr | ant@ldeo.columbia.edu   
------------------------+------------+-------------------+---------------------------
CFCs                    | RSMAS      | Rana Fine         | rfine@rsmas.miami.edu
                        | LDEO       | Bill Smethie      | bsmeth@ldeo.columbia.edu
------------------------+------------+-------------------+---------------------------
DOC, TDN                | UCSB       | Craig Carlson     | carlson@lifesci.ucsb.edu 
------------------------+------------+-------------------+---------------------------
Transmissometry         | TAMU       | Wilf Gardner      | wgardner@ocean.tamu.edu  
------------------------+------------+-------------------+---------------------------
Chipod                  | OSU,       | Jonathan Nash     | nash@coas.oregonstate.edu 
                        | UCSD       | Jen Mackinnon     | jmackinnon@ucsd.edu   
------------------------+------------+-------------------+---------------------------
CDOM, HPLC, POC         | UCSB       | Norm Nelson       | norm@icess.ucsb.edu      
------------------------+------------+-------------------+---------------------------
13C/14C                 | WHOI,      | Ann McNichol      | amcnichol@whoi.edu,      
                        | Princeton  | Robert Key        | key@princeton.edu        
------------------------+------------+-------------------+---------------------------
δO18                    | LDEO       | Peter Schlosser   | schlosser@ldeo.columbia. 
                        |            |                   | edu                      
------------------------+------------+-------------------+---------------------------
δN15 and δO18 in NO3    | WHOI       | Chawalit          | ccharoenpong@whoi.edu   
                        |            | Charoenpong       |
------------------------+------------+-------------------+---------------------------
Genomics/POC            | UCI        | Adam Martiny      | amartiny@ucsi.edu        
------------------------+------------+-------------------+---------------------------
Phytoplankton, δN15/13C | Bigelow    | Mike Lomas        | mlomas@bigelow.org       
------------------------+------------+-------------------+---------------------------
Trace Metals            | Bigelow    | Benjamin Twining  | btwining@bigelow.org     
------------------------+------------+-------------------+---------------------------
Argo/O2 Floats          | UW, PMEL   | Greg Johnson      | gregory.c.johnson@noaa.gov
------------------------+------------+-------------------+---------------------------
Bathymetry/Nav Underway | NOAA       | Leticia Barbero   | leticia.barbero@noaa.gov
Thermosalinograph/Met   |            |                   |                          
------------------------+------------+-------------------+---------------------------
N03 Isotopes            | MPIC       | Francois Fripiat  | ffripiat@mpic.de      






1.2  Science Team and Responsibilities

Duty               | Name                   | Affiliation| Email Address             
=====================================================================================
Chief Scientist    | Letticia Barbero       | AOML       | leticia.barbero@noaa.gov  
-------------------+------------------------+------------+---------------------------
Co-Chief Scientist | Carmen Rodriguez       | UCSD       | crodriguez@rsmas.miami.edu
                   |                        |            |                           
-------------------+------------------------+------------+---------------------------
CTD Watchstander,  | Chawalit Charoenpong   | WHOI       | ccharoenpong@whoi.edu     
NO3 Isotopes       |                        |            |                           
-------------------+------------------------+------------+---------------------------
CTD Watchstander,  | Amanda Fay             | U.         | arfay@wisc.edu            
Weather            |                        | Wisconsin  |
-------------------+------------------------+------------+---------------------------
CTD Watchstander,  | Karina Khazmutdinova   | FSU        | kk11m@my.fsu.edu          
Chipods            |                        |            |
-------------------+------------------------+------------+---------------------------
CTD Watchstander,  | Patrick Mears          | Coastal    | patrickamears@gmail.com   
LADCP              |                        | Carolina   |
-------------------+------------------------+------------+---------------------------
Res Tech           | Matthew Durham         | UCSD       | mjdurham@ucsd.edu         
-------------------+------------------------+------------+---------------------------
Res Tech           | John Edward Cumminskey | UCSD       | jecummiskey@ucsd.edu      
-------------------+------------------------+------------+---------------------------
Computer Tech      | Brent Devries          | UCSD       | bdevries@ucsd.edu         
-------------------+------------------------+------------+---------------------------
Nutrients, ODF     | Susan Becker           | UCSD ODF   | sbecker@ucsd.edu          
supervisor,        |                        |            |                           
SOCCOM floats      |                        |            |                           
-------------------+------------------------+------------+---------------------------
Nutrients          | John Ballard           | UCSD ODF   | jrballar@ucsd.edu         
-------------------+------------------------+------------+---------------------------
CTDO Processing,   | Courtney Schatzman     | UCSD ODF   | cschatzman@ucsd.edu       
Database Management|                        |            |                           
-------------------+------------------------+------------+---------------------------
Salts, ET, Deck    | Sergey Tepyuk          | UCSD SEG   | sergey1@ucsd.edu          
-------------------+------------------------+------------+---------------------------
Dissolved O2,      | Andrew Barna           | UCSD ODF   | abarna@gmail.com          
Database Management|                        |            |                           
-------------------+------------------------+------------+---------------------------
Dissolved O2,      | Joseph Gum             | UCSD ODF   | jgum@ucsd.edu             
Database Support   |                        |            |                           
-------------------+------------------------+------------+---------------------------
SADCP, LADCP       | Takaya Uchida          | LDEO       | tuchida@ldeo.columbia.edu 
-------------------+------------------------+------------+---------------------------
DIC, underway pCO2 | Robert Castle          | AOML       | robert.castle@noaa.gov    
-------------------+------------------------+------------+---------------------------
DIC                | Morgan Ostendorf       | PMEL       | morgan.ostendorf@noaa.gov 
-------------------+------------------------+------------+---------------------------
CFCs, SF6          | Eugene Gorman          | LDEO       | egorman@ldeo.columbia.edu 
-------------------+------------------------+------------+---------------------------
CFCs, SF6          | Benjamin Hickman       | LDEO       | hickmanb@hawaii.edu       
-------------------+------------------------+------------+---------------------------
CFCs, SF6 student  | Molly Martin           | RSMAS      | mmmartin@rsmas.miami.edu  
-------------------+------------------------+------------+---------------------------
Total Alkalinity   | David Cervantes        | UCSD       | d1cervantes@ucsd.edu      
-------------------+------------------------+------------+---------------------------
Total Alkalinity   | Ellen Briggs           | UCSD       | ebriggs@ucsd.edu          
-------------------+------------------------+------------+---------------------------
pH                 | Stephanie Mumma        | UCSD       | stephaniemumma@hotmail.com
-------------------+------------------------+------------+---------------------------
CDOM               | Erik Stassinos         | UCSB       | norm@icess.ucsb.edu       
---------------------+----------------------+------------+---------------------------
CDOM               | Jeremy Kravitz         | U. Puerto  | jeremy.kraviz@gmail.com   
                   |                        | Rico       |
-------------------+------------------------+------------+---------------------------
DOC, TDN, Radio    | Jacqui Comstock        | UCSB       | jacquicomstock@gmail.com  
Carbon             |                        |            |                           
-------------------+------------------------+------------+---------------------------
Phytoplankton,     | Steven Baer            | Bigelow    | sbaer@bigelow.org         
15N/13C            |                        |            |
-------------------+------------------------+------------+---------------------------
Genomics/POM       | Cathy Garcia           | UCI        | catgar@uci.edu            
-------------------+------------------------+------------+---------------------------
Genomics/POM       | Nathan Garcia          | UCI        | n8garcia@gmail.com        
-------------------+------------------------+------------+---------------------------
Trace Metals       | Sara Rauschenberg      | Bigelow    | srauschenberg@bigelow.org 






1.3  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 10.4L.
Underwater electronic components primarily consisted of a SeaBird
Electronics pressure sensor and housing unit with dual exhaust, dual
pumps, dual temperature, a reference temperature, dual conductivity,
dissolved oxygen, transmissometer, chlorophyll fluorometer and
altimeter. LADCP and chipods instruments were deployed with the
CTD/rosette package and their use is outlined in sections of this
document specific to their analysis.

CTD was mounted horizontally in the CTDO/rosette/LADCP/chipod for all
stations. The cages were mounted at the bottom of the rosette frame and
located to one side of the carousel. The temperature, conductivity,
dissolved oxygen, respective pumps and exhaust tubing were mounted to
the CTD 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 transmissometers were mounted horizontally. The fluorometers and
altimeters were mounted vertically inside the bottom ring of the
rosette frame. The 300 KHz bi-directional Broadband LADCP (RDI)
units, when in use, were mounted vertically on the top and bottom
sides of the frame. The LADCP battery pack was also mounted on the
bottom of the frame.



Equipment        | Model    | S/N    | Cal Date     | Sta     | Resp Party  
============================================================================
Rosette          | 36-place | Yellow |              | 84-196  | *STS*/*ODF* 
-----------------+----------+--------+--------------+---------+-------------
CTD              | SBE9+    | 831    |              | 84-194  | *STS*/*ODF* 
-----------------+----------+--------+--------------+---------+-------------
Pressure Sensor  | Digi-    | 99677  | Nov 17, 2015 | 84-194  | *STS*/*ODF* 
                 | quartz   |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE3+    | 32166  | Nov 17, 2015 | 84-194  | *STS*/*ODF* 
Temperature      |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE4C    | 43399  | Nov 10, 2015 | 84-112  | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE4C    | 43023  | Dec 1, 2015  | 113-114 | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE4C    | 43207  | Jan 20, 2016 | 115-122 | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE4C    | 42819  | Jan 21, 2016 | 115-122 | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary Pump     | SBE5     | 55011  |              | 84-194  | *STS*/*ODF* 
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE3+    | 34226  | Nov 17, 2015 | 84-194  | *STS*/*ODF* 
Temperature      |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE4C    | 41919  | Nov 10, 2015 | 84-102  | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE4C    | 43215  | Nov 10, 2015 | 103-196 | *STS*/*ODF* 
Conductivity     |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary Pump   | SBE5     | 54128  |              | 84-194  | *STS*/*ODF* 
-----------------+----------+--------+--------------+---------+-------------
Transmissometer  | Cstar    | CST-   | Oct 8, 2016  | 84-194  | *TAMU*      
                 |          | 1636DR |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Fluorometer      | WetLabs  | FLRTD- |              | 84-194  | *STS*/*ODF* 
Chloro           |          | 2050   |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE43    | 431138 | Nov 19, 2015 | 84-97,  | *STS*/*ODF* 
Dissolved Oxygen |          |        |              | 105-196 |             
-----------------+----------+--------+--------------+---------+-------------
Primary          | SBE43    | 430848 | Nov 19, 2015 | 98-104  | *STS*/*ODF* 
Dissolved Oxygen |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE43    | 430197 | Feb 09, 2016 | 99-100, | *STS*/*ODF* 
Dissolved Oxygen |          |        |              | 106     |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE43    | 431138 | Nov 19, 2015 | 101-104 | *STS*/*ODF* 
Dissolved Oxygen |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE43    | 430875 | Nov 20, 2015 | 105     | *STS*/*ODF* 
Dissolved Oxygen |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Secondary        | SBE43    | 430275 | Jan 21, 2016 | 107     | *STS*/*ODF* 
Dissolved Oxygen |          |        |              |         |             
-----------------+----------+--------+--------------+---------+-------------
Carousel         | SBE32    |        |              | 84-194  | *STS*/*ODF* 
-----------------+----------+--------+--------------+---------+-------------
Reference        | SBE35    |        |              | 84-127, | *STS*/*ODF* 
Temperature      |          |        |              | 131-194 |             


The CAST6 aft winch deployment system was successfully used for all
stations. 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 I09N-2016. A mechanical termination was
completed after station/cast 114/02. An electrical re-termination took
place after station/cast 115/02 due to signal failure at ~3000 dbar
up-cast.

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. LADCP technician would check for LADCP
battery charge, prepare instrument for data acquisition and disconnect
cables. The chipod battery was monitored for charge and connectors
were checked for fouling and connectivity. Every 20 stations, the
transmissometer windows were cleaned and an on deck blocked and un-
blocked voltage readings were recorded prior to the cast. 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 essentially
the reverse of launching. The rosette, CTD and carousel were rinsed
with fresh water frequently. CTD maintenance included rinsing de-
ionized water through both plumbed sensor lines between casts. On
average, once every 20 stations, 1% Triton-x solution was also rinsed
through both conductivity sensors. The rosette was routinely examined
for valves and o-rings leaks, which were maintained as needed.

Some complications were overcome to complete CTDO/rosette/LADCP/chipod
station casts for I09N. We had some communications issues after a few
full ocean depth casts, and found that the carousel’s bulkhead
connector appeared to have some damage. This was only noticed when the
surface bottle at the top of stations/casts 125/01, 126/01 and
127/01 wouldn’t trip. The carousel would lose communication (the
pressure of the deeper casts was holding the connector seated in place
later allowing seawater ingress towards the surface where pressure
decreased as the cast progressed). Since we do not have a spare 36
place carousel, we have worked to repair this connection by creating
supports for the connector with heat shrink. We used a straight cable
while repairs to the damaged Y-cable were made. The Y-cable enables
communication with the SBE35 reference temperature sensor. While the
Y-cable was repaired (sta: 127-133) we did not have data from SBE35.
Since these repairs, we did not have any more communications errors
with the carousel. However, during the troubleshooting for this issue,
another carousel issue came up with bottle #12 failing to fire on
station/casts 127/03, 130/02, 131/02, 133/01 and 134/01. Our first
suspicion was just a sticky latch, but no amount of cleaning or
swapping of latches was reliably solving the problem. Closer
inspection of the magnet/solenoid for bottle 12 showed some of the
seal starting to protrude from the solenoid housing surface, likely
blocking the latch release mechanism and causing the bottle fire to
fail. As the stations are starting to get closer together and
shallower, losing a single bottle depth has not seemed to be a major
issue for science, so rather than risk further damage to the carousel
by attempting surgery on the damaged seal, we removed bottle 12
from the rosette and bottle firing sequence and operated with 35
bottles. Shortly following the events with carousel trigger 12, the
seals at bottle position #5 (sta: 150) and #20 (sta: 180) were found
to be extruding as well. Both of these bottle positions were taken out
of the firing sequence. Finally bottle 35 showed some leakage during a
couple of casts and was swapped with the replacement bottle from
position 5 to resolve the issue.

















2  CRUISE NARRATIVE


2.1  Summary

The US GO-SHIP I09N 2016 repeat hydrography cruise took place in the
Indian Ocean from March 21 through April 28, 2016. This I09N cruise
track was a repeat of the 2007 occupation and is the northern
extension of the I08S cruise which took place February 14 to March 17,
2016 on the R/V Roger Revelle. This hydrographic survey of the Indian
Ocean included: rosette casts with mounted CTD/DO/LADCP/Chi-
pods/Fluorometer/Transmissometer; bio-optical casts; trace metal
casts; underway shipboard ADCP and pCO2/fluorescence/T/S measurements;
underway sampling for biochemical measurements (HPLC/AP/NH_4/PO*/
nitrogen isotopic composition of POM); as well as ARGO float and XBT
deployments. Mobilization onto the R/V Revelle occurred on March 18th
in Fremantle, Australia and the cruise departed Fremantle on March
21st, 2016 at 13:24 (local). The R/V Revelle arrived to Phuket,
Thailand on April 28, 2016 at 08:00.

The general I09N cruise track is meridional, heading north along the
95E longitude line until approximately 5S, where the occupation veers
northwesterly in order to stay within international waters (see
figure in front page of this report).

Following the cruise track of the 2007 I09N, we reoccupied the so-
called “bow-tie” section in the Bay of Bengal, which is a triangular
track extending zonally from roughly 85-90E on 10N, and meridionally
from roughly 7-10N on 86/85E. The zonal transect along 10N starting on
station 167 is a reoccupation of stations from WOCE line I01E, which
was only occupied once in 1995. Given the time availability at that
point we decided to extend the transect as far west as international
waters would allow, and we added two extra stations to our cruise, a
reoccupation of stations 981 and 980 of the I01E line. This brought
our total number of stations from 111 to 113.

The location of stations 190 and 196 had to be slightly modified with
respect to their counterparts on I09N 2007 because they fell within
the EEZ of India. 190 was moved slightly westward, while 196, our
northernmost station, was moved about 7’ south, to 17.883N instead of
18.0N.

Sampling occurred at 20-30 nm-intervals from March 25 through April
24. A total of 113 stations were occupied and 116 CTD/rosette casts
were deployed. The CTD/rosette package (CTD/DO/LADCP/Chi-
pod/fluorometer/transmissometer) was deployed to within 10-15m of the
bottom on 110 stations. Stations 103-105 were deeper than 6000m. Due
to pressure limitations of the equipment installed on the rosette, the
deepest bottle was fired at 6000m on these stations, regardless of
actual depth. A similar gap occurred during the 1995 and 2007
occupations for similar reasons. At stations 97, 127, and 162 (termed
"Regional Stations,") an additional rosette was deployed to a depth
near 200m for the collection of biochemical samples. Approximately
once per day, if the weather and timing were conducive to sampling,
separate trace metal casts (28 total) and bio-optical casts (23 total)
were deployed from the aft deck.

Water samples from the rosette/CTD package were collected in up to 36
10L Bullister bottles at all stations providing water samples for
CFCs/SF6, dissolved oxygen, Total DIC, pH, Total Alkalinity,
nutrients, salinity, DOC, DO14C, CDOM, Chl-a, HPLC, AP, POC, δ15N2,
N2, N2O, isotopic composition of NO3-, NO2- and NH4- isotopes, DNA
composition. Underway surface pCO2, temperature, salinity, dissolved
oxygen, multi-beam bathymetry and meteorological measurements were
collected, as well as a suite of biochemical samples for subsequent
analysis. Approximately once per day, at the same stations where trace
metals casts were conducted, 3 bottles from the CTD were tripped at 20
meters to be dedicated to genomics and nutrient uptake rate incubation
experiments.

Eight Argo floats were deployed throughout the cruise. XBTs were
deployed on all days that CTD casts were not performed (underway in
international waters) and they provided upper water column temperature
profiles for calibration of the multi-beam. The cruise ended in
Phuket, Thailand on April 28, 2016 with deMOB occurring on April 29,
2016.

A highlight of this cruise has been the number of collaborations and
potential new projects that have sprouted between scientists from
different institutions (UC Irvine, Bigelow and WHOI) for
biogeochemical studies in the Bay of Bengal using underway surface
water from the science seawater line and left-over water from the
CTDs (these samples have been added to the sample log for keeping
track).


2.2  Issues / Goals not Achieved

No major problems were experienced during the cruise and all science
goals were successfully achieved. In fact, the excellent weather and
performance of the equipment allowed us to add two extra “bonus”
stations along 10N, extending the reoccupation of I01E as far west as
international waters would allow us.

The following are some minor issues experienced during the cruise: On
Sunday April 3rd, while on station 115, we had a loss of
communications with the CTD which was then at 3000 m depth and coming
up. We recovered the package and determined that one of the conductor
cables had shorted. We switched to an alternate one in the winch and
proceeded with sampling, redoing a cast on station 115. There were no
further communication issues after that.

In the second half of the cruise, 3 Niskin bottles had to be taken out
of the rosette because of extruded seals on the magnets that trigger
the closing of the bottles. At that point our deepest stations had
been completed and the remaining ones were shallower. Our replacement
carousel was a 24-bottle position, so it was preferable to keep using
the 36-bottle carousel with 33 Niskins. Given the depths of the
stations, this did not significantly impact the vertical resolution of
the profiles.




2.3  Acknowledgements

The successful completion of the cruise relied on dedicated assistance
from many individuals on shore and on the UNOLS ship *Roger Revelle*.
Funded investigators in the project and members of the GO-SHIP
executive committee, Lynne Talley, Greg Johnson and Jim Swift in
particular, were instrumental in the successful planning and executing
of the cruise. The participants in the cruise showed dedication and
camaraderie during their 39 days at sea, often spending time from
their off shift to assist other colleagues. Officers and crew of the
*Roger Revelle* exhibited a high degree of professionalism and
assistance to accomplish the mission and to make us feel at home
during the long voyage. Captain Chris Curl oversaw a smoothly running
ship and engaged with the scientific party. The expertise and
professionalism of the restechs on board is greatly acknowledged.
Their expert instrument and infrastructure troubleshooting experience
ensured that any maintenance to our equipment was performed with
minimal time loss, if any. All officers, deck crew, engineers, and
galley staff contributed to the success of this long cruise. Their
assistance is gratefully acknowledged.

The U.S. GO-SHIP is sponsored by the National Science Foundation and
the NOAA Climate Observation Division of the Climate Program Office
(COD/CPO).

Clearance was requested and granted from the sovereign nation of
Australia for research conducted in their declared territorial waters.
Their permission to execute the research effort in the waters
surrounding Cocos Islands was critical for the repeat occupation and
is greatly appreciated.



























3  CTDO AND HYDROGRAPHIC ANALYSIS


3.1  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 2009 SBE
SeaSave v.7.18c 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 10 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 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 multibeam center beam
depth were all monitored to determine the distance of the package from 
the bottom. The winch was directed to slow decent rate to 30m/min 100m
from the bottom and 10m/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.

After the last bottle was closed, the CWO directed winch to recover
the rosette. Once out of the water 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 as well
as correspondence between rosette bottles and analytical samples
drawn.

Normally the CTD sensors were rinsed after each station using syringes
fitted with Tygon tubing and filled with a fresh solution of dilute
Triton-X in de-ionized water. The syringes were left on the CTD
between casts, with the temperature and conductivity sensors immersed
in the rinsing solution.


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.


3.2  CTDO Data Processing

Shipboard CTD data processing was performed after deployment using
SIO/ODF CTD processing software v.5.1.0. CTD acquisition data were
copied onto the Linux system and database, then processed to a
0.5-second time-series. 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 113 CTD stations were occupied including one test station.
A total of 116 CTDO/rosette/LADCP/chipod casts were completed: 113
standard CTDO/rosette/LADCP/chipod casts, 3 trace metal program casts,
one test cast. We had one aborted cast not included in the completed cast
count. 194 successful CTD casts were complete in combination with the
I08S portion of this cruise. The 36-place (CTD #831) rosette was used
for all station/casts.

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 O2 comparisons were made between
down and up casts as well as between groups of adjacent deployments.
Vertical sections of measured and derived properties from sensor data
were checked for consistency.

A number of issues were encountered during I09N-2016 that directly
impacted CTD analysis. Issues that directly impacted bottle closures,
such as carousel communication problems, were detailed in the
Underwater Sampling Package section of this report. Temperature,
conductivity and oxygen analytical sensor issues are details in the
following respective sections.


3.3  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 Paroscientific Digiquartz pressure transducer S/N: 831-99677 was
calibrated on November 17th, 2015 at the SIO/ Calibration Facility.
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 Serial 831-99677; Station Set 84-196


                         | Start P (dbar) | End P (dbar)
          ==============================================
          Min            |     -0.3       |     0.0     
          ---------------+----------------+-------------
          Max            |      0.0       |     0.3     
          ---------------+----------------+-------------
          Average        |     -0.2       |     0.2     
          ---------------+----------------+-------------
          Applied Offset |                |    -0.215   


An offset of -0.215 was applied to every cast performed by CTD 831.
On-deck pressure reading for CTD 831 varied from -0.3 to 0.0 dbar
before the casts, and 0.0 to 0.3 dbar after the casts. Before and
after average difference was -0.2 and 0.2 dbar respectively. The
overall average offset before and after cast was -0.4 dbar.


3.4  Temperature Analysis

Laboratory calibrations of temperature sensors were performed prior to
the cruise at the SIO/ Calibration Facility. Dates of laboratory
calibrations 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 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.
It 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 5 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 + Offset

                      T(90)  = T + tp(1)P + t(0)

         T(90)  = T + aP(2) + bP + cT(2) + dT + Offset

Temperature correction coefficients for each station are provided in
the APPENDIX. Corrected temperature differences are shown in the
following figures.


Fig. 3.1: SBE35RT-T1 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.2: Deep SBE35RT-T1 by station (Pressure ≥ 2000dbar).

Fig. 3.3: SBE35RT-T2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.4: Deep SBE35RT-T2 by station (Pressure ≥ 2000dbar).

Fig. 3.5: T1-T2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.6: Deep T1-T2 by station (Pressure ≥ 2000dbar).

Fig. 3.7: SBE35RT-T1 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.8: SBE35RT-T2 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.9: T1-T2 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).


The 95% confidence limits for the mean low-gradient (values -0.002°C
≤ T1-T2 ≤ 0.002°C) differences are ±0.0038°C for SBE35RT-T1,
±0.0040°C for SBE35RT-T2 and ±0.0017°C for T1-T2. The 95% confidence
limits for the deep temperature residuals (where pressure ≥
2000dbar) are ±0.00087°C for SBE35RT-T1, ±0.00010°C for SBE35RT-T2 and
±0.0011°C for T1-T2.

Minor complications impacted the temperature sensor data used for the
I09N cruise. The SBE35RT sensor was by-passed with a straight cable
when carousel communication issues arose. As a result of carousel
communications issues, temperature difference data is missing for
stations 127-132. The carousel communication issues are detailed in
the Underwater Sampling Package section of the report. The exhaust
system pumps shut off on up-cast when the primary conductivity sensor
failed on stations 120, 121 and 122. Those complications are detailed
in the following section. The pump failure resulted in poor flow
through ventilation of the temperature sensors particularly in the
primary sensors. The secondary temperature data was reported for
station data 120-122. The resulting affected sections of data have
been coded and documented in the quality code APPENDIX.



3.5  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
shipboard 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. 3.10: Coherence of conductivity differences as a function of
           temperature differences.


Uncorrected conductivity comparisons are shown in the following figures 


Fig. 3.11: Uncorrected C(Bottle) - C1 by station (-0.002°C ≤ T1-T2
           ≤ 0.002°C).

Fig. 3.12: Uncorrected C(Bottle) - C2 by station (-0.002°C ≤ T1-T2
           ≤ 0.002°C).

Fig. 3.13: Uncorrected C1-C2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).


A functioning SBE4C sensor typically exhibits 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, responses to
pressure, temperature and conductivity were examined for each
conductivity sensor. The response model is second order with respect
to pressure, first order with respect to temperature, first order
with respect to conductivity and first order with respect to time.
The functions used to apply shipboard calibrations are as follows.

The residual conductivity differences after correction are shown in
Figures.

Fig. 3.14: Corrected C(Bottle) - C1 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.15: Deep Corrected C(Bottle)  - C1 by station (Pressure >=2000dbar).

Fig. 3.16: Corrected C(Bottle)- C2 by station (-0.002°C ≤ T1-T2 < 0.002°C).

Fig. 3.17: Deep Corrected C(Bottle) - C2 by station (Pressure >=2000dbar).

Fig. 3.18: Corrected C1-C2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.19: Deep Corrected C1-C2 by station (Pressure >= 2000dbar).

Fig. 3.20: Corrected C(Bottle) - C1 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.21: Corrected C(Bottle) - C2 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.22: Corrected C1-C2 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

Fig. 3.23: Corrected C(Bottle) - C1 by conductivity (-0.002°C ≤ T1-T2 ≤ 
           0.002°C).

Fig. 3.24: Corrected C(Bottle) - C2 by conductivity (-0.002°C ≤ T1-T2 ≤ 
           0.002°C).

Fig. 3.25: Corrected C1-C2 by conductivity (-0.002°C ≤ T1-T2 ≤ 0.002°C).


The final corrections for all conductivity sensors used on this cruise
are summarized in APPENDIX. (TO BE MADE AVAILABLE LATER ON SHORE)
Corrections made to all conductivity sensors are of the form:

C:sub: *cor* = C + cp(2) P(^2) + cp(1) P + c(1) C + c(0)

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 also published in the APPENDIX.

The 95% confidence limits for the mean low-gradient (values -0.002°C
≤ T1-T2 ≤ 0.002°C) differences are ±0.0040°C for salnity-C1. The
95% confidence limits for the deep salinity residuals (where pressure
≥ 2000dbar) are ±0.0016°C for salinity-C1.

A number of issues affected conductivity and calculated CTD salinities
during this cruise. We suffered a number of unique conductivity
failures throughout the cruise as follows: * Secondary conductivity
sensor (S/N:41919) failed at the bottom of our deep 5900+ m cast on
102/01. * Primary conductivity sensor (S/N: 3399) failed in a similar
fashion at the bottom of cast 112/01 * Primary conductivity sensor (S/N:
3023) was found to have a significant drift and replaced after cast
114/01 * Primary conductivity sensor (S/N: 3207) had pressure
dependent irregularities that presented like data signal spikes on
cast 120/02. The connectors were examined and reseated. The problem
occurred again on 121/02 at which time the cable was replaced. The
problem persisted on station 122/01 and the sensor was finally
replaced.


Fig. 3.26: Salinity residuals by station (-0.002°C ≤ T1-T2 < 0.002°C).

Fig. 3.27: Salinity residuals by pressure (-0.002°C ≤T1-T2 ≤ 0.002°C).

Fig. 3.28: Deep Salinity residuals by station (Pressure >= 2000dbar).





3.6  CTD Dissolved Oxygen

Laboratory calibrations of the dissolved oxygen 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 SBE43 frequencies to µmol/kg oxygen values for acquisition
only. Additional shipoard 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 O2 check
samples taken at bottle stops by matching the down cast CTD data to
the up cast trip locations along isopycnal surfaces. CTD dissolved O2
was then calculated using Clark Cell MPOD O2 sensor response model
for Beckman/SensorMedics and SBE43 dissolved O2 sensors. The residual
differences of bottle check value versus CTD dissolved O2 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 (tau(p)), a slow tau(Tf)
and fast tau(Ts) thermal response, package velocity tau(dP),
thermal diffusion tau(dT) and pressure hysteresis tau(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 O2 concentration is then
calculated:

          ⎛               P(h)     ⎞
          |          C(2) ----      |
O2 ml/l = |C • V  • e     5000 +C   | • f   (T,P)•
          ⎝ 1   DO               3 ⎠     sat
          
                                                dOc        dP
               (C(4)t(1)+C(5)t(2)+C(7)P(1)+C(6) --- + C(8) --- + C(9)dT)
              e                                 dT         dTt


Where:

• O2 ml/l           Dissolved O2 concentration in ml/l

• V(DO)             Raw sensor output

• C(1)              Sensor slope

• C(2)              Hysteresis response 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-response low-pass filtered temperature (°C)

• T(s)              Short-response low-pass filtered temperature (°C)

• P(l)              Low-pass filtered pressure (decibars)

• dOc / 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)       Response coefficients


CTD dissolved O_2 residuals are shown in the following figures:

Fig.3.29: O2 residuals by station (-0.01°C ≤ T1-T2 ≤ 0.01°C).


The standard deviations of 1.58 (µmol/kg) for all oxygens and 0.65
(µmol/kg) for deep oxygens are only presented as general indicators of
goodness of fit. SIO makes no claims regarding the precision or
accuracy of CTD dissolved O2 data.


Fig.3.30: O2 residuals by pressure (-0.01°C ≤ T1-T2 ≤ 0.01°C).

Fig.3.31: Deep O2 residuals by station (Pressure >= 2000dbar).


A few minor problems with acquisition of data complicated the CTD
dissolved oxygen fits as follows: SBE43 (S/N: 431138) data signal was
steadily growing noisier with each progressive cast. It was replaced
after station/cast 97/01 with SBE43 (S/N: 430848), which appeared to 
have an even worse signal past 3500 dbar on down cast. A secondary SBE43 
(S/N:430197) sensor was added to AUX 3 on station/cast 100/01 and both
primary SBE43 (S/N: 430848) and secondary presented the same deep cast 
gradual increase of signal to noise ratio. Both sensors were moved to 
AUX 2 on station/cast 101/02 and symptoms persisted. We rerouted the 
exhaust lines from both sensors to vent slightly higher than initially 
set on station cast 102/01. This solved this issue. SBE43 (S/N: 431138) 
had a stronger signal and was moved back to the primary position on 
station/cast 105/01. All compromised data signals were recorded and 
coded in the data files. The bottle trip levels affected by the signals 
are reflected 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).














































4  SALINITY


4.1  Equipment and Techniques

A single Guildline Autosal, model 8400B salinometer (S/N 65-740)
located in salinity analysis room, was used for all salinity
measurements. The autosal was recently calibrated before the last
cruise, I08S. The salinometer readings were logged on a computer using
in house LabView program developed by Carl Mattson. The Autosal's
water bath temperature was set to 21°C, until station 135. After which
the Autosal was set to 24°C due to the rising ambient tempertures of
the Northern Indian Ocean. The laboratory's temperature was also set
and maintained to just below 21°C until station 135 and just below 24°
C after. This is to ensure stabilize reading values and improve
accuracy. Salinity analyses were performed after samples had
equilibrated to laboratory temperature, usually 8 hours after
collection. The salinometer was standardized for each group of samples
analyzed (usually 2 casts and 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. Prior to each run a sub-standard
flush, approximately 200 ml, of the conductivity cell was conducted to
flush out the DI water used in between runs. For each calibration
standard, the salinometer cell was initially flushed 6 times before a
set of conductivity ratio reading was taken. For each sample, the
salinometer cell was initially flushed at least 3 times before a set
of conductivity ratio readings were taken.

IAPSO Standard Seawater Batch P-158 was used to standardize all casts.


Fig. 4.1: Salinity standard IAPSO Batch P-158


4.2  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.

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

PIs
   • Susan Becker
   • James Swift

Technicians
   • Susan Becker
   • John Ballard


5.1  Summary of Analysis

• 3887 samples from 113 ctd stations

• The cruise started with new pump tubes and they were changed prior
  to stations 115 and 166.

• 4 sets of nitrate, phosphate, and silicate Primary/Secondary
  standards were made up over the course of the cruise.

• 2 sets of Primary and 26 sets of Secondary nitrite and ammonia
  standards were made up over the course of the cruise.

• The cadmium column efficiency was checked periodically and ranged
  between 88%-100%.  A new column was put on if the efficiency fell
  below 97%.


5.2  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
GO-SHIP repeat hydrography manual (Hydes et al., 2010) [Hydes2010].


5.3  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 540nm. 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 l liter volume.
   Add 5ml of 2% CuSO4 solution to this NH4Cl stock. This should last
   many months.


5.4  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 (880nm after station
59, see section on analytical problems for details).

**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.


5.5  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.


5.6  Ammonium Analysis

**Fluorometric method**
   Ammonia is analyzed using the method described by Kerouel and
   Aminot [Kerouel1997]. The sample is combined with a working reagent
   made up of ortho-phthalaldehyde, sodium sulfite and borate buffer
   and heated to 75degC. Fluorescence proportional to the NH4
   concentration is emitted at 460nm following excitation at 370nm.

**REAGENTS**

Ortho-phthalaldehyde stock (OPH):
   Dissolve 8g of ortho-phthalaldehyde in 200mls ethanol and mix
   thoroughly. Store in a dark glass bottle and keep refrigerated.

Sodium sulfite stock:
   Dissolve 0.8g sodium sulfite in DIW and dilute up to 100ml. Store
   in a glass bottle, replace weekly.

Borate buffer
   Dissolve 120g disodium tetraborate in DIW and bring up to 4L
   volume.

Working reagent:
   In the following order and proportions combine: 1L borate buffer
   20ml stock orthophthalaldehyde, 2 ml stock sodium sulfite, 4 drops
   40% Surfynol 465/485 surfactant and mix. Store in a glass bottle
   and protect from light. Replace weekly. Make this up at least one
   day prior to use. Store in dark bottle and protect from outside
   air/nh4 contamination.


5.7  Sampling

Nutrient samples were drawn into 40 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.


5.8  Data collection and processing

Data collection and processing was done with the software (ACCE ver
6.10) 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.



5.9  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 prior to each run from a
secondary. Working standards were made up in low nutrient seawater
(LNSW). LNSW used for this cruise was deep water collected at a test
station at the beginning of the cruise track. 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   | PO4   | SiO3  | NO2   | NH4
                | (uM)  | (uM)  | (uM)  | (uM)  | (uM)
             ===+=======+=======+=======+=======+=====
              0 | 0.0   | 0.0   | 0.0   | 0.0   | 0.0 
             ---+-------+-------+-------+-------+-----
              3 | 15.50 | 1.2   | 60    | 0.50  | 2.0 
             ---+-------+-------+-------+-------+-----
              5 | 31.00 | 2.4   | 120   | 1.00  | 4.0 
             ---+-------+-------+-------+-------+-----
              7 | 46.50 | 3.6   | 180   | 1.50  | 6.0 


5.10  Quality Control

All final data were reported in micro-moles/kg. NO3, PO4, NO2 and
NH4 were reported to two decimals places and SIL to one. Accuracy is
based on the quality of the standards the levels are:


                 NO3 | 0.05 µM (micro moles/Liter)
                 ----+----------------------------
                 PO4 | 0.004 µM                   
                 ----+----------------------------
                 SIL | 2-4 µM                     
                 ----+----------------------------
                 NO2 | 0.05 µM                    
                 ----+----------------------------
                 NH4 | 0.03 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
              ----------+--------------------+-------
              NO3       | 31.00              | 0.17  
              ----------+--------------------+-------
              PO4       | 2.14               | 0.02  
              ----------+--------------------+-------
              SIL       | 98.9               | 0.55  


SIO/ODF has been using Reference Materials for Nutrients in Seawater
(RMNS) on repeat Hydrography cruises as another estimate of accuracy
and precision for each cruise since 2009. The accuracy and precision
(standard deviation) for this cruise were measured by analysis of a
RMNS with each run. The RMNS preparation, verification, and suggested
protocol for use of the material are described by Aoyama [Aoyama2006]
[Aoyama2007], [Aoyama2008] and Sato [Sato2010]. RMNS batch BV was used
on this cruise, with each bottle being used twice before being
discarded and a new one opened. Data are tabulated below.

    Parameter | Concentration | stddev | assigned conc | diff  
    ==========+===============+========+===============+====== 
        -     |   (µmol/kg)   |   -    |   (µmol/kg)   |  -   
    ----------+---------------+--------+---------------+------
       NO3    |     35.19     | 0.17   |    35.36      | 0.16 
    ----------+---------------+--------+---------------+------
       PO4    |      2.49     | 0.02   |     2.498     | 0.008
    ----------+---------------+--------+---------------+------
       Sil    |    101.5      | 0.55   |   102.2       | 0.71 
    ----------+---------------+--------+---------------+------
       NO2    |      0.05     | 0.003  |     0.047     |-0.002


5.11  Analytical problems

Distilled deionized water was checked for all nutrients during cruise
after reporting a POC filter change warning. All nutrient levels were
below detection limit and good for duration of cruise.

Sulfite reagent was replaced once due to degradation in detected in
OPA working reagent. Occasional phosphate baseline drifts and jumps
were mitigated with periodic soap and bleach cleaning.

[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).

[Hydes2010]     Hydes, D.J., Aoyama, M., Aminot, A., Bakker,
                K., Becker, S., Coverly, S., Daniel, A.,Dickson,A.G.,
                Grosso, O., Kerouel, R., Ooijen, J. van, Sato, K., Tanhua,
                T., Woodward, E.M.S., Zhang, J.Z., 2010. Determination of
                Dissolved Nutrients (N, P, Si) in Seawater with High
                Precision and Inter-Comparability Using Gas-Segmented
                Continuous Flow Analysers, In: GO-SHIP Repeat Hydrography
                Manual: A Collection of Expert Reports and Guidelines.
                IOCCP Report No. 14, ICPO Publication Series No 134.

[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.







6  OXYGEN ANALYSIS

PIs
   • Susan Becker
   • James Swift

Technicians
   • Andrew Barna
   • Joseph Gum


6.1  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 765 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 approximately 0.012N, and thiosulfate
solution approximately 55 gm/l. Pre-made liquid potassium iodate
standards were run every day (approximately every 4-5 stations),
unless changes were made to the system or reagents. Reagent/distilled
water blanks were determined every day or more often if a change in
reagents required it to account for presence of oxidizing or reducing
agents.



6.2  Sampling and Data Processing

3884 oxygen measurements were made. Samples were collected for
dissolved oxygen analyses soon after the rosette was brought on board.
Using a silicone drawing tube, nominal 125ml volume-calibrated iodine
flasks were rinsed 3 times with minimal agitation, then filled and
allowed to overflow for at least 3 flask volumes. The sample drawing
temperatures were measured with an electronic resistance temperature
detector (RTD) embedded in the drawing tube. These temperatures were
used to calculate umol/kg concentrations, and as a diagnostic check of
bottle integrity. Reagents (MnCl2 then NaI/NaOH) were added to fix
the oxygen before stoppering. The flasks were shaken twice (10-12
inversions) to assure thorough dispersion of the precipitate, once
immediately after drawing, and then again after about 30-40 minutes.

The samples were analyzed within 2-14 hours of collection, and the
data incorporated into the cruise database.

Thiosulfate normalities were calculated for each standardization and
corrected to 20 deg C. The 20 deg C normalities and the blanks were
plotted versus time and were reviewed for possible problems. The
blanks and thiosulfate normalities for each batch of thiosulfate were
stable enough that no smoothing was necessary.



6.3  Volumetric Calibration

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


6.4  Standards

Liquid potassium iodate standards were prepared in 6 liter 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 oxidizing and reducing
impurities prior to use.


6.5  Narrative
 
All equipment was set up on the previous leg, I08S. Reagents were made
once the ship was underway and evap water was available.

Standards were run about every 24 hours during the transit to the
first station, 84, to monitor thiosulfate stability. Underway samples
were also being collected and analyzed during the transit.

After station 125, the thiosulfate was replaced with a new batch.

No samples were lost due to analytical error.



[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 determination of dissolved oxygen in
                seawater,” Report WHPO 91-2, WOCE Hydrographic
                Programme Office (Aug 1991).










7  TOTAL ALKALINITY

PI
   * Andrew G. Dickson – Scripps Institution of Oceanography

Technicians
   * David Cervantes
   * Ellen Briggs (Graduate Student)


7.1  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.


7.2  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 0.04 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 is performed automatically using LabVIEW 2012.






7.3  Sample Collection

Samples for total alkalinity measurements were taken at all I09N
Stations (84-196). Two Niskin bottles at each station were sampled
twice for duplicate measurements except for stations where 15 or less
Niskin bottles were sampled. 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 0.06 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 RTE water bath.


7.4  Problems and Troubleshooting

The R/V Roger Revelle is a fantastic research vessel. However, our
electrodes appeared to continually pick up larger than expected
interference from the lab’s neighboring instruments or the ship
itself. Electrode plots could show increased electrode sensitivity
over time. Luckily, enough electrodes were brought on I09N so this
never resulted in a bad measurement. Any unusual measurements (poor
electrode plot / profile outlier) were always rerun.

Normally after samples are collected, they are placed into a water
bath to equilibrate the sample temperature near 20°C, the temperature
at which the sample is measured. This is normally fine when the lab
temperature is within 2°C of 20°C. The lab temperature for I09N was
normally near 25°C. This constantly delayed the titration start times.
To remedy the situation, we equilibrated the sample temperatures to
15°C in a water bath so when it met the 25°C room, it wouldn’t get too
warm waiting for its titration to begin.

Near the end of I09N, a suspected clog in the Sample Delivery System
prevented samples from being dispensed normally into their cells,
causing smaller samples sizes of unknown volumes. Pipette Board A on
the SDS was replaced with Pipette Board B and sample flow resumed
appropriate and reliable continuity. However, shortly after switching
in Pipette Board B, a leaky valve was discovered. Although no
measurements were affected because of the operators’ quick responses,
the valve was replaced to prevent any future samples from being lost.


7.5  Quality Control

Dickson laboratory Certified Reference Material (CRM) Batch 152 and
Batch 153 were used to determine the accuracy of the total alkalinity
analyses. The total alkalinity certified value for each batch is:

  • Batch 152     2216.94 ± 0.60 μmol/kg (33;16)
  • Batch 153     2225.59 ± 0.77 μmol/kg (32;16)

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 I09N stations
resulting in 110 reference material analyses. On I09N, the measured
total alkalinity value for each batch is:

  • Batch 152     2216.75 ± 0.66 μmol kg-1 (57) [mean ± std. dev. (n)]
  • Batch 153     2225.03 ± 0.43 μmol kg-1 (14) [mean ± std. dev. (n)]

If greater than 15 Niskin bottles were sampled at a station, two
Niskin bottles on that station were sampled twice to conduct duplicate
analyses. If 15 or less Niskin bottles were sampled at a station, only
one Niskin on that station was sampled twice for duplicate analyses.
The standard deviation for the duplicates measured on I09N is:

Duplicate Standard Deviation ± 0.84 µmol kg–1 (177) [± std. dev.(n)]

The total alkalinity measurements for each I09N station were compared
to measurements taken from the neighboring I09N 2016 stations and the
I09N 2007 stations of similar if not identical coordinates.

2671 total alkalinity values were submitted for I09N. The total
alkalinity of the entire transect is shown as a section in:ref:
*talk-figure*. Although most corrections have been applied and it is
unlikely that any additional corrections will need to be performed,
this data should be considered preliminary until a more thorough
analysis of the data can take place on shore, especially during the
stations where the SDS Pipette Boards were having problems.


fig: Section of total alkalinity along I09N (Stations 84 to 196).




























8  DISSOLVED INORGANIC CARBON (DIC)

PI’s
   • Rik Wanninkhof (NOAA/AOML)
   • Richard A. Feely (NOAA/PMEL)

Technicians
   • Robert Castle (NOAA/AOML)
   • Morgan Ostendorf (UW/JISAO)


8.1  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 HgCl2 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.


8.2  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 Roger Revelle.


8.3  DIC Analysis

In coulometric analysis of DIC, all carbonate species are converted to
CO2 (gas) by addition of excess hydrogen ion (acid) to the seawater
sample, and the evolved CO2 gas is swept into the titration cell of
the coulometer with pure air or compressed nitrogen, where it reacts
quantitatively 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 CO2 that enters the cell is
determined by integrating the total change during the titration.


8.4  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
   [CO2] = Cal. Factor * ------------------------------------------ 
                             pipette volume * density of sample


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

The instrument uses a default value of 35.00 for salinity, but all DIC
values were recalculated to a molar weight (µmol/kg) using density
obtained from the CTD’s salinity when available, otherwise (in about
32 cases) from the bottle salinity. The DIC values were corrected for
dilution due to the addition of 0.16 ml of saturated HgCl2 used for
sample preservation. The total water volume of the sample bottles was
288 ml (calibrated by Esa Peltola, AOML). The correction factor used
for dilution was 1.00055. 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
correction was 0.91 µmol/kg for AOML 3 and 5.16 µmol/kg for AOML 4.

The coulometer cell solution was replaced after 25 – 30 mg of carbon
was titrated, typically after 9 – 12 hours of continuous use. Normally
the blank is in the 40 - 50 range.


8.5  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. CRMs 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 152 or 153
CRM value. The CRM certified value for batch 152 is 2020.88 µmol/kg
and for batch 153 is 2017.95 µmol/k.

The precision of the two DICE systems can be demonstrated via the
replicate samples. Approximately 7% 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
absolute difference from the mean of these replicates is 1.69 µmol/kg
(n=257, stdev=1.51). 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
======  ========  ========  =========  ============  =======
AOML 3  1.003698  1.001461  27.927 ml  -0.91, N= 59   3.12   
AOML 4  0.999765  0.999121  29.306 ml  -5.16, N= 60   1.53   


8.6  Underway DIC Samples

Underway samples were collected from the flow thru system in the
forward Main Lab during transit. Discrete DIC samples were collected
approximately every 4 hours. A total of 19 discrete DIC samples
including duplicates were collected while underway.


8.7  Summary

The overall performance of the analytical equipment was good during
the cruise. There was one minor problem with AOML-3 that occurred near
the equator when the gas sampling valve became obstructed. This caused
an approximately 3-hour delay while the problem was repaired.

There were 2899 samples analyzed and 2648 DIC values submitted from
113 CTD casts which means that there is a DIC value for approximately
65% 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
  





9  DISCRETE pH ANALYSES

PI
   • Dr. Andrew Dickson

Cruise Participant
   • David Cervantes
   • Stephanie Mumma



9.1  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
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 (HgCl2). 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, two duplicate samples were collected from
almost all stations for quality control purposes.


9.2  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 NESLAB
RTE-7 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 immediately after the spectrophotometric measurements
were taken. The indicator meta-cresol purple (mCP) was 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 conductivity
sensor on the CTD.


9.3  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 2 batches were
used during Leg 1 of the cruise. The pHs of these batches was adjusted
with 0.1 M solutions of HCl and NaOH (in 0.6 M NaCl background) to
approximately 7.3, measured with a pH meter calibrated with NBS
buffers. The indicator was obtained from Dr. Robert Byrne at the
University and Southern Florida and was purified using the flash
chromatography technique described by Patsavas et al., 2013
[Patsavas2013].


9.4  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)


9.5  Problems and Troubleshooting

Many of the samples had a high dissolved gas content and degassed when
brought to room temperature. This could be clearly seen in the
formation of bubbles inside the sealed sample bottles and in the
spectrophotometric pH system (Kloehn syringe pump, sample tubing, and
the 10 cm cell). Bubbles were especially difficult to eliminate in the
Kloehn syringe pump, which would accumulate large bubbles at the top
after running a number of samples in each station. Efforts were made
to reduce bubble formation by verifying all pump fittings were tight,
slowing down the speed of the syringe pump, and holding samples below
25°C. When bubbles formed during station analysis, they were cleared
by the aforementioned methods between samples. Bubbles were also
cleared from the syringe after every station by flushing with ethanol,
followed by DI water. This method of flushing with ethanol and DI
water proved to be effective and removed bubbles when accumulated.
These bubbles appeared to have no effect on the samples' pH values.

The Labview software that controls the automated pH system crashed
three times during I09N, resulting in the loss of data for three
samples. The uncorrected pH values were documented in the pH lab
notebook but the usually generated data line is not available to apply
the necessary dye correction. These three data points were flagged as
questionable because they could not be corrected.

Near the end of I09N, the sample outlet tube of the cell sprang a slow
leak overnight when the system was not being used. Luckily, no damage
by the leak was done to the cell, spectrophotometer, or any of the pH
System's components.


9.6  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 152 and Batch
153 (provided by Dr. Andrew Dickson, UCSD). Two duplicate and two
replicate measurements were performed on every station when at least
fifteen Niskins were sampled. If less than fifteen Niskins were
sampled, only one duplicate and one replicate measurement were
performed. CRMs were measured at the beginning and ending of each day.
The precision statistics for I09N are:

  • Duplicate precision ± 0.00046   (n=182)
  • Replicate precision ± 0.00082   (n=177)
  • B152 7.8706 ± 0.00066           (n=37)
  • B152 within-bottle SD ± 0.00020 (n=37)
  • B153 7.8948 ± 0.00073           (n=29)
  • B153 within-bottle SD ± 0.00023 (n=29)

The pH measurements for each I09N station were compared to
measurements taken from the neighboring I09N 2016 stations and the
I09N 2007 stations of similar if not identical coordinates.

2671 pH values were submitted for I09N. The pH of the entire transect
is shown as a section in pH Section. Although most corrections have
been applied and it is unlikely that any additional corrections will
need to be performed, this data should be considered preliminary until
a more thorough analysis of the data can take place on shore.


Fig. 9.1:  pH Section
           Section of pH on the total scale at 25.0°C along I09N (Stations 84
           to 196).


[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.
     
[Lueker2000]   Lueker, T.J., Dickson, A.G., Keeling, C.D.
               "Ocean pCO2 calculated from dissolved inorganic carbon,
               alkalinity, and equations for K1 and K2: validation based
               on laboratory measurements of CO2 in gas and seawater at
               equilibrium," Marine Chemistry, 2000.

[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.














































10  CFC-11, CFC-12, CFC-113, and SF6

Analysts
   • Eugene Gorman (LDEO)
   • Ben Hickman (LDEO)
   • Molly Martin (RSMAS)


10.1  Sample Collection

All samples were collected from depth using 10.4 liter Niskin bottles.
None of the Niskin bottles used showed a CFC contamination throughout
the cruise. All bottles in use remained inside the CTD hanger between
casts.

Sampling was conducted first at each station, according to WOCE
protocol. This avoids contamination by air introduced at the top of
the Niskin bottle as water was being removed. A water sample was
collected from the Niskin bottle petcock using viton tubing to fill a
300 ml BOD bottle. The viton tubing was flushed of air bubbles. The
BOD bottle was placed into a plastic overflow container. Water was
allowed to fill BOD bottle from the bottom into the overflow
container. The stopper was held in the overflow container to be
rinsed. Once water started to flow out of the overflow container the
overflow container/BOD bottle was moved down so the viton tubing came
out and the bottle was stoppered under water while still in the
overflow container. A plastic cap was snapped on to hold the stopper
in place. One duplicate sample was taken on every other station from
random Niskin bottles. Air samples, pumped into the system using an
Air Cadet pump from a Dekoron air intake hose mounted high on the
Foremast, were run when time permitted. Air measurements are used as a
check on accuracy.


10.2  Equipment and Technique

CFC-11 and CFC-12 were measured on most of the 96 stations for a total
of xxxx samples. Due to the non-conservative nature of F113 it was not
measured on this trip. From the beginning this system was not capable
of measuring SF6: all attempts to measure SF6 failed. Equipment
problems led to a failure to sample some stations.

Analyses were performed on a gas chromatograph (GC) equipped with an
electron capture detector (ECD). Samples were introduced into the GC-
EDC via a purge and dual trap system. 202 ml water samples were purged
with nitrogen and the compounds of interest were trapped on a main
Porapack N/Carboxen 1000 trap held at ~ -20°C with a Vortec Tube
cooler. After the sample had been purged and trapped for 6 minutes at
250ml/min flow, the gas stream was stripped of any water vapor via a
magnesium perchlorate trap prior to transfer to the main trap. The
main trap was isolated and heated by direct resistance to 150°C. The
desorbed contents of the main trap were back-flushed and transferred,
with helium gas, over a short period of time, to a small volume focus
trap in order to improve chromatographic peak shape. The focus trap
was Porapak N and is held at ~ -20°C with a Vortec Tube cooler. The
focus trap was flash heated by direct resistance to 180°C to release
the compounds of interest onto the analytical pre-columns. The first
precolumn was a 5 cm length of 1/16” tubing packed with 80/100 mesh
molecular sieve 5A. This column was used to hold back N2O and keep it
from entering the main column. The second precolumn was the first 5
meters of a 60 m Gaspro capillary column with the main column
consisting of the remaining 55 meters. The analytical pre-columns were
held in-line with the main analytical column for the first 50 seconds
of the chromatographic run. After 35 seconds, all of the compounds of
interest were on the main column and the pre-column was switched out
of line and back-flushed with a relatively high flow of nitrogen gas.
This prevented later eluting compounds from building up on the
analytical column, eventually eluting and causing the detector
baseline signal to increase.

The samples were stored at room temperature and analyzed within 6
hours of collection. At the end of every station water measurements
were followed by a purge blank, standard, and system blank. The
surface sample was held after measurement and was sent through the
process in order to “restrip” it to determine the efficiency of the
purging process.


10.3  System performance

Troubles were many; they were deep as a well. I doubt there is a
heaven but I now know there is a hell. It’s the Miami CFC system -
used on the Revelle. It made me want to holler; it made me want to
yell. With that experience, I bid you all farewell. Why I never became
a poet is not hard to tell.


10.4  Calibration

A gas phase standard, 33780, was used for calibration. The
concentrations of the compounds in this standard are reported on the
SIO 2005 absolute calibration scale. 5 calibration curves were run
over the course of the cruise. Estimated accuracy is ±2%. Precision
for CFC-12, CFC-11 error bars will be substantially higher on several
stations which will be noted in the final report. Estimated limit of
detection is 1 fmol/kg for CFC-11, 3 fmol/kg for CFC-12.


















11  UNDERWAY pCO2 ANALYSIS

PIs
   • Rik Wanninkhof (NOAA/AOML)
   • Denis Pierrot (UM/CIMAS)

Technicians
   • Robert Castle (NOAA/AOML)

An automated underway pCO2 system from AOML was installed in the
Hydro Lab of the RV Roger Revelle. The design of the instrumental
system is based on Wanninkhof and Thoning [Wanninkhof1993] and Feely
et al. [Feely1998], while the details of the instrument and of the
data processing are described in Pierrot, et al. [Pierrot2009].

The repeating cycle of the system included 4 gas standards, 5 ambient
air samples, and 100 headspace samples from its equilibrator every 3
hours. The concentrations of the standards range from 233 to 463 ppm
CO2 in compressed air. These field standards were calibrated with
primary standards that are directly traceable to the WMO scale. A gas
cylinder of ultra-high purity air was used every 18 hours to set the
zero of the analyzer.

The system included an equilibrator where approximately 0.6 liters of
constantly refreshed surface seawater from the bow or mid-ship intake
was equilibrated with 0.8 liters of gaseous headspace. The water flow
rate through the equilibrator was 1.5 to 2.2 liters/min.

The equilibrator headspace was circulated through a non-dispersive
infrared (IR) analyzer, a LI-COR™ 6262, at 50 to 120 ml/min and then
returned to the equilibrator. When ambient air or standard gases were
analyzed, the gas leaving the analyzer was vented to the lab. A KNF
pump constantly pulled 6-8 liter/min of marine air through 100 m of
0.95 cm (= 3/8") OD Dekoron™ tubing from an intake on the bow mast.
The intake had a rain guard and a filter of glass wool to prevent
water and larger particles from contaminating the intake line and
reaching the pump. The headspace gas and marine air were dried before
flushing the IR analyzer.

A custom program developed using LabView™ controlled the system and
graphically displayed the air and water results. The program recorded
the output of the IR analyzer, the GPS position, water and gas flows,
water and air temperatures, internal and external pressures, and a
variety of other sensors. The program recorded all of these data for
each analysis.

The system worked well throughout the cruise.


Standard Gas Cylinders

                         Cylinder# | ppm CO2
                         =========   ========
                         JAO2646   | 233.46 
                         JAO2264   | 326.18 
                         JAO2285   | 406.05 
                         JAO2280   | 463.00 


[Pierrot2009]    Pierrot, D.; Neill, C.; Sullivan, K.;
                 Castle, R.; Wanninkhof, R.; Luger, H.; Johannessen, T.;
                 Olsen, A.; Feely, R.A.; and Cosca, C.E. (2009).
                 *Recommendations for autonomous underway pCO2 measuring
                 systems and data- reduction routines.* Deep-Sea Res.,
                 II, v. 56, pp. 512-522.

[Wanninkhof1993] Wanninkhof, R., and Thoning, K.
                 (1993). *Measurement of fugacity of CO2 in surface
                 water using continuous and discrete sampling
                 methods.* Mar. Chem., v. 44, no. 2-4, pp. 189-205.












































12  ISOTOPIC COMPOSITION OF NITROGEN SPECIES

PI
   • Chawalit "Net" Charoenpong


Samples from Niskin bottles and underway system were taken for
analyses of isotopic composition of multiple nitrogen (N)
ions/compounds with the goals to determine the isotopic distribution
of N species in the study region and to understand the cycling of N on
the I09N transect traversing through different oceanic regimes
including the subtropical gyre, equatorial upwelling and the Bay of
Bengal. Natural abundance isotopic composition is a powerful tool to
elucidate the sources and the processes and reactions that affect the
compounds of interest. No onboard analysis was carried out and all
samples will be analyzed back in the Wankel lab for stable isotope
biogeochemistry at WHOI.


12.1  Dissolved N gases (N2O and N2)

Nitrous oxide gas (N2O) is an intermediate compound in many N
reactions and more importantly it is a potent greenhouse gas. The
sample will be analyzed for its concentration and isotopes (δ(^15)N-
N2O, δ(^18)O-N2O and site preference—isotopic asymmetry of the N2O
molecule). With this information, we can deduce the flux of N2O at
the air-sea interface and determine the microbial processes
responsible for its production. Nitrogen gas (N2), on the other hand,
is an inert gas for most part of the ocean where the water is
oxygenated. This make it a conservative tracer for different water
masses as it records the history of water parcels when they were last
in contact with the atmosphere. However, under anoxic condition, N2
is a product of several microbially-mediated reactions including
denitrification and anaerobic ammonium oxidation (anammox). Hence,
concentration and isotopic composition (δ(^15)N-N2) will help deduce
the source of N2 and rates of these processes.

Parameters

   • δ(^15)N-N2O

   • δ(^18)O-N2O

   • N2O site preference

   • [N2O]

   * N2/Ar ratio

   • δ(^15)N-N2

Sampling Procedure: Samples were collected using borosilicate septum
bottles by filling directly from the Niskin bottles. Capping with
butyl rubber stoppers were done while all bottles were completely
underwater. Great care was taken to ensure absence of any bubbles and
samples were poisoned with saturated HgCl2 to stop biological
activities.

Analysis: High precision measurements of N2/Ar and δ(^15)N-N2 were
made on septum sealed samples using on-line gas extraction system
coupled to a multicollector continuous-flow isotope ratio mass
spectrometer (CF-IRMS) as described in [Charoenpong2014]. O2 was
removed from the samples prior to δ(^15)N-N2 analysis using a CuO/Cu
reduction column placed in a 500°C furnace to avoid interferences
caused by interaction between O2, N2 and their fragments within the
IRMS ion source. Additional purge and trap system similar to that
previously described in [McIlvin2010] will be used for N2O analysis.



12.2  Nitrate and Nitrite

Nitrate (NO3(^-)) is the dominant dissolved inorganic nitrogen ions.
Like other nutrients, it is depleted in the surface due to biological
consumption and abundant in the ocean interior due to
remineralization. By looking at the dual isotopes of NO3(^-) (δ(^15)N and
δ(^18)O), we can effectively constrain the nutrient utilization in the
euphotic zone and its loss process in the OMZ. Nitrite (NO2(^-)), on
the other hand, is typically found spatially constrained within close
proximity to the deep chlorophyll maxima (DCM) in the open
ocean—primary nitrite maxima. In addition, we can also find secondary
nitrite maxima deeper down in the intense OMZ. Interestingly, the
latter feature (though pronounced in other OMZs including the Arabian
Sea) is lacking in the Bay of Bengal.

Parameters

   • δ(^15)N-NO3(^-)

   • δ(^18)O-NO3(^-)

   • δ(^15)N-NO2(^-)

   • δ(^18)O-NO2(^-)

Sampling Procedure: Samples for NO3(^-) isotopic analysis (30ml HDPE
bottles) were preserved by mild acidification with hydrochloric and
sulfuric acid to pH 2 to 3 while samples for NO2(^-) isotopic analysis
(60mL HDPE bottles) were preserved by raising the pH with NaOH until
the sample reaches the pH of 12.5. These steps are in place to ensure
the retention of the δ(^15)N and δ(^18)O signatures. Samples bottles were
stored at room temperature until analysis.

Analysis: The denitrifier method ([Casciotti2002]; [Sigman2001]) and
the azide method ([McIlvin2010]) will be used to analyze NO3(^-) and
NO2(^-) respectively. These methods quantitatively convert
NO3(^-)/NO2(^-) to N2O before being extracted and purified (as in
[McIlvin2010]) before being analyzed by the IRMS.


12.3  Ammonium

Ammonium (NH4(^+)) is produced from the organic N degradation and
consumed by multiple processes including NH4(^+) assimilation,
nitrification and anammox. Typically found in submicromolar
concentration in the open ocean notably around the same depths as the
primary nitrite maxima, NH4(^+) is one of the N species that is most
poorly constrained in terms of isotopic composition. Previous studies
(e.g., Sama et al., in prep) indicates several pockets of high NH4(^+)
(up to 0.5uM) in the Bay of Bengal.

Parameter

   • δ(^15)N-NH4(^+)

Sampling procedure: Sample water was filled directly into 500-mL glass
media bottles. Care was taken to ensure minimal contamination (e.g.,
no cigarette smoke or no painting near the sampling area). An ammonia
trap consisting of a pre-combusted (500°C for 4 h) and acidified (20
μL of 2 N H2SO4) GF/D glass fiber filter sandwiched between two sealed
Teflon membranes (the passive ammonia diffusion method as described in
[Sigman1997]), was added to the bottles. Prior to closing the bottles,
pH was raised above 9.2 by adding combusted magnesium oxide powder
(MgO). Samples were kept agitated on at room temperature for at least
5 days before the traps were removed and kept frozen inside clean
1.2mL cryogenic vials until analysis.

Analysis: Persulfate oxidation ([Knapp2005]) and the denitrifier
method ([Sigman2001]) will be used for the analysis of δ^15N-NH_4^+.
In short, the NH4(^+) in the trap will be oxidized to NO3(^-) using
persulfate reagents and then converted to N2O before the introduction
to the IRMS.

Potential problem: Ammonium concentrations on this cruise as analyzed
on board by the nutrient team were typically below the detection limit
for most part of the transect. Even within the Bay of Bengal where
higher [NH4(^+)] is expected, we could not find high enough [NH4(^+)] 
to warrant accurate isotopic measurements.


12.4  Suspended particulate organic matter (POM)

The isotopic composition of particulate organic matter reflects the
balance between the source of N and the isotopic fractionation during
assimilation. Here I use size fractionation to separate different
phytoplankton group to investigate whether there is potentially a
difference of N source between the larger and small size fractions.

Parameters:

   • δ(^15)N-suspended POM

   • δ(^13)C-suspended POM

Sampling Procedure: Suspended particulate organic matter was collected
from either the underway system or the Niskin bottles. Pre-filtration
with 200-micron Nitex mesh was in place to remove larger zooplankton.
Two size fractions were collected using GF/A (1.6 micron) and GF/F
(0.7 micron) filters. Most samples are from underway (5m intake) and
around deep chlorophyll maxima. Samples are kept frozen until
analysis.

Analysis: Filters will first be kept inside a jar with concentrated
HCl overnight to remove any particulate inorganic carbon (i.e.,
calcium carbonate) and then analyzed using elemental analyzer coupled
with IRMS (EA-IRMS). In short, they will be combusted and organic
carbon and nitrogen will be converted into their gas phases: CO2 and
N2, respectively. In the case where there is too little biomass
retained on the filters, the persulfate oxidation coupled with the
denitrifier method (as described earlier) will be used instead.


[Casciotti2002]   Casciotti, K. L., D. M. Sigman, M. G.
                  Hastings, J. K. Böhlke, and A. Hilkert (2002),
                  Measurement of the oxygen isotopic composition of
                  nitrate in seawater and freshwater using the
                  denitrifier method, *Anal. Chem.*, 74(19), 4905–4912,
                  doi:10.1021/ac020113w.

[Charoenpong2014] Charoenpong C. N., L. A. Bristow
                  and M. A. Altabet. (2014). A continuous flow isotope
                  ratio mass spectrometry method for high precision
                  determination of dissolved gas ratios and isotopic
                  composition, *Limnol. Oceanogr.: Methods*, 12,
                  323–337, doi: 10.4319/lom.2014.12.323

[Knapp2005]       Knapp, A. N., D. M. Sigman, and F. Lipschultz.
                  (2005). N iso- topic composition of dissolved organic
                  nitrogen and nitrate at the Bermuda Atlantic Time-Series
                  Study site, *Global Biogeochem. Cycles*, 19, GB1018,
                  doi:10.1029/2004GB002320.
  
[McIlvin2005]     McIlvin M. R. and Altabet M. A. (2005).
                  Chemical Conversion of Nitrate and Nitrite to Nitrous
                  Oxide for Nitrogen and Oxygen Isotopic Analysis in
                  Freshwater and Seawater, *Anal. Chem.*, 77, 5589–5595,
                  doi: 10.1021/ac050528s

[McIlvin2010]     McIlvin M. R., Casciotti K. L. (2010).
                  Fully automated system for stable isotopic analyses of
                  dissolved nitrous oxide at natural abundance levels.
                  *Limnology and Oceanography: Methods* 8, 54-66, doi:
                  10.4319/lom.2010.8.54

[Sigman2001]      Sigman, D. M., K. L. Casciotti, M. Andreani,
                  C. Barford, M. Galanter, and J. K. Böhlke (2001). A
                  bacterial method for the nitrogen isotopic analysis of
                  nitrate in seawater and freshwater, *Anal. Chem.*,
                  73(17), 4145–4153, doi:10.1021/ ac010088e.

[Sigman1997]      Sigman, D. M., M. A. Altabet, R. Michener,
                  D. C. McCorkle, B. Fry, and R. M. Holmes (1997). Natural
                  abundance-level measurement of the nitrogen isotopic
                  composition of oceanic nitrate: An adaptation of the
                  ammonia diffusion method, *Mar. Chem.*, 57(3–4), 227–242,
                  doi:10.1016/S0304- 4203(97)00009-1.




13  ∆(^18)O SAMPLING

PIs

   • Peter Schlosser (LDEO)
   • Lynne Talley (SIO)


Samples for ∆(^18)O were taken by the CTD-watch for Schlosser and
Talley. A total of 1073 brown glass bottles were used to collect XX ml
samples according to the protocol provided.

1. The sample bottles came stored in annotated boxes that were each
   labeled with a box number (1-20) as it was filled samples.

2. The container with the empty sample bottles and documentation
   was kept in the forward bio-lab. Before the return of the CTD to
   the deck, 36 bottles were prepared with Bullister bottle numbers
   written in the caps. The 24 bottle plastic rack, which sat in a
   plastic basin (both provided) was filled with the empty bottles.
   The 12 extra bottles were placed upright in the basin.

3. Seawater was taken directly from the Bullister bottles using the
   tube provided. Sample bottles were rinsed once with seawater from
   the Bullister prior to sampling.

4. After sampling the 36 bottles were taken back to the forward
   bio- lab where they were dried with paper towels, caps were
   tightened and wrapped in tape, and labels were filled out and
   applied.

5. The sample IDs, Bullister bottle numbers, date and box number
   were recorded on a log sheet provided. After all sampling was
   complete this log sheet was converted to the electronic version,
   which will be sent to the PIs.

The agreed upon sampling plan followed the basic outline of the I06S
sampling provided by Robert Key (Princeton) with concentrated sampling
at the southernmost stations and less concentrated to the north. The
table below summarizes the sampling.















Note: Note there was a mix up in the assigning ID numbers so there
      are IDs 432A, B. and C and 452A, and B.


∆O18   ∆O18   ∆O18  STA  CAST    DATE      #      LAT       LON     DEPTH 
Box     ID     ID    #           (UTC)    SAM-                       (m)  
                                          PLES
-----  -----  ----  ---  ----  ---------  ----  --------  --------  ----- 
START  START   END        
 -END  
-----  -----  ----  ---  ----  ---------  ----  --------  --------  ----- 
 1-1      1     19    1    1   19-Feb-16   19   -66.6027   78.3815    468 
 1-1     20     40    2    3   19-Feb-16   21   -66.4997   78.2986    953 
 1-2     41     67    3    1   19-Feb-16   27   -66.45     78.2494   1497 
 2-2     68     98    4    1   19-Feb-16   31   -66.4      78.1993   1979 
 2-3     99    132    5    1   20-Feb-16   34   -66.2999   78.1253   2731 
 3-4    133    168    6    1   20-Feb-16   35   -66.15     78.0102   3009 
 4      169    203    7    2   20-Feb-16   35   -65.6248   78.8085   3313 
 4-5    204    239    8    1   20-Feb-16   35   -65.1      79.6066   3525 
 5-6    240    275    9    1   21-Feb-16   36   -64.5799   80.3926   3667 
 6      276    311   10    1   21-Feb-16   36   -64.05     81.2022   3700 
 6-7    312    347   11    1   21-Feb-16   35   -63.535    82.0005   3450 
 7      348    378   12    1   21-Feb-16   31   -63.003    82.0103   2748 
 8      379    402   13    1   22-Feb-16   23   -62.5003   82.0002   1919 
 8      403    429   15    1   22-Feb-16   27   -61.4999   82.0002   2175 
 8-9    430    451   16    1   22-Feb-16   24   -61        82.0005   1858 
 9      452    475   19    2   23-Feb-16   25   -59.5002   82.0003   1706 
 9-10   476    496   20    2   23-Feb-16   21   -59.0001   82        1291 
10      497    518   21    1   24-Feb-16   22   -58.6101   82.0101   1549 
11      519    553   25    1   24-Feb-16   35   -57.5131   82.5226   4438 
11      554    589   26    1   25-Feb-16   36   -57.3209   82.7791   4240 
11-12   590    625   29    1   25-Feb-16   36   -56.058    84.2612   4822 
12-13   626    661   32    1   26-Feb-16   36   -54.7862   85.6644   4712 
13      662    697   33    1   26-Feb-16   36   -54.367    86.1421   4641 
13-14   698    733   35    1   28-Feb-16   36   -53.5264   87.0235   4602 
14-15   734    761   37    1   28-Feb-16   28   -52.531    87.954    4405 
15      762    796   40    1    1-Mar-16   35   -51.037    89.3503   4141 
15-16   797    832   43    1    1-Mar-16   36   -49.5429   90.7469   3868 
16-17   833    868   44    1    2-Mar-16   36   -49.0449   91.2121   3815 
17      869    903   47    1    2-Mar-16   35   -47.551    92.6087   3616 
17-18   904    936   48    1    3-Mar-16   33   -47.053    93.0739   3490 
18      937    970   51    1    3-Mar-16   33   -45.559    94.4702   3219 
19      971   1003   52    1    3-Mar-16   33   -44.992    95.0002   2903 
19-20  1003   1037   55    1    4-Mar-16   34   -43.068    95.0001   3168 
20     1038   1073   58    1    5-Mar-16   36   -41.1441   95.0003   3564 












14  CDOM

UCSB Global CDOM Group

    • Eric Stassinos, Earth Research Institute UCSB, Technician
    • Jeremy Kravitz, U. Puerto Rico, Volunteer Graduate Student


14.1  Chromophoric Dissolved Organic Matter (CDOM)

Sampling: We nominally sampled one cast per day, on the cast nearest
the overpass times of the ocean color instrument bearing satellites
Aqua (MODIS) and NPP (VIIRS). Each Niskin bottle would be sampled,
with two randomly selected replicates.

Preparation: The standard method involves collecting 60 mL samples
into glass EPA vials, then filtering the samples at low vacuum
pressure (-0.05 MPa) through 25mm 0.2 micron Nuclepore filters which
have been preconditioned with ultrapure water to remove organic
contaminants. For the underway samples we used 0.2 micron nylon
ZenPure cartridge filters to remove particles. Sample vials are rinsed
with the filtrate and the filtrate is returned to the vial. Filtered
samples are stored at 4°C until analysis ([Nelson2007],
[Nelson2009]).

Original plan was to analyze samples at sea using the WPI UltraPath
200cm liquid waveguide cell spectrophotometer system. However, the cell
developed an air leak on I08S that could not be corrected in-field, so
we opted to collect samples to return to UCSB for analysis. We
collected 16 samples and two replicates on each cast, filtered and
stored them. CDOM samples will be returned from Phuket Thailand to
UCSB.

We collected samples on 16 stations, for a total of 288 samples with
32 being replicates.

Analysis: Filtered seawater samples are analyzed for absorption in the
250-734 nm range using a WPI UltraPath spectrophotometer system. The
UltraPath is a single-beam spectrophotometer system consisting of a
UV-Visible light source, a 200 cm liquid waveguide cell, and a diode
array spectrometer. Samples (appx. 12 mL volume) are injected into the
cell using a peristaltic pump. Light is introduced to the cell via a
fiber-optic and travels the length of the cell because of total
internal reflection, as in a fiber optic filament. Absorbance is
calculated by computing the logarithm of the spectrum of transmitted
light through a sample divided by the spectrum of transmitted light
through a reference solution (in this case ultrapure water prepared
each day with our Barnstead Nanopure Diamond UV system using potable
water as input). Because of the difference in real refractive index
between seawater and ultrapure water, the raw data have an apparent
negative absorbance signal that must be removed before computing
absorption coefficient (m(^-1)) (as absorbance x 2.303/l, where l is 
the effective pathlength of the cell, [Nelson2007]).

For this expedition we are testing a new protocol for CDOM absorption
spectra measurement and refractive index correction as part of a NASA
methodological development effort. The protocol involves measuring
standard solutions of Suwanee River Fulvic Acid ~0.25 mg/L and sodium
chloride at 30 and 40 g/L to monitor instrument performance and obtain
data for correction of apparent absorption due to refractive
differences between ultrapure water and seawater.

Selected CDOM absorption data from discrete wavelengths will be
submitted to CCHDO upon completion of quality control. More complete
data sets including raw data and processing code will be available via
the NASA bio-optical field data SeaBASS (seabass.gsfc.nasa.gov).


14.2  Chlorophyll a

Sampling: We collected ~500mL samples from the top 6 depths on the mid
day CTD cast associated with out radiometer deployment and CDOM
sampling, one cast daily, total of approximately 192 samples.

Preparation: Samples were collected into 500mL brown HDPE bottles and
were subsequently filtered onto 25mm 0.45μm pore nitrocellulose
filters. The filters were placed in polypropylene Falcon tubes and
extracted 48 hours at 4°C temperature in 10 mL of 90% acetone (with
Barnstead Nanopure UV prepared water); and were shaken after 24 hours
to ensure complete filter dissolution.

Analysis: The acetone extracts were analyzed using the acidification
technique [Mueller2003] on a Turner Designs AU-10 fluorometer with the
standard chlorophyll fluorescence set. The fluorescence (in relative
units) was measured before (Rb) and after (Ra) acidification with two
drops of 10% HCl. Chlorophylla was computed according to the standard
formula:
                   Chla(µg/l) = (τ/τ - 1)Fd(Rb - Ra)

Where \tau is the fluorescence ratio of pure chlorophyll a to pure
phaeophytin a and Fd is the calibration coefficient (μg/L). τ and
Fd for each of the three sensitivity ranges of the instrument were
determined in August 2014 by Janice Jones and Nathalie Guillocheau,
UCSB; using solutions of pure Anacystis nidulans chlorophyll a (Sigma)
in 90% acetone.

                       HIGH Tau =        1.9539 
                       MED Tau =         1.9496 
                       LOW Tau =         1.8885 
                       Med/High Tau =    1.9520 
                       Low/Med Tau =     1.9274 
                       overallavg Tau =  1.9393 


                  [Chla] Rb    [Chla] ((tau/(tau-1))*     Slope       
                                     (Rb-Ra))                         
  --------------  -----------  ----------------------  -----------
  HIGH Fd =       0.138925422      0.138925422         0.142718147    
  MED Fd =        0.138626676      0.138626676         0.141249987    
  LOW Fd =        0.126879138      0.126879138         0.128316741    
  Med/High Fd =   0.1388           0.138794721         0.141417549    
  Low/Med Fd =    0.1344           0.134354844         0.141000945    
  overallavgFd =  0.1364           0.136411604         0.141201691    


Instrument performance was checked daily with a Turner Designs solid
fluorescence standard. No apparent trend was observed.

Preliminary Results: Preliminary quality control based on phaeophytin
a to chlorophyll a ratios suggest almost all samples collected to date
from shallower than 200m were good. Samples collected at 200m and
below were effectively zero in most cases, putting a tentative lower
limit for chlorophyll determination at 0.01 mg/m(^3). Results show a
general trend of increasing subsurface chlorophyll concentrations and
a shallower deep chlorophyll a maximum as stations progressed from
south of the equator to the Bay of Bengal. The largest deep
chlorophyll a maximum concentrations were observed just north of the
equator between ranges of ~0.5-0.7 mg/m(^3) while surface concentration
ranges remained low under 0.1 mg/m(^3) and reaching below 0.04 mg/m(^3).

Problems: All values of computed chlorophyll a were within normal
values for the region. One sample was omitted (station 104/1, sample
35, flagged 5) due to a contaminated filter pad. All other samples
were flagged as 2 for high confidence in the values.

Fig. 14.1: Chlorophyll a profiles from Station 91 (-24.1S), Station 139
           (-0.32S) and station 167 (9.97N).


14.3  CDOM Rosette Fluorometer

Equipment and Techniques: On I08S, a WETLabs CDOM fluorometer FLCDRTD
was deployed on the rosette. The instrument exhibited unusual offsets
in the data output between 1200 and 1500 db, that were not resolved
before the instrument was lost with the rosette on February 22. There
was not a replacement for the instrument on this leg.

Sampling and Analysis: Instrument data are saved as analog volts DC
and are vicariously calibrated post cruise using laboratory-measured
fluorescence spectra standardized to quinine sulfate fluorescence
equivalents (ppb) of archived samples using a Horiba Jobin Yvon
Fluoromax-4 ([Nelson2009], [Nelson2016]).


14.4  Spectroradiometer casts

Acquisition: Each day near local noon (with one exception; see below)
we deployed a Biospherical C-OPS profiling spectroradiometer system
(system 023) off the port quarter. The instrument measures downwelling
irradiance and upwelling radiance in 19 channels stretching from the
UV-B to the NIR wavebands. The system includes a surface reference
unit with matching channels and a shadowband system for measuring
direct and diffuse contributions to total irradiance. All instruments
acquire data at 15 Hz. The profiler is hand deployed and recovered to
allow drift away from the ship to avoid shadow influence. The maximum
depth reached on every profile was approximately 100 m.

Data Processing: Collected data are subjected to quality control for
tilt and surface irradiance change during the profile [Mueller2003]
and derived products include attenuation coefficient spectra and
water-leaving radiance reflectance (for ocean color remote sensing
data validation). Resulting products will be made available via NASA’s
field bio-optics archive SeaBASS (seabass.gsfc.nasa.gov).

   C-OPS cast summary to 04/24/16

   Cast 084/2
   Cast Start: 25-Mar-2016  06:04:23 UT
   Cast End  : 25-Mar-2016  06:18:26 UT
   Max Depth : 98.6

   Cast 088/1
   Cast Start: 26-Mar-2016  06:03:64 UT
   Cast End  : 26-Mar-2016  06:16:46 UT
   Max Depth : 102.1

   Cast 091/2
   Cast Start: 27-Mar-2016  08:11:24 UT
   Cast End  : 27-Mar-2016  08:25:04 UT
   Max Depth : 98.9

   Cast 97/05
   Cast Start: 29-Mar-2016 06:05:48 UT
   Cast End  : 29-Mar-2016 06:17:56 UT
   Max Depth : 110.8 m

   101/2
   Cast Start: 30-Mar-2016 06:01:15 UT
   Cast End  : 30-Mar-2016 06:14:30 UT
   Max Depth : 101.2 m

   104/2
   Cast Start: 31-Mar-2016 08:13:06 UT
   Cast End  : 31-Mar-2016 08:26:21 UT
   Max Depth : 99.9 m

   108/1
   Cast Start: 01-Apr-2016 07:45:44 UT
   Cast End  : 01-Apr-2016 07:59:19 UT
   Max Depth : 106.3 m

   111/2
   Cast Start: 02-Apr-2016 08:02:33 UT
   Cast End  : 02-Apr-2016 08:17:00 UT
   Max Depth : 97.5 m

   115/01
   Cast Start: 03-Apr-2016 06:43:39 UT
   Cast End  : 03-Apr-2016 06:57:18 UT
   Max Depth : 82.1 m

   121/1
   Cast Start: 05-Apr-2016 08:11:00 UT
   Cast End  : 05-Apr-2016 08:26:59 UT
   Max Depth : 90.6 m


   124/2
   Cast Start: 06-Apr-2016 08:24:41 UT
   Cast End  : 06-Apr-2016 08:40:25 UT
   Max Depth : 91.4 m

   127/6
   Cast Start: 07-Apr-2016 08:02:47 UT
   Cast End  : 07-Apr-2016 08:15:09 UT
   Max Depth : 108.3 m

   131/1
   Cast Start: 08-Apr-2016 05:46:28 UT
   Cast End  : 08-Apr-2016 06:00:34 UT
   Max Depth : 107.0 m

   135/1
   Cast Start: 09-Apr-2016 07:32:35 UT
   Cast End  : 09-Apr-2016 07:46:07 UT
   Max Depth : 108.5 m

   139/1
   Cast Start: 10-Apr-2016 06:00:40 UT
   Cast End  : 10-Apr-2016 06:16:17 UT
   Max Depth : 71.4 m

   143/1
   Cast Start: 11-Apr-2016 07:08:05 UT
   Cast End  : 11-Apr-2016 07:28:24 UT
   Max Depth : 106.9 m

   146/2
   Cast Start: 12-Apr-2016 07:06:23 UT
   Cast End  : 12-Apr-2016 07:18:41 UT
   Max Depth : 109.7 m

   150/2
   Cast Start: 13-Apr-2016 08:21:17 UT
   Cast End  : 13-Apr-2016 08:35:04 UT
   Max Depth : 101.6 m

   154/2
   Cast Start: 14-Apr-2016 06:12:45 UT
   Cast End  : 14-Apr-2016 06:27:10 UT
   Max Depth : 96.5 m

   159/2
   Cast Start: 15-Apr-2016 08:29:53 UT
   Cast End  : 15-Apr-2016 08:42:27 UT
   Max Depth : 122.0 m

   167/1
   Cast Start: 17-Apr-2016 08:20:20 UT
   Cast End  : 17-Apr-2016 08:33:47 UT
   Max Depth : 110.4 m

   175/1
   Cast Start: 19-Apr-2016 08:59:40 UT
   Cast End  : 19-Apr-2016 09:07:41 UT
   Max Depth : 116.0 m

   183/1
   Cast Start: 21-Apr-2016 08:24:10 UT
   Cast End  : 21-Apr-2016 08:37:53 UT
   Max Depth : 84.1 m

   186/2
   Cast Start: 22-Apr-2016 05:30:41 UT
   Cast End  : 22-Apr-2016 05:43:57 UT
   Max Depth : 108.3 m

   190/2
   Cast Start: 23-Apr-2016 06:32:35 UT
   Cast End  : 23-Apr-2016 06:47:34 UT
   Max Depth : 111.3 m

   195/2
   Cast Start: 24-Apr-2016 08:19:34 UT
   Cast End  : 24-Apr-2016 08:34:16 UT
   Max Depth : 70.2 m

Problems: A manufacturing defect caused excessive stress on the
termination of the underwater cable for the instrument which caused a
failure in the communications and loss of two stations samples. After
repairs to the cable, problems with excessive heat, and a motor
position error on the deck unit caused complications with two other
casts leading to aborted profiles.  Deck unit heating issues were
minimized by reducing power to the unit.


Fig. 14.2: C-OPS- 443 nm downwelling irradiance (top left) and upwelling
           radiance (lower left), station 190, cast 2. 443 nm surface 
           irradiance collected at the same moment is shown in cyan. 
           Surface unit (ship) and profiler tilt and roll are shown in 
           the right-hand panels. Strong inflections in the profiles 
           (shown on a logarithmic scale) are due to the presence of
           a chlorophyll maximum near 70m.


14.5  Underway optics system

Equipment and Techniques: We installed our underway inherent optical
property measuring system in the hydro lab and supplied it with ship's
uncontaminated seawater at appx 10 L/min. The system includes a
computer-controlled valve that switches between whole water and a 0.2
μm filter (ZenPure nylon cartridge) which feeds an MSRC vortex
debubbler. The debubbled water is supplied through a PVC manifold to a
SeaBird TSG and an array of optical instruments: a WETLabs ECO BB3
backscattering sensor installed in a custom light trap (Slade et al.
2010), a WETLabs AC-S hyperspectral absorption and attenuation meter,
a Sequoia Scientific LISST 100X type B laser diffraction particle
counter/sizer, and a Satlantic in-situ FIRe in vivo fluorescence
excitation/relaxation sensor.


Fig. 14.3: Particulate backscattering coefficient from the southernmost
           end of the transit and beginning of the section.
           Note near exact overlap of the section south of 66.3S


Analysis: The system includes a computer-controlled data acquisition
system that automatically switches between filtered and whole water
supply to the instruments on a user-defined schedule. The filtered
seawater baseline is used to correct the instrument data for
calibration and offset drift, variable CDOM, and temperature effects
[Slade2010]. With the system operating in unfiltered mode the
instruments are sampled at 1 Hz and data are generally collected in
one minute bins. It takes around 15 minutes to completely flush the
system following a switch two or from filter mode, so no data
collection takes place during this time period. Approximately five
"filter" periods are scheduled each day. Instruments are also powered
off for one minute in ten to mitigate overheating and to extend lamp
life.

System optics were cleaned each day using isopropanol and the filter
cartridge was changed on alternate days.

Data from the system require extensive post processing and quality
control, which will be performed on land. Resulting data will be made
available via NASA’s field bio-optics archive SeaBASS
(seabass.gsfc.nasa.gov).


14.6  POC sampling

Sampling: Large volume HPLC/AP/POC samples were processed on our
filtration rig approximately every 5 days depending on water budget.
Samples were stored in our liquid nitrogen Dewar during the cruise. We
collected ~2 L samples into polyethylene sample bottles from four
depths defined by sharp profile gradients in beam transmission data
from the CTD. Samples were typically drawn above 300m bracketing
transmissometer features and one at 2000m.

Preparation: Samples were filtered onto precombusted 25 mm GF/F glass
fiber filters at < -0.05 MPa vacuum pressure. The filters were folded
into foil packets and immediately frozen in liquid nitrogen. The
samples will be returned to UCSB via liquid nitrogen dry shipper.

Analysis: POC samples will be analyzed for C and N content at the UCSB
Marine Science Institute Analytical Laboratory. Samples are acidified,
combusted at 100°C and analyzed using a Control Equipment, Inc.
CEC440HA elemental analyzer (http://msi.ucsb.edu/services/analytical-
lab/instruments/organic-elemental-analyzer-chn). Detection limits are
approximately 2 μg carbon and 5 μg nitrogen.

HPLC samples will be analyzed by Crystal Thomas at the NASA Goddard
Spaceflight Center HPLC lab (Greenbelt, MD). The full suite of
measurements, procedures, and quality control information is available
at: http://oceancolor.gsfc.nasa.gov/cms/



14.7  Phytoplankton Pigments and Particulate Absorption

Sampling: Once daily, in approximate synchronization with our C-OPS
casts and satellite overpasses we collected samples from the ship's
uncontaminated seawater supply for shore analysis of phytoplankton
pigments via HPLC and for particulate absorption spectra (AP). ~2 L
samples were collected into polyethylene sample bottles.

Preparation: Samples were filtered onto 25 mm GF/F glass fiber filters
and frozen in liquid nitrogen [Mueller2003]. The samples will be
returned for analysis to UCSB (AP) and to NASA GSFC (HPLC).

Analysis: Particulate absorption spectra of the AP sample filters are
measured a Shimadzu UV-2401 spectrophotometer with an integrating
sphere attachment, using a moistened GF/F filter as a blank.
Absorbance of filters is converted to absorption coefficient spectra
using the Quantitative Filter Technique [Mueller2003] using multiple
scattering corrections developed by Nelson et al. [Nelson1998].

Samples for phytoplankton pigment analysis will be analyzed at NASA
GSFC by the Ocean Ecology Laboratory Field Support Group
(http://oceancolor.gsfc.nasa.gov/cms/hplc/). Acetone extracts of the
particles collected on GF/F filters will be separated using an HP HPLC
system with a C8 column, and detected using a diode array
spectrophotometer system to confirm pigment identity. Resulting data
will be made available via NASA’s field bio-optics archive SeaBASS
(seabass.gsfc.nasa.gov).

[Mueller2003] Mueller, J.L., G.S Fargion, and C.R. McClain (eds), 2003. 
              Ocean Optics Protocols For Satellite Ocean Color Sensor 
              Validation, Revision 4. Greenbelt, MD, NASA Goddard 
              Spaceflight Center, NASA/TM-2003-211621/Rev4.

[Nelson1998]  Nelson, N.B., D.A. Siegel, and A.F. Michaels, 1998. 
              Seasonal dynamics of colored dissolved organic matter in 
              the Sargasso Sea. Deep-Sea Res. 45, 931-957.

[Nelson2007]  Nelson, N.B., D.A. Siegel, C.A. Carlson, C. Swan, W.M. 
              Smethie, Jr., and S. Khatiwala,. 2007. Hydrography of 
              chromophoric dissolved organic matter in the North 
              Atlantic. Deep-Sea Res. 54, 710-731.

[Nelson2009]  Nelson, N.B., and P.G. Coble, 2009. Optical analysis of 
              chromophoric dissolved organic matter. In: Practical 
              Guidelines for the Analysis of Seawater, Wurl. O. (ed). 
              San Diego: CRC Press.

[Nelson2016]  Nelson, N.B., and J.M. Gauglitz, 2016. Optical signatures 
              of dissolved organic matter transformation in the global 
              ocean. Front. Mar. Sci. 2:118. doi: 
              10.3389/fmars.2015.00118.

[Slade2010]   Slade, W.H., E. Boss, G. Dall’Omo, M.R. Langner, J. 
              Loftin, M.J. Behrenfeld, C. Roesler, and T.K. Westberry, 
              2010. Underway and Moored Methods for Improving Accuracy 
              in Measurement of Spectral Particulate Absorption and 
              Attenuation. J. Atmos. Ocean. Tech. 27: 1733-1746.




15.  DISSOLVED ORGANIC CARBON


PI 

   Craig Carlson (UCSB)

Technician

   Jacqueline Comstock


Dissolved Organic Carbon (DOC) samples were collected from all Niskin
bottles at all even numbered stations, as well as station 1. A total
of 1415 samples were collected from 43 stations. At each sampled
station, one duplicate sample was taken from a random depth. Samples
from 500m and shallower in the water column were filtered through a
47mm in-line GF/F filter. All samples were rinsed 3 times with
seawater, collected in 40 mL glass EPA vials, and stored at 4°C. 65µl
of 4N Hydrochloric acid were added to preserve samples.

Sample vials were prepared for this cruise by soaking in 10%
Hydrochloric acid, followed by 3 times rinse with DI water. The vials
were then combusted at 450°C for 4 hours to remove any organic matter.
Vial caps were cleaned by soaking in DI water overnight, followed by a
3 times rinse, and then left out to air dry.

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























16  CARBON ISOTOPES IN SEAWATER (14/13C)

PI

   Ann McNichol (WHOI)

Technician

   Jacqueline Comstock


A total of 352 samples were collected from 16 stations. Ten stations
were partially sampled (16 samples) while the rest were full cast (32
samples). Duplicates were collected at six different stations. Samples
were collected in 500 ml airtight glass bottles. Using silicone
tubing, the flasks were rinsed 2 times with the seawater from the
correspondent Niskin bottle. While keeping the tubing at the bottom of
the flask, the flask was filled and flushed by allowing it to overflow
one and a half times its full volume. Once the sample was taken, a
small amount (about 30 cc) of water was removed to create a headspace
and 100 ul of 50% saturated mercuric chloride solution was added in
the sampling bay. In order to avoid contamination, gloves were used
during all collection, handling, and storage processes. Sample
handling was done on a clean table covered with plastic trash bags.

After all samples were collected from a station the glass stoppers
were dried and greased with Apiezon-M grease to ensure an air tight
seal. The stoppers were secured with a rubber band which wrapped over
the entire bottle. The samples were stored in AMS crates or boxes
inside the ship’s main laboratory during the cruise. The samples will
be shipped to WHOI for analysis.

The radiocarbon/DIC content of seawater (DI14C) is measured by
extracting the inorganic carbon as CO2 gas, converting the gas to
graphite, then counting the number of 14C atoms in the sample directly
using an accelerator 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 a CO2 gas
standard calibrated to the PDB standard using an isotope radio mass
spectrometer (IRMS) at NOSAMS.















17  PHYTOPLANKTON, 15N/13C AND TRACE METALS

PI

   • Mike Lomas (Bigelow)
   • Banjamine Twining (Bigelow)

Technician

   • Steven Baer
   • Sara Rauschenberg


The goal of this project is to supplement the GO-SHIP data set with
measurements of microbial abundance and diversity, dissolved and
particulate iron (Fe), along with nitrogen (N) uptake rates in the
surface waters across the central Indian Ocean.

Trace metal clean water was collected from the surface water (20m) at
25 stations. Additional depths were sampled at 6 of these stations,
creating four-point depth profiles of the upper 200m (stations 97,
110, 127, 162, and 189). Samples for dissolved, particulate, and
cellular Fe were collected at each of the 25 stations. In total, 42
dissolved Fe, 42 particulate Fe, and 65 cellular Fe samples will be
brought back to Bigelow Laboratory for later analysis.

At these same 25 stations, water was collected from the “main” rosette
at 20m depth for measurement of chlorophyll a, urea, and total
dissolved phosphorus concentrations, and nutrient uptake incubations.
For measurement of N uptake rates, duplicate 2 L bottles were set up
with tracer additions of stable-isotopically labeled ammonium,
nitrate, and urea. Additionally, stable-isotopically labeled
bicarbonate was added to each bottle for measurement of inorganic
carbon (C) uptake rates (i.e. primary production). Bottles were
incubated on deck for six hours in ambient light and temperature
conditions, before being filtered over GF/F filters (nominal pore size
= 0.7 μm), or concentrated via CellTraps (Memteq Co. UK) for later
separation by a high-speed sorting flow cytometer for analysis of
taxon-specific uptake rates.

Samples for small phytoplankton (*Prochlorococcus, Synechococcus*,
pico- and nano-eukaryotes) and bacterial abundance were obtained from
euphotic zone depths, fixed with paraformaldehyde, and frozen for flow
cytometry analysis on shore. An additional Niskin was reverse-
concentrated and analyzed immediately onboard with a FlowCAM (Fluid
Imaging Systems, Inc.) for enumeration of larger (>10 μm)
phytoplankton.

The transect data will provide an overall picture to latitudinal
gradients in trace metals and biological diversity. Additionally, this
project breaks the central Indian Ocean into three major
biogeochemical regimes: Inter Monsoon Gyre in the North, a region from
~0-10°S, and the Indian Southern Subtropical Gyre in the south. A
series of incubations and bioassays were set up in the center of each
of these biogeochemical regions: stations 97, 127, and 162. These
stations were “regional stations”. Each regional station collected
samples for biological diversity and Fe at depths representing both
the surface and the deep chlorophyll maximum. In addition, samples
were collected for taxon-specific cellular quotas of C, N, and
phosphorus (P). The incubations at the regional stations included the
same uptake rates as described above for the 25 surface water
stations. An additional set of bottles were incubated for the
generation of kinetics curves of ammonium, nitrate, and urea. This
consists of tracer additions of stable-isotopically labeled N, along
with increasing amounts of unlabeled substrate to generate uptake
rates across a spectrum of concentrations (from 0.05 – 5.0 μM).

Bioassays were conducted to test for N, P, or Fe limitation of
phytoplankton growth. Triplicate trace-metal clean bottles were
inoculated with ammonium, phosphate, Fe, all three nutrients together,
or none (control). Bottles were incubated in the on-deck incubator for
three days. Initial and daily samples were taken for nutrient analysis
(performed by S. Becker and J. Ballard), variable chlorophyll
fluorescence (F(v)/F(m)), and preserved samples for flow cytometry
counts of bacteria and phytoplankton. At the conclusion of the
bioassay, additional samples were collected to measure chlorophyll a,
cellular Fe, and particulate organic C.





































18  PLANKTON GENOMIC ANALYSIS

Cruise Participant
   
    Cathy Garcia


The Martiny lab at UC Irvine, in collaboration with the Lomas and
Twining labs at Bigelow Laboratory of Ocean Science, have the goal to
link diversity to biogeochemical cycles in the Indian Ocean. The Lomas
group focused on phytoplankton diversity and nutrient uptake, Twining
on trace metal parameters, and Martiny on particulate organic matter
(POM) ratios and metagenomics.

Both institutions collected samples from a full cast at three
"regional stations". These were identified as the Indian Southern
Subtropical Gyre, an equatorial upwelling region at 10°S, and an Inter
Monsoon Gyre in the Bay of Bengal. The subtropical gyre surface
nutrient concentrations were below detection limit. A shoaling of the
nutricline occurred in the upwelling region, approximately 12°S to
5°S. The Bay of Bengal station is near a large oxygen minimum zone and
freshwater inputs from river runoff. The stations took place at
approximately 20°S, 5°S, and 8°N to capture representative stations
within each region. Triplicate samples for POM) with its constituents
of carbon (POC), nitrogen (PON), and phosphorus (POP), were collected
at 20m. Duplicate samples for DNA were collected at 20m and the deep
chlorophyll maximum (DCM), as described below.

Along the entire IO9N transect, we had a goal to establish very high
latitudinal resolution of genomics and POM data. Utilizing the ship’s
flow-through seawater system, water was collected at each station and
approximately halfway between each station, giving a sampling
resolution of 1/4 to 1/2 degree for the entire transect. On average
samples were taken 2-3 hours apart. Giving a high degree of temporal
as well as spatial resolution. Additionally, we collected water at 15
stations between Fremantle, Australia and the first station at 28°S =
station 84.

Triplicate samples for POM were filtered through 30μm nylon mesh into
8L polycarbonate carboys, which were rinsed once with sample water.
Eight liters were filtered through a GF/F filter (nominal pore size =
7 um) for POM and chemical oxygen demand each. At the same time,
duplicate genomics samples were obtained from the flow-through system.
Ten liters of unfiltered seawater was collected into 10L cubitainers
and passed through 0.22um Sterivex filters. The entire microbial
community larger than 0.22um was preserved and frozen for future
metagenomic analysis. These DNA samples will help identify the
diversity of the microbial population. Gene frequency of identifiable
nutrient uptake genes will assist in understanding patterns of
nutrient regimes and potential links to the surface microbial
community.


  POP     POC/POC   Oxygen Demand    Genomics         Fv/Fm         
--------  --------  -------------  ------------  ------------------
705 GF/F  705 GF/F    351 GF/F     600 Sterivex  Continuous Station 
filters   filters     filters        filters        173 onwards 


In addition to the regional and underway sampling, genomics samples
were collected at or below the deep chlorophyll maximum (DCM). Below
the DCM was chosen to target the primary nitrite layer. This occurred
at all odd numbered stations between April 2nd and April 28th
(stations 113 to 195). In collaboration with Chawalit Charoenpong from
Woods Hole Oceanographic Institution, DNA samples to identify ammonia
oxidizing and/or nitrifying populations were obtained from the oxygen
minimum zone, lower oxycline, and upper oxycline from the rosette from
selected Bay of Bengal stations beginning at station 149.














































19  LADCP

PI

    Dr. Andras Thurnherr

Cruise Participant
  
    Takaya Uchiya



Lowered Acoustic Doppler Current Profiler (LADCP) data were collected
on all stations (84-XXXX). For all profiles a dual head system was
used consisting of a downlooker and an uplooker. All profiles were
sent daily to A. Thurnherr for shore-based processing and QC.
Preliminary processing for horizontal velocity was also performed
onboard using the LDEO_IX software (www.ldeo.columbia.edu/LADCP ).
*ladcp-figure*. and *ladcp-figure*. show the zonal and meridional
velocity components, respectively, including the profiles from cruise
leg 1 (I08S). Due to instrument problems no LADCP data were collected
on leg-1 stations 14-27 and, in addition, the data quality of
horizontal velocities on stations 28-59 were low. The upper panels
show the upper ocean down to 800m using data from the ship-board ADCP
(SADCP) because the data are continuous; the lower panels show the
horizontal velocities from the LADCP.


Fig. 19.1: Zonal velocity [m/s] acquired from the LADCP (upper panel 
           SADCP, lower panel LADCP). The potential density contours 
           (grey solid lines), topography (black solid line) and the 
           intersection of the two cruise legs (red solid line) are 
           shown. Due to instrument problems and data quality issues, 
           LADCP data are masked out on stations 14-59.


The figures clearly show strong horizontal velocities in the Antarctic
Circumpolar Current (ACC) (~45-57S) and in the zonal equatorial
undercurrent region near the Equator. Additionally there are strong
currents around the Broken Plateau (30S). Based on satellite data, the
Broken Plateau coincides with the southern edge of a wedge of high
surface eddy kinetic energy (EKE) apparently emanating from the
western coast of Australia (e.g. Jia et al., 2011) [Jia2011]. Regions
with high vertical kinetic energy (VKE) derived from our LADCP data
do not seem to propagate southern of the Broken Plateau consistent with 
the results by Jia et al., 2011 [Jia2011]. The west coast of Australia 
is an upwelling zone, which results in baroclinically unstable
conditions, making it potentially the source for the high EKE
emanating from the Australian coast. Menezes et al., 2014
[Menzenes2014] also emphasize three separate eastward “jets” near the
surface in the Wharton Sea and the SADCP velocities near the surface
seem quite consistent with this inference. Based on solely the data
from the present cruise, we cannot determine whether the northwestward
flow along the southern flank of the Broken Plateau is part of the
mean circulation or a transitory feature.


Fig. 19.2: Meridional velocity [m/s] acquired from the ADCP (upper panel 
           SADCP, lower panel LADCP). The potential density contours 
           (grey solid lines), topography (black solid line) and the 
           intersection of the two cruise legs (red solid line) are 
           shown. Due to instrument problems and data quality issues, 
           LADCP data are masked out on stations 14-59.


The vertical shear of the horizontal velocity, buoyancy frequency and
the local Richardson number for the upper 300m are shown in *ladcp-
figure* and *ladcp-figure*. The buoyancy frequency was derived using
temperature and salinity data from the CTD and the Thermodynamic
Equation of Seawater - 2010 (TEOS-10: https://github.com/TEOS-10
/python-gsw ) package. The Richardson number was defined as:


              R(i) = N(^2) / (du/dz)(^2) + (dv/dz)(^2)


and the vertical resolution of the Richardson number was restricted by
the SADCP data with vertical scales of 10m. The Richardson number is
an indicator of how susceptible the water column is to shear
instability. It is interesting that we see low values right around the
equator, due to the large vertical shear of horizontal velocities. The
ACC region also has low values due to small buoyancy frequency. We
also show the mixed-layer depth (MLD) which was derived as the depth
at which the potential density exceeded by 0.1 kg/m3 from the surface
value following Fernández-Castro et al., 2014 [Fernández2014]. As
expected the MLD is deep in the ACC region, agreeing quite well with
the MLD provided by Dong et al., 2008 [Dong2008], and shallows up
towards the equator.

Fig. 19.3: LADCP-derived turbulence levels (W/kg) from vertical
           velocity measurements, using a novel finestructure 
           parameterization method (Thurnherr et al., GRL 2015), 
           which yields unbiased results at latitudes of 10 degrees 
           and higher but overestimates turbulence levels close to 
           the equator. Grey contours show equally spaced neutral 
           surfaces. The red vertical line separates the two cruise 
           legs.

Fig. 19.4: Figure 4. Vertical shear of the zonal velocity (left), 
           meridional velocity (middle) from the SADCP and buoyancy
           frequency in log10 scale from CTD (right). The black line
           shows the MLD and the red vertical line separates the two
           cruise legs. The top 400 meters of velocity has been 
           masked out due to low data quality.

Fig. 19.5: Richardson number in log10 scale. The black line shows the
           MLD and the red vertical line separates the two cruise legs. 
           The top 40 meters has been masked out due to low quality of 
           Velocity data.

Post-cruise processing and additional QC will be conducted at LDEO. At
that point it will be determined which profiles are of sufficient
quality for inclusion in the final CLIVAR ADCP archives.


[Dong2008]      Dong S., J. Sprintall, and L. Talley. Souther
                Ocean mixed- layer depth from ARGO float profiles. Journal
                of Geophys. Res.: Oceans. 113(C6) (2008): 2156—2202

[Fernández2014] Fernández-Castro B., B. Mouriño-
                Carballido, V. Benítez-Barrios, P. Couchiño, E.
                Fraile-Nuez, R. Graña, M. Piedeleu, and A. Rodríguez-
                Santana. Microstructure turbulence and diffusivity
                parameterization in the tropical and subtropical
                Atlantic, Pacific and Indian Oceans during the
                Malaspina 2010 expedition. Deep-Sea Res.I(Accepted for
                publication).

[Jia2011]       Jia F., L. Wu, and B. Qiu. Seasonal Modulation of
                Eddy Kinetic Energy and Its Formation Mechanism in the
                Southeast Indian Ocean. Journal of Phys. Ocean. 41.4 (2011):
                657—665.

[McDougall2011] McDougall T., and P. Barker. Getting
                started with TEOS-10 and the Gibbs Seawater (GSW)
                Oceanographic Toolbox. SCOR/IAPSO. WG127 (2011): 28

[Menzenes2014]  Menzenes V., H. Phillips, A. Schiller,
                B. Nathaniel, Dominigues C., and M. Vianna. South
                Indian Countercurrent and associated fronts. Journal of
                Geophys. Res. 119.10 (2014): 6763--6791.

[Thurnherr2015] Thurnherr A., L. St. Laurent, K.
                Richards, J. Toole, E. Kunze, and A. Ruiz Angulo.
                Vertical kinetic energy and turbulent dissipation in
                the ocean. Geophys. Res. Lett. 42 (2015): 794--807























20  Chipods

PI

   Jonathan Nash

Cruise Participant

   Karina Khazmutdinova



20.1  Overview

Chipods are independent, internally-recording devices that measure the
dissipation rate of temperature variance (chi) from a shipboard CTD.
From this, the turbulent diffusivity of heat (K) is computed, which is
an important quantity for quantifying vertical mixing in the ocean.
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.


20.2  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 (Chipod Figure A). The
third one was pointed downwards (Chipod Figure B). Chipod
pressure cases, containing the logger board and batteries, are showed
on Chipod Figure C.


Fig. 20.1: Chipod Figure A, B and C


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.

Below is a table describing the chipod configuration used, along with
the component’s serial numbers. Several replacements were made during
the cruise. Memory cards were replaced in pressure case SN2009 and
SN1013. Temperature sensor 13-05D on pressure case SN2002 was replaced
with sensor 10-06D on station 111, likely because the sensor bead of
13-05D developed a crack/leak.

  Logger Board  Pressure  Sensor   Sensor     Up/Down   Cast Used
       SN       Case SN     SN    Holder SN   Looker              
  ------------  --------  ------  ---------  ---------  ---------
      2002      Ti44-12   13-05D    14 14    Down Down   084-110 
                          10-06D                         111-196 
      2009      Ti44-12   11-25D     10         Up       084-196 
      1003      Ti44-11   14-34D     15         Up       084-196 


20.3  Data

Chipods were quite independent, and easy to manage during the cruise.
Chipods were turned on by connecting the sensors to the pressure cases
in the beginning of the cruise and were continuously taking
measurements for 39 days. Data was uploaded every three-four days to
check if the sensors are functioning properly. The figure below shows
typical cast measurements from a down-looking sensor.


20.4  Chipod issues: Mini-logger freezing when downloading data

Occasionally the mini-logger software used to download data from
chipods froze while downloading the data. As a result, the downloaded
data from the casts would look gibberish, unphysical. Apparently this
is a known problem and that the recorded data has been properly logged
and can be covered once the units have been shipped back to Oregon. If
one or two files could not be downloaded, the units would be power-
cycled and the chipod would continue recording and the next files
would look normal.


























21  ARGO FLOAT DEPLOYMENTS

PI

   Greg Johnson (UW, PMEL)


21.1  Overview

Eight Argo profiling CTD floats were deployed during this cruise at
the request of the University of Washington and NOAA’s Pacific Marine
Environmental Laboratory (PMEL). These floats are part of the Argo
array, a global network of over 3000 profiling floats. The floats are
designed to sink to a depth of 1000m. They then drift freely at depth
for ten days, before sinking to 2000m and then immediately rising to
the surface, collecting CTD data as they rise. Conductivity
(salinity), temperature, and pressure are measured and recorded at
various levels during each float ascent. At the surface, before the
next dive begins, the acquired data is transmitted to shore via
satellite, along with a location estimate taken while the float sits
at the surface. The typical lifetime of the floats in the water is
about four years. All Argo float data is made publicly available on
the web in real-time at http://www.usgodae.org/argo/argo.html.

When in position, each float was launched by carefully lowering it
into the water using a hand-held line strung through the deployment
collar. Deployments were done after the completion of the CTD station
nearest to the requested deployment location, immediately after the
ship had turned, and begun its course to the next station and had
reached a speed of approximately one knot. All eight floats were
deployed successfully. An e-mail report was sent to UW and PMEL, to
report the float ID number, exact float deployment time, location, and
deployer’s name(s). The following table shows the location of each
Argo Float deployment made on GO-SHIP I09N.


#  Float ID   I09N    Lat.   Lon.     Date &   Deployers      
              stn                       time
                                        (UTC)                
-  ---------  ----  -------  -------  -------  ---------------------
1  UW 9758     85   -27.71°  95°E     3/25/16  Matt Durham &  
                                        13:05   Cathy Garcia   
2  UW 9737     90   -24.73°  95°E     3/27/16  Ted Cummiskey & 
                                        01:00   Chawalit Charoenpong
3  UW 9768     98   -20.20°  95°E     3/29/16  Matt Durham &  
                                        13:30   Patrick Mears  
4  PMEL 0597  105   -16.27°  95°E     3/31/16  Matt Durham &  
                                        15:49   Leticia Barbero
5  UW 9763    107   -15.17°  95°E      4/1/16  Ted Cummiskey & 
                                        04:53   Amanda Fay   
6  PMEL 0593  118    -9.28°  95°E      4/4/16  Matt Durham &  
                                        13:30   Karina Khazmutdinova
7  PMEL 0591  132    -2.51°  94.24°E   4/8/16  Ted Cummiskey  
                                        17:45   & David Cervantes
8  PMEL 0598  148     2.60°  91.89°E  4/12/16  Ted Cummiskey  
                                        19:54   & Stephanie Mumma 


Note: Table: Summary of the deployment time and locations of each
  float.


Student Statements
==================


Chawalit Charoenpong
--------------------

   [image]

I09N has been a fantastic 40-day cruise for me! I have been in several
oceanographic cruises in the past but this is the first time as a CTD
watch-stander. This experience has given me a great appreciation for
those who work tirelessly to ensure that the science party gets the
water from the right depths and things are kept in order during
sampling. Preparing the rosette before deployment may look like an
easy task but it is essential to the success in water sample
collection. Also, I had a chance to help out with the sampling for
several parameters including salinity, radiocarbon, alkalinity and
DIC. The 12-hour shifts from midnight to noon sounded long but time
really flew by as things were constantly happening.

I also have my own project on this cruise as I sample for the isotopic
composition of multiple nitrogen species in the Nitrate δ15N and δ18N
Sampling section of this report. Doing this on top of the CTD duty was
challenging but I managed it through a lot of help and encouragement
from my fellow CTD watch-stander and others. Our two co-chief
scientists have been fantastic in accommodating this sampling and
sharing my excitement throughout the cruise.

One other aspect that I enjoyed tremendously on this cruise was the
interaction I had with fellow scientists. I have learned so much from
talking with them and seeing how different analyses were carried out
on board. In collaboration with scientists from University of
California, Irvine and Bigelow Laboratory for Ocean Sciences, I
initiated three small projects that we carried out together to: (1)
Look at the isotopic ratios and stoichiometry of suspended particles
from different size fractions from the underway seawater system and in
water samples collected from the Niskin bottles. (2) Quantify the
relative gene abundance of the anaerobic ammonium oxidizing bacteria
(anammox) in the Bay of Bengal oxygen minimum zone (OMZ). (3) Look at
the microbial community residing in the deep chlorophyll maxima (DCM)
through metagenomics.

Finally, I would like to thank Leticia Barbero for accepting my
application to participate on this cruise and making my sample
collection for nitrogen biogeochemistry possible. I look forward to
being involved in the future GO-SHIP campaigns!





Amanda Fay
----------

   [image]

What an incredible 5 weeks aboard the R/V Revelle! This was my second
GO-SHIP cruise experience, this time serving as a CTD-watchstander on
the I09N cruise from Fremantle, Australia to Phuket, Thailand. The
experience gained from my last cruise definitely aided in making the
transition to ship-life smoother, and the calm seas were much
appreciated by all onboard. Working with the Cast6 winch was a new
experience, but the expertise and abilities of our wonderful restechs
and winch handlers made things go efficiently. As a CTD-watchstander I
spent much of my time in the computer lab, monitoring the instruments
on the rosette during the downcast, and firing the Niskin bottles on
the upcast. My co-watchstander and I spent many hours googling
watermasses and sharing papers and textbooks in order to learn about
the circulation patterns we were seeing as we transited north through
this dynamic region (what’s that blip at 230db from? Why does the
oxygen level increase right above the seafloor?). His expertise in
nitrogen cycling was an asset and I learned much from him during our
time at the computer.

Once the rosette was back onboard, our work moved outside. My tasks
alternated between sampling for alkalinity and/or salinity, and
serving as sample cop, as well as the music coordinator for our
midnight to noon shift. The camaraderie and teamwork displayed during
sampling was impressive. Everyone pitched in to make the process quick
and smooth, especially when breakfast time approached. Samplers would
often stay longer to help with salinity, and our chief and co-chief
were consistently outside, always willing to lend a hand with samples.
Prepping the rosette for deployment was probably my least favorite
task, but as time went on and our callouses grew thicker, the strains
on our fingers and arms subsided as we increased our proficiency at
getting all the bottles cocked and ready to go.

Another task I took on during the cruise was to download daily updates
of weather maps in order to keep the crew abreast of what ocean
conditions would be like over the upcoming days. I updated a script
initially produced by the CTD-watchstanders on I08S, to accommodate
our more northern cruise track and schedule of stations. We enjoyed
watching the storms pass ahead and behind our track, and also marveled
at a prominent cyclone developing in the western part of the basin.
Turns out, it was the strongest tropical cyclone ever on record in the
Indian Ocean, Tropical cycle Fantala, with winds exceeding 175 mph.
The category 4/5 storm persisted for over a week, fueled by above
average sea surface temperatures in the area. We all were thankful
that our cruise track did not put us anywhere near that dangerous
storm.

   [image]Tropical cyclone fantala, wind speed.

   [image]Tropical cyclone fantala, wave height.

Outside of my watchstander duties, I maintained a blog on my personal
website as an outreach project (fayamanda.weebly.com). Many of my
friends are elementary and middle school science teachers. Their
classes followed along during our adventures and when I return, I plan
to go present in their classrooms, answering questions and encouraging
the students to consider the broad spectrum of potential areas of
study in the earth sciences.

I was lucky enough to share my CTD-watch shift with a Thai national,
currently working on his PhD at WHOI. This offered me the chance to
learn and practice Thai phrases and hear about the history and customs
of the Thai people.  What a great addition to the cruise! I think
everyone would agree that the relationships built onboard are the
highlights of the cruise and something I will cherish for years to
come.


Karina Khazmutdinova
--------------------

   [image]

As CTD-watchers, Patrick and I were in charge of preparing the rosette
and making sure it will come back with all the Niskin bottles full of
water for samplers. In the beginning of the cruise we had to switch
around a few oxygen sensors and I became a master of redoing hose
clumps and zip tides. Most of our shifts went smoothly and we got into
the CTD-watchers routine pretty quickly. My other duty on the ship was
uploading data from the chipods and troubleshooting the problems if
chipods data didn't look normal.

Being on board of the RV Revelle has been an amazing experience!
Unfortunately, we saw more trash floating in the ocean than the
wildlife. However, seeing flying fish playing by the ship was
incredible. Star gazing was my favorite thing to do after the shift
especially in the Southern hemisphere! We were blessed with calm
weather and there were a few days when the ocean was so flat that it
was hard to believe that we are in the middle of the Indian Ocean. I
truly enjoyed being back at the sea! Had met incredible people, had
learned a lot and enjoyed doing the science right at the spot!


Patrick Mears
-------------

   [image]

My duties as a CTD watch stander primarily included preparing the
rosette for deployment, monitoring its decent while recording regions
of interest for the samplers, coordinating stops with the winch
operator to match specific depths according to a sampling scheme, and
coordinating sample collecting once it is on deck and occasionally
assisting with sample collection. I also assisted the Research
Technician in replacing sensors and conducting minor maintenance on
the rosette when needed. In addition to those duties, I was also
responsible for setting up the LADCP before each deployment on my
watch and downloading the data after each cast.




CCHDO Data Processing Notes


*  File Merge Carolina Berys
ucsb_cdom_i8si9n_s7a_20170511.txt (download) #66ba3 
Date: 2019-11-05 
Current Status: merged


*  File Submission Andrew Barna
i09n_original_resolution_cnv.zip (download) #79cf5 
Date: 2019-11-01 
Current Status: intermediate


*  File Submission Andrew Barna
i09n_original_acquisition_hex_xmlcon.zip (download) #7d09b 
Date: 2019-11-01 
Current Status: raw


*  File Merge Carolina Berys
33RR20160321_hy1.csv (download) #ed9f5 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
33RR20160321_nc_hyd.zip (download) #f6b56 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
33RR20160321.exc.csv (download) #5be44 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
Final 2016 I09N CFC data.xlsx (download) #12bf0 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
33RR20160321.exc.csv (download) #97137 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
ucsb_cdom_i8si9n_s7a_20170511.txt (download) #66ba3 
Date: 2019-08-29 
Current Status: merged


*  File Merge Carolina Berys
33RR20160321.exc.csv (download) #84bfe 
Date: 2019-08-29 
Current Status: merged


*  Bottle data update CFC-11, CFC-12, DOC, CDOMs Carolina Berys 
Date: 2019-08-29 
Data Type: Bottle 
Action: Website Update 
Note: 
I09N 2016 33RR20160321 processing - BTL/merge - CFC-11, CFC-12, DOC, CDOMs 

2019-08-29

C Berys

Submissions

   id  submit date submit by                  file name
-----  ----------- -------------------------  -------------------------------
--
14068  2018-07-05  R                          33RR20160321.exc.csv
14623  2019-08-20  Robert Key                 33RR20160321.exc.csv
14082  2018-07-12  Carolina for Bill Smethie  Final 2016 I09N CFC data.xlsx
14564  2019-06-25  Norm Nelson                
ucsb_cdom_i8si9n_s7a_20170511.txt
14091  2018-07-18  Robert  Key                33RR20160321.exc.csv


Changes

* changed CDOMLS to CDOMSL
* DOC at station-cast-sample 98-1-11, flag changed from 0 to 2. QC by Bob 
Key, approved by Craig Carlson
* removed SF6 and CFC113 columns, no data included, approved by Rana Fine. 
* CTDSAL, CTDOXY at station-cast-sample 95-3-32, flag changed to 9 for fill 
value, approved by Andrew Barna
* edits to header comments 
                                                           
                                                                
Merges

33RR20160321.exc.csv merged into 33RR20160321_hy1.csv using hydro hydro 
0.8.2-57-g8aa7d7a.

:Updated parameters: CFC-11 CFC-11_FLAG_W CFC-12 CFC-12_FLAG_W 
:New parameters: DOC DOC_FLAG_W

ucsb_cdom_i8si9n_s7a_20170511.txt merged into 33RR20160321_hy1.csv using 
hydro hydro 0.8.2-57-g8aa7d7a.

:New parameters: CDOM325 CDOM325_FLAG_W CDOM340 CDOM340_FLAG_W CDOM380 
CDOM380_FLAG_W CDOM412 CDOM412_FLAG_W CDOM443 CDOM443_FLAG_W CDOM490 
CDOM490_FLAG_W CDOM555 CDOM555_FLAG_W CDOMSL CDOMSL_FLAG_W CDOMSN 
CDOMSN_FLAG_W

33RR20160321_hy1.csv opened in JOA with no apparent problems.


Conversions

file                    converted from       software               
----------------------- -------------------- -----------------------
33RR20160321_nc_hyd.zip 33RR20160321_hy1.csv hydro 0.8.2-57-g8aa7d7a

Updated Files Manifest

file                    stamp            
----------------------- -----------------
33RR20160321_hy1.csv    20190829CCHSIOCBG
33RR20160321_nc_hyd.zip 20190829CCHSIOCBG

					
*  File Merge Carolina Berys
index copy_Leti.txt (download) #5a924 
Date: 2019-08-23 
Current Status: merged


*  File Online Carolina Berys
33RR20160321.exc.csv (download) #84bfe 
Date: 2019-08-20 
Current Status: merged


*  File Submission Robert Key
33RR20160321.exc.csv (download) #84bfe 
Date: 2019-08-20 
Current Status: merged 
Notes
CDOM data submitted by Norm on 6/25/19 merged. I'm not qualified to QC
Numerous header edits


*  File Online Lynne Merchant
ucsb_cdom_i8si9n_s7a_20170511.txt (download) #66ba3 
Date: 2019-06-25 
Current Status: merged


*  File Submission Norm Nelson
ucsb_cdom_i8si9n_s7a_20170511.txt (download) #66ba3 
Date: 2019-06-25 
Current Status: merged 
Notes
I8S I9N 2016 


*  File Submission Norm Nelson
ucsb_cdom_i8si9n_s7a_20170511.txt (download) #66ba3 
Date: 2019-06-25 
Current Status: merged 
Notes
I8S I9N 2016 


*  File Online Carolina Berys
33RR20160321.exc.csv (download) #97137 
Date: 2018-08-06 
Current Status: merged


*  File Online Carolina Berys
33RR20160321.exc.csv (download) #5be44 
Date: 2018-08-01 
Current Status: merged


*  File Submission Robert Key
33RR20160321.exc.csv (download) #97137 
Date: 2018-07-18 
Current Status: merged 
Notes
Submission contains final CFC-11 and 12 submitted by Bill Smethie on 7/12/18
Header updated. There are no CFC-113 nor SF6 data so those columns have been 
removed from the file


*  File Online Carolina Berys
Final 2016 I09N CFC data.xlsx (download) #12bf0 
Date: 2018-07-12 
Current Status: merged


*  File Submission Carolina for Bill Smethie
Final 2016 I09N CFC data.xlsx (download) #12bf0 
Date: 2018-07-12 
Current Status: merged 
Notes
The I09N cruise CFC data currently at CCHDO is the preliminary shipboard 
data.  The raw data were reprocessed after the cruise, but the revised 
concentrations were not submitted.  The attached file contains the final 
reprocessed data with revised quality flags.


*  File Submission R
33RR20160321.exc.csv (download) #5be44 
Date: 2018-07-05 
Current Status: merged 
Notes
Updated bottle file for I09N.2016
Significant header revisions
DOC data from Craig Carlson added
Empty and unexpected to ever receive columns removed

Copy to Barbaro.
Requested final CFC, Alk and pH data


*  File Merge Roxanne Lee
33RR20160321_hy1.csv (download) #68ca1 
Date: 2017-10-15 
Current Status: merged


*  File Merge Roxanne Lee
i09_hy1.csv (download) #588bc 
Date: 2017-10-15 
Current Status: merged


*  Bottle data Roxanne Lee 
Date: 2017-10-15 
Data Type: Bottle 
Action: New 
Note: 
I09N 2016 33RR20160321 processing - BTL/merge - CTDSAL, CTDSAL_FLAG_W, 
CTDOXY, CTDOXY_FLAG_W
 
2017-10-15
 
R Lee
 
Submission
 
filename                               submitted by  date        id  
----------------------------------------------------------------------
33RR20160321_hy1.csv                   Andrew Barna  2016-07-08  12263
i09_hy1.csv	                  Courtney Schatzman 2016-07-19  12277
                                                               

Changes
- DEPTH values were rounded to the nearest whole meter.
- D15N-NO3 to D15N_NO3
- D18O-NO3 to D18O_NO3
                                                                
Merge
 
i09_hy1.csv merged into 33RR20160321_hy1.csv
 
:Updated parameters from i09_hy1.csv: CTDSAL, CTDSAL_FLAG_W, CTDOXY, 
CTDOXY_FLAG_W
 
33RR20160321_hy1.csv and 33RR20160321_nc_hyd.zip opened in JOA with no 
apparent problems.
 
 
Conversion
----------
 
file                    converted from       software               
--------------------------------------------------------------------
33RR20160321_nc_hyd.zip 33RR20160321_hy1.zip hydro 0.8.2-48-g594e1cb
 
 
Updated Files Manifest
----------------------
 
file                    stamp            
-------------------------------------------
33RR20160321_hy1.csv    20171015CCHSIORJL
33RR20160321_nc_hyd.zip 20171015CCHSIORJL
					

*  File Merge see
i09-2016-ctd-data.tar.gz (download) #94f62 
Date: 2017-05-31 
Current Status: merged


*  File Merge see
2016I09.TXT.zip (download) #f282c 
Date: 2017-05-31 
Current Status: merged


*  CTD exchange and netcdf formats online; Merged CTDBEAMCP data see 
Date: 2017-05-31 
Data Type: CTD 
Action: Website Update 
Note: 
I09N 2016 33RR20160321 processing - CTD/merge - 
CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDNOBS,CTDETIME,CTDBEAMCP

2017-05-31

SEE


Submission

filename                 submitted by       date       id  
------------------------ ------------------ ---------- -----
i09-2016-ctd-data.tar.gz Courtney Schatzman 2016-07-19 12276 
2016I09.TXT.zip          Wilf Gardner       2017-05-23 12740 

Changes
-------

33RR20160321_ct1.zip
       - removed DEPTH from header, as values for all casts are -999
       - changed param name from FLUORC to CTDFLUOR
       - removed DEPTH parameter from exchange file
       - removed TRANS parameter from exchange file, raw no longer needed
       - merged CTDBEAMCP data from Wilf Gardner, to replace raw TRANS
       - changed SECT_ID from I09 to I09N to match CCHDO collections
       - added header comments for units and cruise
       - changed file names to conform to CCHDO format

Conversion
----------

file                    converted from       software               
----------------------- -------------------- -----------------
33RR20160321_nc_ctd.zip 33RR20160321_ct1.zip 0.8.2-48-g594e1cb


Updated Files Manifest
----------------------

file                    stamp            
----------------------- -----------------
33RR20160321_ct1.zip    20170531CCHSIOSEE
33RR20160321_nc_ctd.zip 20170531CCHSIOSEE

:Updated parameters: CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDNOBS,CTDETIME
:Merged parameters: CTDBEAMCP

opened in JOA with no apparent problems:
       33RR20160321_ct1.zip 
       33RR20160321_nc_ctd.zip

opened in ODV with no apparent problems:
       33RR20160321_ct1.zip

					
*  File Online Carolina Berys
2016I09.TXT.zip (download) #f282c 
Date: 2017-05-30 
Current Status: merged


*  File Submission see
2016I09.TXT.zip (download) #f282c 
Date: 2017-05-23 
Current Status: merged 
Notes
From W.Gardner;  Beam Attenuation Numbers to be merged into CTD files as 
CTDBEAMCP.   Status: Final


*  File Merge Carolina Berys
33RR20160321_do.pdf (download) #5a4bc 
Date: 2016-11-07 
Current Status: dataset


*  File Merge Carolina Berys
33RR20160321_do.txt (download) #22621 
Date: 2016-11-07 
Current Status: dataset


*  File Submission Jerry Kappa
33RR20160321_do.txt (download) #22621 
Date: 2016-10-24 
Current Status: dataset 
Notes
This is the text version of the I09N_2016 cruise report which contains 
corrections requested by L. Barbero on 2016-09-26, ready to be added to the 
CCHDO web site.


*  File Submission Jerry Kappa
33RR20160321_do.pdf (download) #5a4bc 
Date: 2016-10-21 
Current Status: dataset 
Notes
This updated pdf version of the cruise report is ready to go online in the 
documentation section of the CCHDO web site.  It includes corrections 
submitted by L. Barbero on 2016-09-26.


*  File Online Carolina Berys
index copy_Leti.txt (download) #5a924 
Date: 2016-09-26 
Current Status: merged


*  File Submission Carolina for Leticia Barbero
index copy_Leti.txt (download) #5a924 
Date: 2016-09-26 
Current Status: merged 
Notes
Updated cruise report, edits to PI for PH and others


*  File Online Carolina Berys
i09-2016-ctd-data.tar.gz (download) #94f62 
Date: 2016-07-19 
Current Status: merged


*  File Online Carolina Berys
i09_hy1.csv (download) #588bc 
Date: 2016-07-19 
Current Status: merged


*  File Submission Courtney Schatzman
i09_hy1.csv (download) #588bc 
Date: 2016-07-19 
Current Status: merged 
Notes
Updated 115/03, 112/01, 098/01 CTD salinity, oxygen data and flags. 


*  File Submission Courtney Schatzman
i09-2016-ctd-data.tar.gz (download) #94f62 
Date: 2016-07-19 
Current Status: merged 
Notes
Updated 115/03, 112/01, 098/01 CTD salinity, oxygen data and flags. 


*  File Online Carolina Berys
33RR20160321_hy1.csv (download) #68ca1 
Date: 2016-07-11 
Current Status: merged


*  File Submission Andrew Barna
33RR20160321_hy1.csv (download) #68ca1 
Date: 2016-07-08 
Current Status: merged 
Notes
These data are preliminary, updates expected in the next few weeks.


