CRUISE REPORT: P06E
(Updated APR 2018)



Highlights



                              Cruise Summary Information

               Section Designation:  P06E
Expedition designation (ExpoCodes):  320620170820
                  Chief Scientists:  Kevin Speer/FSU
                                     Lena Schulze/FSU (Co-Chief)
                             Dates:  2017-AUG-20 to 2017-SEP-30
                              Ship:  Nathaniel B Palmer
                     Ports of call:  Papeete, Tahiti to Valparaiso, Chile

                                                -28.9597
             Geographic Boundaries:  -148.9698              -71.585
                                                -32.5051

                          Stations:  106
      Floats and drifters deployed:  31 Argo/O2 floats, 4 SOCCOM floats, 6 drifters 
    Moorings deployed or recovered:  0

                                 Contact Information:

              Kevin Speer                            Lena Schulze
       Florida State University                Florida State University
Geophysical Fluid Dynamics Institution  Geophysical Fluid Dynamics Institution
        Email: kspeer@fsu.edu                  Email: lschulze@fsu.edu
         Phone: 850-644-5594



















                          Cruise Report for the 2017 Reoccupation of P06E




1  GO-SHIP P06E 2017 HYDROGRAPHIC PROGRAM

                                                        Table of Contents


1 GO-SHIP P06E 2017 Hydrographic Program  . . . . . . . . . . . . . .   2
  1.1 Programs and Principal Investigators  . . . . . . . . . . . . .   5
  1.2 Science Team and Responsibilities . . . . . . . . . . . . . . .   5
  1.3 Underwater Sampling Package . . . . . . . . . . . . . . . . . .   7

2 Cruise Narrative  . . . . . . . . . . . . . . . . . . . . . . . . .   8
  2.1 Narrative . . . . . . . . . . . . . . . . . . . . . . . . . . .   9
  2.2 Preliminary Science remarks . . . . . . . . . . . . . . . . . .  11
  2.3 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . .  12

3 CTDO and Hydrographic Analysis  . . . . . . . . . . . . . . . . . .  12
  3.1 CTDO and Bottle Data Acquisition  . . . . . . . . . . . . . . .  13
  3.2 CTDO Data Processing  . . . . . . . . . . . . . . . . . . . . .  14
  3.3 Pressure Analysis . . . . . . . . . . . . . . . . . . . . . . .  14
  3.4 Temperature Analysis  . . . . . . . . . . . . . . . . . . . . .  15
  3.5 Conductivity Analysis . . . . . . . . . . . . . . . . . . . . .  16
  3.6 CTD Dissolved Oxygen  . . . . . . . . . . . . . . . . . . . . .  19

4 Salinity  . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  21
  4.1 Equipment and Techniques  . . . . . . . . . . . . . . . . . . .  21
  4.2 Sampling and Data Processing  . . . . . . . . . . . . . . . . .  22
  4.3 Narrative . . . . . . . . . . . . . . . . . . . . . . . . . . .  22

5 Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  23
  5.1 Summary of Analysis . . . . . . . . . . . . . . . . . . . . . .  23
  5.2 Equipment and Techniques  . . . . . . . . . . . . . . . . . . .  24
  5.3 Nitrate/Nitrite Analysis  . . . . . . . . . . . . . . . . . . .  24
  5.4 Phosphate Analysis  . . . . . . . . . . . . . . . . . . . . . .  25
  5.5 Silicate Analysis . . . . . . . . . . . . . . . . . . . . . . .  25
  5.6 Sampling  . . . . . . . . . . . . . . . . . . . . . . . . . . .  26
  5.7 Data Collection and Processing  . . . . . . . . . . . . . . . .  26
  5.8 Standards and Glassware Calibration . . . . . . . . . . . . . .  26
  5.9 Quality Control . . . . . . . . . . . . . . . . . . . . . . . .  27
  5.10 Analytical Problems  . . . . . . . . . . . . . . . . . . . . .  28

6 Oxygen Analysis . . . . . . . . . . . . . . . . . . . . . . . . . .  30
  6.1 Equipment and Techniques  . . . . . . . . . . . . . . . . . . .  30
  6.2 Sampling and Data Processing  . . . . . . . . . . . . . . . . .  30
  6.3 Volumetric Calibration  . . . . . . . . . . . . . . . . . . . .  31
  6.4 Standards . . . . . . . . . . . . . . . . . . . . . . . . . . .  31
  6.5 Narrative . . . . . . . . . . . . . . . . . . . . . . . . . . .  31

7 Total Alkalinity  . . . . . . . . . . . . . . . . . . . . . . . . .  32
  7.1 Total Alkalinity  . . . . . . . . . . . . . . . . . . . . . . .  32
  7.2 Total Alkalinity Measurement System . . . . . . . . . . . . . .  32
  7.3 Sample Collection . . . . . . . . . . . . . . . . . . . . . . .  33
  7.4 Problems and Troubleshooting  . . . . . . . . . . . . . . . . .  33
  7.5 Quality Control . . . . . . . . . . . . . . . . . . . . . . . .  34

8 Dissolved Inorganic Carbon (DIC)  . . . . . . . . . . . . . . . . .  35
  8.1 Sample collection . . . . . . . . . . . . . . . . . . . . . . .  35
  8.2 Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . .  35
  8.3 DIC Analysis  . . . . . . . . . . . . . . . . . . . . . . . . .  36
  8.4 DIC Calculation . . . . . . . . . . . . . . . . . . . . . . . .  36
  8.5 Calibration, Accuracy, and Precision  . . . . . . . . . . . . .  37
  8.6 Underway DIC Samples  . . . . . . . . . . . . . . . . . . . . .  38
  8.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . .  38

9 Discrete pH Analyses (Total Scale)  . . . . . . . . . . . . . . . .  39
  9.1 Sampling  . . . . . . . . . . . . . . . . . . . . . . . . . . .  39
  9.2 Analysis  . . . . . . . . . . . . . . . . . . . . . . . . . . .  40
  9.3 Reagents  . . . . . . . . . . . . . . . . . . . . . . . . . . .  40
  9.4 Data Processing . . . . . . . . . . . . . . . . . . . . . . . .  40
  9.5 Problems and Troubleshooting  . . . . . . . . . . . . . . . . .  41
  9.6 Standardization/Results . . . . . . . . . . . . . . . . . . . .  42

10 CFC-11, CFC-12, CFC-113, and SF6 . . . . . . . . . . . . . . . . .  43
   10.1 Sample Collection . . . . . . . . . . . . . . . . . . . . . .  43
   10.2 Equipment and Technique . . . . . . . . . . . . . . . . . . .  43
   10.3 Calibration . . . . . . . . . . . . . . . . . . . . . . . . .  44

11 Dissolved Organic Phosphorus . . . . . . . . . . . . . . . . . . .  44

12 Nitrate 𝛿15N and 𝛿18O  . . . . . . . . . . . . . . . . . . . . . .  45

13 Dissolved Organic Carbon and Total Dissolved Nitrogen  . . . . . .  46
   13.1 Project Goals . . . . . . . . . . . . . . . . . . . . . . . .  46
   13.2 Sampling  . . . . . . . . . . . . . . . . . . . . . . . . . .  46
   13.3 Standard Operating Procedure for DOC Analyses-Carlson Lab UCSB 47
   13.4 DOC calculation . . . . . . . . . . . . . . . . . . . . . . .  48
   13.5 Standard Operating Procedure for TDN analyses-Carlson Lab UCSB 48
   13.6 TDN calculation . . . . . . . . . . . . . . . . . . . . . . .  49

14 Carbon Isotopes in seawater (14/13C) . . . . . . . . . . . . . . .  49

15 Marine Microbes, Phosphorus, and Metabolic Energy Potential  . . .  50

16 NASA Ocean Biology/Biogeochemistry Program . . . . . . . . . . . .  51
   16.1 NASA Science Objectives . . . . . . . . . . . . . . . . . . .  51

17 LADCP  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  54
   17.1 LADCP system configuration  . . . . . . . . . . . . . . . . .  54
   17.2 Problems/Setup changes  . . . . . . . . . . . . . . . . . . .  55
   17.3 Data Processing and Quality Control . . . . . . . . . . . . .  57

18 Chipods  . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  57
   18.1 Overview  . . . . . . . . . . . . . . . . . . . . . . . . . .  57
   18.2 System Configuration and Sampling . . . . . . . . . . . . . .  58
   18.3 Data  . . . . . . . . . . . . . . . . . . . . . . . . . . . .  58

19 Float Deployments  . . . . . . . . . . . . . . . . . . . . . . . .  60
   19.1 SOCCOM floats . . . . . . . . . . . . . . . . . . . . . . . .  60
   19.2 SIO floats  . . . . . . . . . . . . . . . . . . . . . . . . .  62
   19.3 UW floats . . . . . . . . . . . . . . . . . . . . . . . . . .  63

20 Drifter Deployments  . . . . . . . . . . . . . . . . . . . . . . .  64

21 Student Statements . . . . . . . . . . . . . . . . . . . . . . . .  65
   21.1 Cristobal Aguilera  . . . . . . . . . . . . . . . . . . . . .  65
   21.2 Dario Marconi . . . . . . . . . . . . . . . . . . . . . . . .  65
   21.3 Lucie Knor  . . . . . . . . . . . . . . . . . . . . . . . . .  66
   21.4 Luz Zarate-Jimenez  . . . . . . . . . . . . . . . . . . . . .  66
   21.5 Rudolph Herbstaedt Gomez  . . . . . . . . . . . . . . . . . .  67
   21.6 Sherry Chou . . . . . . . . . . . . . . . . . . . . . . . . .  68



   [image]Cruise track of P06E 2017

The Pacific Ocean P06E repeat hydrographic line was reoccupied for the
US Global Ocean Carbon and Repeat Hydrography Program. Reoccupation of
the P06E transect occurred on the RVIB Nathaniel B Palmer from August
20, 2017 to September 30, 2017. The survey of P06E 2017 consisted of
*CTDO*, rosette, *LADCP*, chipod, water samples and underway
measurements. The ship departed from the port of Papeete on the island
of Tahiti, French Polynesia and completed the cruise in the port of
Valparaiso, Chile.

A total of 106 stations were occupied with one
CTDO/rosette/LADCP/chipod package. 106 stations and 106
CTDO/rosette/LADCP/chipod casts including 2 test casts were performed.
The stations were, for the most part, a reoccupation of P06E 2009 and
detailed in the following sections. 31 Argo/O2 floats were deployed
on P06E 2017 and detailed in the Float Deployments section of the
cruise report. 4 *SOCCOM* floats were deployed on P06E 2017 and are
detailed in the SOCCOM floats section of the cruise report. 6 drifters
were deployed on P06E 2017 and are detailed in the Drifter Deployments
section of the cruise report.

   [image]Distribution of samples by longitude.

   [image]Distribution of samples by station number.

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 Nitrate
𝛿15N and 𝛿18O, *DOC*/*TDN*, 13C/14C, *POC*, *HPLC*, *DOP*, *DON*,
cell counts, *DOP*, *DIP*, *POP*, particulate ATP, and dissolved ATP.

A sea-going science team assembled from 11 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

                                          Principal 
Program                  Affiliation      Investigator       Email 
———————————————————————  ———————————————  —————————————————  ——————————————————————————
*CTDO* Data, Salinity,   *UCSD*, *SIO*    Susan Becker,      sbecker@ucsd.edu,         
Nutrients, Dissolved O2                   Jim Swift          jswift@ucsd.edu           
-----------------------  ----------------------------------  --------------------------
Total CO2 (DIC)          *PMEL*, *AOML*,  Richard Feely,     Richard.A.Feely@noaa.gov, 
                          *NOAA*          Rik Wanninkhof     Rik.Wanninkhof@noaa.gov   
-----------------------  ----------------------------------  --------------------------
Underway Temperature,    *AOML*, *NOAA*,  Rik Wanninkhof,    Rik.Wanninkhof@noaa.gov,  
Salinity, and pCO2       *ASC*            *ASC*              admin@nbp.usap.gov        
-----------------------  ----------------------------------  --------------------------
Total Alkalinity, pH     *U Miami*        Frank Millero      fmillero@rsmas.miami.edu  
-----------------------  ----------------------------------  --------------------------
ADCP                     *UH*             Eric Firing        efiring@soest.hawaii.edu  
-----------------------  ----------------------------------  --------------------------
*LADCP*                  *LDEO*           Andreas Thurnherr  ant@ldeo.columbia.edu     
-----------------------  ---------------  -----------------  --------------------------
*CFCs*, *SF6*            *U Miami*,       Rana Fine,         rfine@rsmas.miami.edu,    
                         *UT*             Dong-Ha Min        dongha@mail.utexas.edu    
-----------------------  ---------------  -----------------  --------------------------
*DOC*, *TDN*             *UCSB*           Craig Carlson      carlson@lifesci.ucsb.edu  
-----------------------  ---------------  -----------------  --------------------------
C13 & C14                *WHOI*,          Ann McNichol,      amcnichol@whoi.edu,       
                         *Princeton*      Robert Key         key@princeton.edu         
-----------------------  ---------------  -----------------  --------------------------
Transmissometry          *TAMU*           Wilf Gardner       wgardner@ocean.tamu.edu   
-----------------------  ---------------  -----------------  --------------------------
Fluorescence and         *U Maine*        Emmanuel Boss      emmanuel.boss@maine.edu   
Backscatter (*SOCCOM*),
HPLC & POC                                                                 
-----------------------  ---------------  -----------------  --------------------------
Chipod                   *OSU*            Jonathan Nash      nash@coas.oregonstate.edu 
-----------------------  ---------------  -----------------  --------------------------
Nitrate Ni15N and 𝛿18O    *Princeton*       Daniel Sigman     sigman@princeton.edu      
-----------------------  ---------------  -----------------  --------------------------
DON and DOP              *FSU*            Angela Knapp       anknapp@fsu.edu           
-----------------------  ---------------  -----------------  --------------------------
Cell counts, *DOP*,      *U Miami*,       Kimberly           kpopendorf@rsmas.miami.edu  
*DIP*, *POP*, particu-   *RSMAS*          Popendorf                                               
late ATP, and                                                             
dissolved ATP
-----------------------  ---------------  -----------------  --------------------------
Optical profilers,       *NASA*           Antonio Mannino    antonio.mannino-1@nasa.gov  
profiling radiometer                                                              
and above water radio-                                                                
meter, *POC*, *CDOM*,                                                                   
*DOC*, *TDN*, FlowCAM,                                                                  
Oxygen primary produc-                                                                  
tivity, *HPLC* pigments                                                                        
-----------------------  ---------------  -----------------  --------------------------
Argo Floats              *UW*, *UCSD*,    Steve Riser,       riser@ocean.washington.edu,  
                         *SIO*            Dean Roemmich,     droemmich@ucsd.edu,   
                                          John Gilson        jegilson@gmail.com        
-----------------------  ---------------  -----------------  --------------------------
*SOCCOM* Floats          *UW*,            Steve Riser,       riser@ocean.washington.edu,  
                         *UCSD*, *SIO*    Lynne Talley       ltalley@ucsd.edu      
-----------------------  ---------------  -----------------  --------------------------
Surface Drifters         *NOAA*, *AOML*   Shaun Dolk         Shaun.dolk@noaa.gov       
-----------------------  ---------------  -----------------  --------------------------
Underway Bathymetry and  *ASC*            *ASC*              admin@nbp.usap.gov        
Meteorological Data                                                                    
-----------------------  ---------------  -----------------  --------------------------


1.2  Science Team and Responsibilities

Duty                   Name                 Affiliation   Email Address        
—————————————————————  ———————————————————  ————————————  ————————————————————————
Chief Scientist        Kevin Speer          *FSU*         kspeer@fsu.edu          
---------------------  -------------------  ------------  ------------------------
Co-Chief Scientist     Lena Schulze         *FSU*         lschulze@fsu.edu        
---------------------  -------------------  ------------  ------------------------
CTD Watchstander,      Dario Marconi        *Princeton*   dmarconi@princeton.edu  
Nitrate 𝛿1N and 𝛿18O,                                                            
*DOP*
---------------------  -------------------  ------------  ------------------------
CTD Watchstander       Luz Zarate-Jimenez   *TAMU*        luzareli@tamu.edu       
---------------------  -------------------  ------------  ------------------------
CTD Watchstander,      Sherry Chou          *UH*          wawa.sherry@gmail.com   
Chipods
---------------------  -------------------  ------------  ------------------------
Chilean Observer, CTD  Rudolph Herbstaedt   *UNAB*        r.herbstaedtgomez@uandre
Watchstander           Gomez                              sbello.edu              
---------------------  -------------------  ------------  ------------------------
CTD Watchstander       Cristobal Aguilera   *UdeC*        cris.aguilera.bravo.90@g
                                                          mail.com                
---------------------  -------------------  ------------  ------------------------
Nutrients, *ODF*       Susan Becker         *UCSD* *ODF*  sbecker@ucsd.edu        
supervisor, *SOCCOM*                                                              
floats                                                                            
---------------------  -------------------  ------------  ------------------------
Nutrients              David Cervantes      *UCSD* *ODF*  d1cervantes@ucsd.edu    
---------------------  -------------------  ------------  ------------------------
CTDO Processing,       Joseph Gum           *UCSD* *ODF*  jgum@ucsd.edu           
Database Management                                                                        
---------------------  -------------------  ------------  ------------------------
Salts                  Kenneth Jackson      *UCSD* *ODF*  k3jackson@ucsd.edu      
---------------------  -------------------  ------------  ------------------------
Salts                  Kelsey Vogel         *UCSD* *STS*  kdvogel@ucsd.edu        
---------------------  -------------------  ------------  ------------------------
Dissolved O2,          Andrew Barna         *UCSD* *ODF*  abarna@ucsd.edu         
Database Management                                                                        
---------------------  -------------------  ------------  ------------------------
Dissolved O2           John Ballard         *UCSD* *ODF*  jrballard@ucsd.edu      
---------------------  -------------------  ------------  ------------------------
SADCP, *LADCP*,        Elizabeth Simons     *FSU*         egs07d@my.fsu.edu       
floats and drifters                                                                      
---------------------  -------------------  ------------  ------------------------
*DIC*, underway pCO2   Julian Herndon       *PMEL*        julian.herndon@noaa.gov 
---------------------  -------------------  ------------  ------------------------
*DIC*                  Jackie Long                                                
---------------------  -------------------  ------------  ------------------------
*CFCs*, SF6            David Cooper                       davidcooper59@gmail.com 
---------------------  -------------------  ------------  ------------------------
*CFCs*, SF6            Charlene Grall       *U Miami*     cgrall@rsmas.miami.edu  
---------------------  -------------------  ------------  ------------------------
*CFCs*, SF6 student    Lucie Knor           *UH*          luciek@hawaii.edu       
---------------------  -------------------  ------------  ------------------------
Total Alkalinity       Ryan Woosley         *U Miami*     rwoosley@rsmas.miami.edu
---------------------  -------------------  ------------  ------------------------
Total Alkalinity       Fen Huang            *U Miami*     fhuang@rsmas.miami.edu  
---------------------  -------------------  ------------  ------------------------
pH, cell counts,       Kaycie Lanpher       *U Miami*     klanpher@rsmas.miami.edu
*DOP*, *DIP*, *POP*,                                                          
particulateATP,                                                                 
dissolved ATP
---------------------  -------------------  ------------  ------------------------
*DOC*, *TDN*, Radio    Chance English       *UCSB*        cje@umail.ucsb.edu      
Carbon                                                                            
---------------------  -------------------  ------------  ------------------------
Ocean Optics           Joaquin Chaves       *NASA*        joaquin.chaves@nasa.gov 
---------------------  -------------------  ------------  ------------------------
Ocean Optics           Scott Freeman        *NASA*        scott.a.freeman@nasa.gov
---------------------  -------------------  ------------  ------------------------
Ocean Optics           Michael Novak        *NASA*        michael.novak@nasa.gov  
---------------------  -------------------  ------------  ------------------------
Marine Projects        Ken Vicknair         *ASC*         mpc@nbp.usap.gov        
Coordinator                                                                       
---------------------  -------------------  ------------  ------------------------
Marine Lab Technician  Lindsey Ekern        *ASC*         mlt@nbp.usap.gov        
---------------------  -------------------  ------------  ------------------------
Marine Technician      Rich Thompson        *ASC*         mt@nbp.usap.gov         
---------------------  -------------------  ------------  ------------------------
Marine Technician      Shannon Zellerhoff   *ASC*         mt@nbp.usap.gov         
---------------------  -------------------  ------------  ------------------------
Marine Technician      Rosemary McGuire     *ASC*         mt@nbp.usap.gov         
---------------------  -------------------  ------------  ------------------------
Electronic Technician  Sheldon Blackman     *ASC*         et@nbp.usap.gov         
---------------------  -------------------  ------------  ------------------------
Electronic Technician  Julian Race          *ASC*         et@nbp.usap.gov         
---------------------  -------------------  ------------  ------------------------
Network Administrator  Scott Walker         *ASC*         admin@nbp.usap.gov      
---------------------  -------------------  ------------  ------------------------
Network Administrator  Richard Jeong        *ASC*         admin@nbp.usap.gov      
---------------------  -------------------  ------------  ------------------------


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 10.6L.
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
backscatter meter, oxygen optode, 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 titled
analysis.

CTD and cage were vertically mounted at the bottom of the rosette
frame, located below the carousel for all stations. The temperature,
conductivity, dissolved oxygen, respective pumps and exhaust tubing
was mounted to the CTD and cage housing as recommended by SBE. The
reference temperature sensor was mounted between the primary and
secondary temperature sensors at the same level as the intake tubes
for the exhaust lines. The transmissometer was mounted horizontally.
The fluorometer, oxygen optode, and altimeters were mounted vertically
inside the bottom ring of the rosette frames. The 150 KHz bi-
directional Broadband LADCP (RDI) unit was mounted vertically on the
bottom side of the frame. The 300 KHz bi-directional Broadband LADCP
(RDI) unit was mounted vertically on the top side of the frame. The
LADCP battery pack was also mounted on the bottom of the frame.

Equipment         Model            S/N           Cal Date      Stations          Responsible Party
————————————————  ———————————————  ————————————  ————————————  ————————————————  —————————————————
Rosette           36-place         Yellow        _             144-250           *STS*/*ODF*      
----------------  ---------------  ------------  ------------  ----------------  -----------------
CTD               SBE9+            1281          _             144-250           *STS*/*ODF*      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Pressure Sensor   Digiquartz       136428        Apr 10, 2017  144-250           *STS*/*ODF*      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Primary           SBE3+            35844         Apr 11, 2017  144-250           *STS*/*ODF*      
Temperature                                                                                       
----------------  ---------------  ------------  ------------  ----------------  -----------------
Primary           SBE4C            43399         Apr 7, 2017   144-250           *STS*/*ODF*      
Conductivity                                                                                      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Primary Pump      SBE5             51646         _             144-250           *ASC*            
----------------  ---------------  ------------  ------------  ----------------  -----------------
Secondary         SBE3+            32309         Apr 18, 2017  144-250           *STS*/*ODF*      
Temperature                                                                                       
--------------------------------------------------------------------------------------------------
Secondary         SBE4C            42819         Apr 11, 2017  144-250           *STS*/*ODF*      
Conductivity                                                                                      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Secondary Pump    SBE5             55644         _             144-250           *ASC*            
----------------  ---------------  ------------  ------------  ----------------  -----------------
Transmissometer   Cstar            CST-1803DR    Sep 16, 2016  144-250           *TAMU*           
----------------  ---------------  ------------  ------------  ----------------  -----------------
Fluorometer       WetLabs          FLBBRTD-3698  Sep 23, 2014  144-250           *U Maine*        
Chlorophyll and                                                                                   
Backscatter                                                                                       
----------------  ---------------  ------------  ------------  ----------------  -----------------
Primary           SBE43            431138        July 6, 2017  144-250           *ODF*            
Dissolved Oxygen                                                                                  
----------------  ---------------  ------------  ------------  ----------------  -----------------
Oxygen Optode     RINKO            0297          Apr 7, 2017   144-250           *STS*/*ODF*      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Reference         SBE35            0035          Apr 13, 2017  144-250           *STS*/*ODF*      
Temperature                                                                                       
----------------  ---------------  ------------  ------------  ----------------  -----------------
Carousel          SBE32            1178          _             144-250           *STS*/*ODF*      
----------------  ---------------  ------------  ------------  ----------------  -----------------
Altimeter         Valeport 500     51520         _             144-250           *ASC*            
----------------  ---------------  ------------  ------------  ----------------  -----------------


The DUSH5 baltic room 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 P06E 2017.

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 flushing fresh
water through both plumbed sensor lines between casts. 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 P06E 2017. Storms caused casts to proceed slower
than normal, limiting deployment speed to 20 meters per minute for the
first 1000 meters on some stations during storms. Adverse weather
conditions caused surface bottles (nominal 5 meters) to be fired on
the fly, instead of soaking for 30 seconds. Part way through the
cruise the LADCP dipped unacceptably low to the rails upon which the
rosette was mounted. Different solutions were tried before settling on
a set of aluminum skids u-bolted onto the rosette frame to gain
clearance for the LADCP. Spare nylon fishing line used for bottle
lanyards were also rigged to support the weight of the LADCP. One skid
blocked an LADCP head, so the LADCP was rotated in order to have the
bad, unusable head pointed at the skid. The other skid was covered in
black tape to minimize reflection of light off of the aluminum for the
FLBB mounted next to it. The black tape helped until it peeled away,
at which point the data became more noisy.




2  CRUISE NARRATIVE


A hydrographic survey (P06, Leg 2) was conducted in the South Pacific
Ocean from 20 August - 30 Sept. 2017 aboard the RV Ice Breaker
Nathaniel B. Palmer. Leg 2 is the continuation of Leg 1, which arrived
in Papeete, French Polynesia on 17 Aug. 2017. A total of 107 CTD
casts, with a 36 bottle rosette, LADCP and other instruments were
occupied on a transect running along 32° 30’S, from 148.97 W, almost
due south of Papeete, Tahiti, to Valparaiso, Chile.

CTD casts normally went to 10-12 meters above the seafloor. During a
few casts, the CTD was stopped slightly higher due to wave action;
similarly, some of the "surface" bottles nominally at 5m depth were
made at 10m, or, as the console operators became familiar with the
process, fired at 5m depth on the fly (only in conditions where the MT
would not stop the package at shallow depths). In addition to the
(pair of) CTD sensors, two oxygen sensors, upward and downward looking
lowered acoustic doppler current profilers (LADCPs), a
transmissometer, a fluorometer (including backscatter sensor), Chipods
unit, and an altimeter were mounted onto the rosette frame.

Other work was done by the NASA group with 200m optical properties
casts and water sampling. Float and drifter deployments continued on
Leg 2, with a total of 16 UW Argo floats, 15 SIO Argo floats, 4 SOCCOM
floats, and 6 NOAA drifters deployed on Leg 2.

Salinity and dissolved oxygen, nutrients (nitrate, nitrite, phosphate,
silicate), total CO2/TCO2 (dissolved inorganic carbon/DIC), pH,
total alkalinity, and transient tracers (chlorofluorocarbons/CFCs and
sulfur hexafluoride/SF6) were analyzed onboard.

Additional samples were collected for onshore analysis: dissolved
organic carbon (DOC), dissolved organic phosphorus (DOP), radiocarbon
(𝛿13C/𝛿14C), nitrogen and oxygen isotopes of nitrate (𝛿15N, 𝛿18O),
phytoplankton pigment using high performance liquid chromatography
(HPLC), and particulate organic carbon (POC).

Underway measurements included GPS navigation, EM 112 multibeam and
Knudsen bathymetry, ADCP, meteorological parameters, and sea surface
measurements (including temperature, conductivity/salinity, dissolved
oxygen, fluorescence, pCO2 and gravity.


2.1  Narrative

The Leg 2 science party assembled in Papeete, Tahiti to meet the ship
upon its arrival on August 17, 2017. The primary task for Leg 2 was to
complete the transect of CTD/rosette casts beginning at Australia and
ending at Chile.

As the equipment and lab supplies were already set up for Leg 1 in
Sydney, the amount of preparation required in port for the scientific
program was limited to some shipping and receiving and the new
activity of the NASA team. Technical work on the Palmer is supported
by the Contractor (ASC) and new technicians arrived for Leg 2,
including 3 new Marine Technicians for CTD operations. Departure went
smoothly, leaving the dock at 1100 on the 20 Aug. 2017. A 4 day steam
to the first station on Leg 2 allowed new science crew members time to
get their sea legs, adjust to the ship's schedule, take part in safety
drills and become familiar with the ship’s operations.

A test cast was carried out just outside French EZZ to exercise the
system and provide clean water for the chemists. The first station on
the line, Stn. 144, was a repeat of the last station of Leg 1, on 24
Aug. NASA operations were tested and programmed for the time slot
between local 1000-1400 to catch the high sun angles.

On 25 Aug Stn. 147 waves occasionally entered the Baltic room during
the CTD cast. In order to save time, bottle firing stops were aborted
about halfway up and Niskins were closed on the fly. While not normal
procedure for bottle stops, the impact on sampling and calibration was
relatively minor. As a result of wind and waves, on 26 Aug 2017 the
ship steamed at 4kn to Stn 148, to re-evaluate situation at 0600, a
roughly 12 hour delay. The problem is not simply wave height but
cross-chop - waves that appear from an angle to the prevailing
direction and enter the Baltic room uninvited. The situation was more
manageable at daylight and operations continue in the morning. Early
on 1 Sept., CTD ops were again on standby with winds at 40kn and waves
of 15-20 ft. Again the decision was made to wait and re- evaluate the
situation during the daylight hours. The situation and safety of the
CTD package and operators in the Baltic room was regularly evaluated
with winds continuing at 20-25 kt with 10-15ft, choppy seas. On 2
Sept. at the 0000 evaluation on bridge, the decision was made to open
the Baltic room door at 0545 and check for waves entering the room.
With winds and waves down, CTD operations proceeded normally after
that.

Over time the LADCP showed some tendency to slip down and touch the
railing system put in place to receive the CTD package into the Baltic
room. After some iteration, an agreement was reached to attach an
aluminum bar with stainless u-bolts to the base of the CTD frame. The
fluorometer and altimeter were moved to avoid being blocked. The new
arrangement did not result in an increase in the rotation of the
package during the casts.

Weather built again 18 Sept., with the occasional waves entering
Baltic room. Operations continued, however, with the surface bottle
taken on the fly. As on Leg 1, winch speeds were generally slowed in
the upper ocean to accommodate wave motion and reduce wire tension.

Up on reaching the Chile Trench on September 26, 2017, station spacing
was significantly tighter, between 3.5 - 7.5 nm, to resolve
complicated flow and smaller scale chemical property variations along
the eastern boundary and in the trench. In total, 15 stations were
occupied across the trench and onto the shelf reaching 71.585 W and a
water depth of 200m. To allow water samples to be analyzed between
stations, a minimum wait time of 2 hours was implemented between each
station.

The merging of CTD ops and NASA ops went well due the flexibility of
the NASA group on the time of day constraint for the deployment of
their instruments. The Baltic room winch performed well, bottle trips
and water sampling had essentially no problems, and as a whole the new
CTD package was very successful.

Station spacing on Leg 2 ranged from a few miles in the trench, to as
much as 45nm. Aside from a limited area above the eastern flank of the
EPR, most stations in the interior had a 45nm spacing. This was larger
than the spacing on Leg 1, and the previous occupation in 2009/2010.
Spacing was increased owing to fewer available days and a longer track
compared to leg 1; 41 days were allocated to Leg 2, versus 46 days on
Leg 1, and the distance along the line was about 900nm longer on Leg 2
than Leg 1. The number of stations per day actually available for
work, obtained by subtracting the steam time along the line, produces
a similar rate on both legs (c. 5 stations per day available on the
P06 line). Another factor was the enhanced sampling at the eastern
boundary. If we had chosen not to do this, and given the time
constraints, the interior spacing in the Chile Basin portion of the
track could have been reduced somewhat, to about 40 nm. Resolution of
the eastern boundary circulation was deemed a higher priority.

Data quality was examined together with the CTD Watchstanders to help
the students gain some insight to the measurements made during the
cruise. Students were assigned properties and plotted sections and
property relations to try to understand the distributions, recognize
real ocean features and more subtle differences due to sensor behavior
or the various factors involved with chemical analysis, for instance
the temperature of the autosal room (which varied with time). No
unusual data quality issues were found and the overall quality is very
high.

CTD operations ended on Stn. 250 at 0830 29 Sept. 2017, water sampling
continued another hour or so; chemical analysis continued through the
rest of the day, and packing commenced. NASA carried out a final
optical set of casts from 1030-1130 at which point science operations
ended (1200 was the final deadline for science operations in order for
the ship to prepare for entry to the port). Leg 2 ended at Valparaiso,
Chile on 30 Sept. 2017.


2.2  Preliminary Science remarks

P06 was first occupied during WOCE in 1992 over the course of 3 legs,
with stops at Easter Island and Tahiti, then again in 2003, and once
more in 2009- 2010. Not too far to the north, the SCORPIO section at
28 S also traversed this territory in 1967. Motivated by the potential
for climate change effects, GO-SHIP is re-occupying the line 50 years
after the SCORPIO expedition to investigate changes in circulation and
ocean properties, in particular those related to the carbon system,
and to improve sampling where possible and practical.

Leg 2 entered the P6 line over the western flank of the East Pacific
Rise (EPR), well to the east of the deep western boundary current
system above the Kermadec Trench. Previous analysis of the WOCE P6
line by Wijffels et al (2001) showed broad southward deep and bottom
water flow in this region, with little indication of net meridional
flow at shallower levels.

A layering of deep water masses was found at the crest of the EPR. We
were able to occupy an axial valley station, possibly for the first
time on P6, determined to the best of our abilities from Etopo1
bathymetry, and interpreted with the help of our Chilean observer who
is a marine geologist. No obvious properties anomalies were evident
from the preliminary data, but a distinctive, 200m thick mixed-layer
was observed with the characteristics of water found within a nearby
fracture zone on the eastern flank. Above the mixed layer, water
properties indicate regional western flank water masses, switching
back to eastern conditions farther up the water column.

The SCORPIO observations revealed a broad, weak northward flow at 43 S
and to a lesser extent at 28 S in the deep water below 2000m depth,
above the eastern flank of the EPR. New hints of higher oxygen within
the bottom topography might suggest control on the route taken by this
flow. Similarly, indications of bottom water flow occurred here and
there along the route down the eastern flank.

The eastern South Pacific Ocean shows an extraordinary stacking of
salinity and oxygen extrema in the upper 1500m or so. These increase
in magnitude toward the east, arising from the combination of
biological activity and eastern boundary currents bringing properties
both southward and northward along the slope. The termination of the
shallow oxygen minimum is rather abrupt, and tentative results suggest
a balance between eastward advection and eddy mixing.


2.3  Acknowledgments

The professionalism of the analysis groups enabled steady progress and
mutual aid when needed. The CTD Watchstanders did an excellent job,
even as their assignments multiplied over the course of the cruise. We
extend our sincere thanks to MLT Lindsey Ekern for sampling help.
Joaquin Chaves shared his enthusiasm for optical measurements in a
science presentation. Thanks also to Jim Swift, Lynne Talley, Tomomi
Ushii, Sabine Mecking, and Isa Rosso for pre-cruise help and
suggestions. NSF and NOAA are acknowledged for funding provided to the
GO-SHIP program. Pre-cruise planning was done in collaboration with
ASC (Adam Jenkins and Brad Fabling). ASC was also responsible for
marine operations while at sea, and we appreciate the support we
received from the Marine Projects Coordinator Ken Vicknair and ASC
techs, with the deployment and recovery of the rosette and the repair
of the LADCP cable. Captain Brandon Bell (ECO) and the crew helped to
maintain smooth vessel operations throughout.




3  CTDO AND HYDROGRAPHIC ANALYSIS


PIs
   * Susan Becker
   * James Swift

Technicians
   * Joseph Gum


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. SBE SeaSave7
v.7.26.1.8 software was used for data acquisition and to close bottles
on the rosette.

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

Once the deck watch had deployed the rosette, the winch operator would
lower it to 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 no more than 5
meters in high seas. The winch was then instructed to lower the
package to the initial target wire-out at no more than 30m/min to 100m
and no more than 60m/min after 100m depending on sea-cable tension and
the sea state.

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

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

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

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

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

A total of 106 CTD stations were occupied including one test station.
A total of 106 CTDO/rosette/LADCP/chipod casts were completed. 106
standard CTDO/rosette/LADCP/chipod casts and one test cast completed
with a single 36-place (CTD #1281) 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 P06E 2017 that directly
impacted CTD analysis. Issues that directly impacted bottle closures,
such as slipping guide rings, were detailed in the Underwater Sampling
Package section of this report. Temperature, conductivity and oxygen
analytical sensor issues are detailed in the following respective
sections.


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 1281-99677; Station Set 144 - 250

                           Start P (dbar)  End P (dbar)
                           ——————————————  ————————————
           Min                  0.0           -0.1        
           Max                  0.3            0.2         
           Average              0.2            0.1         
           Applied Offset                      0.1081      


An offset of 0.1081 was applied to every cast performed by CTD 1281.
On-deck pressure reading for CTD 1281 varied from 0.0 to 0.3 dbar
before the casts, and -0.1 to 0.2 dbar after the casts. Before and
after average difference was 0.2 and 0.1 dbar respectively. The
overall average offset before and after cast was 0.1081 dbar.


3.4  Temperature Analysis

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

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

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

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

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

                     T_{90} = T + tp_1 P + t_0

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

Corrected temperature differences are shown in the following figures.

   [image]SBE35RT-T1 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

   [image]Deep SBE35RT-T1 by station (Pressure ≥ 2000dbar).

   [image]SBE35RT-T2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

   [image]Deep SBE35RT-T2 by station (Pressure ≥ 2000dbar).

   [image]T1-T2 by station (-0.002°C ≤ T1-T2 ≤ 0.002°C).

   [image]Deep T1-T2 by station (Pressure ≥ 2000dbar).

   [image]SBE35RT-T1 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

   [image]SBE35RT-T2 by pressure (-0.002°C ≤ T1-T2 ≤ 0.002°C).

   [image]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 ±0.0077°C for SBE35RT-T1,
±0.0077°C for SBE35RT-T2 and ±0.0055°C for T1-T2. The 95% confidence
limits for the deep temperature residuals (where pressure ≥
2000dbar) are ±0.00081°C for SBE35RT-T1, ±0.00094°C for SBE35RT-T2 and
±0.00079°C for T1-T2.

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

   * The SBE35RT sensor memory was partially full, and there are
     partial data reported for casts on station 148.

   * Rough weather caused tripping on the fly for the surface bottle
     on many stations, leading to some surface SBE35RT averaging
     periods out of the water.

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
ship-board calibrations were performed to correct sensor bias.
Corrections for both pressure and temperature sensors were finalized
before analyzing conductivity differences. Two independent metrics of
calibration accuracy were examined. At each bottle closure, the
primary and secondary conductivity were compared with each other. Each
sensor was also compared to conductivity calculated from check sample
salinities using CTD pressure and temperature.

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

   [image]Coherence of conductivity differences as a function of
   temperature differences.

Uncorrected conductivity comparisons are shown in figures Uncorrected
CBottle - C1 by station (-0.002 mS/cm  BTLCOND-C1  0.002 mS/cm).
through Uncorrected C1-C2 by station (-0.002 mS/cm  C1-C2  0.002
mS/cm)..

   [image]Uncorrected C_Bottle - C1 by station (-0.002 mS/cm ≤
   BTLCOND-C1 ≤ 0.002 mS/cm).

   [image]Uncorrected C_Bottle - C2 by station (-0.002 mS/cm ≤
   BTLCOND-C2 ≤ 0.002 mS/cm).

   [image]Uncorrected C1-C2 by station (-0.002 mS/cm ≤ C1-C2 ≤
   0.002 mS/cm).

The residual conductivity differences after correction are shown in
figures Corrected CBottle - C1 by station (-0.002 mS/cm  BTLCOND-C1
0.002 mS/cm). through Corrected C1-C2 by conductivity (-0.002 mS/cm
C1-C2  0.002 mS/cm).

   [image]Corrected C_Bottle - C1 by station (-0.002 mS/cm ≤
   BTLCOND-C1 ≤ 0.002 mS/cm).

   [image]Deep Corrected C_Bottle - C1 by station (Pressure >=
   2000dbar).

   [image]Corrected C_Bottle - C2 by station (-0.002 mS/cm ≤
   BTLCOND-C2 ≤ 0.002 mS/cm).

   [image]Deep Corrected C_Bottle - C2 by station (Pressure >=
   2000dbar).

   [image]Corrected C1-C2 by station (-0.002 mS/cm ≤ C1-C2 ≤
   0.002 mS/cm).

   [image]Deep Corrected C1-C2 by station (Pressure >= 2000dbar).

   [image]Corrected C_Bottle - C1 by pressure (-0.002 mS/cm ≤
   BTLCOND-C1 ≤ 0.002 mS/cm).

   [image]Corrected C_Bottle - C2 by pressure (-0.002 mS/cm ≤
   BTLCOND-C2 ≤ 0.002 mS/cm).

   [image]Corrected C1-C2 by pressure (-0.002 mS/cm ≤ C1-C2 ≤
   0.002 mS/cm).

   [image]Corrected C_Bottle - C1 by conductivity (-0.002 mS/cm ≤
   BTLCOND-C1 ≤ 0.002 mS/cm).

   [image]Corrected C_Bottle - C2 by conductivity (-0.002 mS/cm ≤
   BTLCOND-C2 ≤ 0.002 mS/cm).

   [image]Corrected C1-C2 by conductivity (-0.002 mS/cm ≤ C1-C2
   ≤ 0.002 mS/cm).

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

Corrections made to all conductivity sensors are of the form:

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

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

   [image]Salinity residuals by station (-0.002 mPSU ≤ SALNTY-C1SAL
   ≤ 0.002 mPSU).

   [image]Salinity residuals by pressure (-0.002 mPSU ≤ SALNTY-
   C1SAL ≤ 0.002 mPSU).

   [image]Deep Salinity residuals by station (Pressure >= 2000dbar).

The 95% confidence limits for the mean low-gradient (values -0.002
mPSU ≤ T1-T2 ≤ 0.002 mPSU) differences are ±0.0051 PSU for
salinity-C1SAL. The 95% confidence limits for the deep salinity
residuals (where pressure ≥ 2000dbar) are ±0.0021 PSU for salinity-
C1SAL.

A number of issues affected conductivity and calculated CTD salinities
during this cruise.
   * Bottle salinity analysis was complicated due to problems with
     the two Autosals, leading to knock-on problems when attempting to
     calibrate conductivity against bottle salinity.

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

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


3.6  CTD Dissolved Oxygen

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

The pre-cruise laboratory calibration coefficients were used to
convert SBE43 frequencies to µmol/kg oxygen values for acquisition
only. Additional shipboard fitting were performed to correct for the
sensors non-linear response. Corrections for pressure, temperature and
conductivity sensors were finalized before analyzing dissolved oxygen
data. The SBE43 sensor data were compared to dissolved 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 [Millard82] and Owens [Owens85]
SIO models DO sensor secondary responses with lagged CTD data. In-situ
pressure and temperature are filtered to match the sensor responses.
Time constants for the pressure response (τ_p), a slow τ_{Tf}
and fast τ_{Ts} thermal response, package velocity τ_{dP},
thermal diffusion τ_{dT} and pressure hysteresis τ_h are fitting
parameters. Once determined for a given sensor, these time constants
typically remain constant for a cruise. The thermal diffusion term is
derived by low-pass filtering the difference between the fast response
T_s and slow response T_l temperatures. This term is intended to
correct non-linearity in sensor response introduced by inappropriate
analog thermal compensation. Package velocity is approximated by low-
pass filtering 1st-order pressure differences, and is intended to
correct flow-dependent response. Dissolved O2 concentration is then
calculated:

                        P_h                       /                       dO_c      dP        \
                    C_2 ————                     | C t  + C t  + C P + C  ———— + C  ——— + C dT |
O ml/l = [C · V  · e    5000 + C_3] · ƒ   (T,P)·e \ 4 1    5 s    7 l   6  dT     8 dTt    9  /
 2         1   DO                      sat

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)

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

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

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

* C_4 - C_9     response coefficients

CTD dissolved O2 residuals are shown in the following figures O2
residuals by station (-0.01 µmol/kg  OXYGEN-BTLOXY  0.01 µmol/kg).
through Deep O2 residuals by station (Pressure >= 2000dbar)..

   [image]O2 residuals by station (-0.01 µmol/kg ≤ OXYGEN-BTLOXY
   ≤ 0.01 µmol/kg).

   [image]O2 residuals by pressure (-0.01 µmol/kg ≤ OXYGEN-BTLOXY
   ≤ 0.01 µmol/kg).

   [image]Deep O2 residuals by station (Pressure >= 2000dbar).

The second standard deviations of 9.04 (µmol/kg) for all dissolved
oxygen bottle data values and 2.45 (µmol/kg) for deep dissolved oxygen
values are only presented as general indicators of the goodness of
fit. CLIVAR GO-SHIP standards for CTD dissolved oxygen data are < 1%
accuracy against on board Winkler titrated dissolved O2 lab
measurements.

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

   * New software used to fit the data is not working as intended,
     and the data will be re-fit post cruise after a thorough checking
     of the code.

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

[Millard82] 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).

[Owens85] 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


PIs
   * Susan Becker
   * James Swift

Technicians
   * Kelsey Vogel
   * Kenneth Jackson


4.1  Equipment and Techniques

Two Guildline Autosals, model 8400B salinometer (S/N 69-180) and model
8400A salinometer (S/N 57-526) located in salinity analysis room, were
used for all salinity measurements. Autosal model 8400B was serviced
prior to NBP1701 and remained on ship. Autosal model 8400A was
serviced prior to P06W and sent with other equipment in June. The
salinometer readings were logged on a computer using in house LabView
program developed by Carl Mattson. The Autosal water bath temperature
was set to 24°C. The laboratory’s temperature was also set and
maintained to 22°C. This is to ensure stabilize reading values and
improve accuracy. Salinity analyses were performed after samples had
equilibrated to laboratory temperature range of 22-25°C, usually 6
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 2 times before a
set of conductivity ratio reading was taken. For each sample, the
salinometer cell was initially flushed at least 2 times before a set
of conductivity ratio readings were taken.

IAPSO Standard Seawater Batch P-160 was used to standardize all casts.

   [image]


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.


4.3  Narrative

Autosal 69-180 was used to perform the salinity analysis for the
entirety of P06E. Throughout the cruise, there were several issues
found in regards to the salinometer. During station 170 (2017-09-05)
and the running of the salts from station 168, Autosal 69-180 stopped
pumping water due to salt buildup in the sampling tube. As a result,
sample 13 from that cast was aborted and the clogged tubing was
replaced by new Tygon tubing of similar length. From that point on,
only one box was run at a time until it was certain that there were no
adverse effects from the tubing change; it was found to be safe to run
two boxes at a time starting from the analysis of the salts from
station 173 onwards (2017-09-07). During station 174 (2017-09-06),
lint, or some other form of buildup was found to be collecting inside
of the sampling chamber and getting stuck on the platinum sensors of
the Autosal. This problem was addressed by flushing the chamber
multiple times with DI water, soapy water, a small amount of NaOH and
DI water, then a small amount of isopropyl alcohol and DI water, and
then thoroughly rinsed with DI water to flush the tubing and chambers
clean, in that order. This process removed most of the buildup,
however some still remained in the chamber. During Station 175
(2017-09-06), salt run 172, the ending standard looked bad with a
conductivity ratio that read 1.99977 when it was expected to have read
somewhere around 1.99966. The chambers were flushed again with DI
water and the conductivity ratio was measured with a reading of
~0.0205. From that point on, all salt sampling runs were ended by
multiple flushes of the chamber with DI water until it read a
conductivity ratio of ~0.0030-0.0040 in efforts to prevent salt
buildup and other forms of sample contamination. It was also noted
that during station 191 (2017-09-11) that there was a buildup of some
sort of brown residue in some of the bottles (boxes S and X) that were
subsequently cleaned out.

Room and bottle temperature proved difficult to keep consistent
throughout the cruise, causing certain changes to be made throughout
P06E. Towards the beginning of the leg, on station 170 (2017-09-05),
the thermometer of the of the Autosal was found to have a temperature
offset of anywhere between 1.5 to 1.7°C and the room temperature was
adjusted in order to compensate. The initial room temperature was set
to 22°C, raised to 23°C, and subsequently raised to 24°C. Temperature
fluctuations also were observed during this leg. Room temperature was
noted before analyzing a box of salts and these temperatures ranged
from 22.4°C (analysis of Station 172, 2017-09-07) to 26.5°C (analysis
of Station 190, 2017-09-12), this and sample time, resulted in
fluctuations of bottle temperatures when ran. These bottle
temperatures at the time of sampling, ranged from 22.4°C (analysis of
Station 175, 2017-09-08) to 26.0°C (analysis of Station 200,
2017-09-14).

[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
   • David Cervantes


5.1  Summary of Analysis

• 3660 samples from 107 ctd stations

• The cruise started with new pump tubes and they were changed prior
  to stations 163, 198 and 223.

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

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

• The cadmium column efficiency was checked periodically and ranged
  between 94%-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  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.


5.7  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.


5.8  Standards and Glassware Calibration

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

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

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

Standardizations were performed at the beginning of each group of
analyses with working standards prepared every 10-12 hours from a
secondary. Working standards were made up in low nutrient seawater
(LNSW). Batches of LNSW were used on the cruise. Batches of LNSW, were
collected. The actual concentration of nutrients in this water was
empirically determined during the standardization calculations.

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


                -  N+N    PO_4  SIL   NO2   NH_4
                   (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 


5.9  Quality Control

All final data was reported in micro-moles/kg. NO^3, PO_4, and NO2
were reported to two decimals places and SIL to one. Accuracy is based
on the quality of the standards the levels are:


                NO^3  0.05 µM (micro moles/Liter) 
                PO_4  0.004 µM                    
                SIL   2-4 µM                      
                NO2   0.05 µM                     


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


              Parameter  Concentration (µM)  stddev 
              —————————  ——————————————————  ——————
                NO^3           36.05          0.20   
                PO_4           2.53           0.01   
                SIL            113.7          0.9    


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


         Parameter  Concentration  stddev  assigned conc 
             -        (µmol/kg)      -       (µmol/kg)     
         —————————  —————————————  ——————  —————————————
           NO^3         36.14       0.07       36.19     
           PO_4         2.56        0.01       2.56      
           Sil          104.9       0.4        104.6     
           NO2          0.06        0.00       0.05      


5.10  Analytical Problems

No major analytical problems.

[Armstrong1967] Armstrong, F.A.J., Stearns, C.A., and
                Strickland, J.D.H., "The measurement of upwelling and
                subsequent biological processes by means of the
                Technicon Autoanalyzer and associated equipment,"
                Deep-Sea Research, 14, pp.381-389 (1967).

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

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

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

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

[Bernhardt1967] Bernhardt, H., and  Wilhelms, A., "The
                continuous determination of low level iron, soluble
                phosphate and total phosphate with the AutoAnalyzer,"
                Technicon Symposia, I,pp.385-389 (1967).

[Gordon1992] Gordon, L.I., Jennings, J.C., Ross, A.A.,
             Krest, J.M., "A suggested Protocol for Continuous Flow
             Automated Analysis of Seawater Nutrients in the WOCE
             Hydrographic Program and the Joint Global Ocean Fluxes
             Study," Grp. Tech Rpt 92-1, OSU College of Oceanography
             Descr. Chem Oc. (1992).

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

[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
   • John Ballard


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

3661 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 (MnCl_2 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°C. The 20°C normalities and the blanks were plotted
versus time and were reviewed for possible problems. The blanks and
thiosulfate normalities for each batch of thiosulfate were 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

Since the analytical equipment from the Sydney to Papeete leg was to
continue on leg 2, no set up was necessary in Papeete. A limited
supply of Oxygen Standards meant the rig was not regularly
standardized during the transit from station 143 to Papeete, the
entire 4 day port period, and the transit back to the P06 section
line. While the period between standardization was long (approx. 10
days) the change in thiosulfate normality was within the day to day
allowed change. Samples taken from the underway system were stored
until the first station occupation at which time they were analyzed.

The normality of the thiosulfate was monitored daily. Each 1L batch of
thiosulfate was very stable, the difference between the highest and
lowest measured thiosulfate normality for the entire lifetime of a
batch never even exceeded the allowed daily change.

A few samples were lost due to errors made by the analysts:
accidentally dumping an unanalyzed sample, not adding enough acid to
dissolved the precipitant. In a region of especially low (~10 µmol/kg)
oxygen off the coast of Chile, extra care was taken to eliminate
microbubbles and minimize the time between the opening of a niskin and
the fixing of the oxygen sample.

   [image]Oxygen section for P06

[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 (P06W)
   • Frank J. Millero - University of Miami, Rosenstiel School of
     Marine and Atmospheric Science (P06E)

Technicians
   • Manuel Belmonte (P06W)
   • Derek Smith (P06W)
   • Ryan Woosley (P06E)
   • Fen Huang (P06E)


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 are performed automatically using LabVIEW 2012.


7.3  Sample Collection

Samples for total alkalinity measurements were taken at all P06W
Stations (1-143) except for stations 16, 20, 56, 60, 69 and 72. Two
Niskin bottles at each station were sampled twice for duplicate
measurements except for stations where 24 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 0.12 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 RVIB Nathaniel B. Palmer 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 P06W and
replacing them minimized bad measurements. Any unusual measurements
(poor electrode plot / profile outlier) were reran when possible. No
such interference occurred on P06E and the same electrode was used for
the entire leg.

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 P06W ranged
from 19°C to 25°C due to some air conditioning issues. At the
beginning of the cruise, before the air conditioning was fixed, lab
temperatures ranged from 20°C to 25°C. Once the air conditioning was
fixed, the temperature ranged from 19°C to 22°C. This constantly
delayed the titration start times. To remedy the situation, we
equilibrated the sample temperatures to about 22.5°C at the start of
the cruise and 20°C after the lab temperatures were more stable. This
strategy enabled most of the sample temperatures to not exceed a 0.2°C
range while being titrated. During P06E temperature control was not an
issue.

Throughout the cruise, varying issues resulted from the Sample
Delivery System. At the start of the cruise (during station 5), Sample
Delivery System B would not fill the pipette compleately so it was
replaced with Sample Delivery System A. About a third of the way into
the leg (before station 55), a shift in Sample Delivery System A’s
delivery volume was noticed causing smaller samples sizes to be
dispensed: A calibration using a manual pipette resolved this issue.
Once again, towards the end of the leg (during station 140) Sample
Delivery Station A’s dispensed volume shifted and another calibration
was performed. No volume recalibration was required during P06E.
Lastly, throughout the cruise, the Sample Delivery System's program
would freeze in Deliver Sample mode or Prepare Pipette mode and caused
a few sample bottles to be emptied. This resulted in lost samples due
to the novice operators. Despite these issues, a minimal amount of
samples were lost, and the ammount of samples that were suspected of
being low in volume were reran or flagged if a rerun was not possible.


7.5  Quality Control

Dickson laboratory Certified Reference Material (CRM) Batch 165 and
166 was used to determine the accuracy of the total alkalinity
analyses. The total alkalinity certified value for this batch is:

• Batch 165 2214.09 ± 0.41 µmol/kg (32;16)

• Batch 166 2212.56 ± 0.39 µmol/kg

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 station analyzed
resulting in 380 reference material analyses. The measured total
alkalinity value for each batch is:

P06W

   • Batch 165 2213.37 ± 3.94 µmol kg-1 (179) [mean ± std. dev. (n)]

And for P06E

   • Batch 165: 2212.72  1.92 µmol kg-1 (163) [mean ± std. dev. (n)]

   • Batch 166: 2210.62  2.10 µmol kg-1 (26) [mean ± std. dev. (n)]

If greater than 24 Niskin bottles were sampled at a station, two
Niskin bottles on that station were sampled twice to conduct duplicate
analyses. If 24 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 are: For P06W:   ±
3.52 µmol kg-1 (196) [± std. dev. (n)] For P06E.   ± 0.95 µmol kg-1
(196) [± abs std. dev. (n)]

The total alkalinity measurements for each P06W stations have not been
compared to measurements taken from the neighboring P06W 2017 stations
and the P06W 2009 stations of similar if not identical coordinates.

3136 total alkalinity values were submitted for P06W and 2,808 for
P06E. The total alkalinity of the entire transect is shown as a
section in P06W Alkalinity Section. No corrections have been applied
therefor this data should be considered preliminary until a more
thorough analysis of the data can take place on shore.

   [image]P06W Alkalinity Section

   Section of total alkalinity along P06W (Stations 1 to 143).




8  DISSOLVED INORGANIC CARBON (DIC)


PIs
   • Richard A. Feely (NOAA/PMEL)
   • Rik Wanninkhof (NOAA/AOML)

Technicians
   • Julian Herndon (UW/NOAA/PMEL)
   • Jacki Long (UM)


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 310 ml
borosilicate glass bottles using silicone tubing. The flasks were
rinsed three times and filled from the bottom with care not to entrain
any bubbles, overflowing by at least one-full volume. The sample tube
was pinched off and withdrawn, creating a ~6 ml headspace, followed by
0.12 ml of saturated HgCl_2 solution which was added as a
preservative. The sample bottles were then sealed with glass stoppers
lightly coated 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 (PMEL
1 and PMEL2) used simultaneously on the cruise. Each system consisted
of a coulometer (CM5015-O UIC Inc) coupled with a Dissolved Inorganic
Carbon Extractor (DICE). 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 (PMEL 1 and PMEL 2) were set up in the aft dry
lab onboard the RVIB Nathaniel B. Palmer.


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 has a salinity sensor, but all DIC values were
recalculated to a molar weight (µmol/kg) using density obtained from
the CTD’s salinity. The DIC values were corrected for dilution due to
the addition of 0.12 ml of saturated HgCl_2 used for sample
preservation. The total water volume of the sample bottles was 305.55
ml (calibrated by Dana Greeley, AOML). The correction factor used for
dilution was 1.0004. A correction was also applied for the offset from
the CRM. This additive correction was applied for each cell using the
CRM value obtained at the beginning of the cell. The average (± SD)
correction was 0.86 ± 1.08 µmol/kg for PMEL 1 and 1.43 ± 1.57 µmol/kg
for PMEL 2.

The coulometer cell solution was replaced after 25 - 28 mg of carbon
was titrated, typically after 9 - 12 hours of continuous use. The
average (± SD) blanks for PMEL 1 and PMEL 2 were 15.6 ± 3.94 and 17.9
± 4.17 counts, respectively.


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

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

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

The accuracy of the DICE measurement is determined with the use of
standards (Certified Reference Materials (CRMs), consisting of
filtered and UV irradiated seawater) supplied by Dr. A. Dickson of
Scripps Institution of Oceanography (SIO). The CRM accuracy is
determined manometrically on land in San Diego and the DIC data
reported to the data base have been corrected to this batch 165 CRM
value. The CRM certified value for this batch is 2064.33 µmol/kg.

The precision of the two DICE systems can be demonstrated via the
replicate samples. Approximately 10% 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 0.76 µmol/kg.

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.

Table 1: PO6 Leg 2 Calibration data. Includes results up to station
#238 of a total of 250 stations. The additional stations should not
significantly change these reported values.


 UNIT    L Loop    S Loop    Pipette       Ave CRM1     Std Dev  Avg rep. diff.
——————  ————————  ————————  ——————————  ——————————————  ———————  ——————————————
PMEL 1  1.003407  1.007279  27.5812 ml  2064.43, N= 61   1.08        0.74          
PMEL 2  1.004569  1.002407  26.3417 ml  2065.05, N= 52   1.57        0.78          



8.6  Underway DIC Samples

Underway samples were collected from the flow thru system in the Hydro
Lab during transit after departing Tahiti. Discrete DIC samples were
collected approximately every 4 hours. A total of 16 discrete DIC
samples were collected.


8.7  Summary

The overall performance of the analytical equipment during the second
leg of PO6 was very good. Including the duplicates, 3,256 samples were
analyzed from 107 CTD casts and underway sampling for dissolved
inorganic carbon (DIC). The distribution of DIC with depth along the
second leg of PO6 2017 cruise track can be seen in Figure 1. The DIC
data reported to the ODF database directly from the ship are to be
considered preliminary until a more thorough post-cruise data quality
review can be completed ashore.

   [image]Dissolved Inorganic Carbon. Preliminary data from Leg1 and
   Leg2 of PO6 2017 up to station #238. An additional 12 stations (not
   included here) were conducted in the Chile Trench. Courtesy of Ms.
   Luz Zarate, Texas A&M University.

[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., K√∂rtzinger, 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 (Total Scale)


PI
   • Dr. Andrew Dickson (P06W)
   • Frank J. Millero (P06E)

Technicians
   • Stephanie Mumma  (P06W)
   • Kaycie B. Lanpher (P06E)


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 (HgCl_2). Samples were collected only from Niskin
bottles that were also being sampled for both total alkalinity and
dissolved inorganic carbon in order to completely characterize the
carbon system. Additionally, duplicate samples were collected from all
stations for quality control purposes.


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 four batches
were used during P06, Leg 1. The pHs of these batches were adjusted
with 0.1 mol kg^-1 solutions of HCl and NaOH (in 0.6 mol kg^-1 NaCl
background) to approximately 7.75, measured with a pH meter calibrated
with NBS buffers. The indicator was obtained from Dr. Robert Byrne at
the University of Southern Florida and was purified using the flash
chromatography technique described by Patsavas et al., 2013.
[Patsavas2013].


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 from 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 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.

On two occasions near the beginning of the P06W, the valve on the
Kloehn syringe pump appeared to be "sticking" in between ports,
resulting in cross-port contamination of the measured sample. The
spare Kloehn pump was installed and this issue was not encountered
again. The two affected Niskin samples were measured again from the
original sample bottles with good results. The Labview software that
controls the automated pH system crashed once during P06W, resulting
in the loss of data for one measurement. The uncorrected pH values
were documented in the pH lab notebook. This sample was run again and
the resulting pH value for the second analysis was used for data
submission.


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 165 (provided by
Dr. Andrew Dickson, UCSD). Two duplicate and two replicate
measurements were performed on every station when at least twenty-
three Niskins were sampled. If less than twenty-three 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 P06W are:


             Duplicate precision    ± 0.00057 (n=206)      
             Replicate precision    ± 0.00039 (n=244)      
             B165                   7.7598 ± 0.00104 (n=78)
             B165 within-bottle SD  ± 0.00026 (n=78)       



The precision statistics for P06E are:


             Duplicate precision  ± 0.00048 (n=201)        
             B165                 7.7085 ± 0.00085 (n=140) 
            
            
3478 pH values were submitted for P06W, and 2808 on P06E. Additional
corrections will need to be performed and these data should be
considered preliminary until a more thorough analysis of the data can
take place on shore. The preliminary pH of the entire transect is
shown as a section in Fig. %s.


   [image]Section of preliminary pH measurements on the total scale
   along P06 cruise track.


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

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

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




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


Analysts
   • Jim Happell
   • David Cooper
   • Kelly McCabe


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, CFC-12, and SF6 were measured on 129 0f 143 stations for a
total of 3500 samples. Salt water flooded the analytical system just
after analyzing station 48, which was the cause of most of the missed
stations, although some of the added stations with very short station
spacing were also skipped. 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 180°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 N_2O and keep it from entering the main
column. The second pre-column was the first 5 meters of a 60 m Gaspro
capillary column with the main column consisting of the remaining 55
meters. The analytical pre-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 24
hours of collection. Every 12 to 18 measurements were followed by a
purge blank and a standard. 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  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, and SF6 was 1.2%, 1.6% and 2.5% respectively.
Estimated limit of detection is 1 fmol/kg for CFC-11, 3 fmol/kg for
CFC-12, and 0.1 fmol/kg for SF6




11  DISSOLVED ORGANIC PHOSPHORUS


PI
   • Daniel Sigman (Princeton University)

Technician
   • Dario Marconi

Marine dissolved organic matter (DOM) is considered a primary
substrate for heterotrophic microbes, but can also be used by some
nutrient-limited phytoplankton that especially consume dissolved
organic phosphorus (DOP) when phosphate (PO_4) is scarce. However,
very few measurements of surface ocean DOP concentration have been
made, which limits our understanding the extent to which DOP is
utilized by phytoplankton. The goal of this data collection is to
increase the spatial coverage of DOP measurements to constrain the use
of DOP as a nutrient source supporting export production and di-
nitrogen fixation in the global marine environment.

DOP samples were collected from the upper 300 meters at stations with
about two-degree longitude spacing. A total of 350 samples from 35
stations were collected. All samples were hand filtered through
Whatman 25mm Puradisc 0.2µm PES filters. The syringe and filter were
rinsed with 40mL of seawater before each 60mL HDPE bottle was rinsed
once with 40mL of filtered seawater. All samples were stored onboard
at -20°C to preserve for land based analysis.

Analysis: All samples will be analyzed for total dissolved P (TDP)
using the high temperature combustion magnesium sulfate oxidation
techniques modified according to Monaghan and Ruttenberg
[Monaghan1999]. DOP concentration will be reported as the difference
between the TDP concentration and the PO_4 concentration determined
onboard by ODF.

[Monaghan1999] Monaghan, E. J., and K. C. Ruttenberg.
               “Dissolved organic phosphorus in the coastal ocean:
               Reassessment of available methods and seasonal
               phosphorus profiles from the Eel River Shelf.” Limnol.
               Oceanogr., 44(7), 1702-1714 (1999)




12  NITRATE 𝛿15N and 𝛿18O


PIs
   • Daniel Sigman (Princeton University)

Technician
   • Dario Marconi

Nitrate (NO_3^-) is the dominant dissolved inorganic form of nitrogen
in the oceans. As a macro-nutrient, nitrate is depleted in the surface
due to biological consumption and abundant in the ocean interior due
to remineralization. The dual isotopes of NO_3^- (𝛿15N and 𝛿18O)
allow us to constrain the utilization and consumption processes
controlling the nitrogen cycle within the South Pacific Subtropical
Gyre.

Nitrate 𝛿15N samples were collected from all depths at about every
two degrees of longitude. Two 60mL samples were collected from each
niskin bottle fired in the shallowest six depths. One 30mL sample was
taken from all other depths. All samples collected above 400 meters
were hand filtered with a BD 60mL Luer-Lok tip syringe and a 25mm
Puradisc 0.2µm PES filter. The syringe and filter were rinsed with
40mL of seawater before each HDPE (both 60mL and 30mL) bottles were
rinsed once with half their full volume of filtered seawater. The
samples were stored onboard at -20°C to preserve for land based
analysis.

Analysis: The denitrifier method [Casciotti2002] [Sigman2001] will be
used to analyze NO_3^- 𝛿15N and 𝛿18O. Briefly, this method converts
all NO_3^- to nitrous oxide (N_2O) via denitrifying bacteria before
the sample is analyzed by an IRMS.

[Casciotti2002] Casciotti, K. L., D. M. Sigman, M. G.
                Hastings, J. K. Bohlke, and A. Hilkert. “Measurement
                of the oxygen isotopic composition of nitrate in
                seawater and freshwater using the denitrifier method.”
                Anal. Chem., 74, 4905-4912 (2002)

[Sigman2001] Sigman, D. M., K. L. Casciotti, M. Andreani,
             C. Barford, M. Calanter, and J. K. Bohlke. “A bacterial
             method for the nitrogen isotopic analysis of nitrate in
             seawater and freshwater.” Anal. Chem., 73, 4145-4153
             (2001)




13  DISSOLVED ORGANIC CARBON AND TOTAL DISSOLVED NITROGEN


PI
   • Craig Carlson (UCSB)

Technician
   • Chance English

Analysts
   • Keri Opalk
   • Elisa Halewood

Support
   NSF


13.1  Project Goals

The goal of the DOM project is to evaluate dissolved organic carbon
(DOC) and total dissolved nitrogen (TDN) concentrations along the P06
zonal transect (30 to 32.5°S & 153°E to 72°W). During the P06 cruise
Leg 1 (July - Aug 2017), casts were specifically targeted in order to
overlap with the TCO2 sampling program.


13.2  Sampling

DOC profiles were taken at approximately every other station from 26
of 36 niskin bottles ranging the full depth of the water column (68
stations; ~1800 DOC and 600 TDN samples. DOC samples were passed
through an inline filter holding a combusted GF/F filter attached
directly to the Niskin for samples in the top 500 m of each cast. This
was done to eliminated particles larger than 0.7 µm from the sample.
Samples from deeper depths were not filtered. Previous work has
demonstrated that there is no resolvable difference between filtered
and unfiltered samples in waters below the upper 500 m at the µmol
kg^-1 resolution. All samples were rinsed 3 times with about 5 mL of
seawater and collected into combusted 40 mL glass EPA vials. Samples
were fixed with 50 µL of 4N Hydrochloric acid and stored at 4°C on
board. Samples were shipped back to UCSB for analysis via high
temperature combustion on Shimadzu TOC-V or TOC L analyzers.

Sample Vials were prepared for this cruise by soaking in 10%
Hydrochloric acid, followed by a 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 with DI water and left out to dry.

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


13.3  Standard Operating Procedure for DOC Analyses- Carlson Lab UCSB

DOC samples will be analyzed via high temperature combustion using a
Shimadzu TOC-V or Shimadzu TOC-L at an in shore based laboratory at
the University of California, Santa Barbara. The operating conditions
of the Shimadzu TOC-V have been slightly modified from the
manufacturer's model system. The condensation coil has been removed
and the headspace of an internal water trap was reduced to minimize
the system's dead space. The combustion tube contains 0.5 cm Pt
pillows placed on top of Pt alumina beads to improve peak shape and to
reduce alteration of combustion matrix throughout the run. CO2 free
carrier gas is produced with a Whatman® gas generator [Carlson2010].
Samples are drawn into a 5 ml injection syringe and acidified with 2M
HCL (1.5%) and sparged for 1.5 minutes with CO2 free gas Three to five
replicate 100 µl of sample are injected into a combustion tube heated
to 680°C. The resulting gas stream is passed though several water and
halide traps, including an added magnesium perchlorate trap. The CO2
in the carrier gas is analyzed with a non-dispersive infrared detector
and the resulting peak area is integrated with Shimadzu
chromatographic software. Injections continue until the at least three
injections meet the specified range of a SD of 0.1 area counts, CV
≤ 2% or best 3 of 5 injections.

Extensive conditioning of the combustion tube with repeated injections
of low carbon water (LCW) and deep seawater is essential to minimize
the machine blanks. After conditioning, the system blank is assessed
with UV oxidized low carbon water. The system response is standardized
daily with a four-point calibration curve of potassium hydrogen
phthalate solution in LCW. All samples are systematically referenced
against low carbon water and deep Sargasso Sea (2600 m) or Santa
Barbara Channel (400 m) reference waters and surface Sargasso Sea or
Santa Barbara Channel sea water every 6 - 8 analyses [Hansell1998].
The standard deviation of the deep and surface references analyzed
throughout a run generally have a coefficient of variation ranging
between 1-3% over the 3-7 independent analyses (number of references
depends on size of the run). Daily reference waters were calibrated
with DOC CRM provided by D. Hansell (University of Miami;
[Hansell2005]).


13.3  DOC calculation


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


13.5  Standard Operating Procedure for TDN analyses- Carlson Lab UCSB

TDN samples were analyzed via high temperature combustion using a
Shimadzu TOC-V with attached Shimadzu TNM1 unit at an in-shore based
laboratory at the University of California, Santa Barbara. The
operating conditions of the Shimadzu TOC-V were slightly modified from
the manufacturer's model system. The condensation coil was removed and
the headspace of an internal water trap was reduced to minimize the
system's dead space. The combustion tube contained 0.5 cm Pt pillows
placed on top of Pt alumina beads to improve peak shape and to reduce
alteration of combustion matrix throughout the run. Carrier gas was
produced with a Whatman® gas generator [Carlson2010] and ozone was
generated by the TNM1 unit at 0.5L/min flow rate. Three to five
replicate 100 µl of sample were injected at 130mL/min flow rate into
the combustion tube heated to 680°C, where the TN in the sample was
converted to nitric oxide (NO). The resulting gas stream was passed
through an electronic dehumidifier. The dried NO gas then reacted with
ozone producing an excited chemiluminescence NO2 species [Walsh1989]
and the fluorescence signal was detected with a Shimadzu TNMI
chemiluminescence detector. The resulting peak area was integrated
with Shimadzu chromatographic software. Injections continue until at
least three injections meet the specified range of a SD of 0.1 area
counts, CV ≤2\% or best 3 of 5 injections.

Extensive conditioning of the combustion tube with repeated injections
of low nitrogen water and deep seawater was essential to minimize the
machine blanks. After conditioning, the system blank was assessed with
UV oxidized low nitrogen water. The system response was standardized
daily with a four-point calibration curve of potassium nitrate
solution in blank water. All samples were systematically referenced
against low nitrogen water and deep Sargasso Sea reference waters
(2600 m) and surface Sargasso Sea water every 6 - 8 analyses
[Hansell1998]. Daily reference waters were calibrated with deep CRM
provided by D. Hansell (University of Miami; [Hansell2005]).

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


13.6  TDN calculation


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


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

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

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

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




14  CARBON ISOTOPES IN SEAWATER (14/13C)


PI
   • Ann McNichol (WHOI)

Technician
   • Chance English

A total of 27 samples were collected from 24 stations along Leg 1 of
the P06 zonal transect (30-32.5°S & 153°E to 72°W). Samples were taken
from only the surface bottle (~ 5m) at each station with approximately
2.5 degrees of spacing between each station. Duplicates were made at
three separate stations. Samples were collected in 500 mL airtight
glass bottles. Using silicone tubing, the flasks were rinsed 2 times
with seawater from the surface niskin. While keeping the tubing at the
bottom of the flask, the flask was filled and flushed by allowing it
to overflow 1.5 times its volume. Once the sample was taken, about 10
mL of water was removed to create a headspace and 120 µL of 50%
saturated mercuric chloride solution was added to the sample. To avoid
contamination, gloves were used when handling all sampling equipment
and plastic bags were used to cover any surface where sampling or
processing occurred.

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

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

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




15  MARINE MICROBES, PHOSPHORUS, AND METABOLIC ENERGY POTENTIAL


PI
   • Kimberly J Popendorf

Cruise Participant
   • Kaycie B Lanpher

Important factors for ocean productivity are the relative availability
of nutrients and the generation and storage of metabolic energy to
convert these nutrients into biomass. Adenosine triphosphate (ATP) is
a primary energy trafficking molecule and plays a key role in
providing intracellular energy for metabolism. We are investigating
ATP, as a measure for metabolic energy potential, relative to other
biogeochemical parameters: biomass, community composition, and
nutrient resources in two dissolved phosphorus pools. These
comparisons will address the relationship between energy compounds and
biomass with the availability of nutrient resources. We will be
testing the hypothesis that the allocation of energy compounds as a
fraction of biomass will have an inverse relationship with nutrient
concentrations and will vary across a latitudinal gradient and within
depth profiles. We collected data across the P06 transect in the
Southern Pacific Ocean with depth profiles of the upper 200 m for cell
counts and concentrations of dissolved organic phosphorus (DOP),
dissolved inorganic phosphorus (DIP), particulate organic phosphorus
(POP), particulate ATP, and dissolved ATP. From the cross correlations
of these data we will explore the variation in microbial allocation to
energy storage, the role of DOP in supporting the microbial community,
and the relationship between microbial abundance and the dissolved and
particulate phosphorus pools.

Samples were collected at 12 stations, 6 depths per station with a
maximum at 215 m, and 3 times using the ship’s flow-through system,
spread out across the transect. Water was collected in a 250 mL HPDE
bottle at the CTD rosette for total dissolved phosphorus (TDP), which
was immediately placed in the freezer to be analyzed on land.
Additionally, 2 L of water was collected from the same niskin bottles
on the CTD. From this, 2 mL was taken in duplicate from each bottle
and put into two cryogenic vials containing 0.5% formaldehyde final
concentration. These cryogenic vials were placed in the refrigerator
for 30 minutes before being stored in a dewar containing liquid
nitrogen to return to the lab for analysis of cell counts. Then, 1 L
of each sample was filtered using a 47mm, 0.3 um glass fiber filter.
Each of those filters were boiled for 5 minutes in a 20mM Tris buffer
and then frozen and returned to the lab for analysis of particulate
ATP. The filtrate from three of those filters was also frozen for
land-based analysis of dissolved ATP. The remaining 1 L for each
sample was then filtered using the 47 mm, 0.3 um glass fiber filters,
the filters were rinsed with 1 mL of 0.17 M sodium sulfate before
being stored in combusted foil and placed in a liquid nitrogen dewar
and returned to the lab for land-based analysis of particulate organic
phosphorus (POP).




16  NASA OCEAN BIOLOGY/BIOGEOCHEMISTRY PROGRAM


NASA Goddard Space Flight Center, Ocean Ecology Laboratory, Field
Support Group

Participating team members:
   • Joaquín E. Chaves
   • Scott A. Freeman
   • Michael G. Novak

The NASA Goddard Space Flight Center (GSFC), Field Support Group
participated in the 2017 P06 Leg 2 GO-SHIP campaign on board the R/V
Nathaniel B. Palmer. The campaign departed from the Papeete, French
Polynesia, on August 20, 2017, and arrived in Valparaiso, Chile, on
September 30, 2017. Measurements were mainly conducted along 32.5° S
just south of the South Pacific Gyre, starting at approximately 149°
W, along a zonal west-to-east transect ending at ~74° W off the coast
of Chile.


16.1  NASA Science Objectives

The P06 campaign presented a valuable opportunity to collect in-water
optical measurements concurrently with phytoplankton pigments and
other biogeochemical parameters to support NASA's satellite ocean
color validation across a wide dynamic range of water optical
properties. The P06 line traversed from the clear, oligotrophic Gyre,
to the hypertrophic waters of the Chile upwelling system. Pigment and
biogeochemical samples were also collected concurrently with the
deployment of SOCCOM biogeochemical ARGO floats to support their
calibration.

   [image]Summary of NASA’s sampling during GO-SHIP P06, 2017.


16.1.1  Phytoplankton pigments and taxonomy, and biogeochemical 
        measurements

Near-surface samples (~2 m) were collected for measure the
concentration of phytoplankton pigments using high performance liquid
chromatography (HPLC), particulate organic carbon (POC), particulate
inorganic carbon (PIC), dissolved organic carbon (DOC), and spectral
particulate (a_{p}(λ)), and CDOM (a_{g}(λ)) absorptions. Samples for 
the determination of phytoplankton species composition and cell abundance 
were also collected and preserved for later analysis. A FlowCam imaging 
flow cytometer (Fluid Imaging Technologies, Inc., Scarborough, ME) was 
used to quantitatively image live phytoplankton cells for taxonomic 
classification and enumeration. For the parameters above, surface samples 
were collected with a peristaltic pump outfitted with an acid-clean 
silicon rubber hose deployed over the side while on station. Additional 
subsurface samples from two depths within the photic zone (< 200 m) were 
collected from the CTD rosette at stations where concurrent optical 
measurements were conducted. The depths for these subsurface samples were 
chosen based on the location of the chlorophyll maximum. Niskins bottles 
were fired at and above the chlorophyll maximum, the latter depth was 
determined by the inflection point of the chlorophyll fluorescence above 
the maximum. All filtration and cold sample preservation were conducted 
on board. Samples were transported to NASA-GSFC for further analyses. An
inventory of all samples collected for each parameter is presented in
Table %s.


16.1.2  In-Water Optical Measurements (AOPs, IOPs)

The package to measure inherent optical properties (IOPs) was equipped
with two attenuation and absorption spectrometers (ac-s, ac-9; WET
Labs, Inc.). The ac-9 was equipped with a 0.2 um pre-filter to allow
the in-situ measurement of spectral particulate absorption
(a_{p}(λ)). The IOP package also included two scattering
meters (bb-3, VSF-9; WET Labs, Inc.), and a Sea Bird SBE 49 CTD. The
ac-s and ac-9 meters measure absorption and attenuation (and total
scattering by difference) at 90 and 9 wavelengths, respectively,
between 400 and 740 nm, while the bb-3 measures backscatter at 3
wavelengths and 117°. The VSF-9 measures scattering at 9 angles from
60° to 170° at 532 nm. The package performed casts down to 200m depth
at 36 stations during the campaign (Table %s).

Apparent optical properties (AOPs), both downwelling irradiance
(E_{d}(λ)) and upwelling radiance (L_{u}(λ)), were measured using a 
Satlantic, Inc., HyperPro radiometer system and/or a Biospherical 
Instruments C-OPS system. For both instrument systems, incoming solar 
irradiance (E_{s}(λ)) was measured with a matching reference radiometer. 
The HyperPro system measured radiance and irradiance at 255 wavelengths 
between 305 and 1140 nm, while the C-OPS measured the same parameters at 
19 wavelengths between 305 and 900 nm. AOP measurements were conducted 
once daily within ± 2 h of local solar noon when weather conditions 
permitted down to the 20% of surface light level.

Additionally, we conducted solar radiometry at 10 stations using a
Microtops Sun Photometer. The Microtops is a small, handheld
instrument, which measures solar radiance at five wavelengths. These
data will be incorporated into NASA’s AERONET database.


16.1.3  Underway IOP Measurements

During the entire campaign, with the exception of the transit through
the French EEZ, we conducted IOP measurements with an underway system
that included an ac-s meter, a VSF-3 scattering meter, a bb-3
scattering meter, and a chlorophyll fluorometer. All the above
instruments in the underway system are from WET Labs, Inc. A Turner
integrated cavity absorption meter (ICAM) also provided absorption
data at 9 wavelengths. In addition to the optical instruments, the
system included a SeaBird SBE45 thermosalinograph and a Sequoia Inc.
valve flow control unit, which switched hourly between whole seawater
and 0.2 um filtered water to measure a_{p}. Twice per day, distilled 
water was run through the entire system to calibrate the optical 
instruments.


Table 16.1: Biogeochemical samples collected during the P06 campaign by 
            the NASA team.

       Parameter                          Number of samples 
       —————————————————————————————————  —————————————————
       a_{p}                                    213               
       a_{g}                                    122               
       DOC                                      301               
       HPLC pigments                            226               
       POC                                      646               
       PIC                                      137               
       Phytoplankton abundance, taxonomy        108               
       —————————————————————————————————  —————————————————
       **Total**                               1753              



Table 16.2: Inherent optical properties (IOPs) instrument casts during 
            the P06 GO-SHIP campaign.

Date, UTC  Beg time  Duration  End time  Sta-  Latitude  Longitude
yyyymmdd     UTC                 UTC     tion                     
—————————  ————————  ————————  ————————  ————  ————————  —————————
20170824   00:05:26  00:10:41  00:16:07  902   -28.9596  -148.9672
20170824   00:23:01  00:30:00  00:53:01  902   -28.9596  -148.9672
20170824   22:19:54  00:30:16  22:50:10  144   -32.4996  -148.9693
20170825   20:28:41  00:29:32  20:58:13  146   -32.5009  -147.3892
20170826   20:27:47  00:29:05  20:56:52  148   -32.5001  -145.709 
20170828   18:40:19  00:21:25  19:01:44  152   -32.5032  -142.2516
20170829   22:24:34  00:20:14  22:44:48  155   -32.4992  -139.4796
20170830   20:15:00  00:34:56  20:49:56  157   -32.5003  -137.6989
20170831   19:22:55  00:19:03  19:41:58  160   -32.5001  -135.0277
20170902   17:32:45  00:22:20  17:55:05  162   -32.4998  -133.2433
20170903   18:52:53  00:15:48  19:08:41  165   -32.4998  -130.5776
20170904   19:59:07  00:20:58  20:20:05  168   -32.5003  -127.9669
20170905   17:18:56  00:20:14  17:39:10  171   -32.501   -125.8766
20170906   19:03:54  00:20:58  19:24:52  175   -32.5     -122.9989
20170907   17:35:59  00:19:19  17:55:18  178   -32.4997  -120.5564
20170908   18:25:35  00:19:34  18:45:09  181   -32.4998  -118.0661
20170909   21:14:20  00:23:04  21:37:24  184   -32.4896  -115.5716
20170910   18:56:35  00:20:28  19:17:03  187   -32.5001  -113.0855
20170911   18:17:36  00:20:06  18:37:42  191   -32.5001  -110.3258
20170912   18:03:34  00:21:51  18:25:25  194   -32.5     -108.256 
20170913   18:52:25  00:26:43  19:19:08  198   -32.5     -105.4966
20170914   18:54:19  00:26:28  19:20:47  201   -32.5002  -103.4259
20170915   19:49:13  00:23:12  20:12:25  205   -32.5005  -100.6656
20170916   15:29:38  00:24:19  15:53:57  207   -32.5002  -98.8853 
20170917   15:06:44  00:19:53  15:26:37  210   -32.5004  -96.2146 
20170918   15:57:44  00:20:38  16:18:22  213   -32.4998  -93.544  
20170919   17:00:21  00:22:07  17:22:28  216   -32.5031  -90.8778 
20170920   17:25:56  00:22:16  17:48:12  219   -32.4999  -88.205  
20170921   15:12:56  00:22:22  15:35:18  222   -32.4999  -85.5353 
20170922   15:47:19  00:21:52  16:09:11  225   -32.5008  -82.8655 
20170923   16:25:33  00:21:32  16:47:05  228   -32.5002  -80.1938 
20170924   16:39:59  00:22:34  17:02:33  231   -32.5002  -77.5246 
20170925   13:20:32  00:20:35  13:41:07  233   -32.4997  -75.7453 
20170926   15:44:33  00:32:15  16:16:48  237   -32.5004  -73.0834 
20170927   15:34:50  00:25:36  16:00:26  241   -32.5001  -72.5573 
20170928   16:45:02  00:24:58  17:10:00  245   -32.5     -72.1956 
20170929   13:32:31  00:10:31  13:43:02  250   -32.5005  -71.585  
20170929   13:48:52  00:22:06  14:10:58  250   -32.5172  -71.585  



Table 16.3: Apparent optical properties (AOPs) instrument casts during 
            the P06 GO-SHIP campaign.

Date, UTC  Beg time  End time  Sta-  Latitude  Longitude   Sky
yyyymmdd     UTC       UTC     tion                       Condi-
                                                          tions
                                                            %
                                                          clouds
—————————  ————————  ————————  ————  ————————  —————————  ——————
20170823   21:15:00  21:25:00   902  -28.9638  -148.9673   100 
20170823   21:26:00  21:30:00   902  -28.9638  -148.9673    60  
20170828   19:07:00  19:22:00   152  -32.5032  -142.2516    50  
20170829   22:07:00  22:20:00   155  -32.4992  -139.4796   100 
20170903   19:15:27  19:17:25   165  -32.4998  -130.5776    60  
20170903   19:17:32  19:25:00   165  -32.4998  -130.5776    60  
20170904   20:26:49  20:41:22   168  -32.5003  -127.9669    40  
20170905   17:39:03  17:40:21   171  -32.501   -125.8766    10  
20170906   19:35:14  19:45:43   175  -32.5     -122.9989    30  
20170907   18:12:00  18:14:00   178  -32.4997  -120.5564    10  
20170907   18:14:00  18:18:00   178  -32.4997  -120.5564    10  
20170908   18:53:00  19:12:00   181  -32.4998  -118.0661    80  
20170909   20:37:48  21:05:00   184  -32.4896  -115.5716    30  
20170910   19:25:42  19:41:27   187  -32.5001  -113.0855    60  
20170911   18:52:25  19:04:08   191  -32.5001  -110.3258    10  
20170912   18:53:38  18:45:35   194  -32.5     -108.256     30  
20170915   20:24:25  20:31:05   205  -32.5005  -100.6656    80  
20170917   15:32:56  15:36:41   210  -32.5004  -96.2146     40  
20170917   15:47:00  15:50:42   210  -32.5004  -96.2146     40  
20170918   16:26:28  16:38:05   213  -32.4998  -93.544      30  
20170919   17:37:59  17:46:28   216  -32.5031  -90.8778     30  
20170920   17:56:45  18:19:43   219  -32.4999  -88.205      80  
20170920   17:56:45  18:19:43   219  -32.4999  -88.205      80  
20170921   15:47:37  16:03:20   222  -32.4999  -85.5353    100 
20170921   15:47:37  16:03:20   222  -32.4999  -85.5353    100 
20170922   16:22:07  16:33:07   225  -32.5008  -82.8655    100 
20170923   16:57:17  17:06:51   228  -32.5002  -80.1938    100 
20170924   17:03:52  17:12:40   231  -32.5002  -77.5246     20  
20170927   16:31:32  16:43:45   241  -32.5001  -72.5573     40  
20170928   17:23:11  17:36:41   245  -32.5     -72.1956     40  
20170929   14:20:04  14:30:13   250  -32.5172  -71.585     100 




17  LADCP


PI
   • Dr. Andreas Thurnherr

Cruise Participant
   • Elizabeth Simons

LADCP was collected during full depth CTD casts at all stations by
Elizabeth Simons and Lena Schulze. Preliminary processing and QC was
made on board by Elizabeth Simons. Approximately every 5 casts or when
data was questionable post-processed data was sent to Andreas
Thurnherr for further review and QC.


17.1  LADCP system configuration

An upward-looking (UL) and a downward-looking (DL) ADCPs and a
rechargeable battery were affixed to the rosette using custom brackets
(Figure 1 and 2). The UL instrument was positioned ~5 inches over the
top rosette ring while the DL instrument was positioned between Niskin
bottles 4 and 6 and affixed through the brackets to the rosette bottom
center bar.

A star cable was used to connect both UL and DL LADCPs to the battery
and deck/connection cables.

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

Two different ADCP instruments were used during the cruise. The
Teledyne RDI WHM150 (S/N:24544) as DL and the Teledyne RDI WHM300
(S/N:24997) as the UL. The battery package was a Deepsea Power and
Light SB 48 V/16 A (S/N: 01283). All instruments were set up to record
velocity data with 8 m bins and zero blanking distance. Staggered
pinging was used to avoid previous ping interference.

DCP programming and data acquisition were carried out by Elizabeth
Simons and Lena Schulze using the LDEO Acquire software running on a
MAC computer. Prior to each cast, the corresponding command files were
send to both the UL and DL ADCPs, communications were then terminated,
deck cables disconnected and all connections were secured and sealed
with dummy plugs. After the rosette was brought back up on desk
following a cast, the communication and power cables were connected to
the MAC computer. Data acquisition were terminated and files were
downloaded with the corresponding command using the Acquire software.
The battery was disconnected from the star cable and connected to a
charger via a deck cable running from the the baltic room to the dry
aft lab. The battery remained connected to the charger between
stations. The battery pack was periodically vented manually to prevent
pressure build up. Log files were kept for each cast with LADCP and
CTD information to ensure all steps were made properly.


17.2  Problems/Setup changes

The battery package from Leg 1 was overcharging and needed to be
vented after every cast so it was replaced after the test cast (902).
After station 161 a pigtail connection between the on deck power and
star cable was crushed while landing the rosette on deck. It was
replaced with a spare before station 162, and more fully secured.
After the initial stations, it was noted that the DL instrument was
seated lower on the rosette. It turned out that the bracket the
instrument was attached to was slightly twisted and tilting the DL
forward, bringing it closer to the floor. After a rough landing on
deck due to rough seas, skids were attached to the bottom of the
rosette cage, gaining enough clearance for the heads of the DL to
clear the floor. The DL was rotated so the broken beam 3 was looking
at the top of the skid to reduce signal contamination in the working
heads.

Communication issues with the LADCP started early, with multiple files
created for the UL instrument and occasional trouble interacting with
the both the UL and DL. It was assumed that the star cable was faulty,
but working. An extra star cable was hand carried to the ship for Leg
2, and held in reserve for when the cable on the rosette failed
completely. After station 219, the star cable was replaced with the
new cable.

At the beginning of station 220 there were problems with power to the
instruments and on recovery the UL and DL would not communicate using
either LADCP2 command or interact2 command. Partial communication was
restored before station 221, however due to time constraints only the
DL was set-up to record. Once on board after station 221,
troubleshooting found a bad link between the UL and UL deck cables
through the replacement star cable. The star cables were switched
again, with the original faulty, but working cable reattached on the
rosette. The broken star cable was found to have a bad RS232 wire on
the UL connected side of cables. This was repaired by the ETs (Sheldon
Blackman and Julian Race) on board, bypassing the faulty section on
the cables. The original star cable remained in place on the rosette,
with the repaired replacement as a back-up. After the last cable
switch, the original star cable operated acceptably.

   • Station 144: Manually downloaded data.

   • Station 175: Manually downloaded data.

   • Station 183: No UL data.

   • Station 194: Difficulty communicating.

   • Station 200: Manually downloaded data.

   • Station 214: Difficulty communicating with UL.

   • Station 219: Communication issues and multiple files were
     downloaded.

   • Station 220: Manually downloaded data.

   • Station 221: Only DL data.

Multiple stations had multiple files associated with the UL. Some were
the result of user error, usually disconnecting direct power before
comms were established, others were caused for unknown reasons.


17.3  Data Processing and Quality Control

The ADCP data was processed daily by Elizabeth Simons using the
Matlab-based LDEO LADCP processing software version IX (1). Processing
warnings and figures created through the software were reviewed for
signs of anomalies such as rosette rotation and tilt, biased shear,
agreement between LADCP and SADCP velocities, beam strength and range
and ADCP distance to the sea bottom. Data was sent to Andreas
Thurnherr every 5 stations or when questionable profiles were
observed.

Available for download at¬†http://www.ldeo.columbia.edu/LADCP

   [image]Downward looking ADCP

   [image]Upward looking ADCP




18  CHIPODS


PI
   • Jonathan Nash

Cruise Participants
   • Ratnaksha Lele
   • Sherry Chou


18.1  Overview

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


System Configuration and Sampling
---------------------------------

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

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

   [image]Chipod pressure case attached on the rosette


          Logger  Pressure  Up/Down    Station Numbers     
          Board     Case    Looker
           SN        SN
          ——————  ————————  ———————  ———————————————————
          2025    Ti 44-7     Up     1-143, 902, 144-168 
          2030    Ti 44-11    Up     1-107, 169-250      
          2032    Ti 44-15   Down    1-143, 902, 144-172 
          2027    Ti 44-3    Down    173-250             
          2027    Ti 44-3     Up     112-143, 902        
          2026    Ti 44-2     Up     144-146             
          2031    Ti 44-6     Up     147-250             


18.3  Data


18.3.1  Leg 1

The chipods were turned on by connecting the sensors to the pressure
case at the beginning of the cruise. They continuously recorded data
until the end of the leg. Data was uploaded onto the computer once
every day to ensure proper functioning and data collection. SN2030 was
replaced by SN2027 before cast 112 due to problems with file
acquisition and communicating with the device possibly due to a memory
card issue. SN2030 memory card and batteries were replaced soon after.

   [image]A typical plot of chipod raw data


18.3.2  Leg 2

On 8/24/17 we had a test cast at Station 902. Loggers SN2025
(uplooker), SN2027 (uplooker), and SN2032 (downlooker) were deployed.
For this test cast logger SN2027 recorded zeros for temperature and
acceleration values, and the other two loggers recorded normal looking
data. Logger SN2027 was switched out and SN2026 took its place
(batteries inside the units were switched because those from SN2027
were newer). For the first CTD cast, at Station 144, logger SN2026
recorded normal temperature values but the acceleration values were
low compared to the other units. The problem continued during the next
2 CTD casts (Stations 145-146). Logger SN2026 was switched out and
SN2031 took its place starting with Station 147. Data from the 4th CTD
cast of Leg 2, at Station 147, looked fine for all three deployed
loggers: SN2025, SN2031, and SN2032 (except that there are vertical
lines in the plots for data from SN2032 at 3:30 on 08/26/17).

Loggers SN2032 and SN2025 both had problems on 09/2/17 and didn't
record data for Stations 164-168; they both show corrosion on usb
connector plug (pictures were sent to June Marion).

On 9/6/17 logger SN2032 couldn’t communicate with computer and it was
switched out with SN2027.

Chipod sensors seemed to be working fine and loggers were recording
data, but there were continued problems with downloading data. The
computer program for getting data from loggers froze often, especially
with logger SN2031 (uplooker). Logger SN2031 did not record data for
Stations 185-188. Frequency of downloading data was decreased, as
advised by Jonathan Nash.

On 9/19/17, data was retrieved from logger SN2027, but there were
multiple problems with the other 2 loggers. Logger SN2031 froze the
computer program but did not need to be power-cycled; files 78-79
showed incorrectly large maximum time values but otherwise the data
seemed fine - this had happened before and reloading the file had
removed the problem.

Logger SN2030 (uplooker) froze the computer program and then did not
record data for Stations 215-216. On 9/29/17 data was successfully
downloaded from all 3 loggers after the last cast.

**Status of Spares** Logger SN2026 recorded low acceleration values,
it was switched out (with SN2027) on 8/24/17.

Logger SN2025 might have had a faulty memory card, it was switched out
(with SN2030) on 9/6/17 and a new memory card was installed.

The "insides" of SN2026 and SN2025 were switched because SN2026 had a
newer usb plug but unidentified hardware issue, and this way SN2026
was ready to use.

Logger SN2032 was switched out (with SN2031) on 9/6/17 due to problem
recording data (possibly related to corroded usb plug).

**Summary** Data was attained by (at least one) uplooking chipod for
all stations. For the downlooking chipod there is no data for Stations
164-172.




19  FLOAT DEPLOYMENTS


During P06E 2017 a total of 35 profiling floats were deployed, which
were part of several programs: 16 UW Argo, 15 SIO SOLO II, and 4
biogeochemical SOCCOM floats. Elisabeth Simons was responsible for all
deployments, recording and communicating their deployment details to
the various PIs of the programs. The assistance from the ASC marine
technicians was necessary for all deployments, first because it was
required for any operation on the back deck, and second in order to
reduce any possible difficulties with the floats’ deployment. Each
deployment occurred with the use of line strung to the float, with one
end of the line tied to a cleat and the other held by the technician.
Deployments were always done on departure from a CTD station while the
ship was steaming at 1 knot. Before the deployment, the marine
technician communicated with the bridge to disengage the propeller on
the side of the deployment, in order to avoid any risk of having the
float going through the propeller. The cruise participant was
primarily responsible for deployments, with additional assistance from
CTD watchstanders. Elisabeth Simons oversaw operations on the midnight
to noon watch, while Lena Schulze oversaw operations on the noon to
midnight watch.

A 10-day cycle is set for the UW Argo, SOLO II, and SOCCOM floats:
after an initial dive to a parking depth of 1000m, the floats drift
for 10 days with the ocean currents at this depth; after a subsequent
dive to 2000m, the floats then ascend to the surface, during which
data are collected. The 2000m-surface data profiles are then sent to
shore via satellite, using an antenna located at the top of the float.
Measurements comprehend temperature, salinity, pressure and additional
biogeochemical measurements for the SOCCOM type.

The SIO Deep SOLO profiling floats have a different cycle: they dive
down to the full ocean depth and drift at 5000 dbar, or 500 dbar
shallower than the bottom, with a cycle of approximately 15 days, in
order to balance data collection with battery life.

Each of these floats was self-activating, so no initial operations
where required before their deployment to activate them, except for
the case of Deep SOLO floats for which John Gilson sent some commands
few hours before their deployment.

In the following, each float program is discussed.


19.1  SOCCOM floats

PIs
   • Steve Riser
   • Ken Johnson
   • Lynne Talley

Two biogeochemical floats have been deployed, as part of the “Southern
Ocean Carbon and Climate Observations and Modeling” project (SOCCOM).
SOCCOM is a U.S. project sponsored by NSF that focuses on carbon and
climate in the Southern Ocean. Its goal is to deepen our knowledge of
the processes that regulate the carbon export in the Southern Ocean.
So far, SOCCOM has 86 active floats, and the data are available to the
public at http://soccom.princeton.edu/content/float-data. The floats
are equipped with CTD, oxygen (Anderaa optode 4330), nitrate
(MBARI/ISUS), FLBB bio-optical (Wetlabs) and pH (Deep-Sea DuraFET)
sensors. Data acquisition is made available through Iridium Satellite
communication and GPS.

Rick Rupan and Andrew Meyer (UW) tested each float (for both leg 1 and
leg 2 of the P06 occupation) at the beginning of the voyage during the
port call in Sydney, Australia. They found a malfunction on one of the
floats assigned to leg 2, and this float has been sent back to UW for
investigation and repair.

Before the deployment of each float, the fluorometer/backscatter and
the pH sensors were carefully cleaned using lens paper, 99% isopropyl
alcohol and DI water. The procedure required the use of a line strung
through the deployment collar of the float. Each deployment occurred
on the starboard side, mid-ship, while the ship was steaming at no
more than 1 kn. No issues were encountered during the deployments.

The deployments occurred after the completion of the CTD station that
was chosen to be the closest to the planned deployment location and
had a bottom depth greater than 2500m. Samples for HPLC and POC
analyses were taken from the Niskin bottles, tripped as duplicates, at
the surface and at the chlorophyll maxima depths. These samples will
be sent to the U.S., where NASA (HPLC) and UCSB (POC) groups will
perform the analyses. On board, only the filtration of the samples was
required. Full-depth samples of other ocean properties (salts, pH,
nitrate, oxygen) were collected and analyzed by the different groups
on board, in order to calibrate the floats’ sensors. In particular, pH
samples were collected and analyzed by personnel from U Miami, Millero
lab; dissolved inorganic carbon samples by personnel from AOML and
PMEL; oxygen, nitrate and salinity samples by the ODF group at SIO.

After the deployment, the cruise participant recorded the details and
sent them to the SOCCOM PIs. The location and date of the float
deployments are indicated in the table below, with hull and serial
numbers, list of parameters measured by the floats and the CTD cast at
the location of deployment. Both floats have reported their first
profiles and their sensors are working well.


Table 19.1: summary of the deployment details of the four SOCCOM floats

Float I.D.  Inst./   Date        Lat          Lon        P06  Depth  Confirm
            Prog.    (UTC)                               Stn          (Y/N) 
——————————  ——————  ————————  ———————————  ————————————  ———  —————  ———————
12396(2)    SOCCOM  31/08/17  32 30S       135 01.65W    160  4375      Y   
                    23:45                                                   
----------  ------  --------  -----------  ------------  ---  -----  -------
8204(2)     SOCCOM  10/9/17   32 29.887S   114 44.59W    185  2800      Y   
                    04:52                                                   
----------  ------  --------  -----------  ------------  ---  -----  -------
12369       SOCCOM  22/09/17  32 30.00S    084 37.746W   223  3930      Y   
                    03:17                                                   
----------  ------  --------  -----------  ------------  ---  -----  -------
12540(4)    SOCCOM  26/09/17  32 30.0737S  073 57.8215W  235  4100      Y   
                    06:50                                                   


19.2  SIO floats

PIs
   • Dean Roemmich
   • John Gilson

15 SIO SOLO II floats were deployed during the cruise. The SIO SOLO II
are part of a global 3°x3° array. The float is programmed to do a
first dive, and to come back to the surface after one hour. The data
of this first dive are used by the SIO team to check that the float is
working correctly. We have received confirmation that all the floats
have reported correctly after one hour, and their data look good.

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

Each deployment proceeded smoothly, with the exception of SIO float
8568. A stabilizing disk was lost on 8568. This float’s water release
did not function properly so the float was released under rougher
conditions. After each deployment, the details were recorded by the
scientist responsible for the deployment and sent to John Gilson by
the cruise participant. The location and date of the SIO float
deployments are indicated in the table below, with serial numbers, CTD
cast at the location of deployment and name of the personnel who
deployed the floats.


Table 19.2: summary of the deployment details of the 15 SIO SOLO II 
            floats

Float    Date (UTC)    Lat          Lon           P06  Depth  Confirm
 I.D.                                             Stn          (Y/N)
—————  ——————————————  ———————————  ————————————  ———  —————  ———————
8556   25/08/17 21:04  32 30.0948S  147 23.3340W  146  4570      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8557   28/08/17 14:12  32 30.0316S  143 02.5397W  151  5100      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8558   30/08/17 11:47  32 29.9881S  138 35.3137W  156  4575      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8559   3/9/17 19:26    32 30.3797S  130 34.5309W  165  4115      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8560   5/9/17 11:11    32 29.894S   126 18.517W   170  3134      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8562   6/9/17 23:26    32 30.0057S  122 59.6086W  175  3550      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8563   8/9/17 13:37    32 30.0023S  118 53.7286W  180  3500      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8564   10/9/17 12:09   32 30.0098S  113 54.7810W  186  2960      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8565   11/9/17 08:09   32 30.0378S  111 42.2823W  189  2472      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8566   12/9/17 18:49   32 30.4237S  108 15.6862W  194  3209      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8567   15/09/17 14:30  32 30.00S    102 44.131W   202  3686      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8568   18/09/17 16:38  32 30.358S   093 32.839W   213  3710      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8569   19/09/17 17:40  32 30.1856S  090 52.669W   216  3910      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8570   21/09/17 02:08  32 30.0902S  87 19.0324    220  3870      Y   
-----  --------------  -----------  ------------  ---  -----  -------
8571   25/09/17 05:13  32 30.0787S  076 38.1230W  232  3966      Y   
-----  --------------  -----------  ------------  ---  -----  -------


19.3  UW floats

PI
   Steve Riser

16 UW floats have been deployed during P06 leg 1, as part of the
global Argo array. Rick Rupan and Andrew Meyer had tested the floats,
during the port call in Sydney, Australia. The floats were all
successfully deployed, with no issues. After the deployment, the
details were recorded by the scientist responsible for the deployment
and sent to Steve Riser, Dana Swift and Rick Rupan by the cruise
participant. Date, time, location of the deployment, CTD cast
associated with the deployments and the name of the deployers are
reported in the Table below.


Table 19.3: summary of the deployment details of the 16 UW floats

Float        Date (UTC)    Lat          Lon           P06  Depth  Confirm
 I.D.                                                 Stn          (Y/N)
—————————  ——————————————  ———————————  ————————————  ———  —————  ———————
12444(9)   27/08/17 06:48  32 29.863S   144 49.334W   149  6185      Y   
---------  --------------  -----------  ------------  ---  -----  -------
6963(5)    29/08/17 08:36  32 30.015S   141 15.559W   154  5000      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12643(9)   31/08/17 05:52  32 29.85S    136 48.421W   158  4421      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12550      4/9/17 12:05    32 30.0057S  128 47.8830W  167  4279      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12426(10)  6/9/17 01:05    32 30.015S   125 10.11W    172  3750      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12374(6)   7/9/17 14:03    32 30.0137S  121 20.1727W  177  3190      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12420(10)  9/9/17 06:00    32 29.85S    117 14.01W    182  3300      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12428(11)  10/9/17 19:45   32 30.01S    113 06.84W    187  2400      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12770(6)   11/9/17 22:35   32 29.944S   110 19.511W   191  3350      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12611(11)  13/09/17 08:30  32 29.8814S  106 52.4863W  196  3278      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12626(12)  16/09/17 15:50  32 30.0169S  098 53.1386W  207  3820      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12623(12)  17/09/17 15:55  32 30.4816S  096 13.5855W  210  3940      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12608(13)  19/09/17 08:56  32 29.9966S  091 45.9192W  215  3480      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12644      20/09/17 09:26  32 30.1707S  089 05.7669W  218  3380      Y   
---------  --------------  -----------  ------------  ---  -----  -------
12609      21/09/17 19:45  32 30.00S    085 31.96W    222  3720      Y   
---------  --------------  -----------  ------------  ---  -----  -------
11096(14)  22/09/17 20:11  32 30.00S    082 51.899W   225  3730      Y   
---------  --------------  -----------  ------------  ---  -----  -------




20  DRIFTER DEPLOYMENTS


PI
   • Shaun Dolk (*AOML*)

Cruise Participants
   • Elizabeth Simons

Six drifters were deployed on P06E 2017 for the Global Drifter
Program. Elizabeth Simons was responsible for deployment of the
drifters, and the CTD watchstanders of each shift helped with the
deployment. Secondary assistance was provided by ASC Marine
Technicians.

The simple deployment process involved: (1) removing the plastic
wrapping from the drifter; (2) carrying the drifter to the back deck;
(3) deployment of the drifter, after received confirmation from the
bridge; (4) recoding of the deployment details. In case two
deployments were required at the same location, the drifter release
occurred with 30 seconds of distance between each other, in order to
avoid any entanglement amongst the drifters' drogues. After the
deployment, the scientist responsible for the operation recorded the
details from the monitor in the wet lab, wrote them in the log sheet
and Elizabeth Simons sent the details to Shaun Dolk at AOML. The Table
below reports the details for each deployment.


Table 20.1: Table of deployments of the six drifters


Float I.D.    Date (UTC)        Lat          Lon       P06 Stn  Depth
——————————  ——————————————  ———————————  ————————————  ———————  —————
64829530    25/08/17 12:24  32 30.073S   148 10.879W     145    4603 
----------  --------------  -----------  ------------  -------  -----
64831280    19/09/17 17:40  32 30.1856S  090 52.669W     216    3910 
----------  --------------  -----------  ------------  -------  -----
64829550    20/09/17 01:50  32 30.08S    089 58.95W      217    3713 
----------  --------------  -----------  ------------  -------  -----
64829040    20/09/17 18:09  32 30.005S   088 12.299W     219    3680 
----------  --------------  -----------  ------------  -------  -----
64828490    21/09/17 10:10  32 30.0263S  086 25.5327W    221    3960 
----------  --------------  -----------  ------------  -------  -----
64828500    22/09/17 03:29  32 30.00S    084 37.753W     223    3950 
----------  --------------  -----------  ------------  -------  -----




21  STUDENT STATEMENTS


21.1  Cristobal Aguilera

   [image]In the picture, from left to right: me, Luz, Dr. Speer, Rich
   (MT), Lucie (fellow student), and Kenny.

I guess I could say I got into this cruise for pure chance, or sheer
luck. My advisor was supposed to come, but he couldn’t find the time:
too many obligations and duties. After him, his right hand man was the
next on the line, but he couldn’t either, for the same reasons. So
here I am, almost at the end of this fantastic experience! I had high
expectations for what this cruise would be, but they were far
surpassed. I have met a lot of fun people onboard the Nathaniel B.
Palmer, and a 40 days long ship adventure is something to be lived! I
actually didn’t even realize how the days passed by: it looked like we
were just starting, and now we are a few miles from land. Part of that
may be due to the huge amount of work to be done; no rest for CTD
watchstanders! (Not to mention the super fun ping-pong tournament!!)
But I think it’s just that when you enjoy what you do, time flies. I’d
like to mention  my fellow watchstanders Luz, Kenny, Dario, Rudi and
Cherry, they were all really nice and spending time and working with
them was easy and rewarding.

On a more academic side, this cruise experience will undoubtedly leave
its mark in my academic life. As a physical oceanographer in
formation, this hands-on experience has helped me to get a better
understanding on how the oceanographic data is acquired. On campus, we
students are often used to only use the data, without thinking or
taking into consideration how the data was collected, where does it
come from. Being outside, on the actual open ocean, has given me a
different perspective, has helped me to set the idea that data are not
just numbers in a matrix. Great efforts must be done to acquire it,
and good quality data is not being produced by itself. As part of my
duties onboard, I had to make some plots of the data we were
collecting. Here is an example of what we have been up to:

   [image]Cross-section of the bottle dissolved oxygen concentration
   along 32.5¬∫S

As some final words, I just want to point out that this was a great
experience overall, I have made links and bounds that will remain in
time, and I have actually been lucky enough to get a master’s degree
thesis project off this journey, in collaboration with Dr. Kevin
Speer. So there is no doubt for me that it was definitely worth it!


21.2  Dario Marconi

Take a walk on the wild side.... I started the cruise that I was seek
as I have never been. When Ken was taking my temperature on Day 1 I
thought: well, I guess that my time on the ship finishes now. Nope,
the antibiotics did their job. I recovered, lost weight and I leave
the ship in great shape. Thanks Ocean to clean my body and make my
mind sharper: "mens sana in corpore sano". Thanks to my team: Lena,
Rudi and Cherry. I return home with an amazing dataset for nitrate
isotope analyses. In my previous work I studied Nitrogen fixation in
the Atlantic, a basin that does not host significant rates of water
column denitrification. It's now time to use my tool bag in the
Pacific where N fixation and denitrification are co-occurring in the
same basin. Buon vento to whom will sail on the NBP in the next
future!


21.3  Lucie Knor

   [image]Photo: Joaqu√≠n Chaves

GO-SHIP P06E from Pape'ete to Valpara√≠so was my first experience at
sea, and a wonderful one at that. I helped David Cooper and Charlene
Grall with sampling and analysis of chlorofluorocarbons (CFCs) and
sulfur hexafluoride (SF6), anthropogenic gaseous compounds that are
used as tracers for ocean circulation and ventilation. I learned how
to sample CTD casts for volatile gases, and how to measure CFCs and
SF6 using a gas chromatograph. Throughout both smooth routine and
white-knuckle troubleshooting, I was impressed with David and
Charlene’s patience and insight, and I consider myself lucky to have
learned from them.

The 42 days on the Nathaniel Palmer made me realize that I have chosen
the right field, and I want to thank GO-SHIP for providing me with the
opportunity to get to this very satisfying conclusion. My traveling
companions all had interesting things to say about their various
projects, from nitrate isotopes and dissolved organic carbon to
Pacific water masses and ocean color remote sensing. I especially
enjoyed hearing about the on-the-ground research for NASA’s earth
observing satellites.

I'm looking forward to crossing paths again with the scientists and
crew I got to know on this adventure.


21.4  Luz Zarate-Jimenez

First of all, I would like to extend my gratitude for the opportunity
to participate on this oceanographic research cruise. This at-sea
experience has broadened my vision, allowing me to interact with and
learn from researchers in different fields and made me appreciate the
opportunity of being part of an international effort to improve the
understanding of the ocean and its variability. The scientific team
and crew of the vessel were beyond professional at all times and
shared the common goal of creating a successful oceanographic
expedition. Being surrounded by such knowledgeable and committed
scientists enhanced my interest in learning more and participating
actively within the scientific community.

Part of my duties as watch-stander included preparing the rosette
before every cast to ensure the proper collection of water, monitoring
the deployment and descent of the CTD, communicating with the winch
operators to adjust speed, recording depths of interest (including O2
minimum and maximum and chlorophyll maximum), as well as firing the
Niskin bottles using the right depth scheme. Once the rosette was on
board, I supported the sampling personnel serving as "sample cop",
helping to ensure that each research group was able to get the water
they needed. With practice, being a CTD operator along with Cristobal
Aguilera was enjoyable and fun. Keeping track of the changes in
temperature, salinity, and oxygen both vertically (depth) and
horizontally (west to east transect), provided us with enough material
to have discussions about the variations that we were observing. Most
of the time, these discussions were led by Dr. Kevin Speer, whom I
will always remember for being a challenging mentor from whom I have
learned a lot during these last weeks.

Dr. Kevin encouraged critical thinking among the students. One of my
favorite activities was spending time with Dr. Speer and Cristobal
looking at the bathymetric plots to decide the best location and
estimate the timing for the next station. Also, Dr. Speer kept the
watch-standers engaged with the data analyzed by the chemists. To do
so, we helped produce different sections for the properties being
analyzed during the cruise, so that the chemists could detect
important changes or problems with the data as we continued our
transect along the 32¬∫S line. Some of these properties included
salinity, temperature, oxygen, alkalinity, pH, and dissolved inorganic
carbon.

   [image]Cross-section of the pH concentration along the 32.5¬∫S

This cruise represented a great opportunity to grow personally and
professionally. Cristobal Aguilera, Elizabeth Simons, and Dr. Dario
Maconi were great support when coding. As a geophysicist, I enjoyed
the talk given by Rudolph Herbstaedt Gomez, where he explained to us
the main features of the East Pacific Rise. I wish I had spent more
time with the people from the other shift. However, I had the chance
of learning from my fellow watch-stander’s culture, and enjoy getting
to talk in Spanish with Sherry Chou, who was always willing to have a
conversation.


21.5  Rudolph Herbstaedt Gomez

I went on the GO-SHIP-P06 LEG 2 cruise as a Chilean National Observer.
However, for the most part I was included in the students' activities.
Given that I am in my senior year and have already taken all my course
work, this cruise helped me to see from a broad perspective the
interactions between different subjects I have studied. It was a great
opportunity to deepen my understanding on different natural phenomena,
particularly from a physical oceanography point of view. As a geology
major, learning about oceanography was something absolutely new.

During this cruise, I served as a CTD watchstander and helped collect
alkalinity water samples. I had the privilege of working with
wonderful people who taught me how to use the equipment and were
always willing to help me whenever it was needed. For these reasons, I
am very thankful for all the scientific team for involving me in their
research and paper discussions, which helped me get involved in the
research that was taking place on the ship.

Like every science student, curiosity is innate to me. In this case, I
learned a lot about the Pacific Ocean, and its relationship with
global scale processes. Although geology and oceanography are
different research areas, I realized that there is a significant
connection between them. Lastly, I must say that this experience has
increased my appreciation for those who work at sea, both the ship
crew who impacted my daily life, and the science staff who contribute
to enhance our understanding of the behavior of the ocean.


21.6  Sherry Chou

While I have been on four other research ships for different projects,
this cruise on the RVIB Nathaniel B. Palmer for GO-SHIP P06E has been
the longest and the most rewarding. Previously I had experienced a
variety of serious problems during research cruises, and signing up
for this opportunity was my way of giving ocean field work one more
(perhaps last) chance. I told myself that no matter what happens I
will be able to get through it, and that alone will be a worthwhile
experience. I was often thinking about it like a marathon, something
seemingly intimidating but very feasible to accomplish, with patience
and perseverance. Like a marathon, signing up was the hardest part in
many ways.

In spite of my positive self-talk, I was rather anxious prior to the
start of the cruise. Luckily, we had a few days in port so I came on
the ship early and asked around for help to get settled in. Everyone
was very nice and understanding, and slowly but surely I got adjusted
to ship life and trained for my new responsibilities.

From the start there were a variety of problems with the chipods, and
troubleshooting them and replacing malfunctioning parts was sometimes
tiring, but also a great learning opportunity. Jonathan Nash and June
Marion always replied to my inquiries promptly, even late at night,
and gave me lots of encouragement. While at first I was slightly
overwhelmed at the idea of being the "expert" on the ship, slowly I
became confident that I could take care of these instruments and the
important data they were collecting. The training session with
Ratnaksha Lele from Leg1, and the consistent and reliable support from
Jonathan and June were central to my climbing quickly along the
learning curve. Also invaluable was knowing that I could rely on the
expertise and help of the Marine and Electronics techs and the Chief-
Scientists when needed.

For my other two duties, as CTD Watchstander and "sample cop", there
were many others who shared the responsibilities, and I witnessed the
beauty of the scientific process at work. I think central to the
scientific method is the idea that humans are fallible, and human
error is inevitable. However, we can minimize the impact of human
error, by implementing a careful protocol. For the most important
tasks we often have many people checking on each other, catching each
other's mistakes. Mistakes were frequent, by almost everyone, but they
did not compromise the integrity of the data. Everything was carefully
and honestly noted. Along these lines, I was also greatly impressed
with the protocol for sampling water from the rosette. There was a
specific order which was understood and accepted, and everyone
followed the protocol. These are principles which are central to
science, common place even, but I couldn't help but think how
wonderful it would be if other aspects of society worked so rationally
and cooperatively, that it could be common place in our everyday
lives.

On the purely scientific level, I totally geeked out after our first
sampling session, where I recorded the temperature measured from water
collected from the Niskin bottles. After about an hour of writing down
very similar numbers, the numbers started jumping dramatically. It was
the thermocline, which I have known about for the last eight years,
but which I was vicariously "experiencing" for the first time. I was
really excited, and I couldn't stop telling everyone about it,
including to Dad back home. It's like the first time I pointed a
telescope at a random spot in the night sky, and saw light from
Jupiter and its moons. I felt the thrill of discovery in both cases,
and very close to nature and its beautiful mysteries.

I learned that there are some things which need to be experienced
first hand, in situ, in real time, and that scientific discovery is
what I hope to have the privilege to be a part of for the rest of my
life. I have to thank GO-SHIP and my advisor for this opportunity. It
has been one of the most special experiences of my life.







                      2017 P6 GO SHIP Repeat Hydrography Section
                             LADCP Post-Cruise QC Report
                                   A.M. Thurnherr
                                  December 15, 2017


Figure 1: Cross-Pacific zonal section of p0, a measure of finescale (100{320m vertical 
          wavelength) Vertical Kinetic Energy (VKE), along 32°S derived from the 
          vertical LADCP velocities collected during the 2017 occupation of the GO-
          SHIP P6 section; the orange contours show neutral density from uncalibrated 
          CTD data.


1 Summary

This report describes the results from the post-cruise quality control of the LADCP 
data collected during the two legs of the 2017 P6 GO-SHIP (CLIVAR repeat hydrography) 
cruise on the UNOLS R/V Nathaniel B. Palmer. Using two ADCPs installed on the 
hydrographic rosette (Section 2), one looking downward (DL) and the other upward 
(UL), full-depth profiles of all three components of the oceanic velocity field were 
collected at most stations. Entirely different methods are used for processing 
LADCP/CTD data for horizontal and vertical velocity, requiring separate QC (Sections 
3 and 4, respectively).

Main Findings: 1) There is good overall agreement (<∆u(rms)>≈4 cm·s^(-1)) between the 
independent upper-ocean horizontal velocity measurements from the LADCP and SADCP 
systems, indicating that the LADCP-derived horizontal velocities from the 2017 re-
occupation of the P6 repeat-hydrography line are of excellent quality. 2) Based on 
correlations between the independent vertical velocity measurements provided by the 
two ADCPs, the LADCP-derived w(ocean) profiles are of high quality as well.



2  Instruments and Data Acquisition

During the first (profiles^(1) 1-143) and second (144-250) cruise legs, Alma Castillo 
Trujillo and Elizabeth Simons, respectively, were responsible for LADCP data 
acquisition and shipboard QC. Additionally, the processing figures from every 5th 
profile and from profiles with suspected problems were sent to Thurnherr for 
additional checks.

Two different ADCP instruments were used during this cruise: the WHM15O #24544 as 
down-looker (DL) and the WHM300 #24497 as uplooker (UL). Initially (stations 1{13) 
the ADCPs were mounted on the rosette together with the "IMP" magnetometer/ 
accelerometer package that also serves as connection between the instruments and the 
battery. Almost immediately there were intermittent but frequent communications 
problems that were eventually traced to a leak in the IMP pressure case. As a result 
there are insufficient LADCP data for processing the profiles of stations 6 and 10-
13. On station 14 the IMP was replaced with a TRDI star cable and there are 
processable LADCP data from all remaining stations. However, intermittent 
communications problems continued during the entire cruise. The resulting profiles 
with multiple data files were processed with the largest files only. Five out of the 
final profiles (9, 60, 183, 200 and 221) were processed without any valid UL data.

During profile 97 beam #3 of the DL ADCP failed. Because the performance of the 
instrument remained otherwise good, because no spare WM150 was available, and because 
the range of the WH300 uplooker was marginal in that region of relatively weak 
acoustic backscatter it was decided to continue data acquisition without replacing 
the ADCP with the bad beam with a 300 kHz instrument. The UL performed well 
throughout the entire cruise. Both ADCPs were set up to record velocity data with 8 m 
pulses/bins and zero blanking. Staggered pinging was used to avoid previous ping 
interference, which is particularly important for 150 kHz instruments. See cruise 
report for additional information.

The left panel of Figure 2 shows the maximum profile depths. The topography of the 
first part of the cruise (the first 100 stations or so) is characterized by 
significant roughness in the Coral Sea and across a backarc basin just north of New 
Zealand. After crossing the deep Kermadec Trench around station 100 the seafloor 
becomes much smoother and rises gradually toward the EPR crest near station 188 
before descending into the Chile Basin and, finally, rising again at the South 
American continental slope. Except for the three profiles from stations 93, 94 and 
119, which were located in water deeper than 6000 m, bottom-track information is 
available for all profiles.

The right panel of Figure 2 shows the number of rotations experienced by the rosette. 
The fact that the instrument rotated primarily counterclockwise during the downcasts 
and clockwise during the upcasts with approximately equal number of rotations 
suggests that there was comparatively little stress on the wire during this cruise.

LADCP data quality is sensitively dependent on instrument range (Figure 3, left 
panel), which depends on the acoustic scattering environment. During the second half 
of the P6 cruise, acoustic backscatter was quite weak, with WH300 ranges below 65 m 
(an empirical limit for good horizontal-velocity profiles collected with single-ADCP 
systems) in most profiles after station 90 or so. The problem was compounded by a DL 
beam going bad on station 97, causing a significant reduction in instrument range, 
but the range of the 3-beam 150 kHz ADCP nevertheless remained above the 4-beam range 
of the 300 kHz UL for the remainder of the cruise, and the combined range of the two 
ADCPs was greater than 80 m in all dual-head profiles. Since the DL-only profiles (9, 
60, 183, 200 and 221) all have ranges greater than 65 m, too, all P6 LADCP profiles 
are expected to yield good horizontal velocities.

———————————————————————————————

(1) LADCP profile numbers, which are equal to the CTD station numbers of this cruise, 
    are used throughout in this report. The LADCP data distribution contains the file 
    STATIONNUMBERS.nc, which associates LADCP profile numbers with CTD station and 
    cast numbers. The CTD station and cast numbers are also printed in the titles of 
    all diagnostic figures produced by the LDEO IX software.


Figure 2: Profiling parameters. Left panel: Maximum depth. Right panel: Net package 
          rotations.

Figure 3: Left panel: Instrument range. Right panel: rms acceleration due to vessel 
          heave (sea state).


Package motion due to surface waves (sea state) is also known to affect LADCP data 
quality; in the right panel of Figure 3 sea state is quantified as the rms vertical 
package acceleration. Calm seas are typically associated with accelerations below 
0.2m·s^(-2) or so, implying significant wave-related package motion roughly in the 
middle third of the cruise. For context, the peak values around 0.35m·s^(-2) are 
small compared to values from the Southern Ocean, which frequently exceed 0.4m·s^(-2), 
indicating that sea state is not expected to have a strong detrimental effect on the 
quality of the P6 LADCP profiles.


Figure 4: rms LADCP-SADCP horizontal velocity differences; low values indicate good 
          agreement.



3  Horizontal Velocity

The overall quality of the horizontal LADCP velocities is assessed by processing all 
profiles with the velocity-inversion method (LDEO IX 13 software), using the bottom-
track (BT) and ship-drift (GPS) constraints and comparing the resulting LADCP 
velocities near the sea surface to the corresponding SADCP velocities. Based on data 
from other cruises, high-quality LADCP and SADCP velocities typically agree within 3-
6 cm·s^(-1) when averaged over a few profiles. The data from the 2017 P6 occupation 
clearly fit this criterion (Figure 4). Only in the middle of the section, roughly 
between profiles 90 and 170, are there velocity discrepancies around 6 cm·s^(-1), and 
the number of profiles with significantly higher discrepancies is small. Both low 
acoustic backscatter and sea state likely contributed to this pattern (Figure 3). 
Diagnostic plots were inspected from all profiles with velocity discrepancies 
exceeding 6 cm·s^(-1), but no data anomalies were found.

For final horizontal-velocity processing, the LADCP data were re-processed with all 
available referencing constraints, including the SADCP velocities. As a result, the 
final velocity uncertainties are smaller than the discrepancies shown in Figure 4, at 
least for the profiles with errors above 3 cm·s^(-1), which is the nominal accuracy of 
horizontal velocity from high-quality LADCP profiles. In summary, the quality of the 
final processed horizontal velocities derived from the 2017 P18 LADCP data is 
excellent. (Possible exceptions are profiles 1 and 2, both short and shallow casts 
where the seabed was not detected correctly and for which no good SADCP data are 
available. There are no indications that the resulting horizontal velocity profiles, 
referenced with GPS data alone, are bad, however, and they are included in the 
archive.)


Figure 5: Left panel: Correlation coefficient of DL/UL vertical velocity correlation 
          vs. profile number, averaged in groups of 10 profiles with error bars from 
          bootstrapping. Right Panel: Vertical-velocity signal (red; rms w) and noise 
          (blue; rms DL/UL regression residuals scaled by 2^(-0.5)) vs. profile 
          number. Data from the uppermost 300m are excluded.




4  Vertical Velocity

In order to process the LADCP data for vertical ocean velocity the LADCP w software, 
version 1.4, was used. In addition to high-quality velocity data from the ADCPs, 
vertical-velocity processing also requires 24 Hz CTD time series with very few or no 
missing scans. In contrast to other recent GO-SHIP cruises, there are no indication 
for CTD data transmission problems during P6, attesting to the high quality of the 
CTD winch system on the Palmer.

There are vertical-velocity profiles from all P6 stations with valid LADCP data. 
Dissipation estimates from a finestructure parameterization method (Thurnherr et al., 
GRL 2015) are available from all stations except those without valid LADCP data (6 & 
10{13) and two stations at both ends of the section (1, 2, 249, 250), which are not 
deep enough for the spectral method to be applied.

In contrast to LADCP-derived horizontal velocity, the two w measurements at a given 
depth (from the DL and UL ADCP) are largely^(2) independent. Diagnostics based on 
linear regressions between UL vs. DL-derived w are therefore useful measures of 
profile quality. The left panel of Figure 5 shows the resulting correlation 
coefficients for the P6 LADCP data below 300 m, calculated from w(ocean) profiles 
processed at the default 40m vertical resolution. Based on experience with other data 
sets, high-quality LADCP profiles typically have DL-UL correlation coefficients above 
0.3 when averaged over a few profiles. The P6 LADCP profiles clearly fit this 
criterion - the apparent outlier group with correlation coefficients consistently 
above 0.5 are profiles 81{89 crossing the Havre Trough, where the highest VKE levels 
were observed on this cruise.

The right panel of Figure 5 shows the vertical velocity signal and noise levels for 
all dual-head profiles. The red bars show profile-averaged w(ocean) below 300 m. 
(LADCP vertical velocity measurements near the surface are often contaminated by 
biological effects.) The blue bars show the corresponding rms noise estimates, 
defined here as the DL-UL regression residuals scaled by 1/√2. Based on experience 
with other data sets, high-quality LADCP w profiles typically have residual noise 
levels in the range 0.003-0.006 m·s^(-1) . The P6 LADCP profiles clearly fit this 
criterion, too. The profile-averaged Vertical Kinetic Energy (VKE) levels observed 
during P6 ranged between 0.004 m·s^(-1)  and 0.015 m·s^(-1) , with the w  signal 
exceeding the noise level in all profiles. East of the EPR crest (station 188) 
profile-averaged VKE levels are generally lower than west of the EPR crest. A section 
plot of finescale VKE reveals, among other patterns, that the cross-EPR difference is 
due to a thick layer of elevated finescale VKE over the entire western EPR flank 
(Figure 1). Average EPR- profiles of finescale VKE, rescaled as dissipation using an 
empirical scaling (Thurnherr et al., GRL 2015), indicate that the differences are 
significant (Figure 6).

———————————————————————————————————-

(2) Only errors in the CTD package-velocity time series that persist over time scales 
    of minutes can give rise to vertical-velocity errors that are correlated between 
    the two ADCPs.


Figure 6: Average height-above-bottom profiles of finescale VKE from the eastern and 
          western of the EPR. VKE is rescaled as dissipation using an empirical 
          scaling (Thurnherr et al.,  GRL 2015). Error bars indicate 95% confidence 
          from bootstrapping.



CCHDO DATA PROCESSING NOTES

•  File Merge Carolina Berys
320620170820_do.pdf (download) #5aadd
Date: 2018-04-05
Current Status: merged

•  File Merge Jerry Kappa
320620170820_do.pdf (download) #cdc68
Date: 2018-04-05
Current Status: dataset

•  File Submission Jerry Kappa
320620170820_do.pdf (download) #cdc68
Date: 2018-04-05
Current Status: dataset
Notes
The pdf version of P06E_2017 is ready to go online.  It contains all of the 
PI-provided data reports as well as an LADCP QC report.

•  File Merge CCHSIO
320620170820_ct1.zip (download) #53589
Date: 2018-03-05
Current Status: merged

•  Update files from As Received to Dataset CCHSIO 
Date: 2018-03-05
Data Type: CTD
Action: Website Update
Note: 
    2017 320620170820 processing - CTD/merge - 
CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDXMISS,CTDBBP700RAW,CTDRINKO

2018-03-05

CCHSIO

Submission

filename             submitted by date       id  
-------------------- ------------ ---------- -----
320620170820_ct1.zip Joseph Gum   2017-11-20 13773

Changes
-------

320620170820_ct1.zip
        - This is a GO-SHIP Cruise:  CTDOXY flags are all uncalibrated
        - added cruise comments
        - removed DEPTH from header, as all values are -999
        - removed space before DATA header
        - changed SECT_ID description from nbp1707 to P06E
        - changed parameter name from CTDBACKSCATTER to CTDBBP700RAW (and 
          flag)
        - renamed files to match CCHDO format
        - RINKO: no stations have RINKO data:  data were submitted as 
          "0.0000,1"


Conversion
----------

file                    converted from       software               
----------------------- -------------------- -----------------------
320620170820_nc_ctd.zip 320620170820_ct1.zip hydro 0.8.2-48-g594e1cb


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

file                    stamp            
----------------------- --------------
320620170820_ct1.zip    20170305CCHSIO
320620170820_nc_ctd.zip 20170305CCHSIO

:Updated parameters: CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDBBP700RAW,CTDXMISS,CTDRINKO

opened in JOA with no apparent problems:
     320620170820_ct1.zip
     320620170820_nc_ctd.zip

opened in ODV with no apparent problems:
     320620170820_ct1.zip


					
•  File Online Carolina Berys
320620170820_ct1.zip (download) #53589
Date: 2017-11-20
Current Status: merged

•  File Submission Joseph Gum
320620170820_ct1.zip (download) #53589
Date: 2017-11-20
Current Status: merged

•  File Online Carolina Berys
320620170820_hy1.csv (download) #fe10d
Date: 2017-11-20
Current Status: unprocessed

•  File Online Carolina Berys
320620170820_do.txt (download) #67c9d
Date: 2017-11-20
Current Status: unprocessed

•  File Online Carolina Berys
320620170820_do.pdf (download) #5aadd
Date: 2017-11-20
Current Status: merged

•  File Submission Joseph Gum
320620170820_do.pdf (download) #5aadd
Date: 2017-11-20
Current Status: merged

•  File Submission Joseph Gum
320620170820_do.txt (download) #67c9d
Date: 2017-11-20
Current Status: unprocessed
•  File Submission Andrew Barna
320620170820_hy1.csv (download) #fe10d
Date: 2017-11-20
Current Status: unprocessed
Notes
These data can go online in the dataset, the cruise report will be submitted 
as soon the CTD/Bottle residual plots are updated.

