Cruise Report for the 2022 Reoccupation of P02E
***********************************************


GO-SHIP P02E 2022 Hydrographic Program
======================================


Summary
-------

The 2022 reoccupation of leg 2 of the GO-SHIP P02 hydrographic line,
RR2205 (Fig. 1), included 130 profiles collected on 89 stations using
a 36-bottle rosette. This includes a shallow test dip carried out on
the way to the first station of the section, reoccupation of 10
stations in the California Current region near the eastern end of the
section, as well as 1000-m casts for the BIO-GO-SHIP [1] program
collected on every third station. Additionally, four GO_BGC floats
with biochemical sensors were deployed. All floats were deployed on
stations with bio profiles, using an extended bottle sampling
schedule. Most of the P2 section, including the entire zonal component
along 30N, was collected with the target 30nm station spacing. For the
2022 occupation it was decided to follow mostly the original cross-
slope/-shelf approach to the Californian coast from the 1993 WOCE
cruises, which coincides with the southernmost repeat section of the
CalCOFI program. One of the stations had to be moved slightly because
of Navy operations in the area. Stations along this approach were
spaced less than 30nm apart, with particularly close spacing over the
steep continental slope. The rosette instruments included a pumped CTD
with dual temperature and conductivity lines, one with oxygen (SBE43),
a secondary separate RINKO oxygen sensor, fluorometer,
transmissometer, upward and downward-looking LADCPs, an underwater
vision profiler (UVP), two upward-looking and one downward-looking
Chi-POD. Niskin bottle samples were collected and analyzed for the
standard GO-SHIP set of parameters. Along all transits continuous
underway shipboard multibeam bathymetry, TSG, met and pCO2 data were
collected and a flow-through cytometer was run. The SADCP ran
continuously. The EK-80 ran during each cast. There was also discrete
underway sampling three times a day that included HPLC, POM, POC/N and
DNA/RNA. See individual sections for further detail.

   [image]Red rings: Bio stations. Green: stations of the partial re-
   occupation of the CCS with two full profiles (bio stations also
   have 2 bio profiles).

In spite of the failure of the primary winch after the first deep
profile there were no significant delays due to technical problems.
Therefore, and also because of the perfect weather and sea state
prevailing during the cruise, the full science plan could be carried
out, including an optional partial second crossing of the California
Current system. Preliminary results include observations of strong
climate-change trends in the abyssal temperatures and salinities in
the subtropical gyre since the previous occupation of P02 in 2013, as
well as the mapping of a large plume of SF6 in the eastern part of the
section, that is likely caused by the propulsion system of a
particular type of Navy torpedoes.


Programs and Principal Investigators
------------------------------------

+---------------------------+---------------------------+---------------------------+---------------------------+
| Program                   | Affiliation               | Principal Investigator    | Email                     |
|===========================|===========================|===========================|===========================|
| BGC Floats                | *SIO*                     | Lynne Talley              | ltalley@ucsd.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| C13 & C14                 | *UW*, *WHOI*              | Rolf Sonnerup, Roberta    | rolf@uw.edu,              |
|                           |                           | Hansman                   | rhansman@whoi.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *CFCs*, *SF6*             | *UT*                      | Dong-Ha Min               | dongha@austin.utexas.edu  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Chipods                   | *OSU*                     | Jonathan Nash             | nash@coas.oregonstate.edu |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *CTDO* Data, Salinity,    | *UCSD*, *SIO*             | Susan Becker, Todd Martz  | sbecker@ucsd.edu,         |
| Nutrients, Dissolved O_2  |                           |                           | trmartz@ucsd.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Underway pCO_2            | *PMEL*, *NOAA*            | Simone Alin               | simone.r.alin@noaa.gov    |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *DOC*, *TDN*              | *UCSB*                    | Craig Carlson             | craig_carlson@ucsb.edu    |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Lowered *ADCP*            | *LDEO*                    | Andreas Thurnherr         | ant@ldeo.columbia.edu     |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *POC*, *HPLC*             | *UCSD*                    | Adam Martiny              | amartiny@uci.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Shipboard *ADCP*          | *UH*                      | Julia Hummon              | hummon@hawaii.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Total Alkalinity, pH      | *SIO*                     | Andrew Dickson            | adickson@ucsd.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Total CO_2 (DIC)          | *PMEL*, *NOAA*            | Richard Feely             | richard.a.feely@noaa.gov  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Transmissometer           | *UCI*, *OSU*              | Adam Martiny, Jason Graff | amartiny@uci.edu, jason.  |
|                           |                           |                           | graff@oregonstate.edu     |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *UVP*-5                   | *UAF*                     | Andrew McDonnell          | amcdonnell@alaska.edu     |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Viral Abundance           | *UoE*                     | Ben Temperton             | b.temperton@exeter.ac.uk  |
+---------------------------+---------------------------+---------------------------+---------------------------+


Science Team and Responsibilities
---------------------------------

+---------------------------+---------------------------+---------------------------+---------------------------+
| Duty                      | Name                      | Affiliation               | Email Address             |
|===========================|===========================|===========================|===========================|
| Chief Scientist           | Andreas Thurnherr         | *LDEO*                    | ant@ldeo.columbia.edu     |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Co-Chief Scientist        | Sebastien Bigorre         | *WHOI*                    | sbigorre@whoi.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CTD Watchstander          | Bailey Amos               | *TAMU*                    | barmos@tamu.edu           |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CTD Watchstander          | Turner Johnson            | *UCSD*                    | turner.e.johnson@gmail.c  |
|                           |                           |                           | om                        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CTD Watchstander          | Alyssa Schultz            | *TAMU*                    | aschultz@tamu.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CTD Watchstander          | Dylan Shafer              | *UCSD*                    | dshafer@ucsd.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Nutrients                 | John Ballard              | *UCSD* *ODF*              | jrballard@ucsd.edu        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Nutrients                 | Tania Leung               | *UCSD* *ODF*              | taleung@ucsd.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CTDO Processing, Database | Michael Kovatch           | *UCSD* *ODF*              | mkovatch@ucsd.edu         |
| Management                |                           |                           |                           |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Salts, Marine Technician  | Gabriel Matthias          | *TAMU*                    | EscaMTS@gmail.com         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Salts                     | Laurette Roy              | *TAMU*                    | laurette.m.roy@gmail.com  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Marine Technician         | Mason Schettig            | *UCSD*                    | mschettig@ucsd.edu        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CR Technician             | Howell Johnson            | *UCSD*                    | hkjohnson@ucsd.edu        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| CR Technician             | Maya Thompson             | *UCSD*                    | m6thompson@ucsd.edu       |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Dissolved O_2             | Elisa Aitoro              | *UCSD* *ODF*              | eaitoro@ucsd.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Dissolved O_2             | Robert “Ben” Freiberger   | *UCSD* *ODF*              | rfreiberger@ucsd.edu      |
+---------------------------+---------------------------+---------------------------+---------------------------+
| LADCP                     | Lilian Dove               | *Caltech*                 | dove@caltech.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Bio/Imaging               | Skylar Gerace             | *UCI*                     | sgerace@uci.edu           |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Bio/Genomics              | Sydney Lewis              | *UH*                      | sydneyl7@hawaii.edu       |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Total Alkalinity          | Daniela Nestory           | *UCSD*                    | dnestory@ucsd.edu         |
+---------------------------+---------------------------+---------------------------+---------------------------+
| Total Alkalinity          | Sidney Wayne              | *UCSD*                    | sidneyelisawayne@gmail.c  |
|                           |                           |                           | om                        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| pH                        | Brison Grey               | *U Miami*                 | bjg136@miami.edu          |
+---------------------------+---------------------------+---------------------------+---------------------------+
| pH                        | Albert Ortiz              | *RSMAS*                   | albert.ortiz@rsmas.miami  |
|                           |                           |                           | .edu                      |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *DIC*                     | Andrew Collins            | *NOAA*                    | djgreel1@gmail.com        |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *DIC*                     | Charles Featherstone      | *NOAA*                    | charles.featherstone@noa  |
|                           |                           |                           | a.gov                     |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *CFCs*                    | David Cooper              | *UT*                      | davidcooper59@gmail.com   |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *CFCs*                    | Carol Gonzalez            | *UT*                      | carolgonzalez@utexas.edu  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *CFCs*                    | Matthew Varas             | *TAMU*                    | mvaras@tamu.edu           |
+---------------------------+---------------------------+---------------------------+---------------------------+
| *DOC*                     | Michelle Michelsen        | *UOE*                     | a.tinari@umiami.edu       |
+---------------------------+---------------------------+---------------------------+---------------------------+

[1] Throughout “core” refers to the regular (GO-SHIP levels 1-2)
    sampling and “bio” refers to the biology sampling performed by the
    Bio GO-SHIP team. See Bio section of this report for the details
    on the bio sampling.


Cruise Narrative
================

After mobilization on June 12 the R/V Roger Revelle left Honolulu port
around 1900 and headed toward the final station of leg one (station
117), which was to be re-occupied as the first station of leg 2.
Before reaching the first station, shortly after noon on June 13 two
shallow test dips of the CTD rosette were carried out along the way
(station 901) to provide training for the student watch standers, to
verify that all instruments are working and to provide the new cruise
participants the opportunity to become familiar with the CTD cast
logistics and sampling. After successful completion the vessel
proceeded to the first station of the P2 section.

While the first CTD cast of the P2 section (station 118) was collected
without problems, soon after the CTD was on deck it was discovered
that the arm of the primary winch system (CAST6) was leaking hydraulic
oil, which took it out of commission for the remainder of the cruise.
The first two attempts at collecting a profile with the backup winch
(DESH5) had to be aborted due to communications problems between the
fish and the deck box. After solving the underlying problem by
removing 100m of CTD wire the system performed well for the remainder
of the cruise. Due to necessity of training new winch operators, many
of the profiles collected during the first week had winch stops during
the downcasts, usually near 100m but sometimes also about 200m above
the sea bed. Additionally a conservative wire tension limit of 4000lbs
prevented winch speeds greater than 20m/min during the initial parts
of the upcasts until it was determined that the slow speed did not
actually decrease wire tension significantly. Also during the first
week there were many Niskin bottle problems including several broken
lanyards and one bottle that was lost entirely, presumably because it
inadvertently closed during the deployment with air trapped inside.
The bottle problems persisted until most of the lanyards were
replaced.

Progressing eastward along 30N stations were occupied every 30nm. The
2022 re-occupation of P2 is the first US GO-SHIP cruise carried out
with additional sampling time allocated to the recently funded Bio GO-
SHIP program. Beginning on station 120 every third full-depth CTD cast
was therefore preceded by a “bio cast” to 1000m, where water was
collected for a variety of biologically relevant parameters, some of
which require large sampling volumes. Samples of the same parameters
were also collected several times per day, guided by solar day time,
using the flow-through system fed by a diaphragm pump (instead of the
usual impeller pump) in order to preserve planktonic particles for
sampling. Additionally, while on station the multifrequency EK80 sonar
system was used to record vertical distributions of backscattering
organisms in the water column.

Profiles 118-142 were collected inside the subtropical gyre,
characterized by warm sea surface temperatures and generally low
particle loads throughout the water column, as indicated by low levels
of acoustic backscatter in the LADCP data. After an oblique crossing
of the subtropical front on stations 143-153 the vessel entered waters
affected by the California Current System, as indicated by a salinity
minimum near 200m and colder sea surface temperatures (Fig. 1). The
cruise track continued eastward along 30N to 123W (station 185) where
it turned northeastward to follow the original WOCE line from 1993
across the continental slope, which is also sampled as part of the
CalCOFI program as line 93.3. (A request for a somewhat more northerly
crossing of the continental slope along CalCOFI line 90, which has
been sampled continuously with gliders since 2007, was denied by the
Navy.) Between 119W and 120W the cruise crossed the steep continental
slope where station spacing was reduced considerably (min 0.98 nm) in
order to avoid bottom-depth steps greater than 500m between adjacent
profiles. The track continued on the shelf along the same heading up
to 118:45 W where a northward dog-leg was required in order to avoid
Navy operations in the FLETA HOT area. As a result, station 200
planned at 32:28.44 N 118:27.18 W  was shifted northwestward by the
Navy to 32:37.33 N 118:40.68 W, from where the remaining stations were
collected in final zonal section following the final approach to San
Diego carried out during the 2004 (CLIVAR) and 2013 (GO-SHIP)
occupations of the P2 repeat-hydrography section.

Due to a lack of weather and significant technical delays the vessel
arrived at the easternmost station (#204) several days before the
scheduled end of the cruise, even though additional sampling time
between CTD profiles had been added beginning at station 186 in order
to allow for a more complete sampling of the Niskin bottles by the CFC
and carbon parameter analysis groups. The available time was used to
re-sample part of the California Current System, starting at station
191 and working westward until station 186.

During the cruise, four BGC Argo Floats were deployed along the P2
section near 159W, 145 W, 131 W and 120 W, all without problems. All
four floats returned their first profiles within a few hours of
deployment, indicating that the sensors were working correctly.

The main purpose of the GO-SHIP repeat-hydrography program is to
monitor the full depth ocean for long-term changes, includes the
effects of global warming. Based on a subsection along 30 N between
160 and 145 W in the subtropical gyre, the upper ocean has warmed
considerably compared to the base-line measurements collected during
WOCE in 1993 with most of the change occurring between 2004 and 2013
(Fig. 2). In contrast to the upper ocean, the temperature at depths
below 4000m has been increasing consistently since 1993, with the
bottom-intensified warming rate increasing with time (Fig. 3). This
abyssal warming is likely the result of a reduction in the volume of
bottom water. Based on bottle salinities it appears that the abyssal
warming has been accompanied by a freshening (Fig. 4) but it must be
noted that the differences are smaller than the uncertainty of the
salinity calibration, which include differences between different
batches of standard sea water. CTD salinity differences compared to
1993 and 2004 are dominated by measurement artifacts (not shown) but
the apparent abyssal differences between the 2013 and 2022 occupations
of P2 are consistent with a freshening accompanying the recent warming
of abyssal waters (Fig. 5).

A variety of tracers are measured as part of GO-SHIP, including SF6
(Sulfur Hexafluoride). On two stations on the California shelf (200
and 203) large concentrations of SF6 peaking at the seabed were
observed (Fig. 6). The near-bottom SF6 concentration on station 200
peaks at more than twice atmospheric values, implying a source on or
near the seabed. A google search revealed that SF6 is used in the
propulsion system of Navy Mark 50 torpedoes making this the most
likely source. While the highest SF6 concentrations were observed on
the shelf, anomalies near 1000m most likely related to this source
were observed several hundreds of miles off shore. A plan to re-sample
station 200 at the end of the cruise in order to verify persistence of
the signal there had to be aborted because the SF6 analysis system
broke upon arriving at the station and repair was not feasible within
the available time.

   [image]Isopycnally mapped upper-ocean salinity along 30N.

   [image]Upper-ocean profiles of average temperature differences
   between 160 and 145W compared to the WOCE base-line hydrography
   collected in 1993.

   [image]Abyssal-ocean profiles of average temperature differences
   between 160 and 145W compared to the WOCE base-line hydrography
   collected in 1993.

   [image]Profiles of average salinity differences from bottle samples
   between 160 and 145W compared to the CLIVAR hydrography collected
   in 2004. (The 1993 WOCE bottle salinities are not consistent with
   the apparent freshening trend.)

   [image]Abyssal-ocean profiles of average salinity differences from
   CTD measurements between 160 and 145W compared to the CLIVAR
   hydrography collected in 2013. (The CTD salinities collected in
   1993 and 2004 are not consistent with the apparent freshening
   trend.)

   [image]Profiles of sulfur hexafluoride (SF6) collected on two
   stations on the California shelf.


Atmospheric Conditions
======================

Between the cruise departure on June 13 and until about June 22,
weather conditions were typical of the Trade Winds regime, driven by
the anticyclonic atmospheric circulation around the subtropical high
pressure system (North Pacific High) that was centered in the
northeastern Pacific. Meteorological conditions measured onboard R/V
Revelle included easterly winds around 15 knots, while sea surface and
air temperature (26.5 ºC and 24.5 ºC respectively at the start of the
cruise) gradually decreased as we steamed eastward. We also observed
predominantly cumulus clouds during the day.

Between June 26 and 28, measurements from the ship sensors indicated a
gradual increase in atmospheric pressure and wind speed values falling
down to 3 m/s. At that time, the ship’s track entered the southern
edge of the North Pacific High. The low wind conditions combined with
high daily shortwave radiation and reduced cloud cover led to
intensified heating of the upper ocean as seen in higher sea surface
temperature values. The calmest sea state  of the cruise were observed
during this period.

In early July, as the ship was entering its southeastern corner, the
North Pacific High started moving west (as seen in weather forecast
imagery from the www.PassageWeather.com, and kindly provided by
Shuwen, the co-chief scientist from leg 1). The weather conditions we
experienced were not tropical anymore, as the wind became more
northerly while air relative humidity increased and stratus clouds
became predominant. Sea surface and air temperature dropped to their
coldest values of the cruise (17.5 ºC and 15 ºC respectively) near
July 10. As the ship entered the shelf off California on July 12,
warmer sea surface and air temperatures increased again.

   [image]Pressure on June 22 2022 from the Global Forecast System
   (GFS) weather forecast model at the National Centers for
   Environmental Prediction (NCEP). Imagery provided from
   www.PassageWeather.com. Track of R/V Revelle during leg 2 (red
   line). Ship’s location on June 22 (pink star) is to the southwest
   of the North Pacific High anticyclone.

   [image]Same as figure above, but for July 4 2022. The North Pacific
   High has moved west.

   [image]Meteorological measurements from R/V Revelle during GOSHIP
   P02 leg 2 in 2022, shown as function of longitude (top subplot) and
   time (bottom subplot). Air temperature  (top left), sea surface
   temperature (top right), wind speed (bottom left), wind speed
   (bottom right).


CTD and Rosette Setup
=====================

For P02E-2022 a *SIO* *STS* 36-place yellow rosette and bottles were
used. The rosette was sent to Guam in early January, 2022 for P02W.
The rosette and bottles were built before P06 2017, making this the
fourteenth time this package has been deployed. A steel bridle was
added to the top of the rosette to adapt to the winch head. The
bottles were made with new PVC, with new non-baked o-rings and
electro-polished steel springs. Springs within the Bullister-style
Niskin bottles were electropolished stainless steel. Bottle lanyards
were made from 300-pound monofilament. No sample contamination has
been noticed by the change in o-rings and springs. The package used on
P02E-2022 weighs roughly 1500 lbs in air without water and 2350 lbs in
air with water. The package used on P02E-2022 weighs roughly 950 lbs
in water. In addition to the standard *CTDO* package on GO-SHIP
cruises three chipods, two *LADCP*, and one *UVP* were mounted on the
rosette.

During the cruise we encountered a handful of problems, most notably
noise between the primary and secondary CTD lines. We describe all of
the above in more detail in the sections below.


Underwater Sampling Package
---------------------------

CTDO/rosette/LADCP/UVP/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 10.6 L.
Underwater electronic components primarily consisted of a SeaBird
Electronics housing unit with Paroscientific pressure sensor with dual
plumbed lines where each line has a pump, temperature sensor,
conductivity sensor, and exhaust line. A SeaBird Electronics membrane
oxygen sensor was mounted on the “primary” line. A reference
thermometer, RINKO oxygen optode, transmissometer, chlorophyll-a
fluorometer, and altimeter were also mounted on the rosette. Chipod,
LADCP, and UVP instruments were deployed with the CTD/rosette package
and their use is outlined in sections of this document specific to
their titled analysis.

CTD and cage were horizontally mounted at the bottom of the rosette
frame, located below the carousel for all stations. The temperature,
conductivity, dissolved oxygen, respective pumps and exhaust tubing
was mounted to the CTD and cage housing as recommended by SBE. The
reference temperature sensor was mounted between the primary and
secondary temperature sensors at the same level as the intakes for the
pumped temperature sensors. The transmissometer was mounted
horizontally on the lower LADCP brace with hose clamps, avoiding shiny
metal inside that would introduce noise in the signal. The hose clamps
for the transmissometer were covered in black electrical tape. The
oxygen optode, fluorometer, and altimeter were mounted vertically
inside the bottom ring of the rosette frames, with nothing obstructing
their line of sight. One 300 KHz bi-directional Broadband LADCP (RDI)
unit was mounted vertically on the bottom side of the frame. Another
300 KHz bi-directional Broadband LADCP (RDI) unit was mounted
vertically on the top side of the frame. The LADCP battery pack was
also mounted on the bottom of the frame. The LADCP and LADCP battery
pack were mounted near (90°) each other at the beginning of the
cruise. Imagining the bow of the ship to be north, the LADCP battery
was mounted on the south side of the rosette, the up/down LADCPs were
on the west side, the UVP on the east, and CTD mounted to the north
(Figure 1).


(*) LADCP was swapped for the partial re-occupation of the California Current System following station 205.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+------------------+------------------+------------------+------------------+------------------+------------------+
| Equipment        | Model            | S/N              | Cal Date         | Stations         | Group            |
|==================|==================|==================|==================|==================|==================|
| Rosette          | 36-place         | Yellow           | –                | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| CTD              | SBE9+            | 1281             | –                | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Pressure Sensor  | Digiquartz       | 136428           | Dec 7, 2021      | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Primary          | SBE3+            | 36049            | Mar 17, 2022     | 118-205          | *STS*/*ODF*      |
| Temperature      |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Primary          | SBE4C            | 43578            | Mar 22, 2022     | 118-205          | *STS*/*ODF*      |
| Conductivity     |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Primary Pump     | SBE5             | 51892            | –                | 118-196          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Primary Pump     | SBE5             | 51781            | –                | 197-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Secondary        | SBE3+            | 34138            | Mar 17, 2022     | 118-205          | *STS*/*ODF*      |
| Temperature      |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Secondary        | SBE4C            | 42569            | Mar 17, 2022     | 118-205          | *STS*/*ODF*      |
| Conductivity     |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Secondary Pump   | SBE5             | 53626            | –                | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Transmissometer  | Cstar            | 1873DR           | Jan 5, 2022      | 118-205          | *TAMU*           |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Fluorometer      | WetLabs ECO-FL-  | 4334             | –                | 118-205          | *STS*/*ODF*      |
| Chlorophyll      | RTD              |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Dissolved Oxygen | SBE43            | 431508           | Oct 8, 2021      | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Oxygen Optode    | JFE Advantech    | 0251             | Apr 7, 2017      | 118-205          | *ODF*            |
|                  | Rinko-III        |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Reference        | SBE35            | 0105             | Mar 15, 2022     | 118-205          | *STS*/*ODF*      |
| Temperature      |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Carousel         | SBE32            | 1178             | –                | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Altimeter        | Valeport 500     | 53821            | –                | 118-205          | *STS*/*ODF*      |
+------------------+------------------+------------------+------------------+------------------+------------------+
| UVP              | –                | 201              | –                | 118-205          | *UAF*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| LADCP (uplooker) | WHM300kHZ        | 12734            |                  | 118-205          | *LDEO*           |
+------------------+------------------+------------------+------------------+------------------+------------------+
| LADCP            | WHM300kHZ        | 3441             |                  | 118-205          | *LDEO*           |
| (downlooker)     |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| LADCP            | WHM300kHZ        | 24477            |                  | 186-191(*)       | *LDEO*           |
| (downlooker)     |                  |                  |                  |                  |                  |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2014 Ti44-8      | –                | 118-162          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2013 TI44-12     | –                | 118-162          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2032 Ti44-15     | –                | 118-162          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2025 Ti44-7      | –                | 163-205          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2017 TI44-6      | –                | 163-205          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+
| Chipods          | Chipod           | 2027 Ti44-?      | –                | 163-205          | *OSU*            |
+------------------+------------------+------------------+------------------+------------------+------------------+

   [image]Package sensor setup from south (for all rosette figures,
   orientation is defined as north being toward the bow).

   [image]Package sensor setup from east.

   [image]Package sensor setup from north.

   [image]Package setup from southwest, from left to right: CTD cage,
   downward facing chipod, downward facing LADCP, transmissometer bar.

   [image]Package setup from southwest, from left to right:
   (Foreground) ECO fluorometer, UVP, RINKO, altimeter.

   [image]Package setup from west.

   [image]Package setup from west, top view.


Winch and Deployment
--------------------

The CAST6 winch and deployment system was used for the two test
stations and the first core station. After a hydraulic oil leak was
found, the rosette was switched to the DESH5 winch for remaining
stations. The rosette system was suspended from a UNOLS-standard
three-conductor 0.322” electro-mechanical sea cable. The sea cable was
terminated with an Evergrip (primary), Guy Grip (secondary), and set
of Crosby Clips (tertiary). No electrical issues occurred on P02E.

The deck watch prepared the rosette 10-30 minutes prior to each cast.
The bottles were cocked and all valves, vents, and lanyards were
checked for proper orientation. Any biofouling noted was cleaned off
the outside of the rosette before the next cast, and the inside of the
bottles were checked for biofouling and sprayed down. The LADCP
technician would check for LADCP battery charge, prepare instrument
for data acquisition, and disconnect cables. The LADCP technician also
dealt with the UVP, disconnecting cables at the same time. Once
stopped on station, the Marine Technician would check the sea state
prior to cast and decide if conditions were acceptable for deployment.
The rosette was moved from the sampling bay out to the deck using the
*Revelle’s* tugger-driven cart while using the CAST6. Following the
switch to the DESH5, the rosette was moved from the sampling bay using
a pallet jack. Once on deck, sea cable slack was pulled up by the
winch operator. CTD watch standers would then turn on the deckbox and
begin data acquistion, and the cast would begin. For casts performed
with the DESH5, members of the science party used taglines to assist
with deployment and recovery. Recovering the package at the end of the
deployment was the reverse of launching. Once rolled back into the
sampling bay, a technician secured the cart to the deck using
additional ratchet straps. The carousel was rinsed and sensors were
cleaned (as described below) after every cast, and then samplers were
allowed to begin collecting water.


Maintenance and Calibrations
----------------------------

During P02E-2022 routine maintenance was done to the rosette to ensure
quality of the science done. Actions taken included rinsing all
electrical instruments on the rosette down with fresh water after each
cast and adjusting hose clamps and guide rings as needed such that
lanyards had appropriate tension. Care was taken not to rinse the
spigots and other parts of the bottle that might be touched by
samplers in order to not contaminate the samples. After each cast,
syringes of fresh water were connected to the plumbed lines to rinse
the sensors and allow them to soak between casts. The rosette was
routinely examined for valve and o-ring leaks, which were maintained
as needed. SBE35RT temperature data was routinely downloaded each day.

Every 20 stations, the transmissometer windows were cleaned and on
deck blocked and un-blocked voltage readings were recorded prior to
the cast. The transmissometer was also calibrated before the start and
after the end of science operations.

“Dark” bio casts were performed periodically, where the fluorometer
sensor face was covered with black electrical tape. Dark casts allowed
for background noise to be measured as function of depth, since the
fluorometer would not measure any signal.


Logs
----

In port: Preparation of the CTD and rosette was minimal as it had the
same setup as P02W 2022, which had just been completed. Integrity
checks on the rosette, such as checking lanyard angles, o-ring and
lanyard replacement, and spigot movement were performed during fueling
before transit to test station. We are using a new mounting system for
the downward looking LADCP which has the LADCP clamped facing inward
instead of outward, which will cause problems if we need to change
that LADCP in rough weather.

June 14, 2022

90101 - Test bio cast to 1000 m. While cocking bottles, #19 top inner-
lanyard came untied and suddenly released the spring tension. Deferred
fixing lanyard until during transit to first station to save time.

90102 - Test core cast to 1000 m. No issues of note besides missing
bottle #19.

June 16, 2022

11801 - Bottle #19 leaking from bottom o-ring; replacement inner-
lanyard likely too long causing spring to be under-tensioned. CAST6
hydro boom found to be leaking hydraulic fluid after cast; swapping
rosette to DESH5, which will require taglines for deployment and
recovery, manual winch payout, and sampling out on deck instead of the
hangar.

11901 - Bio cast aborted at 40 m due to modulo errors and RS-232 comms
failure. Termination is bad and water was intruding under pressure;
cut off 10 m of cable and there was water inside. Before next cast,
deck was scrubbed with Simple Green to remove oil slick. Sensors were
capped, bottles were closed, and rosette cover put on before
scrubbing.

11902 - Bio cast aborted again at 40 m due to RS-232 comms failure.
Cut off 100 m of cable and conductor wires had much less corrosion.
Reterminated and attempting another cast.

11903 - Bio cast successful to 1000 m and back.

11904 - Bottle #34 outer lanyard broke from abrasion. Bottle #19
inner-lanyard swapped after cast.

June 17, 2022

12001 - Bottle #17 top knot came untied and released spring tension
(same as 90101 bottle #19) during prep; cast performed with capless
bottle #17. Bottle #19 leaking again upon recovery; swapped in a new
Niskin bottle.

12101 - Swapped in new Niskin bottles for #17 and #19 before cast.
Rosette came back to surface missing bottle #30. Bottle #17 leaking
from bottom on recovery after opening air vent; outer lanyard may be
too tight and preventing bottle from staying well sealed.

12201 - Bottle #19 swapped out and bottle #30 replaced, both are
spares from Revelle’s stockpile. Bio cast + float

12202 - Bottle #5 closed on ADCP cable and did not seal; was not
sampled. Bottle #19 has low temp, likely closed early. Adjusted bottle
downward before deployment such that it had sufficient tension when
cocked without being overtensioned after being fired.

June 18, 2022

12301 - Bottle #19 draw temperature a little low; lanyard was a little
loose and likely closed itself during downcast. Tightened up before
next cast.

12401 - Bottle #11 did not fire, trigger is sticky.

12501 - Dark bio cast; fluorometer was not fully taped over and still
had some response.

June 19, 2022

12502 - No issues noted.

12601 - Chipod #12 was flooded, swapped with #11. Bottle #10 lanyard
was routed around neighboring standoff and bottom cap was stuck open;
no water at all in bottle.

12701 - Lowered bottle #6 before cast, top handle was bumping into
frame.

12801 - Bio cast; No issues noted.

12802 - No issues noted.

June 20, 2022

12901 - Bottle #30 had small leak; top bottle mating surface has a
gouge in it, swapping in the original bottle #17. Replaced spigot on
bottle #12.

13001 - No issues noted.

13101 - Bio cast; No issues noted.

13102 - Bottle #33 did not fire. Bottles #15 and 16 had vent caps left
open. Bottle #28 CFC syringe broke so will not have a sample

June 21, 2022

13201 - No issues noted.

13301 - Bottle #2 exceptionally warm; check other params.

13401 - Bio cast; No issues noted.

13402 - Bottle top caps hit with hook during recovery. Oxygen data
makes it appear to be #18 and 19.

June 22, 2022

13501 - No issues noted.

13601 - Altimeter a little spiky at bottom, could be ground
composition causing bad returns.

13701 - Bio cast; No issues noted.

13702 - 1 modulo error around ~5700 m. Mistripped 8 bottles (27-34) at
same depth, keyboard/user error.

13703 - Re-cast to 350 m. Bottle #10 bottom cap was left uncocked,
flag bad.

June 23, 2022

13801 - Lowered bottles #17 and 19 before cast to prevent issue of
hitting bottle tops with gaffing hooks.

13901 - Change out top o-rings and air vents on bottle #4 and 28
before cast.

14001 - Bio cast; No issues noted.

14002 - Bottle #17 top inner-cap lanyard broken at depth, came back
missing spring.

June 24, 2022

14101 - No issues noted.

14201 - No issues noted.

14301 - Bio cast; No issues noted.

14302 - Outer lanyards on bottles #34 and 35 changed before due to
visible chafing.

June 25, 2022

14401 - Noisy T/C residuals during soak, likely due to prop wash
and/or the soak being very near the thermocline.

14501 - New spigot on bottle #1. Swapped clear monofilament on top cap
of bottle #17 for newer, blue mono. New inner-cap lanyards on bottles
#11, 22, and 32 due to slightly abrasion. Zeroes in SBE3+ primary are
back

14601 - Bio cast; No issues noted.

14602 - Bottle #33 did not fire. Salinity bottle #9 from box B was
chipped and replace after cast.

June 26, 2022

14701 - No issues noted.

14801 - Swap cables on T1 and T2 to see if zero frequency issue
follows cable. Zeroes stayed on same sensor (T1), issue believed to be
the SBE9+ (CTD).

14901 - Bio cast; No issues noted.

14902 - No issues noted.

15001 - No issues noted.

June 27, 2022

15101 - No issues noted.

15201 - Bio cast; No issues noted.

15202 - No issues noted.

15301 - No issues noted.

June 28, 2022

15401 - Bottle #14 leaking again, Gabe says PVC weld failing. Swapping
in one from backup rosette.

15501 - Bio cast; No issues noted.

15502 - No issues noted.

15601 - Rusty spring found in bottle #14, replaced after cast.

15701 - RS-232 comms timeout error mid-cast @ 3870m

June 29, 2022

15801 - No issues noted.

15802 - No issues noted.

15901 - Bottle #6 leaking

16001 - Bottle #6 leaking again, changed bottom o-ring.

June 30, 2022

16101 - No issues noted.

16102 - Bottle #6 leaking, velcro stuck in cap.

16201 - No issues noted.

16301 - Swapped all chipod pressure cases before cast. Taglines
wrapped around spigots during deployment.

16401 - Dark bio cast. CFCs sampled bottle #25 but syringe was left
open and leaked.

July 1, 2022

16402 - RS-232 comms timeout error at 1650m, data acquisition was not
interrupted.

16501 - Changed o-ring on bottle #19. O2 resampled bottle #31

16601 - Bottle #4 leaking; swap air vent and top cap o-rings.

16701 - No issues noted.

16702 - No issues noted.

July 2, 2022

16801 - No issues noted.

16901 - No issues noted.

17001 - Bio float; No issues noted.

17002 - No issues noted.

July 3, 2022

17101 - No issues noted.

17201 - Adjusted guide rings on bottles 2 and 22 to tighten up bottom
handles.

17301 - Bio cast; No issues noted.

17302 - SeaSave stopped responding during bottle stop; mouse still
working; fixed itself after 30s or so.

17401 - RS-232 comms timeout error at 750m

July 4, 2022

17501 - No issues noted.

17601 - Bio cast + sampling for “planktoscope”

17602 - No issues noted.

17701 - No issues noted.

17801 - No issues noted.

July 5, 2022

17901 - Bio cast; No issues noted.

17902 - No issues noted.

18001 - Salts sampled by multiple people, bottles in box out of order.

18101 - No issues noted.

18201 - Bio cast; No issues noted.

July 6, 2022

18202 - No issues noted.

18301 - Ship lost power during 20m soak; aborted and recovered.

18302 - No issues noted.

18401 - No issues noted.

18501 - Bio cast; No issues noted.

July 7, 2022

18601 - No issues noted.

18701 - No issues noted.

18801 - Bio cast; No issues noted.

July 8, 2022

18802 - No issues noted.

18901 - No issues noted.

19001 - No issues noted.

19101 - Bio cast, float; No issues noted.

July 9, 2022

19102 - No issues noted.

19201 - No issues noted.

19301 - Primary T/C/O extremely spiky at 300m on upcast, most likely
clogged. Upon recovery, primary plumbing was opaque with biofouling.
Tubes removed and cleaned; re-assembled plumbing and cleaned sensor
line with with 1% Triton-X, flush with fresh water. Secondary line
plumbing was loose from C to pump, slid pump forward to close gap.

July 10, 2022

19401 - Test cast to 100m to make sure plumbing is okay.

19402 - Bio cast; No issues noted.

19403 - Aborted, UVP shunt not removed

19404 - No issues noted.

19501 - No issues noted.

19601 - Primary pump problems again near bottom, no bio-fouling upon
recovery. Top o-ring on impeller was broken with 1/3 fully missing;
swapped in 05-1781.

19701 - Test cast to 100m to check new pump. Primary/secondary
residuals still poor over full cast.

19702 - Swapped y-cable and rotated pump to have exhaust at 45º angle.
Deck to ensure pump flow, looks fine. Test cast turned bio cast.

19703 - No issues noted.

July 11, 2022

19801 - Salt bottle #5 from box S dropped during sampling and broken;
replaced with spare.

19901 - No issues noted.

20001 - Bio cast; No issues noted.

20002 - No issues noted.

July 12, 2022

20101 - RS-232 comms failure on upcast at ~400m, modulo error and
overflow light on deckbox. Power cycled deckbox, restarted acquisition
in 20101_2 file without issue for remainder of cast.

20201 - No issues noted.

20301 - Bio cast; No issues noted.

20302 - Bottle #3 bottom cap found unclipped during recovery, likely
uncocked during deployment.

20401 - No issues noted.

July 13, 2022

19103 - Dark bio cast; No issues noted.

19104 - No issues noted.

19002 - No issues noted.

July 14, 2022

18902 - Salt bottle #33 from box S broken during sampling.

18803 - Bio cast; No issues noted.

18804 - No issues noted.

18702 - No issues noted.

18602 - No issues noted.


Sensor Problems
---------------

*Biofouling*: The SBE5 pump on the primary T/C/O line showed signs of
bad flow starting during the upcast on 19301 (Fig. 1). Upon recovery,
plumbing tubes were opaque with biofouling. Plumbing was disassembled
and cleaned with 1% Triton-X. The lines were then re-attached to the
T/C/O sensors and the entire line was flushed with the same 1%
Triton-X and then flushed with fresh water.

   [image]Biofouling/clog evident at 315m due to oxygen decrease and
   staying constant during upcast.

*Pump problems*: The primary pump became an issue again on cast 19601
with what appeared to possibly be another clog. Upon recovery, no
biofouling was found so the pump was removed and inspected. The top
o-ring on the impeller was broken and assumed to be the cause. Pump
5-1781 was swapped in and deployed for a test cast. T/C residuals
between primary and secondary line were erratic during test cast to
100m. Rosette was recovered and the pump exhaust was re-oriented to
45º and the y-cable was swapped. Deck test and test cast ensured pump
was now working fine.


CTDO and Hydrographic Analysis
==============================

PIs
   * Todd Martz (SIO)

   * Susan Becker (SIO)

Technicians
   * Mike Kovatch (SIO)


CTDO and Bottle Data Acquisition
--------------------------------

The CTD data acquisition system consisted of an SBE-11+ (V1) deck unit
and a networked generic PC workstation running Windows 10. SBE
SeaSave7 v.7.26.7.121 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
log for each attempted cast containing a description of each
deployment event and any problems encountered.

Once the deck watch had deployed the rosette, the winch operator would
lower it to 20 meters. The CTD sensor pumps were configured to start
10 seconds after the primary conductivity cell reports salt water in
the cell. The UVP was configured to turn on after it had descended to
20 meters, and was identified as on when the voltages went above a
certain range. The CWO checked the CTD data for proper sensor
operation, waited for sensors to stabilize, waited for the UVP to turn
on, and then 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 60 m/min after 100 m depending on depth, 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 30 m/min 100 m
from the bottom, and 20 m/min 50 m 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 full upcast, the winch operator was
directed to stop the winch at up to 36 predetermined sampling
pressures. During upcasts specific to bio sampling, the winch operator
was directed to stop at up to 21 predetermined sampling pressures.
These standard depths were staggered every station using 3 sampling
schemes. The CTD CWO waited a minimum of 30 seconds prior to tripping
sample bottles, to ensure package had shed its wake (the effect of
bottle stop time is discussed further at the end of Conductivity
Analysis). 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 13 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
recorded the depths bottles were tripped and correspondence between
rosette bottles and analytical samples drawn.

The CTD sensors were rinsed after every cast using syringes of fresh
water 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.


CTDO Data Processing
--------------------

Shipboard CTD data processing was performed after deployment using
SIO/ODF CTD processing software “ctdcal” v. 0.1.3b. CTD acquisition
data were copied onto a OS X system, and then processed. CTD data at
bottle trips were extracted, and a 2-decibar downcast 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 88 CTD stations were occupied including one test station. A
total of 128 CTDO/rosette/LADCP/UVP/chipod casts were completed.

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

Temperature, salinity and, dissolved O_2 comparisons were made between
down and upcasts 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 P02E-2022 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.


Pressure Analysis
-----------------

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

The lab calibration coefficients provided on the calibration report
were used to convert frequencies to pressure. Initial 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
cast.

CTD #1281:

+-----------------------------------+-----------------------------------+-----------------------------------+
|                                   | Start P (dbar)                    | End P (dbar)                      |
|===================================|===================================|===================================|
| Min                               | -0.15                             | -0.41                             |
+-----------------------------------+-----------------------------------+-----------------------------------+
| Max                               | 0.10                              | 0.24                              |
+-----------------------------------+-----------------------------------+-----------------------------------+
| Average                           | 0.01                              | -0.17                             |
+-----------------------------------+-----------------------------------+-----------------------------------+

On-deck pressure reading varied from -0.15 to 0.10 dbar before the
casts, and -0.41 to 0.24 dbar after the casts. The pressure offset
varied from -0.18 to 0.21, with a mean value of -0.18 dbar.


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 systematic 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 13 samples, approximately 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 and second-order with respect to temperature:

   T_{cor} = T + cp_2 P^2 + cp_1 P + ct_2 T^2 + ct_1 T + c_0

Fit coefficients are shown in the following tables.


Primary temperature (T1) coefficients.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+------------------+------------------+------------------+------------------+------------------+------------------+
| Station          | cp_2             | cp_1             | ct_2             | ct_1             | c_0              |
|==================|==================|==================|==================|==================|==================|
| 118-158          | 0.0              | -1.8791e-8       | 0.0              | -3.1674e-5       | 6.1881e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 159-177          | 0.0              | 9.6475e-9        | 0.0              | 4.6552e-5        | 1.8018e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 178-205          | 0.0              | 9.6475e-9        | 0.0              | 4.6552e-5        | 1.8018e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 19103-18602      | 0.0              | -1.1695e-7       | 0.0              | -1.3419e-4       | 9.0745e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+


Secondary temperature (T2) coefficients.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+------------------+------------------+------------------+------------------+------------------+------------------+
| Station          | cp_2             | cp_1             | ct_2             | ct_1             | c_0              |
|==================|==================|==================|==================|==================|==================|
| 118-155          | 0.0              | 4.8963e-8        | 0.0              | -1.1044e-4       | 6.5189e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 159-177          | 0.0              | -1.3964e-8       | 0.0              | -2.0099e-4       | 8.6626e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 178-205          | 0.0              | 1.084e-7         | 0.0              | 3.7615e-5        | 5.0662e-5        |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 19103-18602      | 0.e              | -2.87e-8         | 0.0              | -2.2966e-4       | 9.1661e-4        |
+------------------+------------------+------------------+------------------+------------------+------------------+

Corrected temperature differences are shown in the following figures.

   [image]SBE35RT-T1 versus station.

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

   [image]SBE35RT-T2 versus station.

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

   [image]T1-T2 versus station.

   [image]Deep T1-T2 versus station (Pressure \geq 2000dbar).

   [image]SBE35RT-T1 versus pressure.

   [image]SBE35RT-T2 versus pressure.

   [image]T1-T2 versus pressure.

The 95% confidence limits for the mean low-gradient (values -0.002 °C
\leq T1-T2 \leq 0.002 °C) differences are ±0.00527 °C for SBE35RT-T1,
±0.00523 °C for SBE35RT-T2 and ±0.00146 °C for T1-T2. The 95%
confidence limits for the deep temperature residuals (where pressure
\geq 2000 dbar) are ±0.00074 °C for SBE35RT-T1, ±0.00076 °C for
SBE35RT-T2 and ±0.00063 °C for T1-T2.

No problems affected primary or secondary temperature sensor (SBE3)
data.

Minor complications impacted the reference temperature sensor (SBE35)
data.
   * During casts designated for bio, many bottles were fired at the
     surface and sometimes were too fast (< 15 seconds) for a reading.

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


Conductivity Analysis
---------------------

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

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

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

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

   [image]Corrected C_Bottle - C1 versus station.

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

   [image]Corrected C_Bottle - C2 versus station.

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

   [image]Corrected C1-C2 versus station.

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

   [image]Corrected C_Bottle - C1 versus pressure.

   [image]Corrected C_Bottle - C2 versus pressure.

   [image]Corrected C1-C2 versus pressure.

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

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

Fit coefficients are shown in the following tables.


Primary conductivity (C1) coefficients.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| Station      | cp_2         | cp_1         | ct_2         | ct_1         | cc_2         | cc_1         | c_0          |
|==============|==============|==============|==============|==============|==============|==============|==============|
| 118-158      | 8.3873e-11   | -6.2573e-7   | 0.0          | 0.0          | 0.0          | -4.7561e-4   | 1.6742e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 159-177      | 0.0          | 2.8021e-8    | 0.0          | 0.0          | 0.0          | 4.6701e-4    | -9.5951e-3   |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 178-205      | 0.0          | -4.2272e-7   | 0.0          | 0.0          | 0.0          | -1.8211e-4   | 1.6624e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 19103-18602  | 0.0          | -3.3734e-7   | 0.0          | 0.0          | 0.0          | -6.8688e-4   | 3.3427e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+


Secondary conductivity (C2) coefficients.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| Station      | cp_2         | cp_1         | ct_2         | ct_1         | cc_2         | cc_1         | c_0          |
|==============|==============|==============|==============|==============|==============|==============|==============|
| 118-158      | 1.1950e-10   | -1.0338e-6   | 0.0          | 0.0          | 0.0          | -5.3619e-4   | 2.3234e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 159-177      | 0.0          | -2.5469e-7   | 0.0          | 0.0          | 0.0          | 2.9271e-5    | 6.2111e-3    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 178-205      | 0.0          | -4.8145e-7   | 0.0          | 0.0          | 0.0          | -4.2052e-5   | 1.0867e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| 19103-18602  | 0.0          | -5.5344e-7   | 0.0          | 0.0          | 0.0          | -1.2683e-3   | 5.0528e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+

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 versus station.

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

   [image]Salinity residuals versus pressure.

The 95% confidence limits for the mean low-gradient (values -0.002 ºC
\leq T1-T2 \leq 0.002 ºC) differences are ±0.00581 mPSU for salinity-
C1SAL. The 95% confidence limits for the deep salinity residuals
(where pressure \geq 2000 dbar) are ±0.00192 mPSU for salinity-C1SAL.

Minimal issues affected conductivity and calculated CTD salinities
during this cruise.
   * Bottle stops in halocline may have had insufficient stop time
     during some casts, leading to measurements biased toward lower
     depth measurements.

   Bottle salinity measurements will be biased high relative to the
   CTD if salinity is decreasing toward the surface, or biased low if
   salinity is increasing toward the surface. Bottle stop time was
   increased from 30 seconds to 60 seconds in the halocline from
   station 187 through the end of the cruise. Preliminary results show
   a smaller residual between CTD salinity and reference salinity at
   the longer bottle stops, suggesting 30 seconds is insufficient.
   This result is consistent with the findings of [Paver2020]. This
   hypothesis will continue to be tested on future cruises.

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


CTD Dissolved Oxygen (SBE43)
----------------------------

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. Corrections for hysteresis are applied following Sea-Bird
Application Note 64-3. The SBE43 sensor data were compared to
dissolved O_2 check samples taken at bottle stops by matching the
downcast CTD data to the upcast trip locations along isopycnal
surfaces. CTD dissolved O_2 was then calculated using Clark Cell MPOD
O_2 sensor response model for Beckman/SensorMedics and SBE43 dissolved
O_2 sensors. The residual differences of bottle check value versus CTD
dissolved O_2 values are minimized by optimizing the PMEL DO sensor
response model coefficients using the BFGS non-linear least-squares
fitting procedure.

The general form of the PMEL DO sensor response model equation for
Clark cells follows Brown and Morrison [Mill82] and Owens [Owen85].
Dissolved O_2 concentration is then calculated:

   O_2 = S_{oc} \cdot (V + V_{\textrm{off}} + \tau_{20} \cdot e^{(D_1
   \cdot p + D_2 \cdot (T - 20))} \cdot dV/dt) \cdot O_{sat} \cdot
   e^{T_{cor} \cdot T} \cdot e^{[(E \cdot p) / (273.15 + T)]}

Where:

* V is oxygen voltage (V)

* D_1 and D_2 are (fixed) SBE calibration coefficients

* T is corrected CTD temperature (°C)

* p is corrected CTD pressure (dbar)

* dV/dt is the time-derivative of voltage (V/s)

* O_sat is oxygen saturation

* S_oc, V_off, \tau_20, T_cor, and E are fit coefficients

All stations were fit together to get an initial coefficient estimate.
Stations were then fit individually to refine the coefficients as the
membrane does not deform the same way with each cast. If the fit of
the individual cast had worse resdiuals than the group, they were
reverted to the original group fit coefficients.


SBE43 group fit coefficients. Coefficients were further refined station-by-station.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+------------------+------------------+------------------+------------------+------------------+------------------+
| Station          | S _oc            | V _off           | tau _20          | T _cor           | E                |
|==================|==================|==================|==================|==================|==================|
| 118-205          | 6.0036e-1        | -5.0138e-1       | 1.4500e+0        | -1.5908e-3       | 3.713e-2         |
+------------------+------------------+------------------+------------------+------------------+------------------+

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

   [image]O_2 residuals versus station.

   [image]Deep O_2 residuals versus station (Pressure >= 2000dbar).

   [image]O_2 residuals versus pressure.

The 95% confidence limits of 1.50 (µmol/kg) for all acceptable (flag
2) dissolved oxygen bottle data values and 1.15 (µmol/kg) for deep
dissolved oxygen values are only presented as general indicators of
the goodness of fit. CLIVAR GO-SHIP standards for CTD dissolved oxygen
data are < 1% accuracy against on board Winkler titrated dissolved O_2
lab measurements.

No issues arose with the acquisition and processing of CTD dissolved
oxygen data (SBE43).


CTD Dissolved Oxygen (RINKO)
----------------------------

A two-point calibration was performed prior and after deployment on
the rosette. These calibrations produced sets of calibration
coefficients (G and H) to adjust factory calibration of dissolved
oxygen raw voltage. The calibrations also provided an assessment of
foil degradation over the course of the 90 stations. As per
manufacturer (JFE Advantech Co., Ltd.) recommendation, 100% saturation
points were obtained via bubbling ambient air in a stirred beaker of
tap water about 30 minutes, removing air stone, then submersing the
powered Rinko. Zero point calibrations also followed general
manufacturer recommendations, using a sodium sulfite solution (25g in
500mL deionized water). Dissolved oxygen raw voltage (DOout),
atmospheric pressure, and solution temperature were recorded for
calculation of new oxygen sensor coefficients (G and H).

Rinko temperature (factory coefficients) was used for pre-cruise
calibration. Generally, the Rinko III sensor appears to have performed
as expected with no major problems or sharp drift throughout the
deployment. An SBE 43 dissolved oxygen sensor was deployed
simultaneously. Both oxygen sensor data sets were analyzed and quality
controlled with Winkler bottle oxygen data. RinkoIII data used as
primary oxygen for all stations (118-205), excluding stations 10-12
when the RINKO cable needed to be changed.

RINKO data was acquired, converted from volts to oxygen saturation,
and then multipled by the oxygen solubility to find values in µmol/kg.
The resulting data were then fitted using the equations developed by
[Uchida08]:

   [O_2] = (V_0 / V_c - 1) / K_{sv}

   K_{sv} = c_0 + c_1 T + c_2 T^2, \hspace{6pt} V_0 = 1 + d_0 T,
   \hspace{6pt} V_c = d_1 + d_2 V_r

where:

* T is temperature (ºC)

* V_r is raw voltage (V)

* V_0 is voltage at zero O_2 (V)

* c_0, c_1, c_2, d_0, d_1, d_2 are calibration coefficients

Oxygen is further corrected for pressure effects:

   [O_2]_c = [O_2] (1 + c_p P / 1000) ^ {1/3}

where:

* P is pressure (dbar)

* c_p is pressure compensation coefficient

Lastly, salinity corrections are applied [GarciaGordon1992]:

   [O_2]_{sc} = [O_2]_c \exp[{S (B_0 + B_1 T_S + B_2 T_S^2 + B_3
   T_S^3) + C_0 S^2}]

where:

* T_S is scaled temperature (T_S = ln[(298.15 – T)/(273.15 + T)])

* B_0, B_1, B_2, B_3, C_0 are solubility coefficients

All stations excluding 10-12 were fit together to get an initial
coefficient estimate. Stations were then fit in groups of similar
profiles to get a further refined estimate. Individual casts were then
fit to remove the noticeable time drift in coefficients If the fit of
the individual cast had worse resdiuals than the group, they were
reverted to the original group fit coefficients.


Rinko group fit coefficients. Coefficients were further refined station-by-station.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+
| Station      | c_0          | c_1          | c_2          | d_0          | d_1          | d_2          | c_p          |
|==============|==============|==============|==============|==============|==============|==============|==============|
| 118-205      | 1.3182e+0    | 1.8002e-2    | 1.7002e-4    | -1.4178e-3   | -1.2641e-1   | 3.3973e-1    | 8.8540e-2    |
+--------------+--------------+--------------+--------------+--------------+--------------+--------------+--------------+

CTD dissolved O_2 residuals are shown in the following figures.

   [image]O_2 residuals versus station.

   [image]Deep O_2 residuals versus station (Pressure >= 2000dbar).

   [image]O_2 residuals versus pressure.

The 95% confidence limits of 0.86 (µmol/kg) for all acceptable (flag
2) dissolved oxygen bottle data values and 0.36 (µmol/kg) for deep
dissolved oxygen values are only presented as general indicators of
the goodness of fit. CLIVAR GO-SHIP standards for CTD dissolved oxygen
data are < 1% accuracy against on board Winkler titrated dissolved O_2
lab measurements.

No issues arose with the acquisition and processing of CTD dissolved
oxygen data (RINKO).


BIO Casts
---------

Throughout P02E-2022, 31 bio casts were taken prior to the full cast
for separate, large volumes of water for biological analyses. The
first bio cast was cast 3 at station 119. The last bio cast was cast 1
at station 203. Bio casts were done at re-occupations of station 191
and 188. Salinity and oxygen analyses were not performed during these
casts and therefore the CTD was not fit for those parameters.

   [image]CTD bottle values for temperature, salinity, oxygen, and
   fluorometer voltage plotted against CTD pressure across all bottle
   casts.

[Mill82] Millard, R. C., Jr., “CTD calibration and data processing
         techniques at WHOI using the practical salinity scale,” Proc.
         Int. STD Conference and Workshop, p. 19, Mar. Tech. Soc., La
         Jolla, Ca. (1982).

[Owen85] Owens, W. B. and Millard, R. C., Jr., “A new algorithm for
         CTD oxygen calibration,” Journ. of Am. Meteorological Soc.,
         15, p. 621 (1985).

[Uchida08] Uchida, H., Kawano, T., Kaneko, I., Fukasawa, M. “In Situ
           Calibration of Optode-Based Oxygen Sensors,” J. Atmos.
           Oceanic Technol., 2271-2281, (2008)

[GarciaGordon1992] García, H. E., and L. I. Gordon, 1992: Oxygen
                   solubility in sea- water: Better fitting equations.
                   Limnol. Oceanogr., 37, 1307– 1312.

[Paver2020] Paver, C.R., Codispoti, L.A., Coles, V.J. and Cooper, L.W.
            (2020), Sampling errors arising from carousel entrainment
            and insufficient flushing of oceanographic sampling
            bottles. Limnol Oceanogr Methods, 18: 311-326.


Salinity
========

PIs
   * Todd Martz (SIO)

   * Susan Becker (SIO)

Technicians
   * Laurette Roy (Tech Pool)

   * Gabriel Matthias (Tech Pool)


Equipment and Techniques
------------------------

Two Guildline Autosals were on board and operational, SIO-owned 8400A
S/N 57-526 and S/N 55-564. S/N 57-526 was used for all salinity
measurements during this cruise. The salinity analysis was run in the
ship’s Climate Controlled Chamber, a refrigerator port and amidships
between the Computer Lab and Analytical Lab. The chamber temperature
varied between about 21 and 25 degrees Celcius around 3 times each
hour, with an average (based on measuring temperatures of items in the
chamber) of about 23°C.

Both instruments were serviced prior to the cruise by their respective
institutions. S/N 57-526 was shipped to Guam and was the primary on
the first leg of the PO2 occupation. S/N 55-654 was shipped to Hawaii
with other equipment in March. IAPSO Standard Seawater Batch P-165 was
used for all calibrations: K15 = 0.99986, salinity 34.994, expiration
2024-04-15. A LabView program developed by Carl Mattson was used for
monitoring temperatures, logging data and prompting the operator.
Salinity analyses were performed after samples had equilibrated to
laboratory temperature of 23°C, usually 8 hours or more after
collection.

The salinometer was standardized for each group of samples analyzed
(normally 1 or 2 casts, up to 72 samples) using two bottles of
standard seawater: one at the beginning and one at the end of each set
of measurements. For each calibration standard and sample reading, the
salinometer cell was initially flushed at least 2 times before a set
of conductivity ratio readings was recorded. Between runs the water
from the last standard was left in the cell.


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 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 function of elapsed run time.
The corrected salinity data was then incorporated into the cruise
database.


Narrative
---------

No major problems were encountered during this cruise. Some red algae
was seen growing in one case of sample bottles. Acid washing (10% HCl)
solved the problem. Additional red algae was seen at the drain tube of
the salinometer. Solved by leaving DI water in the machine for 8
hours. Capillary tubes were carefully cleaned with MilliQ, followed by
air, 3 times during the course of the cruise, to help with cell
filling. The first cleaning included a run with diluted Triton-X.
3,265 total salinity samples were taken from 128 CTD casts. Four
sample bottles were broken over the course of this cruise.

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


Nutrients
=========

Technicians
   * John Ballard: Scripps Institution of Oceanography

   * Tanya Leung: Scripps Institution of Oceanography


Summary of Analysis
-------------------

* 3265 samples from 94 CTD stations

* The cruise started with new pump tubes and they were changed twice,
  before stations 158, 176, and 200.

* 5 sets of Primary/Secondary mixed standards and 2 sets of primary
  Nitrite standards were made up over the course of the cruise.

* The cadmium column efficiency was checked periodically and ranged
  between 93%-100%.


Equipment and Techniques
------------------------

Nutrient analyses (phosphate, silicate, nitrate+nitrite, and nitrite)
were performed on a Seal Analytical continuous-flow AutoAnalyzer 3
(AA3). The methods used are described by Gordon et al [Gordon1992]
Hager et al. [Hager1972], and Atlas et al. [Atlas1971]. Details of
modification of analytical methods used in this cruise are also
compatible with the methods described in the nutrient section of the
updated GO-SHIP repeat hydrography manual (Becker et al., 2019,
[Becker2019]).


Nitrate/Nitrite Analysis
------------------------

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

**REAGENTS**

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

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

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

Imidazole Buffer
   Dissolve 13.6g imidazole in ~3.8 liters DIW. Stir for at least 30
   minutes to completely dissolve. Add 60 ml of CuSO_4 + NH_4Cl 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.

NH_4Cl + CuSO_4 mix
   Dissolve 2g cupric sulfate in DIW, bring to 100 m1 volume (2%).
   Dissolve 250g ammonium chloride in DIW, bring to 1l liter volume.
   Add 5ml of 2% CuSO_4 solution to this NH_4Cl stock. This should
   last many months.


Phosphate Analysis
------------------

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

**REAGENTS**

Ammonium Molybdate H_2SO_4 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 H_2SO_4. 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.


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
   H_2SO_4. (Dilute H_2SO_4 = 2.8ml conc H_2SO_4  or 6.4ml of H_2SO_4
   diluted for PO_4 moly per liter DW) (dissolve powder, then add
   H_2SO_4) 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.


Sampling
--------

Nutrient samples were drawn into 30 ml polypropylene screw-capped
centrifuge tubes. The tubes and caps were cleaned with 10% HCl and
rinsed 2-3 times with sample before filling. Samples were analyzed
within 4 hours after sample collection, allowing sufficient time for
all samples to reach room temperature. The centrifuge tubes fit
directly onto the sampler.


Data Collection and Processing
------------------------------

Data collection and processing was done with the software provided
with the instrument from Seal Analytical (AACE). 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.


Standards and Glassware Calibration
-----------------------------------

Primary standards for silicate (Na_2SiF_6), nitrate (KNO_3), nitrite
(NaNO_2), and phosphate (KH_2PO_4) 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. 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 12-16 hours from a
secondary. Working standards were made up in low nutrient seawater
(LNSW). Multiple batches of LNSW were used on the cruise. The first
batch of LNSW was treated in the lab. The water was re-circulated for
~8 hours through a 0.2 micron filter, passed a UV lamp and through a
second 0.2 micron filter. The actual concentration of nutrients in
this water was empirically determined during the standardization
calculations.

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

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


Quality Control
---------------

All final data was reported in micro-moles/kg. NO_3, PO_4, and NO_2
were reported to two decimals places and SIL to one. Accuracy is based
on the quality of the standards the levels are:

+-------+-----------------------------+
| NO_3  | 0.05 µM (micro moles/Liter) |
+-------+-----------------------------+
| PO_4  | 0.004 µM                    |
+-------+-----------------------------+
| SIL   | 2-4 µM                      |
+-------+-----------------------------+
| NO_2  | 0.05 µM                     |
+-------+-----------------------------+

Reference materials for nutrients in seawater (RMNS) were used as a
check sample run with every station. The RMNS preparation,
verification, and suggested protocol for use of the material are
described by [Aoyama2006] [Aoyama2007], [Aoyama2008], Sato [Sato2010]
and Becker et al. [Becker2019]. RMNS batch CM was used on this cruise,
with each bottle being used for all runs in one day before being
discarded and a new one opened. Data are tabulated below.

+-----------+---------------+---------+---------------+
| Parameter | Concentration | stddev  | assigned conc |
|===========|===============|=========|===============|
| -         | (µmol/kg)     | -       | (µmol/kg)     |
+-----------+---------------+---------+---------------+
| NO_3      | 33.16         | 0.13    | 33.2          |
+-----------+---------------+---------+---------------+
| PO_4      | 2.38          | 0.01    | 2.38          |
+-----------+---------------+---------+---------------+
| Sil       | 100.4         | 0.61    | 100.5         |
+-----------+---------------+---------+---------------+
| NO_2      | 0.019         | 0.008   | 0.02          |
+-----------+---------------+---------+---------------+


Analytical Problems
-------------------

Occasional excess carryover on phosphate channel was resolved with a
series of cleaning procedures and monitored throughout cruise. A
contamination issue created problems for silicate measurement from a
few individual sample tubes beginning at station 132. The contaminant
(suspect winch wire grease) eventually spread to other sample tubes
and affected about 15 individual silicate measurements between station
132-153. Once tubes were replaced at station 154, the issue was
resolved. The values of the reference material and were used to
monitor data quality. Adjustments based on the values obtained for the
reference material were made as necessary. Final QC checks were not
completed until after the cruise. Comparison of data from adjacent
stations and to historical data revealed that phosphate data for
stations 12-147 was bad due to a bad reagent preparation.

[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.

[Becker2019] Becker, S., Aoyama M., Woodward M., Baaker, K., Covery,
             S., Mahaffey, C., Tanhua, T., “GO-SHIP Repeat Hydrography
             Nutrient Manual, 2019: The Precise and accurate
             determination of dissololved inorganic nutrients in
             seawater;Continuos Flow Analysis methods.  Ocean Best
             Practices, August 2019.

[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).

[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.


Oxygen Analysis
===============

PIs
   * Todd Martz (SIO)

   * Susan Becker (SIO)

Technicians
   * Elisa Aitoro (SIO)

   * Robert “Ben” Freiberger (SIO)


Equipment and Techniques
------------------------

Dissolved oxygen analyses were performed with an SIO/ODF-designed
automated oxygen titrator using photometric end-point detection based
on the absorption of 365nm wavelength ultra-violet light. The
titration of the samples and the data logging were controlled by PC
LabView software. Thiosulfate was dispensed by a Dosimat 665 buret
driver fitted with a 1.0 ml burette.

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

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


Sampling and Data Processing
----------------------------

A total of 3262 oxygen measurements were made, all of which were
niskin samples. Niskin samples were collected soon after the rosette
was secured on deck, either from fresh niskins or immediately
following CFC sampling.

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

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

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

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


Volumetric Calibration
----------------------

Oxygen flask volumes were determined gravimetrically with degassed
deionised water to determine flask volumes at ODF’s chemistry
laboratory. This is done once before using flasks for the first time
and periodically thereafter when a suspect volume is detected. The 10
mL Dosimat buret used to dispense standard iodate solution was
calibrated using the same method.


Standards
---------

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


Narrative
---------

The oxygen analytical rig was setup in the main lab of the Revelle.
During the transit into Honolulu during leg 1, 4L batches were made of
each reagent.

No major analytical issues were encountered. A few high end points
occurred and were corrected for. The analytical computer would freeze
occasionally, but never while doing analysis.

The thiosulfate stability was considered in 3 batches and showed
remarkable stability throughout the entire cruise. No trends were
observed or corrected for.

An OSIL standard was run against the usual ODF working standard using
a hand pipetter. The agreement between the OSIL and the ODF standard
was just within the daily tolerance.

No data updates are expected.

[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).


Total Alkalinity
================

PIs
   * Andrew G. Dickson (SIO)

Technicians
   * Daniela Nestory (SIO)

   * Sidney Wayne (HPU)


Total Alkalinity
----------------

The total alkalinity of sea water 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 < 10E-4.5 at
25°C and zero ionic strength) over proton donors (acids with K >
10E-4.5) in 1 kilogram of sample.


Total Alkalinity Measurement System
-----------------------------------

*Sample Delivery System:*

Samples are dispensed using a Sample Delivery System (SDS) which has
been calibrated for volume in the lab prior to the cruise. Its volume
is confirmed immediately before use at sea to ensure a consistent
volume will be delivered for each sample. The SDS consists of a
volumetric pipette, various relay valves, an air pump, and is
controlled by a program in LabVIEW 2012.

Before attaching a sample bottle to the SDS, the volumetric pipette is
cleared of any residual solution. The pipette is then rinsed and
filled with the sample. The sample overflows and time is allowed 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, along with
the bottle salinity, are used to convert the sample volume to mass for
analysis.

Samples are delivered into a 250-mL water-jacketed open cell for
titration analysis. While one sample is undergoing titration, a second
sample is prepared with the SDS and equilibrated to 20°C for analysis.

*Open-Cell Titration:*

The total alkalinity is measured through an open-cell titration with a
dilute hydrochloric acid titrant of known concentration. A Metrohm 876
Dosimat Plus is used for all standardized hydrochloric acid additions.

An initial aliquot of approximately 2.3-2.4 mL of standardized
hydrochloric acid (~0.1M HCl in ~0.6M NaCl solution) is first
delivered and the sample is stirred for 5 minutes while air is bubbled
into at a rate of 200 scc/m to remove any liberated carbon dioxide
gas.

After equilibration, ~19 aliquots of 0.035 ml are added. Between the
pH range of 3.5 to 3.0, the progress of the titration is monitored
using a pH glass electrode/reference electrode cell, and the total
alkalinity is computed from the titrant volume and e.m.f. measurements
using a non-linear least-squares approach ([Dickson2007]).

A Thermo Scientific Isotemp water bath is connected to the water-
jacketed open cell to maintain a cell temperature of approximately
20oC. 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.


Sample Collection
-----------------

Alkalinity samples are drawn using silicone tubing connected to the
Niskin bottles and collected into 250 mL Pyrex bottles. The sample
bottles and Teflon-sleeved glass stoppers were rinsed at least twice
before the final filling. A headspace of approximately 3 mL was
removed and 0.1 mL of 50% saturated mercuric chloride solution was
added to each sample for preservation. The samples were equilibrated
prior to analysis at approximately 20°C using a Thermo Scientific
Isotemp water bath.

Samples for total alkalinity were taken at all stations during Leg 2
of P02 (118-204). Except for a few instances, alkalinity samples were
collected from all niskins where DIC and pH were collected, to over-
characterize the CO2 system. The typical sample scheme of partial
collection on all stations (26 bottles), with the exception of a full
collection (36 bottles) on select stations, was followed.

In order to evaluate the reproducibility of the alkalinity system, 2
duplicate samples (two separate alkalinity bottles) were collected on
each cast, with the exception of casts with fewer than 18 bottles, in
which 1 duplicate sample was collected.


Problems and Troubleshooting
----------------------------

The alkalinity system was set up in the hydro lab. Around station 124,
voltage readings from the system’s electrode were suddenly noisy and
values were affected. All parts of the alkalinity system were changed
in hopes of remedying the noise, but to no avail. The system was moved
to the analytical lab around station 125 and the voltage readings /
CRM values were once again normal. Analyses for stations 124 and 125
were the only stations affected by this issue.


Quality Control
---------------

Certified Reference Material (CRMs) and duplicate samples (two bottles
collected from one niskin) were used to quality check the functioning
of the total alkalinity system throughout the cruise.

Dickson laboratory Certified Reference Material (CRM) Batches 200 and
201 were used to determine the accuracy of the total alkalinity
analyses. The total alkalinity certified value for these batches are:

* Batch 200 2186.43 ± 0.42 µmol/kg

* Batch 201 2207.56 ± 0.47 µmol/kg

The cited uncertainties represent the standard deviation.

A CRM sample was analyzed at a minimum frequency of once per every 20
runs, but more often once per every 15 runs. Because total alkalinity
is not affected by gas-exchange, brand new CRM bottles were reserved
for pH and DIC analysis. These pre-opened bottles were subsequently
used for alkalinity analysis.

198 reference material samples were analyzed on Leg 2 of P02.

The average measured total alkalinity value for each batch is:

* Batch 200 2186.59 ± 1.39 µmol/kg (n = 133, 70)

* Batch 201 2208.24 ± 1.25 µmol/kg (n = 65, 40)

Figures in parentheses are the number of analyses made (total number
of analyses; number of separate bottles analyzed).

Duplicate samples were also used to check the reproducibility of the
system. The absolute value of the mean offset between duplicate
samples and the standard deviation are given below.

Mean duplicate sample offset: 1.08 ± 1.00 µmol/kg (n = 164)

2396 total alkalinity values were submitted for Leg 2 of P02.

Further dilution corrections need to be applied to this data back
onshore, therefore, this data is to be considered preliminary.

[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.


Discrete pH Analyses (Total Scale)
==================================

PI
   * Dr. Andrew Dickson (SIO)

Technicians
   * Albert Ortiz (RSMAS)

   * Brison Grey (RSMAS)


Sampling
--------

Samples were collected in 250 mL Pyrex glass bottles and sealed using
grey butyl rubber stoppers held in place by aluminum-crimped caps.
Each bottle was rinsed two times and allowed to overflow by one half
additional bottle volume. Prior to sealing, each sample was given a 1%
headspace and 0.1 mL of 50% saturated mercuric chloride solution was
added to each sample for preservation. 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.


Analysis
--------

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


Reagents
--------

The mCP indicator dye was made up to a concentration of approximately
2.0mM and a total ionic strength of 0.7 M. A total of two batches were
used during Leg 2 of P02. 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 7.80, 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].


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:

   R = \frac{A_{578} - A_{\text{base}}}{A_{434} - A_{\text{base}}}

and

   A_{\text{iso}} = A_{488} - A_{\text{base}}

The change in R for a given change in A_{\text{iso}}, \Delta R/\Delta
A_{\text{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:

   \Delta R/\Delta A_{\text{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_{\text{iso}} (bR + a)


Problems and Troubleshooting
----------------------------

There were no major issues encountered during Leg 2 of P02.


Standardization/Results
-----------------------

The precision of the data was assessed from measurements of duplicate
analyses and certified reference material (CRM) Batch 200 (provided by
Dr. Andrew Dickson, UCSD).

In order to evaluate the reproducibility of the alkalinity system, 2
duplicate samples (two separate alkalinity bottles) were collected on
each cast, with the exception of casts with fewer than 18 niskins, in
which 1 duplicate sample was collected.

CRMs were measured at the beginning and ending of each day.

The precision statistics for Leg 2 of P02 are:

+----------------------------+--------------------------+
| Duplicate precision        | ± 0.0008 (n= 183)        |
+----------------------------+--------------------------+
| B200                       | 7.7987 ± 0.0010 (n= 40)  |
+----------------------------+--------------------------+

2451 pH values were submitted for Leg 2 of P02. Additional corrections
will need to be performed and these data should be considered
preliminary until a more thorough analysis of the data can take place
on shore.

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

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

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


Dissolved Inorganic Carbon (DIC)
================================

PI’s
   * Richard A. Feely (NOAA/PMEL)

   * Rik Wanninkhof (NOAA/AOML)

Technicians
   * Andrew Collins (NOAA/PMEL)

   * Charles Featherstone (NOAA/AOML)


Sample Collection
-----------------

Samples for *DIC* measurements were drawn (according to procedures
outlined in the PICES Special Publication, Guide to Best Practices for
Ocean CO_2 Measurements [Dickson2007]) from Bullister style niskin
bottles into ~310ml borosilicate glass flasks using platinum-cured
silicone tubing. The flasks were rinsed once and filled from the
bottom with care not to entrain any bubbles, overflowing by at least
one-half volume. The sample tube was pinched off and withdrawn,
creating a 6ml headspace and 0.12 ml of saturated HgCl_2 solution was
added as a preservative. The sample bottles were then sealed with
glass stoppers lightly covered with Apiezon-L grease. DIC samples were
collected from a variety of depths with approximately 10% of these
samples taken as duplicates.


Equipment
---------

The analysis was done by coulometry with two analytical systems (PMEL1
and PMEL2) used simultaneously on the cruise. Each system consisted of
a coulometer (5015O UIC Inc) coupled with a Dissolved Inorganic Carbon
Extractor (DICE). The DICE system was developed by Esa Peltola and
Denis Pierrot of NOAA/AOML and Dana Greeley of NOAA/PMEL to modernize
a carbon extractor called SOMMA ([Johnson1985], [Johnson1987],
[Johnson1993], [Johnson1992], [Johnson1999]). The two DICE systems
were set up in a seagoing container modified for use as a shipboard
laboratory on the aft main working deck of the *RV Roger Revelle*.


DIC Analysis
------------

In coulometric analysis of DIC, all carbonate species are converted to
CO_2 by addition of excess hydrogen ion (acid) to the seawater sample,
and the evolved CO_2 is swept into the titration cell of the
coulometer with CO_2 free dry 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
coulometric generation of OH^- ions at the anode. The OH^- ions react
with the H^+ and the solution turns blue again. A beam of light is
shone through the solution, and a photometric detector at the opposite
side of the cell senses the change in transmission. Once the percent
transmission reaches its original value, the coulometric titration is
stopped, and the amount of CO_2 that enters the cell is determined by
integrating the total change during the titration.


DIC Calculation
---------------

The amount of CO_2 injected was calculated according to the 2007 PICES
Special Publication. Each DICE instrument has a modified SBE45
salinity sensor, but all DIC values were recalculated to a molar
weight (µmol \text{kg}^{-1}) using density obtained from the CTD’s
salinity.

The DIC values were corrected for dilution resulting from the addition
of 0.12 ml of saturated HgCl_2 used for sample preservation. The
correction factor used for this dilution is 1.000397. A correction was
also applied for the offset from the Certified Reference Material
(CRM). This additive correction was applied for each cell using the
value of the CRM obtained at the beginning of the cell. The coulometer
cell solution was replaced after 24-28 mg of carbon was titrated,
typically after 10-12 hours of continuous use. The blanks (background
noise per cell) ranged from 20-62.6 on DICE1 and 30-82.3 on DICE2.


Calibration, Accuracy, and Precision
------------------------------------

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

1. Gas loops were always run at the beginning and usually at the end
   of each cell;

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

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

Each coulometer was calibrated by injecting aliquots of pure CO_2
(99.999%), as a standard, 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; and when time allowed at the end of each cell to ensure no
drift during the life of the cell.

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 have
been corrected to batches 200 and 201 CRM values. Batch 200 was used
for the first 44 stations and batch 201 for the remaining 48. The CRM
certified values for batches 200 and 201 are 2022.46 µmol
\text{kg}^{-1} and 2048.19 µmol \text{kg}^{-1}. The summary table
\text{below}^1 lists information for the CRMs.

The precision of the two DICE systems can be demonstrated via the
replicate samples. Approximately 5% 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 0.86 µmol
\text{kg}^{-1}; No systematic differences between the replicates were
\text{observed}^2.


Summary
-------

The overall performance of the analytical equipment was good during
the cruise. No major equipment problems were encountered, nor other
problems that wound up compromising the quality of the data we
collected. As is standard operating procedure, the pipette
calibrations will need to be repeated upon return to shore. Both
systems ran with slightly higher than normal background noise (blanks)
than we are used to seeing. It is believed this extra noise is due to
the new bow thruster the Revelle had installed during the mid-life
refit and the need for all thrusters (Z-drive included) to be
calibrated so they work as a team. This extra instrument noise is
apparent while on station but not while the ship is underway. Further
supporting this belief, we had no extra background noise in Seattle or
while tied up at the pier while in Guam before the first leg of P02.
Even with this additional background noise, the overall precision and
accuracy and comparison to the 2013 P02 data set leads us to believe
the systems were not compromised by this higher blank. Including the
duplicates, 2,672 samples were analyzed for dissolved inorganic
carbon. Therefore, DIC analyzed approximately 75% of the niskins made
available to us. The DIC data reported to the database directly from
the ship are to be considered preliminary until a more thorough
quality assurance can be completed shore side.

Calibration data during this cruise:

+----------+-------------------------------+------------------+------------+
| SYSTEM   | Average Gas Loop Cal Factor   | Pipette Volume   | Observed   |
|==========|===============================|==================|============|
| PMEL1    | 1.00535                       | 27.571 ml        | 0.80       |
+----------+-------------------------------+------------------+------------+
| PMEL2    | 1.00394                       | 26.363 ml        | 0.91       |
+----------+-------------------------------+------------------+------------+

+-----------------+-----------+------+-----------+-----------+------+-----------+
| CRM Info        | PMEL1                        | PMEL2                        |
+-----------------+-----------+------+-----------+-----------+------+-----------+
| Batch - Cert.   | Ave       | N    | Std Dev   | Ave       | N    | Std Dev   |
|=================|===========|======|===========|===========|======|===========|
| 200 - 2022.46   | 2022.76   | 21   | 1.53      | 2022.07   | 21   | 1.59      |
+-----------------+-----------+------+-----------+-----------+------+-----------+
| 201 - 2048.19   | 2047.92   | 26   | 1.12      | 2048.61   | 25   | 1.88      |
+-----------------+-----------+------+-----------+-----------+------+-----------+

   [image]Section plot of DIC from Leg 2 of P02.

[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.

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

[Johnson1987] Johnson, K.M., P.J. Williams, L. Brandstrom, and J. McN.
              Sieburth (1987): *“Coulometric total carbon analysis for
              marine studies: Automation and calibration.”* Mar.
              Chem., 21, 117-133.

[Johnson1992] Johnson, K.M. (1992): Operator’s manual: *“Single
              operator multiparameter metabolic analyzer (SOMMA) for
              total carbon dioxide (CT) with coulometric detection.”*
              Brookhaven National Laboratory, Brookhaven, N.Y., 70 pp.

[Johnson1993] Johnson, K.M., K.D. Wills, D.B. Butler, W.K. Johnson,
              and C.S. Wong (1993): *“Coulometric total carbon dioxide
              analysis for marine studies: Maximizing the performance
              of an automated continuous gas extraction system and
              coulometric detector.”* Mar. Chem., 44, 167-189.

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

[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


Dissolved Organic Carbon and Total Dissolved Nitrogen
=====================================================

PI
   * Craig Carson (UCSB)

Technician
   * Michelle Michelsen (UoE/UCSB)

Analysts
   * Keri Opalk (UCSB)

   * Elisa Halewood (UCSB)

Support
   NSF


Project Goals
-------------

The goal of the DOM project is to evaluate dissolved organic carbon
(DOC) and total dissolved nitrogen (TDN) concentrations along the P02
zonal transect.


Sampling
--------

DOC profiles were taken from every other stations from 12-36 niskins
ranging the full depth of the water column with two duplicates (47 of
94 stations; 1449 DOC/TDN samples). All samples collected above 250
meters were filtered through an inline filter holding a combusted GF/F
filter attached directly to the niskin.

This was done to eliminate particles larger than 0.7 µm from the
sample. To reduce contamination by the filter or filter holder, a new
filter and holder was used for every station. 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 4M Hydrochloric acid
and stored at 4ºC on board. Samples were shipped back to UCSB for
analysis via high temperature combustion 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 450ºC 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.


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 inshore 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 pillow on top of Pt
alumina beads to improve peak shape and to reduce alteration of
combustion matrix throughout the run. CO_2 free carrier gas is
produced with a Whatman® gas generator ([Carlson2010]). Samples are
drawn into a 5 mL injection syringe and acidified with 2M HCL (1.5%)
and sparged for 1.5 minutes with CO_2 free gas. Three to five
replicate 100 µL of sample are injected into a combustion tube headed
to 680°C. The resulting gas stream is passed through several water and
halide traps, including an added magnesium perchlorate trap. The CO_2
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 at least three
injections meet the specified range of a SD of 0.1 area counts, CV
\leq 2% or best 3 of 5 injections.

Extensive conditioning of the combustion tube with repeated injection
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) reference
waters and surface Sargasso Sea water every 6 – 8 analyses ([Hansell
1998]_). The standard deviation of the deep and surface references
analyzed throughout a run generally have a coefficient of variation
ranging between 1-3% over the 3-7 independent analyses (number of
references depends on the size of the run). Daily references waters
were calibrated with DOC CRM provided by D. Hansell (University of
Miami; ([Hansell 2005]_)).


DOC Calculation
~~~~~~~~~~~~~~~

   \mu\text{MC} = \frac{\text{average sample area} - \text{average
   machine blank area}}{\text{slope of std curve}}


Standard Operating Procedure for TDN analyses – Carlson Lab UCSB
----------------------------------------------------------------

TDN samples were analyzed via high temperature combustion using
Shimadzu TOC-V with attached Shimadzu TNMI unit at an inshore 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 resuce
alteration of combustion matrix throughout the run. Carrier gas was
produced with a Whatman® gas generator ([Carlson2010]) and ozone was
generated by the TNMI unite at 0.5L/min flow rate. Three to five
replicate 100 µL of sample were injected at 130 mL/min flow rate into
the combustion tube headed to 680°C, where the TN in the sample was
converted to nitric oxide (NO). The resulting gas stream was passed
through an electronic dehumidifier. The dried NO gas then reacted with
ozone producing an excited chemiluminescence NO_2 species
([Walsh1989]) and the fluorescence signal was detected with a Shimadzu
TNMI chemiluminescence detector. The resulting peak area was
integrated with Shimadzu chromatographic software. Injections continue
until at least three injections meet the specified range of a SD of
0.1 area counts, CV \leq 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 ever 6-8 analyses
([Hansell1998]). Daily references waters were calibrated with deep CRM
provided by D. Hansell (University of Miami; [Hansell2005])).


TDN calculation
~~~~~~~~~~~~~~~

   \mu\text{MN} = \frac{\text{average sample area} - \text{average
   machine blank area}}{\text{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.


Carbon Isotopes in Seawater (14/13C)
====================================

PI
   * Roberta Hansman (WHOI)

   * Rolf Sonnerup (UW)

Technician
   * Michelle Michelsen (UoE/UCSB)

A total of 512 samples were collected along the P02 transect between
station 188-198. Radiocarbon profiles were 32 samples from each
station with one duplicate and five randomised skips between 4000m-
1600m. Station locations mostly followed previous P02 transects.

Samples were collected in 500 mL airtight glass bottles. Using
silicone tubing, the flasks were rinsed 3 times with seawater. 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 saturate 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 (\delta^14C) is measured
by extracting the inorganic carbon as CO_2 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 CO_2
extracted from seawater is measured relative to the ^13C/^12C of a
CO_2 gas standard calibrated to the PDB standard using and isotope
radio mass spectrometer (IRMS) at NOSAMS.


CFC, SF_6, and N_2O
===================

PIs
   * Dong-Ha Min (UT)

Analysts
   * David Cooper (UT)

   * Carol Gonzalez (UT)

   * Matthew Varas (TAMU)

Samples for the analyses of the dissolved chlorofluorocarbons (CFCs,
freons) F11 and F12, sulfur hexafluoride (SF_6) and nitrous oxide
(N_2O) were collected and analyzed during RR2205. Seawater samples
were taken from all casts, with full profiles generally taken from
alternating casts and strategically determined bottles sampled from
the remaining casts. These measurements are complemented by periodic
measurements of air samples.

Seawater samples were drawn from 10 liter Niskin bottles. Samples for
CFC and SF_6 were the first samples drawn, taking care to check the
integrity of the sample and coordinate the sampling analysts to
minimize any time between the initial opening of each bottle and the
completion of sample drawing. To minimize contact with air, the CFC
samples were drawn directly through the stopcocks of the Niskin
bottles into 250 ml precision glass syringes. Syringes were rinsed and
filled via three-way plastic stopcocks. The syringes were subsequently
held at 0-5 degrees C until 30 minutes before being analyzed. At that
time, the syringe was placed in a bath of surface seawater heated at
approximately 28 °C.

For atmospheric sampling, a ~90 m length of 3/8” OD Dekaron tubing was
run from the main lab to the bow of the ship. A flow of air was drawn
through this line into the main laboratory using an air-cadet pump.
The air was compressed in the pump, with the downstream pressure held
at ~1.5 atm. using a backpressure regulator. A tee allowed a flow (100
ml min-1) of the compressed air to be directed to the gas sample valve
of the CFC analytical system, while the bulk flow of the air (>7 l
min-1) was vented through the backpressure regulator. Analysis of bow
air was performed at several locations along the cruise track.
Approximately five measurements were made at each location to increase
the precision. Atmospheric data were not submitted to the database,
but were found to be in excellent agreement with current global
databases.

Concentrations of CFC-1l, CFC-12, SF_6 and N_2O in air samples,
seawater samples and gas standards were measured by shipboard electron
capture gas chromatography (ECD-GC) using techniques described by
[Bullister2008]. This method has been modified with the addition of an
extra ECD to accommodate N_2O analysis. For seawater analyses, water
was transferred from a glass syringe to a glass sparging chamber (~200
ml). The dissolved gases in the seawater sample were extracted by
passing a supply of CFC-free purge gas through the sparging chamber
for a period of 6 minutes at 120 - 140 ml/min. Water vapor was removed
from the purge gas by passage through a Nafion drier, backed up by a
18 cm long, 3/8” diameter glass tube packed with the desiccant
magnesium perchlorate. This tube also contained a short length of
Ascarite to remove carbon dioxide, a potential interferent in N_2O
analysis. The sample gases were concentrated on a cold-trap consisting
of a 1/16” OD stainless steel tube with a ~5 cm section packed tightly
with Porapak Q (60-80 mesh), a 22 cm section packed with Carboxen 1004
and a 2.5 cm section packed with molecular sieve MS5A. A neslab
cryocool was used to cool the trap, to below -50°C. After 6 minutes of
purging, the trap was isolated, and it was heated electrically to
~150°C. The sample gases held in the trap were then injected onto a
precolumn (~60 cm of 1/8” O.D. stainless steel tubing packed with
80-100 mesh Porasil B, held at 80°C) for the initial separation of
CFC-12 and CFC-11 from later eluting peaks. After the F12 had passed
from the pre-column through the second pre-column (22 cm of 1/8” O.D.
Stainless steel tubing packed with Molecular Sieve 5A, 100/120 mesh)
and into the analytical column #1 (~170 cm of 1/8” OD stainless steel
tubing packed with MS5A and held at 80°C) the outflow from the first
precolumn was diverted to the second analytical column (~150 cm 1/8”
OD stainless steel tubing packed with Carbograph 1AC, 80-100 mesh,
held at 80°C). After F11 had passed through the first precolumn, the
flow was diverted to a third analytical column (1/8” stainless steel
tube with 30cm Molecular Sieve 5A, 60/80 mesh) for N_2O analysis. The
first pre-column was then backflushed and vented. The first two
analytical columns and precolumn 1 were held isothermal at 80 degrees
C in an Agilent (HP) 6890N gas chromatograph with two electron capture
detectors (250°C). The third analytical column and second pre-column
were held at 160C in a Shimadzu GC-8A gas chromatogram. The ECD in the
Shimadzu was held at 250°C.

The analytical system was calibrated using a blended standard gas
(seawater ratio, PMEL 464568), with available further reference to a
second atmospheric ratio standard. Gas sample loops of known volume
were thoroughly flushed with standard gas and injected into the
system. The temperature and pressure was recorded so that the amount
of gas injected could be calculated. The procedures used to transfer
the standard gas to the trap, precolumn, main chromatographic column,
and EC detector were similar to those used for analyzing water
samples. Four sizes of gas sample loops were used. Multiple injections
of these loop volumes could be made to allow the system to be
calibrated over a relatively wide range of concentrations. Air samples
and system blanks (injections of loops of CFC-free gas) were injected
and analyzed in a similar manner. The typical analysis time for
seawater, air, standard or blank samples was ~12 minutes.
Concentrations of the CFCs in air, seawater samples, and gas standards
are reported relative to the SIO98 calibration scale (e.g.
[Bullister2010]). Concentrations in air and standard gas are reported
in units of mole fraction CFC in dry gas, and are typically in the
parts per trillion (ppt) range. Dissolved CFC concentrations are given
in units of picomoles per kilogram seawater (pmol kg-1). CFC
concentrations in air and seawater samples were determined by fitting
their chromatographic peak areas to multi-point calibration curves,
generated by injecting multiple sample loops of gas from a working
standard (PMEL cylinder 464568) into the analytical instrument. The
response of the detector to the range of moles of CFC passing through
the detector remained relatively constant during the cruise. Full-and
partial-range calibration curves were run several times during the
cruise. Single injections of a fixed volume of standard gas at one
atmosphere were run much more frequently (at intervals of ~90 minutes)
to monitor short-term changes in detector sensitivity.

The purging efficiency of the stripper was estimated by re-purging a
water sample in the upper concentration range and measuring the
residual signal. At a flow rate of 120 cc/min for 6 minutes, the
purging efficiency for SF_6 and F12 was greater than 99% and the
efficiency for F11 was about 99%. The purging efficiency for N_2O was
about 95%, but subject to some degree of variability due to changes in
flow rate and purging temperature. Although correction is made for
this variability, N_2O data from stations 1-22 were rather more
compromised than subsequent data.

Results of 2795 seawater samples are reported from 86 of the 87
original stations, with station 185 omitted due to system problems,
and 5 of the 6 re-occupation stations. Duplicates were taken from 55
stations to estimate precision and variability. Low-level samples were
selected from deep samples and higher level (surface) samples were
mostly taken from the upper water column. Based on similar data from
PO2 Leg 1, we calculate the average deviation to be less than 1.0%
from the mean of the pairs for F12, F11 and N_2O measurements in the
higher concentration samples, and 2.0% from the mean for SF_6
measurements. Deviation from the mean of pairs from deeper samples
averaged less than 5% (or 0.01 pM) from the mean for F12 and F11 and
approximately 10% for SF_6. Due to the exceedingly low levels of SF_6
present in deeper water, accurate estimates of precision are not
possible. A small number of additional water samples had anomalous
SF_6 or CFC concentrations relative to adjacent samples. These samples
occurred sporadically during the cruise, were not clearly associated
with other features in the water column (e.g., anomalous dissolved
oxygen, salinity, or temperature features) and are omitted from the
reported data.

[Bullister2010] Bullister, J.L. and T. Tanhua. 2010. Sampling and
                Measurement of Chlorofluorocarbons and Sulfur
                Hexafluoride in Seawater. In: The GO-SHIP Repeat
                Hydrography Manual: A Collection of Expert Reports and
                Guidelines. IOCCP Report No. 14, ICPO Publication
                series No. 134, Version 1.

[Bullister2008] Bullister, J.L. and D.P. Wisegarver. 2008. The
                shipboard analysis of trace levels of sulfur
                hexafluoride, chlorofluorocarbon-11 and
                chlorofluorocarbon-12 in seawater. Deep-Sea Res. I, v.
                55, pp. 1063-1074.


LADCP
=====

PI
   * Dr. Andreas Thurnherr (LDEO)

Cruise Participant (Responsible for LADCP Data Acquisition)
   * Lily Dove (Caltech)


Data Acquisition and QC
-----------------------

In order to collect full-depth profiles of horizontal and vertical
ocean velocity, two Acoustic Doppler Current Profilers (ADCPs), one
facing upward (uplooker, UL) and the other downward (downlooker, DL),
as well as a Deep Sea Power And Light rechargeable 48V battery and
cables were installed on the CTD rosette. This lowered ADCP (LADCP)
system was provided by the Lamont-Doherty Earth Observatory (LDEO).
The LADCP system is self-contained, requiring on-deck cable
connections to charge the battery and for communicating with the
acquisition computer. The battery charger was affixed to an elevated
cable run in the CTD bay and connected, via a waterproof power switch,
to an outdoor extension power cable connected to vessel power inside
the wet lab. The LADCP data acquisition computer, a Mac Mini, as well
as a bench-top power supply for the ADCPs connected to a waterproof
power switch were installed on a bench in the same lab.

Between casts the LADCP system in the CTD bay was left unpowered, with
the battery connected to the (usually powered) battery charger, and
the two deck cables leading to the data acquisition computer also
connected, but with the bench top power supply turned off. A dummy
plug was installed to protect the male battery connector pins on the
rosette.

A few minutes before the CTD rosette was moved out of the hangar for
deployment, the charger was turned off, the battery was disconnected
from the charger and connected to the ADCPs on the rosette, and the
now free dummy was used to dummy up the battery charger. Then data
acquisition was started on the computer in the wet lab using a set of
operator scripts created by the PI. After verifying that the data from
the previous cast had been fully downloaded and backed up, the old
data files were deleted from the instruments, before these were
programmed to acquire data for the new cast. Due to weak backscatter
observed in many of the profiles from leg 1, the instrument setup was
optimized for range, with 10-m bins and 4-m blanking, rather than the
stardard 8-m bins without blanking used in regions of sufficient
backscatter. The two ADCPs on the rosette used synchronized pings and
they followed a staggered ping rate alternating between 1.3 and 1.6
seconds, which is designed to mitigate contamination from acoustic
reflection from the sea bed. With the instruments pinging the rosette
was disconnected from the LADCP deck cables, and all four ends were
dummied up. The loose cables on the rosette were secured with orange
Velcro strap to prevent whiplashing during the casts. The same type of
Velcro strap was also used to attach some of the permanently installed
LADCP cables to the rosettes in an attempt to minimize plastic waste
(zip ties). Once everything was set up, the CTD operator and the
ResTech were notified that the LADCP system was ready for deployment.
Deployment information was logged on LADCP log sheets once the rosette
had entered the water.

After recovery of the CTD the Velcro straps securing the dummied pig-
tail ends to the rosette were removed, the connectors were rinsed with
fresh water, the dummy plugs were removed and the ADCPs on the rosette
were connected to the deck cables. The battery was then disconnected
from the rosette cable and connected to the charger, with the dummy
being switched from charger to the rosette in the process. After
turning on the bench-top power supply, LADCP data acquisition was
stopped on the acquisition computer and the data download was
initiated.

After the data from the cast had finished downloading (after about 20
minutes for deep casts, 5 minutes for bio casts), the bench top power
supply was turned off with power toggle switch. Then the data files,
one for each the UL and DL, were checked by integrating the measured
vertical velocities in time, which yields estimates for the maximum
depth (zmax) and the end depth (zend) of the profile, both of which
were recorded on the log sheet. Occasionally, after the battery was
fully charged (usually about an hour after charging was initiated, as
indicated by LEDs on the charger) the charger was disconnected from
power in the wet lab and the time was noted on the log sheet. The
battery was more often left on the charger in trickle-charge mode,
however.

Communication between the acquisition computer and the ADCPs was
handled by the “acquire2” set of software scripts, implemented as a
set of UNIX shell commands designed to minimize the possibility of
operator errors. Five different commands are available:

*Ldir*: Lists the status of the LADCP memory, including number of
files, file size, etc. Used primarily to verify that the LADCP is
operational while connected to the bench power.

*Lstart*: Wakes the instruments, lists their memory contents, clears
the memory (after operator confirmation) and programs the instruments
to start pinging by uploading command files. CTD station and cast
numbers must be provided by the operator since the LADCP files use an
independent numbering scheme.

*Ldownload*: Interrupts the running data acquisition, downloads the
data, and backs up the data files to a network drive.

*Lcheck*: Integrates the measured vertical velocities from both ADCPs
to estimate zmax and zend, which are displayed together with other
useful profile statistics before the data files are backed up on the
network drive.

*Lreset*: Reset the ADCPs after swapping instruments and in case of
communications problems.

During the night watch, the LADCP data were processed for horizontal
velocity using the LDEO_IX processing software and for vertical
velocity using the LADCP_w processing software, both installed on the
acquisition computer and accessed on a personal computer using Screen
Sharing. CTD .cnv data were obtained from the ship’s shared drive and
processed into 1 and 6 Hz formats using the LADCP_w processing
software. In addition to the zend and zmax processing diagnostics,
LADCP data quality was monitored by creating section plots, seen in
Figure 1. Over most of the section the LADCP data quality appears to
be good, although the lack of backscattering particles throughout the
intermediate and abyssal depths of the water column off the shelf lead
to potentially unconstrained velocities. A more comprehensive post-
cruise LADCP QC will be carried out by Thurnherr in his lab before
submission of the combined P02 leg 1 and 2 data to the archives.


Instrumentation
---------------

Two 300kHz Teledyne RDI Workhorse Monitor ADCPs (WHM300) were used for
all profiles up to 20401, which covers the full extent of the P2
section: a primary/DL (S/N 3441) and secondary/UL (S/N 12734). The UL
instrument replaced another instrument used on leg 1 (S/N 754) before
any profiles began on leg 2. The replacement UL (S/N 12734) was fitted
with a custom self-recording accelerometer/magnetometer package called
Independent Measurement Package (IMP). Due to a hardware fault the IMP
did not record any data up to profile 13001. After repairing the
instrument its performance was monitored using its built-in WiFi
access point. Wireless data download with rsync proved easy with data
rates at 20 feet distance typically around 700Mbps. However, the
initial connection with a laptop could not be made at any distance
until first another connection had been made with an iPhone, which
typically was no problems at distances of 2-3 feet. After profile
20401, the final cast of the full P02 transect, the DL instrument was
replaced with a different instrument (S/N 24477), this one fitted with
the most recent prototype of the IMP, which includes MEMS gyros. This
DL was used for the remainder of the profiles, during which a partial
repeat sample of the California Current system was collected. The data
from the IMPs will be merged with the ADCP data for final post-cruise
processing and QC.

A single Deep Sea Power And Light rechargeable 48V battery (S/N 1223)
experienced no problems with charging or operation over the duration
of the cruise.


Preliminary Results
-------------------

ADCPs rely on particles, such as marine life and sinking detritus, in
the water column in order to measure the water velocities. The measure
of particles in the water is called backscatter. Backscatter is
variable across the global ocean and throughout the water column.
Figure 2 shows the backscatter from Leg 2 of P02. Note the double
layer of backscatter in the upper 1000 meters from station 11801 to
station 18401. There is also a significant increase in backscatter at
intermediate and abyssal depths near the coast (stations 18901
onwards). Regions with low backscatter make it difficult to constrain
the calculated horizontal velocities, so further quality control is
needed in the intermediate and abyssal depths of the first part of Leg
2.

There are three “boundary conditions” imposed on the calculation of
horizontal velocities from the LADCP: the GPS, the bottom track, and
the shipboard ADCP (SADCP). Figure 3 shows the root mean squared error
[m/s] from the removal of the bottom track and SADCP from calculations
of the horizontal velocities. Note the decrease of error upon approach
to the shelf (past station 18401), likely as a result of increased
backscatter.


Figures
-------

   [image]Figure 1: (a) Zonal (east-west) and (b) meridional (north-
   south) velocities calculated from the LADCP across the full Leg 2
   of P02.

   [image]Figure 2: Backscatter [decibels] along the P02 Leg 2
   transect. The colorbar is designed so each block of color contains
   an equal number of points.

   [image]Figure 3: Root mean squared error [m/s] resulting from the
   removal of the bottom track (blue) and shipboard ADCP (orange)
   boundary conditions.


BIO GO-SHIP
===========

PIs
   * Adam Martiny (UCI)

   * Jason Graff (OSU)

   * Nicole Poulton (Bigelow)

   * Sophie Clayton (ODU)

Samplers
   * Skylar Gerace (UCI)

   * Sydney Lewis (UH)


Underway Sampling
-----------------

DNA/RNA, Large Volume Particulate Organic Matter (POC, PON, POP,
PCOD), HPLC, and FCM samples were collected at approximately 0600,
1200, and 2000 local time via the underway tap (59 stations). The
underway system was pumped with a diaphragm pump instead of the
impeller pump so that organic matter would not be shredded up. The
timing for collecting samples around 2000 was based on each day’s
solar noon + 8 hours. Underway samplings were skipped if the CTD
rosette were to collect biological samples within a three to four hour
window of an underway sampling time.


Bio CTD Station Sampling
------------------------

At every third GO-SHIP P2 station, the CTD rosette was casted twice
(32 stations). The first cast only collected biological samples
(called the “bio cast”) and the second cast only collected core GO-
SHIP samples (pH, nutrients, etc.). For the bio cast, the CTD rosette
was sent to a maximum depth of 1000 m. As the rosette surfaced, it
collected seawater only to be used for biological samples (ie.
DNA/RNA, Large Volume POM, HPLC, and FCM). Niskin bottles were fired
at depths of 1000 m, 500 m, 200 m, 150 m, 100 m, 75 m, 40 m, and 5 m.
The CTD rosette was then recovered, the seawater was collected, and
then the CTD was cast again to collect the core GO-SHIP samples.


BGC Argo Float Station Sampling
-------------------------------

At each station where a BGC Argo float was deployed, the sampling
scheme for DNA/RNA, Large Volume Particulate Organic Matter (POC, PON,
POP, PCOD), HPLC, and FCM was different than the usual bio cast
sampling. For every bio cast at a float station, Niskin bottles were
fired at depths of 1000 m, 500 m, 200 m, ~30 m below the chlorophyl
maximum depth, at the chlorophyl maximum depth, ~ 30 m above the
chlorophyl maximum depth, at the bottom of the mixed layer, and 5 m.
For Leg 2, four out of the thirty-two bio cast stations were float
stations (GO-SHIP P2 stations 122, 146, 170, and 191).


DNA/RNA
-------

DNA/RNA samples were collected at each underway sampling, with
duplicates collected at 2000. For bio casts, seawater for DNA/RNA was
collected at depths of 1000 m, 200 m, 100 m and 5 m. For bio casts at
float stations, seawater for DNA/RNA was collected at depths of 1000
m, 200 m, at the chlorophyll maximum depth, and 5 m. 100 DNA/RNA
samples were collected from the underway and 120 were collected from
the rosette, resulting in a total of 220 DNA/RNA samples collected
throughout Leg 2.

Each sample was a Sterivex 0.22µm filter cartridge that had seawater
filtered through it. For DNA/RNA, seawater was transported from the
underway or rosette to the filtration system using 4L plastic
cubitainers. Volumes of 4 - 8L of seawater were filtered through a
Sterivex 0.22µm filter cartridge via a peristaltic pump set to a low
speed. After the seawater had been filtered, air was pumped out of the
filter cartridge using a 5 mL syringe. The cartridge bottom was then
sealed with Crito-Seal before pipetting 1620µL of sterile lysis buffer
into the cartridge. The cartridge was then capped with a luer-lock. 10
of the 100 underway samples were duplicates that had RNA/DNA Shield
buffer added instead of lysis buffer in order to compare these two
buffer types. Each filter was placed in a Ziplok bag and stored at -80
°C until time for analysis. Final filtration volume was recorded for
all samples. Samplers wore nitrile gloves throughout the entirety of
sample collection and filtration.

Before Leg 1, all silicone tubing, Omnifit caps and cubitainers were
soaked with soap water, 10% HCl acid, and Milli-Q water. At the end of
every week of the cruise, the peristaltic pump tubing and Omnifit caps
were cleaned with 10% bleach solution and then rinsed with Milli-Q
water. All cubitainers were rinsed three times with sample water
before being filled.


Large Volume Particulate Organic Matter (POM)
---------------------------------------------

Whatman GF/F filters (pore size 0.7 µm, diameter of 25 mm) were
filtered with 2 - 8 L of seawater to serve as particulate organic
matter (POM) samples. Filters were collected for post-cruise analyses
that determined either particulate organic carbon/nitrogen (POC/N),
phosphorous (POP) or particulate chemical oxygen demand (PCOD). POM
samples were collected via the underway tap or the CTD rosette at a
depth of 5 m (91 stations). A total of 801 samples was collected (297
from the underway and 504 from the rosette).

Nine 8 L carboys were filled with 2 - 8 L of seawater for each POM
filtration. The carboys were divided into three groups for desired
sample type: POC/N, POP, and PCOD. As a result, triplicates were
collected for POC/N, POP, and PCOD at each sampling. Seawater was
drawn through the filters using an aspirator pump with a vacuum
setting of -0.06 to -0.08 MPa. After all seawater had been filtered,
filters for POP were rinsed with 5 mL of 0.017 M Na2SO4 to remove any
dissolved organic phosphorous. PCOD filters were rinsed with 5 mL of
Milli-Q water to remove excess chloride. Filters were folded and then
stored at -80°C in pre-combusted aluminum foil.

Before starting Leg 2, GF/F filters and foil squares were precombusted
at 500°C for 5 hours. All silicone tubing, filter cartridges, and
carboys were soaked with soap water, 10% HCl acid, and then Milli-Q
water. Samplers wore nitrile gloves throughout the entirety of sample
filtration. All carboys were rinsed three times with sample water
before being filled.


Small Volume Particulate Organic Carbon/Nitrogen (POC/N)
--------------------------------------------------------

Small volume particulate organic carbon/nitrogen (POC/N) samples were
only collected at the four float stations. The CTD rosette collected
seawater for these samples at a depth of 200 m, ~30 m below the
chlorophyl maximum depth, at the chlorophyl maximum depth, ~30 m above
the chlorophyl maximum depth, at the bottom of the mixed layer, and at
a depth of 5 m. From each of these depths, 2 L of seawater was
collected and a single duplicate of 2 L was collected from one of
these depths. The depth from which the duplicate was collected was
decided at random and varied across float stations. Small volume POC/N
were collected to compare the carbon/nitrogen quantified from large
volume POC/N samples.

Seawater was transported from the rosette to a filtration manifold
using 1 -2 L clear plastic bottles. The filtration manifold was hooked
to a vacuum pump set at 100 mmHg. Seawater was filtered onto pre-
combusted Whatman GF/F filters (pore size 0.7 µm, diameter of 25 mm).
A dry blank and a wet blank were also collected at each float station.
A dry blank consisted of taking a GF/F filter out of the pre-combusted
foil it was stored in, and then putting it pack into the foil without
filtering any seawater. The wet blank consisted of placing another
GF/F filter below one of the GF/F filters before filtering seawater
through them. The bottom filter was collected and saved as the wet
blank. For Leg 2, the wet blank was always placed under the duplicate
sample filter, thus the seawater filtered through it also came from a
random depth and varied across float stations. All filters were then
stored at -80 °C in pre-combusted aluminum foil. Samplers wore nitrile
gloves throughout the entirety of seawater collection and filtration.
All bottles were rinsed three times with sample water before being
filled.


Particulate Chemical Oxygen Demand (PCOD) Volume Trial
------------------------------------------------------

Volume trials for PCOD samples were performed three times during Leg
2. These trials happened randomly when there was enough time in-
between underway or rosette sampling. The volume trial consisted of
filling the POM carboys via the underway with volumes ranging from 1 -
8 L. Starting with a carboy filled with 8 L, each consecutive carboy
was filled with 1 L less than the carboy filled before it (ie. the
second carboy was filled with 7 L, the third was filled with 6 L,
etc.). The seawater from each carboy was filtered onto a Whatman GF/F
(pore size 0.7 µm, diameter of 25 mm) in the same method for POM
filtration. Filters were then rinsed with 5 mL of Milli-Q water to
remove excess chloride. The purpose of the volume trials is to test
the sensitivity of the PCOD analysis after the cruise.

All carboys were rinsed three times with sample water before being
filled. GF/F filters and foil squares were also pre-combusted and then
stored at - 80 °C. Nitrile gloves were worn for all steps mentioned
above.


High Performance Liquid Chromatography (HPLC)
---------------------------------------------

HPLC samples were collected with each underway sampling and at each
bio cast. For bio casts, seawater for HPLC samples was collected at
100 m, 40 m, and 5 m. For float stations, seawater for HPLC samples
was collected at a depth of 200 m, ~30 m below the chlorophyl maximum
depth, at the chlorophyl maximum depth, ~30 m above the chlorophyl
maximum depth, at bottom of the mixed layer, and at a depth of 5. A
total of 181 samples was collected (111 from the rosette and 70 from
the underway). The purpose of HPLC samples was to quantify
photosynthetic pigment content.

For HPLC samples, 2 L of seawater was transported from the underway or
rosette with 1 L amber HPDE bottles. Seawater was then filtered with
Whatman GF/F filters (pore size 0.7 µm, diameter of 25 mm) using a
vacuum pump set at 100 mmHg. Filters were folded twice, placed into 1
mL cryovials, and then stored at -80 °C. Nitrile gloves were worn
throughout seawater collection and filtration. All HPDE bottles were
rinsed three times with sample water before being filled.

A duplicate HPLC sample was collected for every other underway
sampling. This was to ensure that roughly 10% of total HPLC samples
were duplicates. At float stations, a single duplicate of 2 L was also
collected from one of the depths chosen by random. The depth chosen
for the duplicate varied across float stations.


Flow Cytometry (FCM)
--------------------

FCM samples were collected with each underway sampling and at each bio
cast. For bio casts, seawater for FCM samples was collected at depths
of 1000 m, 500 m, 200 m, 150 m, 100 m, 75 m, 40 m, and 5 m. For float
stations, seawater for FCM samples was collected at depths of 1000 m,
500 m, 200 m, ~30 m below the chlorophyl maximum depth, at the
chlorophyl maximum depth, ~30 m above the chlorophyl maximum depth, at
bottom of the mixed layer, and 5 m. A total of 305 samples was
collected (245 from the rosette and 59 from the underway). FCM samples
were to be analysed after the cruise with a flow cytometer.

Seawater for FCM samples was collected with 50 mL tinted falcon tubes.
From the tubes, 1.8 mL of seawater was pipetted into a 2 mL cryovial.
While under a fume hood, 18 µL of a preservation mixture (half 25%
Glutaraldehyde and half 2% Kolliphor) was added to each cryovial. The
cryovial was then inverted several times and then placed on a vial
stand for about for 10 minutes. The vials were then flash frozen with
liquid nitrogen and stored at -80 °C.


Planktoscope
------------

At most stations with a bio cast, 40 - 100 L of seawater from the
underway tap was filtered by a 10 µm mesh to concentrate >10 µm
particles into a volume of ~250 mL (27 stations). The volume used from
the underway was determined by filling a 20 L carboy multiple times.
For two of the twenty-seven stations, about 4 L of seawater from the
chlorophyl maximum depth was concentrated to ~250 mL instead.
Chlorophyl maximum depth seawater was collected via the CTD rosette.
100 mL from the ~250 mL was preserved with 0.5 mL of Lugols solution
for post-cruise analysis. 1.8 mL was also taken from the ~250 mL and
preserved by the same method used for FCM samples. About 5 - 20 mL of
the ~250 mL was also fed into a planktoscope. The purpose of the
planktoscope was to quantify plankton abundance.

The planktoscope took 100 pictures as 5 mL of seawater flowed in front
of a 20 mm tube lens and a 16 mm objective lens. Seawater was set to
flow at a rate of 2 mL/min. The planktoscope then segmented parts of
the pictures that contained distinct outlines and dark shapes against
a white background. The segmenting program was optimized to detect
objects in the size range of 40 µm - 200 µm. The lens were focused and
a white-balanced was performed before filming each sample


Underwater Vision Profiler 5 HD (UVP)
=====================================

PI
   * Andrew McDonnell (UAF)

Cruise Participant
   * Lily Dove (Caltech)


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

The Underwater Vision Profiler 5 (UVP5) HD (High Definition) serial
number 201 was programmed, mounted on the rosette, and charged. This
instrument is owned by Emmanuel Boss at University of Maine. The UVP5
is outfitted with a High Definition 4 Mp camera with an acquisition
frequency of up to 20 Hz. This optical imaging device obtains in situ
concentrations and images of marine particles and plankton throughout
the water column, capturing objects sized ~100 µm to several cm in
diameter. The camera of the UVP5 HD is different from the previous
non-HD version, but the operations are identical for both. The
instrument and data processing are described in [Picheral2010]. Depth
trigger mode was used throughout the entirety of the cruise,
programmed to turn on at 15 m with a maximum depth of 6000 m. A 20 m
soak for one minute was used throughout the cruise.


Problems
--------

See Leg 1 report for details on UVP problems.

No data were downloaded during Leg 2 due to inability to establish
communication with the unit. The intrument was run on all core
stations and left off for bio stations. The instrument will be sent to
the manufacturers for maintenance who will open the bulkhead and
hopefully download the data from the remaining stations.


Future Data Analysis
--------------------

A combination of machine learning and manual validation will be used
to sort images using the Ecotaxa database. Images will be sorted into
various zooplankton taxa and detrital categories. Zooplankton
categories will include crustacea (including copepods and krill),
gelatinous (larvacean, jellyfish, salps), and rhizaria. Examples of
these images are shown in Fig. 1.


Figures
-------

   [image]Fig. 1: Examples of particle and plankton images captured by
   the UVP5HD and processed by custom software. The scale bar
   indicates 2 millimeters. Station number, image number for that
   cast, and depth at which the image was captured are also given in
   the image.

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


Underway pCO_2
==============

PIs
   * Simone Alin (NOAA/PMEL)

Technicians
   * Julian Herndon (UW/NOAA/PMEL)

   * Andrew Collins (UW/NOAA/PMEL)

The partial pressure of carbon dioxide (pCO_2) in the surface ocean
was measured throughout the cruise track of this cruise with a General
Oceanics 8050 pCO_2 Measuring System. Uncontaminated seawater was
continuously passed (~1.7-2.1 L/min) through a chamber where the
seawater concentration of dissolved CO_2 was equilibrated with an
overlaying headspace gas. The CO_2 mole fraction of this headspace gas
(xCO_2) was measured every two minutes via a non-dispersive infrared
analyzer (LiCor 7000) for 60 consecutive measurements. At the end of
these 60 discrete measurements, a set of five standard gases was
analyzed; four of these standards have known CO_2 concentrations
certified by the NOAA Earth Science Research Laboratory (ESRL) ranging
from ~300 to ~900 ppm CO_2 (see Table 1). The fifth standard is a tank
of 99.9995% ultra-high purity nitrogen gas, used as a baseline 0%
CO_2. Following the measurements of standard gases, six consecutive
measurements of atmospheric xCO_2 were made of air supplied through
tubing fastened to the ships forward jack staff. Twice a day, the
infrared analyzer was zeroed and spanned using the nitrogen gas and
the highest concentration CO_2 standard (911.41 ppm). In addition to
measurements of seawater xCO_2, atmospheric xCO_2, and standard gases,
other variables were monitored to evaluate system performance (e.g.
gas and water flow rates, pump speeds, equilibrator pressures, etc.).
For more detail on the general design and operation of this underway
pCO_2 system, see [Pierrot2009].

Throughout the duration of the research cruise, the system performed
well. Initial problems with non-ideal water flow (i.e. <1.5 L/min) add
some uncertainty to some of these measurements and will need to be
carefully evaluated before determining their suitability for inclusion
in the dataset (see details regarding water flow below). Of
approximately 18,730 sea surface xCO_2 measurements, 243 have been
flagged questionable (quality flag 3) and 51 have been flagged bad
(quality flag 4) during this preliminary round of data quality control
and assurance.


Notes on seawater source and data:
----------------------------------

For details regarding the source of seawater to the pCO2 system, see
Julian Herndon’s report from Leg One of this research cruise. During
the first several days of this leg, substantial effort was made by
research technicians and the chief engineer to establish sufficient
water flow to the system. Initial efforts included trying to balance
the water flow to meet the needs of the various (i.e. biological,
chemical, shipboard) users onboard. However, insufficient flow
persisted to the pCO_2 system. Flow was increased by closing down a
forward overflow drain, but quickly dropped below 1.5 L/min. After
exhausting nearly every possible avenue by balancing flows, adjusting
pump speeds and pressures, it was determined that an obstruction must
be preventing sufficient flow to the system. John Ballard and Andrew
Collins disassembled the primary equilibrator in the pCO_2 system to
learn that it was indeed obstructed. After cleaning, the flow to the
pCO_2 system was greatly enhanced and remained sufficient for the
remainder of the cruise. No other major problems were encountered
during the cruise that affected data quality. One issue that persists
relates to occasional dropouts from the MET system, likely due to a
timing mismatch in the communications setup.

The Resident Technicians onboard used bleach to clean/sanitize the
scientific seawater system after we departed Hawaii and prior to the
pCO_2 system being turned on. Model and serial numbers for the pCO_2
instrument components and ancillary instruments have been recorded in
a separate Excel file and will reported as part of the metadata that
will accompany the final/processed pCO_2 data submission. This pCO_2
system does not have a Druck or other external barometer installed in
the dry box to measure the pressure in the LiCor cell. The primary
equilibrator in this pCO_2 system is an older, non-jacketed
equilibrator built using a clear plastic filter housing.

To facilitate data processing and future troubleshooting of the
Revelle pCO_2 system, the column headings for data in the pCO_2 files
sourced from the ship are identified in Table #2. Serial numbers and
additional details for the instruments in table #2 are in a separate
excel file and will be reported as part of the metadata for pCO_2 data
submitted from this cruise.


Table 1: Standard gases for P02 2022 cruise UW pCO_2 system.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+-----------------------------------+-----------------------------------+-----------------------------------+
| Standard                          | Concentration (ppm)               | Tank Serial Numbers               |
|===================================|===================================|===================================|
| 1                                 | 0.0                               | Praxair 5.0 Ultra High Purity N2  |
+-----------------------------------+-----------------------------------+-----------------------------------+
| 2                                 | 283.42                            | LL55868                           |
+-----------------------------------+-----------------------------------+-----------------------------------+
| 3                                 | 399.51                            | LL127199                          |
+-----------------------------------+-----------------------------------+-----------------------------------+
| 4                                 | 539.97                            | LL127204                          |
+-----------------------------------+-----------------------------------+-----------------------------------+
| 5                                 | 911.41                            | LL127176                          |
+-----------------------------------+-----------------------------------+-----------------------------------+


Table 2: pCO_2 system ship supplied data column headers for P02 2022 cruise, Leg 1.  MWL = mean water level.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

+---------------------------+---------------------------+---------------------------+---------------------------+
| Column Header             | Instrument                | System                    | Location                  |
|===========================|===========================|===========================|===========================|
| TSGF1                     | SW flow meter             | 3                         | Bow                       |
+---------------------------+---------------------------+---------------------------+---------------------------+
| TSGT2                     | TSG45 temperature         | 2 and 3                   | Hydrolab                  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| TSGS2                     | TSG45 salinity            | 2 and 3                   | Hydrolab                  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| TSGF2                     | SW flow meter to TSG45    | 2 and 3                   | Hydrolab                  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| PCO2F                     | SW flow meter to pCO_2    | 2 and 3                   | Hydrolab                  |
+---------------------------+---------------------------+---------------------------+---------------------------+
| SST                       | SBE 38 temperature        | 3                         | Bow                       |
+---------------------------+---------------------------+---------------------------+---------------------------+
| AT                        | RM Young temperature      | MET                       | 56’ above MWL*            |
+---------------------------+---------------------------+---------------------------+---------------------------+
| BP                        | RM Young barometer        | MET                       | 56’ above MWL*            |
+---------------------------+---------------------------+---------------------------+---------------------------+
| HDG                       | Konsberg GPS              |                           |                           |
+---------------------------+---------------------------+---------------------------+---------------------------+
| SOG                       | Speed over ground         |                           |                           |
+---------------------------+---------------------------+---------------------------+---------------------------+

While the raw data is not reported here, it has been collected and
will be analyzed using MATLAB® routines developed by Dr. Denis Pierrot
of the Atlantic Oceanographic and Meteorological Lab in Miami, FL.
Measurements of gas standards were generally within 1% of their
certified value throughout the duration of the cruise.

The data from the pCO_2 system that is included as part of the ships
data supplied by the onboard Resident Technicians is xCO_2 (not pCO_2)
that has not been processed or evaluated for QA/QC and as such should
be considered preliminary.

[Pierrot2009] Pierrot, D., Neill, C., Sullivan, K., Castle, R.,
              Wanninkof, R.W., Lüger, H., Johannessen, T., Olsen, A.,
              Feely, R.A., Cosca, C.E.; 2009. Recommendations for
              autonomous underway pCO2 measuring systems and data-
              reduction routines. Deep-Sea Research II 56 (2009)
              512–522


Chipods
=======

PI
   * Jonathan Nash (OSU)


Overview
--------

Chipods are instrument packages that measure turbulence and mixing in
the ocean. Specifically, they are used to compute turbulent
diffusivity of heat (K) which is inferred from measuring dissipation
rate of temperature variance (\chi) 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_Nash2009]. 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 December 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.

The chipods from Leg 1 were left on through station 16301, at which
point all pressure cases were swapped. They continuously recorded data
until the end of the leg. Only one issue occurred with the chipods
following the recovery of cast 12601. The sensor tip on chipod #12 had
popped out and flooded the sensor. Sensor was swapped for chipod #11.

   [image]

Upward-looking chipod sensors attached to the rosette.

   [image]

Downward-looking chipod sensor attached to the rosette.

   [image]Highly sensitive temperature probe, which is sampled at
   100Hz.

+------------------+--------------------+-----------------+------------------------+
| Logger Board SN  | Pressure Case SN   | Up/Down Looker  | Cast Used              |
|==================|====================|=================|========================|
| 2013             | Ti 44-12           | Up              | 118-162                |
+------------------+--------------------+-----------------+------------------------+
| 2032             | Ti 44-15           | Up              | 118-162                |
+------------------+--------------------+-----------------+------------------------+
| 2014             | Ti 44-08           | Down            | 118-162                |
+------------------+--------------------+-----------------+------------------------+
| 2027             | Ti 44-3            | Up              | 163-205                |
+------------------+--------------------+-----------------+------------------------+
| 2017             | Ti 44-6            | Up              | 163-205                |
+------------------+--------------------+-----------------+------------------------+
| 2025             | Ti 44-7            | Down            | 163-205                |
+------------------+--------------------+-----------------+------------------------+

[Moum_and_Nash2009] Moum, J., and J. Nash, Mixing Measurements on an
                    Equatorial Ocean Mooring, Journal of Atmospheric
                    and Oceanic Technology, 26(2), 317–336, 2009


Float Deployments
=================


GO-BGC Argo Floats
------------------

PIs
   * Kenneth Johnson (MBARI)

   * Lynne Talley (UCSD/SIO)

   * Susan Wijffels (WHOI)

   * Curtis Deutsch (Princeton)

   * Steven Riser (UW)

   * Jorge Sarmiento (Princeton)

Four GO-BGC Argo floats were deployed during the cruise with the float
numbers continuing from leg-1 (table below). All floats were UW-
modified Teledyne Webb Apex floats equipped with SBE41-CP CTDs, O_2,
NO_3, pH, and FLBB bio-optical sensors, and provided by the UW float
lab (S. Riser Argo lab). Before deployment the float sensors were
prepared (cleaned) according to the written instructions provided with
the floats. Floats were deployed from the aft deck after the last CTD
profile for that station with the ship steaming at 0.5kts. The floats
were lifted over the stern, then carefully lowered into the water with
a slip-line strung through the deployment collar of the float. All of
the floats began reporting data immediately and the initial profiles
indicate that all sensors were operating well.

All deployments occurred at stations where bio casts were carried out.
In addition to the standard bio-cast sampling, additional water
samples were collected below the mixed layer as well as at, above and
below the chlorophyll maximum. The additional samples were analyzed
for FCM, POC and POCN.

All floats were adopted by different schools as part of the
adopt-a-float program (https://www.go-bgc.org/outreach/adopt-a-float).
Names and images provided by the schools were drawn on the floats
before deployment. Each school received details from their deployment
via posts on the GO-BGC expeditions webpage, handled by George
Matsumoto (MBARI) and Jennifer Magnusson.


Float deployments.
^^^^^^^^^^^^^^^^^^

+------------------+------------------+------------------+------------------+------------------+------------------+
| Deployment       | WMO              | Lat              | Lon              | Date and Time    | CTD Station      |
|                  |                  |                  |                  | (UTC)            |                  |
|==================|==================|==================|==================|==================|==================|
| 11               | 9382             | 30:00 N          | 158:54 W         | 2022/06/18 08:25 | 122              |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 12               | 9419             | 30:00 N          | 145:03 W         | 2022/06/26 04:45 | 146              |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 13               | 9422             | 30:00 N          | 131:11 W         | 2022/07/03 06:08 | 170              |
+------------------+------------------+------------------+------------------+------------------+------------------+
| 14               | 9414             | 31:45 N          | 119:49 W         | 2022/07/09 11:28 | 191              |
+------------------+------------------+------------------+------------------+------------------+------------------+


Viral Abundances
================

PI
   * Ben Temperton (UoE)

Technician
   * Michelle Michelsen (UoE)

Analyst
   * Michelle Michelsen (UoE)

Support
   NSF


Project Goals
-------------

The goal of this project is to evaluate viral abundances within the
cellular fraction (0.22µ Sterivex PC filter) and viral fraction (0.02µ
Anotop Filter).


Sampling
--------

Two liters of water were taken from the surface from every other bio-
cast, and the last three bio-cast for a total of 14 stations sampled.
Samples were sequentially filtered through a 0.22µ sterivex and 0.02µ
anotop filter for 1.5-2.5 hours or when the filter clogged. Below is a
table of stations and amount filtered. The filters were then frozen at
-80ºC and hand carried back to UCSB to organize shipping to University
of Exeter for further analysis. The filters will then be used for DNA
extractions at University of Exeter to describe cell associated
viruses and free viral particles [Martinez-Hernandez].

+--------------+-----------------+------------------------------------+
| Station_Cast | Amount Filtered | Amount of Time                     |
|==============|=================|====================================|
| 131_01       | 650mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 137_01       | 600mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 143_01       | 500mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 149_01       | 800mL           | 2 hours                            |
+--------------+-----------------+------------------------------------+
| 155_01       | 500mL           | 2 hours                            |
+--------------+-----------------+------------------------------------+
| 161_01       | 550mL           | 1.75 hours                         |
+--------------+-----------------+------------------------------------+
| 167_01       | 500mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 173_01       | 600mL           | 2 hours                            |
+--------------+-----------------+------------------------------------+
| 179_01       | 600mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 185_01       | 600mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+
| 191_01       | 400mL           | 2 hours                            |
+--------------+-----------------+------------------------------------+
| 197_02       | 500mL           | 2 hours                            |
+--------------+-----------------+------------------------------------+
| 200_01       | 250mL           | 2.5 hours                          |
+--------------+-----------------+------------------------------------+
| 203_01       | 270mL           | 1.5 hours                          |
+--------------+-----------------+------------------------------------+

[Martinez-Hernandez] Martinez-Hernandez Francisco, Garcia-Heredia
                     Inmaculada, Lluesma Gomez Monica, Maestre-
                     Carballa Lucia, Martínez Martínez Joaquín,
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