**NACP West Coast Cruise**

R/V *Wecoma*, **W0705A**

11 May -- 14 June 2007

Newport, OR -- San Diego, CA USA

Chief Scientists: Richard A. Feely and Christopher L. Sabine

NOAA Pacific Marine Environmental Laboratory

![](media/image1.jpeg){width="5.50625in" height="6.115972222222222in"}

**Cruise Report**

**14 June 2007**

**Table of Contents**

**1.0
Summary............................................................................\...2**

**2.0
Introduction........................................................................\...2**

**3.0 Description of Measurements from Vertical
Profiles........................3**

***3.1 CTD/Hydrographic Measurements
Program..........................................3***

***3.2 Salinity
Measurements....................................................................16***

***3.3 Oxygen
Measurements....................................................................17***

***3.4 Nutrient
Measurements......\..........................................\...\...\...\...\...\...\...\....18***

***3.5 DIC
Measurements...........................\.............................................19***

***3.6 TA
Measurements..........................................................................20***

***3.7 Oxygen Isotopes and O~2~/Ar gas ratio sampling
......................................21***

***3.8 Dissolved Organic
Carbon................................................................22***

***3.9 Colored Organic Matter
(CDOM).......................................................22***

***3.10 Particulate Organic Carbon (POC), Particulate Organic***

***Nitrogen (PON), Biogenic Silica and chlorophyll
(chl)..............................22***

***3.11 Phytoplankton
Counts....................................................................23***

**4.0 Underway
Measurements........................\.................................23**

***4.1 OSU Underway DIC/pCO~2~/TSG/O~2~ and bio-optics
system................\..............23***

**5.0 Other
Measurements.............................\..................................24**

***5.1 Floats
.....................................................................................\...\.....24***

***6.0 Preliminary Results for Mexican
Waters......................................................24***

**6.0
Acknowledgements................................................................25**

**7.0
References...........................................................................25**

**1.0 Summary**

The R/V *Wecoma* completed the first North American Carbon Program
(NACP) West Coast Cruise from Queen Charlotte Sound in western Canada in
the north to Cabo San Lazaro, Baja California, Mexico in the south. The
cruise was designed to complete a series of 13 transects approximately
orthogonal to the Pacific Coast (Figure 1). Full water column
CTD/rosette stations were occupied at 111 specified locations along the
transects. A total of 16 scientists from PMEL/AOML and other government
agencies and universities participated on the 33-day cruise which
departed from the Oregon State University Marine Facility in Newport,
Oregon on 11 May, and arrived on schedule in San Diego, California on 14
June. Water samples were collected from the 24-bottle rosette at each
station and analyzed for salinity, oxygen, nutrients, dissolved
inorganic carbon, total alkalinity, dissolved organic matter, colored
dissolved organic matter, particulate organic carbon, Particulate
silica, and chlorophyll. Argo floats were deployed at 4 locations.
Near-surface measurements of seawater and atmospheric pCO~2,~ and
bio-optical properties were also made along the cruise track. No major
problems were encountered on the cruise and all major cruise objectives
were achieved.

**2.0 Introduction**

In support of the interagency North American Carbon Program (NACP) of
the Climate Cycle Science Program (CCSP), NOAA conducted the NACP West
Coast Cruise (Figure 1) along the Pacific west coast to study carbon
cycle processes in the coastal zone over a wide range of oceanographic,
atmospheric, and biogeochemical conditions. The coastal ocean plays a
critical role in the North American carbon cycle and global carbon
dynamics. It is a conduit for transport of terrestrial material from the
land to the open ocean and its specific biological productivity is on
average about three times larger than the average open-ocean values. It
is also the region where the majority of the interior ocean interacts
with the bottom boundary, leading to enhancements of many chemical,
biological and physical processes in mid-water regions of the ocean. The
coastal regions have large air-sea fluxes both into and out of the
ocean. To date, the net magnitude and direction of the flux still have
large uncertainties. Globally, net CO~2~ fluxes as large as 1 Pg C/year,
or about 60% of the oceanic uptake, have been hypothesized for this
region of the oceans. The large flux is due, in part, from the coastal
pump hypothesis in which the coastal margin sink is enhanced by net
offshore carbon transport. The uncertainty in coastal ocean flux would
be reduced with comprehensive measurements of CO~2~ and related
controlling parameters and yields significant improvements in the
understanding of carbon sources and sinks on the continental shelf. The
major goal of the cruise was to identify the sources and sinks of CO~2~
in the U.S. coastal regime, along with their magnitudes, scales of
variability, and controls on CO~2~ fluxes. The coastal zone must be well
quantified regarding carbon sources and sinks in order to make
reasonable projections of future atmospheric CO~2~ levels.

To address this problem, the PMEL/AOML Marine CO~2~ Program has
initiated a coastal carbon studies component to the U.S. North American
Carbon Program to apply a variety of approaches for studying the carbon
cycle (e.g. survey cruises, underway surface observations, and moorings)
in the coastal region to study the invasion and transport of
anthropogenic CO~2~ and other tracers in coastal ocean waters. This
program is designed to establish baseline observational fields for
carbon system parameters, provide comparative data for observations from
other projects, and develop a set of hydrographic transects of full
water column measurements to be re-occupied over time for studies of
inter-annual changes in physical, chemical and biological
characteristics of the coastal ocean.

This NACP West Coast cruise aboard the R/V *Wecoma*, was the first of
what is planned to be a biennial sequence of observations and studies of
carbon in the dynamic coastal ocean region above/adjacent to the
continental shelf along the west coast of the North American continent.
Data from this cruise will provide a robust observational framework to
monitor long-term trends on inter-annual timescales, and determine the
temporal variability of the inorganic carbon system and its relationship
to biological and physical processes in the coastal ocean and their
capacity to withstand the onset of ocean acidification.

Table 1. Cruise Participants of the NACP West Coast Cruise

![](media/image2.wmf){width="6.497916666666667in" height="4.59375in"}

The *Wecoma* W0705A cruise was supported by the NOAA Global Carbon Cycle
(GCC) program. Sixteen scientists representing 5 universities and 3
government research laboratories participated on the cruise (Table 1)
covering the western North American continental shelf region from Queen
Charlotte Sound in western Canada in the north to Cabo San Lazaro, Baja
California, Mexico in the south. The R/V *Wecoma* departed Newport, OR
on 11 May 2007. The ship proceeded north to the first station at
51°1.08'N, 132°50.72'W. The cruise completed a series of 13 transects
approximately orthogonal to the Pacific Coast (Figure 1). Full water
column CTD/rosette stations were occupied at specified locations along
each of the transects. Twenty-four 12L and 10L Niskin-type bottles were
used to collect water samples from throughout the water column at each
station. Each Niskin-type bottle was sub-sampled on deck for a variety
of analyses. A total of 111 stations were occupied on the cruise (Table
2). In addition, underway measurements of salinity, temperature,
dissolved oxygen, pCO~2~ (air and water), total carbon, fluorescence,
light transmittance, and colored dissolved organic matter fluorescence.
As part of the Argo program, floats were deployed at about 4 locations
usually upon departure from a station. The cruise ended in San Diego, CA
on 14 June, 2007.

**3.0 Description of Measurements from Vertical Profiles**

***3.1 CTD/Hydrographic Measurements Program***

The basic CTD/hydrographic measurements consisted of salinity, dissolved
oxygen and nutrient measurements made from water samples taken on a
24-bottle CTD/rosette casts, plus pressure, temperature, salinity,
dissolved oxygen, transmissometer and fluorometer from CTD profiles. A
total of 111 stations were conducted on this cruise, usually to within
10-20m of the bottom (Table 2). Figure 1 shows the sample locations of
the discrete water samples. No major problems were encountered during
the operation.

*3.1.1 Water Sampling Package*

All but four CTD/O~2~ profiles were collected using Sea-Bird
instrumentation mounted vertically in a 24-position stainless steel
frame, 12L and 12 10L Niskin-type Bullister bottles, and 400 lbs lead
weights. Sea-Bird instruments included 24-position carousel s/n 471;
9plus CTD s/n 315; primary 3plus temperature sensor s/n 03P-4569
(stations 1-34) and 03P-4335 (stations 35-111); primary 4C conductivity
sensor s/n 04-3157 (stations 1-34) and 04-2887 (stations 35-111);
secondary 3plus temperature sensor s/n 03P-4341 and secondary 4C
conductivity sensor s/n 04-3068; and oxygen s/n 43-0313 (stations 1-34)
and 43-0315 (stations 35-111). An altimeter, load cell, and pinger were
also mounted on the underwater package, as well as an OSU-supplied WET
Labs fluorometer and transmissometer. Both optical sensors were removed
from the package after severe corrosion at the CTD connector was found
after station 38. The rosette system was suspended from a UNOLS-standard
three-conductor (0.322") electro-mechanical sea cable using the R/V
*Wecoma's* aft winch. The CTD was mounted vertically in an SBE CTD frame
attached to a plate welded in the center of the rosette frame, under the
pylon. The SBE4 conductivity and SBE3plus temperature sensors and their
respective pumps were mounted vertically as recommended by SBE. Pump
exhausts were attached to inside corners of the CTD cage and directed
downward. The transmissometer was mounted horizontally and the
fluorometer vertically. The altimeter was mounted on the inside of the
bottom frame ring.

Table 2. NACP West Coast Cruise rosette station locations

Station Latitude Longitude Date GMT Depth^1^ Wire Out^2^ Pmax^3^

^\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_^

11 50 43.1N 132 49.1W 14-May-07 812 2944 2947 1120

21 51 01.0N 132 10.5W 14-May-07 1412 2756 2712 2753

31 51 18.4N 131 32.1W 14-May-07 2000 2358 2313 2346

41 51 36.0N 130 52.6W 15-May-07 136 2028 1990 2018

51 51 42.5N 130 38.0W 15-May-07 504 928 901 908

61 51 49.8N 130 22.3W 15-May-07 823 238 226 228

71 52 01.0N 129 58.2W 15-May-07 1202 133 118 121

81 52 14.0N 129 27.0W 15-May-07 1548 170 153 155

91 48 16.5N 129 27.2W 16-May-07 1558 2633 2594 2634

101 48 34.2N 128 50.4W 16-May-07 2148 2042 2021 2049

111 48 51.5N 128 13.4W 17-May-07 310 2494 2451 2488

121 49 06.3N 127 41.8W 17-May-07 849 2579 2495 2525

131 49 21.9N 127 06.0W 17-May-07 1602 157 142 143

141 49 26.1N 126 58.2W 17-May-07 1749 129 114 117

151 49 28.5N 126 50.6W 17-May-07 1946 88 70 72

161 49 32.0N 126 42.0W 17-May-07 2120 52 38 41

171 46 00.0N 127 30.0W 19-May-07 2351 2811 2770 2813

181 46 17.4N 126 55.0W 19-May-07 1654 2745 2700 2740

191 46 35.1N 126 19.4W 19-May-07 1023 2677 2638 2676

201 46 52.3N 125 43.6W 19-May-07 432 1905 1863 1887

211 47 09.4N 125 07.5W 18-May-07 2330 1141 1127 1138

221 47 15.2N 124 55.4W 18-May-07 2102 582 543 550

231 47 20.2N 124 44.2W 18-May-07 1554 131 117 119

241 47 25.1N 124 33.7W 18-May-07 1747 55 40 40

251 44 39.0N 124 09.6W 21-May-07 2333 53 40 42

261 44 39.0N 124 20.1W 22-May-07 100 84 73 76

271 44 39.0N 124 34.0W 21-May-07 1354 170 155 159

281 44 39.0N 124 48.1W 21-May-07 1042 391 375 380

291 44 39.0N 125 02.1W 21-May-07 736 1151 1125 1136

301 44 39.1N 125 16.2W 21-May-07 340 2233 2194 2224

311 44 39.0N 125 30.2W 20-May-07 2303 2880 2840 2883

321 44 39.1N 126 12.3W 20-May-07 1656 2884 2844 2888

331 44 39.0N 126 54.4W 20-May-07 1101 2906 2869 2911

341 41 23.1N 127 09.5W 22-May-07 2139 2530 2534 2505

351 41 39.4N 125 56.4W 23-May-07 812 2981 2905 2951

361 41 47.4N 125 17.5W 23-May-07 1604 3117 3055 3101

371 41 50.1N 125 04.5W 23-May-07 2123 1277 1254 1267

381 41 52.4N 124 51.5W 24-May-07 52 792 767 773

391 41 55.2N 124 38.6W 24-May-07 353 601 580 585

401 41 57.5N 124 29.0W 24-May-07 637 110 94 97

411 41 59.6N 124 21.0W 24-May-07 834 52 39 41

421 40 15.4N 124 23.2W 26-May-07 1410 57 42 44

425 40 14.0N 124 26.8W 26-May-07 1235 123 108 110

431 40 10.4N 124 34.4W 26-May-07 930 668 651 656

441 40 05.5N 124 46.0W 26-May-07 543 1055 1032 1045

451 40 00.5N 124 57.2W 26-May-07 200 1412 1383 1397

461 39 55.6N 125 07.0W 25-May-07 2217 1976 1925 1947

471 39 51.6N 125 16.0W 25-May-07 1615 3013 3018

481 39 41.6N 125 38.3W 25-May-07 900 3569 3496 3551

491 39 21.6N 126 23.2W 25-May-07 141 4094 4016 4084

501 37 38.0N 125 04.4W 27-May-07 605 4171 4128 4201

511 37 58.0N 124 21.1W 27-May-07 1432 3859 3827 3891

521 38 08.2N 123 58.8W 27-May-07 2010 3605 405 431

531 38 12.0N 123 50.3W 29-May-07 538 3197 3197 3213

541 38 16.0N 123 41.4W 29-May-07 129 1549 1526 1544

551 38 20.0N 123 32.5W 28-May-07 2146 271 257 262

561 38 24.0N 123 24.0W 28-May-07 1935 129 117 119

571 38 28.0N 123 15.2W 28-May-07 1805 70 57 59

581 35 54.0N 123 48.1W 29-May-07 2041 3853 3820 3884

591 36 14.0N 123 05.3W 30-May-07 401 3465 3435 3488

601 36 24.1N 122 44.1W 30-May-07 918 3063 3016 3060

611 36 32.0N 122 26.6W 30-May-07 1411 2355 2327 2357

621 36 36.0N 122 18.3W 31-May-07 841 2723 2687 261

631 36 40.0N 122 09.5W 31-May-07 424 1145 1125 1299

641 36 44.0N 122 01.1W 31-May-07 32 1314 1286 1136

651 36 48.0N 121 52.3W 30-May-07 2133 262 259 2723

661 34 10.1N 122 33.2W 1-Jun-07 16 3916 3844 3906

671 34 30.1N 121 51.4W 1-Jun-07 802 3778 3742 3800

681 34 40.1N 121 30.4W 1-Jun-07 1442 1274 1248 1265

691 34 44.1N 121 22.2W 1-Jun-07 1729 590 573 577

701 34 52.1N 121 05.3W 1-Jun-07 2153 530 522 520

711 34 56.1N 120 57.1W 2-Jun-07 44 330 315 319

721 35 00.2N 120 48.5W 2-Jun-07 319 106 93 94

731 35 02.1N 120 44.3W 2-Jun-07 559 58 46 48

741 35 03.5N 120 41.5W 2-Jun-07 730 36 22 24

751 32 36.2N 120 59.5W 3-Jun-07 16 3801 3767 3828

761 32 46.2N 120 39.2W 3-Jun-07 624 3809 3782 3843

771 32 56.1N 120 18.4W 3-Jun-07 1255 795 773 780

781 33 06.1N 119 58.2W 3-Jun-07 1803 1098 1077 1089

791 33 12.1N 119 45.6W 3-Jun-07 2244 675 659 666

801 33 26.2N 119 17.1W 4-Jun-07 454 1558 1567 1585

811 33 38.2N 118 52.2W 4-Jun-07 1147 897 875 884

821 33 46.7N 118 34.9W 4-Jun-07 1554 769 743 750

831 33 50.2N 118 27.3W 4-Jun-07 1904 81 73 70

841 33 56.0N 118 43.2W 4-Jun-07 2245 492 478 482

851 33 47.1N 118 51.1W 5-Jun-07 221 908 890 896

861 30 21.1N 119 27.3W 5-Jun-07 2205 3850 3804 3865

871 30 41.1N 118 47.3W 6-Jun-07 458 2808 2574 2608

881 30 51.1N 118 27.2W 6-Jun-07 1112 2372 2334 2361

891 31 01.1N 118 07.2W 6-Jun-07 1731 1751 1714 1735

901 31 11.1N 117 47.2W 6-Jun-07 2324 1733 1726 1745

911 31 21.1N 117 27.1W 7-Jun-07 525 1906 1876 1901

921 31 31.2N 117 06.5W 7-Jun-07 1053 1233 1219 1231

931 31 37.1N 116 54.4W 7-Jun-07 1607 1146 1125 1136

941 31 41.1N 116 46.4W 7-Jun-07 1950 406 391 396

951 28 23.2N 114 14.0W 8-Jun-07 1643 54 42 44

961 28 13.2N 114 34.2W 8-Jun-07 1903 97 85 87

971 28 03.2N 114 53.5W 8-Jun-07 2230 82 74 75

981 27 51.2N 115 17.1W 9-Jun-07 345 101 90 92

991 27 47.2N 115 24.6W 9-Jun-07 641 297 292 295

1001 27 43.2N 115 32.5W 9-Jun-07 1021 2301 2245 2272

1011 27 33.2N 115 52.1W 9-Jun-07 1652 3779 3723 3780

1021 27 23.2N 116 11.3W 9-Jun-07 2347 3681 3681 3738

1031 27 13.2N 116 31.0W 10-Jun-07 726 3747 992 998

1041 26 05.1N 112 49.0W 11-Jun-07 153 87 75 78

1051 25 55.1N 113 08.2W 11-Jun-07 439 194 181 184

1061 25 45.0N 113 27.4W 11-Jun-07 847 873 850 857

1071 25 35.1N 113 46.5W 11-Jun-07 1425 2998 2961 3001

1081 25 25.1N 114 05.6W 11-Jun-07 2106 3287 3264 3310

1091 25 15.1N 114 24.6W 12-Jun-07 333 3521 107 109

1092 25 15.1N 114 24.6W 12-Jun-07 542 3519 2968 3000

1101 25 05.1N 114 43.7W 12-Jun-07 924 3735 108 101

1102 25 05.1N 114 43.7W 12-Jun-07 1121 3707 2970 2195

1111 24 55.2N 115 02.8W 12-Jun-07 1421 3927 109 110

1112 24 55.1N 115 02.7W 12-Jun-07 1625 3927 2969 3000

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_

^1^Depth \[m\] is uncorrected bottom depth from shipboard Knudsen
echosounder

^2^Wire out \[m\] of winch cable at maximum pressure

^3^Maximum pressure \[db\] of CTD package

The deck watch prepared the rosette 10-15 minutes prior to each cast.
The bottles were cocked and all valves, vents and lanyards were checked
for proper orientation. The CTD was powered up about 10 minutes prior to
station. Once stopped on station, the data acquisition system in the
computer lab was started when directed by the deck watch leader. The
rosette was unstrapped from its tiedown location on deck. The pinger was
activated and syringes were removed from the CTD intake ports. The winch
operator was directed by the deck watch leader to raise the package, the
A-frame and rosette were extended outboard and the package quickly
lowered into the water. The package was lowered to at least 10 meters
and held there for 1 minute after the sensor pumps had turned on. The
winch operator was then directed to bring the package back to the
surface (0 winch wireout) and to begin the descent. At most stations the
CTD rosette was lowered to within 10-20 meters of the bottom (Table 2)
depending on weather conditions and bottom slope, using both the pinger
and altimeter to determine the height above bottom. During the upcast
the winch operator was directed to stop the winch at each bottle trip
depth. The CTD console operator waited 30 seconds before tripping a
bottle to insure the package wake had dissipated and the bottles were
flushed, then an additional 10 seconds after bottle closure to insure
that stable CTD comparison data had been acquired. Once a bottle had
been closed, the console operator directed the winch operator to bring
in the package to the next bottle stop. Standard sampling depths were
used throughout the cruise (Figure 1). Recovering the package at the end
of the deployment was essentially the reverse of launching, with the
additional use of poles and snap-hooks to attach tag lines. The rosette
was secured on deck under the block for sampling. The bottles and
rosette were examined before samples were taken, and anything unusual
noted on the sample log.

Each bottle on the rosette had a unique serial number. This bottle
identification was maintained independently of the bottle position on
the rosette, which was used for sample identification. No bottles were
replaced on this cruise, but various parts of bottles were occasionally
changed or repaired. Routine CTD maintenance included soaking the
conductivity and DO sensors in dilute Triton-X solution between casts to
maintain sensor stability by eliminating any accumulating biofilms.
Rosette maintenance was performed on a regular basis. O-rings were
changed and lanyards repaired as necessary. Bottle maintenance was
performed each day to insure proper closure and sealing. Valves were
inspected for leaks and repaired or replaced as needed.

*3.1.2 Underwater Electronics Packages*

The ship's CTD/rosette package was employed for stations 103, 109, 110,
and 111 while the aft winch was under repair. Similar Sea-Bird
instrumentation, including a horizontally mounted 9plus CTD s/n 256 and
vertically mounted sensors, was housed in a 12-position stainless steel
frame with 12 10-liter Niskin bottles and Sea-Bird 12-position carousel
s/n 89. The sensors included primary temperature s/n 03-0997, primary
conductivity s/n 04-1018, oxygen s/n 43-0387, secondary temperature s/n
03-1008, and secondary conductivity s/n 04-0670. Due to time restraints,
this was a 1000 m profile instead of a deep cast.

Data were acquired at full 24 Hz resolution using a 0.322" three-wire
conducting cable on the aft winch. Data were telemetered through the
ship's Sea-Bird 11plus V2 deck unit s/n 11P6193-0252 onto the ship\'s
dedicated PC using Sea-Bird Seasave Win32 version 5.37m acquisition
software. The pumps were primed for 1 minute at a depth of 10 m before
starting the profile near the surface. The altimeter and pinger were
used to determine the height above the bottom. At each bottle depth, the
console operator waited 30 seconds before closing a bottle to ensure the
package wake had dissipated and the bottles were flushed, and 10 seconds
after bottle closure to ensure that stable CTD comparison data had been
acquired. CTD sensors were flushed and stored with a dilute Triton-X
solution between casts to maintain sensor stability by reducing
biofouling. Near real-time digital data were backed up onto a networked
PMEL laptop. No real-time data were lost.

At station 1, profile data were truncated at 1121dbar owing to a bad
primary conductivity cable that caused both pumps to shut off. At
station 34, the package hit bottom and the primary TCO sensor suite had
to be replaced. Profile data were truncated at 2507 dbar. At station 47,
the package hit bottom and resulted in several kinks in the sea cable.
Eighty-seven meters of cable was cut off before it was reterminated.
Deep station 52 was aborted at 420 dbar owing to bad weather.

Table 3a. NACP West Coast Cruise PMEL underwater electronics

  ----------------- ----------------- ----------------- -----------------
  **Sensor**        **Serial Number** **Calibration     **Calibration
                                      Date**            Facility**

  SBE 32            3232696-0471      n/a               n/a
  24-position                                           
  carousel                                              

  SBE 9plus CTD     09P8431-0315      n/a               n/a

  Paroscientific    53960             January 22, 2007  Sea-Bird
  Digiquartz                                            Electronics
  Pressure Sensor                                       

  SBE 3plus         03P-4569          April 24, 2007    Sea-Bird
  Temperature       (primary,                           Electronics
  Sensor            stations 1-34)                      

  SBE 3plus         03P-4335          April 24, 2007    Sea-Bird
  Temperature       (primary,                           Electronics
  Sensor            stations 35-111)                    

  SBE 3plus         03P-4341          April 25, 2007    Sea-Bird
  Temperature       (secondary, all                     Electronics
  Sensor            stations)                           

  SBE 4C            04-3157 (primary, April 25, 2007    Sea-Bird
  Conductivity      stations 1-34)                      Electronics
  Sensor                                                

  SBE 4C            04-2887 (primary, April 25, 2007    Sea-Bird
  Conductivity      stations 35-111)                    Electronics
  Sensor                                                

  SBE 4C            04-3068           April 25, 2007    Sea-Bird
  Conductivity      (secondary, all                     Electronics
  Sensor            stations                            

  SBE 43 Oxygen     43-0313 (stations April 20, 2007    Sea-Bird
  Sensor            1-34)                               Electronics

  SBE 43 Oxygen     43-0315 (stations May 4, 2007       Sea-Bird
  Sensor            35-111)                             Electronics

  WET Labs          FLRTD-425         November 10, 2005 WET Labs
  Fluorometer                                           

  WET Labs          CST-590DR         January 22, 2007  WET Labs
  Transmissometer                                       

  Benthos 916       1035, 1034        n/a               n/a
  Altimeter                                             

  Metrox Load Cell  8756              n/a               n/a

  Benthos Pinger    1006, 1134        n/a               n/a
  ----------------- ----------------- ----------------- -----------------

Table 3b. NACP West Coast Cruise OSU underwater electronics

  ----------------- ----------------- ----------------- -----------------
  **Sensor**        **Serial Number** **Calibration     **Calibration
                                      Date**            Facility**

  SBE 32            3212395-0089      n/a               n/a
  12-position                                           
  carousel                                              

  SBE 9plus CTD     09P0000-0256      n/a               n/a

  Paroscientific    50130             February 26, 2007 Sea-Bird
  Digiquartz                                            Electronics
  Pressure Sensor                                       

  SBE 3 Temperature 03-0997           November 16, 2006 Sea-Bird
  Sensor                                                Electronics

  SBE 3 Temperature 03-1008           November 16, 2006 Sea-Bird
  Sensor                                                Electronics

  SBE 4             04-1018           November 17, 2006 Sea-Bird
  Conductivity                                          Electronics
  Sensor                                                

  SBE 4C            04-0670           November 17, 2006 Sea-Bird
  Conductivity                                          Electronics
  Sensor                                                

  SBE 43 Oxygen     43-0387           January 3, 2007   Sea-Bird
  Sensor                                                Electronics

  Benthos PSA-916D  1021              n/a               n/a
  Altimeter                                             
  ----------------- ----------------- ----------------- -----------------

*3.1.3 Navigation and Bathymetry Data Acquisition*

Navigation data were acquired at 1-second intervals from the ship\'s
P-Code GPS receiver by a Linux system that provided a web-page with
continuous updates to the ship's position and to the arrival times for
upcoming stations throughout the cruise. Bathymetric data were collected
using the Ship\'s 12khz Knudsen echosounder system. These data were
logged using the R/V *Wecoma's* DAS system. Interruptions to the
acquisition of the bathymetric data occurred when the Knudsen system was
switched to receive the frequency of the pinger to track the distance
between the CTD rosette package and the bottom.

*3.1.4 CTD Data Acquisition and Rosette Operation*

The CTD data acquisition system consisted of an SBE-11plus (V2) deck
unit and a networked generic PC workstation running Windows XP. SBE
SeaSave software was used for data acquisition and to close bottles on
the rosette. CTD deployments were initiated by the console watch after
the ship had stopped on station. The watch maintained a console
operations log containing a description of each deployment, a record of
every attempt to close a bottle and any pertinent comments. Once the
deck watch had deployed the rosette, the winch operator would lower it
to 10 meters. The CTD sensor pumps were configured with a 60 second
startup delay, and were usually on by this time. The console operator
checked the CTD data for proper sensor operation, waited an additional
60 seconds for sensors to stabilize, then instructed the winch operator
to bring the package to the surface, pause for 10 seconds, and descend
to a target depth (wire-out). The profiling rate was no more than
30m/min to 50m, no more than 45m/min to 200m and no more than 50m/min
deeper than 200m varying with sea cable tension and the sea state.

The console watch monitored the progress of the deployment and quality
of the CTD data through interactive graphics and operational displays.
Additionally, the watch created a sample log for the deployment which
would be later used to record the correspondence between rosette bottles
and analytical samples taken. The altimeter channel, CTD pressure,
wire-out, pinger and bathymetric depth were all monitored to determine
the distance of the package from the bottom, usually allowing a safe
approach to within 10 meters. Bottles were closed on the up cast by
operating an on-screen control. Bottles were tripped 30 seconds after
stopping at the trip location to allow the rosette wake to dissipate and
the bottles to flush. The winch operator was instructed to proceed to
the next bottle stop 10 seconds after closing bottles to insure that
stable CTD data were associated with the trip. After the last bottle was
closed, the console operator directed the deck watch to bring the
rosette on deck. Once out of the water, the console operator terminated
the data acquisition, turned off the deck unit and assisted with rosette
sampling.

*3.1.5 CTD/O~2~ Data Processing*

The reduction of profile data began with a standard suite of processing
modules (process.bat) using Sea-Bird Data Processing Win32 version 5.37e
software in the following order:

1\. DATCNV converts raw data into engineering units and creates a .ROS
bottle file. Both down and up casts were processed for scan, elapsed
time(s), pressure, t0, t1, c0, c1, and oxygen voltage. Optical sensor
data were converted to voltages but not carried further through the
processing stream. MARKSCAN was used to skip over scans acquired on deck
and while priming the system under water. MARKSCAN values were entered
at the DATCNV menu prompt.

2\. ALIGNCTD aligns temperature, conductivity, and oxygen measurements
in time relative to pressure to ensure that derived parameters are made
using measurements from the same parcel of water. Both conductivities
are automatically advanced in the V2 deck unit by 0.073 seconds. No
additional alignment was necessary for primary conductivity sensors s/n
3157 and 2887. An additional alignment of .020 seconds was made to
secondary conductivity sensor s/n 3068 for a net advance of .093
seconds. It was not necessary to align temperature or oxygen.

3\. BOTTLESUM averages burst data over an 8-second interval (+/- 4
seconds of the confirm bit) and derives both primary and secondary
salinity, primary potential temperature (θ), primary potential density
anomaly (σ~θ~), and oxygen (in μmol/kg).

4\. WILDEDIT makes two passes through the data in 100 scan bins. The
first pass flags points greater than 2 standard deviations; the second
pass removes points greater than 20 standard deviations from the mean
with the flagged points excluded. Data were kept within 100 of the mean
(i.e. all data).

5\. FILTER applies a low pass filter to pressure with a time constant of
0.15 seconds. In order to produce zero phase (no time shift) the filter
is first run forward through the file and then run backwards through the
file.

6\. CELLTM uses a recursive filter to remove conductivity cell thermal
mass effects from measured conductivity. In areas with steep temperature
gradients the thermal mass correction is on the order of 0.005 PSS-78.
In other areas the correction is negligible. The value used for the
thermal anomaly amplitude (α) was 0.03. The value used for the thermal
anomaly time constant (β^-1^) was 7.0 s.

7\. LOOPEDIT removes scans associated with pressure slowdowns and
reversals. If the CTD velocity is less than 0.25 m s^-1^ or the pressure
is not greater than the previous maximum scan, the scan is omitted.

8\. BINAVG averages the data into 1-dbar bins. Each bin is centered on
an integer pressure value, e.g. the 1-dbar bin averages scans where
pressure is between 0.5 dbar and 1.5 dbar. There is no surface bin. The
number of points averaged in each bin is included in the data file.

9\. DERIVE uses 1-dbar averaged pressure, temperature, and conductivity
to compute primary and secondary salinity.

10\. TRANS converts the binary data file to ASCII format.

Package slowdowns and reversals owing to ship roll can move mixed water
in tow to in front of the CTD sensors and create artificial density
inversions and other artifacts. In addition to Seasoft module LOOPEDIT,
MATLAB program deloop.m computes values of density locally referenced
between every 1 dbar of pressure to compute the square of the buoyancy
frequency, N^2^, and linearly interpolates temperature, conductivity,
and oxygen voltage over those records where N^2^ is less than or equal
to -1 × 10^-5^ s^-2^. Twelve profiles failed this criteria in the top 10
meters. These data were retained by program delooppost.m and flagged as
questionable in the final WOCE formatted files.Program calctd.m reads
the delooped data files and applies final calibrations to primary
temperature and conductivity, and computes salinity and calibrated
oxygen. Program cnv_eps.f computes ITS-90 temperature, potential
temperature (θ), density anomalies σ~t~ and σ~θ~, and dynamic height;
creates WOCE quality flags, and converts the ASCII calibrated data files
into NetCDF format for PMEL's database. Program wocelst.f converts the
ASCII calibrated data files into ASCII WOCE format for submission to the
WHPO.

*3.1.6 CTD Shipboard Calibration Procedures*

CTD 09P8431-0315 was used for all casts (Table 3). The CTD was deployed
with all sensors and pumps aligned vertically, as recommended by SBE.
The primary temperature and conductivity sensors (T1 & C1) were used for
all reported CTD data. In-situ salinity and dissolved O2 check samples
collected during each cast were used to calibrate the conductivity and
dissolved O2 sensors.

*3.1.7 CTD Pressure*

Pressure calibrations for the CTD instrument used during this cruise
were pre-cruise. No additional adjustments were applied. On deck
pressure readings prior to each cast were examined and remained within
0.5 dbar of calibration.

3.1.8 CTD Temperature

In addition to a viscous heating correction of -0.0006 °C, a linearly
interpolated temperature sensor drift correction using pre and
post-cruise calibration data for the midpoint of the cruise will be
determined. Viscous and drift corrections are applied to profile data
using program calctd.m, and to burst data using calclo.m.

*3.1.9 CTD Conductivity*

Seasoft module BOTTLESUM creates a sample file for each cast. These
files were appended using program sbecal1.f. Program addsal.f matched
sample salinities flagged as good to CTD salinities by station/sample
number. Primary sensors s/n 3157 and 2887 were selected for calibration.
For s/n 3157, program calcos0.m produced the best results for an overall
linear fit of sample data from stations 1-34:

number of points used: 71

total number of points: 88

\% of points used in fit: 80.68

fit standard deviation : 0.002516

fit bias: 0.032562618

fit slope: 0.99893265

For s/n 2887, program calcop1.m produced the best results for a
station-dependent linear fit with a pressure term of two groups of
sample data, 35-46 and 47-111 respectively:

Group: 35-46

number of points used: 1797

total number of points : 2057

\% of points used in fit: 87.36

fit standard deviation : 0.001389

fit bias: -0.00093990233

fit slope: 0.99997966

Group: 47-111

number of points used: 1797

total number of points: 2057

\% of points used in fit: 87.36

fit standard deviation : 0.001389

fit bias : -0.00093990233

fit slope: 0.99997966

For s/n 1018, program calcos0.m produced the best results for an overall
linear fit of sample data from stations 103 and 109-111:

number of points used: 8

total number of points: 8

\% of points used in fit: 100

fit standard deviation: 0.002184

fit bias: 0.006008887

fit slope: 0.99990618

Conductivity calibrations were applied to profile data using program
calctd.m, and to burst data using calclo.m.

Primary sensor CTD - bottle conductivity differences plotted against
station number (Figure 2) and pressure (Figure 3) are used to allow a
visual assessment of the success of the fit.

![](media/image3.jpeg){width="5.786111111111111in"
height="4.339583333333334in"}

![](media/image4.jpeg){width="5.770833333333333in"
height="4.141666666666667in"}

*3.1.10 CTD Oxygen Calibration*

Program addoxy.f matched bottle sample oxygen values flagged as good (2
or 6) to CTD oxygen values by station/sample number. Because of sensor
hysteresis, programs match_sg_n_313.m (stations 1-34) and
match_sg_n_315.m (stations 35-111) were used to match up-cast oxygen
data to downcast oxygen data by potential density anomalies referenced
to the closest 1000-m interval. A least-squares station-dependent fit
was determined for groups of stations using program run_oxygen_cal_1.m:

Station Slope Range Bias Lag Tcor Pcor Points Used StdDev

1- 4 0.3309-0.3399 -0.4972 3.0197 0.0029 0.0001 100 98.0% 0.4481

5-20 0.3511-0.3645 -0.5119 3.1121 0.0023 0.0001 528 90.5% 0.7684

21-22 0.3731-0.3731 -0.5271 3.7915 0.0016 0.0001 68 88.2% 0.6854

23-43 0.3620-0.3693 -0.5059 3.3016 0.0023 0.0001 628 89.6% 0.8648

44-66 0.3756-0.3820 -0.5145 7.3144 0.0017 0.0001 783 89.8% 0.8288

67-67 0.3612-0.3612 -0.4606 3.7839 0.0102 0.0002 29 96.6% 0.6001

68-84 0.4244-0.4359 -0.4600 6.7851 -0.0056 0.0001 524 82.1% 0.7518

Oxygen calibration coefficients were applied to profile data using
program calctd.m, and to burst data using calclo.m.

Primary sensor CTD - bottle oxygen differences plotted against station
number (Figure 4) and pressure (Figure 5) are used to allow a visual
assessment of the success of the fits.

![](media/image5.jpeg){width="6.26875in" height="3.7625in"}

![](media/image6.jpeg){width="6.144444444444445in"
height="3.948611111111111in"}

Dissolved O~2~ concentration is calculated via the equation:

O~2~(ml/l) =
\[c1\*Oc+c2\]\*fsat(S,T,P)\*e\*\*(c3\*Pl+c4\*Tf+c5\*Ts+c6\*dOc/dt) (1)

where:

O~2~(ml/l) = Dissolved O~2~ concentration in ml/l;

Oc = Sensor current (µamps);

fsat(S,T,P) = O~2~ saturation concentration at S,T,P (ml/l);

S = Salinity at O~2~ response-time;

T = Temperature at O~2~ response-time (°C);

P = Pressure at O~2~ response-time (decibars);

Pl = Low-pass filtered pressure (decibars);

Tf = Fast low-pass filtered temperature (°C);

Ts = Slow low-pass filtered temperature (°C);

dOc/dt = Sensor current gradient (µamps/secs);

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

*3.1.11 Bottle Sampling*

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

o O~2~

o Ar and O~2~ isotopes

o Dissolved Inorganic Carbon (DIC)

o Total Alkalinity

o Dissolved Organic Carbon (DOC)

o Total Organic Carbon

o CDOM

o Chlorophyll

o Salinity

o Nutrients

o Particulate Organic Carbon

o Particulate Si

o Stained Paticulate Matter

The correspondence between individual sample containers and the rosette
bottle position (1-24) from which the sample was drawn was recorded on
the sample log for the cast. This log also included any comments or
anomalous conditions noted about the rosette and bottles. One member of
the sampling team was designated the sample cop, whose sole
responsibility was to maintain this log and insure that sampling
progressed in the proper drawing order.

Normal sampling practice included opening the drain valve and then the
air vent on the bottle, indicating an air leak if water escaped. This
observation together with other diagnostic comments (e.g., "lanyard
caught in lid," "valve left open") that might later prove useful in
determining sample integrity were routinely noted on the sample log.
Drawing oxygen samples also involved taking the sample draw temperature
from the bottle. The temperature was noted on the sample log and was
sometimes useful in determining leaking or mis-tripped bottles.

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

*3.1.11 Bottle Data Processing*

Water samples collected and properties analyzed shipboard were managed
centrally in a Excel data base and processed in Ocean DataView. The
sample logs was entered into the database once sampling was completed.
Quality flags associated with sampled properties were set to indicate
that the property had been sampled, and sample container identifications
were noted where applicable (e.g., oxygen flask number). Analytical
results were provided on a regular basis by the various analytical
groups and incorporated into the database. Various consistency checks
and detailed examination of the data continued throughout the cruise.

***3.2 Salinity Measurements***

Sample salinity measurements were made using Guildline 8400B Autosal
salinometer s/n 68807 located in a container lab on the upper deck aft.
Two samples were collected from each cast, one from the surface mixed
layer and one from the deepest Niskin. Samples were collected in 200 ml
Kimax high-alumina borosilicate bottles, sealed with custom clear
plastic inserts and Nalgene caps, and externally rinsed with fresh water
to reduce salt contamination. Salinity samples were allowed to
equilibrate in an open tray on the counter next to the Autosal for a
minimum of eight hours. A batch of measurements, sorted by depth in
descending order, was performed at the end of each transect, roughly
every third day of the cruise. A total of 260 sample salinity
measurements were made during this cruise, including 40 duplicates.

The Autosal bath temperature was set to 21C. An air conditioner was
mounted in the van to regulate temperature around 19-20C. Fluctuations
were monitored using a wall-mounted thermometer. A logging thermometer
recorded ambient temperature in1-minute increments during a run, which
usually remained stable to within 1C. Power to the Autosal was
conditioned through a UPS to reduce noise in the readings. An Ocean
Scientific Instruments interface box connected the Autosal to a laptop
with ACI2003 software installed.

After initiating the software program, a bottle of standard seawater
(batch P145) was used to determine an offset correction to be applied to
the following measurements. Each water sample was flushed through the
Autosal's conductivity cell 3-5 times before taking the first reading.
After waiting five seconds, ten seconds of 4 Hz data (40 values) were
averaged for a conductivity ratio. Three corrected conductivity ratios
were averaged and one salinity value was calculated for each water
sample. After all samples were analyzed, a second bottle of standard
seawater was run and may be used post-cruise to determine a drift
correction during the run. A dilute solution of Triton-X surfactant was
flushed through the cell at the end of each session, followed by 400 ml
is distilled water. Distilled water remained in the cell between uses.

***3.3 Oxygen Measurements***

Samples were drawn from Niskin bottles into calibrated 125 ml iodine
titration flasks using Tygon tubing with a silicone adaptor that fit
over the petcock to avoid contamination of DOC samples. Bottles were
rinsed three times and filled from the bottom, overflowing three volumes
while taking care not to entrain any bubbles. The draw temperature was
taken using a digital thermometer with a flexible thermistor probe that
was inserted into the flask while the sample was being drawn during the
overflow period. These temperatures were used to calculate µmol kg^-1^
concentrations, and a diagnostic check of bottle integrity. One-ml of
MnCl~2~ and one-ml of NaOH/NaI were added immediately after drawing the
sample was concluded using a Repipetor, the flasks were then stoppered
and shaken well about 20 times. DIW was added to the neck of each flask
to create a water seal. The flasks were stored in the lab in plastic
totes at room temperature for 6-7 hours before analysis. Twenty-four
samples plus two duplicates were drawn from each station except the
shallow costal stations where only ten to fifteen samples were drawn
with one to two duplicates. Total number of samples collected was 2419
with a test cast of 10 samples; total number of samples flagged after
initial shipboard reduction of quality control: Questionable (QC=6 ):
Bad (QC=11 ): Not reported (QC=5 ).

Dissolved oxygen analyses were performed with a MBARI-designed automated
oxygen titrator using photometric end-point detection based on the
absorption of 365 nm wavelength ultra-violet light. The titration of the
samples and the data logging were controlled by a 386 PC running the

Oxygen program written by Gernot Friedrich. The titrations were
preformed in a climate controlled lab van at 18.5°C-20°C. Thiosulfate
was dispensed by a Dosimat 665 fitted with a 5.0 ml buret. The
whole-bottle titration technique of Carpenter (1965) with modifications
by Culberson et al. (1991) was used, but with more dilute solution of
thiosulfate (10 g L^-1^). Replicate 10 ml iodate standards were run
every 36 hours. The reagent blank determined as the difference between
V2 and V1, the volumes of thiosulfate required to titrate 1 ml aliquots
of the iodate standard was determined at the beginning of the cruise.
This method was found during pre-cruise testing to produce a more
reproducible blank value than the value determined as the intercept of a
standard curve. Periodic spot checks of the thiosulfate was done between
standards along with checks of the blank measurement to insure its
initial quality. The molarity of the thiosulfate titrant was determined
as given in Dickson (1994).

![](media/image7.wmf){width="6.49375in" height="3.9555555555555557in"}

***3.4 Nutrient Measurements***

Nutrient samples were collected from the Niskin bottles in acid washed
25-ml linear polyethylene bottles after three complete seawater rinses
and analyzed within 1 hour of sample collection Nutrients were analyzed
with a continuous flow analyzer (CFA) using the protocols for the WOCE
hydrographic program as set forth in the manual by L.I. Gordon, et al
(2000). \~2350 samples were taken at discrete depths and analyzed for
phosphate (PO~4~), nitrate (NO~3~) plus nitrite (NO~2~)\--(N+N), nitrite
and silicic acid (Sil). The A and B standards for PO4, NO~3~ and Sil for
the cruise were prepared in the laboratory at PMEL. An A standard for
NO~2~ was prepared weekly. Working standards were prepared at sea for
each run of the CFA. Output from the detectors was recorded as peak
heights of the analog voltage signal using a VI program on a laptop
computer and converted to μM/L using an Excel spreadsheet. A refractive
index analysis was run every other day and a linearity test of the
detectors was run weekly.

*3.4.1 Nitrate and Nitrite*

Nitrite was determined by diazotizing with sulfanilamide and coupling
with N-1 naphthyl ethylenediamine dihydrochloride to form an azo dye.
The color produced is measured at 540 nm (Zhang et al., 1997). Samples
for nitrate analysis were passed through a home made cadmium column
(Zhang et al., 2000), which reduced nitrate to nitrite and the resulting
nitrite concentration was then determined as described above. Nitrate
concentrations were determined from the difference of nitrate + nitrite
and nitrite.

*3.4.2 Phosphate*

Phosphate in the samples was determined by reacting with molybdenum (VI)
and antimony (III) in an acidic medium to form an
antimonyphosphomolybdate complex a temperature of 55°C. This complex was
subsequently reduced with hydrazine to form a blue complex and the
absorbance was measured at 815 nm (Zhang et al., 2001).

*3.4.3 Silicic Acid*

Silicic acid in the sample was analyzed by reacting the aliquote with
molybdate in a acidic solution to form molybdosilicic acid. The
molybdosilicic acid was then reduced by SnCl~2~ to form molybdenum blue
(Gordon et al., 1995). The absorbance of the molybdenum blue was
measured at 660 nm.

*3.4.4 Calibration and Standards*

Stock standard solutions were prepared by dissolving high purity
standard materials (KNO~3~, NaNO~2~, KH~2~PO~4~ and Na~2~SiF~6~ ) in
deionized water. Working standards were freshly made at each station by
diluting the stock solutions in low nutrient seawater. The low nutrient
seawater used for the preparation of working standards, determination of
blank, and wash between samples was filtered seawater obtained from
low-nutrient Pacific surface waters. Standardizations were performed
prior to each sample run with working standard solutions. Replicates
were usually collected at the deepest Niskin bottle from each cast. The
relative standard deviation from the results of these replicate samples
was used to estimate the overall precision obtained by the sampling and
analytical procedures. The precisions of these samples were 0.04 µmol/kg
for nitrate, 0.01 µmol/kg for phosphate and 0.1 µmol/kg for silicic
acid.

***3.5 DIC Measurements***

The DIC analytical instrumentation was set up in a seagoing container
modified for use as a shipboard laboratory. The analysis was done by
coulometry with two analytical systems (PMEL-1 and PMEL-2) used
simultaneously on the cruise. Each system consisted of a 5011 coulometer
(UIC, Inc.) coupled with a system designed to improve upon the original
SOMMA (Single Operator Multiparameter Metabolic Analyzer) inlet system.
The original SOMMA was developed by Ken Johnson (Johnson et al.,
1985,1987,1993; Johnson, 1992; Wilke et al., 1993) of Brookhaven
National Laboratory (BNL). In the coulometric analysis of DIC, all
carbonate species are converted to CO~2~ (gas) by addition of excess
hydrogen to the seawater sample, and the evolved CO~2~ gas is carried
into the titration cell of the coulometer, where it reacts
quantitatively with a proprietary reagent based on ethanolamine to
generate hydrogen ions. These are subsequently titrated with
coulometrically generated hydroxide. CO~2~ is thus measured by
integrating the total change required to balance the reaction.

For this NACP West Coast Cruise, our primary standards (Certified
Reference Materials (CRMs supplied by Dr. A. Dickson of Scripps
Institution of Oceanography (SIO). The CRM accuracy is determined
shoreside manometrically. The CRMS were run approximately every 24
samples on each analytical system. We also re-used (or re-analyzed)
these standards as a "secondary standard" -- these were also analyzed
approximately every 24 samples -- though offset from the primary
standard. On this cruise, the overall accuracy and precision for the
primary CRMs on both instruments combined was 0.54 ± 1.5 µmol/kg (n=87,
as of June 4). Preliminary DIC data reported to the database have not
yet been completely corrected to the Batch 79 CRM value, but a more
careful quality assurance to be completed shoreside will have final data
corrected to the secondary standard on a per instrument basis.

Samples were drawn from the Niskin-type bottles into cleaned,
precombusted 300-mL Pyrex bottles using Tygon tubing with silicone ends.
Bottles were rinsed twice and filled from the bottom, overflowing half a
volume and taking care not to entrain any bubbles. The tube was pinched
off and withdrawn, creating a 6-mL headspace, and 0.18 mL of 50%
saturated HgCl~2~ solution was added as a preservative. The sample
bottles were sealed with glass stoppers lightly covered with Apiezon-L
grease, and were stored at room temperature for a maximum of 5 hours
prior to analysis. Over 2000 samples were analyzed for discrete DIC;
full profiles were completed on every station after some initial
instrument adjustment during line number 1. Replicate samples were
typically taken from the two bottom depths out of the Niskin-type
bottles. The replicate samples were interspersed throughout the station
analysis for quality assurance of the integrity of the coulometer cell
solutions. No systematic differences between the replicates were
observed.

***3.6 TA Measurements***

Seawater total alkalinity (*TA*) was measured by acidimetric titration.
The specific method used was based upon the open cell method described
by Dickson et al (2003). This method involves first acidifying the
sample to reduce the sample pH to less than 3.6 followed by bubbling
CO~2~-free air through the sample to facilitate removal of the CO~2~
evolved by the acid addition. After removal of the carbonate species
from solution, the titration proceeds until a pH of less than 3.0 is
attained. Titration progress is monitored by measuring the electromotive
force (*E*) of a combination glass-reference electrode. The
electromotive force is directly related to solution pH via the Nernst
Equation

\[H^+^\] = *k* exp(*E*/*RTF*^-1^) = exp(*E* -- *E^0^*/*RTF*^-1^), (Eq.
1)

where *E^0^* is the electrode reference potential, *R* is the universal
gas constant, *T* is the solution temperature, and *F* is the Faraday
constant. A non-linear least squares method is used to fit the titration
data to an equation that takes into account the various acid-base
equilibria in solution during the titration. The two adjustable
parameters in this fit equation are *A~T\ ~*and *E^0^*.

Samples were drawn from the Niskin-type bottles into cleaned, amber, 250
mL borosilicate glass bottles using Tygon tubing with silicone ends.
Bottles were rinsed twice and filled from the bottom, overflowing half a
volume and taking care not to entrain any bubbles. The sample tube was
closed off and withdrawn from the sample bottle, creating a 5 mL
headspace. Samples were preserved by poisoning with 0.18 mL of a 50%
saturated HgCl~2~ solution. Sample bottles were sealed with glass
stoppers lightly coated with Apiezon-L grease, and were stored at room
temperature (21-25 °C) for a maximum of 12 hours prior to analysis.

Titrations were carried out in water-jacketed, 250 mL beakers. The
beakers were kept at 24.0 ± 0.2 °C with water from a constant
temperature bath. Prior to analysis, samples were placed in the water
bath to bring them to the same temperature as the reaction beakers.
Seawater samples were dispensed into the water-jacketed beaker using a
fixed volume (108.30 +/ 0.03 mL) glass syringe. A Metrohm Dosimat 765
was used to deliver acid to the sample beaker in increments of 0.040 mL.
The acid titrant used was 0.1 mol kg^-1^ HCl prepared in 0.6 mol kg^-1^
NaCl background to approximate the ionic strength of seawater (0.7 mol
kg^-1^). Three batches of titrant were used over the course of the
cruise: PMEL 050607-1, PMEL 050607-2, and PMEL 050607-3. Acid
concentrations determined from laboratory preparation are 0.09923,
0.10031, and 0.10002 mol kg^-1^, respectively.Titration pH was monitored
with a Radiometer (model PHC 2002-8) combination pH glass-reference
electrode. Electrode *E* was measured using a National Instruments
high-precision data acquisition card (NI-4351). This same data
acquisition card was used to provide the 100 mA excitation current and
record the resistance of the Pt RTDs used to monitor sample, titrant,
and reaction temperatures. Pt RTDs were calibrated to +/- 0.01 °C.
Degassing air was flowed through a Drierite column and then an Ascarite
column prior to bubbling through the sample to remove all water and
CO~2~ from the gas stream.Instrument control and data acquisition was
with custom software developed at NOAA/PMEL using the National
Instruments LabView programming environment. Over the course of the
cruise we analyzed over 2,500 samples, including duplicate samples and
certified reference materials (CRMs). Typical titrations were completed
in 10 - 14 minutes and required 20 - 24 acid additions to reach a pH of
3.0. Analytical accuracy was assessed by periodic analysis of CRMs
(Batch 79: supplied by Dr. A. Dickson of Scripps Institution of
Oceanography; <http://andrew.ucsd.edu/co2qc/>) throughout the cruise.
References were analyzed approximately every 24 samples. Deviation from
the certified reference alkalinity (2262.31 umol/kg) varied between acid
batches, but was never greater than 5.0 umol/kg. Analytical precision
over the course of the cruise, calculated as the standard deviation of
all CRM analyses, was +/- 2.0 umol/kg. The electrode reference
potential, *E^0^*, was monitored over the course of the cruise to assess
electrode condition and stability. With the exception of a step in
*E^0^* near the beginning of the cruise, coinciding with a change in
reaction temperature from 20 to 24 °C, *E^0^* increased steadily and in
a linear fashion from 0.380 to 0.383.

***3.7 Oxygen Isotope and O~2~/Ar gas ratio sampling***

Samples for dissolved oxygen isotopes and O~2~/Ar gas ratios were
collected from a near-surface (10-15m) Niskin at all stations except
station 85. At 20 stations an additional 1-2 samples were collected in
the upper 100m below the mixed layer. Roughly, these additional
subsurface samples were taken at one inshore (shelf) station and one
offshore station on each line. Samples were collected in 500 ml
pre-evacuated glass sampling bottles equipped with Louwers™ high vacuum
single o-ring valves. Each bottle had been pre-poisoned with mercuric
chloride during flask preparation. Great care was taken to prevent
atmospheric contamination of the sample during collection by filling the
flask sidearm with water, tapping all air bubbles free, then slowly
opening the o-ring to the flask while maintaining a water lock between
the atmosphere and the o-ring. Roughly 250 ml of sample was collected in
each 500 ml flask, allowing half the flask volume for dissolved gases to
exsolve into the headspace.

Samples will be returned to the University of Washington stable isotope
laboratory for analysis of ^18^O/^16^O, ^17^O/^16^O, and O~2~/Ar by a
Thermo-Finnigan isotope ratio mass spectrometer after cryogenic
separation of water vapor and CO~2~ and chromatographic separation of
N~2~ from the O~2~ and Ar in the collected gas mixture. Seventy-five
determinations of the ^18^O/^16^O and ^17^O/^16^O ratio relative to an
internal reference standard will be used to compute ^17^∆, which is
defined as

> ^17^∆=10^6^ \[ln(δ^17^O/1000 -1) -- 0.518\*ln(δ^18^O/1000 -1)\],

where δ^17^O = 10^3^\[(^17^O/^16^O)sample/(^17^O/^16^O)standard -1\] and
δ^18^O is defined analogously. Final ^17^∆ values will be reported
relative to air based on air standards analyzed each day with samples.
The O~2~/Ar ratio will also be determined on each sample by a separate
determination of mass peaks 32 and 40. The ratio will then be reported
relative to the O~2~/Ar ratio expected at solubility equilibrium using
the O~2~ and Ar solubility relationships of Garcia and Gordon (1992) and
Hamme and Emerson (2004).

The ^17^∆ of dissolved O~2~ will yield an estimate of in situ gross
primary productivity following Luz and Barkan (2000), while the
dissolved O~2~/Ar gas ratio will yield an estimate of net biological
O~2~ production (e.g., Craig and Hayward, 1987; Emerson et al., 1997).
These data will be used to determine the spatial variability of gross
and net organic carbon production and export along the west coast during
the upwelling season and help to constrain the influence of biological
activities on the west coast inorganic carbon budget.

***3.8 Dissolved Organic Carbon***

DOC samples were collected using two slightly different sampling
protocols for different laboratories (Craig Carlson, University of
California Santa Barbara, UCSB, and Debby Ianson, Institute of Ocean
Sciences, IOS). Approximately 1250 samples were collected for the UCSB
lab and 200 samples for the IOS lab (including some TOC samples).
Vertical profiles from surface to 2000m (or depth of water column) were
sampled at all lines and all stations (with the exception of two
nearshore locations). Samples can easily be contaminated so great care
was taken when sampling. Nitrile gloves (not latex) were worn and only
silicon tubing was used for all samples drawn from the rosette. Samples
were filtered in line from the Niskin bottles using a nominal 0.7 µm
pore size glass fibre filter (GFF) into 60 ml high density polyethylene
bottles (UCSB) or a 0.2 µm Teflon filter into 40 ml glass vials with
Teflon caps (IOS). TOC samples were collected directly from the Niskin
bottles (no filtering). DOC samples below 250 m going to the UCSB lab
were not filtered. All samples were frozen immediately after collection.
The 0.7 um filters were discarded and new filters used for each cast.
The filter cartridges were acid rinsed between each cast. The 0.2 µm
filter was acid rinsed between each line and flushed with 1 l of
seawater before sampling at each station.

All analysis will occur at the respective labs. For analysis the sample
is thawed and acidified, sparged with oxygen to remove inorganic carbon.
The organic carbon is combusted and converted to carbon dioxide which is
measured by a non-dispersive infrared detector.

***3.9 Colored Dissolved Organic Matter (CDOM)***

CDOM samples were collected using the 0.2 µm Teflon filter (same filter
and procedure as the DOC samples above) into a 125 ml amber glass bottle
and refrigerated immediately. Surface samples were collected at 4-5
stations on each line including the 3 profile stations per line
(described below, section 3.10). At these 3 stations 3 depths were
sampled; surface, mixed layer and below the mixed layer. Approximately
150 samples were collected. Analysis will be completed at IOS by Sophia
Johannessen using a dual beam spectrophotometer.

***3.10 Particulate Organic Carbon (POC), Particulate Organic Nitrogen
(PON), Biogenic Silica and chlorophyll a (chl)***

At 3 stations per line vertical profiles of POC, PON, BSi and chl were
sampled. The stations were chosen to be representative of the shelf,
shelf break and immediately offshore. For POC, PON and BSi 4 depths were
sampled; 5m, middle of surface mixed layer (ML), base of ML and one
depth well below the ML (usually 175m). Chl was sampled at the upper 3
depths, but not below the ML. Chl was also sampled at 5m at an
additional station on each line.

The collection of POC, PON, BSi and chl samples from the rosette is
similar. A volume of water (0.5 l for chl; 2 l for POC and PON; 2 1 for
BSi) was collected from the rosette and filtered immediately after
collection onboard in the wet lab using a filtration manifold and a low
pressure vacuum pump. Note that POC and PON are measured from the same
filter. Polycarbonate filters (0.6 µm) were used for BSi samples and GFF
(0.7 µm) filters were used for POC, PON and also chl. The filters were
frozen immediately after filtering to await analysis.

The BSi samples will be analyzed at the University of Victoria (UVic) by
Diana Varela\'s lab. These filters will be dried at 60 °C, transferred
to a 15-ml centrifuge tubes where the BSi is dissolved with NaOH at 95
°C for 1 hour. Dissolved Si will then be measured spectophotometrically.
Chl and phaeopigments will be analyzed fluorometrically (also in the
Varela lab at UVic). POC and PON will be analyzed at the University of
California, Davis Stable Isotope Facility. Filters will be dried at 60
°C and prepared for mass spectrometric analysis.

***3.11 Phytoplankton Counts***

Samples for phytoplankton species composition were collected at one
station per line, above the shelf and in the surface. Seawater was
collected and fixed (cells are killed, preserved and stained) with a
Lugols solution. Aliquots of the sample will be counted using an
inverted microscope.

**4.0 Underway Measurements**

*4.1 OSU Underway DIC/pCO~2~/TSG/O~2~, bio-optics system*

An integrated suite of underway surface measurements was attempted using
the ship's uncontaminated seawater supply, flowing at \> 20 liters per
minute. Approximately 8 liters per minute were diverted to flow
sequentially through a \'bio-optics\' sensor suite, consisting of a
SeaBird Electronics (SBE) SBE45 Thermosalinograph, an SBE43 dissolved
oxygen sensor, and WetLabs transmissometer, chlorophyll fluorometer, and
CDOM fluorometer sensors. Continuous *p*CO~2~ determinations were made
by equilibrating at about 200 -- 400 ml/min of this seawater stream with
marine air using a miniature version of the microporous membrane
contactor as described in Hales, Chipman, and Takahashi, 2004. A stream
of air flowing counter to the liquid stream equilibrated with the
seawater, and then passed through a LI- COR LI-840 dual-channel NDIR
analyzer, where the CO~2~ and water vapor content of the carrier gas
were analyzed at a frequency of 1 Hz. Accuracy was ensured by regular
analyses of standard gases of known CO~2~ mixing ratio. Precision of the
LI-840 is reported by LI-COR to be about 2 ppm, however our high
sampling rate and subsequent data reduction improves this statistic.
Repeat analyses of standard gases shows that polynomial data-smoothing
at ca 10-second resolution reduces the analytical precision to \<1 ppm.

Continuous underway measurement of DIC was accomplished by passing an
acidified subsample of the surface seawater through a second microporous
membrane contactor where it is stripped of CO~2~ by CO~2~-free air which
is then analyzed by a LiCor 6262 infrared analyzer. The method is
essentially that described in Bandstra, Hales, and Takahashi, 2006. The
DIC measurements were calibrated by both CO~2~ standard gases and liquid
sodium bicarbonate standards prepared in artificial seawater. Discrete
subsamples of the liquid bicarbonate standards were analyzed by
coulometry on board the ship by NOAA personnel.

Unprecedented problems with the interface between the data collection
and control system and the pCO~2~ analytical hardware plagued the pCO~2~
system. These problems manifested themselves as data-transmission
dropouts, connectivity issues, valve mis-alignment, and mass flow
controller (MFC) inaccuracy. Trouble-shooting at sea by PMEL\'s Paul
Covert appeared to isolate the problems to a USB hub that was used to
merge the signals from several instruments. The hub was bypassed, with
the result that the MFC was no longer actively controlled, and the SBE45
TSG was no longer logging data. These issues were overcome by manually
setting the MFC, and verifying that the TSG and the Wecoma\'s underway
TSG system were supplying essentially identical readings. The system ran
in this mode after 31 May. Unfortunately, the MFC issues arose again,
even when the MFC was operating independently of the other components.
Joe Jennings and Paul Covert discovered that the MFC would operate
properly with a set point of 60 ml/min. This was double the desired flow
rate, and required that we verify the extent of equilibration. Joe
Jennings ran tests with high and low standard gases and found that the
carrier gas was 92% equilibrated at that flow rate, as opposed to the
\>99.5% at 30 ml/ min. This correction will be made in the post-cruise
data processing. The problem also raises the suspicion that the MFC was
the source of the earlier issues, as the system -wide problems were
absent when the MFC was isolated, and the MFC problems continued.

**5.0 Other Measurements**

*5.1 ARGO Floats*

As part of the ARGO program, ARGO floats were deployed upon departure
from each of 4 stations. Each deployment required 30 minutes of startup
time to unpack, inspect, and test the float. All floats passed their
self-check routines and were launched successfully. Immediately
following deployment, an email was sent to Dr. Greg Johnson of PMEL to
report the exact time and position of the float. Return emails from Dr.
Johnson confirmed that all floats were working properly.

**6.0 Preliminary Results for Mexican Waters**

The California Current System (CCS) extends along the coasts of
California, USA and Baja California, Mexico. Along Mexico's coast the
most intense upwelling events occur in spring and early summer. For this
region there are no historical measurements of inorganic carbon. Most of
what is known about the dynamics of the CCS has been built from the
CalCOFI program, which began sampling in 1949. Coastal Baja California
was included in the spatial and temporal coverage of the original
CalCOFI grid, but at a reduced sampling grid, including only southern
California, was established in 1985, with the sampling of Mexican waters
ending in 1984 (Hewitt, 1988). In particular, the coastal ocean off Baja
California is important because it is the southern end of the CCS and
also because it is the transitional region between the mid-latitudes and
the tropics along the eastern boundary of the North Pacific (Durazo and
Baumgartner, 2002). Recognizing the need for more complete spatial
coverage, a multi-institutional monitoring program supported by the
Mexican government was initiated off Baja California (25--31°N) in
October 1997. These surveys follow the original CalCOFI grid in Mexican
waters and were scheduled to coincide as closely as possible with the
CalCOFI cruises in central and southern California. Thus, a regular
program of oceanographic observations called IMECOCAL (Investigaciones
Mexicanas de la Corriente de California) now exists in Mexican waters to
provide the coverage needed to match the scale of observation to the
scale of variability in the CCS (Durazo and Baumgartner, 2002). However,
it was not until 2006 when measurements of CO~2~ system parameters (pH,
DIC and TA) were included as a part of this program. These measurements
are especially significant as they will form the spatial and seasonal
baseline of CO~2~ system chemistry in this region of the North Pacific
West coast. In addition, the concern about the long-term fate of
anthropogenic CO~2~ in the atmosphere will permit to examine the
fundamental processes controlling the distributions of DIC and TA onto
the continental shelf of the coastal off Baja California.

During the NACP West Coast cruise, three lines were included along
Mexico's coast: one located between the California Bight; a second
located in Pta. Eugenia, where several studies identify this area as the
transition between CC (California Current) and subtropical waters; and
the third located in San Lazaro Bay, where subtropical waters are
predominant. As was reported in the NACP West Coast Cruise Week 4
Report, evidence for upwelling of corrosive "ocean acidified" water onto
the North American west coast continental shelf was observed. The extent
of the ocean acidification impacted is between 50^o^ and 32^o^N. The
ocean acidification appears to be also occurring on the continental
shelf off Ensenada Baja California, but deeper in comparison with the
observed on higher latitudes probably as a result of less intense
upwelling events. In this region, the upwelling occurred offshore with
*p*CO~2~ in near surface depths (\~20m) at about 700 µatm. Corrosive
waters with pH\<7.775 were upwelled from depths of approximately 100-150
m in the offshore region and were observed about 30m from the surface.
Furthermore, both calcite and aragonite saturation horizons were deeper
than the northern lines but very similar to the conditions observed off
San Luis Obispo and Los Angeles (LA). However, the aragonite and calcite
saturation horizons were deeper by 30m and 50m, respectively, off
Ensenada than off LA. The first line in Mexico supports the idea that
upwelling processes transport corrosive water onto the continental shelf
in this region. These results also represent the first evidence that in
Mexico the continental shelf is being seasonally impacted by ocean
acidification.

**6.0 Acknowledgements.** The scientific party of the NACP West Coast
Cruise W0705A would like to express sincere thanks to Captain Rick
Verlini and all of the crew of the R/V *Wecoma* for their outstanding
work in support of our cruise despite some very difficult weather
conditions in the North Pacific Ocean.

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