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Summer CalCOFI
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UNITED STATES DEPARTMENT OF COMMERCE
National Oceanic and Atmospheric Administration
National Marine Fisheries Service
Southwest Fisheries Science Center
8604 La Jolla Shores Drive
La Jolla, CA 92037
February 15, 2007
F/SWC1:DAG
CRUISE REPORT
VESSEL:
NOAA Vessel David Starr Jordan, 0701-JD, DS 07-01.
CRUISE DATES:
January 12 - February 3, 2007.
PROJECT:
CalCOFI Survey, Fisheries Resources Division.
ITINERARY:
Leg I: Departed the Nimitz Marine Facility at 0800 on January 12,
2007 and moved to the Navy fuel pier to begin fueling. Departed
the fuel pier around 15:00 and proceeded to the first station
(93.3/26.7 - position 32° 57.38N 117° 18.32W). Continued to occupy
stations up to 76.7 100.0 at which time operations were
discontinued and the ship pulled into Monterey, California to
complete leg I on January 31.
Leg II: Departed Monterey on January 31 after exchanging scientific
personnel and began occupying stations on line 66.7. Completed
stations out to 85.0 and then returned to San Diego on February 3,
2007.
OBJECTIVES: 1.
To continue an ongoing assessment of pelagic fish stocks between
Monterey Bay and La Jolla, California.
2.
To monitor environmental conditions within the CalCOFI survey area.
3.
To conduct a continuous sampling of surface waters using the ship’s
underway system. Temperature, salinity and chlorophyll were
automatically logged by computer with the output from the GPS
navigational unit.
4.
To record current profiles throughout the duration of the cruise
with the Acoustic Doppler Current Profiler (ADCP).
5.
To measure optical profiles within the California bight. The
optical profile measurements will include pigment concentration and
particle absorption.
6.
To make continuous observations of sea birds and marine mammals.
PROCEDURES: 1.
Each standard CalCOFI station included the following:
a. A CTD/Rosette consisting of 24 10-liter hydrographic bottles
was lowered to 500 meters (depth permitting) to measure physical
parameters and collect water at discrete depths. Additional
intermediate stations were added to line 66.7 and the CTD casts
were sent down to 1000 meters. Sea water from each hydrographic
bottle was analyzed for chlorophyll, salinity, and nutrients.
Continuous profiling during the cast was obtained for
oxygen, temperature, conductivity, light transmittance
and chlorophyll fluorescence.
b. A CalBOBL (CalCOFI Bongo) standard oblique plankton
tow with 300 meters of wire out, depth permitting, used
paired 505 :m mesh nets with 71 cm diameter openings.

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The technical requirements for this tow were: Descent rate of 50
meters per minute, ascent rate of 20 meters per minute. All tows
with ascending wire angles lower than 38° or higher than 51° in the
final 100 meters of wire were repeated. Additionally, a 45° wire
angle was closely maintained during the ascent and descent of the
net frame. Contents of the starboard side net were preserved in
buffered formalin for later identification. The port side net
contents were preserved in buffered ethanol for later
identification of ichthyoplankton and DNA studies for stations at
and inshore of station 70.
c. A Manta net (surface) tow, using a 505 :m mesh net on a frame
with a mouth area of 0.1333 m². The duration of each tow is 15
minutes at approximately 1½ knots.
d. Weather observations.
e. A Pairovet (vertical) plankton tow was taken at all stations
inshore of, and including station 70. The Pairovet net was fished
from 70 meters (depth permitting) to the surface using a 25 cm
diameter 150 :m mesh net. The technical requirements for Pairovet
tows are: Descent rate of 70 meters per minute, ascent rate of 70
meters per minute. All tows with wire angles exceeding 15/ during
the ascent were repeated.
f. A PRPOOS(Planktonic Rate Processes in Oligotrophic Ocean
Systems) net tow was taken at all stations on line 90.0 and 80.0
as well as stations out to and including station 70.0 on lines 86.7
and 83.3. These stations were occupied as part of the LTER(Long
Term Ecological Research) project. The mesh of the PRPOOS net is
202 :m and the tow is a vertical cast up from 210 meters, depth
permitting.
g.
Up to and including line 76.7, at about 1100 hours on each
day of the cruise a primary productivity CTD cast consisting of six
10-liter hydrographic bottles was carried out. The cast
arrangement were determined by a Secchi disc observation. The
purpose of the cast was to collect water from 6 discrete depths for
daily in situ productivity experiments. Measurements of extracted
chlorophyll and phaeophytin were obtained with a fluorometer.
Primary production was measured as C14 uptake in a 6 hour in situ
incubation. Nutrients were measured with an auto-analyzer. All
radioisotope work areas were given a wipe test before the departure
of the SIO technical staff.
h. During transit between stations, a bird observer and marine
mammal observer recorded locations and species of various sea birds
and marine mammals.
i. During transit between most daylight stations, an acoustic
hydrophone array was towed off the stern with a cable/winch to
record sounds from marine mammals. Upon approaching a station, a
sonobuoy was deployed one nautical mile prior to stopping for
station work.
2.
The egg pump (CUFES - Continuous Underway Fish Egg Sampler)was
mounted inside the ship’s hull drawing water from a depth of three
meters. During the grid occupation, the pump ran continuously
between stations to sample any pelagic fish eggs.
3.
An additional nine stations were occupied within the CalCOFI
pattern for SCCOOS(Southern California Coastal Ocean Observation
System). These were 20 meter depth stations and consisted of a CTD
lowered to within a few meters from the bottom and a Bongo tow.

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These stations were included in the original station plans provided
to the ship.
RESULTS:
Activity
Requested
Completed
Aborted
Bongo tows
94
79
15
Manta
85
71
14
Pairovet
61
46
15
PRPOOS tows
35
35
0
CTD
95
84
11
Salinity
95
84
11
Oxygen
95
84
11
Nutrients
95
84
11
Chlorophyll
95
84
11
Phytoplankton
66
66
0
Primary productivity
16
16
0
Weather
95
84
11
Surface Temp.
95
84
11
Underway data (hours)
552
552
0
ADCP (hours)
552
552
0
CUFES samples
417
417
0
In addition, approximately 500 total hours of bird and marine
mammal observations were logged by Annie Douglas, Lisa Sheffield,
Greg Campbell and Nadia Rubio.
DISPOSITION
OF DATA:
CalBOBL, Manta tow data sheets and formalin preserved samples -
Richard Charter, FRD (SWFSC).
Station activity logs, weather data and surface temperature data
- Richard Charter, FRD (SWFSC) and Ralf Goericke, IOD (SIO).
ADCP data - Richard Charter, FRD (SWFSC).
CTD data - Ralf Goericke, IOD (SIO)and Tim Pennington (MBARI).
Water analysis data (temperatures, salinities, nutrients and
chlorophylls) - Ralf Goericke, IOD (SIO) and Tim Pennington
(MBARI) .
CUFES data - Richard Charter, FRD (SWFSC).
Underway data - Richard Charter, FRD (SWFSC).
Alcohol preserved bongo samples - William Watson, FRD (SWFSC).
Marine mammal observation and acoustic data - John Hildebrand,
GRD, MPL (SIO).
Bird observation data - William Sydeman, MED (PRBO).
Underway CO2 data - Gernot Friederich, (MBARI).
INCIDENTS &
MALFUNCTIONS:
The ship moved to the Navy fuel pier at 0800 and arrived around
0900. Departed fuel pier around 1500 and arrived at first
station 1730. Due to fueling at departure, we were unable to
occupy the first primary productivity station. Initially there
were problems with a starboard main engine cylinder running hot,
but by adjusting the fuel mixture, the problem was corrected. On
the first station, the starboard winch rate could not achieve 70
m/min. Problem was corrected by station 93.3 40.0.

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The LOPC mounted in the bongo frame stopped working on station
93.3 50.0 and was later removed on station 93.3 60.0 and replaced
by the standard CalBOBL setup.
At station 93.3 100.0, one of the high pressure hoses to the
starboard side winch burst and a replacement hose was built and
re-installed. Total time for repair was a little over an hour.
Completed station 90.120 and decided to break off from the
pattern and head into Dana Point to drop off scientific personnel
due to family emergency. A loss of approximately 1½ days. During
transit into Dana Point, steering was lost for approximately 30
minutes but no time was lost to the survey.
COMMENDATIONS:
The personnel of the David Starr Jordan should be recognized and
commended for their dedication and professional manner, ensuring
the completion of the cruise:
The deck department for their ability to meet the needs of all
types of gear with speed and expertise.
The bridge officers for their assistance with all sampling
operations as well as assuring the safety and well-being of all
personnel aboard. Efforts to complete stations in a timely
manner and meet specific time schedules contributed to the
completion of the majority of the scheduled work.
The engineering department for their performance and ability
correcting major and minor malfunctions to allow the completion
of the cruise with little or no loss of time.
The electronics specialist for his assistance with communications
and correcting any electronic malfunctions for both the ship and
scientific gear.
The stewards department for providing excellent meals and
accommodations in all weather conditions.
In addition, the combined scientific staff from SWFSC, SIO,
MBARI, CDFG, PRBO and Cascadia Research should be commended on
their ability to continuously collect high quality data
throughout the duration of the cruise.
PERSONNEL:
Leg I:
Dave Griffith, Cruise Leader
SWFSC
Ron Dotson
SWFSC
Amy Hays*
SWFSC
Sue Manion**
SWFSC
Bryan Overcash
CDFG
Dave Wolgast, SIO coordinator
SIO
Jim Wilkinson
SIO
Jennifer Sheldon
SIO
Kathryn Stanaway
SIO
Greg Campbell†
SIO
Nadia Rubio‡
SIO
Shonna Dovel
SIO
Megan Roadman
SIO
Susan Becker, chemist
SIO
Annie Douglas
CR
Lisa Sheffield
PRBO
Jeffrey Lewis, volunteer
SIO
* Disembarked in Dana Point, CA

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** Embarked in Dana Point, CA
† Disembarked in Port San Luis, CA
‡ Embarked in Port San Luis, CA
Leg II:
Dave Griffith, Cruise Leader
SWFSC
Ron Dotson
SWFSC
Sue Manion
SWFSC
Bryan Overcash
CDFG
Dave Wolgast, SIO coordinator
SIO
Jennifer Sheldon
SIO
Nadia Rubio
SIO
Annie Douglas
CR
Lisa Sheffield
PRBO
Marguerite Blum
MBARI
SWFSC personnel authorized per diem at the rate of $3.00 per day
to be paid via the Imprest Fund at the termination of the cruise.
SWFSC PERSONNEL
WATCH HOURS:
1200 - 2359
Charge to account #28LEF01-P15
0000 - 1159
Date:
Prepared by:
David Griffith
Approved by:
William W. Fox Ph.D
Science & Research Director
Southwest Region

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