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Final Project Instructions (click for full pdf)

Date Submitted: February 7, 2017
Platform: NOAA Ship Bell M. Shimada
Project Number: SH-17-04 (OMAO), 1704SH (SWFSC)
Project Title: Spring CalCOFI and Saildrone Ground Truthing, SWFSC/PMEL
Project Dates: March 19, 2017 to April 21, 2017

 

I. Overview

A. Brief Summary and Project Period

I.A.1. Survey the distributions and abundances of pelagic fish stocks, their prey, and their biotic and abiotic environments in the area of the California Current between San Francisco, California and San Diego, California during the period of March 28 to April 21, 2017.

I.A.2. Ground truth the Saildrone UAS instrument suite with the Shimada.

B. Days at Sea (DAS)

I.B.1. Of the 31 DAS scheduled for this project, 25 are funded by a Line Office Allocation according to the Fleet Allocation Plan. This project is estimated to exhibit a High Operational Tempo.

I.B.2. 1 UxS day is funded for OAR-PMEL to run instrument comparisons between the SHIMADA and a Carbon Saildrone.

I.B.3 5 days are funded for OMAO for transit from Newport, Oregon to San Diego, California.

C. Operating Area

I.C.1. The area covered during this survey will be from San Diego to San Francisco and extend approximately 200 miles offshore (please see appendices 1b & 2a).

I.C.2. UxS Saildrone: The SHIMADA – Saildrone comparison will take place somewhere along the CA coast between San Francisco and Santa Barbara in less than 300m water depth. The exact location will be determined based on observations from SH-17-02. The requirements are an area with fish aggregates in the water column in less than 300m.

D. Summary of Objectives

Survey the distributions and abundances of pelagic fish stocks, their prey, and their biotic and abiotic environments in the area of the California Current between San Francisco, California and San Diego, California.

The following are specific objectives for the spring CalCOFI.

I.D.1. Continuously sample pelagic fish eggs using the Continuous Underway Fish Egg Sampler (CUFES). The data will be used to estimate the distributions and abundances of spawning hake, anchovy, mackerel, and Pacific sardine.

I.D.2. Continuously sample sea-surface temperature, salinity, and chlorophyll-a using a thermosalinometer and fluorometer. These data will be used to estimate the physical oceanographic habitats for target species.

I.D.3. Continuously sample air temperature, barometric pressure, and wind speed and direction using an integrated weather station.

I.D.4. Sample profiles of seawater temperature, salinity, chlorophyll-a, nutrients, and phytoplankton using a CTD with water-sampling rosette and other instruments at prescribed stations. Measurements of extracted chlorophyll and phaeophytin will be obtained with a fluorometer. Primary production will be measured as C14 uptake in a six hour in situ incubation. Nutrients will be measured with an auto-analyzer. These data will be used to estimate primary productivity and the biotic and abiotic habitats for target species.

I.D.5. Sample the light intensity in the photic zone using a standard Secchi disk once per day in conjunction with a daytime CTD station. These data will be used to interpret the measurements of primary production.

I.D.6. Sample plankton using a CalBOBL (CalCOFI Bongo Oblique) at prescribed stations. These data will be used to estimate the distributions and abundances of ichthyoplankton and zooplankton species.

I.D.7. Sample plankton using a Manta (neuston) net at prescribed stations. These data will be used to estimate the distributions and abundances of ichthyoplankton species.

I.D.8. Sample the vertically integrated abundance of fish eggs using a Pairovet net at prescribed stations. These data will be used to quantify the abundances and distributions of fish eggs.

I.D.9. Sample plankton using a PRPOOS (Planktonic Rate Processes in Oligotrophic Ocean Systems net) at all prescribed CalCOFI stations on lines 90.0 and 80.0 as well as stations out to and including station 70.0 on lines 86.7 and 83.3 and station 81.8 46.9. PRPOOS will not be towed on SCCOOS stations. These data will be used in analyses by the LTER (Long Term Ecological Research) project.

I.D.10. Continuously sample profiles of currents using the RDI/Teledyne Acoustic Doppler Current Profiler.

I.D.11. Continuously observe, during daylight hours, seabirds and mammals. These data will be used to estimate the distributions and abundances of seabirds and marine mammals.

I.D.12. Conduct 24 hrs of Saildrone comparison operations to validate carbon, fisheries acoustics, ADCP, oceanographic, and meteorological sensors integrated onto the Saildrone UAS.

E. Participating Institutions

I.E.1 Southwest Fisheries Science Center (SWFSC)

I.E.2 Scripps Institution of Oceanography (SIO)

I.E.3 Farallon Institute Advanced Ecosystem Research (FIAER)

I.E.4 California Department of Fish and Wildlife (CDF&W)

I.E.5 Monterey Bay Aquarium Research Institution (MBARI)

I.E.6 J. Craig Venter Institute (JCVI)

I.E.7. Pacific Marine Environmental Laboratory (PMEL)

F. Personnel/Science Party: name, title, gender, affiliation, and nationality

Name (Last, First) Title DateAboard DateDisembark Gender Affiliation Nationality
Julian Herndon Research Scientist(UxS Chief Sci) March 19, 2017 March 24, 2017 M JISAO/PMEL US
Amy Hays Chief Scientist March 28, 2017 April 21, 2017 F SWFSC US
Bryan Overcash Biologist March 28, 2017 April 21, 2017 M SWFSC US
David Wolgast* Oceanographer March 28, 2017 April 14, 2017 M SIO US
Jennifer Rodgers-Wolgast* Oceanographer March 28, 2017 April 14, 2017 F SIO US
James Wilkinson* Oceanographer March 28, 2017 April 14, 2017 M SIO US
Megan Roadman LTER March 28, 2017 April 21, 2017 F SIO US
Shonna Dovel* LTER March 28, 2017 April 14, 2017 F SIO US
Daniel Schuller* Chemist March 28, 2017 April 14, 2017 M SIO US
Matthias Scheer Marine MammalObserver March 28, 2017 April 21, 2017 M SIO US
Melody Baran Marine MammalObserver March 28, 2017 April 21, 2017 F SIO US
Regina Guazzo Marine MammalAcoustician/Observer March 28, 2017 April 21, 2017 F SIO US
Sophie Webb Bird Observer March 28, 2017 April 21, 2017 F FIAER US
Stephanie Ostresh Volunteer March 28, 2017 April 21, 2017 F SIO US
Hailey Rosenthal Volunteer March 28, 2017 April 21, 2017 F SIO US
Dovi Kacev Geneticist April 14, 2017 April 21, 2017 M NOAA US
Luke Thompson Geneticist April 14, 2017 April 21, 2017 M NOAA US
Lisa Zeigler Geneticist April 14, 2017 April 21, 2017 F JCVI US

*Personnel will be transferred ashore in Monterey or Santa Cruz, California by small boat at the completion of line 70.0.

**Personnel will be transferred from Monterey or Santa Cruz, California by small boat to the Shimada for Leg II.

G. Administrative

1. Points of Contacts:

Chief Scientist/alternate: Amy Hays/Bryan Overcash (858-546-7130/858-5467126); 8901 La Jolla Shores Drive, La Jolla, CA, 92037 ( This email address is being protected from spambots. You need JavaScript enabled to view it./This email address is being protected from spambots. You need JavaScript enabled to view it. )

UxS Saildrone Chief Scientist/ alternate: Julian Herndon / Noah Lawrence-Slavas (206-526-6256 / 206-498-4666); 7600 Sand Point Way NE, Seattle, WA 98115 (This email address is being protected from spambots. You need JavaScript enabled to view it./This email address is being protected from spambots. You need JavaScript enabled to view it. )

Project Operation Lead: Sam McClatchie (858-546-7183); 8901 La Jolla Shores Drive, La Jolla, CA, 92037 (This email address is being protected from spambots. You need JavaScript enabled to view it. )

Ops Officer: LT Sara Sheehan (808-684-5457) NOAA Ship Bell M. Shimada (This email address is being protected from spambots. You need JavaScript enabled to view it. )

Saildrone: Contact: Richard Jenkins, ( 510-326-0946), E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

  1. Diplomatic Clearances None Required.
    1. Licenses and Permits
      1. All marine mammal work is covered under a federal research permit NMFS Permit 17312 issued to Dr. John Hildebrand of SIO.
      2. CDFW ON April 2, 2015 to NOAA-SWFSC-FRD-Cisco Werner(SC12372)

II. Operations

A. Project Itinerary Leg II: March 19: Depart Newport, OR – UxS and Transit March 24: Arrive San Diego, CA Leg II: March 28: Depart San Diego, CA – CalCOFI April 14: Small boat transfer via Monterey or Santa Cruz, CA

April 14: Complete Small boat transfer in Depart Monterey or Santa Cruz, CA – continue CalCOFI April 21: Arrive San Francisco, CA

B. Staging and Destaging

Staging will be conducted in San Diego, CA at the 10th Ave Marine Terminal. Staging will require at least two full days. Destaging will be conducted in San Francisco, CA at Pier 30/32, San Francisco.

We request one laboratory van to be craned onto the afterdeck and secured in San Diego prior to departure. The dimension of the van is approximately 8x8x10 feet weighing 6500 lbs. Power requirement is 110V.

We request one SWFSC MMTD Acoustic Hydraulic Winch and Portable HPU be craned onto the afterdeck and secured in San Diego prior to departure. Specifications are as follows:

HPU as backup to ship’s HPU. Hydraulic hoses will be installed at the beginning of the project, and not disconnected until the end of the project. This best management practice will mitigate the leaking of hydraulic oil through the hoses. Efforts will be coordinated between the ship and the scientific compliment to ensure proper measures are in place to reduce environmental impacts in the event of a spill casualty.

C. Operations to be Conducted

II.C.1. UxS Saildrone Comparison Operations

  1. The objective is to ground truth the Saildrone’s scientific payload using the Bell M. Shimada. We would like to do this under a variety of Saildrone operating conditions, which will replicate different wind approach angles, water speeds, heel angles, and wave approach angles. During the inter-comparison, the ship will follow the Saildrone, behind, and if possible downwind, at distances ranging from 100 to 500 meters. The procedure will be as follows: The Saildrone will be placed on a course, either a straight run or a box course by the Saildrone operator.
  2. The ship will verify, with the Saildrone operator over the phone & e-mail (Contact: Richard Jenkins, Phone: 510 326 0946, E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it. ), the box waypoint positions and that the Saildrone is on the box course. Additional information, such as the width of the corridor between the waypoints, nominally 200m that the sail drone will stay within while tacking, current position, speed through water, etc. will also be relayed.
  3. The ship will then approach the Saildrone to a comfortable distance and the ship will shadow the Saildrone as it moves around the box course. The ship will verify with the Saildrone operator, via e-mail & phone, when they are making their approach and are in position with visual ID. The Saildrone will then maintain its current operating scheme, until the ship calls again to disengage or ask the Saildrone to change its operation mode.

II.C.1.a. Underway pCO2 Comparison. During the entire 24 hours of comparison work the ship will run the underway pCO2 system and follow as closely as practical to the Saildrone.

II.C.1.b. Water sample collection. Every 6 hours during the comparison period the ship will take surface water samples with either the ship’s CTD rosette, or a Van Dorn sampler supplied by PMEL. The ship should approach to within 100m of the Saildrone to collect these samples. Water samples will be collected by the PMEL scientist.

II.C.1.c. Oceanographic and Meteorological sensor comparison. During the entire 24 hour period the ship will log the scientific sensors as requested.

II.C.1.d. EK60 Comparison. During the first 12 hours of the comparison the ship will conduct an EK60 comparison with the Saildrone. The frequency we are interested in collecting is 38 khz. The ship should secure all other active acoustics during this time as they will interfere with the Saildrone’s and the Ship’s EK60.

II.C.1.e. ADCP Current Comparison. During the second 12 hours of the comparison the ship will conduct an ADCP comparison to validate Saildrone’s ADCP system. The ship should secure the EK60 and all other active acoustics during this time so they do not interfere with the Saildrone’s ADCP.

II.C.2. Underway Operations

II.C.2.a. Thermosalinometer sampling -The ship will provide and maintain a thermosalinometer (TSG), which is calibrated and in working order, for continuous measurement of surface water temperature and salinity. A backup unit (calibrated and in working order) will also be provided by the vessel and remain aboard during the project. The Scientific Computing System (SCS) will serve as the main data collection system. All SCS data will be provided to SWFSC personnel at the completion of the project.

II.C.2.b. Acoustics: Calibration of the EK60 is not requested or planned. EK60 echosounder data will not be collected during the survey.

II.C.2.c. ADCP: The ship’s ADCP should run continuously and be logged to a data acquisition system. Complete system settings will be provided by the oceanographer, but will include 5-minute averaging of currents, AGC and 4 beam returns in 60 8-meter bins.

II.C.2.d. CUFES: The egg pump will be mounted inside the ship’s hull drawing water from a depth of three meters. The pump will run continuously between stations to sample any pelagic fish eggs. Approximately 640 liters/minute is sent through a concentrator which filters all material larger than 505µm. The sieved material is then collected and identified. All fish eggs are identified to lowest taxa, counted and entered into the data acquisition software. Each sample entry is coupled with sea surface temperature, geographical position, wind speed and direction, date and time, pump speed and surface salinity. Sampling intervals will vary in length, depending on the number of fish eggs seen, from five to 30 minutes.

It is requested that prior to departure on March 28 that the CUFES intake be cleared from all marine growth.

• Dive completed dockside in Newport on March 3. CUFES intake was cleared of all marine growth. Acceptable to chief scientist.

II.C.2.e. Bird Observations: During daylight hours a bird observer will be posted on the flying bridge to identify and count birds while the ship is underway during project transects.

II.C.2.f. Acoustic hydrophone: During transit between most daylight stations, an acoustic hydrophone array will be towed from the stern at a distance of 300 meters with a deck loaded winch to record sounds from marine mammals. The winch is a hydraulic Sauer Danfoss DH-200 with a deck pattern of 6 by 6 feet. Upon approaching a station, a sonobuoy will be deployed one nautical mile prior to stopping for station work.

II.C.3. Station Operations

Each standard station will include the following:

II.C.3.a. CTD/Rosette consisting of 24 10-liter hydrographic bottles will be lowered to approximately 500 meters (depth permitting) at each station to measure physical parameters and collect water at discrete depths for analysis of: salinity, nutrients, oxygen, chlorophyll, etc.

NOTE: SIO will provide their own CTD sensor and 24 bottle (10 liter) rosette unit.Please record CTD deployed, CTD at depth and CTD recovered for SCS.

II.C.3.b. CalBOBL (CalCOFI Bongo): standard oblique plankton tow with 300 meters of wire out, depth permitting, using paired 505 µm mesh nets with 71 cm diameter openings. The technical requirements for this tow are: Descent wire rate of 50 meters per minute and an ascent wire 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 will be repeated. Additionally, a 45° wire angle should be closely maintained during the ascent and descent of the net frame. A self-contained LOPC (Laser Optical Particle Counter) will be mounted in the port side opening during each tow. The port side sample will be preserved in buffered ethanol at every station.

Please record Bongo deployed and Bongo recovered for SCS.

II.C.3.c. Manta net (neuston) tow: using a 505 µm mesh net on a frame with a mouth area of 0.1333 m². Tows are 15 minutes in duration at towing speed of approximately 1.5 -2.0 knots. Wire angles should be kept between 15° and 25°.

Please record Manta deployed and Manta recovered in SCS.

II.C.3.d. Pairovet net: will be fished from 70 meters to the surface (depth permitting) using paired 25 cm diameter 150 µm mesh nets. The technical requirements for Pairovet tows are: Descent rate of 70 meters per minute, a terminal depth time of 10 seconds and an ascent rate of 70 meters per minute. All tows with wire angles exceeding 15° during the ascent will be repeated.

Please record Pairovet deployed and Pairovet recovered for SCS.

II.C.3.e. PRPOOS (Planktonic Rate Processes in Oligotrophic Ocean Systems) net will be 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 and station 81.8 46.9. These stations are occupied as part of the LTER (Long Term Ecological Research) project. The mesh of the PRPOOS net is 202 µm and the tow is a vertical cast up from 210 meters. The technical requirements for the PRPOOS tows are: Decent rate of 40 meters per minute, a terminal depth time of 20 seconds and an ascent rate of 50 meters per minute.

Please record PRPOOS deployed and PRPOOS recovered for SCS.

II.C.3.f. Primary productivity: at about 1100 hours on each day a primary productivity CTD cast consisting of six 10-liter hydrographic bottles (mounted on CTD frame) will be carried out. The cast arrangement will be determined by a Secchi disc observation. This cast will be in conjunction with an already scheduled station. The purpose of the cast is to collect water from six discrete depths for daily in situ productivity experiments. Measurements of extracted chlorophyll and phaeophytin will be obtained with a fluorometer. Primary production will be measured as C14 uptake in a six hour in situ incubation. Nutrients will be measured with an auto-analyzer. All radioisotope work areas will be given a wipe test before the departure of the SIO technical staff. Primary productivity on leg II after line 76.7 will not be measured.

II.C.3.g. A light meter (Secchi disk) will be used to measure the light intensity in the euphotic zone once a day with the primary productivity cast and all daytime stations.

Please record Secchi deployed and Secchi recovered for SCS.

II.C.3.h. Weather observations.

II.C.4.a. Order of Operations for each standard station:

1) CTD to 515 meters with 24 bottle rosette (depth permitting).

2) Secchi disk (daylight stations only, Secchi will be first prior to CTD on Primary Productivity station of the day which is typically 0900-1100). Secchi disk will not be measured on Leg II after completion of line 76.7.

3) PRPOOS net tow [lines 90.0, 86.7 (out to station 70), 83.3 (out to station 70)

and 80.0 ; station 81.8 46.9]. No PRPOOS on near shore SCCOOS stations.

Total of 35 stations).

4) Pairovet net tow (on all lines out to station 100 but not to include near shore SCCOOS).

5) Manta net tow (on all stations except for near shore SCCOOS).

6) Bongo net tow (on all stations).

II.C.4.b. Plankton Nets, Oceanographic Sampling Devices, Video Camera and ROV Deployments: The SWFSC deploys a wide variety of gear to sample the marine environment during all of their research projects. These types of gear are not considered to pose any risk to protected species and are therefore not subject to specific mitigation measures. However, the OOD and crew monitor for any unusual circumstances that may arise at a sampling site and use their professional judgment and discretion to avoid any potential risks to protected species during deployment of all research equipment.

Marine mammal watches are now a standard part of conducting fisheries research activities, particularly those that use gear (e.g., longlines and mid-water trawls) known to interact with marine mammals or that we believe have a reasonable likelihood of doing so in the future. Marine mammal watches are conducted in two ways. First, watches are conducted by lookouts (those navigating the vessel and other crew) at all times when the vessel is being operated. Second, marine mammal watches and monitoring occur for 30 minutes prior to deployment of gear, and they continue until gear is brought back on board, for longlines and mid-water trawl gear. Watches in the first category are not done by dedicated staff; these personnel primary duties as lookout according to the Rules of the Road are “maintaining a proper lookout by sight and hearing as well as by all available means appropriate in the prevailing circumstances and conditions so as to make a full appraisal of the situation and of the risk of collision.” Watches in the second category are done by dedicated scientists with no other responsibilities during the watch period. If marine mammals are sighted within 1 nm of the planned set location then the sampling station is either moved or canceled. Watch-standers record the estimated species and number of animals present and their behaviors. This information can be valuable in understanding whether some species may be attracted to vessels or gear. While underway:

We will have a bird observer on the flying bridge during all daylight transects.

We will have 2 marine mammal observers on the flying bridge during all daylight transects.

We will have a marine mammal acoustician with a towed hydrophone. The hydrophone will be towed off the stern at a distance of 300 meters between daylight stations. The hydrophone will be deployed at a ship speed of 5 knots while leaving a station. Once deployed, ship can travel at full speed. The hydrophone can be retrieved at ship’s full speed. If the ship must make sudden course changes, notify the marine mammal acoustician and marine mammal observers.

At 1 mile prior to each daylight station marine mammal observers will deploy 2 sonobuoys. The hydrophone will be retrieved at this time.

Communication will be open to bridge during all hydrophone deployments and retrievals.

D. Dive Plan

All dives are to be conducted in accordance with the requirements and regulations of the NOAA Diving Program ( http://www.ndc.noaa.gov/dr.html ) and require the approval of the ship’s Commanding Officer.

E. Applicable Restrictions

Conditions which preclude normal operations:

In the event of poor weather conditions, we will work with the ship’s officers on developing the best strategy for completion of all stations safely.

We have replacement gear for all operations. Equipment failure should not impact our project.

III. Equipment

A. Equipment and Capabilities provided by the ship

We request the following systems and their associated support services, sufficient consumables, back-up units, and on-site spares. All measurement instruments are assumed to have current calibrations and we request that all pertinent calibration information be included in the data package.

Starboard hydro winch with 0.375” cable for standard Pairovet, Manta, Bongo and PRPOOS tows

A-frame w/blocks to accommodate 0.375" cable

Constant temperature room set at 22oC ± 1oC (71.5oF ± 2oF)

NOTE: The vessel has no constant temperature room. The constant environment room is sufficient if we are allowed to open and close the door to control temperature and ventilation.

Winch monitoring system

EK60 18 kHz depth recorder or comparable to measure bottom depth to 4000+ meters Acoustic Doppler Current Profiler

Scientific computing system

12-bottle rosette frame capable of carrying 10-liter niskin bottles, fitted with SBE911+ CTD unit

(spare only to be used in case of equipment loss or failure)

Pump, collector and concentrator unit for CUFES water sampling

GPS feed to flying bridge for use by bird observer

110V power to science van on main deck

1500 PSI hydraulic power to science winch on main deck for use as backup

440V power hookup for project’s Portable HPU

-80oC Freezer

For UxS Saildrone comparison operations we request the following measurement systems. All measurement instruments are assumed to have current calibrations and we request that all pertinent calibration information be included in the data package.

  1. The Underway pCO2 system
  2. The EK-60 fish finder (38 khz),
  3. The ADCP with associated POS-MV, Gyro and GPS systems to get current information.
    1. The ship should log the scientific sensors listed below for comparison with the Saildrone at a 60-second SCS logging rate. Please make sure that the filters are cleaned on the ship’s underway seawater system and that the flow rate is reasonable. Please Bleach the intake and pipes just before the cruise
      1. Wind Speed & Direction
      2. Near-surface (i.e. from ship’s underway seawater system) water temperature
      3. Near-surface salinity
      4. Near-surface dissolved oxygen
      5. Atmospheric LWR and SWR from ship’s mast
      6. Air temperature/relative humidity
      7. Barometric pressure
      8. Near-surface chlorophyll-a concentration
      9. GPS data
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