Woods Hole Oceanographic Institution

Cruise Planning Synopsis

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AT42-13: Cowen "Mesozooplankton Food Webs"


R/V Atlantis

Cruise Party

Kelly Sutherland: Principal Investigator
University of Oregon USA
+1 541 346 8783

Robert Cowen: Chief Scientist
Oregon State University, Hatfield USA
+1 541 867 0211

Departure: Jul 15, 2019

Newport, OR

Arrival: Jul 26, 2019

Newport, OR

Operations Area

Off Newport, OR and off Trinidad, CA
Lat/Lon: 44° 39.12′ N / 125° 7.02′ W
Depth Range: 50 / 120
Will the vessel be operating within 200 NM of a foreign country? no

Science Objectives

MEsoZooplankton trophodynamics in the CALifornia Current (MEZCAL)

General approach

Our overall approach is to sample the summer trophic web off the coast of Newport, OR and Trinidad, CA. Cruise data will be combined with a winter and summer cruise from 2018 and this year's winter cruise in order to investigate differences in the activity of the traditional food web as well as the microbial foodweb with regard to season (summer/winter) and upwelling (continuous off the coast of CA and intermittent off OR). For that we sample with a high resolution in situ plankton imaging device (In Situ Ichthyoplankton Imaging System, ISIIS) to obtain an accurate description of plankton communities: their abundances, patchiness, and horizontal and vertical spatial distributions. In parallel, we collect depth-discrete mesozooplankton samples to quantify diets for larval fishes and gelatinous zooplankton and prey-specific growth rates of larval fishes.

Science Activities

This is the fourth of four research cruises in the NCC. Cross-shelf transects will be located off of (1) Newport, OR and (2) Trinidad Head, CA to capitalize on historic records of ocean conditions.

We will deploy ISIIS along transects from East to West during daylight hours and then West to East at night. Traversing the transect again, we will sample as many of the stations as possible with a coupled MOCNESS from East to West in daylight hours, and then we do as many stations as possible again on the way back from West to East, during night time. Sampling is adaptive and follows marine dawn and sunset. We also deploy a ½ m diameter ring net down to 25 m before or after each MOCNESS deployment.

To collect water samples for Particulate Organic Matter (POM) we will utilize CTD/Niskin bottle deployments at each MOCNESS station during the daylight transect. This complete sampling of a transect with ISIIS, MOCNESS, ring nets, and CTD will take 48 hrs. We will repeat this sampling of the transect off Oregon, taking another 48 hrs, and then transit (24 hrs) to the northern CA site and repeat the same sampling regime (96 hrs total) on the onshore-offshore transect off Trinidad Head, CA. The ship will need a final 24 hrs to return to Newport following the CA sampling, resulting in a total at-sea cruise time of 10 days.

Sampling technology: 

In Situ Ichthyoplankton Imaging System (ISIIS)– Our central sampling technology is the In Situ Ichthyoplankton Imaging System (ISIIS), a high resolution imaging system designed to image sufficient volumes of water to accurately quantify rare meso- and macroplankton such as larval fishes and gelatinous zooplankton in situ). The current system (ISIIS-2) consists of two separate cameras: the first capable of imaging up to 140 L s-1, with pixel resolution of 68 µm, and the second, small camera capable of imaging to 35 µm pixel resolution. Together, the dual camera system enables resolution of in situplanktonic taxa from large ciliates to medusae. The ISIIS is also instrumented with a set of environmental sensors including: CTD, PAR, O2, and fluorometry. All data are passed via fiber optic cable to an onboard computer, time-stamped for cross-referencing, and saved on a high-speed disk array (also experimental Amazon snowball setup as discussed on this cruise). The line-scan cameras build continuous images; if the instrument is towed for 100 km, it has a 100-km long image with 68-µm or 35-µm line (pixel) resolution. Thus, ISIIS can assess distributions ranging from cm to 10s of km (or more if the instrument is towed farther).

 For the ISIIS we will bring a Hawblodt 0.322 fibre optic winch from the WHOI winch pool with us. 

Coupled Multiple Opening and Closing Net and Environmental Sampling System (coupled MOCNESS)– To sample a range of zooplankton simultaneously, we will use a coupled MOCNESS system consisting of a 4m2net fitted with 1 mm mesh and a 1 m2net with 333 µm mesh. A series of five paired nets that can be remotely triggered to open and close will enable us to sample different depths discretely. MOCNESS samples will be used to validate and compare to ISIIS imagery, but primarily to collect biological specimens for analysis of diet (gut contents), growth (larval fish otolith microstructure), fatty acids, and stable isotopes composition. Immediately after collection, a sub sample of each net sample will be sorted for common gelatinous zooplankters for diet analysis and then preserved individually in 5% buffered formalin. The remaining contents of all samples will be fixed and preserved in 70% ethanol. Net 0 samples are integrated across all depths as this net is open on initial deployment to depth. To provide direct comparison of MOCNESS sampling to existing time series sampling along these two historical transect lines, we will also deploy the standard vertical ring net casts at each day station. All biological samples are either stored in ethanol, formalin, or frozen in the -80C freezers, no fatty acid or stable isotope analyses will be processed on board.

 For MOCNESS we will rely on one of your ship winch systems, please.

Additional Info

Pre-cruise Planning Meeting: Teleconference
Meeting Notes: Collaborators from Trinidad CA, Portland OR, Eugene OR and Newport OR will join together with you via teleconference.
Media personnel on board: Video, Artist at Sea
Dear Sir or Madam, We have one photographer/videographer, plus one Artist at Sea. What kind of art this Artist at Sea will make is still to be determined. The final selection for that will be made in late spring 2019. So, most likely 2 representatives of the arts. Just to confirm, these are not from traditional media (as in for a TV network etc). Cheers, Moritz


Supporting documentation:



Funding Agency: NSF
Grant or contract number: 1737399

Scientific Instrumentation for R/V Atlantis

Shipboard Equipment

ADCP 75 kHz
Deionized Water System
Science Underway Seawater System
Navigation - Heading
Fume Hood
Navigation - Position

Shipboard Communication

Basic Internet access via HiSeasNet

CTD/Water Sampling

911+ Rosette 24-position, 10-liter bottle Rosette with dual T/C sensors
Biospherical underwater PAR (1000m depth limit) with reference Surface PAR
SBE43 oxygen sensor
Seapoint STM turbidity sensor
Wet Labs ECO-AFL fluorometer
Wet Labs C*Star transmissometer (660nm wavelength)

Critical CTD Sensors

If possible we would like to request 1m square net opening 333 micron MOCNESS nets with cod ends

MET Sensors

Barometric Pressure
Air temperature
Relative Humidity
Wind speed and direction

Sample Storage

Climate Controlled Walk-in
Freezer -70°C 25 cu. ft.
Freezer -70°C 3.2 cu. ft. ea.
Storage Notes: The walk in freezer should be set to around 0 deg C, please.

We can start with one -70 deg C freezer, and if needed the second could be used depending on how many plankton samples we want to freeze.


Will you be using Long Base Line (LBL) navigation? no
How many nets? null
How many tansponders? null
Will you be using Ultra-short baseline (USBL) navigation?no


Navigation Notes: ISIIS needs a serial input GPS signal please. We have a serial to USB adapter that plugs into the ISIIS topside computer. Could you send us a snippet from the Atlantis GPS stream so we can check for compatibility with the ISIIS system please?

We would like to ask for radios to talk to the bridge during ISIIS deployments (speed of ship through water has to be increased and decreased on a regular basis), and well as a second set of radios to talk to the person driving the ISIIS FO winch.


CTD Winch with .322" Electro-mechanical wire
Hydro Winch with .25" hydro wire
Other Portable Winch
Trawl Winch with 9/16th trawl wire
Winch Notes: - CTD winch for deploying the CTD
- The 0.681 coax trawl winch would be the best for our MOCNESS based on our experience.
- Other portable winch is the Hawboldt 0.322 FO winch we bring onboard for ISIIS.
- Hydro winch 0.25 might be good to deploy the small ring net. Although it only goes down to 25m it needs a weight with a wire clamp to keep the net straight on the way down. Thus, from our experience it's too much for hand deployment. Maybe the smaller hydro winch or something off the crane would be best suited. When I requested the crane a few sections above that was only as a potential deployment mechanism for the ringnet. If something else is used, no crane is needed (apart form loading of course). Would you be able to supply the ball weight and wire clamp for ringnet deployment? Thanks!

Wire use and application

Hydro Winch with .25" hydro wire
CTD Winch with .322" Electro-mechanical wire
Trawl Winch with .680 Coax
Winch Notes: The tethered, undulating ISIIS underwater imager: 900 lbs. We bring a WHOI winch pool Hawboldt 0.322 fibre optic winch and cable for that, ISIIS contains < 1l of water when taken out of the water, max depth of deployment is 105m. Has floatation devices, weighs less in water.

Coupled MOCNESS: 2000 lbs. Deployed using one of your winches, as per above, let's discuss which is best suited but I believe the 0.680 coax that is listed here fits best. Our MOCNESS is outfitted with the new Scripps SIO upgrade where the net release motors are triggered by a SBE9 CTD (we are borrowing the CTD that will be on our MOCNESS from Brian Guest, WHOI winch pool, loan agreement is finalized). Only contains water in the cod-ends (± 30 l). Max depth of deployment is also 105m.

1/2 m ringnet: potentially (after discussion with you) deployed on the 0.25 hydro winch and wire. 10 lbs without the weight. Contains 1l of water upon retrieval. Max depth of deployment 25 m.

We would like to attach a small frame that holds 2 GoPro cameras and 2 lights to the frame of the CTD (0.322 EM wire). Weight approx 20 lbs. Contains no seawater.

Standard Oceanographic Cables

Slip ring required? no
Non-standard wire required? no
Traction winch required? no

Specialized Deck Equipment

Mooring Deployment/Recovery Equipment Required: no Type: 
Cruise Specific Science Winch Required: yes Type: Hawblodt FO winch for ISIIS
Nets Required: yes Type: 10 nets attached to MOCNESS

Over the Side Equipment

Will you be bringing any equipment (winches, blocks, etc.) that lowers instruments over the side? yes
Details: Hawboldt FO winch and associated block described above lower ISIIS over the side.

Special Requirements

Elecrical Power: yes Identify Hawboldt Winch requires 480V. ISIIS power source connects to standard 110V receptacle
Equipment Handling: yes Identify: during loading/offloading and deployments/recoveries please
Inter/intraship Communications: yes Identify: GPS feed for ISIIS and MOCNESS
Science Stowage: no Identify: 
Water: yes Identify: Ultrapure water for rinsing the POM filters if possible

Additional Cruise Items/Activities

Explosive Devices:no
Portable Air Compressors:no
Flammable Gases:no
Small Boat Operations:no
SCUBA Diving Operations:no

Hazardous Material

Will hazardous material be utilized?yes
Describe deployment method and quantity:
Please see attached Hazardous materials file.

Ethanol drums are stored outside (6x), as well as one waste ethanol drum (from swapping Ethanol from our plankton samples).

Radioactive Material


Additional Information

Is night time work anticipated on this cruise?yes
Specialized tech support (Seabeam, coring, other):
Yes, the same operations that happen during day also happen during night. Except during transit, 24h operations are expected. In an ideal scenario tech support (or Bosun and his crew depending on how the deck is run) would help with deployments and recovery of MOCNESS, ISIIS, and Ringnet. The science crew on this cruise has been working together now on 3 cruises, but the CTD was always operated by a Restech (bottle firing by scientists though); however, if needed we can learn to drive the CTD.
Other required equipment and special needs:
While we are trained in fibre optic terminations for ISIIS, it would be good if Atlantis restechs would be in charge of the MOCNESS termination please.

As noted we will have a SBE9 from Brian Guest, WHOI, on our MOCNESS, as well as using "his" deck unit. Is it possible that you have a computer setup for us for flying MOCNESS with the new SIO software (lvpki 0.99s or higher version)? Otherwise we will bring our own MOCNESS topside computer.

If we could have radios for communication between lab and bridge, as well as lab and ISIIS winch, that would be great, thanks.

Based on our experiences in the past we would like to request the maximum amount of seawater sinks (4 would be good) since we can catch quite a lot of plankton, and in the summer especially, pyrosomes, which slow our processing down.

We would like to use the e-logger website system where we can input deployments and retrievals (automatically pulls GPS from ship's stream), if possible.

ADCP: Are the more frequencies available other than 75khz?

Is there a EK60 or 80 on board?

Checklist & Notes


U.S. Customs Form: no
Diplomatic Clearance: no
Date Submitted:
Date Approved:
Agent Information:
Isotope Use Approval: no
Isotope Notes:
SCUBA Diving: no


SSSG Tech: