Sampling is in Full Swing on the Spring 2018 Bottom Trawl Survey

Post and Photos by Christine Kircun, NOAA/NEFSC

The spring survey has officially begun, and I am on night watch with a great team!  After a couple of nights to adjust to the sleeping schedule, we’re back in the full swing of sampling.

Not all fish are sampled the same.  For some species, such as shortnose greeneye (Chlorophthalmus agassizi), only lengths are taken.  For others, such as bluefish (Pomatomus saltatrix), we take length, weight, sex, maturity, stomach contents and otoliths.  The bluefish pictured is a 46.5cm (just over 18 inches long) resting (after spawning) female.


A longfin squid and unidentified squid were found in the stomach (image below).


Since the otoliths (pictured below) for bluefish are very fragile, the heads are frozen so the otoliths can be taken out back at the lab.


This is the most common workup.  There may also be additional requests from researchers inside and outside the lab for fin clips, gonad samples, muscle samples or whole frozen fish for identification, maturity, and stomach workshops.

For this leg, we’ve had some beautiful weather.  On night watch, it’s sometimes easy to forget to go outside, but on those nice days, it’s wonderful to feel the sun and watch the water, hoping to catch a glimpse of a shark, fish, or pod of dolphins.

6 sunrise

Though, it’s not always sunny and calm, and we had a little window of unpleasant weather.  When the waves and wind are too rough to fish, the main job becomes not


Seas are getting rougher and winds are increasing as another storm approaches. 

flying out of your chair when the ship takes a roll, keeping your balance while walking, and trying not to get sick.  If you’ve never been sea sick, count yourself lucky because it is miserable.  But that’s just another part of life on a ship.  Sometimes it’s really tough to be out here, but ultimately, it’s all worth it.  There’s a lot of dedicated and excited scientists, volunteers, officers, deckhands and engineers who are all committed to gathering the best data possible, no matter what.

Christine Kircun
NEFSC Fishery Biology Program, Age and Growth Technician
Aboard the NOAA Ship Henry B. Bigelow
HB18-02-Leg 1

Delicate Jellies, Video Stars

Hi! I’m Liese Siemann, and I am primarily a computational biologist. I spend my time running statistical and fluid dynamics models and writing programs to analyze images. So when I was invited to participate in this research cruise to develop a new camera system to survey jellyfish and other gelatinous animals, I jumped at the chance. Getting to work with sea turtles again and spend time watching whales all over the North Atlantic made the opportunity even more enticing.

The scientists at Coonamessett Farm Foundation have been attaching cameras and lights to scallop dredges for years, so I had a wide array of cameras, lights, and attachment hardware to choose from when designing the camera system.

As a first step, I spent many hours kayaking in ponds and coastal waters near home, testing camera settings with GoPro cameras attached to long poles. Preliminary testing of the whole set-up on a mock PVC frame was conducted at night in coastal waters off of docks in Falmouth, Massachusetts. Even if the jellyfish survey tows were conducted only during the day, it would still be dark at many of the depths we were likely to survey with the video system.

I did as much prep work as possible because the first time the camera system would be attached to a net frame and towed behind a big vessel is now, during this cruise. I had no idea if the system would work as planned. Luckily, the project has been successful beyond my expectations.

Small transluscent jellies form a chain

A pair of salp chains. Salps are gelatinous planktonic tunicates that often link together to form long chains. When collected in survey nets, these chains break apart, but the camera system records the salps as they enter the net with their chains intact. Photo by Liese Siemann

Transparent jellyfish and it's shadow

Ctenophores, or comb jellies, have rows of cilia along their transparent bodies for locomotion. These combs are particularly visible in the ctenophore shadow. Photo by Liese Siemann

We have collected imagery of small gelatinous animals that are normally damaged during typical survey trawls. By analyzing the videos with behavioral observation software and coupling the results with tow data collected by NOAA scientists, we will be able to estimate the abundance of these smaller, delicate organisms in a new way.

Liese Siemann, Coonamessett Farm Foundation

Aboard the NOAA Ship Henry Bigelow

Little Boat, Big Whales

On March 6, we took advantage of fair weather and calm winds to look for North Atlantic right whales south of Martha’s Vineyard.  By day’s end we’d seen 5, and the New England Aquarium aerial survey team we are working with spotted another 9. Colleagues from Woods Hole Oceanographic Institution were also working in the area  were aboard the WHOI R/V Tioga.


Survey crew with cheerful smiles despite freezing air temperatures aboard the R/V Selkie, (left to right) Leah Crowe, Christin Khan, Allison Henry, and Tim Cole of the NEFSC Protected Species Branch. Photo credit NOAA Fisheries NEFSC/Darcie Cole

We’re collecting data important for documenting the distribution, movement, and health of these rare animals.  We also coordinate with the New England Aquarium team that is photographing whales from the air as part of their survey.

We’re focused on gathering several kinds of information: photographs that are used to identify individual animals, and small samples of skin and feces.


R/V Selkie underway (white plume in the water) photographed by the New England Aquarium aerial survey team.  At left, a still camera is pointed out a small window to photograph whales.  Photo credit NOAA Fisheries NEFSC/Ester Quintana, New England Aquarium

Our sightings of 5 whales, along with 9 more spotted by the aerial survey team were the basis for establishing an 1800 mi2 voluntary speed restriction zone (Dynamic Management Area-DMA) that will remain in place for at least 2 weeks.  Our research is being conducted under federal research permit  #17355-01, NMFS/NEFSC.

The R/V Selkie Survey Team

NEFSC Passive Acoustic Research Group Multi-Recorder Deployment and Recovery Cruise on the R/V Connecticut

NEFSC Cruise Participants: Eric Matzen and Annamaria Izzi



Top: R/V Connecticut‘s deck loaded with 5 HARPs to be deployed. Bottom: Sunset at Avery Point, CT. Photos by Annamaria Izzi, NEFSC/NOAA

After days of preparation, of making sure we crossed our t’s and dotted our i’s, we left Avery Point, Connecticut at 1800 with overcast skies but calm seas. The goal of our trip is to deploy 5 HARPs (High-frequency Acoustic Recording Packages from SCRIPPS), recover 3, and recover, refurbish, and redeploy a noise reference station (NRS, PMEL and Oregon State University). All recorders are off the shelf break, from New Jersey up to the tip of Georges Bank. The HARPS are capable of recording sound from many species including baleen whales, sperm whales, beaked whales, and dolphins. The five that we will be deploying, as well as the three that were out, are part of the Shelf Break Acoustic Ecology project, which includes a total of 8 HARPs spanning Georges Bank to Florida. This is a combined effort of the Northeast and Southeast Fisheries Science Centers to understand biological activity along the shelf break before the planned seismic exploration starts off the United States’ eastern seaboard. The NRS serves a slightly different purpose, to listen to and characterize the ambient noise in the deep ocean. It is part of a larger project that is being conducted by NOAA Fisheries, NOAA Sanctuaries, and the National Park Service, to compare ocean noise throughout a number of sites within U.S. waters on both coasts and the Gulf of Mexico.



Top left: HARP in the Big Apple.  Top right: HARP at the Brooklyn Bridge and the Empire State Building. Bottom left: Eric Matzen getting the first HARP ready to be deployed. Bottom right: Eric launching the HARP with the crew of the R/V Connecticut.  Photos by Annamaria Izzi, NEFSC/NOAA

By 0600 we were sailing through NYC. Skyscrapers, the Brooklyn Bridge, and the Statue of Liberty all greeted us and bade us farewell as we made our way out of New York Harbor. We had traveled down Long Island Sound, hugging the coast for as long as possible before making our way offshore. Today was a day of planning, of outlining how things were going to happen and where we wanted to deploy our units as we made our way full-steam down to the southernmost deployment site. We arrived at the site in the late evening with perfect seas, and dropped it off right where we wanted it without a hitch. Then it was full steam ahead to the next site.


The sea gods were a bit rough with us at the start. Waves slopping on deck, boat rocking back and forth, a few of us fell prey to the rough conditions. But there were enough of us that despite what the weather threw at us, we still managed to get the second HARP out easily. Later on in the day the winds died down, and with it the whitecaps.  We even managed to find a few pods of common dolphins, which took the opportunity to bow-ride our vessel, as well as some ocean sunfish sunbathing.



Top: HARP floating at the surface after being released from the ocean floor. Bottom: Eric extracting the hard drive data from the recovered HARP. Photos by Annamaria Izzi, NEFSC/NOAA

Today was the first day in which we had to recover an existing HARP, and replace it with a new one. There was an air of excitement (and nervousness) about the vessel as there always is when calling out to an instrument that has been underwater for a year. In order to get the unit to surface, a burn signal is sent that when the release “hears” it, acknowledges and scuttles the weights, allowing the unit to rise to the surface. We all didn’t know how long it would take, and were surprised to see it at the surface in a mere 15 minutes. The unit had been down around 1000 m in depth! We carefully extracted the unit from the water and quickly deployed the new one that was to take its place. With the unit we recovered, we cleaned and pulled its guts out, taking the precious data collected on the hard drives and storing them in static-free bags to be analyzed once back at the lab. If that wasn’t enough of an interesting day, we also came across three sperm whales in which one raised its flukes to go on a deep foraging dive, and the other two were logging at the surface and traveling. Bottlenose dolphins kept us company for most of the day, and we also found a few puffins! The sun was high in the sky, temperatures were warm, the sea state was great, and some of the crew could be found on the deck enjoying the nice weather. Definitely a much needed reprieve from the weather the day before!



Top left: The crew of the R/V Connecticut spotting the NRS buoy at the surface after its release from the seafloor. Top right and bottom left: Capturing the NRS mooring and bringing it on deck. Bottom right: All of the crew assisting Eric and Annamaria in recovering the 1.67-mile mooring. Photos by Annamaria Izzi, NEFSC/NOAA

The day started out much like the previous one did. We had taken the night to steam up to our northernmost HARP site to arrive just after daybreak for retrieval, which went without a hitch. However that was not the case for the deployment. The HARP that we had selected did not pass the deck tests we conduct before dropping it over; luckily we still had one other HARP on deck. We prepped that one and launched it right where the old one was. We tried to troubleshoot the problematic HARP, but ran out of time as we started to prepare for the NRS mooring that was to be recovered later on that afternoon. That mooring had been like an uneasy weight on everyone’s minds this past week, as it had 1.67 miles of line, not including the hydrophone, float, acoustic release, and anchor. We all referred to it as the “monster buoy”. Due to the skill of the crew and many recovery planning meetings, the entire mooring was up in 5 hours and went so smoothly, even with the building swells! By the time we were done, it was well into dark so we strapped it all down securely on deck to be deployed first thing the following morning. We spent the rest of the night replacing shackles and any other parts that looked to have some wear to make less work for the morning.



Top left: The newly refurbished NRS mooring. Top right: Annamaria and Eric letting out 1.67 miles of line with assistance from the crew. Bottom left: Annamaria and Eric just before releasing the NRS anchor. Bottom right: cutting the last ropes holding the anchor. Photos by Annamaria Izzi, NEFSC/NOAA

Today was our first overcast day of the trip, but the seas were essentially the same as they had been. We conducted many deployment meetings to make sure that everyone knew what task they needed to perform, and how it was all going to work. By 0700 we were ready to deploy and despite everyone’s trepidation, the deployment went very smoothly, even with towing 1.67 miles of mooring for 5 miles. Including the time it took to tow the mooring behind us, the entire process took half the time it took to recover it. After the deployment, we set to work to ascertain just what was wrong with the last HARP. After a few phone calls to the manufacturers on the West Coast and completely taking apart the internal frame, we were able to solve the problem and get the unit working again. Things were back on schedule to do the recovery of the last HARP that had been in the water, and swapping it with the newly fixed HARP. But the weather kicked up and things weren’t looking very optimistic, which put a damper on our spirits. We decided to hold off the final decision of whether to recover the unit at the bottom until we actually made it to the HARP site. Once there, after a brief planning meeting, and weather check, we decided to go for it. And the decision paid off. We were able to recover and deploy our HARPs, fully completing our mission. By 1800 we were heading home.



It’s That Time of Year in the Gulf of Maine

More North Atlantic right whales have been sighted by the Northeast Fisheries Science Center (NEFSC)’s aerial survey group in recent days. On April 9, four right whales were seen feeding in surface and subsurface waters during an aerial survey of Stellwagen Bank and Wilkinson Basin in the Gulf of Maine.  In addition, 11 fin whales, 17 humpback whales, 4 minke whales, and 125 Atlantic white-sided dolphins were also sighted during the five-hour flight.

Nine North Atlantic right whales were observed on April 17, with excellent conditions during a neatly six-hour aerial survey of Cashes Ledge in the NOAA Twin Otter. The right whales were sighted in transit, feeding.  Also sighted during the survey were 5 humpback whales, 4 fin whales, 15 sei whales, 3 minke whales, 29 Atlantic white-sided dolphins, and 30 harbor porpoise.

The NEFSC Aerial Survey Group

Retrieving the AMARs, Launching the Buoys

On May 29th, the Henry Bigelow reached the easternmost part of the survey area on the northeastern tip of Georges Bank. We are now continuing our coverage of Georges Bank and will venture into the Gulf of Maine next.

Survey Technician Geoff Shook lowers a transducer over the side to communicate with the submerged Autonomous Multi-channel Acoustic Recorder (AMAR) mooring. Photo by Jerry Prezioso NEFSC / NOAA.

Survey Technician Geoff Shook lowers a transducer over the side to communicate with the submerged Autonomous Multi-channel Acoustic Recorder (AMAR) mooring. Photo by Jerry Prezioso NEFSC / NOAA.

While working our way east along the southern flank of Georges Bank yesterday we made a stop at Lydonia Canyon to retrieve an Autonomous Multi-channel Acoustic Recorder (AMAR) mooring that had been deployed last summer to record whale sounds. With calm seas and sunny skies (but a fog bank on the horizon to add some drama) the retrieval went very smoothly. The ship pinged the recorder and received signals back indicating its distance from the ship. After maneuvering the ship closer to the mooring, a release signal was sent, and the recorder popped to the surface ten minutes later.

AMAR unit on the surface after being released from its mooring on the seafloor. The yellow container has part of the unit inside while the red floats are supporting another component beneath them. Photo by Jerry Prezioso NEFSC / NOAA.

AMAR unit on the surface after being released from its mooring on the seafloor. The yellow container has part of the unit inside while the red floats are supporting another component beneath them. Photo by Jerry Prezioso NEFSC / NOAA.

After being spotted by our sharp-eyed WHOI scientist Emily Peacock, the command and crew worked together to reposition the vessel and scoop the recorder unit and two glass buoyancy floats from the water. The entire process took no more than two hours.

Retrieval of the AMAR unit on the port side of the Henry Bigelow, Photo by Jerry Prezioso NEFSC / NOAA

Retrieval of the AMAR unit on the port side of the Henry Bigelow, Photo by Jerry Prezioso NEFSC / NOAA

This morning our NOAA Teacher-at-Sea, DJ Kast, launched two artistically decorated drifter buoys as part of the NOAA Global Drifter Buoy Program. Equipped with a thermistor, an ARGOS satellite tracking system, and a transmitter, the buoy will send out its location and water temperature for over a year (about 410 days) before its batteries die out. A cylindrical drogue attached to a surface float that the teacher and students decorated will cause the buoy to be moved about by surface currents, not wind gusts on the float.

NOAA Teacher-at-Sea DJ Kast deploying the St. Joseph School buoy while we are on the northeast peak of Georges Bank. Photo by Jerry Prezioso NEFSC / NOAA.

NOAA Teacher-at-Sea DJ Kast deploying the St. Joseph School buoy while we are on the northeast peak of Georges Bank. Photo by Jerry Prezioso NEFSC / NOAA.

Students from a variety of public schools associated with a University of Southern California program and one parochial school, St. Josephs in Fairhaven, MA, will be looking online to follow the progress of “their” buoys across the ocean!

t. Joseph Elementary School students decorating "their" NOAA buoy prior to the cruise. Photo by Harvey Walsh NEFSC / NOAA.

St. Joseph Elementary School students decorating “their” NOAA buoy prior to the cruise. Photo by Harvey Walsh NEFSC / NOAA.

While on the southern flank of Georges the catches were full of phytoplankton, but now on the northeast peak this has dropped off. The present catches are mostly calanoid copepods and some gelatinous zooplankton, mainly Pleurobranchia ctenophores and an assortment of salps. We are still seeing an occasional Phronima amphipod in its salp shelter too!

Our weather continues to be excellent which has been a real boon to our progress. We are currently heading for the shoal portion of Georges Bank before turning north to sample in the Gulf of Maine, which we will sample to the best of our ability in the time remaining.

Jerry Prezioso, chief scientist

HB1502 Ecosystem Monitoring Survey

Sighting an Entangled Humpback

The NEFSC aerial survey group flew more than five hours May 14 to survey Cashes Ledge.  The team sighted an entangled humpback on the first line of the survey, reported it, and and stayed on station until a disentanglement team from the Center for Coastal Studies arrived on the scene. This is the third time the whale, an adult female named Spinnaker, has had an assisted disentanglement.  As Leah Crowe of the aerial team noted, she “is very lucky that all the pieces – area surveyed, people and weather – fell into place to free her.”

entangled humpabck with boat nearby

Entangled humpback whale named Spinnaker sighted by the NEFSC aerial survey group May 14. A disentanglement team stands by.  Heavy fishing gear is puling the whale down,  with a yellow float visible to the right of the whale. Photo by Leah Crowe, NEFSC/NOAA taken under MMPA research permit # 17355.

Shadow of NOAA Twin Otter on surface near Spinnaker

The shadow of the NOAA Twin Otter with the aerial survey team appears on the ocean surface next to Spinnaker. Photo by Leah Crowe, NEFSC/NOAA taken under MMPA research permit # 17355.

close-up of whale trailing float

Closer view of Spinnaker trailing fishing line and a float. Photo by Leah Crowe, NEFSC/NOAA taken under MMPA research permit # 17355.

A second humpback whale, along with 7 fin whales, 8 sei whales, 3 minke whales, 5 harbor porpoise and 3 basking sharks were sighted, along with 4 North Atlantic right whales.

The NEFSC Survey Group