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

A Useful Little Bone

Post and photos by Christine Kircun, NOAA/NEFSC

As we near the end of the 2017 spring bottom trawl survey, we are about 650 miles north of our southernmost station near Cape Hatteras.  With that said, it wouldn’t be surprising to know that the fish are very different in the northern part of the survey.

Here we’ll find haddock, cod, pollock, and American plaice to name a few.  And just like down south, while some fish look very different there are a few that are tricky to differentiate, especially for someone’s first time out.  While external features are used to quickly identify a fish, there is another important structure that can also identify a fish: the otolith.

The otolith is an earbone that we primarily use to figure out the age of a fish, although it can also be used to identify fish.  Otolith shapes vary widely, but the more closely species are related, the more similar they look.  I’ve chosen three fish to highlight this.


This picture appeared in one of my earlier blogs, but I wanted to bring it back because it’s a great example of the otoliths being easier to tell apart than the fish itself.  Silver hake is slightly more silver in color and has 16-20 gill rakers while offshore hake tend to be bluer and have 8-11 gill rakers.


pic 2a_opt

The top fish is a silver hake and the bottom is offshore hake.  Otoliths from these fish are at left

pic 2b_opt


Here’s a close-up of those otoliths. The  offshore hake otolith (top) isn’t as long and slender as the silver hake otolith, even from fish of approximately the same size.  The offshore hake otolith in general is much wider, and its tips are more rounded than the silver hake otolith.




pic 3_opt

Atlantic herring (top) vs Alewife (bottom)

Above are two fish we’re currently catching in almost every tow: Atlantic herring and alewife, a river herring.  While these two fish may seem very different in this picture, it’s not uncommon to toss a couple from the sorting belt into the wrong bucket.  The quickest way to tell the difference by looking at the outside is to run your finger along its top side from tail to head.   It will be smooth on the herring, but not so with the alewife as you’ll get caught on its scutes — spiny, rough scales.  Their otoliths are very small in comparison to their overall body size. You can barely see them in this photo. The Atlantic herring otos are placed in the vertical black band on the measuring board, just below the herring’s jaw. The alewife’s are even smaller, placed in the black tag on the measuring board, just to the right of the number “4”,  above the fish’s eye.

pic 4_opt

Here’s a close-up of those otoliths.  They are very similar in shape, with the rostrum (top portion) being about the same length relative to the total length of the otolith.  The width is where you’ll find the difference.  The alewife otolith is wider relative to its height than is the slightly more slender herring otolith.

pic 5_opt

White hake (top) and red hake (bottom)

Here’s another confusing pair.  Until you get the eye for making distinctions, these two fish are very easy to confuse.  A quick way to tell the difference by just looking at these two is the length of the pelvic fin, that reddish looking string you can see running from near the throat and down the belly.  It extends further along the body of the red hake.  If the pelvic fin — also called a filament — is broken, the silvery color or smaller scales of the white hake are other quick identifying characteristics.  But let’s go to the otoliths!

pic 6_opt

These otoliths (right) came from two very different sized fish, but the size isn’t necessarily what’s going to differentiate these two fish. Look at the rostrum, the pointed top end.  Red hake have a smooth rostrum (left) while white hake’s rostrum (right) is bumpy.  Also, the red hake otolith tends to have a little edge right before the rostrum begins.

I find myself using this skill the most when examining stomach samples to find out what a fish has been eating.  If I am trying to ID a partially digested fish, the otolith is often remains more intact than the rest of the animal.  It can also be used to identify a fish  down to genus or species.  This is just another way we rely on this useful little bone!

Christine Kircun, biologist

Aboard the NOAA Ship Henry Bigelow

They Came from the Deep

Leg III: 2017 Spring Bottom Trawl Survey

Photo credit for all images in this post NOAA/GARFO/William Duffy


Spotted tinselfish, family Zeidae, caught at 275 meters.

Welcome aboard Leg 3 of the NMFS NEFSC bottom trawl survey.  One of the questions I get asked frequently when I get back home is: what are the coolest types of fish you see out there?  My answer is always the same, the deep-water fish species.  They are interesting, they look like aliens, and I am pretty sure some of the more horrific monsters that one would see on TV or in the movies was inspired by a fish caught from the deep depths of the sea.  So while I am guest blogging out here, I thought it would be great to share a few pictures from a couple of our deep-water stations with the rest of you.

In our first deep station of the trip, we towed at 300 meters (900 feet).  When we dumped the bag in the checker there were almost 2,000 pounds of large barndoor skates.  Also brought up from 30 meters were some cutlassfish, pearlsides, shortnose green eyes, and a grenadier.   One of the more interesting types of fishes that come up from the depths are the barracudinas from the family Paralepididae. The specimen in the slideshow below was about 30cm long. .  The other fish pictured here: pearlside, family Sternoptychidae; short-nose green eye, family Chlorophthalmidae; and grenadier, family Macrouridae, are all commonly seen in the deeper waters of the Gulf of Maine and Georges Bank.


Barndoor skates






shortnose green eye





In another station, we towed at 275 meters and caught a few more interesting deep-water fish species that I think most people have never seen before.  These are some of the more colorful, interestingly shaped, and bizarre-looking fish species that we catch on these surveys.  The first is an oddly shaped fish called a spotted tinselfish from the family Zeidae, pictured at the top of this post.  We also had a few “large” Myctophids, also called lanternfishes (above).  Most fish from this family are relatively small, with the largest species not getting more than 30 cm in length.  These fish have light producing organs called photophores and luminous scales throughout its body.  However, as you will see from the picture, most of their scales come off when they are caught in the net.


Crab, Family Grapsidae

While we are out here we also get some really interesting invertebrates, and two types, crabs and squid, are quite common and are represented by quite a few different species.  This brightly colored crab (right) is from the family Grapsidae and this multicolored rossia squid (below) is a type of bobtail squid from the family Sepiolidae.


Rossia squid, also called a “bobtail”squid, Family Sepiolidae

These were just some of the many different types of deep-water species that we see on our surveys.

Bill Duffy, NOAA Fisheries Greater Atlantic Port Agent

Aboard the NOAA Ship Henry B. Bigelow

2017 Spring Bottom Trawl Survey

Leg II: Safety First!

As I write this we are about to leap-frog our original cruise track and pick up stations that would have been done earlier if not for the weather.

A typical New England Nor’easter worked its way up the coast in the last few days.  The Bigelow is able to fish in most weather conditions but when the winds start howling it can become dangerous for the crew operating the equipment on deck.  Plus, scientific collections could be compromised due to the surging nature of the ship in those conditions.  Safety is our primary concern out here.  By altering our cruise track and heading inshore we were able to ride out the storm and only lose about 12 hours of operations.

Today is also drill day.  Preparing for emergencies at sea is a serious business and we are a long way away from any help.  The crew conducts weekly safety drills, including some sort of simulated fire drill.  For the scientists, we basically stay out of the way by gathering on the bow of the ship and assist if necessary.  Several of the regular sea-going scientists are trained to help fight fire if called upon.  This week we conducted a medical emergency drill that included transporting a member of the scientific party via backboard and simulating calls back to land for instructions.


Below deck, preparing for abandon ship drill

Each week there is also an abandon ship drill.  This involves the crew reporting to assigned life rafts and donning survival suits. Actually getting into the suits ensures that we know how do it quickly and that assigned suit  fits, important details if there is a real emergency.  Survival suits are buoyant wet suits that keep us afloat and protect us from getting hypothermia if we have to get in the water.

All of these add up to safe voyages where the health and welfare of the people aboard are paramount.

Sean Lucey

Fishery biologist

Aboard the NOAA Ship Henry B. Bigelow

2017 Spring Bottom Trawl Survey

Leg II:  There’s a lot more going on than just trawling

Greetings from the NOAA Ship Henry B. Bigelow!  Leg II of the NEFSC Spring Bottom Trawl left Newport, RI on Tuesday, March 28th.  We made our way South to pick up where Leg I left off.

While this trip is labeled as a bottom trawl survey, there is a lot more going on than just trawling.  This ship conducts a lot of exciting science:  collecting hydrographic data about the physical characteristics of the water using on-board sensors and special sampling devices, using fine-meshed bongo nets to collect plankton, and of course examining the fish and other marine life that comes up in the trawl.  The Bottom Trawl Survey is definitely an ecosystem survey, designed to capture all aspects of the marine environment and ecology.



Deploying a bongo net. Photo by NOAA/NEFSC

As an ecosystem modeler, I am very interested in how the data is collected out here and ultimately analyzed back on land.  The most basic of fish data that we collect is weight per tow.  Each tow is separated by species and then weighed.  This information is important so we can get a relative sense of the size of the various populations.  From there we take individual length data on most species. Some things are sent back to the lab and counted/measured there.

Just as important as these basic metrics is the biological sampling that we conduct.  For some species a subsample of the catch is selected for further study.  We determine the sex and maturity of the fish to get information on spawning in a population.  We examine their stomach contents to learn more about predators and prey.  We also age them using a variety of techniques.



Still life: Monkfish ear bone on blue PVC insulated glove. Photo by NOAA/NEFSC: Northeast Cooperative Research Program


A bluefish ear-bone section, ready for an ager to read.  Photo by NOAA/NEFSC

The most common way to age a fish is to use their ear bones or otoliths.  This technique works similar to aging a tree.  Seasonal changes in a fish’s growth pattern create rings or annuli.  Each year a new ring is created.  At sea we remove the ear bones and send them back to land.  Each species requires some processing of the ear bones before an age reader can count the rings.

The end result is we have an age structure of the population and can track how each year’s cohort is growing and, along with the other data we’ve collected, help forecast sustainable catch levels for the future.

Sean Lucey, ecosystem modeller

Aboard the NOAA Ship Henry B. Bigelow

2017 Spring Bottom Trawl Survey

Leg I: Sometimes It’s All About the Little Things

All photos in this post by NOAA/NEFSC/Christine Kirkun

Fish identification is an important part of the job on the bottom trawl survey.  When the catch comes down the sorting belt, it is our job to separate them into baskets, buckets and pails.  Some fish look extremely different from each other.  Others may appear almost exactly the same, especially if it’s your first time looking at them.  The sorting belt is constantly moving so even the most seasoned scientist may get their eyes crossed as they pick through the unsorted catch.

The people at the top of the line typically pick up the large animals, such as dogfish, skates, rays, and goosefish, or a single fish, if the catch has a lot of a particular species, such as haddock, Acadian redfish, or silver hake.  This makes it easier for the people at the bottom of the line to pick up the smaller animals, such as juvenile fishes, squid and crabs, and the more difficult fish to pick up, such and windowpane and fourspot flounders.  Ultimately, if there are two species that look similar, and you’re unsure, you can ask someone or, if it’s busy, place them both in a bucket to be sorted separately at the end.

pic 1_spiny dog back-smooth dog front_opt

A spiny dogfish and a smooth dogfish

Dogfish have been everywhere so far, and we’ve caught a lot of them.  Spiny dogfish is our most commonly caught shark, but there are areas where the smooth dogfish is abundant as well.  At first glance, these two sharks may seem identical, but on close inspection, it is quite clear that they are very distinct from each other.  But remember, we’re not looking at them, perfectly lined up and still.  They are moving down the sorting belt all mixed together with the rest of the catch.  In this case, the sorter looks specifically for the presence or absence or the dorsal spines, although on closer inspection, it is clear the shape of the head, eyes, and caudal tail are very different.

pic 3_2nd dorsal fin_spiny back-smooth front_opt

The telltale spine

The two main sea robins we’ll find are striped and northern.  While both species can reach into the 20cm range for length, the northern sea robin is usually smaller.  Much about them looks very similar except for the prominent dark lateral stripe of the, you guessed it, striped sea robin.

pic 4_striped back-northern front_opt

A striped and a northern sea robin

Squid is also a very common species caught along the entire survey track.  Loligo, or longfin squid, is most dominantly in our survey, although it’s not uncommon to have a mixed catch with Illex, the shortfin squid.  Right away, there is an obvious color difference, with the Illex being more golden/orange and the Loligo a deep red/maroon or light purple, depending on its mood.  The fin length on the mantle is another identifier.  Notice the fin on the Illex is about one-third of the mantle length, while on the Loligo, it’s about half the length of its mantle.

pic 5_illex top-loligo bottom_opt

Shortfin and longfin squid

Silver hake is another fish we catch throughout the entire survey, but when trawling offshore, we keep our eyes out for the very similar looking offshore hake.  The slight color difference is what pops out on the sorting belt.  Silver hake reflect a golden color along their dorsal side while offshore hake show more of a bluish hue.  The best way to tell these two apart is to count the gill rakers—the stiff filaments on the gill arch used to filter solids away from the gills.  Silver hake have 16-20 and offshore have 8-11.

pic 6_silver top-offshore bottom_opt

The nearly identical hakes

Christine Kirkun, fishery biologist

Aboard the NOAA Ship Henry B.  Bigelow

2017 Spring Bottom Trawl Survey

Leg I: Fast Prey and Slow Predators

All photos in this post by NOAA/NEFSC Wesley Rand

One of my responsibilities as part of the scientific party on the Bigelow is to open animals’ stomachs to see what they have been preying on. I had a couple of interesting finds today.  I didn’t know these predators were capable of catching what I found in their stomachs!

The first find is something we are seeing pretty regularly, and that is winter skate (below,top two panels) with spotted hake (below lower panel) in their stomachs. If you just look at the two fish, you wouldn’t think skates could catch hake. Notice that the skate’s mouth is on its underside and not in a particularly maneuverable place. Pure speculation, but maybe the hakes rely on hiding in the ocean’s bottom instead of swimming away to avoid predators?  If that were so, skates could easily suck them up when they hiding in the mud or sand.

The second find of the day was something we had not yet seen on this trip; a fat spiny dogfish with a whole Atlantic menhaden in her stomach.


Spiny dogfish female we examined, with a full gut.

The menhaden was about 8 inches long and almost perfectly intact! Atlantic menhaden, commonly known as bunker or pogies, are fast-swimming, schooling fish. Spiny dogfish spend most of the time on the ocean floor and aren’t known to be the fastest swimmers, but I’m sure if one swam into a big bait-ball of menhaden, it could nab one.


Atlantic menhaden, spiny dogfish victim!

It’s all just conjecture, but that’s one of the great things about being a part of this survey. You get to see things that are happening in the wild, like predator/prey relationships that challenge your view of the world.  When your findings contradict what you thought was possible, you have to think of new ideas to explain how it’s possible. The other half of the fun is bouncing ideas off of colleagues to see if they have any merit or if maybe there’s some part of the picture you’re missing.

Wesley Rand, fishery biologist

Aboard the NOAA Ship Henry B.  Bigelow


2017 Spring Bottom Trawl Survey

Leg I: Southern Fish Make Things Interesting

We’d made it all the way south and had just begun working our way north when bad weather drove us to shelter in Norfolk, VA.  Our work and research primarily revolves around northern fish species so sampling down south affords us the opportunity to briefly dip into the gulf stream and find fish that mostly live to the south of us, but that can also come into northerly waters when currents and temperatures are right.  Sometimes we are familiar enough with a fish to identify it down to its species.  Other times, we may only get down to its family classification.  In any case, when it comes to these southern and/or deep-water fish, we bring them back to the lab where there is more time to closely and carefully key out the species.  The following pictures show the diversity in body shape and color of these beautiful animals.  Enjoy!

Christine Kirkun, fishery biologist

Aboard the NOAA Ship Henry B. Bigelow

All Photos by NOAA NEFSC/Christine Kirkun

This slideshow requires JavaScript.


2017 Spring Bottom Trawl Survey

Leg I: Sampling Underway– One Fish at a Time

It’s been more than  a week since we sailed from Newport, RI, sampling is well underway, and we’re still heading south.  If we’re not working up fish, we’re waiting to work up fish.  A question constantly being asked is “what is the net doing” or “where are we”?  In other words, are we fishing, are we steaming (heading for the next sampling station), is a work-up currently happening, or are we sampling for water salinity, temperature and depth or for plankton.  Ultimately, the action begins when the net comes onboard!


The checker filled with mostly dogfish. Photo by NOAA NEFSC/Christine Kircun

The net is pulled out of the water by large winches, and with help from a crane, the contents are dumped into a checker, or a big, metal holding bin.  The little door in the checker allows a scientist to push the fish onto a ladder conveyor belt that brings them onto a sorting belt inside the lab.

Conveyor belts are used at all parts of the sampling process to move catch where it needs to go.  The scientists on watch sort the fish into small, medium or large baskets.  As the baskets are filled and sent to the watch chief, they are entered into the sampling program and sent down another conveyor belt to the three sampling stations.


Sorting squid coming into the wet lab on the conveyor belt. Photo by NOAA NEFSC/ Christine Kircun

There’s where scientists weigh the catch, record lengths and weights, and can take stomachs for food habits studies, remove hard parts like earbones and scales for aging studies, and make observations about fish condition and whether they are ready to spawn. After a basket is worked up, the remains are placed on a lower conveyor belt which leads to a shoot emptying into the ocean.

Depending on the area and time of year, we have a rough idea of what we’ll catch, but there are always surprises.  I’m on night watch (midnight to noon), and while the catch has mostly been spiny dogfish, we’ve also caught a blueline tilefish  and a mola.

Blueline tilefish, Caulolatilus microps, are found on mud and rubble bottoms, and is thought to inhabit burrows and may get up to 15 years old.  Their diet is mostly invertebrates that live on the ocean bottom, and the occasional fish.  Blueline tilefish range from around Virginia to southern Florida/Mexico and at depths of 30-130m.


Blueline tilefish. Photo by NOAA NEFSC/Christine Kircun

The mola (sunfish) we caught was a  Mola mola, one of the world’s three species of mola. It is the heaviest known bony fish, and can weigh in at up to 5000 pounds.  They can be up to 14 feet long and 10 feet wide.  This fish swims in the uppermost waters of the ocean and is often found swimming lethargically and relaxing at the surface; sometimes laying on their side to let birds and small fish eat the many parasites off their skin.  Their diet consists mostly of jellyfish but also eat algae and zooplankton.


Dogfish haul. Photo by NOAA NEFSC/Christine Kircun

Sometimes, it’s not just the unique fish we catch that is impressive, but the amount.  Just before breakfast, we brought up a very large deck-tow of spiny and smooth dogfish.  With the help of our survey tech and a deck-hand, it took 8 of us 5 hours to count the entire bag!  We finished just before watch change, which was perfect timing as we were definitely ready to go to bed.

Christine Kircun

NEFSC fishery biologist

Aboard the NOAA Ship Henry B. Bigelow

2017 Spring Bottom Trawl Survey

Leg 1: Wintery Weather Tests Your Bones

Anybody who has worked at sea knows that your efforts are limited to what the elements will allow. On Friday, March 10 we experienced that first hand. We hit a bit of a squall off the coast of North Carolina. The conditions changed very quickly. In just a few hours the waves went from 3-4 feet to 12 footers with even larger swells.


Rough seas on Leg I.  Photo by NOAA NEFSC/Kateryn Thompson-Delgado

Kateryn Thompson-Delgado

Fortunately, the Bigelow is equipped to fish in rough conditions so we continued to plug away at stations. Working on a rocking vessel takes a lot of energy. Your body has to use so many more muscles just to walk around, and even if you are just sitting, it can get very uncomfortable. I felt even worse for the night watch, who needed to sleep while Mother Nature attempted to throw them out of their racks.

Just as the day-watch’s shift was ending, the winds started to turn again. With everyone drained, the day watch turned in for the night. When we woke up, we found the seas had calmed down significantly. The waves were back down to 2-3 feet. What a difference 12 hours can make on the ocean! Compared to yesterday, you can barely feel the Bigelow’s rocking and I think everyone is a lot happier for it.


Sunrise and clams seas. Photo by NOAA NEFSC/Kateryn Thompson-Delgado

Dealing with rough seas is the part of the “price of doing business” when collecting data at sea. We plan for it and are prepared. Like one NOAA Corps officer told us during our initial trip briefing, “We call it the Spring Survey but this is the month of March. It’s still winter. We expect to hit some winter weather.” When log books and back packs start to go flying across the room, it’s good to know you’re in the hands of capable people who are well prepared.


Wesley Rand

NEFSC fishery biologist

Aboard the NOAA Ship Henry B. Bigelow