Merging Science and Technology at Sea

Science and technology come together to execute the Spring Bottom Trawl Survey onboard the NOAA Ship Henry B. Bigelow.  Gone are the days of pencil, paper, and tally marks to record data collected at sea.  Various methods are employed to ensure efficient, accurate and rapid recording of not only biological data but also ship sensors, position, and performance of protocols.

Where the ship, nets, and other data devices are located and collecting information in the Northeast Atlantic Ocean both spatially and vertically in the water column are recorded (see images below).  This provides the NOAA Corps Officers, the Chief Scientist, and Watch Chiefs with data graphically displayed via many different screens.

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Pictured top left:  sonar track of the Bigelow over bottom topography; right: spatial location of the vessel and one of the stations; bottom left: vertical sensors on the trawl net, with the orange line showing the net being recovered aboard ship.  Photo credit:  NOAA Fisheries/Heidi Marotta


While working up the specimens collected in the net, technology provides the solution with barcoding.  Species are sorted into barcoded baskets, buckets and pails and recorded into the database via the FSCS2 (Fisheries Scientific Computing System 2.0) software by the Watch Chief.  Accurate weights are calculated and stored automatically.  As samples move down conveyor belts to the scientific crew for workup, they are pulled off the belt and scanned with waterproof barcode scanners.  The software then displays the species for confirmation and sampling begins.  As physical samples are prepared (freezing partial or whole specimens, or removing otoliths used for aging fish), a barcode printer at each sampling location instantaneously prints a waterproof label for the bag or envelope.  These samples are placed into a big walk-in freezer or into bins on the wall of the wet lab.

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Barcodes rule!  Top left:  The container barcode is assigned to a specific species and scanned into the FSCS2 program to open up that species sampling protocol. Top right: barcoded labels are printed for and attached to all samples that are collected at sea. Note the specific details on the label.  Bottom: Bins holding otolith samples. Other samples that may be barcoded are stomach contents, reproductive samples, and whole fish and invertebrates sent back for identification, research,  or training purposes. Each envelope has a barcode label noting the common name and the scientific name for the species, along with a lot of other information. Photo credit: NOAA Fisheries/Heidi Marotta


Electronic, motion compensated scales weigh in containers, individual fish and electronic measuring boards record weight and lengths respectively, at the touch of a button or a touch of a magnet sending the data to the server.  These data are audited real time (using known algorithms for species length/weight calculations, for example), ensuring immediate at sea correction so that when the survey is complete the data is readily available soon after.

The wet lab where the biological data are collected is a harsh environment with flushing water constantly running, scientific crew dressed in foul weather gear and big blue rubber gloves, in addition to large amounts of wet, slimy, fish. Touch screens are the main interface to the science crew to record observed characteristics of specimens such as sex, maturity, and stomach contents.  All of the technology in this area is rugged, waterproof, reliable and interacts with the software and database to quickly and accurately save the data.

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Top : screen shot of a FSCS2 protocol screen.  Bottom Right: a fish on the measuring board, with measuring magnet visible at far right.  Bottom left:  scale screen showing specimen weight. Data from the electronic scale and the measuring board (right) are all recorded into the database. (Photo credit: NOAA Fisheries/Heidi Marotta


At the end of the two and a half month survey the final physical specimens are offloaded to be brought back to the NEFSC’
s Woods Hole Laboratory for land-based processing.  The database with the sensor data and biological data is exported onto a thumbdrive to be loaded onto the servers back at the lab for scientific analysis.  The barcodes allow for individual specimen identification in the database when scanned by other land-based software applications.  Where the specimen was collected, the temperature of the sea water, and all of the individual measurements are available for scientific use.

When asking the crew out of this final leg of the spring survey if they could imaging collecting data any other way than with sophisticated computer technology, they all answered with a resounding “No way!” (at least not the volume, speed, or accuracy).  Granted the majority of this crew grew up on video games, personal computers and cell phones, so they fully trust in all things computer and technology related to make life easier and information more accurate.  As a computer scientist responsible for providing these solutions, I couldn’t agree more!

Heidi Marotta
IT Specialist, NEFSC
Acting Data and Development Branch Chief
Aboard the FSV Henry B. Bigelow
Spring 2019 Bottom Trawl Survey Leg 4

Easter on Georges Bank and Northeast Channel

During Easter weekend, we were sampling along the northeastern part of Georges Bank and even made it into Canadian waters.  We’ve been seeing a lot of large winter skate, Leucoraja ocellata.

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A winter skate on the measuring board. Photo credit: NOAA Fisheries/Christine Kircun

This species may be confused with little skate, but at these sizes, there’s no dispute.  It’s not uncommon to see a winter skate measure in at over a meter long!  At that size, some caution is needed when handling this bottom dweller because it has very sharp dermal denticles on its wing.  Dermal denticles are tough, and in this case, extremely pointy, scales that help with protection.  As I was sorting fish, my Grundens (waterproof outerwear) got snagged onto some of these denticles and nearly caused a tear!

The fish tend to get bigger the further north we go.  We caught some sizable fourspot flounder, Paralichthys oblongus, that were over 40cm.

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Fourspot flounder. Photo credit: NOAA Fisheries/Christine Kircun

This one was the largest one I remember seeing at 50 cm!  Their characteristic four spots are easy to see and with their large mouths, it’s not uncommon to find fish, shrimp and crabs in their stomach.

A yellowfin bass, Anthias nicholsi, was caught during the day shift. Its neon yellow and pink colors definitely catch your eye among the more brown and muted colors commonly found in the area.

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Yellowfin bass. Photo credit NOAA Fisheries/Christine Kircun

And just for fun, we had an egg decorating contest. After the eggs were decorated, we were able to cast our votes. It wasn’t easy because there were so many fun and creative eggs, but there were some that stood out.
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Congratulations to Katelyn Depot for ‘Best Overall Egg’ (#14), Joseph Warren for ‘Most Traditional Egg’ (#15), and Jakub Kircun for ‘Most Creative Egg’ (#1)!

Christine Kircun
Aboard the FSV Henry B. Bigelow
Spring 2019 Bottom Trawl Survey Leg 3

Habitat in a Bucket

April 15, 2019

Did you know most animals in the ocean don’t have backbones?

We’re half a week into leg 3 of the NEFSC spring bottom trawl survey and into the full swing of survey life.  Our first tow this morning, around 1:30 am, was a little southeast of Chatham harbor, Massachusetts.  Even though the catch was fairly small, it was full of really interesting benthic invertebrates.  These are the animals that live on the ocean floor and lack vertebrae, the small bones that form a backbone.

This morning we had a small bucket of very diverse specimens.  At first, it may seem difficult to get a grasp of what you’re looking, but it becomes much easier to comprehend after taking some time to separate everything into groups.

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Habitat in a bucket. Photo credit: NOAA Fisheries/Christine Kircun

Here are some highlights from what I found: a diverse range of animals!

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A mussel, some sea stars, sponges, a sea mouse, comb jelly, sand dollar, sea urchin, and fish eggs. Photo credit: NOAA Fisheries/Christine Kircun

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The eggs in one of the clusters were really large, and the larval fish could be seen inside. Note the empty egg in the lower right hand corner of the picture.  Photo credit: NOAA Fisheries/Christine Kircun

Another neat find (pictured below) was a large  orange-footed sea cucumber, Cucumaria frondosa.

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Sea cucumber. Photo credit: NOAA Fisheries/Christine Kircun

I quickly placed this animal in a bucket of fresh salt water, and after some time, it relaxed enough to expose its tentacles.  It was surprising to see!  In my experience, they are mostly seen closed up after coming up in the net.

It’s always fun to see tows like these.  Even though it may be harder to pick through on the sorting belt, it’s a great opportunity to see the diversity of life that lives on the ocean floor.

Christine Kircun
Aboard the FSV Henry B. Bigelow
Spring 2019 Bottom Trawl Survey Leg 3

 

NEFSC Science Update: At Work, Looking Toward Spring

February 20, 2019

NEFSC Science and Research Director Jon Hare is stepping into the blogging business for a while. He’ll be updating readers as we restart our research year in the run-up to our 2019 field season. Go, Jon!

Starting our new year in February has been an adventure for the NEFSC. Stakeholders from across the region have been in touch with me and others on our staff asking about our plans for the rest of the year.

Almost everyone has heard about “the machinery of government” and I have had a chance recently to see the upside of it: the ability of our staff to quickly assess priorities and get on with delivering quality science to marine researchers, resource managers, and business operators.

This blog is generally used to highlight field work. Since I don’t do too much of that anymore (the downside of the director’s chair!) I have decided to use the blog to give updates on the status of projects that our stakeholders have asked about the most in recent weeks. I will be writing more of these as we gear up for spring and summer.

So here goes:

2019 Science Status Update 1,  by Jon Hare

Our spring bottom trawl survey aboard the NOAA Ship Henry B. Bigelow is set to leave Newport, RI March 9. That’s a few days later than first planned, but we are also extending the cruise by a few days. We plan to complete a full survey. This fieldwork is always influenced by weather, as well as vessel and equipment performance, so our staff is trained to make adjustments while still obtaining the best possible data.

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NEFSC R/V Gloria Michelle.  NOAA/NEFSC photo by Adam Poquette

Our Canadian colleagues are leaving this week for their regular bottom trawl survey which, as usual, includes some stations in U.S. waters of the Gulf of Maine.  The NEFSC research vessel Gloria Michelle is on track to complete the annual spring trawl survey of Massachusetts state waters.

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One of seven rare newborn right whales spotted so far this year off Florida rubs its mother’s head. Photo by Florida Fish and Wildlife Conservation Commission, NOAA Research Permit # 20556-01

This time of year is also key for our work to recover endangered North Atlantic right whales.  In comparison with last year’s zero newborns, there’s good news from the calving grounds off the southeastern U.S.: 7 new right whale calves have been confirmed so far this year. Our aerial surveys in the Northeast were also busy this winter with a large number of whales sighted south of Cape Cod. These sightings triggered short-term protection areas for these animals.

We will be revising our stock assessment plans for the remainder of the year. We are working through timelines for biological sample and data processing, analyses, meetings, and other activities that underlie the many assessment products completed every year. We are in ongoing contact with fishery management partners in the region as we set priorities.

That’s it for my first blog.  Let me know what you want to hear about in my next one!

Jon Hare

NEFSC Science and Research Director

Leg I Home Stretch!

September 20, 2018

With a couple days left to fish, we’re closing in on the end of leg 1!  It’s that point in the leg when everything begins to look familiar and routine may have taken over.  But if you’re patient and keep your eyes open, you’re sure to see something.  With that said, here are some highlights from the last couple of days!

We woke up to an announcement that a large pod of common dolphins were jumping and swimming straight towards the boat.  There were at least 50 of them!  The whole show lasted 5-10 minutes, and just like that, they were gone.  It’s amazing how quickly these sightings come and go.

Video by Jennifer Casey, NOAA Fisheries

We’ve been sampling in deeper water these last couple of days, and a neat Scorpaenidae fish came up in the net.  It may look similar to our black belly rosefishHelicolenus dactylopterus, but there are some noticeable differences.  This fish is a bright orange color and has one extremely long dorsal spine.  When the mouth is open, you’ll see a bright yellow throat while the blackbelly rosefish’s is, as you would expect, black.

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Scorpaenidae are a group of predatory marine fish that includes scoropionfishes or rockfishes,   Photo credit: NOAA Fisheries/Christine Kircun

Some lobsters we catch have lost one or both of their arms.  Though, it’s not a permanent state because they can be regrown, and that’s exactly what one of the lobsters we caught was doing!  At first glance, it may seem like it has only one arm, but look closer, and you can see that a replacement arm has just started growing.

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Lobster regrowing a new arm.  Photo credit: NOAA Fisheries/Christine Kircun

At another station, we caught a beautiful starfish. We are wondering if it belongs to the genus Coronaster.  This animal has 11 delicate arms and is an orange-red color.  After pictures were taken, some arms were detached.  It seemed odd for that to happen so quickly and after minimal handling.  Perhaps it could be some kind of defense mechanism.  It will be brought back to the lab for further identification.

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Coronaster is a species of starfish, or sea star. Photo credit: NOAA Fisheries/Christine Kircun.

A benefit of being on day watch, noon to midnight, is the chance to witness amazing sunsets.  When the weather is just right, the sky can be remarkable, and it’s difficult to resist taking a moment to be still and enjoy the view.

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Some day watch scientists,  watching the sunset after working up a station. Left to right: Kelcie Bean, Zackery Fyke, Lacey Bluemel, and Jennifer Casey.

Christine Kircun
Aboard the FSV Henry B. Bigelow
Fall 2018 Bottom Trawl Survey Leg 1

Very Small but Very Important

Sept. 14, 2018

Despite Hurricane Florence’s destruction on the Carolina coasts, the FSV Henry B. Bigelow has kept sampling stations at a steady pace.  We are currently outside Long Island, well out of the reach of the hurricane’s wind and rain.  As of now, it’s all clear for us to keep sampling stations and working up fish, but fish aren’t the only thing we’re catching in nets.

The ocean is amazingly diverse.  There are well known animals such as tuna, cod, and whales.  They could be valued for recreational enjoyment, commercial importance or intrinsic pleasure.  And there are numerous animals such as starfish, sea urchins, jellyfish, corals, and sponges that are only found in the ocean.  But there are hundreds of easily overlooked, very small yet vitally important species that benefit all living creatures, aquatic and terrestrial: plankton.

Simply put, plankton are very small, sometimes microscopic animals (zooplankton) and plants (phytoplankton) that drift in the water.  Found in both fresh and salt water, they are the base of the aquatic food web.  Not just that, but phytoplankton produce about half of Earth’s oxygen!  Because of their crucial environmental role, it is extremely important to study and monitor these fascinating organisms, and we have a protocol for doing just that on the bottom trawl surveys.

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Bongo nets. Photo credit: NOAA Fisheries/Christine Kircun

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Survey Technician Mark Bradley spraying the contents of a plankton net into a sieve. Photo credit: NOAA Fisheries/Christine Kircun

Plankton tows are cast at select stations on the FSV Henry B. Bigelow.  This is called a ‘bongo’ because the two nets used look like bongos.  The bongo is lowered over the sidesampling station to about 5-10m from the bottom, depending on the ground type and weather conditions.  As soon as it reaches its appropriate depth, it’s brought back to the surface.  This gives us a vertical profile of the organisms in that area.The nets are washed down into a sieve, and the plankton are preserved with formalin in glass jars which will be examined back on land after the survey is completed.

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Jar filled with plankton. Photo credit: NOAA Fisheries/Christine Kircun

Before the jars are preserved, a quick, first glance may leave the observer uninterested.  But simply wait a moment, and the jar comes to life!  Depending on the sampling location and time of year, ostracods, copepods, protozoans, jellyfish, mysids…. can be seen moving and zooming all over.  So the next time you’re enjoying the beach and gazing out on the water, know that it is far from empty!  You are actually watching thousands and thousands of plankton, working hard to support life in the ocean and on land.  So take a deep breath and say “Thank you!”

Plankton studies is not my area of focus, but it is for the people in the NEFSC Oceans and Climate Branch!  Check out their website at Oceans and Climate Branch for more information.

Christine Kircun
Aboard the FSV Henry B. Bigelow
Fall 2018 Bottom Trawl Survey Leg 1

Approaching hurricane, sampling underway

September 11, 2018

We’re almost a week into leg I of the bottom trawl survey on the FSV Henry B. Bigelow, and it’s off to a great start!  Despite Hurricane Florence slowly approaching from the southeast, the weather has been absolutely gorgeous.  The water is flat, and the sky is full of beautiful clouds.  One of them briefly produced a water spout.

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Water spout forming. Photo credit: NOAA Fisheries/Christine Kircun

While off the coast of North Carolina, we saw the Diamond Shoals Lighthouse. With so many shoals along the coast of North Carolina, lighthouses were extremely important to warn sailors of the dangers below.

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Diamond Shoals Lighthouse. Photo credit: NOAa Fisheries/Christine Kircun

This lighthouse was eventually moved offshore because warning signals from land were ultimately ineffective.  Read more at http://lighthousefriends.com/light.asp?ID=169.

And of course, it’s always exciting to see what the net brings up.  Most of the animals have been small, but a couple sizable specimens made it to our sampling stations.  Cobia (Rachycentron canadum) is a pelagic, flatheaded fish that spends most of its time alone except when they aggregate annually to mate.  Currently, efforts to domestically cultivate cobia for food are underway.

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Cobia. Photo credit: NOAA Fisheries/Christine Kircun

Grey triggerfish (Balistes capriscus) is found all along the eastern US coast.  These fish travel through the water with wave-like movements of their dorsal and anal fins.  They communicate with grunting and hissing noises.  Clicking noises are made when the teeth behind its fleshy lips are rubbed together.

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A grey triggerfish. Photo credit: NOAA Fisheries/Christine Kircun

The common octopus (Octopus vulgaris) is an intelligent cephalopod that eats bivalves (mollusks with two shells) and crabs.  They are known to leave the empty shells

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in what’s known as midden piles right outside whatever space they’ve decided to call home.  These piles are a unique way to show researchers what kind of bivalves and crabs are in the area since an octopus can more effectively comb through its habitat as it hunts for food.

Christine Kircun
Aboard the FSV Henry B. Bigelow
Fall Bottom Trawl Survey – Leg 1