sample processing – NOAA Teacher at Sea Blog

September 27, 2013March 12, 2021

John Clark, September 27, 2013

NOAA Teacher at Sea John Clark

Aboard NOAA Ship Henry B. Bigelow

September 23 – October 4, 2013

Mission: Autumn Bottom Trawl Survey
Geographical Area of Cruise: North Atlantic
Date: September 27, 2013

Science and Technology Log

It’s going to be a busy night trawling and processing our catch. Yippee. I like being busy as the time passes more quickly and I learn about more fish. A large number of trawling areas are all clustered together for our shift. For the most part that means the time needed to collect data on one trawl is close to the amount of time needed for the ship to reach the next trawling area. The first trawl was a highlight for me as we collected, for the first time, a few puffer fish and one managed to stay inflated so I had a picture taken with that one.

However, on this night there was more than just puffer fish to be photographed with. On this night we caught the big one that didn’t get away. One trawl brings in an amazing catch of 6 very large striped bass and among them is a new record: The largest striped bass ever hauled in by NOAA Fisheries! The crew let me hold it up. It was very heavy and I kept hoping it would not start flopping around. I could just see myself letting go and watching it slip off the deck and back into the sea. Fortunately, our newly caught prize reacted passively to my photo op. I felt very lucky that the big fish was processed at the station I was working at. When Jakub put the big fish on the scale it was like a game show – special sounds were emitted from our speakers and out came the printed label confirming our prize – “FREEZ – biggest fish ever “-‐-‐the largest Morone Saxatilis (striped bass) ever caught by a NOAA Fisheries research ship. It was four feet long. I kept waiting for the balloons to come down from the ceiling.

Every member of the science team sorts fish but at the data collection tables my role in the fish lab is one of “recorder”. I’m teamed with another scientist who serves as the “cutter”, in this case Jakub. That person collects the information I enter into the computer. The amount of data collected depends on the quantity and type of fish caught in the net. I help record data on length, weight, sex, sexual development, diet, and scales. Sometimes fish specimens or parts of a fish, like the backbone of a goose fish, are preserved. On other occasions, fish, often the small ones are frozen for further study. Not every scientist can make it on to the Bigelow to be directly part of the trip so species data and samples are collected in accordance with their requests.

Collecting data from a fish as large as our striped bass is not easy. It is as big as the processing sink at our data collection station and it takes Jakub’s skill with a hacksaw-‐-‐yes I said hacksaw-‐-‐to open up the back of the head of the striped bass and retrieve the otolith, the two small bones found behind the head that are studied to determine age. When we were done, the fish was bagged and placed in the deep freeze for further study upon our return. On the good side we only froze one of the six striped bass that we caught so we got to enjoy some great seafood for dinner. The team filleted over 18 pounds of striped bass for the chef to cook up.

More Going On:

Processing the trawl is not the only data collection activity taking place on the Bigelow. Before most trawls begin the command comes down to “deploy the bongos”. They are actually a pair of closed end nets similar to nets used to catch butterflies only much longer. The name bongo comes from the deployment apparatus that holds the pair of nets. The top resembles a set of bongo drums with one net attached to each one. Their purpose, once deployed, is to collect plankton samples for further study. Many fish live off plankton until they are themselves eaten by a predator farther up the food chain so the health of plankton is critical to the success of the ecological food chain in the oceans.

Before some other trawls, comes the command to deploy the CTD device. When submerged to a target depth and running in the water as the ship steams forward, this long fire extinguisher sized device measures conductivity and temperature at specified depths of the ocean. It is another tool for measuring the health of the ocean and how current water conditions can impact the health of the marine life and also the food chain in the area.

Personal Log

On a personal note, I filleted a fish for the first time today – a flounder. Tanya, one of the science crew taught me how to do it. I was so excited about the outcome that I did another one!

September 25, 2013March 12, 2021

John Clark, September 25, 2013

NOAA Teacher at Sea John Clark

Aboard NOAA Ship Henry B. Bigelow

September 23 – October 4, 2013

Mission: Autumn Bottom Trawl Survey
Geographical Area of Cruise: North Atlantic
Date: September 25, 2013

Science and Technology Log

I was told that the first 12 hour night watch shift was the hardest for staving off sleep and those who spoke were right. Tonight’s overnight shift seems to be flying by and I’m certainly awake. Lots of trawling and sorting this evening with four sorts complete by 6am. One was just full of dogfish, the shark looking fish, and they process quickly because other than weight and length there is little request for other data. The dogfish were sorted at the bucket end of the job so determining sex had already been completed by the time the fish get to my workstation. Again I’m under the mentorship of Jakub who can process fish faster than I can print and place labels on the storage envelopes. The placement of the labels is my weakness as I have no fingernails and removing the paper backing from the sticky label is awkward and time consuming. Still tonight I’m showing speed improvement over last night. Well at least I’m getting the labels on straight most of the time.

In addition to the dogfish, we have processed large quantities of skate (the one that looks like a sting ray to me), left eyed flounders, croakers (no relation to the frog), and sea robins of which there are two types, northern and stripe. The sea robins are very colorful with the array of spines just behind the mouth. And yes it hurts when one of the spines goes through your glove. Sadly for me sorting has been less exciting tonight. With the big fish being grabbed off at the front of the line there has been little left for me to sort. I feel like the goal keeper in soccer – just don’t let them get past me. To my great surprise, so far I’ve experienced no real fear of touching the fish. The gloves are very nice to work with.

And let us not overlook the squid. There have been pulled in by the hundreds in the runs today. There are two types of squids, long fin (the lolligo) and short fin (the illex). What they both have in common is the ability to make an incredible mess. They are slimy on the outside and inky on the inside. They remind me of a fishy candy bar with really big eyes. And for all the fish that enjoy their squid treat the species is, of course, (wait for it) just eye candy. The stories about the inking are really true. When upset, they give off ink; lots of ink. And they are very upset by the time they reach the data collection stations. If you could bottle their ink you would never need to refill your pen again. They are also very, very plentiful which might explain why there are no requests to collect additional data beyond how long they are. I guess they are not eye candy to marine scientists. However, there vastness is also their virtue. As a food source for many larger species of marine life, an absence of large quantities of squid in our trawling nets would be a bad sign for the marine ecosystem below us.

When the squid are missing, our friend the Skate (which of the four types does not matter) is glad to pick up the slack on the “messy to work with” front. As this species makes it down the sorting and data collecting line the internal panic button goes off and they exude this thick, slimy substance that covers their bodies and makes them very slippery customers at the weigh stations. It turns out the small spines on the tails were placed there so that fisheries researchers could have a fighting chance to handle them without dropping. Still, a skate sliding onto the floor is a frequent event and provides comic relief for all working at the data collection stations.

There was new species in the nets tonight, the Coronet fish which looks like along drink straw with stripes and a string attached to the back end. It is pencil thick and about a foot long without the string. We only caught it twice during the trip. The rest of the hauls replicate past sorting as dogfish, robins, skates, squid, croakers, and flounder are the bulk of the catch. I’ve been told that the diversity and size of the trawl should be more abundant as we steam along the coastline heading north from the lower coast of New Jersey. Our last trawl of the shift, the nets deployed collect two species new for our voyage, but ones I actually recognized despite my limited knowledge of fish – the Horseshoe Crab and a lobster! I grew up seeing those on the Jersey shore. We only got one lobster and after measuring it we let go back to grow some more. It only weighed in at less than two pounds.

Personal Log

The foul weather suit we wear to work the line does not leave the staging room where they are stored as wearing them around the ship is not allowed. After watching others, I have mastered the art of pushing the wader pants over the rubber boots and thus leaving them set-‐up for quick donning and removal of gear throughout the shift.

While the work is very interesting on board, the highlight of each day is meal time. Even though I work the night shift (which ends at noon) I take a nap right after my shift so I can be up and alert in time for dinner. My favorite has been the T-‐bone steaks with Monterey seasoning and any of the fish cooked up from our trawling like scallops or flounder. The chef, Dennis, and his assistant, Jeremy serve up some really fine cuisine. Not fancy but very tasty. There is a new soup every day at lunch and so far my favorite has been the cream of tomato. I went back for seconds! Of course, breakfast is the meal all of us on the night watch look forward to as there is no meal service between midnight and 7am. After 7 hours of just snacking and coffee, we are ready for some solid food by the time breakfast is served.

Seas continue to be very calm and the weather sunny and pleasant. That’s quite a surprise for the North Atlantic in the fall. And the sunrise today was amazing. The Executive Officer, Chad Cary, shared that the weather we are experiencing should continue for at least four more days. I am grateful for the calm weather – less chance to experience sea sickness. That is something I’m determined to avoid if possible.

September 24, 2013March 12, 2021

John Clark, Hi Ho, Hi Ho It’s Off to Work We Go, September 24, 2013

NOAA Teacher at Sea
John Clark
Aboard NOAA Ship Henry B. Bigelow
September 23 – October 4, 2013

Mission: Autumn Bottom Trawl Survey
Geographical Area of Cruise: North Atlantic
Date: September 24, 2013

Science and Technology Log

Today is my first full 12 hour shift day. I’m on the night crew working midnight to noon. Since we left port yesterday I’ve been trying to adjust my internal clock for pulling daily “all night”ers. On Monday, after we left port, safety briefs for all hands occurred once we made it out to sea and I got to complete my initiation into the Teacher at Sea alumni program – the donning of the Gumby suit as I call it. It is actually a bright red wet suit that covers your entire body and makes you look like a TV Claymation figure from the old TV show. In actuality it is designed to help you survive if you need to abandon ship. Pictures are of course taken to preserve this rite of passage.

The Henry B. Bigelow is a specially-built NOAA vessel designed to conduct fisheries research at sea. Its purpose is to collect data that will help scientists assess the health of the Northern Coastal Atlantic Ocean and the fish populations that inhabit it. The work is invaluable to the commercial fishing industry.

Yesterday, I learned how we will go about collecting fisheries data. Our Chief Scientist, Dr. Peter Chase, has selected locations for sampling the local fish population and the ship officers have developed a sailing plan that will enable the ship to visit all those locations, weather permitting, during the course of the voyage. To me its sounds like a well-‐planned game of connecting the dots. At each target location, a trawling net will be deployed and dragged near the bottom of the sea for a 20 minute period at a speed of 3 knots. Hence the reason this voyage is identified as a bottom trawl survey mission. To drag the bottom without damaging the nets is not easy and there are five spare nets on board in case something goes wrong. To minimize the chance of damaging the net during a tow, the survey technicians use the wide beam sonar equipment to survey the bottom prior to deployment. Their goal is to identify a smooth path for the net to follow. The fish collected in the net are sorted and studied, based on selected criteria, once on board. A specially designed transport system moves the fish from the net to the sorting and data collection stations inside the wet lab. I’m very excited to see how it actually works during my upcoming shift.

Work is already underway when our night crew checks in. The ship runs 24/7 and the nets have been down and trawling since 7pm. Fish sorting and data collection are already underway. I don my foul weather gear which looks like a set of waders used for British fly fishing. There is also a top jacket but the weather is pleasant tonight and the layer is not needed. I just need to sport some gloves and get to work. I’m involved with processing two trawls of fish right away. I’m assigned to work with an experienced member of the science team, Jakub. We will be collecting information on the species of fish caught on each trawl. Jakub carries out the role as cutter, collecting the physical information or fish parts needed by the scientists. My role is recorder and I enter data about the particular fish being evaluated as well package up and store the parts of the fish being retained for future study.

Data collection on each fish harvest is a very detailed. Fish are sorted by species as they come down the moving sorting line where they arrive after coming up the conveyer belt system from the “dump” tank, so named because that is where the full nets deposit their bounty. Everybody on the line sorts fish. Big fish get pulled off first by the experienced scientists at the start of belt and then volunteers such as I pull off the smaller fish. Each fish is placed into a bucket by type of fish. There are three types of buckets and each bucket has a bar code tag. The big laundry looking baskets hold the big fish, five gallon paint buckets hold the smaller fish, and one gallon buckets (placed above the sorting line) hold the unexpected or small species. On each run there is generally one fish that is not sorted and goes all the way to the end untouched and unceremoniously ends up in the catch-‐all container at the end of the line. The watch leader weighs the buckets and then links the bar code on the bucket to the type of fish in it. From there the buckets are ready for data collection.

After sorting the fish, individual data collection begins “by the bucket” where simultaneously at three different stations the sizing, weighing, and computer requested activities occur. By random sample certain work is performed on that fish. It gets weighed and usually opened up to retrieve something from inside the fish. Today, I’ve observed several types of data collection. Frequently requested are removal of the otolith, two small bones in the head that are used to help determine the age of the fish. For bigger fish with vertebra, such as the goose fish, there are periodic requests to remove a part of the backbone and ship it off for testing. Determining sex is recorded for many computer tagged fish and several are checked stomach contents.

Of the tools used to record data from the fish, the magic magnetized measuring system is the neatest. It’s rapid fire data collecting at its finest. The fish goes flat on the measuring board; head at the zero point, and then a quick touch with a magnetized block at the end of the fish records the length and weight. Sadly, it marks the end of tall tales about the big one that got away and keeps getting bigger as the story is retold. The length of the specimen is accurately recorded for posterity in an instant.

clark 1e

Personal Log

Flying into Providence over the end of Long Island and the New England coast line is breath taking. A jagged, sandy coast line dotted with summer homes just beyond the sand dunes. To line up for final approach we fly right over Newport where the Henry B. Bigelow is berthed at the Navy base there. However, I am not able to spot the NOAA fisheries vessel that will be my home for the next two weeks from the air.

I arrive a day prior to sailing so I have half a day to see the sites of Newport, Rhode Island and I know exactly where I’m headed – the Tennis Hall of Fame. My father was a first class tennis player who invested many hours attempting to teach his son the game. Despite the passion in our home for the great sport we never made it to the Tennis Hall of Fame in Newport. Today I fulfilled that bucket list goal. I still remember being court side as a young boy at The Philadelphia Indoor Championship watching the likes of Charlie Pasarell, Arthur Ashe, and Pancho Gonzales playing on the canvas tennis court that was stretched out over the basketball arena. Also in the museum, to my surprise, was a picture of the grass court lawn of the Germantown Cricket Club from its days as a USTA championship venue. I grew up playing on those grass tennis courts as my father belonged to that club. After seeing that picture, I left the museum knowing my father got as much out of the visit as I did.

September 21, 2007April 2, 2021

Allison Schaffer, September 21, 2007

NOAA Teacher at Sea
Allison Schaffer
Onboard NOAA Ship Gordon Gunter
September 14 – 27, 2007

Mission: Ichthyoplankton Survey
Geographical Area: Gulf of Mexico
Date: September 21, 2007

Weather Data from Bridge
Visibility: 12 nautical miles
Wind direction: E
Wind speed: 12 kts.
Sea wave height: 1 – 2 feet
Swell wave height: 2 – 3 feet
Seawater temperature: 29.0 degrees
Present Weather: Partly Cloudy

Science and Technology Log

Today we had the opportunity to try out two new sample methods. One method is along the same lines as the bongo and Neuston sample but this one is called a methot. A methot is 2.32 X 2.24 m frame with 1/8” mesh netting. The total length of the methot net is 43 feet. It’s huge! It works just like regular plankton net where it has a large opening and then as it moves towards the end it becomes more and more narrow and eventually ends at a collection container. The reason this is my first time doing one is because they are usually done only at night and since the net is so large they must be done in fairly deep water. The deck personnel helped us put the net in the water and then we waited. As the net was brought back on deck, we rinsed it down and collected samples the same way we would a bongo or Neuston sample. Of course with such a large net we collect bigger animals that we would with the other two. We did collect some fairly large fish along with smaller larvae. Our collection wasn’t the most excited some of the scientists have seen but to me, it was very exciting.

The second collection we took wasn’t a plankton collection but a water sample. It is important to know the physical and biological parameters of different areas when collecting. For this, we used a very large (and expensive) piece of technology: a CTD which stands for conductivity, temperature and depth. The CTD also measures dissolved oxygen and can do all of these measurements without actually collecting any water. We do however collect water to look at chlorophyll levels. The CTD frame has three bottles attached to the frame to collect water throughout the water column. Once we open the bottles on deck and set them, the lab scientist has the capability to fire the bottles shut at different depths. All measurements and water collection happen at three areas in the water column. One data and water collection is done at maximum depth, the second at mid depth at the third just a few feet from the surface. After all of the data has been collected, the CTD is brought back on deck where we bring the water samples up to the lab to test. It was definitely an exciting day on deck today.

Personal Log

It has one week since we left port in Pascagoula and I am having such a great time! I forgot how much fun field work is and how excited I get over the smallest things when it comes to animals. I am so fortunate to have such an experience and I can not wait to get some samples home to share with our students. I already have started making some lesson plans!

Addendum: Glossary of Terms

Visibility is how far ahead you can see from the ship. On a very foggy day you may only have a visibility of 10 ft whereas on a clear day you can see all the way to the horizon, or 12 nautical miles.
Wind direction tells you which way the wind is blowing from: 0° is north, 90° is east, 180° is south, and 270° is west.
Sea wave height is the height of the smaller ripples
Swell height is the estimates larger waves
Sea level pressure (or Barometric Pressure) indicates what the trend of the weather has been. High barometric pressure usually means sunny weather and rain can not build up in clouds if they are being squeezed together by high pressure. Low barometric pressure means rainy or stormy weather is on the way.
Present Weather is a description of what the day’s weather is.

– Courtesy of Thomas Nassif, NOAA Teacher at Sea, 2005 Field Season

Field Party Chief or FPC is in charge of the team of scientists on board the ship. This person oversees all activities having to do with collection of samples and is the go to person in case anything goes wrong that the scientists can’t handle. They also act as an extra set of hands when needed.
Bongo Net is two circular frames 60 cm in diameter sitting side by side with two 333 micron nets and a weight in the center to help it sink. At the base of each net is a plastic container used to collect all the plankton that can be easily removed so we can retrieve the samples
Lab Scientist is the scientist that stays in the lab to work the computers recording the data on sample time, sample depth and is the one that relays information to the deck personnel about when the nets have hit maximum depth. They keep watch in case anything goes wrong underwater.
Deck Scientist is the scientist out on deck getting the nets ready, rinsing the nets, collecting and preserving samples. They are the eyes on deck in case anything goes wrong at the surface or on deck.
Neuston Net is one net 1 X 2 meters with a 947 micron net. Neuston samples are done only at the surface and placed in the water for ten minutes.
CTD
Photic Zone

September 18, 2007April 2, 2021

Allison Schaffer, September 18, 2007

NOAA Teacher at Sea
Allison Schaffer
Onboard NOAA Ship Gordon Gunter
September 14 – 27, 2007

Mission: Ichthyoplankton Survey
Geographical Area: Gulf of Mexico
Date: September 18, 2007

Weather Data from Bridge
Visibility: 12 nautical miles
Wind direction: NE
Wind speed: 18 kts.
Sea wave height: 3 – 4 feet
Swell wave height: 3 – 4 feet
Seawater temperature: 27.5 degrees
Present Weather: Mostly Cloudy

Our sample from one of the bongo collections

Science and Technology Log

I woke up this morning excited and ready to go! My morning doesn’t exactly start bright and early at 6am but tends to start much later around 10am. The way life on board the boat works for the team of scientists is that there are two teams: the night watch which is from midnight to noon and the day watch runs from noon to midnight. The field party (that’s what the team of scientists on board is called) consists of six scientists and the FPC (Field Party Chief). I work as part of the day watch along with two of the other scientists. The remaining three work the night shift. Each of the pre-selected stations is about 30 miles apart, so it takes us close to three hours to commute between stations. Once we arrive at the station, all the sample collections and last about 45 minutes to an hour. After we have completed a station we head back into the lab where we have three hours to wait until our next station. During this time we usually watch a movie, read a book, email friends, family or work, do work, play cards, etc. Or in my case, I like to sit out on the deck and look at the ocean since living in Chicago it’s not something I get to see everyday.

Teacher at Sea, Allison Schaffer, rinsing one of the bongo samples into a glass container to be preserved

So this particular morning, I wake up and get dressed just in time for an early lunch before our shift. Today it happens that we reach our station around 11 and since each station takes about an hour, myself and the other scientists from my shift decided we would head up and relieve the night shift early so they can head down for lunch since lunch is only out until noon. Since they had already done the bongo net sampling and preserving, we finished up the station with a Neuston collection. Once we labeled all the samples, I sat down at one of the computers to do some more emailing and started staring out the window in the lab. It was another beautiful day on the Gulf! At least from my perspective it was. What I didn’t see yet on our horizon was a fairly large storm system was headed our way from the Atlantic across Florida in our direction. We arrived at our second station, did our two sample collections and headed back in for dinner. When we got back in, the FPC said that the Commanding Officer (or CO), Lieutenant Commander Brian Parker, said we were going to be heading south to get away from the storm. He said that was our best bet to avoid any bad weather and that the safety of everyone on board is most important to him. We would definitely not be able to hit anymore stations on my shift but we now had the rest of the night off to relax!

Bongo nets coming out of the water getting rinsed down by one of the scientists — Bongo nets coming out of the water getting rinsed

Personal Log

I have been finding some very cool animals in the samples we have collected! The other deck scientist and I spend more time looking through our sieves to see what caught than we do doing anything else. At our first station we got more jellies—and the stinging ones this time! But at our second station, we caught a bunch of juvenile flat fish and eels. And we are getting tons of crabs and shrimp! Little tiny ones! It is still amazing to me the variety of what we are finding and the different colors of everything! Bright blue copepods, orange or purple crabs, purple amphipods, silvery blue and yellow jacks, silvery blue half beaks, yellow and gray triggers, pink shrimp, and more!

Teacher at Sea, Allison Schaffer, taking wire angle measurements for the bongo nets using the inclinometer. — Allison Schaffer taking wire angle measurements for the bongo nets with the inclinometer

Teacher at Sea, Allison Schaffer holding a cannon ball jelly caught in the Neuston net — Allison Schaffer holding a cannon ball jelly caught in the Neuston net