Carmen Andrews: Transforming Fish into Data, July 15, 2012

NOAA Teacher at Sea
Carmen Andrews
Aboard R/V Savannah
July 7 – 18, 2012

Mission: SEFIS Reef Fish Survey
Location: Atlantic Ocean, off the coast of Cape Canaveral, Florida
Date: July 15, 2012

Latitude:      28 ° 50.28   N
Longitude:   80 ° 26.26’  W       

Weather Data:
Air Temperature: 28.6° C (83.48°F)
Wind Speed: 18 knots
Wind Direction: from the Southeast
Surface Water Temperature: 27.6 °C (81.68°F)
Weather conditions: Sunny and Fair

Science and Technology Log

How are fish catches transformed into data? How can scientists use data derived from fish to help conserve threatened fish species?

The goal of the Southeast Fishery-Independent Survey or SEFIS is to monitor and research reef fish in southeast continental shelf waters.  Marine and fisheries scientists have developed sophisticated protocols and procedures to ensure the best possible sampling of these important natural resources, and to develop fisheries management recommendations for present and future sustainability.

During the cruise, important commercial fish in the snapper and grouper families are caught over as wide an area as possible; they are also taken in large enough numbers that they can be worked up into statistically reliable metrics. In addition to counts and measurements, biological samples are also taken at sea for future analysis in land-based research labs.

Gag grouper ready for its work up
Gag grouper ready for its work-up

Scientists strive to render an informative snapshot of reef fish stocks in a given time interval. Reports that analyze and summarize the data are submitted to policy-makers and legislators to set fisheries rules, restrictions and possible quotas for commercial and sports fishermen.

After fish are caught and put on ice, processing includes several kinds of measurement that occur on deck. This data is referred to as ‘Length Frequency’. Tag information from the trap follows the fish through all processing.  Aggregate weight measurements for all the fish of one species caught in a trap are made and recorded in kilograms.

David is weighing the gag grouper, with Adam P. looking on
David is weighing the gag grouper, with Adam P. looking on

The length for each fish in the trap is noted, using a metrically scaled fish board. Not all fish are kept for further processing.

David measuring the length of the gag grouper
David measuring the length of the gag grouper

Species-specific tally sheets randomly assign which fish from the catch are kept and which ones are tossed back into the ocean. These forms, which specify percentages of fish identified as ‘keepers’, are closely consulted by the data recorder and the information is shared with the scientist who is measuring the catch.

Shelly is recording length frequency measurement data
Shelly is recording length frequency measurement data
Length frequency data entries
Length frequency data entries
Red Porgy keep/toss percentage sheet
Red Porgy keep/toss percentage sheet

Kept fish are put in a seawater and ice slurry. The others are thrown over the side of the boat.

Age and reproductive sampling are done next in the wet lab.

Small yellow envelopes are prepared before fish work up can begin. Each envelope is labeled with cruise information, catch number, fish number, and the taxonomical name of the fish, using  binomial nomenclature of genus and species.

Adam P. and Shelly labeling envelopes and plastic specimen containers
Adam P. and Shelly labeling envelopes and plastic specimen containers

A small color-coded plastic container (the color indicates fish species tissue origin), with the fish’s source information riveted at the top, is also prepared. This container will store fish tissue samples.

The fish trap catch number is documented on another data form, along with boat and science team identification, collection method and other important information about the circumstances surrounding the fish catch.  Each species’ data is separately grouped on the data form, as individual fish in a catch are sequentially numbered down the form.

Me, transcribing fish weight & length data
Me, transcribing fish weight & length data

Each fish is weighed, and the weight is noted in grams. The scale is periodically calibrated to be sure the fish is weighed accurately.

Vermilion snappers and scamp, labeled and  ready for dissection
Vermilion snappers and scamp, labeled and ready for dissection

Three length measurements that are made: standard length (SL), total length (TL), and if the fish species has a fork tail — fork length (FL). The fish is laid, facing left on a fish board. The board is long wooden plank with a metric measuring scale running down the center.

Standard length does not include the caudal fin or tail. It begins at the tip of the fish’s head; then the fish measurer lifts the tail up slightly to form a crease where the backbone ends. Standard length measurement includes the fish’s head to end of backbone dimension only. Total length is the entire length of the fish, including the caudal fin. In fork-tailed species, the fork length measurement begins at the fish’s snout and ends at the v-notch in the tail.

Fish length measurements
Fish length measurements

Source: Australian Government – Department of Environment, Water, Population and Communities

Part of the dissection of every fish (except gray triggerfish) is the extraction of  otoliths from the fish’s head. An otolith is a bone-like structure made of calcium carbonate and located in the inner ear of fish. All vertebrates have similar structures that function as gravity, balance, movement, and directional indicators. Otoliths help fish sense changes in horizontal motion and acceleration.

To extract the otoliths, the scientist makes a deep cut behind the fish’s head and pulls it away from the body. The left and right otoliths are found in small slits below the brain. They must be removed carefully, one at a time with forceps. They can easily break or slip into the brain cavity.

Red snapper with removed otolith
Red snapper with removed otolith

Otoliths reveal many things about a fish’s life. Its age and growth throughout the first year of its life can be determined. Otoliths have concentric rings that are deposited over time. The information they show is analogous tree ring growth patterns that record winter and summer cycles. Other otolith measurements can determine when the fish hatched, as well as helping to calculate spawning times in the fish’s life.

The oxygen atoms in calcium carbonate (CaCO3) can be used to assay oxygen isotopes. Scientists can use these markers to reconstruct temperatures of the waters the fish has lived in. Scientists also look for other trace elements and isotopes to determine various environmental factors.

Each pair of otoliths is put into the small labeled yellow envelope.

The otoliths on the gray triggerfish are too small to be studied, so the spine from its back is collected for age and growth analysis.

Spine removed from a gray triggerfish
Spine removed from a gray triggerfish

The last step standard data collection is determining the sex and maturity of the fish. The fish is cut open at the belly, similar to preparing the fish as a filet to eat it.

Making a cut into a vermilion snapper
Making a cut into a vermilion snapper

If the fish is big, the air bladder must be deflated. The intestines are moved or cut out of the way. The gonads (ovaries and testes) are found, and the fish can be identified as a male or female. (Groupers can be hermaphroditic.) The fish’s stage of maturity can also be determined this way.  Maturational stages can be classified with a series of codes:

U = undetermined

1 = immature virgin (gonads are barely visible)

2 = resting (empty gonads – in between reproductive events)

3 = enlarging/developing (eggs/sperm are beginning to be produced)

4 = running ripe (gonads are full of eggs/sperm and are ready to spawn)

5 = spent (spawning has already occurred)

Dissected gonad specimens are removed from the fish and placed in a plastic containers, snapped shut and stored in a formalin jar to preserve them. These preserved samples will be analyzed later by histology scientists. Histology is the science of organ tissue analysis.

Dissected fish gonads
Dissected fish gonads

Red snappers have their fins clipped to provide a DNA sample. They may also have their stomachs removed and the contents studied to better understand their diets.

Video data from the underwater cameras is downloaded in the dry lab. This data will be analyzed once scientists return to their labs on land.

Personal Log

Many different kinds of echinoderms and other invertebrates have been pulled up in the fish traps. Several are species that I’ve never seen before:

Basket Star
I am holding a basket star. It is a type of brittle star in the echinoderm phylum.
A red sea star
A red sea star
Spikey sea star
Spikey sea star
Small crab, covered in seaweed, shell and sand
Small crab, covered in seaweed, shell and sand

We also catch many unusual large and small fish in the traps and on hooks. Several of these have been tropical species that I’ve only seen in salt water aquariums.

Lizardfish
Lizardfish
Sargassumfish
Sargassumfish
Hooked blacktip shark
Hooked blacktip shark
Scrawld Filefish
Scrawld Filefish
Spotted butterflyfish
Spotted butterflyfish
Jack knife fish
Jack knife fish

Andrea Schmuttermair: Out to Sea, June 24, 2012

NOAA Teacher at Sea
Andrea Schmuttermair
Aboard NOAA Ship Oregon II
June 22 – July 3

Mission: Groundfish Survey
Geographical area of cruise: Gulf of Mexico
Date: June 24, 2012

Ship Data from the Bridge
Latitude: 2858 N
Longitude: 9310.96 W
Speed:  10 mph
Wind Speed: 6.77
Wind Direction: N/NE
Surface Water Salinity: 30.9
Air Temperature: 28.5 C
Relative Humidity: 79%
Barometric Pressure: 1009.84 mb
Water Depth:  24.3 meters

 Personal Log

About ready to set sail!
About ready to set sail!

And the journey has begun! I arrived in Houston on Thursday afternoon, only to be whisked away by Chief Scientist Andre DeBose to meet a few of the other scientists and crew for dinner. I had a great time getting to know a few of the people I will be working with over the next couple of weeks. We arrived to the port at Galveston about 10pm, where I got a quick tour of the Oregon II, my home for the next 2 weeks. Exhausted from traveling, I made myself at home in my stateroom before turning in for the evening.

Because we weren’t scheduled to set sail until 1400, I had a bit of time in the morning to explore Galveston. Being the adventurous type , I took this time to explore the land I would soon be leaving. The Oregon II is docked at Pier 21, located on “The Strand”, a strip filled with historic buildings and tourist shops.  I spent most of my morning snapping photos, checking out the shops, and tracking down a good breakfast burrito at one
of the many Mexican food places that don the strip.

The pier in Galveston
The pier in Galveston

Once back at the ship, we were briefed on the “Do’s and Don’ts” while on board, and what our shifts would look like. I am on the night watch, which means I will be working from midnight until noon each day. This will be a tough schedule to get used to, but I’m hoping we’ll see some neat things at night, and that it will be a little cooler out. I knew I should get to sleep as soon as we set sail, however I couldn’t help hanging out on deck for a little while as we left the port. I was rewarded for this opportunity by watching the pelicans and dolphins seeing our ship out of the port. I snapped a few more photos, enjoyed the cool breeze, and then headed down for bed.

I had quite a blast on my first night shift. I think keeping busy was a good thing, even though it was exhausting. I enjoyed getting to know my team a little better, and of course, checking out all the critters! Some of my favorites were the squid, sharp-nose and dogfish sharks, lizardfish, and my all-time favorite so far – the bashful crab.

Why do you think he is called the "bashful crab"?
Why do you think he is called the “bashful crab”?

Science and Technology Log

I am always under the mindset that if you want to learn something, you need to throw yourself in head first. Well, that’s exactly what I did on my very first shift on the Oregon II. We are split up into 2 shifts — midnight to noon or noon to midnight. On my watch, I am working with our watch leader, Alonzo, 2 scientists, Lindsey and Alex, and a volunteer, Renee. Our Field Party Chief Scientist (FPC), Andre, had to leave unexpectedly. Our new FPC, Brittany, was with us a bit of this first watch to make sure we understood our tasks, as I had lots of questions! Not only did I get the privilege to work the nightshift (I know you’re probably wondering why I said privilege  — I’ll explain soon), but we also had one of the busiest shifts we’re anticipated to have for the length of this cruise. Just after midnight on Saturday morning, we pulled up our first trawl and conducted our first CTD.

The CTD warming up just below the water's surface
The CTD warming up just below the water’s surface
Rinsing out the CTD with freshwater
Rinsing out the CTD with freshwater

A CTD, if you remember from my first blog, stands for Conductivity, Temperature, and Depth. We put the device overboard in the front of the ship (the bow), and let it sit just below the surface for about 3 minutes so the sensors can warm up before we drop it to its scheduled depth. Then we lower it so it is as close to the ocean floor as possible. We do this at every station to collect important information about the oxygen level in the water in these areas. This information is important because we want to find out what the optimal conditions (temperature, salinity and oxygen levels) are for the specimens we collect. Knowing what environmental conditions suit each species allows us to see how shifts in the environment can impact populations. The data from the CTD is displayed on the computer in our dry lab, where the data points are plotted on a graph.

The dry lab is where we process a lot of our data both from the CTD and the sampling. We can monitor our CTD casts and find the weather information here. It is also the area where scientists go when there is a bit of downtime to relax before the next catch is brought in.

Bringing up the trawl- this was a big catch!
Bringing up the trawl — this was a big catch!
Working in the dry lab

Over in the back of the ship, also known as the stern, the trawl picks up all sorts of critters from the ocean bottom. When we’re ready, the deck crew helps us bring up the trawl and dump our catch into large buckets on deck.  We had so much on the first catch that they dumped it out on the floor and we shoveled it into buckets like we were shoveling snow. We then weighed our catch before bringing it in and sorting it. Our first few catches were quite large — we had 6 or 7 baskets full of critters! Each basket can hold roughly 25kg. So, mathematicians, about how many kilograms were our first couple of catches? The nighttime brings on some interesting animals, and there is a certain excitement to staring out at the pitch black ocean.

Our troughs full of the catch, waiting to be sorted
Our troughs full of the catch, waiting to be sorted

With these large catches, jumping in head first was exactly what I had to do. I got a quick crash course in how to identify and sort the fish. I had no idea there would be so many different types! From the entire catch, we were to pull out red snapper, shrimp (pink, white and brown only), blue crabs, and anything unusual. We did this by dumping all the fish in a large trough, which we would then dig through to find our samples and place them in separate baskets.

We are pulling out samples primarily of shrimp because that is one of the main focuses of our survey this summer. The estimated abundance of shrimp, calculated from the trawl catches, is used to set limits for the commercial fishermen.

In addition to sorting out these important critters, we would also take what we call a subsample, the size of which is determined by the size of our total catch. Of this subsample, we sorted out everything in this section of the catch. We often had over 20 different types fish or crustaceans! Once the subsample was sorted, Alonzo would then weigh the total weight of a certain species and enter the data into our computer system. From here the fun part really began.

Lindsey is measuring, weighing and sexing the catch while I enter the data into the computer.
Lindsey is measuring, weighing and sexing the catch while I enter the data into the computer.
Weighing the lizardfish
Weighing the lizardfish

We would measure the length of each critter on our measuring board, which uses a magnetic wand to capture the data and send it directly to the computer database. For most of the species, we would also take the weight of the first fish and every fifth fish thereafter, and, if possible, also determine its sex and stage of maturity. All this information was entered in the database. We typically worked in teams of 2 with one person measuring and weighing the fish and the other entering information into the computer. We were a bit slow to start, but after the first catch we had a system down. Once we had all of our data, we bagged up some of the fish that people have requested for samples while the rest headed back to the ocean. Fish from our survey will go to scientists in lab across the country to study further.

Because all the stations were about 2-5 miles apart on our first watch, we were working nonstop from midnight until about 11am. We pulled up about 7 catches, and almost always had a catch waiting to be sorted on deck.

Hard at work measuring my lizardfish
Hard at work measuring my lizardfish

Got Questions?

Don’t forget, you can leave your questions in the “Comments” section below, and I’ll do my best to answer them!

Critter Query:

Students: Don’t forget to put your name in your response.  Remember, the first one to respond correctly will receive a prize in the fall!

Critter Query #1: What’s the biggest commercial shrimp found in the Gulf of Mexico and what is its scientific name?

Critter Query #2: Name 3 types of shark found in the Gulf of Mexico.  (more than one correct response — all correct responses will receive a prize providing there are no repeats)

Ruth Meadows, July 7, 2009

NOAA Teacher at Sea
Ruth S. Meadows
Onboard NOAA Ship Henry B. Bigelow 
June 12 – July 18, 2009 

Mission: Census of Marine Life (MAR-Eco)
Geographical Area: Mid- Atlantic Ridge; Charlie- Gibbs Fracture Zone
Date: July 7, 2009

Tom Letessier holds a sea urchin fully inflated with water.
Tom Letessier holds a sea urchin still fully inflated.

Weather Data from the Bridge 
Temperature: 8o C
Humidity: 91%
Wind: 9.75 kts

Science and Technology Log 

Usually by the time the catch was on board, the sea urchins were deflated and very flat. These are commonly known as collapsible or flat urchins. When it is taken out of the water, it collapses into a flat shape. There is a red shrimp on the right side. We caught many different sizes of the Bathysaurus during the benthic trawls.  It has a very bony head, large mouth and lots of sharp teeth.  It normally rests stationary on the bottom of the ocean floor with its head slightly elevated.  It feeds primarily on fishes and decapods (type of crustacean).

Lizardfish
Lizardfish
A deep sea crab, Neolithodes grimaldii, was found in two different benthic catches. Its spines are very long and sharp. They were both in remarkably good physical shape and were carefully preserved so their spines would not break.
A deep sea crab, Neolithodes grimaldii, was found in two different benthic catches. Its spines are long and sharp. They were in remarkably good shape and were carefully preserved so their spines would not break.

We are finished with our trawls and are heading back to Newport, Rhode Island.  The trip back will take about 7 days.  During this time, the information that was entered into the computers will be analyzed and checked for any errors. In addition, the organisms that are preserved will be sorted and packaged for delivery to various locations.  Many of the samples will be going to the Virginia Institute of Marine Science (VIMS) and later distributed to various scientists to use in their research. Dr. Tracey Sutton will even send some specimens to me in Opelika for my students to observe.

Personal Log 

Occasionally, when the weather and work schedule allows, the deck chairs come out and we relax and visit with one another outside.  The crew calls this “The Stinky Sailor”. There will be soft drinks, slushy type drinks, sometimes candy and if we are lucky Andrew entertains us with his music. This part of the ship is called the O2 deck, two floors up from the main deck.  The Stinky Sailor is set behind the superstructure of the ship so it is protected from the wind.  When we were sailing east, the afternoon sun would warm the area making it a very pleasant place to visit and relax. 

Screen shot 2013-04-28 at 10.23.07 PM

Ruth Meadows, July 5, 2009

NOAA Teacher at Sea
Ruth S. Meadows
Onboard NOAA Ship Henry B. Bigelow 
June 12 – July 18, 2009 

Mission: Census of Marine Life (MAR-Eco)
Geographical Area: Mid- Atlantic Ridge; Charlie- Gibbs Fracture Zone
Date: July 5, 2009

dumbo octopus
Dumbo octopus

Weather Data from the Bridge 
Temperature: 10.3o C
Humidity: 93%
Wind: 8.9 kts

Science and Technology Log 

Dr. Mike Vecchione holds a very large dumbo octopus from one of the deep sea trawls. This octopus got its name from the large fins that look like the ears of “Dumbo” the elephant. It is a benthic cephalopod (an ancient group in the phylum Mollusca) that lives above the floor of the ocean. It probably feed on copepods and other small crustaceans, but we don’t know much about its biology. This particular species (Cirrothauma magna) has only been caught a few times before.

a very large example of a slickhead
A very large example of a slickhead

John Galbraith and Tom Letessier hold a very large example of a slickhead. These fish are dark in color and their exterior is slippery. These soft-bodied soggy fish are common in waters greater than 1000m deep. They get their common name from the slimy look of their head. They lack a swim bladder and make themselves as light as possible by having weak bones and watery flesh. Chimeras are distantly related to sharks and rays and can be found at depths up to 2500m. These fish have cartilage instead of bones. We caught several of these in the benthic trawls, but this one was the largest.  Most of these fish have a venomous spine at the back of its dorsal fin.

This is a chimaera that weighed in at 12 kilograms.
This is a chimaera that weighed in at 12 kilograms.
Basti (from Germany) is holding another chimaera, Venda (from Portugal) has a slickhead and Meridith (from Boston) has a lizardfish from the last benthic trawl of the cruise.
Basti (from Germany) with a chimaera, Venda (from Portugal) has a slickhead and Meridith (from Boston) has a lizardfish.

Do You Know? 

What would happen between a shark and an octopus? Find out here.   

Taylor Parker, April 21, 2009

NOAA Teacher at Sea
Taylor Parker
Onboard NOAA Ship Oscar Elton Sette
April 19-29, 2009 

Mission: Hawaii Bottom fish Survey
Geographical Area: South side of Oahu
Date: April 21, 2009

The crew does an incredible job of lowering these SAFE boats into the water with Kona coast in the background.
The crew does an incredible job of lowering these SAFE boats into the water with Kona coast in the background.

Weather Data 
Winds: 7-16 knots variable.
3-5 ft swells.
Water temp: 24 C.
Air temp: 70 F.

Science and Technology Log 

Oh man, I am so happy that we’re underway! The swells found us today and we’re finally rocking around – it is great! Today, the game-plan is that at 6am the 15ft SAFE boat runs out into the sapphire blue Hawaiian waters to study the slicks (areas of converging down-welling currents- the glassy parts in the ocean) while the 19ft boat tries to find juvenile bottom-fish. Good luck!

Retrieving the trawl
Retrieving the trawl

I, however, am helping three other scientists with trawling for billfish. We’re working with the Isaacs-Kidd trawl (I/K). This is a 10 meter long net with 5mm mesh that is connected to a detachable cod-end which collects the plankton. The I/K was named after the researchers from Scripps in La Jolla who developed the technology in the 60’s. We dropped the net bearing their names into the water by an A-Frame winch maintaining just below the surface for an hour. At this time the net is retrieved and the cod end is removed for study. It is replaced with a fresh end and the net is thrown back into the water for another hour.

The codend is replaced
The codend is replaced

The cod-end is brought into the hydro-lab and the contents are splayed out into a tray and analyzed. The marine organisms are then sorted, organized and labeled for any rare or special fish – my personal favorite is the long, skinny Lizardfish in the middle of the tray. The different fish in this photo are really interesting. The small one in the top left is a Slender Mola which as an adult lives in the open water, the longer Lizardfish lives on the bottom, the Blenny lives near shore in shallow water while the Lantern-fish grows up, lives in mid-water and develops light organs. As adults they grow into different sizes, scatter into different waters in the ocean and adapt accordingly. But as larvae they are all found together—in the slicks.

The contents of the cod-end are readied for analysis
The contents of the cod-end are readied for analysis

The target specimens for this trawl are Marlin, Swordfish and other billfish larvae. And you know what? We caught a couple; the one pictured is a baby Swordfish. From this photo it is hard to believe this creature grows up to be the extremely muscular fish in the same sub-Order as the one Hemingway writes about, but it is true. Not much is known about the life histories of these fish, that is why we’re here, but it is believed that it takes many years to reach adult. The specimen were photographed and then placed in a 32oz plastic jar with ethyl alcohol for further analyzing later. We repeated this process 6 times throughout the day.

Personal Log 

My personal favorite, the lizardfish
My personal favorite, the lizardfish

The I/K collects a lot of very small marine organisms. It looks like gumbo. Luckily, this isn’t our dinner; we’re fed a lot better looking— and definitely tasting— food on this cruise. We collected numerous jellies, shrimp, fish larvae, debris, eggs, nudibranchs and crabs. All of it is relatively transparent so you don’t notice it while in the ocean. The I/K concentrates the gelatinous biota and truly illustrates what is in the water. And considering the warmer waters of the tropics are less productive than colder waters, this isn’t everything that could be there. Just don’t think about this when you open your mouth underwater!

A baby swordfish
A baby swordfish

The trawl was fun and definitely a new experience. It is truly incredible the amount of life that is in the water. Until you see you it pulled out, you don’t believe it. This is one of the paradigm-shifting results from being on this ship that I am only now beginning to realize. This entire vessel is designed to study the ocean; every facet of this boat is geared toward understanding the marine world. The researchers and crew on the Sette are actively embracing NOAA’s mission of stewardship.

Question of the Day 

"Gumbo" from the trawl
“Gumbo” from the trawl

Why are the fish we catch the colors they are—orange, yellow, red, etc? This was one of the questions I asked some of the expert marine biologists over dinner the other day and I was told that one of the reasons is that the colors makes the fish invisible. Red absorbs the spectrum of light that gets down around 100 fathoms and makes the fish look grey.

New Term/ Phrase/ Word 
New words: Vog –volcanic fog. Here the marine layer is normal condensation coupled with volcanic particulates. Kai – Hawaiian for the sea; Nalu – Hawaiian for waves; Kuliana— Hawaiian for responsibility. This can be responsibility for anything: your job, your family, etc. But as Ensign Norris says, it is also responsibility for the environment and it reminds us to protect what we have.

Animals Seen Today 
We saw a Laysan Albatross (Phoebastria immutabilis) today zooming the boat. It is a beautiful bird that I’ve never seen before and its wings were truly massive. We also caught a few billfish and fish larvae so tiny they look like they are just heads!