Tag: CTD

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Martin McClure: Starting the Survey, July 30, 2023

NOAA Teacher at Sea

Martin McClure

NOAA Ship Oregon II

July 25– August 9, 2023

Mission: Shark/Red Snapper Bottom Longline Survey

Geographic Area of Cruise: Gulf of Mexico/Atlantic Ocean

Date: July 30, 2023

Latitude: 31°21.967’N

Lonfitude: 80°12.135’W

Air Temperature: 27.5° C.

Wind Speed: 6.79 kph

Science and Technology Log: Longline Fishing

Teacher at Sea Stephen Kade created this graphic to help explain longline fishing.

We have started the longline survey and it is well organized and exciting. The first part of the process is called the set. We start the fishing process by baiting circle hooks. These hooks are attached to a 12 foot length of 3 mm line called a gangion (gan-jin). We use mackerel for bait. Each piece of fish is hooked through a circle hook.

Circle hooks ready for baiting

Next we drop over a buoy with a radar reflector on top called a hi flier. Attached to this is a 4 mm line called the main line. Then a weight is attached to the line and dropped. This anchors the beginning of the fishing line to the seafloor. Next, a numbered clip is attached to each gangion. The gangions are attached to the main line in order from 1- 50. A second weight is then attached to the main line and the process is repeated with gangions numbered 51- 100. A third weight is then attached to anchor this end of the line to the seafloor.

Tagging and attaching the gangions

Finally, a second hi flier buoy is attached and released to mark the end of the line.  As each of these steps is done a member of the team records it on a computer. This gives a precise time that each baited hook went in the water as well as when and where the anchors and buoys were released. 

Ready to drop the hi flyer

The next step is to take water measurements. This is done with a remarkable device called a CTD. CTD stands for conductivity, temperature and depth. Conductivity is related to how much salt is in the water (salinity) and is related to how well it will conduct electricity. It also measures the temperature and depth of the ocean at that spot. We attach a camera to it to see what the seafloor is made of at that spot. We want to know if it is a sandy bottom, sea grass, muddy, etc.  

The CTD


Then we wait one hour. 


The second part of the process is called the haul. The haul is simply the set done in reverse, except that we often catch fish. The fishermen use a grappling hook to retrieve the main line attached to the hi flier.

Grappling hook ready to thrown

When it is brought on board, the main line is attached to a winch. The winch is used to pull the main line up of the seafloor. As the main line is pulled in the gangions are detached and replaced in a barrel, the numbered clips are detached and kept on a line in number order. That way,  everything is ready to be used for the next set. Whatever is on, or not on, the hook is recorded on the computer. If the bait is missing or damaged is noted.

Weighing a barracuda

Any fish caught is noted on the computer and the team jumps into action. For sharks there are several things that happen. They are identified by species. The hook is removed and the shark is weighed. It is then measured for three different lengths, precaudal (before the tail fin), fork (at the fork in the tail, and total (the end of the tail fin). The sex, male or female,  and maturity is determined. Tissue samples are taken by cutting off a small piece of a fin. This tissue sample is placed in a small plastic vial and labeled. They are also often given a numbered tag. This information is all recorded and entered into the computer. 

Me, tagging a sandbar shark.

Meet the Crew: Lieutenant James Freed

NOAA Corps Lieutenant James Freed is the operations officer for the Oregon II. He has many responsibilities as part of his job. Part of his job is to liaison, or maintain communication, between the science party and the ship’s commanding officer (CO). That means making sure that everything that the science team needs is on the ship. If the science team has needs then we would go through him and not directly to the CO. As Operations Officer he is also in charge of organizing materials when they come aboard the ship. He posts the Plan of the Day which lets everyone on board know what to expect that day. Lieutenant Freed coordinates port logistics for the ship. This means he coordinates the loading and unloading of materials. His duties also include acting as Officer of the Deck (OOD). During this 4 hour shift he is responsible for the ship’s navigation and safety. His emergency response assignments on the Oregon II include being the nozzleman on the fire team, launching life rafts for abandon ship and he goes out on the rescue boat for man overboard. 
Lieutenant Freed grew up in Santa Rosa, California. He attended Santa Rosa Junior College and then transferred to University of California, Santa Cruz where he studied marine biology. During this time he worked as an intern on a fishing vessel and this is where he first heard about the NOAA Corps. He has now been in the NOAA Corps for 6 years. Before being assigned to the Oregon II he was first assigned to the NOAA Ship Bell M. Shimada in Newport, Oregon. He then moved to Seattle working with the Marine Mammal Laboratory at Alaska Fisheries Science Center. For this assignment his duties were quite varied. They included doing a lot of field work, flying drones, and doing whale biopsies. 
Lieutenant Freed is clearly enthusiastic about his career in the NOAA Corps. He describes it as an “incredible career” that supports his growth with leadership and management training. The NOAA Corps is growing with new ships and aircraft and will need to recruit new members.. The ships participate in a wide variety of tasks including fisheries research, oceanographic and atmospheric data collection and hydrographic mapping. 

Personal Log

Well these last few days have been quite a transition. After 2 1/2 days of transit from Pascagoula, MS to Miami. It was a bit shocking to see how the skyline has changed after 40+ years. It has grown, to say the least. We started fishing just north of Miami. The 10 person science team is split into two shifts. I am on the “day” shift. We work from noon to midnight. These long shifts are filled with alternating periods of activity and waiting. After the set we wait for an hour before the haul. Then, depending on where the next set is, there will be another wait of between two to three hours. The hauls seem to follow the same patterns. As the mile of line is reeled in, there are long periods with not much happening. Then, there might be three fish online within a few hooks. Last night it was two baby tiger sharks and a 1200 mm (3 ft. 11 in.) barracuda within about 5 minutes. When there is a shark too big to haul up by hand on the gangion, the crane is used. We all don hardhats, the crane is moved into place and everyone is busy taking measurements, preparing tags, and taking tissue samples. I was warned to bring a lot of reading material for the down time and I did that. However, with so many things to learn, interesting people to talk to, and beautiful scenery to watch, I have had little time for boredom to creep in.

Ready to release a baby tiger shark.

One of the most common questions that I had before I left concerned getting motion sick. Dare I utter the word… seasick. So far, I have been lucky… hmm, I can’t seem to find any wood around here to knock on. I started the voyage with what I consider to be a rational decision, take the Dramamine. We started with two days of beautiful weather. By the first sign of rough seas I had stopped taking the Dramamine so I went outside and watched the horizon for about an hour. I decided that watching the horizon on a beautiful day at sea had no drawbacks. I never did feel nauseaus. Some people recomended that I buy the accupressure bands which I did. When seas get rough and I am inside I will sometimes wear those. I have not been seasick, yet. I still take precautions like not doing computer work inside when in rough seas but so far I have been fine. In fact, as far as I know none of the volunteers or crew have been sick.

I cannot end this blog without acknowledging the stewards in the gally and the impressive menu available at each meal. I think that there are always three choices for a main dish and a variety of sides. Additonally, a salad bar is always available, snacks, and my favorite, ice cream.

Just one of three delicious options that night

Animals seen: sea turtle, dolphin, snake fish, spotted eel, barracuda, shark sucker. Sharks: sandbar shark, tiger shark, Atlantic sharpnose shark, scalloped hammerhead

shame faced crab

Did you know?

Most of the fish that we catch have parasites living in and on them?

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Elli Simonen: Data, Calibrating Data and Surveying, July 15, 2023

NOAA Teacher at Sea

Elli Simonen (she/her)

Aboard NOAA Ship Fairweather

July 10, 2023 – July 28, 2023

Mission:  Hydrographic Survey of the Pribilof Islands 

Geographic Area of Cruise: Pribilof Islands, Alaska

Date: July 16, 2023

Weather Data

Location: 55’21.02° N, 161’02.02° W

Outside temperature: 11°C

Water temperature: 10°C

True Winds:  337°, 6.5 kts

Skies: Overcast and Cloudy

Science and Technology Log

What is Surveying?

I was in port with the NOAA Ship Fairweather for a little under a week but right now we are en route to the Pribilof Islands.  During the time at port, the survey team surveyed surrounding areas, calibrated equipment and practiced troubleshooting survey systems. The goal of surveying is to gather the bathymetry data of the seafloor, or the depths and shape of the seafloor. 


Surveying equipment is located on NOAA Ship Fairweather as well as four smaller boats called survey launches, which each get deployed from the ship.  Depending on the mission, sea conditions and the project plan, the ship or launches may both be used, or a combination of both. 


Global Positioning System (GPS) records position. The Inertial Measurement Units (IMU) measures the motion of the ship.   Multibeam Echosounder (MBES) is when sound is pinged from a vessel to the seafloor and the time lapse is used to determine the depth of the seafloor.  MBES is a type of sonar that uses multiple beams to get a more complete picture of the seafloor with depths and characteristics.  After the data is pinpointed to a specific location, variability associated with tides is also taken into account by transforming the data vertically to the mean lowest low tide. Bathymetry data taken on NOAA Ship Fairweather as well as its four survey launches appears as strips on a map, as the ship or boat moves. 


Data is measured to the mean lowest low tide because that level of water is on average the lowest of any tide for a given area.  Using the lowest depth in navigation is conservative, thus allowing vessels to navigate safely through mapped waters. 

photo of two adjacent computer monitors with different views of the collected survey data imposed on charts or maps

Survey Data shown as green strips.

a small boat (a survey launch) mounted on the port side of NOAA Ship Fairweather, as seen from the deck in front of another mounted launch (only partially visible). Beyond the side of the ship, the still water of a bay extends toward the steep green hill that lines the far side. Another launch, already deployed, is visible on the water at a distance.

Survey launches being stored on NOAA Ship Fairweather as well as one deployed in the harbor

Elli stands on the deck of a small boat. She's wearing a life vest and her Teacher at Sea hat. We have a partial view of the launch's wheelhouse to her left and an electronic winch to the right. Behind Elli the waters are calm, and we can see mountains in the distance.

TAS Elli Simonen aboard one of the survey launches.

Calibrating the Data

During our time in port we took out some of the survey launches to perform a patch test; that is, calibration procedures to ensure the data we collect is as accurate as possible.  A correctly calibrated system will show the same mapping of the seafloor in repeated tests, without the influence of confounding variables – speed, direction and ship motion. In a patch test, time delay, pitch, roll and heading are calculated multiple times over different depths, obstructions and slopes on the seafloor and compared to known data.  The obstruction we surveyed was a shipwreck.

view of two computer monitors, two keyboards, and two computer mice on a desk

Planning the Patch Test

photo of a computer screen; it is difficult to see what is being displayed, but Elli has circled one area and added the label "shipwreck"

Map of the planned surveys for the Patch Test.

photo of a computer screen displaying bathymetric data. much of the area appears flat (colored teal blue) but there is a small, raised, orange portion in the shape of a ship lying on its side

Survey Data showing the Wreck

To correct for how the speed of sound changes in ocean water, during surveying every four hours Conductivity, Temperature and Depth (CTD) is measured.  The CTD measures Salinity and Pressure of the Water Column, aspects that can change the speed of sound.  The CTD is used to further calibrate data because different depths have different levels of salinity and temperature, and therefore distort how fast the sound travels. CTD data is used in post-processing to correct for any distortions.

a conductivity, temperature, an depth probe stored in front of a computer tower inside the survey launch's wheelhouse. the probe looks like a white cylinder strapped inside a metal frame that tapers at the top

CTD on the survey launches.

three crewmembers, wearing orange life vests and white hard hats, stand around a piece of equipment mounted at the corner of the aft deck of NOAA Ship Fairweather. a computer is mounted in a blue frame; above extends a blue boom and pulley. a coil of rope hangs on the side. Beyond the ship, the waters are gray with some caps, distant mountain ranges appear in shades of dark blue, and a cloudy, gray-white sky tops the picture.

Moving Vessel Profiler (MVP), a type of CTD that can be used while the ship is in motion, being deployed on NOAA Ship Fairweather by members of the surveying team.

Where does the data go?

Once the survey technicians gather bathymetry data, they still need to edit it before passing it along to National Centers for Environmental Information (NCEI), who package it for public view and is the data repository for environmental data in the U.S. and the U.S. Office of Coast Survey who create navigational charts. Editing the data involves rejecting spurious noise that MBES picked up that is out of range or incorrect.  This data then is transformed into charts and more standardized bathymetry data.

two people look at a computer screen in the computer lab. The survey tech, seated at the computer station, points toward multicolored swaths against a black background on the right monitor. Elli stands be hind him to view over his shoulder. On the desk are messy folders and papers, a small potted plant, and an action figure.

Survey Technician showing TAS Elli Simonen the process of cleaning survey data

Personal Log

Members of the survey team are all smart, respectful and patient and take the time to explain to me the science at play no matter how many questions I have.  I spend the majority of my day with the survey team but also explore other areas of the ship.  I have now been onboard for over a week and things are beginning to feel routine.  The sun does not set here until about 10:30pm and rises around 6am.  Meals are served at regular times and more importantly, at least to me, coffee is available 24/7.

a view of Elli's stateroom. To the left is a metal warddrobe and a metal sink. To the right is a filing cabinet, a simple bed, and the edge of a metal chest of drawers. There's an open porthole along the back wall, and light shines through it onto the wall, forming a bright circle above the bed.

This is TAS Elli’s room aboard NOAA Ship Fairweather at 9:45pm

view through a sea-sprayed porthole of water and mountains. the sun is low in the sky.

View out my window in the Gulf of Alaska.

Did you know?

screenshot of a political map of the continents of the world, with North America at the center. Neon green lines color the North American coastline and extend in webs throughout the rest of the ocean. the map is titled "Data Centre for Digital Bathymetry Viewer."

This map shows, in green, the areas of the world that have bathymetry data, from NCEI, https://www.ncei.noaa.gov/maps/iho_dcdb/

Animals Seen

an otter floats on its back in the water.

Otter swimming near NOAA Ship Fairweather

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Lisa Carlson: Where Did You Come From, Where Did You Go? July 13, 2023

NOAA Teacher at Sea

Lisa Carlson

NOAA Ship Bell M. Shimada

July 5, 2023 – July 19, 2023

Mission: Fisheries: Pacific Hake Survey (More info here)

Geographic Region: Pacific Ocean, off the coast of California

Date: July 13, 2023

– – ⚓ – –

Weather Data from the bridge:

July 11 (1200 PT, 1500 EST)
Location: 37° 46.7’ N, 123° 26.6’ W
43nm (50mi) West of San Francisco, CA

Visibility: 2 nautical miles
Sky condition: Overcast, fog
Wind: 20 knots from N 250°
Barometer: 1015.2 mbar
Sea wave height: 2-3 feet
Swell: 6-7 ft from NW 320°
Sea temperature: 12.2°C (57.2°F)
Air temperature: 12.7°C (57.9°F)
Course Over Ground: (COG): 270°
Speed Over Ground (SOG): 10 knots

July 12 (1200 PT, 1500 EST)
Location: 38° 06.8’ N, 123° 01.6’ W
7nm (8mi) North of Point Reyes Lighthouse, Inverness, CA

Visibility: 2 nautical miles
Sky condition: Overcast, fog
Wind: 12 knots from N 350°
Barometer: 1016.0 mbar
Sea wave height: 1-2 feet
Swell: 3-4 ft from W 280°
Sea temperature: 11.0°C (57.2°F)
Air temperature: 11.5°C (57.9°F)
Course Over Ground: (COG): 270°
Speed Over Ground (SOG): 10 knots

July 13 (1200 PT, 1500 EST)
Location: 38° 17.3’ N, 123° 06.1’ W
2.5nm (4mi) Southwest of Bodega Bay, CA

Visibility: 3 nautical miles
Sky condition: Few clouds, fog
Wind: 13 knots from NW 300°
Barometer: 1015.9 mbar
Sea wave height: 1-2 feet 1-2
Swell: 3-4 ft from NW 300°
Sea temperature: 10.7°C (51.3°F)
Air temperature: 13.7°C (56.6°F)
Course Over Ground: (COG): 340°
Speed Over Ground (SOG): 10 knots

– – ⚓ – –

In my July 6 post, I explained how NOAA Ship Bell M. Shimada is equipped to collect acoustic data in the form of echo grams and therefore find fish to trawl for. In my July 10 post, I explained how we get the fish onboard, and what we do with the sample once it is collected from the net. These entries described what work is done in the Acoustics Lab and the Wet Lab, but there is one more Lab onboard to explore and explain: the Chemistry Lab.

view down the starboard side of NOAA Ship Bell M Shimada shows a wooden nameplate (reading Bell M Shimada) on a railing, the fast rescue boat mounted aftward, and the Golden Gate Bridge in the background.
NOAA Ship Bell M. Shimada leaving Pier 30/32 in San Francisco, CA on July 5, 2023. (Just a nice photo taken by me that I wanted to include)

Science and Technology Log

Each morning after breakfast, we usually gather in the Acoustics Lab, determine what transect we are on, if we are inshore or offshore, and in some ways: hurry up and wait. Once certain patterns and blips show up on the echo grams, the Acoustics team talks with the bridge and may request to turn around and attempt a trawl. After all marine mammal observations are completed, the net is retrieved, and the samples are brought to the Wet Lab, we sort and collect data on the samples. These operations usually take place between 0800 and 2000. (8am to 8pm)

So what happens at night? In the Chemistry Lab, scientists work with the Deck and Surveys Departments to deploy a collection of electronic instruments and 12 Niskin bottles (open bottles used to collect and hold water samples, about one meter long) secured to a cylindrical frame called a rosette. It is deployed from the side sampling station instead of the stern. Scientists onboard NOAA Ship Bell M. Shimada use the instruments and collection of water samples in two ways: measuring Conductivity, Temperature, and Depth (CTD) within a water column to study oceanography, and collecting environmental DNA (eDNA).

photo of a large piece of sampling equipment on deck. a large white metal cylindrical frame houses a ring of perhaps ten tall gray canisters - the Niskin bottles. The bottles circle the conductivity, temperature, and depth probe, which is barely visible. Behind the frame, past the ship's rail, we see vivid blue water with a few white caps and a coastal mountain range beyond.

CTD Niskin bottles arranged on a circular rosette frame.

“Nighttime operations primarily consists of deploying the Conductivity-Temperature [-Depth] (CTD) rosette which gathers oceanographic data such as conductivity, temperature, dissolved oxygen, and chlorophyll fluorescence. The CTD can also be triggered to collect water at specific depths.”

NOAA Fisheries: “eDNA Part 2: There’s a Lot of Water in the Sea – and the Chemistry Lab”
NOAA Ocean Exploration: “What does “CTD” stand for?”

Conductivity, Temperature and Depth: CTD

CTD stands for conductivity (ability to pass an electrical current), temperature, and depth. Scientists use the rosette frame, which is attached to the ship by cables, and has the CTD and 12 Niskin bottles attached, to collect electronic data and multiple water samples.

“A CTD device’s primary function is to detect how the conductivity and temperature of the water column changes relative to depth. Conductivity is a measure of how well a solution conducts electricity and it is directly related to salinity. By measuring the conductivity of seawater, the salinity can be derived from the temperature and pressure of the same water. The depth is then derived from the pressure measurement by calculating the density of water from the temperature and the salinity.”

NOAA Ocean Exploration: “What does “CTD” stand for?”
Elysha, wearing an orange life vest and white NOAA logo hard hat, sits at a metal desk with two computer monitors and a keyboard. The monitors display data from the CTD. Elysha has her right hand on a computer mouse while her left grips a pen over a yellow legal pad. She is turning to smile at the camera.
Senior Survey Technician Elysha Agne gives commands to the Deck Department running the winch and cable to the rosette, and ensures quality data is being collected at each sampling depth.

“For more detailed analyses back in the lab, each of the large gray bottles captures a water sample at a different depth. The data provide scientists important information about the local aquatic environment.”

NOAA: “Photo story: Virtually cruise aboard a NOAA ship for a fish trawl survey”

Depending on the depth at which the vessel is currently operating, the rosette will descend to one to five predetermined depths (50m-500m) for sampling. For example, if the vessel depth reads 400m, water samples will occur at 50m, 150m, 200m, and 300m (more information in Table 1 below). A water sample is also taken just below the ocean surface using a through hull fitting, which allows seawater to be collected via a hole in the hull that feeds directly to the Chem Lab.

Table 1. Sample depths for eDNA. Two independent samples should be taken at each depth. The total ocean depth of location for the CTD cast determines the depths at which water samples will be collected. The rows of the table are labeled Sampling Depth (m) and the columns are labeled Topography depth of CTD cast.
Table 1 in Protocol manual, written by Chem Lab member and eDNA scientist Abi Wells.

While the rosette descends, data is recorded from multiple sensors and are later used by scientists to compare with Acoustic and Wet Lab data and compile and categorize new information from the survey. Pressure, depth, temperature, conductivity, salinity, oxygen, fluorescence, and turbidity were all being recorded during this leg of the survey mission.

photo of a computer screen displaying data. two graphs depict depth (m) on the y-axis and salinity or dissolved oxygen on the x-axes.
Program displaying data collected from the CTD rosette in real time.

Environmental DNA: eDNA

During the day, Hake stay in deeper waters, averaging around 200-350m, but at night the nocturnal feeders start their daily migration through the water column to shallower depths. They feed primarily on zooplankton, shrimp, myctophids (Lanternfish), and even young Hake at this depth. As Hake move throughout the water column, they leave behind DNA in the water that can be collected later as sort of a signature of their presence in that location. The collection, filtering, and preservation of sampled water in the ocean environment is categorized as collecting eDNA. This environmental DNA can be in the form of gametes (reproductive cells), fish scales, feces, etc.

Collecting water samples at different depths in the same vertical column can show what marine life was present at that location, and what depth they were at. I relate it to reviewing school security cameras or talking to other teachers at the end of the school day, to determine where a student was at a certain time and why.

The apparatus housing the CTD probe and Niskin rosette sits on deck. Abi, wearing a yellow hard hat, orange life vest, blue gloves and brown rubber boots, stands between the equipment and the rail of the ship to empty water from a Niskin bottle into a plastic bag. The profile of her face is mostly obscured by her long yellow ponytail.
Chem Lab member and eDNA scientist Abi Wells collecting a 2.5L water sample from a Niskin bottle after a successful CTD deployment.

When the rosette is back on deck, scientists use gloves and new collection bags called Whirlpacks, to collect approximately 2.5L of water from each 10L Niskin bottle. This process is conducted with a great emphasis on sterility, including wiping the bottle spigot with DNAway to remove any contaminants, using new materials, and not allowing fingers or the spigot to touch the collection bag.

White paper is taped down on a bench in the wet lab. On it are rows of water filtering cups mounted on gray horizontal pipes attached to hoses. Each filter cup is topped with a paper filter. Two have funnels attached; additional funnels, still sealed, line the workbench behind the filtering cups.
Sterile work site being set up to pour water samples into the cups and strain through the filters.
blue gloved hands pour water from a clear plastic bag into a funnel attached to a filtering cup. nearby, three plastic pitchers serve as holders for open plastic bags will filled with water.
Chem Lab member and eDNA scientist Abi Wells pouring a 2.5L water sample into the corresponding cup to strain through the filter.

Once the collection bags are filled and brought to the Chem Lab, filtration occurs using 1.0 micron filters. Although this size of filter, compared to smaller filters, allows some cells to pass through and not be collected, it is faster and results in less breakage of cells and loss of DNA. After 2.5L of the water sample is poured through individual filters for each depth sample, they are placed in pre-labeled (location and depth information) tubes with 2mL of preservative buffer. The tubes are stored at room temperature and away from UV light until NOAA Ship Bell M. Shimada is back in port and the samples can be further researched in on-land laboratories. Results from additional studies help to compile lists of marine life that was present in the water column and can be compared to acoustic data and species caught and logged in the Wet Lab.

– – ⚓ – –

Personal Log

So, there you have it. Three Labs onboard that conduct very different research, but fit together in the puzzle of Hake development, migration, diet, niches, ecosystem, biomass, and supporting sustainable commercial fisheries. Each additional piece of data; whether it be echo sounds, physical samples, eDNA, or CTD information, strengthens the others and helps to create a cohesive summary of the data. 

This was a lot to learn in the first few days, but as I’ve said before, all of the crew has been welcoming, supportive, and educational. Having a strong team that works together is priceless, and thoroughly noticed and appreciated. 

A few days into the mission my Mom asked me what the best part of my day was. I had three answers and haven’t had a day yet with only one answer. I replied that it was the great salmon dinner, clean clothes, and seeing Risso’s Dolphins for the first time.

Video taken by me of Risso’s Dolphins surfacing for air. (Plays on loop)

We are now a little more than halfway through the mission and it has truly flown by. We’ve shared riddles and daily Final Jeopardy questions. We’ve laughed over daily experiences and the faces Hake fish make. We’ve played music and watched baseball during dinner. We enjoy watching marine life and breathe in the salt air while strengthening our sea legs. Sometimes we just drink coffee and snack and enjoy this opportunity with each other, and that makes every part of the day the best part.

– – ⚓ – –

Did You Know?

Although Hake are occasionally cannibalistic, they are not at the top of their food chain. Humboldt Squid (Remember those 15 foot long tentacles in my Wet Lab post?), Dogfish Sharks, and marine mammals are all predators, as well as commercial fishing.
Today well over 100 Spiny Dogfish Sharks were inadvertently caught in the trawl, in the same location as the baskets of Hake we sampled from.
Maybe there were baby Hake fish in the sharks’ stomachs… we didn’t attempt to find out.

a white plastic basket of small sharks
Basket one of Spiny Dogfish
a white plastic basket of small sharks
Basket two of Spiny Dogfish

– – ⚓ – –

New Terms/Phrases

Although I had learned the terms a few days earlier, I got to help Wet Lab Lead Ethan Beyer collect otolith and stomach samples for the first time from a sub-sample of Hake the other day.

I watched and learned, then helped scan barcodes of otolith sample bottles, add 95% ethanol that is diluted 50/50 with water, and delicately pick up the ear bones with tweezers and place them in the bottle.

Additionally, each Hake in the sub-sample has its weight recorded, along with length, sex, and developmental stage. From that sub-sample, five stomachs are removed for later analysis, and five have their stomachs opened and their diet is recorded. We often find Lanternfish (Myctophids), Krill (Euphausiidae) and small Hake.

Two orange-gloved hands reach toward a fish on an electronic scale. the ichthystick measuring board is on the table in front of the scale. To the right, in the foreground of the photo, is a large styrofoam case holding small glass sample bottles upright. about two thirds are capped with black caps, while the rest are empty.
Wet Lab Lead Ethan Beyer weighing a Hake sample. Otolith tubes are in the foreground, those with lids have samples inside them and have been scanned into the database with other measurements and samples data from the Hake.
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Julie Hayes: Days at Sea! April 26, 2023

NOAA Teacher at Sea

Julie Hayes

Aboard NOAA Ship Pisces

April 22-May 5, 2023

Mission: SEAMAP Reef Fish

Geographic Area of Cruise: Gulf of Mexico

Date: April 26, 2023

Weather Data

Clouds: Scattered

Temperature: 77 degrees F

Wind: 12 kt.

Waves: 2-4 ft.

Science and Technology Log

Each day is started and then ended with a water sample from the ocean. The technology is called a CTD, but the procedure would be called a CTD cast (as if we were casting it in the ocean). CTD stands for conductivity, temperature, and depth. The CTD consists of a collection of electronic instruments that measure the properties of the water, including a laser that checks the clarity of the water. Sampling water bottles are connected to a metal frame called a “rosette”. This information on water characteristics is important to both the scientists and the survey mapping team that use cameras and sonar. This information lets them know how well the clarity of the water is and the speed of sound that helps with the depth finders and sonar.

The apparatus containing the conductivity, temperature, and depth probe sits on the deck of NOAA Ship Pisces, awaiting deployment.
CTD used to check water quality, conductivity, temperature, and depth.

Vocabulary Check

What is Conductivity?

Conductivity is a measure of the ability of water to pass an electrical current.

What is Salinity?

Salinity is the dissolved salt content of a body of water and is a strong conductor of water.

So why is it important for scientist to know what each of these are?

The higher salinity the water is, the higher the conductivity of electrical currents.

Temperature also plays a role in the density. Knowing each of these is important because it lets the scientists know the water quality at different depths so they can make adjustments to their cameras and sonar.

Jack Prior, Chief Scientist

Jack is a pretty “chill” guy, and I have enjoyed watching him in action the past few days. Jack is the field party chief of this mission which involves everything from planning the trip, to deciding the daily sampling locations, deploying cameras, mapping, and figuring out what to do when things go wrong. Jack is in charge of planning and submitting the protocol for the entire mission and also is responsible for the end reports of the mission. You will find Jack on this leg sitting behind multiple computers regulating and keeping a watchful eye on all of the important information regarding this mission. Jack attended the University of West Florida to get his degree in marine biology.

Jack sits at a computer desk with multiple monitors. He smiles at the camera, his right hand giving a thumbs up.
Chief Scientist Jack Prior

Student Question of the Day

Whenever I get a chance, I ask random crew members questions that my students back home were curious about. Here is how Jack answered some of the students’ questions.

Konnor, Nichole, Lillian ask: What degree do you have and what all is needed to do your job?

Jack started his major in biology and had originally planned on going on to be a pharmacist, but then moved to Florida where he ended up getting his degree in marine biology instead. Jack continued to also get his Masters at the University of West Florida, too. Jack changed his career path because he enjoyed marine life. Volunteer work is crucial to get experience, and can benefit you on becoming more diverse when it comes to getting a job in marine biology.

Alyson asks: What would be your dream job?

Someday Jack wants to explore the seafloor in a submarine.

Blake, Sailor, Lilli, Jenna ask: What is your favorite food on the ship?

Taco Tuesdays seem to be a huge hit on the ship, as well as Friday pizza day.

Auburn, Ashton M., Karson, Liam: What would you consider to be the coolest marine life you have seen?

Seeing large diverse reef habitats is what Jack says he finds the most interesting, especially uncommon invertebrates that you’d never see on the beach.

Jaxon and Dwight: Can you be on the ship if you have health issues and what happens if there is a medical emergency?

The ship is a pretty confined space with steep stairs, uneven footing, areas you have to be able to step over, and have the ability to carry heavy weight. If there is ever a medical emergency, the ship works alongside the United States Coast Guard to get them the help they need. However, the ship is great working with all issues and plans accordingly to those who may have special diet restrictions.

Personal Log

Well, I will say that I am getting better at having my sea legs but that is still a work in progress. I have really enjoyed getting to understand the life on this ship, and I am just amazed at how diverse everyone is and yet still make this an amazing environment. It has taken me a few days to get the hang of where things are and to get out of my comfort zone to ask what I feel like has to be a million questions about everything. I have really enjoyed getting to hear and learn about the crew’s background and how they ended up on NOAA Ship Pisces. I greatly appreciate their willingness to answer my questions, even though I am sure I am in their way at moments. Everyone has a job to do and work different hours and shifts. It is great to see how they all respect each other’s space and sleeping hours.

There is so much science around me that I never knew existed, and I am shocked on how much technology is actually being used and heavily relied upon. Today was the first day the waves were calm enough that I was able to go out on the stern (learning names of different areas of the ship) to work on the blog and soak up a little bit of Sun. It was nice to be able to get some fresh air. The food has been amazing on the ship. I love how everyone is so courteous by thanking the cooks, as well as cleaning up after themselves before leaving the mess. The mess is the area in which we eat and the kitchen is called the galley. It has taken me a few days to understand the boat “lingo” but I am starting to catch on. The stairs are pretty steep, and everyone on board says to use 3 points of contact when walking. This is so that if they hit a wave while walking you are more stable. I could definitely see this being an issue going up and down the stairs. The doors are super heavy and I am still learning how to get those twisted and sealed tight the first time I close it (I am getting there).

A view of the mess: that is, the ship's the dining area. At the moment, it is unoccupied. There are five long tables, bolted to the floor, covered in blue vinyl or plastic table clothes. Black chairs surround each one. The chair's legs are all capped in cut-open tennis balls. The tables are supplied with condiments and paper towel holders. A large television screen mounted on the wall shows a football game.
The mess where we eat. It is spotless and a great size to fit everyone on board.

A staircase, as seen looking down from the top stair. There are railings and anti-slip applications.
A heavy metal door, with rounded edges, and a steering-wheel shaped handle. The door is stamped "Keep Closed."
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George Hademenos: A Day in the Life…of a Marine Science Researcher, August 25, 2022

NOAA Teacher at Sea

George Hademenos

Aboard R/V Tommy Munro

July 19 – 27, 2022

Mission: Gulf of Mexico Summer Groundfish Survey

Geographic Area of Cruise: Eastern Gulf of Mexico

Date: August 25, 2022

In this post, I would like to walk you through my interactions and observations with the science research being conducted aboard the R/V Tommy Munro, in particular, the steps that were taken during a trawling process. The entire process involved three stages: Preparing for Sampling, Conducting the Sampling, and Analyzing the Sampling with each stage consisting of six distinct steps.

View the following steps in an interactive tour here: Trawl Sampling Process (Genially)

I. Preparing for Sampling

Step 1: The ship travels to designated coordinates for sampling sites as determined for the particular leg of the Survey by SEAMAP (Southeast Area Monitoring and Assessment Program).

screenshot of a computer screen showing the path that R/V Tommy Munro traveled among sampling sites. The ship's path is a bold blue line connecting sample sites marked in yellow. It's superimposed on an electronic nautical chart. This survey occurred southeast of Florida's Apalachicola Bay and St. George Island.
Ship Transport to Sampling Site

Step 2: Once the ship reaches the site, a Secchi disk is attached to a cable and lowered into the water off the side of the ship to determine visibility. When the disk can no longer be seen, the depth is recorded and the disk is raised and secured on ship. 

a scientist wearing a life vest stands on a small grated platform that has folded down off the fantail of R/V Tommy Munro. With his left land, he grasps a cable hanging from an A-Frame that extends out of the photo. The cable is attached to a white disk, about the size of an old record, with a weight underneath.
Deployment of Secchi Disk

Step 3: A CTD (Conductivity, Temperature, and Depth) unit is then prepared for deployment. It is a rectangular chamber with sensors designed to measure physical properties of the water below including dissolved oxygen, conductivity, transmissivity, and depth. 

a conductivity, temperature, and depth probe, mounted inside a rectangular metal cage about 1 foot square and about 3 feet high, sits on deck. a crew member wearing white shrimp boots hooks a cable onto the top of the CTD frame. Another person, mostly out of frame, touches the CTD frame with their right hand, covered in a blue latex glove.
Preparation of CTD Unit

Step 4: The CTD unit is powered on and first is submerged just below the surface of the water and left there for three minutes for sensors to calibrate. It is then lowered to a specified depth which is 2 meters above the floor of the body of water to protect the sensors from damage. 

the CTD unit, attached to a cable, sinks into dark blue water.
Deployment of CTD Unit

Step 5: Once the CTD unit has reached the designated depth, it remains there only for seconds until it is raised up and secured on board the ship.  

a science team member, wearing a blue hat, a blue life vest, and blue latext gloves, stands on the deployment platform out the back of R/V Tommy Munro. He grasps the top of the CTD frame as a cable lifts it back out of the water.
Recovery of CTD Unit

Step 6: The CTD unit is then turned off and the unit is connected through a cable to a computer in the dry lab for data upload. Once the data upload is completed, the CTD unit is flushed with deionized water using a syringe and plastic tubing and then secured on the side of the ship.   

the CTD unit sits on deck, now connected to a computer via a cable to upload the data it collected.
Data Upload from CTD Unit

II. Conducting the Sampling

Step 1: The trawling process now begins with the trawl nets thrown off the back of the ship. The nets are connected to two planks, each weighing about 350 lbs, which not only submerges the nets but also provide an angled resistance which keeps the nets open in the form of a cone – optimal for sampling while the ship is in motion.

a view of the fantail of R/V Tommy Munro, from an upper deck. we are looking through the rigging of the trawl frames. two large planks rest on the lower deck, connected to ropes and lines. the trawl net, connected to the planks, extends out the back of the fantail. It is just visible below the surface, a turquoise-colored cone submerged in a blue sea.
Preparation of the Trawling Process Part 1
another view of the fantail of R/V Tommy Munro from an upper deck, through extensive rigging and frames. the trawl net is further extended; now the large planks are lowering off the back deck as well, suspended by lines connected to a pulley in an A-frame. it is a clear day and the water is very smooth.
Preparation of the Trawling Process Part 2

Step 2: Once the trawl nets have been released into the water from the ship, the ship starts up and continues on its path for 30 minutes as the nets are trapping marine life it encounters.

a view of the fantail of R/V Tommy Munro from an upper deck. the trawl net is fully deployed and no longer visible. a crew member sweeps the deck.
Onset of the Trawling Process

Step 3: After 30 minutes has transpired, a siren sounds and the ship comes to a stop. The two weighted planks are pulled upon the ship followed by the trawl nets.

a view of the A-frame at the fantail R/V Tommy Munro as the trawl net rises from the ocean. The two spreader panels are suspended from separate lines running through the central pulley. behind those, the top of the trawl net is visible above the water. a crew member guides the spreader doors with his left hand, holding the lines with his right hand.
Conclusion of the Trawling Process Part 1
the spreader doors are now resting on the fantail deck again. two crewmembers, wearing life jackets, pull the trawl net back on board.
Conclusion of the Trawling Process Part 2

Step 4: The trawl nets are raised and hoisted above buckets for all specimens to be collected. Then begins the process of separation. In the first separation, the marine life is separated from seaweed, kelp and other debris. The buckets with marine life and debris are then weighed and recorded.

a crewmember (only partially visible) empties the contents of the trawl net into a blue plastic basket. it looks like it's mostly sargassum.
Content Collection from the Trawl Part 1
four plastic baskets on deck hold the sorted contents of the trawl. one has larger fish; another contains only a single fish; a third is a jumble of seaweed and sargassum, and may represent the remainder to sort; the contents of the fourth are not visible. a crewmember wearing a life vest and gloves leans over the baskets. another crewmember, only partially visible, looks on.
Content Collection from the Trawl Part 2

Step 5: The bucket(s) with marine life are emptied upon a large table on the ship’s stern for separation according to species.

a pile of fish on a large metal sorting table. we can see snappers, a trigger fish, and many lionfish. a stack of white sorting baskets rests adjacent to the pile.
Separation Based on Species Part 1
a gloved hand reaches toward the pile of fish on the metal sorting table. (this photo was taken from the same vantage point as the previous one.)
Separation Based on Species Part 2

Step 6: Each species of marine life is placed in their own tray for identification, examination, and measurements inside the wet lab. 

two gloved crewmembers sort fish into smaller white baskets on a large metal sorting table. the table is on the back deck of the ship, and we can see smooth ocean conditions in the background. the crewmember in the foreground considers a small fish he has picked up from the remaining unsorted pile. the other crewmember looks on.
Species Sorted in Trays Part 1
a close-up view of the sorting basket containing only lionfish.
Species Sorted in Trays Part 2

III. Analyzing the Sampling

Step 1: After all species were grouped in their trays, all trays were taken into the wet lab for analysis. Each species was positively identified, counted, and recorded.  

a direct view of three fish of different species, lined up on the metal sorting table. the third is a spotfin butterflyfish.
Tray Transport to Wet Lab

Step 2: Once each species was identified and counted, the total number of species was weighed while in the tray (accounting for the mass of the tray) and recorded on a spreadsheet to a connected computer display system.   

a view of a scale.
Total Weight Measurements

Step 3: For each species, the length of each specimen was recorded using a magnetic wand with a sensor that facilitated the electronic recording of the value into a spreadsheet.   

two hands, wearing latex gloves, measure a small lionfish on the electronic measuring board. the scientist holds the fish against the board with his left hand and with his right hand marks the length with the magnetic stylus.
Individual Length Measurements

Step 4: Weights of the collected species were recorded for the first sample and every fifth one that followed.   

the gloved arm places the small lionfish on the scale behind the fish measuring board.
Individual Weight Measurements

Step 5: If time permitted between samplings, the sex of selected specimens for a species was determined and recorded.   

gloved hands cut into a small lionfish to remove the fish's gonads.
Individual Species Sex Identification

Step 6:Once the entire sampling was analyzed, selected samples of specimens were placed in a baggie and stored in a freezer for further analysis with the remaining specimens returned to a larger bucket and thrown overboard into the waters. The separation table was cleaned with a hose and buckets were piled in preparation for the next sampling. 

view out the fantail of R/V Tommy Munro from the lower deck. the trawl net and spreader doors lay on the deck, not currently in use. the sun shines on calm seas.
Finalize Process and Prepare for Next

In this installment of my exercise of the Ocean Literacy Framework, I would like to ask you

to respond to three questions about the fifth essential principle (The ocean supports a great diversity of life and ecosystems.), presented in a Padlet accessed by the following link:

https://tinyurl.com/427xp9p3

Remember, there are no right or wrong answers – the questions serve not as an opportunity to answer yes or no, or to get answers right or wrong; rather, these questions serve as an opportunity not only to assess what you know or think about the scope of the principle but also to learn, explore, and investigate the demonstrated principle. If you have any questions or would like to discuss further, please indicate so in the blog and I would be glad to answer your questions and initiate a discussion.