chem lab – NOAA Teacher at Sea Blog

July 13, 2023July 19, 2023

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

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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

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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?”

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.

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. — Sterile work site being set up to pour water samples into the cups and strain through the filters.

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.

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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.

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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

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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.

May 7, 2016August 21, 2021

Nichia Huxtable: Life on board, you won’t be bored!, May 6, 2016

NOAA Teacher at Sea

Nichia Huxtable

Aboard NOAA Ship Bell M. Shimada

April 28-May 9, 2016

Mission: Mapping CINMS Geographical area of cruise: Channel Islands, California Date: May 6, 2016

Weather Data from the Bridge: 2-3 ft swells; storm clouds over land, clear at sea

Science and Technology Log

Dismantling the REMUS 600 AUV for its trip home — Goodbye, AUV. Until we meet again.

The AUV is no longer my favorite thing on Shimada. As I write this, it is being dismantled and packed into shipping boxes for its return trip home to Maryland. To keep a long, sad story short, the AUV had a big electrical problem that was fixed, but when the scientists turned it on for a test run, a tiny $6 lithium battery broke open and oozed all over the motherboard. Game over for the AUV. So now my favorite thing on Shimada is the ice cream.

Personal Log

Enough about science and technology for now. I bet you’re really wondering what it’s like day in and day out on board Shimada. Well, my intrepid future NOAA crew members, this blog post is for you! We’ll start what’s most important: the food.

Dinner options onboard Shimada.

Cooking in the galley

Lunchtime!

Need some tea

Breakfast, lunch, and dinner are all served at the same time everyday. The food is prepared in the galley and everyone eats in the mess. Beverages, cereal, yogurt, fruit, snacks, the salad bar, and ice cream are available 24 hours a day, so there is no need to ever be hungry. Not all ships are the same, however. In one of the many anecdotes told to me by master storyteller Fabio Campanella, an Italian research ship he once worked on served fresh bread and authentic pizza everyday…sign me up for that cruise!

DSC_0470[1] — Unlike the AUV, the ice cream freezer never disappoints

Next, you’re probably wondering where everyone sleeps. Sleeping quarters are called staterooms and most commonly sleep two people, although larger staterooms might sleep four. Each stateroom has its own television and a bathroom, which is called a head. As you can see in the photo, the bunks have these neat curtains that keep out the light in case your roommate needs to get up at 1 a.m. for the night-shift.

Stateroom on NOAA Bell M. Shimada

Stateroom on NOAA Ship Bell M. Shimada

Stateroom hallway on NOAA Ship Shimada

"Working — Working in the Acoustics Lab on *Shimada*

The Shimada has lots and lots of work and storage rooms, each serving a different function. There is a wet lab, dry lab, chem lab, and acoustics lab for doing SCIENCE (woohoo!), as well as a tech room for the computer specialist (called an ET), storage lockers for paint, cleaning supplies, and linens, plus other rooms full of gear and machinery. There’s also a laundry room, so you can take care of your stinky socks before your roommate starts to complain!

Gear storage on NOAA Sip Shimada

Dry Lab on NOAA Ship Shimada

Laundry room on NOAA Ship Shimada

Electrical technician’s office on Shimada

Computer room for Shimada’s crew

An office for a NOAA Corps officer on Shimada

Trash on board is separated into recyclable bottles and cans, food waste, and trash. The food waste is ground up into tiny pieces and dumped in the ocean outside of the sanctuary, while the trash is INCINERATED! That’s right, it’s set on fire…a really, really, hot fire. Ash from the incinerator is disposed of onshore.

Another important part of the ship is the bridge. Operations occur 24 hours a day, so the ship never sleeps. Officers on the bridge must know what is happening on the ship, what the weather and traffic is like around the ship, and they must make sure to properly pass down this information between watches. The bridge has radar to spot obstacles and other ships, a radio to communicate with other ships, and a radio to communicate with the crew and scientists.

"Looking — Looking for wildlife on the NOAA Ship *Bell M. Shimada*

3rd Engineers E. Simmons and C. Danus

Painting the deck of NOAA Ship Shimada

Last, but not least, is the lounge that comes complete with surround-sound, a big screen TV, super-comfy recliners, and about 700 movies, including the newest of the new releases.

Did you know?

A female elephant seal was once recorded diving underwater for two continuous hours (they usually stay underwater for 1/2 hour); the deepest recorded dive was by a male and was 5,141ft.

Stay tuned for the next post: Multibeam? You Mean Multi-AWESOME!

September 16, 2014April 28, 2021

Sue Zupko, Diversity, September 13, 2014

NOAA Teacher at Sea
Sue Zupko
Aboard NOAA Ship Henry B. Bigelow
September 7-19, 2014

Mission: Autumn Bottom Trawl Leg I
Geographical Area of Cruise: Atlantic Ocean from Cape May, NJ to Cape Hatteras, NC
Date: September 13, 2014

Weather Data from the Bridge
Lat 35°38.1’N Lon 074°50’W

Present Weather PC
Visibility 10 nm
Wind 220° 5kts

Sea Level Pressure 1016.6
Sea Wave Height 1-2 ft
Temperature: Sea Water 27.2°C
Air 28.4°

Science and Technology Log

If you want to learn about biodiversity, come on a NOAA Fisheries Cruise. We hear about the numerous fish in the ocean, but nothing really makes it come alive as does seeing it. There are pockets of animals in each of the strata. Different depths have different temperatures, bottom type, plants, etc. Let me explain a bit about my watch and what we are doing.

I was amazed by the diverse sounds. A crow. A jaguar screaming. A frog croak. Sloshing. Thumps. “Fine”. A ringing telephone. A whip cracking. A waterfall. Thunder. A pinball machine. Music playing. Some people singing along. Laughter. Chatter. The list is seemingly endless.

There are platforms we each stand on along the conveyor belt which brings the fish in to be processed from the checker on the deck. The first person in line and pulls out fish which might be harmful such as electric rays and large sharks. Hope she gets the Lionfish as well. Don’t want to be stuck by those spines. As the animals come down the line we sort them based on the instructions of the watch chief who has been outside to see the catch, comparing what we have.

Heath, our watch chief, programming our catch

Heath is my watch chief. So, he suits up in his PFD (life jacket–personal flotation device) and hardhat(helmet) to see what was put in the catcher and then tells us what to leave on the conveyor belt as it goes by. That is usually what is most numerous. Sometimes it’s trash, such as starfish and jellies , other times it’s Loligo squid One night we had a huge amount of scallops so a seemingly endless stream of scallops passed us by. I love eating scallops. It is amazing to view them up close. They have numerous eyes lining the inside of the shell.

Atlantic Calico Scallops Argopecten gibbus — Atlantic Calico Scallops (Argopecten gibbus)

Starfish (Astropecten) and jellies on the conveyor

Containers Small, Gallon, 10 Gallon, 1.47 Cubic Feet Baskets

Once the animals are sorted by species into containers, they then make their way down the conveyor to Heath. Heath scans the container which makes a telephone ringing sound. He enters/selects the name of the animal on his monitor (crow caws–actually except for animal id every time he does something his “ok” sound is a crow), checks our work to be sure the animals in the container are all the same, weighs the catch of that entire species, and sends the container on its way down the conveyor belt.

There are three processing stations along the conveyor. I have mostly worked with Nicole this week so far. She is a fabulous teacher. Very patient with my inexperience and points out when I do something correctly. That way I will repeat things the correct way. She also suggests better ways when I struggle. Heath explained that we process the containers with the most organisms in them first so no one is stuck at the end of the line doing a large container of animals when others are cleaning up. Some containers might just have one animal. This system works pretty well since everyone seems to finish at the same time.

There are two people at each of the three stations. One person is the fish processor and the other is the recorder. First, the processor scans the container. It buzzes and identifies the container and what the animal is. I was very proud of myself today. I have been assigned to work with Larry now. He left me on my own to process (though he was watching from across the conveyor). When I checked to see how to measure the fish I was working with, it said to measure the width of the carapace. Carapaces are found on turtles or crabs. It is their hard shell. I had a tiny fish. On a rocking ship, it is easy to push a wrong button on a screen and this container had the wrong name on it. Easy fix. Sent it back for reassigning a species and I picked it up when it came by again. “Nice catch on that,” Larry said. Made me feel proud that I recognized how to use the equipment, recognize certain species, and fix the problem. Nicole said if we make a mistake, it can always be fixed. Remember, we learn from mistakes. That’s what we stress in my classroom. Try it. If you fail, learn from the mistake and redo. That works with adults as well.

My favorite sound is the pinball machine that says the weight has been recorded. If the animal needs more processing than just being weighed, there is a sound (a jaguar scream or a whip cracking) to tell the team what to do. Sometimes we need to put the animal in a jar to be preserved. )

Other times we need to take a photograph, or it will ask what the animal’s sex is. We have had a lot of requests for fish to be frozen for study back in the lab. These are bagged and put into a large freezer for the requesting scientist. The most common seems to be getting the otolith, the part of a fish that aids it in orientation, balance, and sound detection. These are tiny in most fish and require a little manila envelope that we put a sticker on identifying it. These special requests from the computer are all preset requests from scientists working in a scientific area back on shore.

Chemicals preserve the speciman for further research.

The sound of the waterfall is the constant stream of salt water running down a shoot onto the floor. This picks up animals and trash that have dropped and washes them down drains or out the scuppers (small rectangular openings on the bottom of the wall at the floor which opens to the outside) on the sides of the room. The water is very warm and I’ve noticed that the sea water has been warmer than the air temperature. Another sound is the water sloshing around, similar to the sound in a bathtub when you move the water.

Saltwater helps keep the floor clean in the wet lab.

When I began this blog I was sitting on the O2 deck at a small table under the stairs. We kept changing direction at relatively slow speeds. I have learned that we were using the multi-beam sonar to look at the bottom to find an acceptable spot to trawl. I was excited to sit outside to work and gaze out over the ocean. During that time I spotted three pods of dolphins swimming. John Galbraith, our chief scientist, and I discussed last night how if you aren’t spending time observing something you will miss many things. So true. If I wasn’t observing the ocean frequently, what are the odds I would see a whale?

Meet Scientist Nicole Charriere

Nicole has been my mentor for the past week. She is a sea-going biological technician, sailing about 130 days out of a year. She usually is on scallop surveys, but seems pretty expert in fish, shrimp, and clams as well. Her job on this cruise is to help provide leadership. There are several volunteers on this cruise, me included, and some are novices just learning about fish. She explains about the protocols (a formal set of rules and procedures to be followed during a particular research experiment).

What Nicole likes about her job is she isn’t in an office all the time. Trawls are different every day. No two tows are the same, and there are a huge variety of species. She really enjoys the diversity of people she gets to work with. There are different scientists and crew members to meet each time. She is a scuba diver and knew she wanted a career with NOAA when she graduated college. She had a job on a commercial fishing vessel and was contacted by NOAA. Someone probably noticed her great work and let someone hiring at NOAA know.

There is something very ironic about Nicole working on a fishing vessel. She doesn’t like sea food. She recognizes its importance and that it is important for the world to have a reliable food source, but it isn’t her favorite.

Nicole’s advice to my students is to talk to everyone and learn. Make connections about what you learn. Work hard, since working hard and getting along with people on a team gets you noticed and when a job comes available, guess who gets hired? Not the person who is difficult to work with and is late constantly.

Nicole has an active lifestyle. In addition to scuba diving, she roller blades, plays guitar and keyboard, and plays soft ball and soccer. She knows a lot of people who are still looking for the perfect career for them. Nicole is thrilled to have found her dream job so early in her life. I am grateful to have had the opportunity to work with this eloquent, interesting, and fun scientist.

Personal Log

Yeah! The captain put out an all-call and said there were pilot whales off the port side. We had just finished our watch and I headed out to the port side. There they were. I said, “They look like dolphins.” Both are cetaceans, both hunt fish, both are smart, both have a dorsal fin that sticks up out of the water. I believe I saw some earlier. One remained in one place with a huge fin sticking up. I hadn’t seen a dolphin do that before. They might swim in a circle going after a fish, but this behavior was a bit unusual. At the time I just thought how big that dolphin was. Now, upon reflection, I believe that was a Pilot Whale. That was so kind of the captain to announce the whales’ presence. The XO, Chad Cary, told me that Pilot Whales got their name since they are indicators of where the fish were. The fisherman just piloted their boats to where those whales were. Interesting way to get a name. Obviously, I’m pretty excited. Did you say I would see a whale on that poll?

Did You Know?

CTD stands for conductivity, sea water temperature, and depth (of where measurements are taken).

According to NOAA, salinity measurements can be used to determine seawater density which is a primary driving force for major ocean currents which help drive the Earth’s climates. This seems analogous (similar) to the causes of wind when air moves from warm air to cold and back again.

Question of the Day

The CTD protocol states that it must stop 5 meters from the bottom to take its measurements. If the CTD descends at 37 m/s, how long will it take for the CTD to get in position to measure its readings and return to the surface if the bottom is 338 m from the surface?

Vocabulary

Salinity: The percentage of salt in the water. Think of it as if you had 1000 grams of water and mixed one gram of salt into it. This would be 1 ppt salinity. Our ocean averages about 35 ppt salinity. Our CTD found that the ocean’s salinity where we tested today was 34 ppt.

Something to Think About

We actually let out 361 m of wire with the CTD, but the bottom was only 338 m. Why did we let out more wire than the distance to the bottom when we dropped the CTD?

Animals Seen Today

Balloonfish Diodon holocanthus — Balloonfish (Diodon holocanthus)

Longnose Greeneye (Parasudis truculenta)

Lancer Stargazer (Kathetostoma albigutta)

July 8, 2012August 11, 2021

Stacey Jambura: The Adventure Begins, July 8, 2012

NOAA Teacher at Sea

Stacey Jambura

Aboard NOAA Ship Oregon II

July 6 – 17, 2012

Mission: SEAMAP Summer Groundfish Survey

Geographical Area of Cruise: Gulf of Mexico

(You can also view the NOAA ShipTracker here: http://shiptracker.noaa.gov/shiptracker.html)

Date: July 8, 2012

Weather Details from Bridge: (at 18:45 GMT)

Air Temperature: 29.50 ◦C

Water Temperature: 30.70 ◦C

Relative Humidity: 66%

Wind Speed: 1.52 kts

Barometric Pressure: 1,017.82 mb

Science and Technology Log

Virtual Tour of the Oregon II

I know many of you may have never been on a ship before and are probably curious to know what it is like to be aboard the Oregon II. I’m going to take you on a little virtual tour, but first you will need to know some common terms that are used to refer to certain areas on the ship.

Ship Term	What It Means
Bow	The front of the ship.
Stern	The back of the ship.
Starboard	The right side of the ship when facing the bow.
Port	The left side of the ship when facing the bow.
Forward	The direction towards the bow of the ship.
Aft	The direction towards the stern of the ship.
Bridge	The location of the command center for the ship.
Galley	The kitchen.
Mess Hall	The dining area.
Head	The bathroom.
Stateroom	Where crew members sleep.

On Deck

The Bow

At the bow of the ship is where most of the scientific collection equipment is deployed/released. The CTD (conductivity, temperature, depth), the neuston net, and the bongo nets. (I will talk about each one of these in upcoming blogs.) There are several large cranes that help lift these up off the deck and swing them over the edge of the ship to be released into the water. When you are at the bow and the cranes are running, it is very important to keep yourself safe. Everyone who is at the bow when the cranes are operating is required to wear a hard hat and a PFD (personal floatation device). You never know if a cable will snap or the wind will swing the equipment towards you. There is a sensor on the PFD that is activated when large amounts of saltwater touches it, like if you were to fall overboard. Once salt water touches the sensor, the PFD will inflate and keep you afloat until you can be rescued.

The Stern

At the stern is where the samples from the neuston cod end and the bongo cod ends are collected and preserved in jars for scientists to examine at a lab. This is also where the large trawling net is deployed. The scientists spend most of their time at this part of the ship.

What Makes the Ship Sail?

Bridge

The bridge is where the officers of the Oregon II work. It is located toward the bow of the ship. The bridge has all of the navigation tools necessary to steer the ship to the next sampling station. There is also a lot of weather equipment that is monitored and recorded throughout the day. The bridge is where you’ll find the best views of the ocean because it is almost completely surrounded by windows and it’s higher than any other room on the ship.

Chart Room

This room is where all of the maps are stored. While there are more technologically advanced methods used for navigation on the ship located in the bridge, it is important to have physical maps on hand to refer to, especially if the instruments stop working for any reason.

Engine Room

Before we untied our ship from the dock I received a full tour of the engine room. This is where the heart of the ship is. Everything in the engine room powers the ship. Our water is even purified down here using reverse osmosis (passing water through a membrane to filter the water). Because of this machine, we can filter salt water into fresh water to use on the ship.

It was great to venture down to the engine room before we set sail because I was told that it can get up to 110 degrees when the engines are running! It is a large space, but it feels small because of the large equipment. There are two of everything, which is especially important if something needs repair. Below is a picture of the two engines. The other is a picture of one of the generators.

Living on a Ship
Stateroom

My stateroom is compact, but its main purpose is for sleeping so size isn’t really an issue. There is a bunk bed, a sink with a mirror, latching drawers for clothes, and a hide-away desk. There is also a compact tv that is attached to the bottom of the top bunk and folds up when it is not in use. I only use the room to sleep and get ready for my shift because my bunkmate works the opposite watch shift as mine (midnight to noon), and I want to be the least disruptive as possible. After 12 hours shifts, sleep is really needed and helps reenergize you in time for the next watch.

The Head

The head is the same as a bathroom. On the Oregon II there are private and communal heads. The private heads are for the officers and are typically connected to their staterooms. The communal heads are open for any crew member to use. There are also communal showers for the crew to use. All of the toilets use salt water that is pumped onboard. The reason fresh water is not used is because it is a precious source on the ship and is not readily available from the ship’s surroundings. The sinks, showers, drinking fountains, and ice machines all use fresh water. Fresh water on the ship should never be wasted. Water for the sinks is timed so that there will never be a faucet that is accidentally left on. Showers are to be kept to a maximum of 10 minutes, though it is encouraged that they be even shorter.

Galley and Mess Hall

This is one of my favorite places. The galley is where our ship’s cooks prepare all of the wonderful food for the crew. The mess hall is where we all eat during meal times. During meal times it can be quite crowded in the mess hall as there are only 12 available seats and over 30 crew members onboard who are ready to eat. There is an “eat it and beat it” policy to help ensure that everyone who comes down to eat will be able to find a spot. Despite this, it is still a great way to converse with the crew and talk about events from the day before giving up your set to another hungry crew member.

Crew Lounge

This is the place where crew members who have some down time can gather and socialize, though down time can be rare. There is satellite tv, a couple of computers, and hundreds of movies to choose from. Some available movies haven’t even been released onto DVD for the common household yet, but they are available to the military. They do this because not everyone has access to current movies when they are away from home for extended periods of time. All of the DVDs are encrypted and can ONLY work on the machines aboard the ship. I was excited to find a copy of The Hunger Games and I plan on trying to watch it before my trip is over.

Labs on the Oregon II

The Wet Lab

The Wet Lab is where all of the samples from the groundfish trawls are sorted, counted, measured, weighed, and sexed (gender identified). Buckets filled with animals from the nets are dumped onto a large conveyor belt and spread out to make sorting the different species out into individual baskets easier. Everything in the wet lab can get wet except the sensors connected to the machines. We need to be cautious around the sensors when we are cleaning up after a sampling so as not to get water in them.

The Dry Lab

The Dry Lab is where all of the computers are located that record all of the data from the samplings. As the name of this lab states, everything in it is dry. Water should never come into contact with the equipment in here because it can seriously damage it. In between samplings, this is typically where the scientists gather to wait for arrival at the next sampling station.

The Chem Lab

This is where all of the plankton samples are stored. It is also where water samples taken from the CTD are tested for dissolved oxygen (DO). The CTD does have its own DO sensor, but it is always best to test something more than once to ensure you are collecting accurate data.

Personal Log

Day 1 – July 5th

I arrived in Gulfport/Biloxi, Mississippi late in the afternoon of July 5th. The chief scientist, Brittany Palm, met me at the airport and drove me over to the Port of Pascagoula where the Oregon II was docked. We met up with two college volunteers, Kayla and Andrew, and got a quick tour of the ship (the air conditioning was out!) before we headed over to a wonderful local barbecue restaurant. We returned after dark and were welcomed with a fixed AC! I unpacked my belongs into my latched drawers and made up my bunk bed up so that everything would be in place when I was ready to hit the sack. It took a couple of nights for me to get use to the sounds of the ship, but now I hardly notice them.

Day 2 – July 6th

When I woke up the next morning, I decided to venture out into downtown Pascagoula which was only a 5 minute walk away from the ship. It is a quaint area with little shops and restaurants. I met up with the two volunteers and we picked a business that had the best of both worlds, a restaurant and a shop, to have a wonderful breakfast. We had to be back on the ship by 12:30 for a welcome meeting, but we took some time to snap a few pictures of our floating home for the next 12 days. We were underway shortly after 2 pm (1400 hours in military time). It was fun to watch our ship depart from the dock and enjoy the light breeze. It wasn’t long until we had another meeting, this time with the deck crew. We learned about the safety rules of working on deck and discussed its importance. The rest of the afternoon was spent relaxing and getting my sea legs. The gentle rocking does require you to step carefully, especially when you have to step through the water tight doors!

Day 3 – July 7th

Our first day out at sea was slow to start. We didn’t reach our first sampling station until early in the morning on the 7th, even though we left the Oregon II’s port in Pascagoula mid-afternoon on the 6th. I was sound asleep when we arrived because my shift runs noon to midnight every day, so my first sampling experience didn’t happen until almost 24 hours after we set sail. This was nice because it gave me time to explore the ship and meet some of the crew.

Right after lunch I got to jump right in and help finish bagging, labeling, and cleaning up the wet lab for the team that was just finishing up their shift. After we had finished it was time to conduct my first plankton sampling. We went out on deck at the bow of the ship to prepare the CTD (conductivity, temperature, depth) device for deployment/release. After the CTD was released and brought back on deck, we deployed the neuston net to collect species samples from that same station. (I’ll explain the importance of this type of net in a later blog.) Once the collection time was complete, the neuston net was brought back on deck where we detached the cod end and placed it into a large bucket. Cod ends are plastic cylindrical attachments with screened holes to let water run through but keep living things inside during collection. The neuston cod end’s screens have 0.947mm sized openings. We then deployed the bongo nets to collect samples of even smaller species like plankton. (I will describe the purpose of the bongo nets in a later blog.) When the nets were brought back on deck, we detached the cod ends from the two bongo nets and placed those into buckets as well. The screens on the cod ends for the bongo net are even smaller than the neuston’s at only 0.333mm. When all of the nets were rinsed to make sure nothing was still stuck to the inside of the nets, we brought the buckets back to the stern of the ship to further rinse the samples and place them into jars for further examination by scientists.

Day 4 – July 8th

Blowfish — Holding a blowfish collected from a trawling

Today was a lot of fun because I completed my first groundfish trawl. The net for this trawl is located at the stern of the ship. When the net was brought back up on deck, it was emptied into a large box. There was quite the commotion when the fish were emptied out of the net. Not only were the fish flopping around like crazy and splattering water everywhere, their scales flew everywhere and it looked like shiny confetti! Anyone who was in a 6 foot radius was bound to be covered in scales. By the end of the day I thought I was part mermaid with the amount of scales that had stuck to me!

There were so many fish in one of our trawls that we had to use large shovels to place the fish into more manageable sized baskets. The baskets were brought inside the wet lab to be sorted, weighed, measured, and labeled.

The coolest animals I saw today were sea urchins, a sharpnose shark, and a blowfish. It was also fun to observe the different crab species, so long as I kept my fingers away from their claws!

Question of the Day

There is only one right answer to this question. ? You’ll be able to find it at one of the links I placed in my blog. Can you find the answer?

Good Luck!

May 24, 2010April 7, 2021

Laura Rodriguez, May 24th, 2010

NOAA Teacher at Sea
Laura Rodriguez
Aboard NOAA Ship Oscar Dyson
May 24 – June 2, 2012

Mission: Fisheries Surveys
Geographical Area: Eastern Bering Sea
Date: May 24, 2010

Pollock Survey Begins

Robert-and-Kerri-CTD-web-300x225 — Robert and Kerri deploy the CTD

deploying-bongos-1-web-225x300 — Deploying the Bongo nets

deploying-bongos-2-web-300x225 — The bongo nets are almost in

retrieving-bongos-225x300 — Retrieving the bongo nets, full of algae and hopefully full of Pollock Larvae

On Saturday, my watch began at 10:00 AM. Two of the scientists, Annette Dougherty and Kevin Bailey have watch from 4 AM until 4 PM. The other two scientists, Tiffany Vance and Steve Porter, have watch from 4 PM until 4 AM. I guess being the teacher they took pity on me and gave me half and half. Before getting to one of the stations, the scientists make sure that everything is ready. They lay out the bongo nets on the deck where they will be used. The bongo nets are two nets that from the top look like bongo drums. (See picture) There is an instrument attached to the bongo nets called a SEACAT that takes conductivity, temperature and salinity measurements during the tow. Inside the lab, buckets, bowls and tweezers are all laid out ready to be used.

As we approach each station, the bridge informs the scientists and survey technicians. The bongo nets have already been readied and are set to be deployed (put into the ocean) from the hero platform. When the OK is given, the nets are lifted by the hydrowinch to a point where they can be maneuvered over the rail and then they are lowered into the water. The nets are lowered until they are at 100 meters or 10 meters off the bottom. As they are lowered, the pilot of the boat keeps the wire at a 45° angle by moving the boat slowly forward. Once the nets reach their maximum depth, they are slowly brought back up again. ( I tried to upload a video showing the deployment and retrieval of the bongo, but it won’t work so I’ll show you the video when I get back.

pollock-larvae-001-300x225 — Pollock larvae under the microscope

When the nets clear the water, they are hosed down to get any organisms into the bottle on the end of the net (called the cod end.) The cod end is then removed and the contents of one net are poured into a bucket for sorting. The contents of the other net are preserved and sent to a lab in Poland where they use instruments to get a very accurate count of the Pollock.

lab-work-web1-300x225 — Annette Dougherty and Kevin Bailey in the chem Lab

Inside the chem lab, the contents of the bucket are scooped out and poured little by little into a mixing bowl. We then perform a rough count by removing the very small Pollock larvae and any other fish larvae and put them into a petri dish with cold water (the petri dish is placed on top of ice.) They are only a few mm long (averaging between 6-10mm.) Once we have gone through the entire contents, the Pollock larvae are counted, photographed and the length measured. They are then placed into a labeled vial with 95% ethanol. The other fish larvae are placed in a separate vial in 100% ethanol. They are kept in case another scientific team needs the data. The Pollock larvae will be sent to the scientists’ lab back in Seattle where they will perform further analysis on them. I’ll tell you more about that in the next blog.

Answers to your questions:

Annalise – The ship travels at 12 knots when we are going between stations.

survival-suit-web1-225x300 — Abandon Ship drill – You need to know how to put on your survival suit

Matt T– The ship is very safe. Drills are conducted every week. My first day on the ship, we had a fire drill and abandon ship drill. (See photo of me in my survival suit.)

Dan – The Oscar Dyson observes and records a number of environmental conditions. The bridge takes weather readings every hour and keeps them in a weather log. These include wind direction, wind speed, seawater temperature, air temperature, air pressure, cloud cover, sea swell height and direction. Conditions in the water are also constantly monitored such as temperature, conductivity, salinity, and amount of oxygen.

Olivia – The bongo tow is one way to get fish eggs. The mesh used on the bongo nets is very fine). It is able to filter out these very small larval fish and fish eggs, too.

Brittany – There is no specific number of fish that need to be caught for this experiment. Part of the experiment is to see how many larval fish there are. For our rough count, the scientists measure 20 larvae to get an estimate of their size. They will then look at the otoliths (small inner ear bones) to estimate their age.

copepods-and-amphipods-003-300x225 — Copepod

Amy – Aside from the Pollock larvae in the nets, we have caught cod larvae, larval squid, fish eggs, amphipods, terapods, jellies, Euphausids or krill, copepods and the larvae of other fish. The nets are small enough that we don’t catch any large fish or other animals.

Josh W. and Jon – Joel Kellogg has the night shift, so I haven’t met him yet. Stephen Macri is not on this cruise so I can’t ask him your questions.

Questions for today

In your answers to the last blog, many of you researched the large animals that live here in the Gulf of Alaska. The most abundant organisms, however, are much smaller. Two organisms that are very important to the survival of the large animals here are copepods and Euphausids. The larval Pollock feed on the larval copepods that are called copepodites.

Find out what other animals feed on copepods and euphausids. Then, describe at least one food chain that includes copepods and one that includes krill. In your food chain start with a producer or autotroph Ex. Algae) and end with the highest level of consumer or predator (Ex. blue Whale)

Again, Please be sure to include the link to the website where you got your information. Answer the questions in your own words writing complete sentences with as much detail as you can.