Mission: Integrated West Coast Pelagics Survey (Leg 2)
Geographic Area of Cruise: Pacific Ocean, California Coast
Date: July 14, 2025
Science team group photo
Jojo and the Golden Gate Bridge
Weather Data from the Bridge
It is our last full day at sea, and the visibility is minimal. Currently, the bridge is reporting a temperature of 57.2°F and a wind speed of 19 knots. Our sky condition is OVC, with the entire sky filled with clouds; additionally, there is a lot of fog. Our OPS officer, Brandon Schleiger, emptied the mess hall of every human soul eating lunch when he reported over the loudspeaker, “There is a blue whale spotted port side, very close…maybe about 100 yards.”
Blue whale spotted port side of NOAA Ship Bell M. Shimada
Surrounded by Salt Water
The number three is an important one for human survival. It has been said that humans will die after three minutes without oxygen, three days without water, and three weeks without food. On the Shimada, both oxygen and food have been plentiful, but the water situation is an interesting story. For a human stranded at sea, the ocean becomes a desert, and finding freshwater might require some unpleasant alternatives like eating fish eyeballs or drinking turtle blood—definitely (and thankfully) not on Chef Phil’s menu. Drinking salt water is generally a bad idea, as it can lead to further dehydration.
First Assistant Engineer Matt Swanson
On board NOAA Ship Bell M. Shimada, desalination is happening all the time—like magic, but with a lot more plumbing. I interviewed Matt Swanson (First Assistant Engineer) about how this salt-to-sip transformation happens. The ship has two methods for converting salt water into freshwater: flash evaporators and reverse osmosis. Let’s talk about flash evaporation, which sounds like a superhero skill, but it’s just advanced engineering. First, there are two types of water involved with this: jacket water and salt water. Jacket water is water that’s purchased on land. It is dyed traffic-cone orange and used to cool down the ship’s engines, which get much hotter than an August car seat in Arizona.
Using saltwater for this function would be a one-way ticket to Rustville for the engine’s metal parts, so it’s 100% jacket water for Shimada’s engines. As it circulates through, it absorbs engine heat, becoming hot enough to help boil the nearby saltwater—but don’t worry, the two waters never actually touch. They’re separated by titanium plates like awkward dance partners at a middle school dance. When the steam turns back into water, voila! Shimada’s got distilled water that can be used for drinking, showering, and flushing toilets.
Desalinated water station
Home for me is on the island of Oʻahu. Here, we’re surrounded by saltwater on all sides—but surprisingly, we don’t have a way to convert seawater to drinkable water on a large scale. Hopefully, at some point in the future, this situation may change. Improvements in Hawaii happen slowly. Twenty years ago, a seawater desalination facility was approved by Congress. With a projected cost of $204 million, the Kalaeloa Seawater Desalination Facility is designed to produce 1.7 million gallons of freshwater per day, drawn and desalinated straight from the ocean. Oahu desperately needs this important resource for fresh water, but unfortunately, the project is still awaiting permit approval.
Science: Environmental DNA
The Conductivity, Temperature, and Depth (CTD) rosette includes a ring of water sampling bottles.
Environmental DNA, or eDNA, is nature’s version of leaving fingerprints—except instead of prints, organisms leave behind tiny traces of genetic material in the water. Fish, mammals, birds… they’re all unknowingly contributing to a floating soup of clues. By collecting just a bit of water, scientists can discover the species that have recently passed through, like detectives reading the guest list to an underwater party.
Why take eDNA samples? NOAA reports that eDNA can identify species and characterize their role in the area’s food web and ecosystem. Also, it offers a powerful, non-invasive way to monitor marine life without disturbing it—no giant nets, no hake fish hauls mixed in with baby sharks called spiny dogfish. This new technology allows scientists to gather information without bycatch.
Jojo holds a spiny dogfish
Spiny dogfish are sticky! This large haul of hake fish was so stuck together with the dogfish that we had to pull out the fire hose to get them out of the hopper.
Maddy and Sam are eDNA NOAA scientists. According to Sam, there are about 100 specific sampling stations along the U.S. West Coast (excluding Alaska), where water is collected and sampled for ocean species each year. In 2024 alone, the Pacific NOAA team took approximately 2,500 water samples.
NOAA scientists Sam and Maddy study environmental DNA.
Despite being a non-invasive way to sample species, there are a few drawbacks to this research method. According to Maddy, there is no way to currently assess the age or sex of the fish being surveyed through eDNA methods. This limits a scientist’s ability to know the health and future of a species. As eDNA improves, it may be possible to create a full picture of a fish population. For now, eDNA and fish trawling surveys are working together to get a better picture of what is happening under the sea.
Visual Art and Music in Seafloor Mapping and Acoustics:
Oceantransect lines
During a “leg” at sea, NOAA scientist Rebecca Thomas (respectfully called “RT” by her science crew) calls herself a “fancy fish finder.” She is not only using sound equipment to locate hake fish underwater, but she is also presenting this information in both visual and musical forms.
Take her ocean floor maps, for example. Mapping the depths of the ocean floor is a remarkable human accomplishment, and knowledge of these depths is important to Rebecca’s work. Rebecca even customized the color palette to match her mental map of the sea—deeper water in darker tones, shallower areas in lighter ones. As she puts it, “It just made more sense.” And it works—the color gradient helps her instantly read depth and spot the elusive “hake snake,” the long, wriggly trail of fish she’s after.
Bathymetric map of the seafloor in Monterey BayThis is an example of what the “hake snake” looks like on the sonar data. The green wavey line represents what the scientists are looking for. When they see this, they will make a decision on deploying the huge nets to fish.
But she didn’t stop there. Rebecca’s also experimenting with turning sonar data into sound, essentially making music out of marine science. Here she explains a composition she created that includes music for a CTD going down into the ocean, an alarm clock waking her up, and a sunrise. While it’s not the catchy tune of Alan Menken’s, Under the Sea, it is a helpful way to form a greater understanding of an elaborate water world that is challenging for us, land animals, to understand.
Rebecca Thomas is explaining the sound and music she’s added to her sonar data.
Animals Seen Today: Humpback whales, blue whale, Pacific whiteside dolphins, hookarm squid, chili pepper rockfish, tiny octopus, hake, anchovy, purple striped jellyfish, lamprey, seabugs
If possible, it was important to me to help our tiny creatures stay alive. This octopus is an example of one of my favorite wet lab buddies.
Personal
Another thing—sleeping on this boat? It’s pretty great! In Hawaii, I opt for the ocean breeze over air conditioning, but out here, the cabin turns into an arctic tundra every night. So naturally, I’ve assembled a fortress of five blankets—a Shimada sea cocoon. Sometimes it feels like I’m gently swaying on a waterbed. Other times, it’s a full-blown rolling magic carpet ride through the waves. Either way, I’m snoozing like a champion, beneath a sky full of Pacific fog off the coast of California.
Mission: Oceanographic and Biological Monitoring of Davidson Seamount
Geographic Area: Davidson Seamount/Monterey Bay National Marine Sanctuary
Date: July 22, 2025
Weather Data from the Bridge
Latitude: 35° 45.51’ N
Longitude: 122° 36.14’ W
Wind Speed: 18 knots
Wave Height: 3’
Air Temperature: 15.6°C/60°F
Sky: Overcast
Science and Technology Log:
We have now finished our planned transects and are using our two additional days at sea to repeat two of the transect lines. This will allow us to see changes along the lines with observations 5 days apart. Our deep drops for eDNA (the genetic material shed by organisms in the water) will be at 2400m.
I have had a chance to help with the collection of samples of eDNA. The process begins right after the CTD rosette is lifted to the deck. Water is collected from the specific Niskin bottle that was filled at the various depths- either surface (0 m.), 500 m., 1000 m. or 2400 m. Next, the water samples are taken to the wet lab, where under laboratory conditions, they are filtered to collect eDNA which is then stored for future processing by MBARI.
I loved having a chance to participate in collecting the sample. Working with the equipment reminded me a lot of the joy I had in my college chemistry classes and it felt amazing to be making a contribution to science that will help understand this very special environment of Monterey Bay National Marine Sanctuary.
Collecting water for eDNA sampling from the CTD rosetteCompleted water collectionSetting up filtration with Chad KingAttaching filter to collect eDNAPreserving eDNAeDNA ready for testing by MBARI
I have also been learning more about the ocean by looking at the CTD (water conductivity (salinity), temperature, and depth) profiles with the Reuben Lasker survey technicians, CC and Jaclyn. The survey technicians observe and record the data as the rosette descends. They also monitor how deep the rosette descends based on what they see on the sonar data, which is showing the overall distance to seamount. At the targeted depths and with a press of a mouse button, they close the Niskin bottle caps to capture water for eDNA sampling.
CTD Data Monitoring
The data screens in the lab show how oxygen, temperature, salinity and chlorophyll change as we descend. At the surface the water temperature is 15°C (59°F) while at 1000m it is 3.5°C (38.3°F) and at 2400m it is 1.9°C (35.4 °F). Salinity at the surface is 33.25ppt, at 1000m it is 34.4ppt and at 2400m it is 34.65 ppt. Oxygen is 0.6 ml/L at the surface and is at its lowest 0.2 ml/L between 600 – 800m. The oxygen rises again as you go deeper than 800m and at 2400 it’s more than 2.0 ml/L. Chlorophyll is at its maximum at 43 m and is an indicator of the amount of phytoplankton in the upper layer of the ocean. Phytoplankton (microscopic algae) is the base of most food webs in the ocean. Thus, this data helps us better understand the ecosystem of the deep ocean.
Our seabird and marine mammal counts are going well, though we had the slowest day on Monday with only 47 animal sightings (11 mammals and 36 birds). Yet, all together for the week (with the 994 sightings shared in the last post), we had a total of 1,041 animal sightings for the 500 miles of survey.
As we repeated the survey line (16W) today (Tuesday), we had an exciting sighting of a pod of seven orcas! I have never seen orcas in California. I’ve also become far more skilled at sighting whale blows on the horizon and spotting sharks from the two black triangles peeking out of the water as they glide by. The various types of seabirds – like Leach’s Storm Petrels and Red-necked Phalaropes- are now second nature to me. Some of the most exciting moments have been finding the waving flippers of Guadalupe fur seals as they drift by clinging to a branch of kelp.
So far, I have probably put in 50 hours of observation time and I have been delighted in every moment of it. It is a bit like an easter egg hunt in the ocean. I have learned so much thanks to the support of the scientists who always think of me when any special sighting arises. Everyone makes the extra effort to make sure I have a chance to see it too.
Fin Whale Sighting! Photo Credit: Jim Tietz
Personal Log
I have been savoring the days at sea and the ever changing colors of the ocean from the deepest blue to silvery greys. I spend most of my days outdoors on the flying bridge perfecting my observation skills. Our shifts are complemented with delicious meals, after dinner card games and evenings in the gym. Life couldn’t be better and it is a real privilege to be part of this experience. Beside participating in science, I have been very busy interviewing people to better understand how everyone works together to make the mission successful. I’d like to share the stories of some of the people I have met.
NOAA Corps and the Crew: The Team at Sea that Makes Science Possible
Besides the 11 of us on the science team, we have the team that runs the ship composed of seven NOAA Corps officers and 18 crew. The crew includes survey technicians, electronics technicians, engineers, deckhands and stewards. NOAA Corps is one of the eight uniformed services of the United States. They are commissioned officers who support NOAA’s scientific and navigational missions by operating NOAA ships and aircraft. The Commanding Officer of the Lasker, CDR Aaron Maggied, shared that some NOAA Corps officers fly planes as hurricane hunters to collect data for forecasting hurricanes. Others, like himself, sail ships to make sure our ocean and its inhabitants are studied so that we can better understand and responsibly manage our natural resources, like our current sanctuary project. He also mentioned that early in his career he was called on to help in the Deepwater Horizon oil spill response effort in 2010. The officers have all been very supportive of having a teacher on board and readily answer any questions about their work.
NOAA CorpsWomen of NOAA Corps
Lt Cdr. Kelli-Ann Bliss Interview
LCDR Kelli-Ann Bliss
Kell was the first officer I met on the ship. She welcomed me at the entrance to Coast Guard Island in Alameda and escorted me to the ship, kindly carrying my heavy duffle on her shoulders.
What is your job?
On Reuben Lasker, I am the XO, which stands for Executive Officer, and second in command. I have a background in science, like all NOAA Corps officers, and I support the scientists on the ship during sea assignments, and in different capacities when on land assignments. I work on the bridge and sail the ship safely to help the scientists get the data they need. This work is important because we need to understand how our planet works so we can survive as a species. I also mentor the Junior Officers (JOOD) as they work toward being Officers of the Deck (OOD). I also manage the crew details (payroll, vacation, staffing, approving purchasing, etc.) like an administrative assistant.
How did you come to NOAA?
I grew up in Rhode Island and spent summers sailing with my family all over New England. I went to Maine Maritime Academy and earned a degree in marine science. I worked in a lab on Cape Cod doing water testing after college. My college classmates encouraged me to apply for NOAA.
I have been in the NOAA Corps for 16 years and have been on 8 different NOAA ships. I have also served on various land assignments — including in Antarctica for 13 months. In Antarctica, I was half of a team with a NOAA technician. We were running experiments and collecting samples on behalf of scientists in their home locations. While staying over the winter, I enjoyed the gorgeous auroras (natural light displays in the sky) and the flat, snowy landscape of Antarctica. Currently I am stationed in Louisiana and awaiting the completion of the newest NOAA ship to the fleet, the NOAA Ship Oceanographer, where I will also serve as XO. My tasks will be much the same as here on Reuben Lasker, but additionally, I will hire the new crew and be part of the team that gets her ready for scientific missions.
What do you love about your job?
I love being at sea. You are in a new place every day and it is gorgeous. There is always something new to learn either through presentations, different weather conditions, or a new tool or technology on the ship.
What is your greatest challenge?
As you go up in the ranks, there is a lot of paperwork, which tends to mean a lot of sitting – but there’s always the ability to go up and stand a watch on the bridge to break it up. I also work to keep harmony and help to set a positive culture with the team which starts at the top.
When did you know you wanted to have an ocean focused career?
In middle school in Coventry, Rhode Island, I joined the shell club and learned all about shells and their history. For example, the ancient Romans boiled the murex shell and infused the purple color into fabric. Once a month, the club would travel to Boston and connect with the Malacological Club at Harvard and I would be exposed to even more people who were passionate about shells. I knew that I wanted to study science. For college, my family wanted me close by so I chose Maine Maritime Academy, this allowed me to merge my interests in science and being on the water.
What do you recommend to students who are interested in an ocean focused career?
Stay curious and ask questions. There are many ways to get into the field and people will share their knowledge. Always keep learning.
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Interview of JOOD Camille Cube (Junior Officer of the Deck)
I met Camille Cube on my first visit to the bridge. I was so impressed by the calm and confident way she was steering the ship. In conversation, we were happy to discover that we both had Filipino roots. Camille kindly agreed to be interviewed.
ENS Camille Cube
What is your job/position?
I am the newest officer. My rank is Ensign and my position is called JOOD (Junior Officer of the Deck). I am learning to safely drive the ship and ensure everyone’s safety onboard. To steer the ship, I use navigational charts, radar, look out the windows, and other tools.
How did you come to NOAA?
I grew up in Northern Virginia. Then, I went to the University of Washington and majored in Environmental Science. I love the environment of both land and sea. During college, I did many internships. Two were with NOAA Fisheries. I also studied at Friday Harbor Labs on San Juan Island; in this 11 week residential program, I learned marine biology, went tidepooling and saw orcas. I also spent three months as an intern in Cambridge, England with the International Whaling Commission. After graduating from college, I worked for NOAA Fisheries in Sacramento (CA) as a natural resource and management specialist. I joined the NOAA Corps for a more hands-on experience. I love how the NOAA Corps changes jobs every few years. I will be on Reuben Lasker for two years; three months have passed so far.
How does the NOAA Corps work?
To apply, you fill out an application online, go to an interview and pass medical processing. If you are chosen, you begin three months of training at the US Coast Guard Academy in New London, Connecticut, alongside US Coast Guard officer candidates. This training has hands-on learning about navigation, the parts of a ship, safety, CPR, and fire fighting alongside classroom learning. I learned leadership and public speaking skills in my training and the experience has built my self-confidence. You begin your service as a junior officer and after 120 days of sailing, completing a workbook and proving that you can safely drive the ship, you become OOD (Officer of the Deck) qualified, which means you can drive the ship without supervision.
What is your work day like?
My watch, which is when I am driving the ship, begins at 11:15 p.m. and goes to 3:30 a.m. From 3:30 to 7:00 a.m., I do administrative work and eat breakfast. Sometimes, I exercise in the ship’s gym; our requirement is to work out 180 minutes a week. My second watch is from 7:15 to 11:30 a.m. After that, I am off duty, and I read, sleep or crochet. Right now I am making a purse that looks like a sheep.
What do you love about your job?
I love helping make science happen. NOAA’s work in science is really important. Often we work on research on fish populations and fish are very important for the economy and ecosystem. Collecting weather data is also important for weather forecasters. I love being able to do cool things on the ocean that I was never able to do in the office like steer the ship and see lots of wildlife. I also love the community in NOAA; we support each other, especially the other officers and the crew because we live and work so close together. A shout out to the stewards (ship’s cooks) for making Filipino food that reminds me of my family.
What is your greatest challenge?
Being away from home for long periods of time is a challenge. I live in San Diego now. Even though my husband visits me when we are in port, I have only been able to see my cat Mio once this year.
What was your favorite book in elementary school?
I was obsessed with Percy Jackson and wanted to be a demigod of Poseidon. I wished for water powers!
What do you recommend to students who are interested in an ocean focused career?
If you are near the ocean, get out and explore it in a hands-on way like tidepooling. If you are not near the ocean, watch documentaries and keep learning about the ocean. If you can, join a marine biology club.
I am excited to share information about career opportunities with NOAA with my students and family. I had never heard of this service before and now after experiencing the work of the NOAA Corps, I believe it is a wonderful opportunity. I also learned about another new to me career-the careers of wage mariners. It takes many essential skilled workers to sail these ships that make science happen.
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Interview of Nick Sampson (Oiler)
I had a chance to interview Nick Sampson. He is a mariner and specifically works as an Oiler. We met in the mess hall (dining room) as he is outgoing and very curious about all the science we are doing on our mission. He also kindly took us on a tour of the engine room with fellow mariner Joe Johnston.
Oiler Nick Sampson
Nick Sampson is from Jacksonville Florida. He has a 5 year old daughter and his wife is expecting another child soon.
What is your job?
I am an Oiler on the ship which means I check the temperature gauges and maintain the ship. I keep the ship running, secure and dependable.
What do you love about your job?
I love that I am doing something positive. I enjoy people–I am a people person and I love to learn from others. You can see the world with this job, make good money and learn a lot. I have been to Hawaii, Guam, Saipan, Japan, South Korea, Germany and recently I spent 43 days in Alaska.
What is a challenge in your job?
Learning more about the machinery is a challenge but I am eager to learn. The job is good if you are single, but if you have kids it is difficult to be away. It is still a good job for supporting a family.
How did you know you wanted an ocean focused career?
My older brother is a mariner so I decided to do the same. I graduated from Blue Water Maritime School in Florida and have been working on ships for the last 7 years.
What are your words of advice?
Give it a try! Invest in yourself and you can learn a lot.
The Most Essential Crew: The Stewards
A final shout out- as Camille says- has to go to the stewards. From the first day, the food has been AMAZING!!! The smells of the cooking waft all the way up to the flying bridge. Our meals are at 7 am, 11 am, and 5 pm. Since the crew and scientist work a range of shifts, including the night shift, there is always a wide array of assorted snacks as well as easy to prepare meals like fancy ramen bowls. There are lots of organic choices, a fruit salad bar at breakfast, and a green salad bar at lunch. I have been enjoying the organic grassfed milk in my tea every morning.
The stewards, Arnold Dones and Judeni De Los Reyes, create food with great care and an element of magic. Since both have Filipino roots, they love to make some of the traditional foods like adobo and pancit (my favorite Filipino food). But they also love to test out new recipes. I am still thinking about the cabbage rolls from the first day. They tasted like a special grandmother’s recipe; Arnold shares that he researches recipes and gives them a try. Before working for NOAA, he was a cook for the Navy for 10 years.
Arnold loves his job on Lasker and takes great pride in carefully planning the menu even up to a year in advance. This way he can plan to have the right equipment and the right cooking time. Arnold “loves to cook everything” and likes to explore new foods. “Good food makes everyone function well both in terms of energy and morale. It makes people happy and I love to make everyone happy by giving them the best quality food and snacks.”
Arnold Dones (Chief Steward) and Judeni Delos Reyes (Steward)Breakfast: Avocado Toast Bar Lunch: Couscous Stuffed Tomatoes Salad BarDinner with Pancit (Filipino Noodles)MenusWell Stocked FridgeIce Cream Anytime
Did You Know?
Guadalupe Fur Seal Sighting. Photo Credit: Jim Tietz
Guadalupe Fur seals are members of the “eared fur seal” family. They breed on Guadalupe Island (off the coast of Mexico) and on the Channel Islands. They have been making a comeback since they were once hunted to near extinction in the 1700’s and 1800’s. They are now considered “threatened” on the Endangered Species list and research and conservation is helping their recovery. They feed on squid and small fish mostly at night. They dive from an average of 65’ to a maximum of 250’. They rest with their heads under water and their flippers poking out above water as pictured below. On this mission, we have been seeing both Northern Fur Seals and Guadalupe Fur Seals.
Geographic Area of Cruise: Pacific Coast, near Northern California
Date: September 6, 2024
Weather Data from the Bridge (Mendocino Ridge Essential Fish Habitat Conservation Area):
Latitude: 40º18.178’ N
Longitude: 124º48.470’W
Wind Speed: 5.87 knots
Air Temperature: 14.3ºC/57.74ºF
Conditions: Foggy
Science and Technology Log
There are many methods of studying the ecosystem of the ocean on the mission that I am on, and another method we are utilizing is that of Environmental DNA (referred to as eDNA). Every living organism in the ocean leaves behind traces of its existence. Much like humans shed skin cells and hair, and cats and dogs shed fur, ocean organisms leave behind skin, scales, and waste products. These artifacts contain DNA, and can last in the water for anywhere from 7 to 21 days. Scientists have ways of collecting eDNA using the CTD (Conductivity, Temperature, and Depth) rosette.
Deploying the CTD
CTD off the side of the ship.
A CTD rosette is a device that is routinely lowered off of the ship to monitor the temperature and conductivity of the water at measured depths in the water column. NOAA Ship Bell M. Shimada’s rosette has 12 containers, called Niskin bottles, that are opened before deployment, and then triggered at different depths one at a time as the rosette ascends, trapping the water from that depth inside. Separate from these collections, sensors analyze the temperature, salinity (salt levels), pressure, dissolved oxygen, turbidity (cloudiness), and other useful information. The data collected from the CTD shows up instantaneously on a computer screen aboard the ship.
Data coming in from the CTD dive
To collect eDNA, the scientists look at where the biggest temperature changes happen (called the thermocline). Once the CTD is back aboard the ship’s deck, the scientists pump the water collected in the Niskin bottles triggered at the depths surrounding the thermocline through a filter. The eDNA material is collected and strained into this filter, where it is preserved to be sent to a lab for further analysis. Once the eDNA gets to the lab, scientists look at the DNA “fingerprints” left behind by organisms and match them to a database of known DNA. The scientists then have knowledge of what organisms were present in that location in the ocean at the depths those samples were collected from.
Scientist Alice Kojima-Clarke pointing out the eDNA filter
This goes hand in hand with the work I blogged about last on the MultiNet. The identification of the plankton that Jenn is doing is part of the work that goes into the database helping scientists identify DNA from the eDNA samples.
Personal Log
I’ve gotten a lot of questions about what the food is like on the ship, and anyone who knows me knows that food is a big part of my life! The ship’s cook, Ronnie, is amazing. He cooks the food from scratch, and it is not uncommon to see meatballs being rolled out for the next meal, or other prep taking place. The meals are served buffet-style, and there is no shortage of food. Even the pickiest eater would be happily satisfied here.
The menu from a few days ago
Dinner from tonight
For Labor Day, we got to have a cookout on the ship’s back deck. It was quite the feast, featuring all of the grilled meat and fixings you could want.
Grilling steaks for Labor Day
Also, if at any meal you ‘forget’ to take dessert, Ed, the steward, will remind you. He’s always looking out for your best interest! He also always has the best jazz music playing in the kitchen.
Ed always has the biggest smile on his face – you can tell he takes great pride in his job! Ronnie is in the background, and his food is spoiling us!
Finally, I have to take a minute to wish my Dad a happy birthday! I had some cake to celebrate you today, Dad!!!
I saved you a piece of Red Velvet Cake!
Music Connections
In looking at how the eDNA analysis works, I’m going to compare it to listening to an audio recording of a high school band. When a person listens to a recording of the band, they can tell what instruments are represented in the recording. For example, you may notice that there are flutes, oboes, clarinets, and saxophones, but perhaps the band is missing a bassoonist. If the group does a really good job of section playing, you would have a very tough time picking out HOW MANY flutists are in the recording. You may be able to hear that there are a lot of them, based on the depth of sound you hear throughout the dynamics being played, but you could not say with any confidence whether there are 7, 8, or 9 flutists. You also would not know whether one of the high school students was absent that day, or whether a guest was playing on the recording as well. The process of eDNA analysis is the same way – scientists can tell what was present in that one snapshot of time, based on the DNA present in the sample. They cannot tell you how many of each organism is present, or whether those organisms live there or were merely just migrating through the area.
For today’s audio clip, I recorded the ship’s horn being blown as a result of the reduced visibility from the fog. I learned that there are several different patterns for the horn to blow, and the example I have for you here is the long fog horn blast followed by two short blasts, signaling that we are unable to change course (in this case, due to the fact that we are acoustically tethered to the AUV that was in the water at the time)
The ship’s fog horn
Student Questions
Students asked me to be on the lookout for dolphins. On our third day at sea, we saw a whole pod of dolphins right next to the ship! Here’s a very short video to watch them all, and I am not zoomed in at all with my phone!
Pod of dolphins swimming past NOAA Ship Bell M. Shimada
Mission: Pacific hake (Merluccius productus) Survey (Leg 3 of 5) Geographic Area of Cruise: Pacific Ocean off the Northern California Coast working north back toward coastal waters off Oregon. Date: Friday, August 4, 2023
Weather Data from the Bridge Sunrise 0614 | Sunset 2037 Current Time: 0700 (7am Pacific Daylight Time) Lat 43 16.7 N, Lon 124 38.0 W Visibility: 10 nm (nautical miles) Sky condition: partly cloudy Wind Speed: 5 knots Wind Direction: 030° Barometer: 1020.3 mb Sea Wave height: 1 ft | Swell: 340°, 1-2 ft Sea temp: 13.7°C | Air Temp: 16.2°C
Science and Technology Log
On Wednesday night I stayed up to participate in the first CTD cast of the evening. What is a CTD? The short version: a water sample collection to measure conductivity, temperature, and depth. eDNA information is also collected during the CTD casts.
The longer version: As is true of all operations, all departments collaborate to get the science done. The bridge delayed casting due to erratic behavior from marine traffic in the area. When that vessel moved away, the deck crew got busy operating the crane that lowered the CTD unit to 500 meters. The Survey Technicians, along with the Electronics Technician, had just rebuilt the CTD unit days before, due to some hardware failures at sea. The eDNA scientist prepared the Chem Lab for receiving samples that would confirm the presence of hake as well as other species.
When I arrived, Senior Survey Technician Elysha Agne was watching a live feed of the sensors on the CTD unit. Agne explained what was happening on the feed: There are two sensors per item being tested, then both sensors are compared for reliability of the data. There is one exception: A dual channel fluorometer, which gauges turbidity and fluorescence (which measures chlorophyll). Turbidity spikes toward the bottom in shallow areas due to wave action. Salinity is calculated by temperature and conductivity. Sometimes there are salinity spikes at the surface, but it’s not usually “real data” if just one sensor spikes. The CTD unit is sent down to 500 meters as requested by scientists. Measurements and water collection occur at 500, 300, 150 and 50 meters. The number of CTDs allocated to a transect line varies according to how many nautical miles the line is. For example, multiple readings at the 500 meter mark may be taken on a line. CTD casts west of the one done at the 500m depth contour are spaced every 5 nm apart. Scientists are not currently taking CTD samples beyond the ocean bottom’s 1500m contour line.
The main “fish,” called an SBE 9plus, has calibrated internal pressure. As it descends you can tell the depth the “fish” is at. Sea-Bird Electronics (the origin of the SBE acronym) manufactures the majority of scientific sensors used on board, with the exception of meteorological sensors. The Seabird deck box (computer) is connected to the winch wire. The winch wire is terminated to a plug that is plugged into the main “fish.”
The other day, the termination failed. Termination means the winch wire is cut, threaded out, and the computer wire plugged into the winch wire. The spot it’s terminated can be exposed to damage if internal wires aren’t laid flat. Tension and tears may occur anyway because it’s a weak point. The plug on the main “fish” where the winch wire cable connects broke too, so the whole CTD had to be rebuilt. The “Chinese finger,” the metal spiral that pulls the load of the CTD on the winch wire, was also defective, so modifications were made.
Broken plug on the “fish.”What you need for a moisture proof seal (electrical insulating compound).Niskin bottles in a pile while CTD unit is rebuilt.Termination failure.The main “fish” that the sensors are attached to..
When the CTD is at the target depth, Agne presses a button in the chem lab that logs a bunch of meteorological and location data. She remotely “fires” a bottle which sends a signal to the “cake” that sits on top of the CTD. The signal is an electric pulse to release a magnet that holds the niskin bottle open. If it pops correctly, water is sealed inside. Since two bottles of water were requested at each depth, a second signal is sent to the second bottle. There are 12 niskin bottles on the CTD “carousel.” After two were done at 500 m, the winch operator takes the CTD unit up to 300 m; Agne fires two more bottles there, then two more bottles at 200 m, 150 m, and 50 m. About two and a half liters of water are taken per bottle.
Samantha Engster, eDNA Scientist
Once the CTD unit returned to the surface, I got to help “pop the nipples” on the bottles to release the water into plastic bags. Back in the Chem Lab, eDNA Scientist, Samantha Engster, pours the water through a filter 1 micron thin. The filter is then folded in half and placed in a vial of Longmire’s solution until the eDNA can be analyzed in a lab back on land. Microscopes are not used for DNA analysis. Phenol-chloroform is used to remove proteins from nucleic acids. Quantitative polymerase chain reaction (qPCR) technique is then used to perform gene expression. This is the third hake survey that has been done in conjunction with eDNA analysis.
While the CTD “fish” and all its sensors are collecting oceanographic data, Engster collects environmental data from the water samples. Surface water samples are also taken at the underway seawater station courtesy of a pump hooked up near one of the chem lab sinks. The eDNA verifies abundance and distribution of hake. When information from these water samples is partnered with data from the echo sounders, and “ground-truthed” with physical hake bodies in the net, the data set is strengthened by the diverse tests.
The CTD unit fixed and ready for the next deployment. Sensors reattached to the “fish.”The “cake” that sits on top of the unit that seals off the water samples.
Career Feature
Note: A handful of the people I have met aboard are experienced “Observers.” NOAA contracts with companies that deploy observers trained as biological technicians. Find out more here.
Engineers Evan McNeil (Right), and Evan Thomas (Left).
Evan McNeil & Evan Thomas, Engineers
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
Evan M. I’m a manager over our engineers. Below me is the second engineer. We have three third engineers, a junior engineer, and an oiler, also called a GVA (General Vessel Assistant), or wiper. I set the pace of work everyday. I assign all the jobs. Traditionally the Engine Department is under the First Engineer, but technically the Engine Room is mine. The Chief Engineer and the Captain (NOAA Corps Commanding Officer in this case) are in charge of the safety of the whole ship. The Chief Engineer also directs jobs to me that need to get done and I’ll delegate those jobs out.
Evan T. Third Assistant Engineer, soon to be Second. I mostly fix stuff that is broken.
What’s your educational background?
Evan M. I have a Bachelor’s of Science in Marine Engineering Technology with a minor in marine science from California Maritime Academy. I grew up near Bodega Bay, so my background is oriented toward the ocean. I really enjoy it.
Evan T. Graduated from Cal Maritime, 2019. I grew up in Southern California, Redlands, a desert that somehow grows oranges. I applied to all the engineering schools in California, and Cal Maritime was one of the few that replied back. I said “Yeah, I could see myself doing this.” And here I am! What do you enjoy most about your work?
Evan M. I enjoy who I work with. It makes work go by quickly. I enjoy our schedule and our time off. This is what I enjoy about my NOAA job and about sailing jobs in general. Shore leave is a type of leave. There’s also annual leave and sick leave. We call it going on rotation or off rotation. Off rotation is usually for a month, and on rotation is usually two months. Every ship is different but that’s how it is for the Shimada, a two-on, one-off schedule. If you talk to other sailors they’ll tell you ratios for time on and time off. For example, I did Leg 2 of the hake survey, I’m on Leg 3, and then I’m off.
Evan T. Learning new equipment, new ways to do things.
What advice do you have for a young person interested in ocean-related careers?
Evan M. If you are interested in going straight to being an officer, I would go straight to a maritime academy. It’s a very niche thing to know about. No one knows what they want to do at 19. NOAA’s always hiring. If you are interested in being an engineer, you start out as a wiper, then you can work your way up in the engineering department pretty easily.
Evan T. Imagine being stuck in an office and you can’t go home for a month. Find something that will distract you when you are out on the ocean for weeks at a time. Hang out with people, play games, read a book. You have to be ready to fight fires, flooding, that sort of thing.
If you could invent a tool to make your work more efficient—cost is no concern, and the tool wouldn’t eliminate your job—what would it be and why?
Evan M. A slide that goes from the bridge to the engineering operations deck.
Evan T. I would go for an elevator on the ship.
Do you have a favorite book?
Evan M. Modern Marine Engineering volume 1
Evan T. My 5th grade teacher wrote their own book that I found entertaining. I also liked Huckleberry Finn, by Mark Twain.
Vince Welton, Electronics Technician
Vince Welton
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
I’m an electronic technician. I deal with everything that has to do with electronics, which includes: weather, navigation, radars, satellite communications, phone systems, computers, networking, and science equipment. All the ancillary stuff that doesn’t have to do with power or steering. Power and steering belongs to the engineers. What’s your educational background?
When I was in high school my father had an electronics shop and I worked with him. He was career Air Force and an electronics technician as well. My senior year of high school I was also taking night classes at a college in Roseburg, Oregon in electronics. I joined the U.S. Air Force and was sent off to tech school and a year’s worth of education in electronics. Then there was a lot of learning on the job in electronic warfare. I worked on B52s. I was a jammer. In order to learn that you had to learn everybody else’s job. That’s what makes mine so unique. You had to learn radio, satellite, early warning radar, site-to-site radar, learning what other people did so I could fix what was wrong with their electronic tools. I went from preparing for war to saving the whales, so to speak. Saving the whales is better!
What do you enjoy most about your work?
I enjoy the difficulty of the problems. We’re problem solvers.
What are the challenges of your work?
Problems you can’t fix! That’s what disturbs a technician the most, not being able to solve a problem.
What advice do you have for a young person interested in ocean-related careers?
The sciences are important no matter what you do. Having curiosity is the biggest thing. My hope is that education systems are realizing the importance of teaching kids how to think. Young people need to grow the ability to ask questions, instead of just providing answers.
If you could invent a tool to make your work more efficient—cost is no concern, and the tool wouldn’t eliminate your job—what would it be and why?
I think AI has phenomenal potential, but it’s a double-edged sword because there’s a dark side to it as well.
Do you have a favorite book?
The Infinity Concerto, by Greg Bear The Little Book of String Theory, by Steven S. Gubser
What’s the coolest thing you’ve seen at sea?
Actually seeing a whale come out of the water is probably the coolest thing. Watching that enormous tonnage jumping completely out of the ocean. If you look out the window long enough and you’ll see quite a few things.
Markee Meggs, Able Bodied Seaman
Markee Meggs
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
I’m an AB, or Able Bodied Seaman. The job looks different on different ships. On the Shimada I stand watch and look for things that don’t show up on radar. Most ships you drive—only NOAA Corps Officers drive on the Shimada—I can drive rescue boats, tie up the ship, and do maintenance on the outside. I’m a crane operator. On a container ship you make sure the refrigerated containers are fully plugged in. On a refueling ship (tanker) you hookup fuel hoses. Crowley is a major tanker company. On RoRo ships (roll on, roll off) you work with ramps for the vehicle decks, transporting cars from overseas.
AB is a big job on a cruise ship. I did one trip per year for three years, then got stuck on one during the pandemic in 2020. On the cruise ship you stand watch, do maintenance, paint, tie up the ship, drive the ship. There’s even “pool watch” where you do swimming pool maintenance. You also assist with driving small boats and help guests on and off during a port call.
I’m a member of SIU (Seafarers International Union) and work as an independent contractor for NOAA. I like the freedom of choosing where I go.
What’s your educational background?
I’m from Mobile, Alabama. I spent four years in the Navy (my grandad served on submarines during World War Two), one year in active Navy Reserves, then eight years as a contractor supporting the Navy with the Military Sealift Command. I spent a year as a crane operator in an oceaneering oil field, and have an Associate’s Degree in electrical engineering. On the oil field job we used an ROV to scope out the ocean floor first. After identifying a stable location I laid pipe with the crane, and took care not to tip over the boat in the process! My first NOAA ship was the Rainier, sailing in American Samoa.
What do you enjoy most about your work?
I most enjoy meeting different types of people. Once you’ve been to a place you have friends everywhere. I also love to travel—seeing different places. It’s a two-for-one deal because once you’ve finished with the work you are in an amazing vacation place.
What advice do you have for a young person interested in ocean-related careers?
If ships interest you, do the Navy first. They pay for training, and your job is convertible. Becoming a merchant mariner is easier with Navy experience than coming straight off the street. There is a shortcut to becoming a merchant mariner, but you’ll have to pay for classes. Finally, always ask questions! Yes, even ask questions of your superiors in the Navy.
What’s the coolest thing you’ve seen at sea?
The coolest things I’ve seen at sea have been the northern lights in Alaska, whales, volcanic activity, and rainbow-wearing waterfalls in Hawaii.
Do you have a favorite book?
Some of my favorite books are Gifted Hands, and Think Big, both by Ben Carson. Gifted Hands: The Ben Carson Story was turned into a film with Cuba Gooding Jr in 2009. Another book that made an impression was Mastery, by Robert Greene. Its overarching message is “whatever you do, do well.”
Julia Clemons, FEAT Team Lead
Julia Clemons
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
I am the Team Lead of the FEAT (Fisheries Engineering and Acoustic Technologies) Team with the NWFSC (Northwest Fisheries Science Center). The primary mission of our team is to conduct a Pacific hake biomass survey in the California Current ecosystem and the FEAT team was born specifically to take on that mission from another science center. The results of this survey go into the stock assessment for managing the fishery. Fisheries and Oceans Canada are partners in this survey. Hake takes you down many paths because their diet and habitat are tied to other species. For example, krill are a major prey item in the diet of hake, so understanding krill biomass and distribution is important to the hake story as well. Rockfish also have an affinity for a similar habitat to hake in rockier areas near the shelf break, so we use acoustics and trawling to distinguish between the two.
What’s your educational background?
My undergraduate degree from University of Washington was in geological oceanography. I began with NOAA in 1993 and worked for the Pacific Marine Environmental Laboratory’s Vents program to study hydrothermal systems. This involved a diverse team of scientists: chemical and physical oceanographers, biologists, and geologists. I got my Master’s in Geology at Vanderbilt but shifted to NOAA Fisheries in 2000 working in the Habitat Conservation and Engineering (HCE) Program where we looked at habitat associations of rockfish. We looked at ROV and submersible video of the rocky banks off Oregon to identify fish and their geological surroundings. The HCE program shifted its focus to reducing bycatch by experimenting with net modifications and I moved to the FEAT team.
What do you enjoy most about your work?
I think one of the most important components of Team Lead is to be a supporter—supporting the facilitation of good science, supporting people. I also think about what I can do to support the overall mission of NOAA Fisheries. That’s my favorite thing, supporting others. I love when the focus is not on me!
What advice do you have for a young person interested in ocean-related careers?
Think about ways you can put yourself in the right place at the right time. Ask about volunteer opportunities. Ask questions, explore, think about what you want to do and look at people who are doing that—ask them how they got to that position.
What’s the coolest thing you’ve seen at sea?
When I was with the NOAA Vents group in 1994 I got to go to the bottom of the seafloor in the submersible Alvin. I was in there for nine hours with one other scientist and Alvin’s pilot. You think you’re going to know what it looks like, because you’ve seen video, and you think you’re going to understand how it feels, but then you get down there and everything is bigger, more beautiful, in all its variation and glory. We navigated to a mid-ocean ridge system that had an eruption the year previously. There was bright yellow sulfur discharge on black basalt rocks… after all those hours looking at ROV video, to see it in person through the porthole was incredible.
Do you have a favorite book?
The 5 AM Club, by Robin Sharma. I’m a morning person, and this book lays out how to structure those early hours and set you up for a successful day. When I was little I loved The Little Mermaid story by Hans Christian Anderson—the original, not the Disney version. I grew up in Vancouver, Washington and was always asking my parents, “Can we go to the beach?”
Taxonomy of Sights
Day 11. Three lampreys in the bycatch! Risso’s Dolphin (Grampus griseus). Day 12. Blue Whales! I guess they read my blog post about the Gordon Lightfoot song. What may have been a blue shark came up near the surface, next to the ship. Strange creatures from the deep in the bycatch: gremlin looking grenadier fish. Day 13. Pod of porpoises seen during marine mammal watch.
Blue Whale. Photo by Nick Metheny, marine mammal and bird observerGrenadier Fish
You Might Be Wondering…
How often are safety drills?
Weekly drills keep all aboard well-practiced on what to do in case of fire, man overboard, or abandon ship. Daily meetings of department heads also address safety. One activity of monthly safety meetings is to review stories of safety failures on other ships to learn from those mistakes. Each time a member of NOAA Corps is assigned a new tour at sea they must complete a Survival-at-Sea course. The Fishery Resource Analysis and Monitoring division (FRAM) also requires yearly Sea Safety Training for the scientists. “Ditch Kits,” found throughout the ship, contain: a rescue whistle, leatherman, food rations & water, and emergency blankets. Additionally, there are multiple navigation and communication tools in the ditch kit: a traditional compass, a handheld Garmin GPS, a boat-assigned PLB (personal locator beacon) registered with the Coast Guard, and a VHF radio with battery backup providing access to marine channel 16.
After a tour of the engine rooms, I learned that the diesel engines also have built in Emergency Diesel Generators (EDG). If you look up at the lights on the mess deck you’ll see some of the light fixtures have a red and white “E” next to them. This label indicates which would be powered by the generators, and which would not.
An individual Personal Locator Beacon is also assigned–in addition to ditch kit and lifeboat supplies. Teacher at Sea Gapp, trying on an immersion suit.
Floating Facts
The NOAA Corps is not a part of a union, however there are unions that advocate for other NOAA employees. Licensed engineers are a part of MEBA, The Marine Engineers’ Beneficial Association. Non-licensed positions are represented by SIU, Seafarers International Union. Both of these unions are a part of AFL-CIO, the largest federation of unions in the U.S.
I had been curious whether there was a database that housed an inclusive list of NOAA Fisheries field research, and NOAA did not disappoint. You can find the Fishery-Independent Surveys System (FINNS) here, and browse as a guest. I’m now brainstorming how I might use the database with students—perhaps as a scavenger hunt—to have them practice their search skills. You can search by: fiscal year, fiscal quarter, science center, survey status, and platform type.
Which Cook Inlet species is the subject of Alaska Fisheries Science Center (AFSC) 2023 research, which is underway in a small boat? Hint: Raffi
Another tool I’m looking forward to using in the classroom is NOAA’s Species Directory, which can serve as a scientifically sound encyclopedia for ocean animal reports conducted by students.
Librarian at Sea
“The sea is a desert of waves, A wilderness of water.”― Langston Hughes, Selected Poems
This quote from Hughes’ poem, Long Trip, had me thinking about the surface of the ocean. I have seen the surface in many states over the past days: soft folds, jagged white-tipped peaks, teal, turquoise, indigo. Sometimes there are long snaking paths of water that have an entirely different surface than water adjacent. Whether it is due to currents colliding, chemical process, biological process, temperature difference—I cannot say. If I were to anthropomorphize the phenomena, I’d say these lines are wrinkles, as the ocean creases into different expressions. A hint of what lies within and beneath.
It also has me thinking about the interviews I’ve conducted with the people on NOAA Ship Bell M. Shimada. I started with a superficial name and title, a face on a board near the Acoustics Lab depicting all hands on Leg 3. When I sat down to talk with people representing Scientists, Engineers, Deck Crew, Electronics, Officers, Survey, and Steward, I began to unspool colorful stories from a broad spectrum of life experiences, many from divergent habitats, all who have converged here to do in essence what the concierge at my Newport hotel said to me as I walked out the door, “Keep our oceans safe!” A tall order in so few words. From shore we’re a small white blip on the horizon; up close there’s a frenzy of activity, a range of expertise, a conviction that our actions can improve living for humans, for hake, and for all the species in Earth’s collective ecosystem.
A wilderness of blue water.
Hook, Line, and Thinker
We opened up a hake in the Wet Lab today to find it had a green liver. Why? Parasites? A bacterial infection? An allergy to krill? There’s always more beneath the surface, more stories to suss out. This is what makes science exciting, what makes living with 30+ strangers exciting. It’s what I enjoy about teaching.
How do the albatross know when we’re hauling back a net full of hake? They seem to appear out of nowhere. First a couple, then maybe 40 of them materialize around the net, squabbling over fish bits.
Have you ever discovered something unexpected and wondered about its origins? How could the scientific method support you in finding out an answer… or to at least develop a theory?
A Bobbing Bibliography
Known as “charts” at sea and “maps” on land, NOAA Ship Bell M. Shimada has a small library of charts. Find out more at NOAA’s Office of Coast Survey. Paper charts are actually being phased out. “NOAA has already started to cancel individual charts and will shut down all production and maintenance of traditional paper nautical charts and the associated raster chart products and services by January 2025.”
Mission: Fisheries: Pacific Hake Survey (More info here)
GeographicRegion: Pacific Ocean, off the coast of California
Date: July 13, 2023
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Weather Data from the bridge:
July11 (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.
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).
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.”
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.”
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.”
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 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.
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.
Sterile work site being set up to pour water samples into the cups and strain through the filters.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.
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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.
Basket one of Spiny DogfishBasket two 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.
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.
