Imaging Flow Cytobot – NOAA Teacher at Sea Blog

August 17, 2019

Ragupathy Kannan: Starting with Plankton, August 18, 2019

NOAA Teacher at Sea

Ragupathy Kannan

Aboard NOAA Ship Gordon Gunter

August 15-30, 2019

Mission: Summer Ecosystem Monitoring

Geographic Area of Cruise: Northeast Atlantic Ocean

Date: August 18, 2019

Weather Data from the Bridge

Latitude: 38.2494289
Longitude: -75.0853552
Water temperature: 26.3°C
Wind Speed: 4.92 knots
Wind Direction: 122 degrees
Air temperature: 27.1°C
Atmospheric pressure: 1015 millibars
Sky: Partly cloudy

Science and Technology Log

In my previous blog posting, I explained the importance of plankton as base of the ecological pyramid upon which much of marine life in this ecosystem depends. The past few days, I have witnessed and experienced in-person how scientists aboard this sophisticated research vessel collect and analyze sea water samples for plankton.

Yesterday I spent some time with Kyle Turner, a guest researcher from the University of Rhode Island doing his M.S. in Oceanography. He operates a highly sophisticated device called the Imaging FlowCytobot (IFCB). I was fascinated to learn how it works. It is basically a microscope and camera hooked up to the ship’s water intake system. As the waters pass through the system, laser beams capture images of tiny particles, mostly phytoplankton (tiny photosynthetic drifters). As particles do, they scatter the light or even fluoresce (meaning, they emit their own light). Based on this, the computer “zooms in” on the plankton automatically and activates the camera into taking photographs of each of them! I was amazed at the precision and quality of the images, taken continuously as it pipes in the water from below. Kyle says this helps them monitor quality and quantity of plankton on a continual basis.

Kyle Turner and IFCB — Kyle Turner with the Imaging FlowCytobot (IFCB)

Kannan and IFCB — Here I am examining a filamentous (hair-like) phytoplankton in the IFCB monitor.

IFCB computer screen — The various kinds of phytoplankton are neatly displayed on the IFCB’s computer screen. See my previous blog for a photo of the dazzling and colorful array of plankton out there! Plankton may lack the popularity of the more charismatic sea animals like whales, but much of life in the ocean hinges on their welfare.

Career Corner

Hello, students (especially bio majors). In this corner of my blogs, I will interview some key research personnel on the ship to highlight careers. Please learn and be inspired from these folks.

Here is my interview with Kyle Turner.

Q. Tell us something about your graduate program.

A. My research focuses on phytoplankton using bio-optical methods. Basically, how changes in light can tell us about phytoplankton in the water.

Q. How does this IFCB device help you?

A. It gives me real time information on the different types of phytoplankton in the location where we are. We can monitor changes in their composition, like the dominant species, etc.

Q. Why are phytoplankton so important?

A. They are like trees on land. They produce about half the oxygen in the atmosphere, so they’re super important to all life on earth. They are also the base of the marine food web. The larger zooplankton eat them, and they in turn are eaten by fish, and so on all the way to the big whales. They all rely on each other in this big ocean ecosystem.

Q. How are phytoplankton changing?

A. The oceans are warming, so we’re observing shifts in their composition.

Q. What brought you into marine science?

A. I grew up on the coast. I’ve always liked the ocean. I love science. So I combined my passions.

Q. What is your advice to my students exploring a career in marine science?

A. Looking for outside research opportunities is important. There are so many opportunities from organizations like NASA, NSF, and NOAA. I did two summer research internships as an undergrad. First was with NASA when I was a junior. I applied through their website. That was a big stepping stone for me. A couple of years later, I did another summer project with a researcher who is now my advisor in graduate school. That’s how I met her.

Q. What are your future plans?

A. I’d love to get into satellite oceanography to observe plankton and work for NASA or NOAA.

Personal Log

I am pleasantly surprised by how comfortable this ship is. I was expecting something more Spartan. I have my own spacious room with ample work and storage space, a comfortable bed, TV (which I don’t have time for!), and even a small fridge and my own sink. Being gently rocked to sleep by the ship is an added perk!

Sunrise view — A room with a view—sunrise from my window

The food is awesome. We have two expert cooks on board, Margaret and Bronley.

The ship’s mess is a nice place to eat and interact with people. There’s always food available 24/7, even outside of meal hours.

Did You Know?

NOAA Ship Gordon Gunter played a big role in recovery operations following Hurricane Katrina and the Deepwater Horizon oil spill.

Barograph — This photo is displayed in the galley. Note the sharp decline in atmospheric pressure as Katrina thundered through.

Some interesting animals seen so far

Flying fish (they get spooked by the ship, take off and fly several yards low across the water!)
Cow-nosed Rays (see photo and caption below)
Leather-backed Sea-turtle (I’m used to seeing them on the beach in Trinidad—see my previous blog. It was a treat to see one swimming close by. I was even able to see the pink translucent spot on the head).
Bottle-nosed Dolphins
Seabirds (lots of them…. four lifers already—more on this later!)

school of cow-nose rays — We saw large schools of Cow-nosed Rays closer to the coast. These animals feed on bivalve mollusks like clams and oysters with their robust jaws adapted for such hard food. They are classified as Near Threatened due to their reliance on oyster beds which are themselves threatened by pollution and over exploitation.

August 27, 2018September 2, 2018

Martha Loizeaux: Salp Confidence, August 24, 2018

NOAA Teacher at Sea

Martha Loizeaux

Aboard NOAA Ship Gordon Gunter

August 22-31, 2018

Mission: Summer Ecosystem Monitoring Survey

Geographic Area of Cruise: Northeast Atlantic Ocean

Date: August 24, 2018

Weather Data from the Bridge

Latitude: 40.15 N

Longitude: 68.71 W

Wind direction: NE

Wind speed: 14 knots

Water temperature: 23.8 degrees C

Air pressure: 1023 millibars

Air temperature: 24.2 degrees C

Water depth: 165 meters

Science and Technology Log

What an exciting first full day out at sea! I have been so grateful that our science team has allowed me to be completely hands-on and take responsibility for some of the science happening on the ship. In addition to checking the Imaging Flow Cytobot (IFCB) periodically, I am very much involved in the data collection at each of our stations.

There are specific stations along our course where scientists need to collect data. The crew announces when we are close to the station. At that time, along with another volunteer on watch, I don my foul weather gear to head out to the deck. We get pretty splashed as we are working with the equipment so the gear is a good idea. We help the crew as they lower “bongo nets” into the water using a cable and pulley system. Can you guess why they are called bongo nets? These nets have a very fine mesh that helps collect, you guessed it, PLANKTON!

bongos on deck — *bongo nets waiting on the deck to be deployed*

bongos in water — *The bongo net and the “baby” bongo net being deployed.*

We also help raise the bongo nets after several minutes dragging them through the water. We rinse all of the plankton down to the bottom of the net and then open up the end of the net to allow all of the plankton into a sieve where we will collect it. I have been surprised by the amount of jelly-like animals that have shown up in the nets!

Then it’s time to use special liquids (ethanol or formalin) and water to wash the plankton into collection jars. These chemicals will preserve the plankton so scientists can study it back in the lab!

It has been so much fun working with this equipment, asking the scientists questions about the plankton, and being a part of it all.

Harvey, our chief scientist, explained to me that many scientists can use the plankton samples for all different studies. Some of the samples can be used to study larval fish (baby fish) otoliths, the tiny ear bones that can verify the identification of larval hake using genetics. Knowing this, scientists can do research to determine where the larval fish were born! What a great example of the beginning of a scientific

Hake larvae — *Some examples of larval hake. Photo courtesy of Harvey Walsh*

experiment!:

Question – Where are most larval red hake fish born in the Northeast Atlantic Ocean?

Research – Scientists might research currents in the area, wind patterns, and other things that would push plankton from place to place. They also would research what other scientists have already learned about larval red hake.

Hypothesis – Most larval red hake fish are born in the Southern New England and Georges Bank regions in the northeast US shelf.

Didn’t I tell you plankton were amazing?

At some of the stations, we also lower Niskin bottles and CTD instruments into the water to collect a lot more data! More on that to come!

Martha and bongos — *Here I am getting ready to deploy the bongo nets.*

rinsing nets — *Jessica and I rinsing the bongo nets.*

plankton on sieve — *Plankton looks tiny when we filter it into a sieve.*

*Our plankton samples after being rinsed into the jars.*

NOAA Corps Corner

Today I spoke with Lola Ajilore, Officer with NOAA Corps, and asked her a few questions about her important work. A pod of humpback whales off the bow stole the show! Here’s what we got in before the exciting interruption…

Me – Tell me more about your roles on the ship.

Lola – I am the Navigation Officer, Medical Officer, Environmental Officer, Ship Store Officer, and Morale Officer. As you can see, we all have multiple roles on the ship. As Navigation Officer, for example, I plot charts, track directions, and coordinate with the Operations Officer and Commanding Officer on track lines and routes that are requested by the scientists.

Me – Where do you do most of your work?

Lola – I am always with NOAA Ship Gordon Gunter. The ship’s home port is in Pascagoula, Mississippi. Our missions often take place in the Gulf of Mexico but we also run these Northeast Shelf cruises for Ecosystem Monitoring every year.

Me – What kind of training is needed for your line of work?

Lola – We undergo an application process that includes several interview steps. We then train at the Coast Guard Academy. Much of our training parallels that of the Coast Guard, but we also do our own NOAA Corps training as well.

Me – What tool do you use in your work that you could not live without?

Lola – Radar! [Radar aids navigation by detecting things that are far away such as an island or another ship]

Nav officer — *Lola as Navigation Officer.*

humpback from afar — *Can you see the little black dot in the middle of the picture? It’s a humpback whale! It looked a lot closer in real life.*

Personal Log

sunset view — *Sunset on NOAA ship Gordon Gunter*

I cannot believe the amazing views that we have on this ship 24 hrs. a day! The water has been super calm and the sunrise, sunset, breaching whales, and pods of dolphins have taken my breath away.

Yesterday was emergency drill day! Libby, our Operations Officer, had given us directions on how to respond to emergencies prior to leaving the

*Mustering on the deck during the emergency fire drill.*

dock. There are emergency drills for a fire (just like at school!), abandon ship (in the case that we had to immediately leave the ship in an emergency), and man overboard.

We practiced a fire drill and an abandon ship drill. The Officers on the ship sounded the alarm, using a different number and duration of blast based on the type of emergency. For a fire, we all “mustered” (got together in one place) in assigned areas. All of the science team members mustered together. For abandon ship, we all mustered near the life boats along with our life jackets and immersion suits (suits that can help you survive if you end up in the water).

Martha in immersion suit — *Here I am in my immersion suit!*

The fun part of the abandon ship drill was donning our immersion suits in one minute or less! This was a great thing to practice so if there ever was a real emergency, we would know how to put on the suit. I thought I looked pretty cool in my immersion suit.

Did You Know?

Salps are barrel-shaped planktonic tunicates. Our plankton bongo nets always contain some jelly-like salps. Where I live in the Florida Keys, we see mangrove tunicates growing on mangrove roots. Here in the open ocean, salps stick together in long colonies and drift! Sometimes there are so many salps in our nets, we have to filter them out with sieves and put them back in the water.

salps from web — *An example of a colony of salps. Photo courtesy of NOAA*

Something to Think About

We have been finding up to 4,000 phytoplankton in 5 mL of water. A gallon of water is equal to about 3785 mL. There is about 352,670,000,000,000,000,000 gallons of water in the Atlantic Ocean. How much plankton is in the Atlantic? You do the math.

plankton from web — *This is what some plankton look like under the microscope. Photo courtesy of NOAA*

May 27, 2018May 29, 2018

Susan Dee: Microscopic Sea Life – Days 1-4, May 24, 2018

NOAA Teacher at Sea
Susan Dee
Aboard NOAA Ship Henry B. Bigelow
May 23 – June 7, 2018

Mission: Spring Ecosystem Monitoring Survey

Geographic Area of Cruise: Northeastern Coast U.S.
Date: May 24, 2018
Weather Data from Bridge
Latitude: 40°32′
Longitude: 070°45′
Sea Wave Height: 1-2 feet
Wind Speed: 12 knots°
Wind Direction: west
Viability: unrestricted
Air Temperature: 13.5°C
Sky: Few clouds

Science and Technology Log

Tuesday, May 22, I arrived at Newport Naval Base and boarded NOAA Ship Henry B. Bigelow to begin my Teacher at Sea journey by staying overnight on a docked ship. Day 1 was filled with many new experiences as we headed out to sea. The Henry B. Bigelow is part of a fleet of vessels commissioned to conduct fishery surveys. To learn more about the Henry B. Bigelow, check out this website: Henry B. Bigelow. The objective of this cruise is to access the hydrographic, planktonic and pelagic components of North East U.S. continental shelf ecosystem. The majority of the surveys we will take involve the microbiotic parts of the sea – phytoplankton, zooplankton and mesoplankton. Plankton are small microscope organisms in the oceans that are extremely important to the entire Earth ecosystem. These organisms are the foundation of the entire ocean food web. By studying their populations. scientists can get an accurate picture of the state of larger ocean organism populations.

Before leaving the dock, I met with Emily Peacock from Woods Hole Oceanographic Institute (WHOI) to learn how to run an Imaging Flow Cytobot instrument that uses video and flow cytometric technology to capture images of phytoplankton. The IFCB was developed by Dr Heidi Sosik and Rob Olsen (WHOI) to get a better understanding of coastal plankton communities. The IFCB runs 24 hours a day collecting sea water and continuously measuring phytoplankton abundance. Five milliliters of sea water are analyzed every 20 minutes and produces the images shown below.

Imaging Flow Cytobot IFCB — Imaging Flow Cytobot (IFCB)

phytoplankton — Images of Phytoplankton taken by IFCB

The science party on board is made up of scientists from National Marine Fisheries Service (NMFS) part of NOAA Fisheries Division. The chief scientist, Jerry Prezioso, works out of Narragansett Lab and the lead scientist, Tamara Holzworth Davis, is from the Woods Hole Lab, both from the NOAA Northeast Fisheries Science Center. Other members of the Science Party are Seabird/Marine Mammal observers and a student from Maine Maritime Academy. The Crew and scientist group work together to coordinate sampling stations. The crew gets the ship to the site and aid the scientists in deploying instruments. The scientists collect the data and samples at each station. The Crew and scientists work together to find the best and most efficient sea route to each sampling site. Note all the stops for specimen collection on map below. There definitely has to be a plan!

map of proposed route — Proposed Cruise Track and Survey Locations

Personal Log

Because research instrument deployment is done 24 hours a day, the NOAA Corps crew and scientists are divided into two shifts. I am on watch 1200 – 2400 hours, considered the day shift. This schedule is working good for me. I finish duty at midnight, go to sleep till 9:00 AM and rise to be back on duty at noon. Not a bad schedule. Due to clear weather and calm seas, the ship headed east out of Newport Harbor towards the continental shelf and started collecting samples at planned stops. I joined another group of scientists observing bird and marine mammal populations from the flying bridge of the ship. Humpback whales and basking sharks breached several times during the day

It has only been two days but I feel very acclimated to life at sea. I am not seasick, thanks to calm seas and the patch. Finding the way around the ship is getting easier- it is like a maze. Spotting a pod of humpback whales breaching and basking sharks was a highlight of the day. My Biology students back at May River High School scored great on End of Course Exam. Congratulations May River High School Sharks! Thinking of y’all.

Love My SHARKS!