The Biome Beneath the Surface

Author: Victoria Coles

Inhaling and exhaling, the ocean trades gases with the atmosphere; carbon dioxide, oxygen, chlorofluorocarbons and more. Different scientists on IO7 measure each of them. But what happens to the gases away from the sea surface? In the sunlit ocean, phytoplankton busily use energy from the sun to create more oxygen gas, and to convert carbon dioxide gas to plant mass. Equally active are the bacteria and animals who devour the plants as well as each other, respiring, or turning carbon biomass back to carbon dioxide while using up oxygen. The water here all looks blue to us (Fig 1).

Figure 1: Different shades of blue ocean on IO7.

From one day to the next there might be more or fewer whitecaps or torrential rain or fierce sun, but the water looks the same. Below the surface however, there is a hidden world with huge variability in plants and animals. Recently, we have begun to learn that the specific types of plant and animal food webs affect how gasses are processed in the ocean. So, we expect changes in the ecology to influence how much carbon or oxygen the ocean stores, and how much it passes back to the atmosphere.

And this brings us back to how we measure the plant and animal world at and beneath the ocean’s surface.  In the Bio Lab on the ship, Hannah Morrissette (MS student at University of Maryland Center for Environmental Science) and I are working with collaborators (Greg Silsbe, Raleigh Hood, and Joaquim Goes) using funding from NASA to understand the plant and animal communities that lie at the surface where satellites can see them, as well as below where they cannot. This is Hannah’s first time at sea, and I am continually reminded of how lucky we are to be here by experiencing this adventure through her eyes. For NASA, the satellites are our eyes; they measure the wavelength of the light reflected from the sea surface, then convert this to measures of chlorophyll content that can tell us both how many plants are present (Fig 2) and how fast they are growing. These are key measures of the health and state of the ocean, used for managing fisheries (like the tuna industry here in the Indian Ocean), as well as for understanding changes in the ocean’s exhalation of oxygen and carbon dioxide.

Figure 2: Ocean chlorophyll-a composite map using NOAA VIRS and NASA MODIS satellites. (Credit: Dr. Greg Silsbe)

But the satellite measurements of plankton growth must be confirmed and improved using direct measurements from a ship because the equations that convert the satellite reflectance to plankton biomass and growth depend on atmospheric conditions that are changing as well as the specific makeup of the plants that live in a region which is also changing. Here, on the Ronald H. Brown, we filter a lot of water (more than 2600 gallons so far; fig 3) to detect different pigments that each have a unique signature in the wavelengths the satellites measure. From this, we’ll improve the satellite maps to learn how the base of the food web responds to changing climate. We also continuously photograph the plankton community using a FlowCam (fig 4), and measure the size and shape of the cells as well as how they photosynthesize in response to light (using a FIRe instrument; fig 5). Each morning, we also sample the water column to learn how fast the plants and animals are growing by looking at changes in oxygen over time in sealed bottles (fig. 6). This will help us to develop estimates of how much plant based carbon sinks into the deep ocean – affecting the carbon and oxygen breath of the water when it ultimately returns to the surface.

We also tow nets in the upper ocean to learn more about the small animal or zooplankton communities that likely create the fastest source of sinking carbon to the deeper ocean. The water all looks blue, but the plants and animals have been changing radically over the different areas of the Indian Ocean (Figs 4 and 7); from the deserts of the subtropics, to the fertile tropical upwelling areas. These zooplankton samples get photographed and stored at sea for later analysis. Some animals will be examined to learn whether their shells are dissolving in waters with acidic pH. Other samples will be counted (old school) to learn who is there. Some samples will get analyzed with new genetic barcoding techniques (high tech) to find out which DNA occurs in each region. Using old and new school measurements allows us to compare this section with the last one 20 years ago while still staying up to date with modern technologies.

Figure 7: Some of the animals collected across our net tows.

As we steam through these hidden plant and animal habitats we are continually reminded of how little we know about the diverse organisms below the surface that alternately fuel and steal the ocean’s breath (Fig 7).

I07N 101: Intro to Oceanography

Author: Holly Westbrook

Hello! My name is Holly and I am a scientist. When you read the word “scientist” you might imagine a person in a white lab coat, goggles, and gloves, swirling a flask of strange colored liquid, or maybe frowning at a clipboard. Now, sometimes science does look like that, but other times it looks like this:

From left to right, Ian, Andy, and Christian deploying an ARGO float.

The scientists onboard the Ronald H. Brown are “oceanographers,” scientists who study the ocean. It can be a tricky field to study because we have to collect samples from places that can’t be easily reached (for example, the middle of the Indian Ocean).

We collect water samples from the bottom of the ocean all the way up to the top using a piece of equipment called a “rosette.” The rosette has many different things attached to it, to bring up water we use “Niskin bottles” (the gray bottles in the next picture). Once the rosette is on deck and secured we can start sampling. There are many different people who need to get water samples. We have a specific order of who goes when to make sure things stay organized and all the time-sensitive samples are collected quickly. Still, things can get a little crowded.

From left to right, Chuck, Leah, CFCs Chuck, and Ian working in close quarters to get their water samples.

There are a couple of different ways to collect water, many of us use plastic tubes and glass bottles, some use plastic bottles, some use glass syringes, and one person has a bit more of an involved method:

Christian sampling black carbon, looks like a pretty involved process.

A lot of the scientists work 12 hour shifts, we usually have another person who will take over our shift when we are done. That means that no matter the time of day there is always research being done! My shift is from 11:30 pm to 11:30 am. It was a little rough adjusting at first, but by now I’ve gotten used to it. Plus I’ve seen some pretty great sunrises.

A beautiful sunrise I got to see while waiting for my turn at the rosette.

When we’re not working, how we use our time is up to us. We can read outside, watch movies in the lounge, play card games, go to the gym, or talk to friends online—there’s a surprising number of ways to occupy your time!

Breakfast, lunch, and dinner are prepared by the stewards and they are at the same time every day. But there is always something to eat, which is good because I sleep through dinner and wake up several hours before breakfast. There’s things like oatmeal and cereal, but also daily snacks and ice cream at any time.

The days can be repetitive and tend to blend together but the importance of the work and the company we keep makes it all worthwhile!

From left to right: Bonnie, Myself Amanda, Catherine, Carmen, Annelise, and Jenna on a water taxi to Mahé.

Using Sound to Visualize Currents

Author: Amanda Fay

Time is flying! After so many weeks at sea I’m happy to report that spirits are high and everyone is going with the flow. Speaking of flow…let’s learn about currents!

So I am here as the sole person in charge of the LADCP or Lowered Acoustic Doppler Current Profiler, although I get lots of help from Jay and Andy. These instruments are attached to the rosette frame and use the Doppler effect of sound waves to measure the speed of water throughout the water column. ADCPs are very common in oceanographic work and can also be used in an anchored setup on the seafloor as well as mounted on seawalls or bridge pilings. Ships also frequently have ADCPs attached to their hulls, which allows them to take constant current measurements as the boat moves.

In our case, we use LADCPs, which means the instruments are lowered to the ocean floor and then brought back up in order to get a complete profile of the water column. There are 2 LADCP instruments on the platform- one that looks downward (the master) and one that points upward (the slave) as well as a battery pack that provides the instruments with power during their nearly 4 hour ocean voyage (depending on depth of the cast) at each sampling station. When the instruments are on deck between stations, they and the battery are connected to the ship’s power through a train of long black cables.

So what do I do? About 15 minutes before we reach the sampling station, I go into the lab adjacent to the sampling bay and begin the process of getting these instruments up and running in preparation for their next dive into the water. I check their status, erase their current files to make room for new data, and then get them all set to go. They start “ping-ing” and a few minutes later they are in the water.

The ADCP measures water currents with sound using the principles of the Doppler effect. Sound waves have a higher frequency when they move toward you than when they move away from you. The ADCP works by transmitting “pings” at a constant frequency while in the water. As the sound waves travel, they ricochet off particles in the water such as silt or plankton. The reflected sound is then bounced back to the instrument. The waves reflected off of a particle moving away from the instrument send back a slightly lowered frequency, while reflections off particles moving toward the instrument send back slightly higher frequency waves. The difference between what gets sent out and what the instrument receives is called the Doppler shift. The instrument uses this shift to calculate how fast the particle and the water around it are moving.

When the instruments get back on deck I reconnect power to them and the battery and begin downloading the precious data they hold. Some immediate QC is done to ensure things look good (cables haven’t gone bad, the battery is providing sufficient power, etc). Later, I process the data to see what kinds of currents we are seeing in the water. Sometimes this shows that I need to swap out an instrument (no small feat as they are quite heavy and awkward). Currently we have a Master that is operating with only 3 of its 4 beams operational. This is ok- redundancy is key in these types of instruments and they are able to work with just 3 beams, but no less.

And that’s how we use sound to measure the motion of the ocean.


Port of Seychelles: A Break from Operations

Author: Chuck Kleinwort

Life aboard a GO-SHIP cruise can be pretty hectic.  When CTD operations are in progress, work is being done on a twenty-four hour a day, seven days a week schedule.  Samples are drawn and analyzed as fast as they can be processed.  In a little over three weeks, sixty-four CTD casts have been performed and around 1500 samples have been drawn by the scientists working onboard.  This busy schedule leaves little time for rest and relaxation, as the data we are collecting is very important and every sample drawn provides one more snapshot of evidence to the current state of the Indian Ocean.  Luckily for us, there was an opportunity provided by NOAA to visit the Seychelles Islands in the mid-point of our sampling operations.  This stop provides a welcome reprieve from the rigors of the constant sampling scheme and gives both scientists and crew a chance to experience the natural majesty of the region.

The Seychelles Islands are a chain of rocky islands northeast of Madagascar.  They were colonized in the 1700s by French nationals, and a plantation lifestyle similar to the Caribbean Islands was instituted.  Goods such as cinnamon and chilies were grown in the tropical environment initially but shifted to less labor-intensive crops like coconuts later on.  In the early 1800s, the British took control over the island and it remained a colony until its’ independence in 1976.  This time of year is the tail end of the local monsoon season.  It is common during this period for northwest winds to bring large amounts of precipitation to the islands.

View of the eastern shore of the island Mahe from the summit of Morne Blanc, a local hiking trail.
View from the botanical gardens in Victoria.
Scientist Andrew Whitley feeding a giant tortoise. The animals are native to the region and can grow up to 250 kg (over 500 pounds) and have been proven to live longer than 170 years.
Enjoying the tropical beaches of the island.


Life on the Ronald H. Brown as a First-time Field Scientist

Author: Jenna Lee

I first started doing undergraduate research in the Martiny Lab a few months ago, with Cathy as my graduate student advisor. The plan was for her to train me on particulate organic matter (POM) nutrient analysis so that I could continue to run tests when she left in the winter for the I07N research cruise. I never expected to end up on the cruise myself, but by some stroke of luck (lucky for me at least), the cruise was delayed until April and a space on board the Ronald H. Brown opened up.

The ship was scheduled to leave port from South Africa on April 23rd, but I wasn’t guaranteed a spot on the cruise until the last week of March. The few weeks leading up to departure were hectic for me to say the least. I had to book an international flight, get vaccines, and buy everything I’d need for the next couple months. On top of that, I had never been on a boat for more than a day until now! I didn’t even know if I would get seasick or not (I definitely did the first few days). It was all worth it in the end, though, and I’m extremely grateful for the opportunity to be out at sea right now.


For me, the hardest thing to adjust to was my schedule. Cathy and I each take 12 hour POM sampling shifts, and mine is from midnight to noon. It took a few days for me to get used to going to sleep at 2pm and waking up at 10pm, but now I love my shift. It’s peaceful late at night, the stars are absolutely gorgeous, and the time difference from California makes it perfect to use the on-board wifi to talk to friends and family back at home. And whenever I have trouble waking up, I make myself a delicious budget mocha (a cup of the world’s strongest coffee mixed with a packet of instant hot chocolate). Between hourly samples, there’s plenty of time to relax watch a sunrise, catch up on some reading, or work on schoolwork. I’m technically still enrolled in a research thesis course, so I have plenty of reading and writing to do.

It’s great how nice everyone is, too! I’m pretty shy, but the crew and scientists alike really made me feel like family. People have set up a ping-pong table and hammock in the main lab, my saved meals have cute drawings on them, and there are bingo and movie nights.

Talking to all these amazing, supportive, established scientists and other students on board has been inspiring. I can’t wait to continue my education and pursue a career in oceanography. Hopefully I’ll continue to have opportunities like this one!