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.

A Peek into the Life of a CTD Watch Stander

Author: Yashwant Meghare

“DON’T PANIC” are the words I have written in big letters on my notes for how to operate a CTD. My excellent teacher, Kristene McTaggart (Kristy) laughs and agrees that it is indeed a very good thing to keep in mind.

Two days later, I have a dream that I let the CTD hit the bottom while going on an unapproved bathroom break. I woke up, very disappointed with my-dream-self.

May 5th, 2018

CTD: stands for conductivity, temperature and depth, and refers to a package of electronic instruments that measure these properties. Often, CTD is attached to a rosette that holds Niskin bottles for water sampling.

Somewhere in the middle of the Indian Ocean, at the so called “Station 22” I am sitting next to the person who operates CTD when I am off my watch- which goes from midnight to noon.

– Survey. Computer. Deploy the CTD.

– Winch. Computer. Down at 30 m/min. Target depth … (well whatever the depth is at that station)

The communication is very short and limited in order to avoid miscommunication or any kind of confusion. But as the CTD goes down to the unexplored abysmal depths of the ocean, it’s not the just the CTD that’s under pressure. The operator experiences the same feeling of increasing pressure.

– Quick instrument check for any signs of technical error. All good. (Well, at least that’s what we like to see.)

As the CTD goes deeper and deeper and things start to get more consistent, the operator is relieved. (or are they?)



FAST FORWARD >> 3 hours

The process of driving a CTD down to the depth can seem very uneventful. You will have to power through with a cup of coffee or some music that will bang you awake. (Or in my case, once when Kristy hid behind the door to scare me. I didn’t need much coffee after that.)

You keep increasing the speed from 30 meters per minute to 45 and then to 60. While it does seem like an uneventful job, there are spurts of times when there’s a bunch of tasks. Keeping a log of things at the beginning is important to have the final file tell you what data is important and what can be discarded. Keeping an eye for any system errors to mark them in the log is necessary. This works much like a checkpoint system in race. Anytime there’s an issue, flag it to check it later. So, even though there’s no consistent activity, it does require your attention all the time for quality data. This includes several markers in the data file to mark the beginning of the activity, the moment when CTD is underwater, when CTD is at maximum depth, and when it is going up.

The rosette hosting the CTD is not just working to measure the salinity, temperature and depth. It is an assorted set of instruments. It has a transmissometer to measure the clarity of the water, fluorometer, LADCP, oxygen sensors, altimeter that measures the height from bottom.

The altimeter activates when the CTD is within 100 meters of the seafloor. The goal is to keep the CTD off the bottom, but just close enough that the sediments don’t get sucked up into the pump (which can cause trouble).

– All stations, CTD is at maximum depth.



FAST FORWARD >> 3 hours

The journey back up involves collecting water samples at every few hundred meters.

– Winch, standby. Winch, slowdown. Winch stop. Collect water sample.

– Winch, up.

Once the CTD is back on deck, the bottles are checked for any leaks and made sure they had been fired. The real-time data collected is copied and saved on the system. The CTD operator helps with any sampling if needed.

Once all the samples have been collected, there are other simple tasks to take care of such as setting up the CTD for the next cast. There are small details that one must pay attention to for a successful cast. Andrew Stefanick (Andy), who seems like a pro with the CTD instruments helps with and teaches me all the fine details. Uncorking the bottles and cleaning the optical sensors needs to be done in a certain manner so that the equipment is not damaged.

The wording makes it sound like the CTD is some small fragile object, but in reality, it can’t be moved without the help of electrical pulley.

The purpose of GO-SHIP cruises is to observe changes in our oceans over time and this can be done only if we have quality data. From the Niskin bottles, the water is collected to do various types of analysis. Dissolved organic radiocarbon analysis, CO­2 levels, radiometric dating, nutrient concentrations, particulate organic matter, pH and alkalinity levels, dissolved oxygen concentration, CFC gas analysis, calcium analysis and density profiling are all performed on the water collected in the bottles on the CTD. So, this makes CTD a crucial part of the cruise and puts a lot of responsibility on CTD operators. With 132 CTD casts planned between Durban and Goa, this cruise will explore the Western Indian Ocean after a very long time and look for any changes that have occurred over the decades.



POM: The living and the dead

Author: Catherine Garcia

POM – What is it? – POM stands for “particulate organic matter”. Sea water particles could be living plankton, dead material, or even plastic bits that have made it out to sea. The dead material sometimes includes old plankton cells, plant matter, fecal pellets, airborne dust particles, river-borne soil particles, etc. The further the Ronald Brown moves away from the coast and into open water, a higher portion of the particles we capture is living phytoplankton, bacteria, and zooplankton.  Jenna and I are looking at the organic portion of the particulate matter, or the living/dead material. When this POM gets dense enough, it sinks out of the sunlit ocean layer and might make it to the ocean bottom if not consumed by bacteria on the way down. We call this the “Biological Carbon Pump”.

Jenna and Catherine filtering POM samples.

POM – Why and how do scientists measure it? – Scientists care about POM because phytoplankton play a VERY large role in removing carbon dioxide (CO2) from the air in the upper ocean. To understand just how much carbon is being removed, scientists need to measure how much carbon is captured in particles and what percentage sinks into the deep ocean by the Biological Carbon Pump. To know how much is carbon, we measure the elemental composition of particulate organic matter to obtain its concentration. The most abundant elements in organic matter are carbon, hydrogen, nitrogen, phosphorus, oxygen, and sulfur.

In the Western Indian Ocean, we are collecting samples for particulate organic carbon, nitrogen, phosphorus, and oxygen. The NOAA/V Ronald Brown has a sea water pump constantly bringing sea water conveniently to our lab bench.  Once we collect ~6L of sea water, all of it is filtered onto glass fiber filters that let any particles smaller than 0.7um flow though.

Glass fiber filter (on left) used to collect POM samples.

It really isn’t any different from than filtering the coffee grinds out of your coffee, except we keep what’s on the filter! Because larger plankton are rarer and a small fraction of the sea water in this area, we filter out any particles larger than 30um to avoid the occasional zooplankton. The filters are frozen after collection and stored frozen until analysis at Dr. Adam Martiny’s lab at the University of California-Irvine.  Once in the lab, the filters for carbon and hydrogen are eventually baked at more than 900oC in an Elemental Analyzer to turn all the carbon and hydrogen into a gas that can be measured. The phosphorus and oxygen are measured using chemical assays against a standard concentration curve.

POM – What does it tell us? – So, I mentioned why we cared about carbon, but why capture the other elements? Until recently the science community accepted a phytoplankton recipe of sorts: 106 parts carbon: 16 parts nitrogen: 1 parts phosphorus and so on. Mix together some carbon from photosynthesis and nutrients from the deep ocean to get your typical model phytoplankton. This ratio gives scientists a good estimate of how much POM is composed of carbon. Globally, an average phytoplankton does almost converge on this ratio of elements first described by Alfred Redfield in 1934. But not always.

Like us, plankton are what they eat. Phytoplankton in particular have extremely flexible elemental ratios. Just how flexible, and what causes them to change their ratios remains an open question. There are several theories that link elemental composition to environmental conditions, which group is present, or even how fast they grow. Jenna and I will try to track down this mystery on the IO7 cruise track.