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!

International Collaboration at Sea – Being a Japanese scientist on a US vessel

Author: Shinichiro Umeda

The ocean absorbs considerable heat and anthropogenic carbon dioxide (mostly from burning fossil fuels), slowing down the global warming. It is important for the future climate to monitor heat and carbon in the ocean regularly. Although satellite observations and autonomous instruments such as Argo floats are widely used, ship-based hydrography remains the only method for highly accurate measurements of temperature, salinity, and other chemical and biogeochemical parameters over the full water column. The ocean covers about 70% of the Earth surface and international collaboration is inevitable. The international program we are sailing for is called GO-SHIP (Global Ocean Ship-based Hydrographic Investigations Program).

Both JAMSTEC (Japan Agency for Marine-Earth Science and Technology), for which I work, and NOAA are part of GO-SHIP. R/V Ron Brown of NOAA is now observing the I07N section north of 30S. R/V Mirai (Japanese word “future”, see Image 2) of JAMSTEC will occupy the I07S section from 30S to 65S (or ice edge) in the 2019/20 season. The two sections will form a complete trans-basin section, contributing to understanding of the basin scale heat/material circulation of the Indian Ocean.

R/V Mirai has been to the Arctic, Pacific, and Indian Oceans (both subarctic and subtropical) since 1997. Her length is 128.5 m, beam is 19.0 m, depth is 10.5 m, draft is 6.9 m and gross tonnage is 8,706 tons. For hydrographic cruises, she carries 46 scientists on board, deploying CTD, collecting and analyzing water samples, all day and night.

JAMSTEC and NOAA have a long history of collaboration. To better understand and predict climate variations related to El Niño and the Southern Oscillation (ENSO), the TAO/TRITON moored buoy array is operated in the Tropical Pacific Ocean. TAO/TRITON was built over the 10-year period from 1985 to 1994 and is presently supported by JAMSTEC and NOAA.

And another episode of collaboration occurred in 2017. NOAA’s Pacific Marine Environmental Laboratory (PMEL) operates a research mooring at the Kuroshio Extension Observatory (KEO) which is located off the coast of Japan. The KEO surface mooring provides publicly available data including meteorological components such as wind velocity/direction and oceanographic components such as temperature/salinity and surface ocean acidification for international climate researchers worldwide. On October 19, 2017, it broke from its anchor and went adrift. A rescue took place on the high-seas at the end of December 2017, as technicians from JAMSTEC helped recover and redeploy the KEO mooring (See Image 3). The mooring continues to provide important data for the North Pacific research.

There are differences between JAMSTEC and NOAA, such as language, culture onboard, size of scientists onboard, duty team, etc. On the other hand, we (and probably all other sea-going research institutions) all love the sea and science we do, and willing to help each other in need. The collaboration continues.




CFCs: Unintentional Ocean Tracers

Author: Katey Williams

Hi! My name is Katey Williams and I’m working as a CFC analyst with Bonnie Chang and Chuck Kleinwort in the CFC lab aboard the Ronald H. Brown.


What are CFC’s ?

CFC stands for Chlorofluorocarbons. As the name suggests, these are chemicals that contain chlorine, fluorine, and carbon atoms. CFCs exist as a gas in both the atmosphere and dissolved in the ocean. These chemicals don’t occur naturally though. They were first manufactured in the 1930s as a non-toxic refrigerant. Older refrigerators used to use toxic gases as refrigerants. However, after a series of fatal accidents due to refrigerators leaking toxic chemicals, the need for a non-toxic refrigerant was recognized. So CFCs were invented. They worked well and were massively produced in the 1960s in refrigerators, automobiles, air conditioner and aerosols.

Unfortunately, the seemingly perfect chemical came with a catch.  Even though CFCs are non-toxic humans, they can cause some serious damage when they enter the upper atmosphere. The upper atmosphere contains the ozone layer, which protects earth by absorbing harmful ultraviolet radiation from the sun. Exposure to ultraviolet radiation can cause mutation in plants, animals, and humans, and can lead to higher rates of cancer and immune system problems. Once it was discovered that CFCs were creating holes in the ozone layer, governments started to ban the production and usage of CFCs. Since 1996, industries have phased out CFCs and the amount of CFCs in the atmosphere has started to decline.


What do CFCs measure in the ocean’s water column and why these measurements important?

CFCs may not have made great refrigerant chemicals, but what they do make is great ocean tracers. Even though CFCs have been phased out of industry, they still exist as a gas in the atmosphere. When the gases of the atmosphere interact with the surface of the ocean, some of the CFCs dissolve into the ocean and stay there. As these water masses travel around the ocean and throughout the water column, they take the CFCs with them. CFCs act like a dye in ocean currents that scientist can measure and track. Determining the age and the amount of CFCs in the water column can tell us about the rates and pathways ocean circulation and mixing patterns.


How are CFC measured?

Extracting CFCs out of the water column starts with taking water samples from the CTD. We use giant glass syringes to extract water out from the CTD bottles. Since there’s a higher concentration of CFCs in the air in comparison to the ocean, the water sample within the syringe has to be free of air bubbles. Otherwise the amount of CFCs in the water sample won’t be accurate.

After we take our water samples with the syringes, we take them to the CFC lab on the ship to analyze. The CFC lab has a system set up that extracts the CFCs out of the water sample and then runs the gases through a gas chromatogram. The gas chromatogram measures the concentration of CFCs in each of the water samples.

System in the CFC lab used to extract and analyze CFCs from the water samples. Gas chromatograms are the last three machines on the right.


We’re two weeks into the cruise and have already analyzed over 500 water samples! There will be many more to come as we continue to travel throughout the Indian Ocean, measuring CFCs and tracing ocean currents one sample at a time.


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.

Behind the Science: Dissolved Oxygen

Author: Leah Chomiak

Hello from the middle of the Indian Ocean! The skies are blue, the seas are calm, the air is fresh and full of oxygen (O2)… and so is the water column! My name is Leah, one of the scientists onboard I07N running dissolved oxygen analyses along with my counterpart, Sam. Together, we are in charge of sampling, assessing, and quantifying the amount of gaseous oxygen dissolved in the seawater from every bottle of every station… coming to a grand total of 3,432 samples once we close out the transect in India. Wowza!


Dissolved oxygen, the same stuff you and I breathe each second of the day, is crucial to the marine environment; whether that be oceans, lakes, rivers, or ponds, for obvious reasons. Oxygen is essential for life and is taken up by organisms through a process termed cellular respiration where oxygen is taken in and carbon dioxide is spit out in return. The reverse process, photosynthesis, results in the generation of oxygen through the uptake of carbon dioxide. Just like on land, plant cells fill the oceanic environment in the form of plankton, where oxygen is produced. All remaining organisms of the sea, from fish and sharks to corals and giant squids, rely on the presence of dissolved oxygen in the water column just as we rely on oxygen in our atmosphere – to survive! We measure the dissolved oxygen to understand not only the biological and chemical aspects of seawater, but also for understanding the physical movement of currents and water masses too.

o2 titrationWe start by first collecting a sample of seawater out of a Niskin bottle that is closed at a certain depth in the water column from a CTD rosette, yielding samples from 24 different depths spanning the surface to the ocean floor. Immediately after collecting the seawater sample, the sample is ‘fixed’ with two reagents that react to form a precipitate – in simplest terms, all of the dissolved oxygen reacts to form a solid and is suspended in solution. By performing this reaction, we essentially have the power to “freeze” all oxygen in the sample at that given moment, meaning photosynthesis and respiration are halted and no further O2 is produced or consumed. Once the entire CTD has been sampled, the O2 samples are brought back to our lab inside the ship, where we then give them a shot of strong acid to dissolve the precipitate (turning the sample a cool yellow color) and at last perform a titration to determine the amount of oxygen present in the sample.

Since the surface ocean and the atmosphere are in constant exchange with each other, oxygen from the atmosphere is assimilated into the surface waters, and we tend to see high oxygen near the surface for this reason. Due to the availability of sunlight near the surface, plankton aggregate and help to contribute to the surface oxygen levels through photosynthesis. Samples taken near the bottom of the ocean also tend to have high oxygen levels, one being because the extreme pressure and cold temperatures facilitate the dissolution of gas in seawater, and two, certain water masses, such as the cold and dense Antarctic Bottom Water are known to have high O2 content due to recent exposure with the atmosphere. Central in the water column is where the oldest water lies, and oxygen tends to be lacking due to uptake by biological organisms. Not only is oxygen useful in assessing biological productivity, its also a great parameter to use when observing global ocean circulation!

The outflow of the Arabian Sea/northern Indian Ocean is observed as one of the largest and most distinctive oxygen minimum zones (OMZ) in the world, where oxygen concentrations are extremely low due to high biologic consumption and other chemical factors. As we continue to head north along the I07N transit line, it will be very interesting to see how our oxygen profiles change as we enter the OMZ. It has been 23 years since this hydrographic line was last sampled; I wonder what we will observe this time around!