Notes from the Field

Phytoplankton Sampling Strategies

February 20th, 2017 by Zrinka Ljubešić

Plankton comes from the greek word planktos, meaning wanderer. It does not define a specific organism, but rather a specific life style. Plankton consist of all organisms dispersed in water that are passively driven by water currents or are subject to passive sinking process. Some of those organisms have an ability to produce oxygen and sugars using sunlight and CO2, just like terrestrial plants do. We call them phytoplankton (greek: phyton -plant ).

Phytoplankton are the wandering meadows of the ocean and an important base of the food web. Most of the phytoplankton are smaller than the width of the single human hair. They are feeding the hungry ocean, and the phytoplankton composition determines the diversity of organisms developing on the higher trophic levels like fish, birds and mammals. It is not only important for organisms living in the ocean, but it is crucial for all life on Earth. Consider the size of the oceans covering our blue planet for a moment – the amount of phytoplankton every second breath that we take the oxygen is produced by phytoplankton.

This is microscopic picture of a diatom called Leptocylindrus, a kind of phytoplankton. Phytoplankton feeds the ocean, and the phytoplankton composition determines the diversity of organisms developing on the higher trophic levels like fish, birds, and mammals. Colleen Durkin

How To Begin?

When it comes to phytoplankton, it is not just the quantity, but also the quality that matters. You may wonder how can researchers sample something that we cannot see that exists in an environment where we cannot be in? How can we catch something that is passively driven by currents and changing all the time? How can we get the insight of the abundance of some particles that are unevenly dispersed in an ocean? Since the discovery of the microscope scientists have been trying to find answers to those questions.

Here, on R/V Falkor we are combining traditional methods of phytoplankton analysis – such as preservation of water for later, onshore analysis under a microscope – with the new, recently developed methods of onboard image analyses. Discrete samples are taken with the Niskin bottles at the specified depth. The sampling depth is chosen according to the physical, chemical and biological characteristics of the water column that are measured by the instruments mounted on the rosette, and controlled from the science control room. Once the rosette is on deck, the samples are taken from the Niskin bottles and prepared to be either stored until they return to land, or analyzed on board. The great advantage of the onboard image analysis is that it lends an instantaneous snapshot of the phytoplankton composition and abundance, which allows you to adapt your sampling strategy and use the time spent on the ship in a better, more productive way.

Discrete samples are taken with the Niskin bottles in each CTD cast, at specific depths. The sampling depth is chosen according to the physical, chemical, and biological characteristics of the water column. SOI/Mónika Naranjo González

The flow-through system onboard the R/V Falkor allows us for continuous sampling of the surface water for physical, chemical and biological properties, including phytoplankton composition with Imaging Flow Cytobot. This amazing instrument samples from the flow-through system every 20 minutes, and takes images of particles contained in 5 mL (100 drops) of seawater. Therefore, as we steam through the Pacific or as we stop to conduct some other measurements, we are continuously gathering high-spatial information about phytoplankton abundance and composition. The advantage of taking images vs. looking at the cells through the microscope is that you can always go back to your sample if needed. That helps us that help to have comparable results and minimizes the error of phytoplankton counting and taxonomy misidentification.

The Imaging Flow Cytobot is one of the state-of-the-art technologies used on the current expedition. As Falkor sails, a pump runs seawater through the instrument, which takes pictures of all the particles present. SOI/Ivona Cetinić

The Future….

Will the modern methods of high-resolution imaging ever substitute traditional microscopy? I would say – no. While continuous sampling techniques give us amazing insight into the spatial distribution of the phytoplankton and inform best sampling strategies, classical microscopy gives us insight into the detailed morphological characteristics that are needed to be seen from multiple angles to really be understood. The phytoplankton taxonomy is under constant revision and change as the new methodologies develop. With more knowledge and deeper insight, we do find answers to existing questions, but we also encounter more questions that need to be answered. The combination of the traditional and modern methods is the best strategy to understand the secrets of these beautiful oceanic wonders.

Science at Sea: Challenges, Silver Linings, and Success

February 18th, 2017 by Mónika Naranjo González

The sediment traps and the Wirewalker were recovered after three days of collecting data with a big surprise. Some parts were bent, and three out of the four collecting cylinders of the sediment traps were missing. The remaining trap was broken and unusable. One battery pack was lost, another damaged and the bungee had snapped. “What if we are not prepared for the North Pacific in winter?” thought Physical Oceanographer Melissa Omand. Colleen Durkin, Oceanographer, felt her confidence take a hit. Her team had deployed these instruments before, so she was not expecting anything to go wrong. She thought the big waves were the cause.

A fraction of a tooth found stuck in the line told a different story: the North Pacific was not to blame, but instead the instruments were damaged by a Great White Shark. This was certainly a rocky start for the team and a true testament to the unexpected challenges of conducting science at sea.

The Wirewalker came back up with more than just great data at the first station. Due to a tooth being embedded in the line, researchers presume a White Shark attacked the instrument. SOI/ Mónika Naranjo González

Silver Linings

Amazingly, the data extracted from the nine sensors in the Wirewalker was complete. This provided new insights about the instrument’s resilience and capabilities. Even with ripped cables and a lost battery pack, it did not miss a beat and came back with an important discovery from Hawaiian waters: the team was excited to confirm a growth in the amount of particles during daytime, which was surprising for two reasons.

The first reason deals with the behaviour of phytoplankton itself. Confirming that that there is a variation in the amount of organisms found at day or night is key to make a complete characterization of the oceanic carbon cycle. Melissa, Colleen, and Biogeochemical Oceanographer Meg Estapa are studying the Carbon Pump: how particles sinking in the ocean drag carbon down to the depths of the ocean with them, removing carbon from the atmosphere. By learning about variations in the particles through time – as well as in different layers of the water column – scientists can better understand the physical mechanisms involved in particle distribution in the ocean. This also relates to the biochemical processes that the ocean controls.

The second surprise pertains to the Wirewalker and its capabilities. The instrument walks the 150 meter-long wire every seven minutes. A sensor in the walker emits light and then measures how much light bounces back after hitting particles suspended in the water. Counterintuitively, the smaller the particle, the more light it backscatters. The team already knew the Wirewalker would provide info about the particle’s sizes and density, but they did not expect that could also be used to measure community growth. The evident variation in the amount of light backscattered was an indicator of a change in the amount of particles suspended in the water. Other optical instruments confirmed the walker’s findings, which suggests that the Wirewalker could be useful to determine more measurements than previously thought.

This is a composite image containing the findings of one gel sediment trap, created from a series of photographs taken with a microscope. Within it, aggregates, fecal pellets, phytoplankton, zooplankton and other particles can be seen. Image credit: SOI/Melissa Omand


Not even a Great White could stop the team. Three stations and four weeks later, Colleen Durkin and Melissa Omand can barely contain their excitement when, for the first time, they watch the time-lapse photographs taken by a mobile phone deployed along with the Wirewalker. Playing the pictures as a sequence creates a minute-long movie: “This is the movie of your dreams!” exclaims Colleen, “We’re with them, seeing the things we’ve studied for so long.” This is a small victory, but one that Melissa will carry with her proudly when she walks away from Falkor. Her timelapse repurposed phone contraption works, providing new information about the subtle machinery that drives the carbon cycle, and even proving that the instruments work as intended: the movie shows that the particles falling into the gel traps are preserved in an optimal way.

Colleen Durkin and Melissa Omand can barely contain their excitement when they watch for the first time a time-lapse movie created from the images taken every 2 seconds by a newly developed instrument. SOI/ Mónika Naranjo González

New Actors Take the Stage

1750 liters of seawater filtered. 150,000 Flow Cam pictures, 810,000 Cytobot images, 361,200 meters of the ocean profiled. It will take months for the interdisciplinary team on board Falkor to be able to process all the data and then begin cross-referencing it, but some preliminary observations have been made.

Radiolarians are planktonic creatures that up until now have not received much attention when it comes to painting the ecological big picture of the Carbon Cycle. Recently, some articles showed some statistical significance, but offered no clues about the specific role played by them. Aggregates found in the sediment traps suggest that they actually play an important part in the carbon pump. Colleen Durkin suspects this will be an important result of the team’s research, filling in one more piece of the puzzle. “I’m sure other things will pop up as we process the samples,” she adds.

As the expedition approaches its end, Melissa’s question about preparation has been clearly answered: Falkor, the crew, the scientists, and the instruments were all ready to take on winter in the North Pacific. Nearing their return to shore, they are bringing back high-resolution imagery, tens of terabytes of data, and the successful testing of new state of the art technologies.

Radiolarian might not have received the attention they deserve up until now. The findings of some of the sediment traps suggest they play an important role in the Carbon Cycle.

The Ocean’s Colors From Space

February 17th, 2017 by Antonio Mannino

A radiometer installed in the bow of Falkor takes color measurements from both seawater and sky. SOI/Kristen Carlson

Earth’s ocean is vast and deep, and we still need to study many things about it. To investigate and quantify biological and chemical processes, for instance, we need to determine the concentration and size of particles (living and non-living organisms) floating in the water, dissolved materials, and the diversity of organisms such as the microscopic photosynthetic phytoplankton. Their study requires both direct measurements by deploying instruments at sea or analyzing water samples, and satellite remote sensing.

Particles and dissolved organic materials scatter and absorb the sunlight that enters the ocean, which alters the ocean’s color. For instance, the first site that we sampled contained low abundances of particles including phytoplankton and dissolved organic materials, which translated to clear blue waters. Higher abundances of phytoplankton result in greener seas because of their chlorophyll pigments.

Sea to Space

Since 1978, NASA has applied satellite remote sensing to study phytoplankton. The image depicts chlorophyll concentrations in the ocean. NASA/Norman Kuring

Since 1978, NASA has applied satellite remote sensing to study phytoplankton though its experimental Coastal Zone Color Scanner. Several other sensors followed from 1997 to the present. By 2022, NASA expects to launch the next generation ocean color satellite sensor for the Plankton, Aerosol, Cloud, and Ocean Ecosystem (PACE) which is currently being developed. This PACE sensor will provide unprecedented detail on the color spectrum and intensity of the light exiting the ocean’s surface, which will be used to infer a lot of information about our oceans, including the concentration and size of particles and dissolved organic materials, the diversity of phytoplankton, and rates of phytoplankton growth within the ocean’s sunlit surface layer.

To successfully apply the capabilities of the PACE sensor requires the development of relationships between ocean data (such as chlorophyll-a) and how it affects the color and the amount of light that will be measured by the satellite. One of our goals for participating on the Sea to Space Particle Investigation in the northeastern Pacific Ocean aboard Falkor is to collect biological, chemical and optical measurements in order to build these relationships.

To be able to do so, much of our work at sea involves development and evaluation of new methods and measurement capabilities to ensure that the data collected are of sufficient quality for application with satellite remote sensing. For example, to quantify phytoplankton growth rates, we are conducting experiments with phytoplankton and measuring the oxygen produced and carbon dioxide consumed over time.

Only satellite remote sensing can provide the comprehensive data sets across space and time needed to study the state of Earth’s vast ocean. The ocean moderates our weather, provides food, medicine, energy resources, recreation, and many other benefits. Improving our understanding of the ocean will help us better predict how it will change in the future.

Antonio Mannino, Oceanographer, installs a Coulometer in Falkor’s wet lab to measure particle productivity in water samples collected during the expedition. SOI/Mónika Naranjo González

Phytoplankton in Three Phases

February 15th, 2017 by Aimee Neeley

I always knew that one day I wanted to study the ocean, even though I grew up just north of Pittsburgh and had never seen the ocean. After graduating high school, I attended the College of Charleston in South Carolina where my plan from the start was to major in Marine Biology. I began my junior year in college with no idea what I wanted to do with this very broad degree. Then I took the required oceanography course – after that, oceanography and phytoplankton (aquatic plant life that is microscopic) were in my life permanently.

Aimee Neely, Biological Oceanographer, is studying particles using a FlowCam, an instrument that takes pictures of all the particles in the water flowing from a pump located in Falkor’s aft. SOI/Mónika Naranjo González

Phase 1: What Are Phytoplankton?

For an undergraduate project, I measured the response of several species of phytoplankton to different light intensities by measuring the concentration of their photosynthetic pigments, the compounds that collect light for photosynthesis. Pigments can also be used to identify specific groups of phytoplankton. During the second year of my Master’s program for marine biology, I participated in my first research cruise on a Canadian Coast Guard vessel that sailed from Dutch Harbor to Barrow, Alaska. I got my first taste of filtering, which is the collection of particles onto glass fiber pads that can be used for various analyses. Despite my initial bout of sea sickness in a near flat sea state, I was hooked.

In 2007 I pursued a research opportunity at the Bermuda Institute of Ocean Sciences where I was ship-bound once a month measuring the sulfur-based compounds made by phytoplankton that are thought to enhance cloud formation when they are outgassed to the atmosphere. For years, what I knew about phytoplankton was based on chemistry and physiology.

Samples filtered by Aimee will be processed back on land to measure different pigments in order to identify the planktonic organisms contained in it. SOI/Mónika Naranjo González

Phase 2: We Can Measure Phytoplankton from Space?

In late 2008, I left the beautiful island of Bermuda (crazy, right?) for Maryland to work at NASA Goddard Space Flight Center. Before this time, I knew nothing about satellites or ocean color remote sensing. While working at NASA I have learned that everything in the ocean – dissolved compounds, phytoplankton, and particles – absorb and scatter sunlight. Using this information about the color of the light reflecting out of the ocean, we can translate this light into information about what types of phytoplankton are in the water column.

High temporal and spatial resolution observations in the global ocean are just not feasible as we are limited by time and resources. Therefore, we make use of additional tools to fill in the gap for global and regional oceanographic observations. Satellite ocean color observations provide global ocean coverage, reaching time and space beyond our capabilities with research vessels and, therefore, may fill in the data gap where field measurements are limiting.

A satellite image shows Falkor’s track and the colors in ocean water. Colors indicate the amount of chlorophyll, where red is the highest and blue the lowest. SOI/Mónika Naranjo González

Phase 3: Learning How To See Phytoplankton

Ground truthing of these measurements of phytoplankton types through ocean color remote sensing is necessary but challenging. We can use phytoplankton pigments to derive a certain amount of information but the addition of microscopy is ideal, as then we can see which species are in the water. One of the newer technologies in the field is imaging flow cytometry, a technology that combines the best aspects of microscopy, flow cytometry and digital imaging.

Water is fed through the instrument at a specific magnification wherein a camera can be triggered to take a digital image of each particle or phytoplankter that passed by the field of view. Imagine how high spatial resolution of these data will help us to ground truth the phytoplankton type products that we retrieve from satellite imaging. On the RV Falkor, we have two forms of this technology to sample, not only the surface of the ocean, but also at depth. Having never spent much time in front of a microscope myself, I am learning so much from the skilled scientists around me who can look at an image and almost immediately identify to which genus and/or species the phytoplankton belongs. I hope to gain this knowledge as I learn and use this instrumentation.

The Flow Cam is an instrument used by Aimee to identify particles in the water. Water is fed through the instrument at a specific magnification wherein a camera can be triggered to take a digital image of each particle or phytoplankter that passed by the field of view. SOI/Aimee Neeley

Maiden Voyages

February 14th, 2017 by Mónika Naranjo González

Melissa Omand, interdisciplinary physical oceanographer from the University of Rhode Island’s Graduate School of Oceanography, was confronted with a conflict: it was time for an upgrade to her phone, but creating more technological trash did not feel right. Plus, the camera on her older phone was fantastic. Together with her first graduate student Noah Walcutt, she worked on optimizing better battery life, as well as fabricating an underwater housing and a lighting system for her “outdated” gadget. This to her remains the best part of her job: creating and testing new instruments, as well as repurposing existing ones.

Creating and testing new instruments, as well as repurposing existing tools, are some of Melissa Omand’s favorite aspects of her job. Melissa is a Physical Oceanographer currently sailing on board R/V Falkor. SOI/ Mónika Naranjo González


Melissa and Noah are working with two different novel instruments in this cruise. The first one is a time-lapse camera developed after repurposing her previous mobile. The phone will dangle at the base of a 150 meter wire, deployed as part of the Wirewalker assembly. For three or four days, the camera snaps pictures of the base of a sediment trap which collects falling particles called marine snow. Up until now, Melissa and her colleagues Colleen Durkin and Meg Estapa have been able to identify what kind of particles fall into the traps (and at what time this happens) by analyzing the material preserved in a special gel. They have also learned that particles fall in pulses as opposed to a steady flow. However, they are still not sure about which types of marine snow sink with each pulse, and how these are connected to the phytoplankton community above. They hope the images taken by the camera will provide a new piece to complete the puzzle that is carbon storage in the ocean.

Melissa Omand deploys the sediment traps as part of the Wirewalker, while Oliver Hurdwell observes closely. SOI/ Mónika Naranjo González

Stepping in

A second novel instrument Melissa has brought on board is a holographic camera. Unlike traditional photography, a holographic image is obtained when a laser beam hits an object and either bounces off of it or goes through it, bending the light. More a computer than just a camera, the instrument combines diffraction data with math in order to reconstruct the light’s journey after interacting with the object (in this case, a planktonic organism). Tracing the behaviour of the light provides an enormous amount of information about the object’s characteristics in three dimensions. The result is an image that allows the experts to focus on different planes, and not in just one single depth of field.

This is interesting both because it vastly increases the volume sampled by enabling the scientists to choose where to focus on a picture that has already been taken, and in that it enables a very exciting application: Virtual Reality.

Noah Walcutt examines the holographic camera installed in the CTD rosette. The camera is able to capture around 40 000 images in a single CTD cast. SOI/ Mónika Naranjo González

Numbers, numbers…

Cut a single hair a hundred times and you will get something resembling the size of a few microns. That is the resolution that the holographic camera can capture in a single photo: 16 photos per second, 100 particles per hologram in average, 40 thousand holograms per dip in the ocean. The numbers begin adding up fast, so Melissa knows it is time once again to create something from scratch: their own pathway for data management, processing and analysis. This is why she began working with Ben Knorlein, a computer scientist from the Center for Computation and Visualization from Brown University.

Not only is Ben in charge of designing an efficient way to deal with all of the information yielded by the holographic camera, but he is also the mastermind behind the software that allows scientists to step into the holograms and interact with the particles in a Virtual Reality environment. This has been the first time Ben has ever been at sea. He assists researchers in the deployment and recovery of scientific instrumentation, and more importantly, he is gaining a deeper understanding of what they are looking for, becoming familiar with their thought process and expectations. All of this experience is vital for Ben to improve the software so scientists can have faster access to the information they need to extract from each holographic image.

No other ship could have given the team the opportunity to work efficiently with these images on board. Falkor’sHigh Performance Computer enables Ben to process tens of thousands of images in a single day, generating data immediately. Each day Ben sits at his working station in the Dry Lab, fine tuning parameters and settings to offer Melissa and Noah new options. Once back ashore, this cruise’s intense collaboration will have made the trio tighter than ever, and they will walk away from Falkor carrying invaluable new information, instruments and software.

Ben Knorlein, Computer Scientist, observes Melissa Omand as she reacts to the first Virtual Reality experience created on board Falkor from holographic images of plankton suspended in the water. SOI/ Mónika Naranjo González