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Biological oceanography

Growing a Scientist: Undergraduate Research 2017

Each summer, the University of Rhode Island Graduate School of Oceanography (GSO) hosts undergraduate students from all over the country to participate in oceanographic research. These Summer Undergraduate Research Fellows (SURFOs) have not only been working with GSO scientists, but they have spent part of their time learning how to communicate this science to the public. Read on to find out what they have been up to, and why they everyone should be as excited as they are about their work.

The 2017 cohort: Sitting from left to right: Shannon Riley (Oregon State University), Rosalie Cisse (Tougaloo College), Elana Ames (Coastal Carolina University), Melanie Wallace (Purdue University), Maddison Flasco (Otterbein University) and Kierra Jones (Tougaloo College).
Standing from left to right: Christine Gardiner (graduate student liaison), Jackson Sugar (University of Rhode Island), Amanda Love (Lake Superior State University), Nicholas Piskurich (University of Notre Dame), Kyle Turner (George Mason University), Courtney Hill (Tougaloo College), Oliver Lucier (Rice University), and Salvatore Ferrone (Ithaca College).

“Lake Level Rise and Seismic Risk in Haiti” by Oliver Lucier

“What did the ocean do when she caught wind of the Hurricane? She waved” by Salvatore Ferrone

“Building MINIONS” by Jackson Sugar

“Not So Super Superbugs” by Maddie Flasco

“Location, Location, Location – Krill Style” by Shannon Riley

“Fixing the oceans” by Elana Ames

“Light, Ocean, Camera, Action!” by Kyle Turner


Lake Level Rise and Seismic Risk in Haiti

Oliver Lucier – Rice University

Submerged Villages and Flooded Fields

Lake Azuei is a large brackish lake located in the fertile central plain of Haiti (Fig. 1). Over the last fifteen years the lake level of Lake Azuei has risen a remarkable ~5m (15ft)! This lake level rise has created huge problems for the Haitians who live near the lake; submerging their fields, destroying whole villages, and threatening key transportation routes. For the people who live around the lake it is incredibly important to know if the lake will continue rising and if so, by how much and what places will be submerged next.

Figure 1. Lake Azuei and 2010 earthquake fault line

Quantifying and Contextualizing the Lake Level Rise

This summer I am conducting research to precisely quantify and analyze the lake level rise of Lake Azuei in Haiti. In order to calculate and quantify the lake level rise, a team of researchers travelled to Haiti in January of 2017 to map the underwater terrain of Lake Azuei. They used advanced sonar equipment, installed on the underside of a small boat, and drove patterns around the lake collecting data. The equipment on the boat emitted a sound signal, which took a depth reading at every point on the lake and created a 2D profile of the sediment layers that comprise the lakebed.

By leveraging the work done in January, my team has compiled an updated bathymetric map of Lake Azuei, which shows the depth of the lake at every point. We then compared this new bathymetric map with older surface area maps, and it was immediately obvious that the surface area of Lake Azuei had increased substantially and we were even able to see which villages and farms the lake had swallowed. Additionally, because of the very high resolution of the sonar data, we were able to zoom in and specifically study several paleo-shorelines of Lake Azuei. We found a paleo-shoreline at ~5m depth suggestive of the previous shoreline of the lake from fifteen years ago, before the unprecedented lake level rise. We also located an older but more pronounced paleo-shoreline at ~10m depth, indicating that the lake level must have held steady at ~10m below its current level for a significant period of time.

Seismic Risk Below the Lake

An additional component of my research this summer involved searching for active faults below Lake Azuei. In 2010 an extremely large M7.0 magnitude earthquake occurred in Haiti causing horrific damage and loss of life. This earthquake was located on a fault very close to Lake Azuei, and previous studies had indicated that there might also be a fault running under the lake. Our collected data allowed us to confirm the presence of folds present on the lakebed, which can be indicative of active faulting deeper below the lake. The presence of a fault under Lake Azuei indicates that the lake area must be considered as an active fault zone and a possible, if not probable, source of future earthquakes. This new knowledge gleaned from scientific research can go a long way to preparing Haiti for future earthquakes and hopefully minimizing future damage and loss of life.

Future Implications

The research my team has done allows us to say with some certainty that the lake level of Lake Azuei is quite variable over long periods of time. The paleo-shorelines we have found tell us how the lake has risen in the past, and using this information we can extrapolate future lake level rise. We are currently using our data to model the lake level   if it were to rise another three meters from its current level. These models will allow future researchers and local leaders to plan accordingly should the lake continue to rise. Additionally, by providing greater detail on the type of seismic hazards below the lake we hope that policy makers will be better able to judge seismic risk and create precautions better suited to the tectonic environment around the lake.


What did the ocean do when she caught wind of the Hurricane? She waved

Salvatore Ferrone – Ithaca College

Hurricanes are complex weather  systems with strong winds that really rough up the ocean surface; cause powerful waves that pummel ships and upset stomachs everywhere. In order to characterize a hurricane we use many different programs to simulate different aspects of a hurricane. For example, we use a model to calculate wind speed and direction at every location in the Atlantic, a model to predict the path of a hurricane, a model to predict areas that will be affected by storm surge (the overflow of ocean water onto the coast), a model that assess ocean surface waves, etc.

My work involves checking the accuracy an ocean wave model that predicts ocean surface waves Ocean wave characteristics related to hurricane modeling include the distance between each wave (wavelength), and the height of each wave (wave height).

The wave model has been introduced to a new physics engine for waves in shallow waterHave you noticed that waves always travel toward the shore and never alongside the shore? The ground beneath the water causes the waves to bend toward the shore. Waves in water depths less than 30 meters exist in a totally different environment than waves over ocean open.

In order to verify the new model works properly, we need to compare the model’s predictions to actual observations of the real world. One source of data comes from the National Data Buoy Center. The organization has buoys located all around the world that take measurements of the ocean waves. I viewed hurricane Bonnie data from August 1998 because a study had been completed before using Hurricane Bonnie to verify the ocean wave model. Some of the buoys reported some of the tallest waves to be over 14 meters in height. I If put 6 clones of myself on top of each other, this stack of Salvatores would still not be taller than these waves recorded during Hurricane Bonnie.

Figure 2. Model predictions versus observations

Figure 2 showcases an example of our current models predictions of the wave height (grey line) versus the buoys prediction (the dots). From the figure you notice the general trend of agreement, we predict waves around 7 m height between the 26th and 27th and so does the model. Yet the model predicts shorter waves between the August 24th and 26th. In summary, we have a working model that can predict the ocean surface waves competently BUT it’s not perfect and scientists won’t stop until it is.

These models are super complex, and one model needs data from another model to run. I.E. we cannot generate an ocean wave model without the results from the wind generating model, for the wind is a huge factor in generating ocean waves.

Every day I would make comparisons of model wave height predictions against that of buoy observations. Verifying a model is tedious but a necessary step toward improving wave models. When you don’t verify your model you predict waves incorrectly.



Building MINIONS

Jackson Sugar – The University of Rhode Island

Isopycnal [eye·so·pik·nyl]: a layer of the ocean where water density is constant.

Global warming and carbon cycling have been hot topics in the news as far back as I can remember (cue clip from Al Gore’s “An Inconvenient Truth”, 2006). Oceanographic dynamics play a pivotal role in global climate cycles. The uptake and sequestering of carbon by the world’s oceans exists as a major sink in the global carbon cycle. One of the key interests in carbon cycling is quantifying the production and export of marine particulates from the upper ocean to depth. These marine particles, referred collectively to as marine snow, are comprised of biological materials produced in the upper water column, supported by primary production. Gaining insight into the dynamics of carbon cycling in the oceans is of substantial importance for better interpreting climate regimes. Specifically, quantifying rates of carbon export in time and space is a major topic of interest in oceanographic science.

My summer research project tackles the observation of this phenomena through the design of a new type of measurement hardware, allowing us to quantify how carbon reaches the deep sea and becomes isolated from exchange with the atmosphere for thousands or more years. I have been tasked with developing a system to resolve variations in sinking marine snow particles on time scales from hours to days. With this data, scientists can extract not only how much and how fast the particles are sinking into the deep ocean but also the spatial variations of particle size and organic composition.

Figure 1. MINION

Enter the MINION (MINature IsOpycNal float), a specifically designed autonomous undersea float. The goal of the MINION (Fig. 1) project is to develop a fleet of low cost sensors to be deployed over wide areas for large scale analysis of carbon flux. Each float has a suite of hardware for automation and remote sensing all to support the high resolution camera mounted to a transparent settling surface to capture images of the marine snow as it comes to rest on the MINION over the roughly week long deployment.

This system allows for limitless customization and adaptation for future revisions by the incorporation of a Raspberry Pi Zero W single board computer. These low-cost linux systems enable us to interact with the MINION completely wirelessly, allowing for a totally sealed enclosure. Any computer or cell phone has the ability to log on and make changes to every aspect of the MINION’s mission before deployment.

During deployment, MINIONs rely on the steep variation of water density of a targeted isopycnal layer in order to control where the float settles in space. Once properly ballasted the MINION will sit in roughly the same gradient of water density for the duration of its mission. This allows us to control the sensor’s location in the water column without any extraneous hardware. Upon mission completion the MINION drops its ballast weight and floats to the surface. Once surfaced it will automatically alert us of its location via GPS for retrieval.

The MINION project is still in its infancy. As it stands, there are a few key improvements on deck to turn this three week design challenge into a fully realized and integrated instrument. I am currently in the process of upgrading the power circuitry to reduce space taken up inside the sensor and improve overall endurance of the system. This directly translates to longer deployments and more data coming back from each test. I look forward to collecting and publishing what data we receive and to continue learning about the intricacies of carbon cycling on planet earth.


Not So Super Superbugs

Maddie Flasco – Otterbein University

Have you heard of the growing concern about superbugs? These bacterial infections are immune to several types of antibiotics making them extremely difficult to treat. This is believed to be due to the overuse of antibiotics leading to resistance in certain strains. But how do bacteria evolve to have this resistance?

Figure 1. Harvesting knockout strain from nutrient plates.

Horizontal gene transfer (HGT) is a way for bacteria to acquire new genes. This acquisition is not passed from cell to another as it reproduces, but rather entirely different bacterial species. One specific type of HGT is called natural transformation; this process refers to the uptake of environmental DNA into the bacterial cell and integrating it into the genome. Now, not all bacteria are just sucking up random DNA around them. Just as humans are not equipped to breath underwater, not all bacteria are able to take up the free DNA around them. Those species that can undergo natural transformation are referred to as competent.

Those competent species are able to pick up new DNA partially due to the ComEC protein. When turned on, ComEC creates a pore in the cell membrane that allows for DNA to travel into the cell. This protein is widely distributed but can vary in its appearance. Essentially, we have the same protein wearing a bunch of different hats, one hat is your typical baseball cap, another is a knit hat, and finally a bucket hat. All of these hats cover your head, but there may be one that better serves a desired purpose.

If we want to ask which hat will best block the sun on the beach, we can answer a baseball cap. So if we consider all of the different combinations of ComEC, which one is best? In other words, which version allows a cell to take up the most foreign DNA? In an attempt to answer this question, we will look at the problem two ways, computationally and experimentally.

From a computational standpoint, my summer research analyzed bacterial genomes containing the ComEC protein. From here the existing versions were be identified in the genomes. I used genome size as a stand in for transformation efficiency; if one configuration has a larger genome, then it is possible it has integrated more foreign DNA. Through statistical testing, I found that when the Lactamase_B component was present, genome sizes were significantly larger than those configurations lacking it.

Figure 2. In the knockout strain, the comEC gene is replaced by Htk, an antibiotic resistance gene.

Experimentally my research focused on Thermus thermophilus. This species is consistently able to uptake DNA no matter what kind of environment it is found in. I was able to remove the comEC gene in the T. thermophilus genome using the natural transformation machinery already in the cell. This process is referred to as a knockout. This gene was replaced with Htk, an antibiotic resistance gene. The knockout will be used to introduce the cells to DNA that contains variations of the ComEC protein. From here I can test the different combinations to see which is more successful in the uptake of DNA.

The more we can understand how bacteria evolve, the better we can understand how they will react to different environments. Various methods of gene acquisition, such as natural transformation has allowed for bacteria to acquire genes changing the nutrients required for growth, allowed for them to become pathogenic, and even develop antibiotic resistance. If we can understand how these superbugs came to be, it is likely we will have more success in treating them.


Location, Location, Location – Krill Style

Shannon Riley – Oregon State University

What are krill?

Figure 1. Nematobranchion flexipes, a species of euphausiid identified by bilobed eyes and spines on four abdominal segments.

Say the word krill and we’re all more likely to think of whales or penguins than krill themselves. After all, two krill, Will and Bill, were only side characters in Happy Feet 2, a movie about penguins. Krill is the common name for a group of zooplankton called euphausiids (Fig.1). These are small crustaceans that look like shrimp. They are found throughout the world’s oceans, with Antarctica perhaps the most widely known region. Some estimates suggest that there are 6 billion tons of krill in the ocean around Antarctica. For scale, the Great Pyramid in Egypt also weighs approximately 6 billion tons. Krill also live off the coast of the Americas.

Krill eat tiny phytoplankton, making the energy they got from the sun available to bigger animals that can’t eat phytoplankton. Because krill are so widespread and abundant in the ocean, hundreds of species rely on them as their main food, like whales, seals, penguins, herring, and seabirds. Even more species eat animals that survive on krill. Even people eat krill and use them to make Omega-3 pills. Krill also help keep carbon dioxide out of the atmosphere by releasing carbon in fecal pellets, which then sink to the ocean floor and stay there.

What Happens When Water Has Almost No Oxygen?

Oxygen isn’t just important for animals that live on land. Ocean dwelling animals also need oxygen to survive. However, the amount of oxygen in ocean water varies widely. Areas of the ocean with very low oxygen are called Oxygen Minimum Zones (OMZs). You might think these areas would be completely devoid of life. After all, fish such as tuna need ten times more oxygen than is present in some OMZs to survive. But not all animals need this much oxygen. Some, including certain species of krill, can survive in much less oxygen, so they can live in OMZs. OMZs give these animals a safe space to hide from predators in the open ocean, since they can survive there and other animals can’t.

Unfortunately, not all animals, and not even all krill, can survive in the oxygen minimum zone core, which has the lowest oxygen content. This normally doesn’t cause problems, because oxygen minimum zones only cover 8% over the total ocean area. However, certain ocean models have suggested that climate change could cause oxygen minimum zones to increase both horizontally, covering more surface area, and vertically, getting deeper.

This could cause major problems in the oceans. Animals that can’t survive in low oxygen waters will be forced to live in other areas, rendering them more vulnerable to predators or likely to suffer from non-ideal water temperatures and depths.

My Adventure with Krill (My Research)

Figure 2. Euphausia paragibba being identified using a microscope.

This summer, I’m studying krill that were collected off Baja California in one of North America’s Pacific OMZs. I am examining zooplankton samples and removing the krill to further identify them by species. I then look at them under a microscope to identify the details of very small body parts, including the shape of different features of the antennae and the presence or absence of spines (Fig. 2). Some krill species look very similar, so I have to be careful to compare the specimens to each other and to the identification guide I use. Once I sort the samples, I create plots comparing abundances of krill to the oxygen concentration, temperature, and the depth where they were collected (Fig. 3).

These plots show the krill distribution changes between day and night. Krill move up and down in the water column between day and night. Figure 3 shows this migration, with most krill deeper in the water during the day, and in shallower water at night. Plots that compare oxygen concentration to abundance are perhaps the most important, as they allow us to document the optimum conditions for krill survival.

Figure 3. The distribution of krill in the water column changes between day and night.

What to Expect in the Future

This will help us learn where these krill live and what kind of conditions they can tolerate. In the end, we want to know how euphausiids react to the low oxygen waters that may become more prevalent in the future ocean, as their presence and health is extremely important to other species, including penguins, seabirds, tuna, and yes, whales.


Fixing the oceans

Elana Ames – Coastal Carolina University

Figure 1. The phytoplankton Trichodesmium, a cyanobacteria capable of nitrogen fixation

As a kid, you may have learned about photosynthesis as the neat chemical process that plants use to turn carbon dioxide, water and sunshine into the vital oxygen that we breathe. Apparently, I missed the portion of the lecture that only plants could do this, because when I was little, I would bask in the sun and tell my mother I was a plant making oxygen. If anyone interrupted me I would reproachfully tell them: “Shhhh, I’m photosynthesizing!” This process (that humans definitely cannot do, to my dismay), results in primary productivity via the fixation of carbon, making it is the most important chemical reaction on the planet. What you may not have learned in elementary school is that roughly half of the world’s productivity takes place in the oceans. Wilder still is the fact that the majority of productivity in the oceans comes from tiny, sometimes even microscopic, plants and bacteria. These amazing organisms are phytoplankton and they make life in the oceans possible.

Figure 2. The Gulf Stream current shown by the warmer sea surface temperature moving northward.

Phytoplankton need more than CO2 and sunshine; they also require nutrients like nitrogen, phosphorus and iron to grow and photosynthesize. Dissolved nitrogen gas (N2) is abundant in the water column, but it has a very strong chemical bond that most organisms can’t pull apart. So even though they are surrounded by it, nitrogen gas is useless to primary producers like phytoplankton because it is not bio-available. Enter the stars of my research: a special type of phytoplankton, called diazotrophs, can take that stubborn elemental nitrogen and convert it into the bio-available form of ammonia. Ammonia can then be used for photosynthesis. This process is known as “nitrogen fixation” and has huge impacts on global productivity trends. Diazotrophs are incredibly valuable to ecosystems where there is sufficient phosphate and iron, but are deficient in bio-available nitrogen.

Unfortunately for our diazotrophic friends, fixing nitrogen uses up a lot of energy. This process can only take place in relatively warm locations where there is enough excess phosphate in the water to sustain them. Due to their strict nutrient and temperature requirements, diazotrophs are often out-competed by other, non-nitrogen fixing phytoplankton. In the North Atlantic, a strong current called the Gulf Stream runs up the United States east coast bringing warm water up from the tropics. The current’s unique physical properties create a type of barrier from the rest of the ocean. I am trying to figure out if wind and swirling currents are capable of transporting enough excess phosphate across the Gulf Stream to sustain diazotrophic organisms.

Figure 3. Incubation experiments done aboard the R/V Endeavor.
Photo courtesy of: Anna Robuck

By investigating the transport of nutrients across the Gulf Stream using data collected on a cruise from late April, we hope to learn more about the physical processes taking place in the area. Nitrogen fixation can have huge impacts on ecology by controlling how much oxygen is available for fish and other organisms, so this research will be a small part of a larger study to determine and quantify the rates at which it may be taking place. Other aspects of the project include performing seawater incubations to determine fixation rates, examining historical data from a Continuous Plankton Recorder (CPR), and DNA analysis for the diazotrophic gene. Since nitrogen fixation can have such large impacts on nutrient availability, the potential results could effect photosynthesis distributions in the Atlantic Ocean.


Light, Ocean, Camera, Action!

Kyle Turner – George Mason University

What color is the ocean?

If you said blue, then you’re usually right, but not always! Just like the sky may turn red, orange, or pink at sunset, the ocean can be a variety of colors based on how light from the sun interacts with the water, as well as with the tiny particles in the water that are invisible to the naked eye. The study of sunlight in the ocean is called  , and it can reveal a lot more about our watery planet than you may think.

Different substances absorb and scatter light in unique ways. This means that the particular behavior of light in a water body at a given place and time provides information about what types of things are in the water, and can illuminate (pun intended) important processes occurring there. The main constituents that affect the behavior of light in natural waters are commonly grouped into three categories:

1. phytoplankton– microscopic marine organisms that are abundant in the global ocean, produce energy via photosynthesis (converting sunlight and carbon dioxide into useable energy), and form the foundation of the marine food web (Figure 1)

2. Colored Dissolved Organic Matter (CDOM) – dissolved organic compounds originating mainly from decomposed plant material on land and in the ocean, which tend to turn the water a yellowish or brownish color

3. Non-algal Particles – other particles suspended in the water column, such as sediments, microscopic organisms (other than phytoplankton), and detritus (dead stuff)

Figure 1. Different types of phytoplankton cells. Image credit: UTS

Research Spotlight

Figure 2. Filtering apparatus for CDOM (left) and particulate absorption/chlorophyll a (right).

My research this summer, under the mentorship of Dr. Colleen Mouw, is focused on using optical measurements to understand changes in phytoplankton in Narragansett Bay, RI. To do this, I’ve been collecting daily seawater samples from the University of Rhode Island’s Graduate School of Oceanography (GSO) dock, and weekly samples from the world’s longest running plankton survey in Narragansett Bay. These samples are filtered for analysis of chlorophyll a (a light-harvesting pigment present in all phytoplankton), particulate absorption, and CDOM absorption (Figure 2).

Additionally, the samples are run through an instrument called an Imaging FlowCytobot (IFCB) which takes in a small volume of seawater, and images individual phytoplankton cells (Figure 3). One 5 mL water sample produces thousands of images, which are uploaded onto a   and updated daily. From these observations we can get a good sense of how the types of phytoplankton in the bay are changing, even on a daily basis.

Amazingly, sensors onboard satellites can measure light coming from the ocean on a global scale! I’m also using satellite imagery from a sensor called the Medium Resolution Imaging Spectrometer (MERIS), and comparing these measurements with historical data collected in Narragansett Bay.

Figure 3. Imaging FlowCytobot and example images


We hope that these combined efforts will lead to a better understanding of phytoplankton in Narragansett Bay, and will help to enhance the methods used to obtain information from more sophisticated satellite sensors which are planned for launch in the next few years.

Zak Kerrigan
I am a fifth year doctoral candidate at the Graduate School of Oceanography at the University of Rhode Island. I work in the D’Hondt Lab and I am using genetic techniques to determine the community structure and evolution of deep-sea sediment bacteria. I am also a scuba instructor with the University of Rhode Island Dive Safety Program. I earned a B.S. in Aerospace Engineering from the University of Miami and spent 12 years in the US Navy driving submarines before coming back to grad school.


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