Biological oceanography

Growing a Scientist: Undergraduate Research 2018, part 2

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.

Authors: Anna Ward, Cassandra Alexander, Lauren Cook, and Sarah Paulson


Turbulent Conditions: Understanding How Microzooplankton Respond

Anna Ward, Scripps Institution of Oceanography University of California, San Diego

SURFO Advisor: Dr. Susanne Menden-Deuer

Small organisms, big impact:

It only took one look under the microscope to know I had found something special- microzooplankton. These small, single celled organisms were not only swimming throughout the water sample, but also feeding on other living things, both smaller and larger than themselves. Microzooplankton range in size from 2-200 microns, or the size of dust particles to the size of sand. They feed on other microzooplankton and phytoplankton, which produce their own energy through photosynthesis, similar to the way trees do on land. These “bottom of the food chain” organisms are essential for energy transfer to higher trophic level organisms, such as zooplankton and fish. As well, since these organisms respire and photosynthesize, they affect the overall input/output of carbon in the ocean, a necessary element for natural processes.

Preserved microzooplankton samples settling for microscopy analysis

This summer, I am working with Dr. Susanne Menden-Deuer (advisor) and Dr. Gayantonia Franze (mentor) to further understand how turbulenceaffects microzooplankton grazing. Since microzooplankton require physical encounter with their prey species for consumption, turbulence may either enhance grazing because of increasing the encounter rate between predator and prey, or negatively affect grazing by interfering with the capture processes. This research will give us a better understanding of plankton dynamics in coastal ecosystems.

Undergraduate Research Fellow, Anna Ward,
measuring plankton abundances in the laboratory

To assess this research question, I designed an in-lab experiment using organism cultures. Specifically, I used Oxyrrhis marina, Protoperidinium bipes, Gyrodinium dominans, and Gyrodinium sp. predator species. All of these organisms were fed the prey species, Isocrysis galbanaand incubated (similar to refrigerating) at 15 degrees Celsius for five days. Half of the samples were placed in a still condition (0 rotations per minute, rpm), and the other half were placed on a shaker table at 75 rpm, a relatively realistic value for coastal and shelf water turbulence. At different time intervals, the predator and prey abundances were measured and used to calculate growth and grazing rates over time.

Preliminary results show that turbulence affects microzooplankton grazing. There was a significantly higher grazing rate for the turbulent condition as compared to the still condition for O. marina; so the microzooplankton favored the turbulent condition. In comparison, each of the different species responded differently to grazing and no significant difference was seen in their growth rates. I am continuing to analyze the current data and experiment with other predator species to see how they respond.

While these small organisms may not seem like not much in the vast ocean, it is important to understand plankton function and response as they affect energy transfer to higher trophic levels and the global carbon cycle. After all, who doesn’t want to learn more about the ocean? There are so many unique, undiscovered features ready for exploration.

Anna Ward; [email protected]

Anna Ward is a rising undergraduate senior at the University of California, San Diego. There she is studying marine biology within the Scripps Institution of Oceanography, and intends to pursue a career in oceanography. She has particular interest in understanding how phytoplankton and microzooplankton interact with the surrounding environment and within their communities. She hopes to further plankton ecology research, and better understand how these organisms interact with biogeochemical cycles and respond to changing environmental conditions. As well, she is passionate about furthering science communication through non-traditional media platforms, such as dance and performance-centered presentations, and further promoting environmental conservation through education.


A Microscopic Problem in Narragansett Bay

Cassandra E. Alexander, Millersville University

SURFO Advisor: Dr. Colleen Mouw

The Bay

All of us love to eat or at least know someone who loves to eat seafood, right? New England is famous for its delicious fish and shellfish that are freshly caught in the area. Narragansett Bay in New England is an active migration area for multiple fish species and it is responsible for much of New England’s commercial and recreational fishing. Becauseshellfish harvesting is such an important coastal resource in Narragansett Bay, monitory measures need to be in place to watch out for toxin accumulation in our edible shellfish supplies to ensure public safety. In the future, researchers hope to accomplish this using satellite imagery. The yummy shellfish that we consume acquire their nutrients through filter feeding on microorganisms called phytoplankton. Phytoplankton can be thought of as small drifting ocean plants who undergo photosynthesis which is the process of converting sunlight and nutrients into energy.

Figure 1. Map of the Narragansett Bay with stars indicating points of study. Image credit: Kyle Turner

The Problem

Commonly, when we find disease in large fish populations the root of the problem lies with their phytoplankton food source. Harmful Algal Blooms or HABs are when phytoplankton and algae reproduce in uncontrollable numbers and produce dangerous toxins. The direct cause of the photosynthetic organisms producing these toxins is not completely understood, however we do know that an abundance of nutrients introduced into the water from land runoff is a factor. Early detection of toxin-producing species is key to public protection against disease. This demands for regular and constant monitoring of the bay.

Since phytoplankton are so small it is impossible to tell just by looking at the water when a dangerous species population is rising. The bay is home to the world’s longest running plankton survey, known as the Long-Term Plankton Survey (LTPS), which involves taking water samples every week back to a lab to manually count. Phytoplankton blooms can start quickly, so this may not be the best method to catch the beginning of HABs in enough time to warn the public since samples are only taken once a week.

The Narragansett Bay has seen a few bad HABs in its recent history, calling the need for a constant watch for the particularly notable HAB species of the area. To monitor for these species, Colleen Mouw’s lab has acquired an instrument called an Imaging FlowCytobot, or IFCB, which has the ability to continuously survey the bay’s phytoplankton populations. The IFCB collects seawater samples every 20 minutes and is able to take photos of each individual phytoplankton cell from that sample to get a more well-rounded idea of what species are populating the bay. The data that it collects gets updated in real-time to where anyone, no matter where they are located, can take a look at the photos that the IFCB takes.

Figure 2. Two cells of a harmful algal bloom species, Pseudo-nitzschia. Photo taken by the IFCB at the dock 2018/04/09.

After we get these images, we can run them through a code that automatically classifies each photo into groups based on their species. This allows us to look at the distribution of major bay species and groups without going through each image and manually classifying them, saving hours of lab work. The faster that we can analyze and detect the start of HABs in the bay, the faster we can make the public aware of any impending shellfish toxin accumulation that could cause sickness and possibly even death in humans.

A Solution

My study this summer involves lookingtwo different areas of the bay, as shown in Figure 1, to compare their species distributions and give some perspective to understand how well each of the stations collect data. One other goal for the summer is to also take sample water from the long-term plankton survey site and run it through the IFCB and classifier. I plan to compare the species counts I find from the IFCB to the traditional manual counting.

Coastal areas are vital to our ocean ecosystem. Unfortunately, satellites, our fastest data collectors, have a difficult time detecting subtle differences in coastal waters, such as the Narragansett Bay, as many different constituents impacting the color of the ocean vary independently.  It is our hope that through collecting this comprehensive data set on the bay, we will be able to develop methods that allow better discrimination to have a better chance at understanding bays and coastal areas from satellites.


Rising from the deep: the voyage of organisms from the shadow realm influence the surface world

Lauren Cook, University of South Carolina

SURFO Advisor: Dr. Jaime Palter

Dark Voyagers

Though the influence of the sun’s light only touches the uppermost layer of the ocean, a vibrant community teeming with life thrives in the mesopelagic zone of the ocean (200 – 1000 meters or 650 – 3280 feet deep). A suite of fishes and krill (Fig. 1) use the cover of shadow to avoid larger, hungrier sight-feeders (predators that rely on light and vision to find food) at the surface. However, these animals need to eat as well, and though life is by no means scarce in the mesopelagic, it is not half as plentiful as the surface waters.

Figure 1. Iconic small deep-water organisms: a lanternfish (top left), krill (top right), and a bristlemouth (bottom).

Every day, in all of the world’s oceans, an incredible phenomenon occurs: small animals no more than a few centimeters long migrate hundreds of meters to reach the surface to feed. When the sun sets, the alien-like creatures of the mesopelagic ascend upward within a few hours, and gorge themselves in the darkness. When dawn approaches, they quickly descend back to the deep until the sun begins to set once again. Scientists like to call this pattern a diel vertical migration (DVM).

Thrilling – and an amazing feat for creatures so small – but why do they matter?

Their Influence on the Surface World

Mesopelagic migrators are important for us for two reasons. Firstly, they expedite the transfer of carbon to the seafloor by consuming it at the surface, migrating to the mesopelagic, and excreting large fecal pellets (everyone has to do it!) chocked full of carbon. The carbon, having moved from the surface to the deep in only a few hours, sinks to the sea floor packaged in pellets. The carbon then stays stored in the sea floor sediment. Ultimately, these migrating animals help control the partitioning of carbon dioxide between the ocean and the atmosphere…through their poop! This partitioning of a greenhouse gas plays a key role in our global climate. Secondly, migrating mesopelagic animals are an important food source for bigger predators – many of which we eat. Staying in the mesopelagic is helpful to evade predators, but no one’s perfect – and the predators that snack on these migrators are the ones that we catch and put on our plate.

So, here’s the issue: we know that DVMs occur, and that their primary driver may be light (i.e., sunrise and sunset), but other than that, we still have a lot to learn.

More specifically, we don’t know much about how the characteristics of DVMs vary from ocean to ocean. We know even less about variability on other scales. How do DVMs differ in different parts of an ocean basin? How do they change between seasons? If we could characterize the qualities of these DVMs, we could better understand the balance of carbon on our planet, and we could better manage the fish populations that we like to eat.

Adding a Piece to the Puzzle

This summer, I worked to add to our knowledge of DVMs. I analyzed a ten-year long data set that was taken from three unique areas of the north Atlantic: the Slope Sea, the Gulf Stream, and the Sargasso Sea (Fig. 2) on a merchant vessel, Oleander. 

Fig. 2: The cruise path of the Oleander (white) and the general path of the Gulf Stream (orange). The Oleander passed over all three of these areas twice a week for ten years.

It surveyed these areas by having an automated acoustic doppler current profiler (ADCP) mounted onto it, which sends out beams of sound, receives an echo back, then stores that data for us to analyze. Instead of hitting the ocean bottom, though, the sound beams hit small organisms and bounce back to the ship. The larger the echo intensity, the more “stuff” – or animals – are being detected.

Because each region of the north Atlantic has different conditions (e.g., temperature and current speeds), it allowed me to investigate how DVMs change over months and seasons. To do this, I plotted the data and observed any visible differences between the regions. I also looked for consistent, unusual patterns over time.

Fig. 3 is an example of one of the plots from the data set. It reveals a few key characteristics. First, three layers of organisms reside in the Sargasso Sea (warmer, deeper): at the surface, 200 m, and 500 m – interestingly, only a fraction of the animals from the deeper layer migrate up to feed. Second, there appears to be no animals past 250 m in the Gulf Stream (a swift, warm, strong current). Finally, in the Slope Sea (colder, shallower), there is only a layer of organisms at 350 m.

Why are these organisms behaving this way? We aren’t sure yet, but we think that the migrators in the Slope Sea are responding to temperature, while organisms in the Sargasso Sea are responding to changes in light. It is important for us to report these findings so that we may continue the exploration of this dark frontier, and better understand these mysterious little voyagers of the deep.

Fig. 3: A DVM profile from July 2005. Since we detect these organisms by sending out a sound signal, higher echo intensity means more organisms are present. The green and yellow colors are where we see layers of organisms. The wave (top) is local sun angle – the peaks are noon, and the troughs are midnight. (a) Thick surface layer in the Sargasso Sea (b) Second layer of organisms at 200 m (c) Deep layer in Sargasso Sea at approx. 500 m (d) Gulf Stream empty of organisms past 250 m (e) The only layer of the Slope Sea, which migrates to a maximum depth of 350 m. Dashed arrow: the migration of the Slope Sea organisms to 350 m as daytime approaches; you can see they are deep in the ocean around noon. Solid arrows: the DVM in the Sargasso Sea, where organisms from the 200 and 500 m layers migrate to the surface at dusk, and then migrate back down at dawn.


Searching for Pearls of Wisdom: P. marinus and the eastern oyster

Sarah Paulson, Wesleyan University

SURFO advisor: Ying Zhang

Pearl or no pearl, oysters are a vital part of coastal ecosystems around the world. Eastern oysters are one species of oyster that can be found along almost the entire East coast of the Americas. These oysters help to filter seawater as they draw water in, consume algae, and then expel the water. This process improves water quality, which allows light to reach marine plants so that they can grow. Additionally, oysters often grow together in large oyster reefs. These reefs serve as habitats and nurseries for other marine species, and act as a storm barrier to protect coastlines from waves and floods. Oysters also have great economic importance in coastal communities, as aquaculture creates jobs and a food source.

For many years now, a parasite called Perkinsus marinus has been causing decreases in the abundance and productivity of oysters. P. marinus infects the oysters’ equivalent of blood, called the hemolymph, causing a disease called Dermo disease and sometimes even killing the oysters. This parasite tends to thrive in warmer water, so in New England, P. marinus is more prevalent in summer months, peaking around September.

Summer time oyster research

This summer, I am working on a project to study the link between microbiome and P. marinus infections in oysters. The microbiome is the collection of bacteria and other microbes in a given environment. In this case, that environment is the tissue of the oysters. In humans, the microbiome is known to help digest food, acquire nutrients (i.e. vitamins), regulate immune function, and fight off pathogens. Previous experiments have indicated that the oyster microbiome may serve similar purposes, but its exact function is not yet known.

To study the microbiome, it is important to note that not all bacteria can be grown in a lab. If we took a swab from inside the oyster and tried to grow those bacteria in a Petri dish, we would only produce colonies and genetic results from about 1% of the bacteria present. As a result, we use a different method to analyze the bacteria present in our samples.

There is a gene in bacterial DNA called the 16S ribosomal RNA gene. Different strains of bacteria have slightly different versions of this gene, so we are able to use 16S as a marker gene to identify what bacteria are found in each of our samples. In order to do this, we extract all the DNA from each sample and use a process called a polymerase chain reaction (or PCR) to create a lot of copies of the 16S gene. Then we sequence the copies that we created in order to determine what bacteria are in the sample, and how many of them there are.

Based on our results so far, there are significantly variable bacterial communities among different tissues within the oysters, but such variability does not seem to correlate with the infection levels. The oyster gut microbiome samples were significantly different from the other tissue samples collected, indicating a difference between the internal and external bacterial communities of the oyster tissue since the gut represents the only enclosed environment. Additionally, functional analysis of the microbiome showed that functions such as photosynthesis were most commonly found in the gut, which is likely a result of the algae diet of the oyster. There weren’t many oysters in our sample that had severe infections, so further research is being done in collaboration with researchers from the United States Department of Agriculture on a larger group of oysters. Those oysters have been injected with P. marinus in order to collect more data on the potential effects of this parasiteIn general, we hope that this research, as well as future research on the microbiome of the oyster and how that interacts with P. marinus infection, can help with conservation efforts to support these important animals.

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