Undergraduate experiential learning courses

MARN 3001 students at Barn Island mapping the salt marsh elevation. Photo credit: Leonel Romero
Hydrographic survey in Thames River for MARN 3001 aboard the RV Connecticut. Photo credit: Leonel Romero
Students from MARN 4001 presenting their science at a CUSH sponsored public event in the Mystic Seaport Museum. Photo credit: Hung Nguyen
Students in the field for MARN 3030. Photo credit: Pieter Visscher

By Mengyang Zhou

Undergraduate classes within the Department of Marine Sciences (DMS) are bridging the classroom learning, fieldwork and addressing environmental challenges that are relevant to the local community.

As undergraduate students enter their junior and senior year, they engage in experiential learning through classes such as MARN 3001 (Foundations of Marine Sciences, instructed by Pf. Leonel Romero, Pf. Jason Krumholz, and Dr. Claudia Koerting, historically also co-taught by Pf. Craig Tobias who is on sabbatical this year), MARN 4001 (Measurement and Analysis in Coastal Ecosystems, instructed by Pf. Julie Granger and Dr. Claudia Koerting) and MARN 3030 (Coastal Pollution and Bioremediation, instructed by Pf. Pieter Visscher). These classes are designed to provide hands-on experience of fieldwork, lab experiments and data analysis, and empower students to apply classroom knowledge to the real world, making a positive impact on environmental problems in the local community.

The class Foundations of Marine Sciences (MARN 3001) focuses on carrying out and interpreting the most fundamental oceanographic measurements in coastal habitats such as beaches, marshes and estuaries. In the fall semester of 2023, students went on field trips to Long Island Sound and the Thames River aboard the RV Connecticut and RV Lowell Weicker. They collected hydrographic data using CTDs (Conductivity, Temperature and Depth), water samples for nutrient measurements, as well as sediment samples. They also conducted marsh elevation mapping in Bluff Point Beach and Barn Island. Upon analyzing these data and publicly available datasets provided by NOAA (National Oceanic and Atmospheric Administration), students learned how to characterize the changing coastal systems and how organisms adapt to those changes.

Students in the class Measurement and Analysis in Coastal Ecosystems (MARN 4001) assessed the potential causes of water quality impairment in Wequetequock Cove near Stonington, CT and Pawcatuck River, and built connections with the local community. Beyond learning textbook knowledge, they went into the field to collect water and sediment samples that were analyzed in the lab for nutrient and chlorophyll concentrations and O2 consumption rates. They also learned how to analyze, interpret and archive the data they collected, as well as those collected by CUSH (Clean Up Sounds and Harbor), a local non-profit organization who has been conducting a long-term survey of the cove’s water quality. Finally, they tried to address important questions, such as identifying the sources of nutrient overload in the cove, and understanding the causes of summertime O2 depletion in the cover, and constructed scientific posters and presented their scientific findings to a broad audience in Mystic Seaport Museum.

The class Coastal Pollution and Bioremediation (MARN 3030) is another example of a class that is designed to connect students with the real world through service-learning. This class focuses on how pollution in the nearshore marine environment impacts the marine food web. In the fall semester of 2023, students learned the fundamental environmental monitoring techniques and data analysis which were applied to coastal pollution research. They monitored the overall health of the Mystic River through field and lab experiments that included water column profiling, sediment quality and enterococcal counts before and after rain events. Their work provided data for the Alliance of the Mystic River Watershed, a local citizen group that focuses on resilience and social justice along the Mystic River. Upon discussion about local policy related to coordinated resilience planning and watershed protection, they also presented their findings to the public in Mystic Seaport Museum, together with MARN 4001.

To reflect on experiential learning classes, Shannon Jordan, who took MARN 4001 and now a master student in the DMS, said: “MARN 4001, more than any other core class, was an introduction to oceanographic research as it actually occurs. Experimental design, methods of data management and interpretation are not outlined in a manual. In contrast to many undergraduate science labs, this course encourages students to take the reins in each aspect of the scientific method. MARN 4001 was an excellent environment in which to explore individual research interests and the process by which questions are translated into hypotheses, experiments, results, and further questions. The opportunity to develop these practical skills in a collaborative environment – with ready access to the vast knowledge base of experienced faculty – was incredibly valuable.” 

Through these experiential learning classes, students worked on interdisciplinary problems and gained plenty of hands-on experience in the field of oceanography. They also proposed solutions to address the local environmental problems, and presented them to a broad audience. The valuable skill sets they developed in the past semester will prepare them for their future career and academic pursuits.

Dissolved organic matter sets the bioavailability of mercury

(Left) Emily Seelen in the lab. (Right) Robert Mason and Celia Chen in the field


Mechanistic illustration of MeHg bioavailability controlled by dissolved organic matter thiol concentrations (Fig. 5 in Seelen et al., 2023)

By Mengyang Zhou

Connecticut and New England, like many locations around the world, houses many estuaries that suffer from mercury pollution that is largely inorganic, less toxic and not as bioaccumulative as methylmercury (MeHg). The mercury concentrations in these regions are much higher than in the open ocean despite only a small fraction of these concentrations being bioavailable. Eventually,  inorganic Hg is converted to MeHg and enters the food web. Coastal regions, like estuaries, also support marine resource cultivation and supply to communities, and therefore are potentially a source of exposure for humans to elevated levels of MeHg. A key environmental control determining MeHg bioavailability is dissolved organic matter (DOM), and specifically the sulfur-containing thiol binding ligands within the DOM, as they strongly bind to MeHg. Understanding how dissolved organic matter (DOM) influences MeHg bioavailability is crucial for predicting exposure in high-trophic level biota, including humans. Environmental changes, such as eutrophication and altered runoff, impact DOM loading in aquatic ecosystems and therefore can  affect MeHg bioavailability. Historically, using dissolved organic carbon (DOC) as a proxy for MeHg[RM1] -binding capacity has been a standard, but this work shows this assumption may lead to errors depending on the natural environment you are working in. The group hypothesized that the properties of DOM unrelated to total DOC may be impacting MeHg bioavailability, and may underpin the variability in MeHg uptake at low DOC concentrations commonly observed in the environment. Specifically, the group tested whether DOM binding capacity, defined as the concentration of thiol ligands per gram DOC, or the DOM binding strength to MeHg dictated overall MeHg bioavailability in distinct coastal regions.

To address this, the team measured DOM properties associated with MeHg bioavailability across four distinct regions of the nearshore terrestrial-marine aquatic continuum.  They found that the in situ MeHg-binding capacity of DOM varied significantly and systematically across the terrestrial-marine aquatic continuum they explored, but the binding affinity varied but not significantly or systematically across the same system, and ligand exchange kinetics were fast for all types of DOM.

Next, they explored the DOM principles they highlight as driving MeHg uptake by testing it in a phytoplankton uptake experiment using a specific species of diatom.  Their results supported that not only the total DOM concentration but also the concentration of specific DOM-associated sulfur compounds called thiol functional groups binding sites (DOM-RSH) were the primary factors controlling the MeHg bioavailability and accumulation within the phytoplankton.

The project was started by Emily Seelen PhD ’18 (Fig. 1), now a postdoctoral researcher at the University of Southern California, when she was a graduate researcher in Professor Robert Mason’s lab (Fig. 2). Pf. Mason’s funded projects supported the work and Seelen also received an NSF graduate fellowship that enabled a study abroad collaboration with co-authoring chemists Erik Björn, Ulf Skyllberg, and Van Liem-Nguyen from Umeå University in Sweden. Seelen was also advised by Associate Research Professor Zofia Baumann who instructed Seelen on how to perform the phytoplankton uptake experiments, drawing from her previous research tracing heavy metal contaminants through the environment.

Seelen said she was inspired to pursue this work in part as an opportunity to work abroad as a result of her research with Professor Mason. “With Rob I was able to learn a lot about broad coastal Hg cycling, but I knew I wanted to dive a bit deeper into what exactly controlled how much MeHg was able to enter into the food web. I put together a list of potential universities I could study at, and soon got to meet Erik Bjorn at the 2015 Hg conference (ICMGP) in Korea. I instantly knew this was the working group for me and we wrote the proposal soon after!” She then proceeded to apply for the NSF graduate fellowship to pursue this idea and was successful in acquiring one of these highly competitive fellowships.

The study emphasizes the crucial role of dissolved organic matter (DOM) in MeHg bioaccumulation in aquatic ecosystems. It reveals that MeHg uptake by phytoplankton is directly linked to the DOM-RSH rather than the more traditional binding calculation for MeHg -dissolved organic carbon (DOC) interaction. Figure 3 showcases how decreasing trends in DOM-RSH concentrations across the terrestrial to marine aquatic continuum leads to higher MeHg availability and planktonic uptake in systems dominated by marine DOM relative to those impacted by more humic, terrestrial DOM. The research suggests that measuring DOM-RSH concentrations is essential for accurate models in understanding MeHg incorporation in aquatic food webs across different environments. The research highlights the need to consider specific DOM characteristics, specifically the ratio of thiol functional groups to DOC (DOM-RSH/DOC), for more accurate predictions under various environmental scenarios.

Link to UConn Today article

Art Meets Science: ‘Floating Points’ at AVS Gallery

Floating Points Exhibit by artist Oskar Landi in The Alexey von Schlippe Gallery of Art at Avery Point on Nov. 14, 2023. (Sean Flynn/UConn Photo)

The presence of microplastics in the world’s oceans is the focus of the exhibition “Floating Points: Observing the Plastisphere with NASA”, on view at Alexey von Schlippe (AVS) Gallery of Art at Avery Point through Dec. 10. Link to full article in UConn Today.

Meet Felipe Soares: our Ocean Modeling Technician

Photo credit: Beatriz Silva

By Mengyang Zhou

Felipe Soares shared his career journey as an ocean modeler, his experiences, challenges, and the key role he plays in advancing ocean modeling research in the Coastal Biogeochemistry Dynamics Laboratory in our department.

Mengyang: Can you tell us about your career path? 

Felipe: So, let me start from the very beginning. I was always passionate about nature and marine life and had an inclination to be a marine biologist. But when the time arrived to choose a career, I found myself very uncertain. One day my mother suggested that I take a look at the Oceanography course at the Rio de Janeiro State University (UERJ). Initially, it sounded very unconventional to me, and I basically disregarded it. However, after reading about it in a career guidebook it captivated me and suddenly, I couldn’t envision any other option. While I was an Oceanography undergrad student at UERJ, I actively sought opportunities in research labs, and that led me to acquire some skills and expand my network beyond the university. This pursuit led me to get an internship at the IEAPM (a Brazilian Navy research institute) and subsequently at Prooceano, a growing and already well-established oceanography consulting company in Rio de Janeiro in the late 2000’s. So, at this point my career was already leaning towards the industry. Over the next twelve years, I worked at this company, playing a pivotal role in ocean modeling, which involved extensive model preparation, running, and evaluation. Simultaneously, I pursued my master’s at the Rio de Janeiro Federal University (UFRJ) studying the seasonality of the Brazil Current mesoscale activity. Upon discovering an open position at Sam’s lab, which required expertise aligned with my experience, I researched her work. The multidisciplinary aspect of the work was particularly appealing to me, presenting an opportunity to get out of my comfort zone, acquire new skills, and enrich both my career and life. Consequently, I joined the DMS (Department of Marine Sciences) to work at the Coastal Biogeochemistry Dynamics Lab in August 2021. 

Mengyang: What’s your current position in our department? 

Felipe: I am currently a research assistant II, contributing to almost all projects within Sam’s lab. As a technician in a modeling lab, my responsibilities involve running the models, conducting data analyses, comparing the model results with observations, and generating plots and statistics. These outputs are used in presentations, papers, daily research activities, etc. 

Mengyang: What do you enjoy most about your current position, and what are the most challenging parts about this job, if any? 

Felipe: I like tackling problems that demand both programming skills and oceanographic knowledge. This often involves managing large datasets and highlighting the information that will be useful for the scientists in a plot (and maybe make them visually appealing too). Additionally, by participating in diverse and engaging research projects you can learn a lot and be incredibly fulfilling. The most challenging part is the responsibility of overseeing model runs which are often the primary source of data for the lab’s projects. Any technical problems or configuration errors can significantly impact the lab’s research schedule and objectives. 

Mengyang: What do you do outside of work for fun, to balance life and work?

Felipe: Outside of work, I love spending time in nature. Whether it’s hiking with my family or fishing in the streams (and hopefully back to trail running soon), you can probably find me exploring the parks in eastern CT during weekends. Soccer is also another passion (or maybe a religion) for me. I am glad that I can follow all Vasco da Gama matches in the Brazilian league from the US, and that there’s an awesome soccer group in the DMS that plays every Friday here at Avery Point.

Unraveling phytoplankton nutrient proclivity in an ocean desert

Graduate student Catherine Crowley went on research cruises to investigate the contribution of small eukaryotes to new production in the North Pacific Subtropical Gyre.

The RV Kilo-Moana Katie was on.
Katie and her colleagues: Julie Granger, Katie Crowley, Katherine Ackerman, Matt Miller (left to right) Photo credits: Catherine Crowley

By Mengyang Zhou

Catherine (Katie) Crowley, a Ph.D. student in the Granger Laboratory, participated in two research cruises in the North Pacific Subtropical Gyre (NPSG) in the summer of 2023. The cruises, in August and September 2023, were aboard the R/V Kilo Moana as part of the Hawaiian Ocean Time Series (HOT) program at Station ALOHA (A Long-Term Oligotrophic Habitat Assessment). HOT is one of the longest-running time series in the ocean spanning over 30 years. This region of the Pacific Ocean is known as the “ocean desert”, with relatively little nutrients in the surface waters due to the low nutrient supply common in subtropical gyres. However, it is not well understood how certain phytoplankton living in surface waters in summer access the nutrients in the deeper waters. Katie’s research will investigate how particular phytoplankton (eukaryotes) access subsurface nitrogen at Station ALOHA, to better understand how the productivity in subtropical gyres will be impacted by climate change.

On the cruises this summer, she performed isotope incubation experiments and collected samples for nitrogen isotope analyses and cell counts. Back at UConn, she will sort the phytoplankton populations from the samples she collected on a fluorescence-activated cell sorting (FACS) flow cytometer and aim to examine their nitrogen composition, to reveal which nutrients these phytoplankton have a taste preference for in the subtropical gyre. She plans to present this work with her collaborators, the White Lab from the University of Hawaii) and the Marchetti Lab from the University of North Carolina at Chapel Hill) at the upcoming Ocean Science Meeting in 2024. 

To reflect on her cruise experience this summer, Katie says: “These collaborative cruises allowed me to gain hands-on experience and learn about eukaryotic primary production in the Pacific Gyre. As a graduate student, I was able to collect data for my research and assist the HOT team with their time-series collections.”

New multi-study analysis of gut microbiome data from blue mussels

Caption: Graphical abstract depicting that a multi-study analysis of raw 16S gut microbiome data collected from blue mussels revealed that depuration strongly influences the recovered microbial community.

Everybody poops, even mussels! And it turns out that whether a mussels has pooped matters a lot when you sample its gut microbiome. New research published in Environmental Microbiology by the Ward lab and lead author Tyler Griffin reveals that fecal egestion (or depuration) status of mussels is a critically important factor for determining the microbial community composition in the mussel gut. By performing a multistudy re-analysis of microbiome data from several projects conducted by the Ward lab over seven years, they were able to broaden the understanding of gut microbial dynamics of these foundational invertebrates in Long Island Sound. Link to the article.

Microplastics in Shellfish at “Extremely Low” Levels Globally

A group of researchers at DMS joined together under Sandra Shumway and Evan Ward, critically reviewed 750+ publications on microplastics and molluscs in the field and laboratory. This incredible effort has resulted in a thoughtful review of the cluttered scientific literature. Many studies on suspension feeding molluscs and microplastics have perpetuated inaccurate findings based on inappropriate methodologies, poor animal husbandry, and misinterpreted results. All of these false conclusions have caused a damaging narrative for the shellfish industry, raising concerns about the safety of eating shellfish. While microplastics are ingested by shellfish, microplastics in molluscs are extremely low globally as these animals are capable of selective capture, ingestion, and egestion of particles. In reality, the number of microplastics inhaled and consumed by humans in everyday life far outweighs the number of microplastics found in shellfish. Recommendations were provided for future studies in both the field and laboratory that will prevent researchers from falling into the pitfalls discussed in this review. This review is presented from the perspective of experts on shellfish physiology and represents the opinions of, and assessments made by, the authors. The authors hope this review can be used as a starting point for those interested in furthering this field of research with thoughtful experimental questions. Link to the article.

An Interview with Our Retiring Faculty Member – George B. McManus

Retiring Faculty Member - George B. McManus. Photo credit: Mengyang Zhou
Retiring Faculty Member – George B. McManus. Photo credit: Mengyang Zhou

By Mengyang Zhou

George McManus is retiring on February 1, 2024, after 28 years at the university. Graduate student Mengyang Zhou sat down with him to capture George’s reflection on his amazing career and find out what he plans to do next. 


Mengyang: How did you decide to pursue a career in academia? 

George: I was interested in environmental science and had a degree in biology. So I thought I might want to be an environmental lawyer, actually. Then I went to Stony Brook University to get a master’s degree in marine science before going to law school. But when I got there, I really liked science much more, and I said I don’t want to be a lawyer. So I stayed at Stony Brook and got my PhD in 1986. Then I had a postdoc in upstate New York at the Cary Institute, and another postdoc at the University of Maryland. Then I got a faculty job at the University of South Alabama. In 1995, I got the job at UConn, and I’ve been here since then. A lot of changes in that period of time. When I got here, I think there were maybe a dozen of faculty, and there was only one woman. They just started the undergraduate major, which was called Coastal Studies at that time, and they had the graduate program here. And when I started out, I was teaching two days a week at the Stamford campus. But then in 1998, I got transferred here to the Avery Point campus so I had my lab and my teaching here. And I’ve been just here ever since.


Mengyang: What are the changes that you saw in our department over the years?

George: One big change is that the faculty is much bigger now. Also, the undergraduate major has really grown. Now we have around 100 students in this major. A big change is this building. When I got here, there were two kind-of broken down buildings with not very good facilities, and they were crumbling. This building was started in 2001, I think. And it really made a big difference in the facility and labs. I used to be in another building that was taken down, and I could look out across here and see this new building going up. Sometimes I walked over here and stood here when it was just concrete and nothing else, so I knew I was going to be in this office. The department has also grown a lot in research funding. One thing that really hasn’t changed is that it’s still a relatively small department. And people still collaborate a lot with each other. When departments get big, they break down into different groups, and all of a sudden, you’re just a smaller part of the bigger group. But here it’s still small enough that people, from geochemistry or physical oceanography or biology, still talk to each other. The Avery Point campus itself has also changed a lot. The facilities have gotten a lot better. I think we’ve gotten higher quality students here. 


Mengyang: Can you talk about how your research and the field changed over the years?

George: I am always interested in plankton. For my PhD, I studied little tiny flagellates that eat bacteria. And I was always interested in the food chain, the protozoa and how they fit into the food chain. The food chain in the ocean can be very long because it starts with tiny things and takes many steps before you get something big like a fish. I also did a master’s degree about copepods and copepod processing of PCBs (polychlorinated biphenyls), which is an environmental contaminant. I did a postdoc in upstate New York. It was a freshwater environment. I studied a little lake for a whole year, measuring who eats different kinds of bacteria and how the food chain was set up. And then when I got down to Maryland, I got interested a little bit in phytoplankton, because I was interested in using different phytoplankton pigments to identify which kinds of algae were there, and who was grazing on them by changes in the different pigments. Then I got interested in slightly bigger things like ciliates and other kinds of grazers. I continued that work when I went to Alabama. 

One thing that I discovered in graduate school, but it was a side thing, not part of my dissertation, was that there were some ciliates that eat phytoplankton and they digest everything, but they keep the chloroplast, and the chloroplasts can still be functional. So they can photosynthesize based on the food that they eat. They’re called mixotrophs, because they’re eating but also photosynthesizing. And that was something I thought was really fascinating. It was an experience of discovery in my life. I remember looking in the microscope and putting on the fluorescent light and seeing all these chloroplasts inside of ciliates and I just ran out of the room to try to find somebody to show this to. But I didn’t really get back to that until I went on a sabbatical, when I was at UConn in 2002. And I was in Ireland, studying this little mixotrophic ciliate that lives in tide pools. And I started, also at the same time, collaborating with a person at Smith College, Dr. Laura Katz. She’s a molecular biologist. So I would pick these ciliates, and then she would sequence their DNA. And one of the things we found out is we could sequence the chloroplast and find out what kinds of algae they were eating. Huan Zhang and Senjie Lin also helped me with this.   It turns out, they’re eating macro algae. They actually eat the spores from seaweeds. We could tell that from the genome of the chloroplast. And from that point in the early 2000s, I really kind of focused on using molecular methods to document diversity of protozoa, especially ciliates in the natural environment. I still always had an interest in the food chain, and I did some work in Brazil with Hans Dam (also a faculty member in our department) on the tropical upwelling system and how the food chain is structured there. But mostly, a big part of what I have been doing is cultivating the organisms. We’ve had a long time series out here at the dock on campus, collecting ciliates, trying to culture them and identify them. Then we barcode them, in other words, we take a piece of the DNA that we sequence, and that lets us identify them. If we get the same thing later, we can verify from the DNA. So I think my lab developed kind of a specialty in being able to cultivate these organisms because they’re very, very fastidious, and hard to cultivate. And then especially with collaborations with my colleague at Smith College, being able to sequence them and eventually we got to where we could sequence the whole genome or the whole transcriptome. When we first did that, the Moore Foundation funded a study of eukaryotic plankton transcriptomes. Anybody who had anything in culture that they wanted to sequence, the foundation would do it. We had the ciliate that I talked about, that grows in the tide pools and eats seaweed. We had them in culture, but to collect enough RNA, I would have to filter quite a bit and they don’t like to be caught on a filter. They kind of blow up on the filter and they don’t like to be centrifuged. So I picked individuals and I had to pick 22,000 of them. I picked maybe a couple of 1000 every day for two weeks. Within a couple of years, now you can just pick one and get the whole transcriptome from the methods people have now. So even in the short time of my career, things have changed so dramatically. We have a lot of new tools now to look at the genes and the gene expression in these organisms, not only in culture, but also we’ve been on cruises on the shelf here and collected things and sequence them from that.


Mengyang: What are the things you are going to miss after retirement? 

George: I’ll miss the people. One of the things that I really hated about COVID was that everybody was working remotely. And that just does not suit me. From the very beginning, the university let people back into their labs if they had things like cultures to maintain, and I was basically coming in every week. But there weren’t too many other people here. I missed the people because of all the years before and even now since COVID is pretty much over. You see people and interact with them. I will still come in for the first year or two, and go to seminars and talk to people. But I think I won’t be active in the research part of it. I may go to some meetings, but I’m not going to keep any more cultures. I’m part of the SCOR working group. SCOR is the Scientific Committee on Oceanic Research. It’s an international organization. The NSF (National Science Foundation) funds these working groups on specific topics. The one that I’m involved in, with another year and a half to go, is about mixotrophs, organisms that both feed and also photosynthesize. I’ll have a meeting in Brazil next year, and maybe another meeting in Asia after that. So I’ll still be active intellectually, but probably not be doing research directly.


Mengyang: Do you have some final words to reflect on your academic career?

George: I think I’ve been very lucky that every day that I got up, I drove to work and I was happy. I always look forward to what I am going to do today. And it’s a tremendous privilege to have that. And kind of to earn your keep, you teach and you have graduate students and so forth. And that’s also fun. I love doing that. I don’t know if in the future, the structure will be quite the same. There’s more of a movement towards having teaching faculty and then research faculty. I’m not sure if the tenure system is going to stay in there. I hope it does. I hope that young people still have the same opportunities I had. It’s been a really great career and I wouldn’t change anything about it. I really enjoyed it.

PhD student Anagha Payyambally featured in UConn Today

Our PhD student Anagha Payyambally was featured in UConn Today to celebrate her achievement of receiving the Quad Fellowship. Anagha is one of only 100 recipients out of over 3000 applicants to receive this fellowship to her graduate studies. This new fellowship program supports exceptional students who are citizens of the United States, Australia, India, and Japan to support their graduate studies in the United States and build collaboration among scientists and technologists.

Read the story here with quotes from Anagha and her advisor Dr. Manning. Congratulations, Anagha!