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.

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.”

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.

Fall 2021 Department Achievements

Fall 2021 Department Achievements


Prof. Hans Dam

Received the 2021 UConn Faculty Excellence Award for Graduate Teaching. This Award recognizes a faculty member with a distinguished record of sustained teaching excellence through outstanding instruction, engaging students thoroughly in the process of learning, and contributing significantly to the intellectual life of the University.  


CIRCA – Prof. James O’Donnell

The Connecticut legislature’s 2021-23 budget provided an additional $5 million to CIRCA to expand Resilient Connecticut activities and advance fundable projects. CIRCA will continue to support development of innovative adaptation approaches for flood and heat vulnerability along with expert advice on climate issues to communities in Hartford, New London, and Middlesex Counties. 

Prof. Hannes Baumann

Connecticut SeaGrant: PI Baumann together with collaborators from CTDEEP received funding to investigate the causes and ecosystem consequences of the recent, steep increase in Black Sea Bass in Long Island Sound. 

Jo-Marie Kasinak (graduate student, Prof. Vaudrey) & Prof. Vaudrey

Connecticut SeaGrant: Toward a deeper understanding of human connections with ocean environments: Ocean Identity (OI) as a novel construct, research instrument, and assessment tool. (2022-2024), $143,309, PIs Kelly, Kasinak, McKinley, Vaudrey, & Mattei. 

Prof. Robert Mason

NSF Chemical Oceanography: Methylated mercury sources and cycling in the high latitude North Atlantic. (2021-2023), $283,534, PI Mason. 

Prof. Samantha Siedlecki

NSF: Regional climate change projections to enable equitable ocean planning for the blue economy (2021-2022), PIs. Pinsky, Hice-Dunton, Siedlecki, & St. Martin. This project aims to enable climate-ready, coordinated, and inclusive decision making throughout the blue economy and spark a new generation of durable blue development.

Prof. Vlahos

NSF: Arctic Marginal Ice Zone Alkalinity (AMIZA). PI Vlahos. This project is studying the components of carbonate alkalinity in the changing Arctic with a focus on the transient ice melt zones.

NIH: Chronic Kidney Disease. PI Vlahos. Lead PI Shuchi Anand, Stanford University. This project is a continuation of our efforts with colleagues in Sri Lanka and at Stanford to expand our 300 person cohort to a 900 person longitudinal study on the progression of kidney disease and water quality.


Prof. Peter Auster

Prof. Auster presents a chapter as part of an international effort to inform delegations to the United Nations about the status and effects of human activities on the global ocean. (Levin, L. A., Auster, P., Clark, M. R., Hall-Spencer, J. M., Hopcroft, R., Ingels, J., Metaxas, A., Narayanaswamy, B., Tuhumwire, J. T., Yasuhara, M. (2021).  Continental slopes and submarine canyons.  Chapter 7J, p. 395-420, in: The Second World Ocean Assessment, World Ocean Assessment II. United Nations, New York.)

Prof. Auster addresses the confusion in ecological terminology used in international agreements to manage fisheries impacts on the high seas. (Watling, L., Auster, P. J. (2021). Vulnerable marine ecosystems, communities, and indicator species: confusing concepts for conservation of seamounts. Frontiers in Marine Science 8:622586.)

Prof. Auster and colleagues demonstrate that simple GoPro cameras can be used to quantify the role of oyster aquaculture cages as fish habitat. (Mercaldo-Allen, R., Clark, P., Liu, Y., Phillips, G., Redman, D., Auster, P. J., Estela, E., Milke, L., Verkade, A., Rose, J. M.  (2021). Exploring video and eDNA metabarcoding methods to assess oyster aquaculture cages as fish habitat.  Aquaculture Environment Interactions 13:277-294.)

Prof. Paola Batta-Lona

Prof. Batta-Lona and colleagues examined how environmental conditions affect the distribution of zooplankton in the Gulf of Mexico. (Cicala, F., Arteaga, M., Herzka, S., Martinez, M., Hereu, C., Jimenez Rosenberg, S. P. A., Saavedra, A., Robles, J., Gomez, R., Batta-Lona, P. G., Galindo Sanchez, C. E. (2021). Environmental conditions drive zooplankton community structure in the deep-water region of the southern Gulf of Mexico: a molecular approach. Molecular Ecology.) 

Prof. Batta-Lona and colleagues used DNA (metabarcoding) to look at the diversity of zooplankton in the Gulf of Mexico. (Martinez, M., Hereu, C., Galindo Sanchez, C. E., Arteaga, M., Batta-Lona, P. G., Saavedra, A., Robles, J., Jimenez Rosenberg, S. P. A., Herzka, S. (2021). Epipelagic zooplankton diversity in the deep water region of the Gulf of Mexico: A metabarcoding survey.  ICES Journal of Marine Science.)

Prof. Zofia Baumann

Prof. Baumann and colleagues present a study that demonstrates the liver detoxifies previously-bioaccumulated methylmercury based on analyses of tissues from three waterbird species. (Poulin, B.A., Janssen, S.E., Rosera, T.J., Krabbenhoft, D.P., Eagles-Smith, C.A., Ackerman, J.T., Stewart, A.R., Kim, E., Baumann, Z., Kim, J.H. and Manceau, A., 2021. Isotope fractionation from in vivo methylmercury detoxification in waterbirds. ACS Earth and Space Chemistry, 5(5), pp.990-997.)

Prof. Ann Bucklin

Ann Bucklin, chair of the Scientific Committee for Ocean Research (SCOR) Working Group WG157 presents with other members of WG157 a review paper examining global patterns of biodiversity of marine zooplankton using DNA barcodes or short sequences of cytochrome oxidase I (COI) that discriminate and identify species and announce a reference database for identification of species from DNA barcoding and metabarcoding of pelagic biodiversity, with advanced search functions by ocean region and taxonomic group. (Bucklin A., Peijnenburg, K. T. C. A., Kosobokova, K. N., O’Brien, T. D., Blanco-Bercial, L., Cornils, A., Falkenhaug, T., Hopcroft, R. R., Hosia, A., Laakmann, S., Li, C., Martell, L., Questel, J. M., Wall-Palmer, D., Wang, M., Wiebe, P. H., Weydmann-Zwolicka, A. (2021). Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology.)

Photo by R.R. Hopcroft and C. Clarke (UAF) and L.P. Madin (WHOI); see: 

Profs. Hans Dam, Michael Finiguerra, Hannes Baumann

Profs. Dam, Finiguerra, and Baumann show that zooplankton adapt quickly, but with limited capacity, to ocean warming and acidification, which is both encouraging and sobering news for the response of animal populations to rapid climate change. (Dam, H. G., deMayo, J. A., Park, G., Norton, L., He, X., Finiguerra, M. B., Baumann, H., Brennan, R. S., Pespeni, M. H. (2021). Rapid, but limited, zooplankton adaptation to simultaneous warming and acidification. Nature Climate Change, 11, 780-786.)

Prof. Leonel Romero 

Prof. Romero and colleagues propose a new approach to realistically model wave effects on currents, overcoming several limitations of state-of-the-art coupled wave-ocean models. (Romero, L., Hypolite, D., McWilliams, J. C. (2021). Representing Wave Effects on Currents. Ocean Modelling, 167, 101873.)

Prof. Sandy Shumway

Prof. Shumway edited a book titled “Molluscan Shellfish Aquaculture: A Practical Guide” as a usable manual for those interested in an up-to-date introduction to the field. The book covers each of the major cultured species of cultural importance. (Shumway, Sandy, Ed. (2021) Molluscan Shellfish Aquaculture: A Practical Guide. 5M Publishing.)

Prof. Samantha Siedlecki

Prof. Siedlecki and colleagues present work showing that the  projected changes for carbon variables like pCO2 and pH in the California Current System (CCS) using a high resolution model are modified by coastal processes resolved in the downscaled projections relative to the projected global simulation, suggesting downscaled projections are necessary to more accurately project future conditions of these variables. (Siedlecki, S. A., Pilcher, D., Howard, E. M., Deutsch, C., MacCready, P., Norton, E. L., Frenzel, H., Newton, J., Feely, R. A., Alin, S. R., Klinger, T. (2021). Coastal processes modify projections of some climate-driven stressors in the California Current System, Biogeosciences, 18, 2871–2890.)

Prof. Siedlecki, graduate student Kelly McGarry, and colleagues present a combination of regional high-resolution simulations that project ocean acidification (OA) conditions for the Gulf of Maine into 2050, the results of which indicate that the aragonite saturation state (one measure of OA) declines and the entire GOM will experiences biologically critical conditions for most of the year. (Siedlecki, S. A., Salisbury, J., Gledhill, D. K., Bastidas, C., Meseck, S., McGarry, K., … & Morrison, R. (2021). Projecting ocean acidification impacts for the Gulf of Maine to 2050: New tools and expectations. Elementa: Science of the Anthropocene, 9(1):00062.) 

Prof. Penny Vlahos

Prof. Vlahos, graduate student Emma Shipley, and colleagues present an interdisciplinary study that connects drinking water quality to the progression of kidney disease in rice farmers in the Sri Lankan dry zone. (Vlahos, P., Schensul, S., Anand, S., Shipley, E., Diyabalanage, S., Hu, C., Ha, T., Staniec, A., Haider, L., Schensul, J., Hewavitarne, P., Silva, T., Chandrajith, R., Nanayakkara, N. (Accepted). Water Sources and Kidney Function: Investigating Chronic Kidney Disease of Unknown Etiology in a Prospective Study. NPJ Clean Water.)

Halle Berger (graduate student, Profs. Samantha Siedlecki and Catherine Matassa)

Berger and colleagues present a vulnerability assessment for Dungeness crab to climate change which revealed that population-level vulnerability to future hypoxia is most severe overall due to increased exposure of the critical adult stage during the upwelling season. (Berger, H. M., Siedlecki, S. A., Matassa, C. M., Alin, S. R., Kaplan, I. C., Hodgson, E. E., Pilcher, D. J., Norton, E. L., Newton, J. A. (2021). Seasonality and life history complexity determine vulnerability of Dungeness crab to multiple climate stressors. AGU Advances, 2, e2021AV000456.) 

Tyler Griffin (graduate student, Prof. Evan Ward)

Griffin and colleagues demonstrate that antibiotics can be used as effective tools to experimentally diminish the gut microbiomes of suspension-feeding animals, like oysters and mussels. (Griffin, T. W., Pierce, M. L., Nigro, L. M., Holohan, B., & Ward, J. E. (2021). An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension-feeding bivalves. Invertebrate Biology.  e12352.)

Allison Staniec (PhD graduate, Prof. Penny Vlahos)

Staniec and colleagues present a study identifying the role of sea spray in gas exchange in an article that was also featured in Nature Highlights: Big Potential for Tiny Droplets. (Staniec, A., Vlahos, P., Monahan, E. C. (2021) The role of sea spray in atmosphere-ocean gas exchange. Nature Geoscience, 14, 593-598.)

Departmental History: The Feng Graduate Research Colloquium, an Important Professional Development Tool for DMS Graduate Students

The Feng Graduate Research Colloquium has been a tradition in the Marine Science Department since 1996. Named after the first Head of the Department of Marine Sciences, Dr. Sung Y. Feng, the colloquium was started by Prof. Hans Dam. When he joined the department in the early 1990s, he saw a need for better professional development of students, particularly for presenting their research. Hans developed the colloquium to act as a conference in which students receive friendly, constructive criticism, and have the opportunity to work on developing their abstract writing, leadership, and scientific communication skills. 

The format has remained similar over the years, until the COVID-19 pandemic threw a wrench into the schedule. The 2020 colloquium was postponed to 2021 and held entirely online, which presented new challenges for the Steering Committee, the group of graduate students who helped Hans organize and run the colloquium. These challenges included choosing a platform for interactive poster presentations and troubleshooting throughout the day. Hans reflects, “The particularly difficult thing was running the poster session. We found this free software that worked, and it worked pretty well, but it was a little difficult to transition from room to room.” Hannah Collins, a member of the 2021 Feng Steering Committee, added, “Usually, Feng is such a collaborative thing within the department so the challenge was to replicate that virtually. We did our best to create opportunities for good research discussions, even if it was over a computer screen.”

Students benefit in different ways from participating in the colloquium. They prepare by listening to several seminars from faculty about writing abstracts and presenting both posters and oral presentations. Hans works with other faculty to read and critique abstracts students prepare. Hans adds, “One way to make a reputation is to give good talks, whether at conferences or invited seminars. The colloquium is a way to hone many of the skills of professional development and those that are expected of people who graduate from graduate school. We’ve seen the benefits, because our students do very well at conferences.” 

The group photo of the Department of Marine Sciences at the 2018 Feng Colloquium. Hans is kneeling at the far right of the front row (Photo: DMS Archive)

While Masters students typically only have the opportunity to present at one colloquium, PhD students typically get multiple opportunities. Hans acknowledges that he can see improvement in these students from their first colloquium to subsequent ones, “Most PhD students give a poster their first year, so you see that progression from not having an idea formulated to being able to give a talk. The more you present, the better you get, and I see that with the colloquium itself.” 

Given the benefits of the colloquium to students and the department, it’s clear that the tradition isn’t going anywhere, and for now, neither is Hans. “Feng is one of my prides. I do it because I love it, and it’s a great thing. At some point I’m sure I’m going to walk away from it and let somebody else do it, but in the meantime, I’m just enjoying it.” The Department looks forward to another successful Feng Colloquium in 2023.

Investigating the Role of Sea Spray in Gas Exchange

When considering the oceans’ role in climate change, many people focus on the capability of the oceans to store gases from the atmosphere. However, the transfer of gases between the atmosphere and the ocean is actually a complex process facilitated by multiple mechanisms, including sea spray. Sea spray moves matter and energy between the surface ocean and the atmosphere, and its contribution to gas exchange is not yet fully understood by researchers. Strongly linked to wind conditions, sea spray is predicted to increase as long-term climate trends increase wind speeds, particularly in extreme conditions such as hurricanes. Improving the modeling of gas exchange in these scenarios can help inform climate predictions of the future.

In a recent publication, former graduate student Allison Staniec, Professor Penny Vlahos and Emeritus Professor Edward C. Monahan modeled the sea spray gas exchange of non-reactive gases including argon, helium, neon, nitrogen, and oxygen. The goal of the project was to understand the magnitude of flux of these gases between the ocean and the atmosphere via sea spray. Staniec explained the motivation for the work, “There’s been a lot of exploration about how sea spray can carry things like heat and momentum. People have started looking at how it can carry organic compounds. There hasn’t been a ton of work on gases, and part of that is because it’s really difficult to measure in situ or in the laboratory. We wanted to do a proof of concept of whether this spray-mediated gas exchange could theoretically contribute to overall gas exchange.” 

There are several challenges to creating a sea spray model. First, there are many different calculated sea spray generation fluxes from previous work to choose between. Staniec explains that the Anguelova number flux was chosen because it fell right in the middle of the many literature values, but that the range of orders of magnitude of sea spray droplet generation can further complicate calculations. In addition, sea spray droplets have two stages after creation, in the first they cool after separating from the ocean surface and in the second they shrink and evaporate. However, not all droplets have the same fate. Some cool but fall back to the surface before beginning to evaporate, some evaporate entirely, and many fall somewhere in between. Since the studied gases are more soluble at lower temperatures, droplets that cool but then drop back into the ocean transfer gas into the ocean, but droplets that cool and evaporate completely transfer gas into the atmosphere. 

The typical evolution of a sea-spray droplet on injection into the atmosphere. G represents a gas molecule; T, the temperature; R, the radius; white dots represent the salt ions in solution. (Staniec et al. 2021)

After carefully considering how to represent all these factors in their model, the group determined that for gases like He and Ne, sea spray will not have much effect even at high wind speeds. However, for gases like O2, sea spray could have a significant impact on gas flux between the ocean and the atmosphere, particularly at high wind speeds. While this paper doesn’t focus on gases that are relevant to climate change, future models can expand the understanding of gas flux to more complicated and climate-relevant gases, such as CO2. Staniec explains, “We didn’t do specifically climate change relevant gases because CO2 is complicated by the fact that it reacts when it enters the water. But this is a stepping stone for that.” More investigation is needed to understand sea spray mediated gas exchange, particularly in areas of high wind speed such as the Southern Ocean, which is known for high winds and carbon sequestration. Future studies can use the findings and relevant code presented in Staniec’s work to further constrain gas exchange in these regions. 

The percentage change in gas volume (oxygen) of a 100-µm-radius droplet reaching final equilibration, with both steps combined. Darker colors represent regions that will experience higher impacts of gas exchange. (Staniec et al. 2021)

Citation: Staniec, A., Vlahos, P. & Monahan, E.C. The role of sea spray in atmosphere–ocean gas exchange. Nat. Geosci. 14, 593–598 (2021).

Where are they now? Meet Yan Jia

Dr. Yan Jia is a recent graduate of the Marine Sciences Department – he finished his PhD with Prof. Mike Whitney in 2019. His graduate research used drifters and models to understand the seasonal variation of freshwater discharge from the Connecticut River into Long Island Sound. Yan is currently working as a postdoctoral research associate for the Connecticut Institute for Resilience and Climate Adaptation (CIRCA). In his free time, he likes to collect matchbox cars and spend time with his family and his three children. This interview was carried out by Emma Shipley on October 12, 2021.

Yan Jia (Photo: CIRCA)

Q: How did you end up in your current position, and what do you do now?

When I worked as a PhD student, I didn’t pay too much attention to my future work. I knew I wanted to do research, but I didn’t try to apply to that many places, maybe 7 or 8 institutions. Sometimes you get denied, and you have to learn not to take it personally. Sometimes it’s just the job market, or the time window for the position doesn’t line up with your graduation and they are urgently looking for someone to fill the position. Eventually, Jim (Prof. James O’Donnell, UConn) offered this position to me. He was looking for postdocs.

Right now, CIRCA has two postdocs, me and my colleague Chang (Chang Liu, postdoctoral research associate, CIRCA). We are running more realistic studies on how to react to climate change and climate change’s impacts on the local area. We established a 100-year return period chart about how strong the storm surge and highest waves will be. We also run simulations more locally, specifically around New Haven harbor and neighboring coastal towns. One of the projects I finished earlier this year was about salt marsh flooding in Guilford. There is a small inlet with a width of only 8 meters, but it controls the water exchange of a 120-acre salt marsh. The local residents want to build a bridge over an old route that goes across the salt marsh; because of the sea level rising there has been more frequent flooding. It may cost millions of dollars, so they want to know what the flooding conditions are like. We run model simulations, but we also want to know if the results are reasonable. Normally people just run one numerical model, like ROMS (the Regional Ocean Modeling System), but what I did was compare four different hydrodynamic models. We can see why each model is different from the rest and which one is better to be applied in Guilford, and that will help future coastal modeling. Also, we simplified those hydrodynamic models to an idealized mathematical model that can predict the water levels inside the salt marsh much, much quicker. This idealized model is 1000x faster than the original hydrodynamic model and can be easily used by other non-modelers.

Q: It sounds like most of what you do on a day-to-day basis is work on models?

Yes, generally I help supply the scientific results for management and decision making.

Q: What does typical modeling work look like for you?

Since the summer, I have been working on adding wave forecast to an established operational model. It supplies surface current information for the Coast Guard in case they need to rescue a boat or a person in the Sound. Jim and his team have been collecting buoy-observed wave data for over 15 years. It’s one of the longest wave records in a US estuary. We can run hindcast simulations with the historical observations to tune the wave model and find a good set of parameters to support the operational forecast. 

As an aside, Yan shared with me a joke about his work:

In Chinese, ‘physical oceanographer’ has a similar pronunciation as the words meaning “an oceanographer who sits inside the room,” so that’s my job. I just sit inside the room. Very occasionally, I am sent to the field. I think field observations are very necessary. Last spring, I spent several months trying to improve the Guilford simulation, but it wouldn’t give the right answer. So, in the summer, I decided that we needed to have a field trip. When I saw the inlet, I realized it was totally different from what the model was trying to predict. That was the starting point to drag me back to the right place. So, I shouldn’t stay in the room all the time!

Yan uses a side-looking ADCP to measure the inflows at a Guilford salt marsh inlet (Photo: Kay Howard-Strobel)

Q: What about your grad school experience at UConn prepared you the best for this job?

I worked with Mike and got more familiar with ROMS, which laid the foundation for what I do now. Mike and Jim allowed me freedom, they did not regulate me in certain directions, they allowed me to use my wisdom to decide what direction or question I thought was good to pursue, and they always gave good advice. When I worked with Mike, he encouraged me to learn more simulations not just on the ocean side, but also on the atmospheric side. That helped my work with Jim because to make a good simulation of storm surge, you have to have a good simulation of wind.

Q: Do you have any advice for current students?

One of the good courses I learned from was Jim O’Donnell’s mathematical modeling course. I took that course twice. You can bring your own question and get his advice on the direction you should take. My classmates and I all learned a lot from his lecture. And of course, everyone knows to read a lot of papers.

Quarantine Cruising: Oceanographic Cruises During COVID

In early May of 2021, two faculty members and four students from our department set out for an Arctic research cruise. Led by faculty member Prof. Rob Mason, the group spent two weeks quarantining on the remote island of Unalaska in the Aleutian chain before departing on a three-week oceanographic cruise.

The Arctic, defined as the region of the Earth within the Arctic Circle located at approximately 66° 34’ N, contains several seas and parts of the United States, Canada, Scandinavia, Iceland, Greenland, and Sweden. The region is unique, with cold temperatures, varying snow and ice cover, and seasonal sea ice. Prevailing water and air currents facilitate the transport of many long-range pollutants to the Arctic, and the region is heavily impacted by climate change. Global warming has caused the loss of annual and seasonal sea ice cover, increased river discharge, and thawing of permafrost. Many climate models predict greater warming in the Arctic than the global average, compounding the effects of these changes. One of the most effective ways to gather data about these ecosystems is through oceanographic cruises.

Multi-week cruises are the backbone of much research in the oceanographic field. The occurrence of these cruises can often be reduced to a few sentences in the methods section, but the execution requires years of work prior to departure. Planning for this trip began in 2017, when Prof. Mason first submitted a proposal to the National Science Foundation (NSF) along with co-investigator Dr. Dave Kadko of Florida International University. He requested funding for a cruise to the Arctic to examine the role of ice in controlling mercury levels in seawater. 

While the RV Sikuliaq, operated by the University of Alaska Fairbanks, can typically host 20 scientists, due to the COVID-19 pandemic, the cruise was limited to 10. COVID-19 required other changes to the typical cruise experience, too. Everyone on the ship had to undergo a two-week quarantine and two COVID-19 tests prior to boarding. The UConn science party quarantined in Unalaska, Alaska, commonly known as Dutch Harbor. During the quarantine, the group hiked to several different sites on the island, including two sites of WWII bunkers and two different mountains. 

The UConn crew hikes Mt. Ballyhoo in Dutch Harbor. From left to right: Lauren Barrett, Emma Shipley, Penny Vlahos, Hannah Inman, Yipeng He, Rob Mason. (Photo: Yipeng He)
The view from the 03 deck of the Sikuliaq where continuous air sampling instruments were located. During the summer, the sun never sets in the Arctic, but dips close to the horizon before beginning to rise again. This photo was taken near midnight. (Photo: Emma Shipley)

After boarding the ship, the group settled in for three weeks of data collection. To meet research objectives, UConn’s team collected air, water, snow, and ice samples. One unique aspect of cruises to the Arctic is the ability to collect samples from sea ice. During this cruise effort, the science party sampled at 5 different ice stations within the marginal ice zone, the region of seasonal sea ice surrounding annual ice. Sampling on sea ice is a carefully orchestrated process. The ship’s captain and crew meticulously select a section of ice that looks large and stable enough to support several members of the science party. Scientists are briefed on the safe places to walk on the ice, and the Science Operations crew members test the ice before allowing the science party to sample. Equipment and people are typically transported between the ship and the ice using a “man-basket,” or a cage attached to a winch. While on the ice, the science party uses ice-corers to collect ice cores, large augur drills to create holes for collecting ice brine and under-ice water, and shovels for snow. The Arctic environment can be harsh and dangerous, and a team of crew and scientists work as look-outs on the bridge for any potential threats, such as roaming polar bears. In fact, the UConn team saw four different polar bears while on the cruise, three of which were visible while ice sampling was taking place. Seeing polar bears in the wild is a truly unique experience, and observing these animals in their natural habitat was commonly mentioned by the science party as one of their favorite parts of the cruise. Rob adds, “Seeing the bears up close was definitely a highlight. Sampling in the ice and getting out there off the ship was special, but overall being in such a remote beautiful place where very few people go was a highlight.”

The science party poses on the ice in front of the RV Sikuliaq. From left to right, Ethan Roth (Sikuliaq Science Operations Manager), Marissa Despins (Wright State University), Yipeng He (UConn), Doug Hammond (University of Southern California), Laurie Juranek (Oregon State University), Steve Roberts (Sikuliaq Science Systems Engineer), Mark Stephens (Florida International University), Rob Mason (UConn), Emma Shipley (UConn), Hannah Inman (UConn), Penny Vlahos (UConn), Lauren Barrett (UConn), Dan Naber (Sikuliaq Science Systems Technician). (Photo: Siyu Chen)
Ice sampling, as seen from the Sikuliaq. Shown in the foreground is the “man-basket” that is used to transport personnel and supplies between the ship and the ice. In the background, Rob Mason and Dan Naber take an ice core and Ethan Roth, Laurie Juranek, and Emma Shipley take brine and under-ice samples. (Photo: Lauren Barrett)
Two polar bears observe the Sikuliaq from a nearby ice floe. (Photo: Siyu Chen)

Meet Dr. Claudia Koerting, a Woman who Wears Many Hats

Dr. Claudia Koerting has been working in her current professional faculty position for the past 16 years, although she’s had various positions at UConn since 1997. Almost every graduate and undergraduate who gets a degree in the Department of Marine Sciences has had the opportunity to work with Claudia. Her current position includes serving as the marine science undergraduate coordinator and the honors advisor for the major, coordinating the Early College Experience (ECE) Marine Sciences Program, teaching several courses at Avery Point, and maintaining and helping students use the instrumentation in the SMALER (Suspended Matter Analytical Laboratory for Education and Research) Lab. 

Claudia graduated from the University of Rhode Island (URI) with a double degree in chemistry and microbiology, received a Master’s from UConn in Oceanography, and completed a PhD in pharmaceutical sciences at URI. Her interdisciplinary background allowed her to work on a variety of research projects, from Lyme disease to marine pathogens to the inhibition of bacteria that degrade oil and fuel. She emphasized the importance of interdisciplinary projects: “I like to combine all my backgrounds, cell biology, chemistry, and microbiology, (in the context of marine sciences) because any of them alone is boring to me.” She is particularly apt at analytical work, which made her the perfect fit to run the SMALER Labs at Avery Point. After taking on the role of a PhD level academic assistant for DMS in 2005, she has continued to add to her responsibilities by naturally filling vacuums she has observed, such as oversight of undergraduate lab courses. Of her career path, she says “It’s a great example of how everything you’ve done in your life, no matter how irrelevant it seems at the time, can be relevant to your future work.” When asked what a typical day on the job looks like, she laughs and says there is no typical day. 

Her favorite parts of the job center around helping students grow as scientists and researchers. “A big part of what I love to do is connecting undergraduates and high school students with research and ideas. I get to see them coming in as freshmen, and I get to see them going out as seniors. At the end of the day, when I look back and know that I’ve helped someone in some way, then I feel like I’ve done my job. It’s gratifying.”

Outside of work, Claudia has a passion for being outside, particularly sailing. She loves to be on the water year-round, but when she cannot get out onto the water, she also has a passion for hiking. 

Claudia driving the skiff (photo: Charlie Woods)