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 Science (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 MARN4001 and now a master student in the DMS, said: “MARN4001, 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. MARN4001 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.

Brendon Goulette awarded Connecticut Sea Grant Undergraduate Research Fellowship

Congratulations to Brendon Goulette, an undergraduate student in our department who was awarded a Connecticut Sea Grant Undergraduate Research Fellowship for the work he is doing with Professors Catherine Matassa and Samantha Siedlecki and PhD student Halle Berger. Brendon is researching how climate change is affecting sea scallops, a significant commercial fishery in New England.
Caption: Brendon Goulette measures scallop shells in Samantha Siedlecki’s lab at the UConn Avery Point campus. 

Professor Siedlecki awarded tenure and promotion to Associate Professor

Congratulations to Professor Samantha Siedlecki who was recently awarded tenure and promotion to Associate Professor from the University of Connecticut! We are so proud to have Prof. Siedlecki as a member of our department and to see her awarded tenure.

Professor Siedlecki has been a highly valued member of our department since her arrival at UConn in 2017 and has played many leadership roles in our department and the broader scientific community. Dr. Siedlecki’s research group focuses on coastal biogeochemistry using a combination of simulations and observations to characterize historical and ongoing change and forecast future trends. A particular focus of her group’s work is on coastal carbon and oxygen cycling, including the impacts of decreasing ocean pH (ocean acidification) and decreasing oxygen (deoxygenation) resulting from climate change and other human impacts.

Her research accomplishments have been recognized through an Early Career Faculty Innovators Program Fellowship from NCAR and a Kavli Fellowship from the US National Academy of Sciences. Since her arrival at UConn, she has received approximately 16 grants totalling over $4 million in funding from organizations including NOAA and NSF, including serving as co-lead PI on a $1 million grant on assessing the vulnerability of sea scallops to ongoing ocean change. 

Her teaching contributions have included developing two new courses, Ocean Expedition (a very popular course for our graduate students) and Biogeochemical Modeling, and teaching Environmental Reaction and Transport, a course that allows undergraduate students to develop their quantitative and problem solving skills. She has mentored numerous personnel in the department, and currently supervises two PhD students, one masters student, one research associate, one research scientist, and multiple undergraduate students.

Dr. Siedlecki has been highly active in departmental service, having served on several departmental committees, including the Advisory Committee to the Head, and was a founding member of the department’s Justice, Equity, Diversity and Inclusion committee. She was recognized with a Climate, Diversity, Equity and Inclusion Award from the UConn College of Liberal Arts and Sciences in 2022 due to her contributions to fostering an inclusive climate in our department and at UConn.

Outside of UConn, she has had substantial contributions to research organizations and activities at the regional, national and international level, including serving as co-coordinator for the Northeast Coastal Acidification Network (NECAN) and serving as a member of the international scientific committee for the 5th International Symposium on Oceans in a High CO2 World, and also gave an invited plenary presentation at this conference. Dr. Siedlecki makes stakeholder engagement and outreach critical components of her research program and has participated in numerous outreach activities with members of the aquaculture industry and management organizations along with members of her research group. 

Dr. Siedlecki has co-authored approximately 36 publications and some of her recent publications are listed below.

Now that she has been awarded tenure, Prof. Siedlecki looks forward to finalizing her group’s work with east coast coastal communities through a regional vulnerability assessment of scallops and the communities who rely on them. She plans to conduct similar assessments in other regions with the international research community and is currently preparing a proposal with South African colleagues.

Congratulations to Dr. Siedlecki! We are excited to watch the future accomplishments by you and your team!

Recent publications:

Seasonality and life history complexity determine vulnerability of Dungeness crab to multiple climate stressors” by Berger et al. (2021) in AGU Advances. This paper was led by Siedlecki lab graduate student Halle Berger.

Coastal processes modify projections of some climate-driven stressors in the California Current System” by Siedlecki et al. (2021) in Biogeosciences.

Projecting ocean acidification impacts for the Gulf of Maine to 2050: New tools and expectations” by Siedlecki et al. (2021) in Elementa: Science of the Anthropocene.

Prof. Siedlecki at the Avery Point campus


Prof. Siedlecki and PhD student Halle Berger in Norway following a research conference.


Prof. Siedlecki on the R/V Connecticut during the Oceanographic Expedition graduate course in 2022

Congratulations to Dr. Patricia Myer, PhD!

Congratulations to Dr. Patricia Myer, the department’s newest PhD! Here is a description and some photos of Dr. Myer’s PhD journey, in her own words.

My Ph.D. dissertation defense was on March 20th, 2023, and titled “A Critical Examination of the Factors Controlling Methylmercury Uptake into Marine Plankton.”

I am a student in Dr. Robert Mason’s group and my research includes a three-year long time series of methylmercury in phytoplankton in Narragansett Bay, RI, a research cruise in the Northwest Pacific (NOAA GU1905), and laboratory uptake experiments with the dinoflagellate O. marina.

The goal of these projects was ultimately to compare the effects of biological and environmental variables (e.g., cell size, temperature, dissolved organic matter) between laboratory experiments and environmental studies to try to disentangle the leading drivers of methylmercury accumulation into plankton. The main takeaway is that relationships seen in laboratory experiments, both from my work and the literature, are not nearly as straightforward in the environment. There is a lot more work to be done to understand these complex relationships.

Currently, I have one publication from my prior undergraduate work (https://doi.org/10.1007/s10646-022-02548-0) and one from my work in the Mason lab that is not part of my dissertation (https://doi.org/10.1016/j.chemosphere.2022.134609). I am currently preparing three papers relating to my dissertation for publication.

This work was funded by NSF Chemical Oceanography and the UConn Predoctoral Award.

Myer on the GU1905 cruise with a portable fume hood for processing methylmercury samples into particulate and dissolved fractions – October 2019


Myer presenting in Krakow, Poland at the International Conference for Mercury as a Global Pollutant (ICMGP) – September 2019

Anagha Payyambally awarded Quad Fellowship

Congratulations to Anagha Payyambally, a PhD student in Professor Cara Manning’s research group, who has been selected as part of the inaugural class of Quad Fellows. Anagha is one of 100 recipients out of over 3200 applicants across all STEM fields to be selected for this fellowship, which is administered by Schmidt Futures (a philanthropic initiative of Eric and Wendy Schmidt). The rigorous selection process involved a written application, reference letters, and two interviews, and was designed to assess candidates’ academic excellence, intellectual rigor, interest in the intersection of STEM and society, capacity to bridge differences, and orientation towards results.Here is some info on the award, from Quad:
“This program sponsors 100 exceptional American, Japanese, Australian, and Indian master’s and doctoral students in science, technology, engineering, and mathematics (STEM) to study in the United States. The fellowship develops a network of science and technology experts committed to advancing innovation and collaboration in the private, public, and academic sectors, in their own nations and among Quad countries. The program builds foundational understanding among Quad Fellows of one another’s societies and cultures through cohort-wide trips and robust programming with each country’s top scientists, technologists, and politicians.”

The next application for Quad Fellows is expected to open in November 2023.

Mary McGuinness completes MSc on alkalinity in Long Island Sound embayments

Congratulations to Mary McGuinness who presented her MSc thesis research on alkalinity in Long Island Sound embayments on November 17, 2022.  Mary was advised by Dr. Penny Vlahos. Below is a description written by Mary about her research at UConn and her accomplishments during her degree. Check out the photos of her field work, too! Congratulations, Mary, and best wishes for the future!

I came to UConn in June 2020 after receiving the Crandall Fellowship for my commitment to diversity enhancement in higher education and science during my time as a undergraduate of the New Jersey Institute of Technology. While working on the Alkalinity of Long Island Sound Embayments (ALISE) project I was able to conduct field work across the Long Island Sound and help close the gap for alkalinity and inorganic carbon data in these rivers. Over a two year study I observed spatial trends for alkalinity across the Long Island Sound rivers, at their freshwater endmembers and detected help levels of acidification sensitivity. Lastly I produced an attributive model that indicated importance differences between the eastern and western Long Island Sound and presented novel controlling parameters which can be tested with the collection of further data to help fully resolve this system.

I was able to present my work virtually the Ocean Sciences Meeting (2022) and in person at the Long Island Sound Conference (2022) and Society of Environmental Toxicology and Chemistry Conference (SETAC) (2022). At the SETAC Conference I was presented with the best Oral Presentation Award.


Mary sampling on the Connecticut River


Filtering for dissolved organic carbon at the Thames River


Collecting data in the Thames River with labmate Lauren Barrett


Finishing a day of data collection at the Housatonic River


Outreach event for eelgrass restoration

On October 19, members of the Marine Sciences Department participated in an outreach event for a research project that is led by Professors Craig Tobias and Jamie Vaudrey, graduate student Shannon Jordan, and Chris Pickerell from the Cornell Cooperative Extension. The research is funded through the Long Island Sound Study. The researchers are aiming to improve the success of eelgrass restoration by adding a chemical amendment to the sediments when eelgrass shoots are transplanted to a new location.

The outreach event involved bringing community members and scientists together to prepare the eelgrass shoots for transplanting at the new sites in the Niantic River. Shannon and the team have also been conducting lots of field measurements and laboratory experiments in the lead up to the transplanting event. We look forward to learning how the eelgrass grows in its new habitat over the next year!

Shannon Jordan, Josie Mottram, Anagha Payyambally, and Alex Frenzel prepare eelgrass shoots for transplanting

Community members prepare eelgrass shoots for transplanting. Credit: Jamie Vaudrey


Shannon Jordan and Alex Frenzel participate in fieldwork for the project


Shannon, Amelia, Brian and Peter collect sediments for laboratory experiments

Antibiotics as a Method to Perturb the Gut Microbiome

Nearly all living organisms have a collection of bacteria that live within or on their body and provide essential functions, such as aiding digestion and neutralizing toxins. An important community of microbes primarily located in the gastrointestinal tract of animals is known as the gut microbiome. Scientists are working to understand the complex interactions between the gut microbiome and both essential body functions and disease. One way to study the benefits of the microbiome is to analyze organisms with reduced or eliminated microbiomes. These organisms are lacking the bacteria that may help them mediate environmental stressors.

Griffin et al. (2021) presents the development of a methodology to perturb the gut microbiome in bivalves using antibiotics. This methodology can be valuable to further research by providing a technique that produces animals with reduced or eliminated gut microbiomes without killing the hosts. The project began with the PhD work of Dr. Melissa Pierce, a previous student in Prof. Ward’s lab. Her work exposed oysters (Crassostrea virginica) to a cocktail of antibiotics for 4 days, but didn’t observe any significant changes in the diversity of gut microbes. Tyler Griffin’s work extended the exposure period to 3 weeks and used the blue mussel (Mytilus edulis), which is a commonly used bivalve for lab experimentation. As this was his first PhD research project, Griffin reflected that learning when to be independent and learning when to ask for help were some of his biggest challenges. He cited the help of Bridget Holohan and former Ward lab postdoc Dr. Lisa Nigro as invaluable.

The experimental design is shown for both oyster (top) and mussel (bottom) exposures.

As shown in the flow chart, bivalves were exposed to antibiotics in individual microcosms, or mason jars, and fed a microalgae stock culture that was sterilized by boiling. Three antibiotics were chosen to inhibit a broad group of bacteria. At the end of the experiment, mussels were dissected and analyzed by a few different methods to determine the effect on the microbiome. Through a chance conversation with and help from Dr. Brittany Sprecher, a previous PhD student in Dr. Senjie Lin’s lab, Griffin chose quantitative polymerase chain reaction, or qPCR, which is a technology used for quantifying genes, to check for the total number of bacteria in the gut. qPCR results showed that mussels exposed to antibiotics had a reduced number of bacteria, and other techniques showed reduced microbial species richness and shifts in the whole community composition. Essentially, the antibiotics had successfully reduced the number and type of the bacteria in the gut microbiome, which supported the hypothesis that prolonged exposure to antibiotics can perturb the gut microbiome of bivalves. 

Moving forward, Griffin hopes other researchers can use these methods to study other bivalve species, other microbiomes on different body sites, such as the gill, or even other suspension feeders such as gastropods or ascidians.

Tyler Griffin

Griffin, T. W., Pierce, M. L., Nigro, L. M., Holohan, B. A., & 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, 140( 4), e12352. https://doi.org/10.1111/ivb.12352

Elise Hayes: Longstanding DMS Business Manager

For 30 years, Elise Hayes served as the Department of Marine Sciences Business Manager, called the Marine Sciences Institute at the time of her hiring. She began her time at UConn Avery Point as an undergraduate student, spending breaks working with the National Undersea Research Center and ultimately earning a bachelor’s degree through the UConn Account program. During her tenure, she worked with six department heads/center directors including Richard Cooper, Robert Whitlatch, James O’Donnell, Ann Bucklin, James Edson and Evan Ward.

During her time at UConn, Hayes had the opportunity to participate in many exciting moments. She recalls the opportunity to join a research cruise in the Gulf of Maine and participate in a dive on a 2-person submersible, attending the christening and launch of the RV Connecticut in Maine, and participating in an RV Connecticut cruise to release two pilot whales that were rehabilitated at the Mystic Aquarium as highlights of her time here.

Elise Hayes

As Business Manager, Hayes managed all administrative activities including pre-award and post-award grant management as well as payroll and oversight of purchasing, accounts payable and recharge center activities, among other duties. Her valuable ability to manage the many moving parts of dozens of grants and accounts earned her the gratitude and respect of faculty, staff, and students, and the department will sorely miss her after her retirement at the end of March this year. Post-retirement, she plans to spend more time on her hobby farm where she raises a horse and donkey, goats, and recently acquired some lambs, and spend time at her cottage in Maine.