Publications

Winter 2026 Departmental Achievements

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Awards: 

Professor Pieter Visscher

Prof. Visscher received a Distinguished Career Award from The Geological Society of America. Over a distinguished career spanning more than three decades, Dr. Visscher has led advances in our understanding of the complex interactions between microbial communities, biogeochemical cycles, and the formation of sedimentary structures, bridging microbiology and Earth system science. [Read the full citation and reply]

 

Professor Sandra Shumway

Prof. Shumway was honored as Foreign Fellow by the Korean Academy of Marine Science and became Honorary Life Member in the World Aquaculture Society.

 

PhD candidate Hannah Collins

Hannah received a Young Outstanding One Health Biology Researcher award from the FUCOBI Foundation of Ecuador for her work on the microbiomes of suspension-feeding bivalves.

PhD candidate Molly James

Mollys' music and science collaboration, Harmony of Nature, with South Korean pianist Sophy Chung and composer Maxwell Lu was recently featured in a Career Feature article in the magazine Nature. The project transforms environmental data and scientific concepts into classical music.

MSc student Anagha Payyambally

Anagha received the UConn@COP Fellowship and had the honor of attending the United Nations Framework Convention on Climate Change Conference of Parties in November 2025. She traveled to Brazil to observe the climate change negotiations process and meet environmental leaders. She wrote about her experiences in UConn Today.

Grants: 

Professor Catherine Matassa

Prof. Matassa received a grant from the National Science Foundation to perform a series of manipulative field and lab experiments on organisms that live in the rocky intertidal zone of our coasts. The goal is to better understand how the risk of being eaten influences the behavior and physiology of prey organisms.

Collaborative Research: Intergenerational effects of predation risk and resource identity on rocky shores: consequences for populations, communities, and ecosystems. NSF $400,267

 

Professors Elizabeth Weidner & Shuwei Tan

Profs. Weidner and Tan received funding to study the impact of the Connecticut River on sediment transport and deposition in Long Island Sound. The goal of the project is to better understand how changing sediment deposition, due to extreme weather events, may impacts local shellfish beds and provide guidance for aquaculture management and restoration planning.

Mapping Sediment Transport and Deposition Risks to Shellfish Beds in the Tidally Modulated Connecticut River Plume. CT SeaGrant (2026-2028 OMNIBUS, $169,882)

 

Professors Hannes & Zofia Baumann

In collaboration with partners in Massachusetts, this new project will experimentally simulate electromagnetic fields as they are generated by undersea cables, for example those transporting electricity from offshore wind turbines, and then test their potential effects on the behavior and development of sand lance, a burying fish of great ecological importance in North-Atlantic waters.

 Investigating the Impacts of Electromagnetic Interference (EMI) on Adult and Larval Sand Lance in Stellwagen Bank National Marine Sanctuary. Massachusetts Clean Energy Center $503,831

 

Professor Samantha Siedlecki

Prof. Siedlecki together with colleagues from NOAA and co-PIs from other US institutions received funding to improve forecasting and develop practical strategies—combining ocean science, industry input, and social research— to create a resilient, adaptive management framework for the Sea Scallop fishery , which is one of the most valuable in the United States (>$500 million per year). Although scallops have long been resilient, they are becoming more vulnerable as rising ocean temperatures and increasing acidity affect their growth and reproduction.

RVA-OA2025 Project Title: Collaborating with Fishing Communities to Adapt: Co-developing actionable strategies for Atlantic Sea Scallop fishing communities. NOAA, $1,133,554

Publications: 

 

Professor Catherine Matassa

Matassa and recent PhD graduate Sean Ryan investigated how a species of seaweed (Fucus vesiculosus) defends itself from herbivorous snails (Littorina littorea) along its latitudinal range in the coastal northeast USA. Are northern seaweeds built tougher?

Ryan, S. and Matassa, C. Latitudinal variation in the constitutive and inducible defences of a canopy-forming rocky intertidal seaweed (2025) Functional Ecology, 2025, 39(12), 3718-3731

 

Professor David Lund

Lund and graduate student Monica Garity show that changes in ocean circulation and natural alkalinity enhancement played a key role in regulating atmospheric carbon dioxide in the recent geologic past. The research was featured in UConn Today

Garity, M., Lund, D., Jerris, H., and McBride, J. (2025) Progressively greater biological carbon storage in the deep Atlantic during glacial inception. Proceedings of the National Academy of Sciences 122, e2510171122

 

Professor Pieter Visscher

Visscher and colleagues show that instead of whiting events, visible with satellites, calcium carbonate precipitation is mediated in the upper layers of aquatic sediments, and continue there for several millenia. Results suggest a revision of CO2 removal through calcium carbonate precipitation.

Visscher, P.T. et al. (2026) A critical role of heterotrophic bacteria in early diagenesis of carbonates through exopolymer degradation and calcium release. The Depositional Record (16 January 2026)

 

Professor Heidi Dierssen

Dierssen contributed her expertise in remote sensing methods to new published guidelines for assessing seagrass coverage from areal and space observations. These guidelines helf monitoring and assessment of seagrass ecosystems and inform the Kunming–Montreal Global Biodiversity Framework headline indicator “Extent of natural ecosystems”.

Duffy, J.E., ..., Dierssen, H.M., and 21 co-authors (2025) Measuring and Reporting on Seagrass as an Essential Ocean Variable for Science and Management. BioScience biaf199

 

Professor Hans Dam

A joint team from UConn Marine Sciences/Ecology and Evolution (Professors Dam, Finiguerra, Baumann, and former student James de Mayo) and the University of Vermont (Prof. Pespeni and former postdoc Reid Brennan) used experimental evolution on a marine copepod to show that genetic and epigenetic mechanisms underlie resilience to ocean warming and acidification.

Brennan, R.S., J.A. deMayo, M. Finiguerra, H. Baumann, H.G. Dam, and M. Pespeni (2025) Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors. Proceedings of the National Academy of Sciences, 122(29), e2422782122.

Prof. Dam was also part of a large international group recommending key steps to resolve the disconnect between empirical research and models using planktonic organism to simulate ecosystem responses to global change.

Flynn, K. J., ..., Dam, H. G., ... 30 other authors (2025) More realistic plankton simulation models will improve projections of ocean ecosystem responses to global change. Nature Ecology & Evolution, 1-9

 

Professor Senjie Lin

Prof. Lin published two books in July and August, 2025. "Ecological Genomics of Algae" (CRC Taylor & Francis, 406 pp.) provides an integrative framework linking algal genomes to ecological processes, evolutionary innovation, and environmental adaptation across diverse algal lineages.

"Harmful Algal Blooms: Environmental Factors and Molecular Mechanisms" (Elsevier Academic Press, 306 pp.) integrates environmental forcing with molecular, physiological, and genomic mechanisms to explain the dynamics and impacts of harmful algal blooms.

 

Professor Hannes Baumann

Baumann's research tested one possible explanation for the increase in black sea bass abundance in Long Island Sound, i.e., that the species may be able to overwinter now in our coastal waters.

Zavell, M.D., Mouland, E.P., Barnum, D.L., Matassa, C.M., Schultz, E.T., and Baumann, H. (2025) Can adult Black Sea Bass overwinter in Long Island Sound, USA? Marine and Coastal Fisheries 17:vtaf014

 

Professor Robert Mason

A new study showed that atmospheric oxidation of elemental mercury in the Arctic spring can occur over sea ice, not just over land

He, Y. and Mason, R.P. (2026) Direct evidence for sea-ice-driven atmospheric mercury depletion events in the Arctic marginal ice zone. Environmental Science & Technology. Published 1/26.

New laboratory experiments examined how methylmercury accumulates in a dinoflagellate that acquires food via other processes besides photosynthesis

Myer, P.K., Mason, R.P., Baumann, Z.A. (2025) Prey engulfment as the dominant pathway of MeHg uptake in a heterotrophic dinoflagellate. Marine Environmental Research 210:107348

 

Professor Elizabeth Weidner

Weidner describes novel technology in mapping underwater sea ice - a great summary of which can be found here.

Weidner, E. (2025) Measurements of broadband backscattering from the terminus of a tidewater glacier. J. Acoust. Soc. Am. 158, 504–514

 

Professor emeritus Peter Auster

Auster and colleagues at NOAA's Northeast Fisheries Science Center Milford Laboratory show that aquaculture gear can be important fish habitat in coastal waters.

Mercaldo-Allen, R. ..., Auster, P.J., ... (10 authors) (2025) Measures of habitat quality for black sea bass using oyster aquaculture cages. North American Journal of Aquaculture, 2025, 1–16.

 

Professor emerita Ann Bucklin

The MetaZooGene Intercalibration Experiment (MZG-ICE) was a global effort that confirmed the reliability, accuracy and validity of metabarcoding data for monitoring zooplankton biodiversity.

Blanco-Bercial, L., ... (22 authors), and Bucklin, A. (2026) MetaZooGene Intercalibration Experiment (MZG-ICE): Metabarcoding Marine Zooplankton Diversity of the Global Ocean. Mol Ecol Resources 26(1):e70090

 

Graduate student Paban Bhuyan

Bhuyan and Prof. Romero demonstrated that autonomous saildrones can accurately measure small-scale ocean currents and their changes across space.

Bhuyan, P., Rocha, C.B., Romero, L., and Farrar, J.T. (2026) Acoustic Doppler Current Profiler Measurements from Saildrones, with Applications to Submesoscale Studies. Journal of Atmospheric and Oceanic Technology, e240114

 

Graduate student Hannah Collins

Collins performed experiments showing how two common species of freshwater mussels selectively ingest or reject microplastics.

Collins, H.I., Olatunji, P.O., Holohan, B.A., Shor, L.M., and Ward, J.E. (2025) Size-based ingestion of microspheres and microfibers by two freshwater mussel species (Dreissena bugensis and Elliptio complanata): Implications for removal of microplastic particles from aquatic systems. Journal of Shellfish Research 44:309-321.

 

Graduate student Halle Berger

Berger coupled a bioenergetic with a regional ocean model, predicting that warming initially enhances Atlantic sea scallop growth, but by 2100 scallops grow faster yet reach smaller sizes due to the combined effects of acidification and warming.

Berger, H. M., Siedlecki, S. A., Meseck, S. L., Pousse, E., Hart, D. R., Soares, F., Chute, A., & Matassa, C. M. (2026) Modeling the spatiotemporal effects of ocean acidification and warming on Atlantic sea scallop growth to guide adaptive fisheries management. Ecological Modelling 513:111434

 

 

DMS Prof. Pieter Visscher honored with GSA Career Award

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Please join us in congratulating Prof. Pieter Visscher for receiving the Geological Society of America’s 2025 Distinguished Career Award (sponsored by the Geobiology and Geomicrobiology Division). 

Pieter is honored for his decade-long involvement in an NSF-sponsored project that has worked with undergraduate students studying microbial sediments in Puerto Rico. Between 2000 and 2011, Pieter brought 68 of these students to Avery Point for a two-week geomicrobiology short course. None of these first-generation college students had visited the continental US before. His continued encouragement inspired over 60 students in this program to pursue graduate degrees in the US. He taught this course twice in France, once in Argentina, and once in Chile. 

Visscher5
Prof. Pieter Visscher

Pieter is further commended for his pioneering Astrobiology work, pursuing the fundamental questions: Where are we coming from, where are we going, and what is our future? His tireless curiosity ultimately led to the establishment of NASA’s Astrobiology Institute (NAI) in 1998; the product of a four-decade-long collaboration with scholars, scientists, and engineers from around the country. 

We asked Pieter to name a key paper from the many published in his career - he chose his 2020 study of arsenotrophic microbial mats that allow inferring our past: 

Visscher P.T., K.L. Gallagher, A. Bouton, M.E. Farias, D. Kurth, B.P. Burns, M.R. Walter, M. Sancho-Tomas, P. Philippot, A. Somogyi, K. Medjoubi, E. Vennin, R. Bourillot, M. Contreras, C. Dupraz. 2020. Modern arsenotrophic microbial mats provide an analogue for life in the anoxic Archean.  Nature Communications Earth & Environment 1:24

Visscher1
Antelope Island at the Great Salt Lake in Utah is one of 50+ sites in more than 20 countries where Visscher has studied fossil and modern analogues of Earth’s oldest known ecosystems.

Citation

 

by Tracy Frank: 

Pieter T. Visscher. Over a distinguished career spanning more than three decades, Dr. Visscher has led advances in our understanding of the complex interactions between microbial communities, biogeochemical cycles, and the formation of sedimentary structures, bridging microbiology and Earth system science. His pioneering studies of microbial mats and stromatolites across a range of settings have illuminated the role of microbes in shaping Earth’s surface environments through time, while his innovative approaches to microbial processes in modern and ancient settings have inspired new directions in research. His atmospheric biosignature studies were instrumental for NASA’s Astrobiology Institute, of which he was a co-founding member. A prolific scholar and respected mentor, Dr. Visscher has authored hundreds of influential publications and trained generations of graduate students who continue to advance the discipline worldwide. His research, collaborations, and leadership have had a transformative impact on geomicrobiology, leaving a legacy that will guide the science for decades to come. 

Visscher4
A needle microelectrode is being deployed for microscale geochemical measurements in microbial mats.

Visscher2
Visscher performing 24-h measurements of microbial activities in permanently anoxic ecosystems at Salar La Brava in Chiles Atacama Desert. These ecosystems couple the cycling of carbon to those of arsenic and sulfur, making them the only known modern analogues of the Archean world.

Reply

 

Pieter: Thank you, Tracy, for your kind citation. I am honored to receive this recognition, which has been previously awarded to geochemists, paleontologists, sedimentologists, and geobiologists for whom I have great respect.

As many know, the term geobiology was coined by Lourens G.M. Baas Becking, but not in his monograph “Geobiologie”, published in 1934, but in his inaugural lecture at the University of Leiden on January 28, 1931, entitled “Gaia of leven en aarde”. In this lecture, Baas Becking observed a then recent change in natural and physical scientific research that for the first time were deployed jointly to understand our planet. Furthermore, he expanded his observation that chemistry, biology, and geology did not just apply to the understanding of our planet Earth but provided the foundation for understanding the universe, which he argued was fueled by cyclic events - notably chemical element cycles, but also (micro)biological metabolisms, and physical phenomena, the mutual impact of which was captured in geological time and space. In a way, this laid the groundwork for what, 65 years later, became a motivation for NASA’s Pale Blue Dot II meeting that, in turn, started Astrobiology. Baas Becking viewed geobiology as a Copernican-based science, in other words, perceived not from an anthropocentric, Earth-centric viewpoint, but from a geocentric one. What really matters is that geo(micro)biology is a transdisciplinary science, not just a multidisciplinary one. The answer to “big questions” in this discipline is best solved by first assessing which disciplinary tools are needed, not just by combining disciplinary views that address the question. Despite incredible advances in methodologies in the last four decades, each approach has its limitations. This is critical to remember.

My educational background is based on a combination of organic chemistry and the Delft School of Microbiology – that, in addition to Baas Backing, also included Beijerinck, Kluyver, and van Niel. In addition to having a great mentor, Hans van Gemerden, who combined detailed observations and measurements in the field with meaningful ecophysiological laboratory experiments, I have had the good fortune to meet many scientists who have shaped our discipline as we know it today. The list is quite exhaustive, but I would like to mention a handful of them here briefly, some unsung heroes in geomicrobiology, in chronological order.

SEM-cyanos-minerals
Table-top scanning electron micrograph of a carbonate grain surrounded by and bored into by cyanobacteria.

Visscher6
As night settles over the Atacama desert, the measurements continue

Wolfgang Krumbein was instrumental during my PhD work on sulfur cycling at the University of Groningen. After a long 24 hours of fieldwork, being in a group that was the first to use microelectrodes in the field during diel cycles, a very tedious process at the time, he would sit me down in his cigar-smoke-filled office and question me about everything I had observed and was planning to do as follow-up. Early in my grad student years, he sent me a box with well over a hundred of his reprints. Using geology and microbiology, his strong belief that the laminae in stromatolites are the same as those in microbial mats may be wrong, but it nevertheless challenged our thinking and steered us in the right direction to better understand the role of microbes on early Earth and throughout geologic time. Spending three weeks with Dick Castenholz and Bev Pierson in Yellowstone was a life-changing event. The vast diversity of environments in a relatively small area was an eye-opener. Likewise, several long discussions, both in the field and during elegant home-cooked meals with Malcolm Walter, have contributed much to advancing my work. Lynn Margulis, who, by the way, together with James Lovelock reintroduced the term Gaia in 1974, 43 years after Baas Becking, Ed Leadbetter, Ron Oremland, Jack Farmer, and Dave DesMarais were all instrumental as post-doc and early career mentors. Generous scientists who gave selfless advice and listened. I learned a lot from them and expanded my scientific and interpersonal horizons. It takes a village….

I would like to thank the people who are keeping our field alive: the leaders of the professional societies, notably the Division of Geobiology and Geomicrobiology of Geological Society of America, the reviewers of our proposals and manuscripts, the program directors at funding agencies, the educators, who sparked the interest in students who then come as graduate assistants or post-docs to our labs, and all those students and colleagues with whom I had many fruitful/stimulating discussions and rewarding collaborations. I am excited about the direction in which our field is moving, and hope that we jointly continue to combine the many subdisciplines that make up geo(micro)biology in a meaningful way to unlock the secrets that our field holds in shaping our planet and the many worlds beyond.

Visscher7
Visscher at the Galan volcano in Argentina

Seaweed self defense!

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mattassa-snail
Common periwinkles (Littorina littorea) graze upon the intertidal seaweed Fucus vesiculosus and elicit anti-herbivore defenses (credit: C Matassa)

Did you know that seaweed practices self-defense? A new paper from the Matassa Lab led by recent PhD graduate Sean Ryan on seaweed defense plasticity has been published in Functional Ecology. They investigated how a species of seaweed (Fucus vesiculosus) defends itself from herbivorous snails (Littorina littorea) along its latitudinal range in the coastal northeast USA.

Check out the plain language summary of the article here:

Ryan, S. and Matassa, C.M. (2025) Latitudinal variation in the constitutive and inducible defences of a canopy-forming rocky intertidal seaweed. Function Ecology 39:3718–3731.

Spring 2025 Departmental Achievements

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Awards: 

Professor Senjie Lin

Prof. Lin received the Darbaker Prize from the Botanical Society of America, honoring his research to better understand the biology of two distinct groups of marine phytoplankton (diatoms and dinoflagellates) that play a major role in global nutrient cycling and phytoplankton community dynamics.

 

PhD candidate Hannah Collins

Hannah received the World Aquaculture Society Student Spotlight award recognizing the best abstracts submitted by student to the Aquaculture 2025 meeting.

 

PhD candidate Halle Berger

Halle Berger received the Best Student Poster Award at the 2025 winter science meeting of the Southern New England Chapter of the American Fisheries Society. The poster was about Halle's research on modeling the effects of ocean acidification and warming on Atlantic sea scallop growth to inform adaptive fisheries management.

Grants: 

Professors Cara Manning, Leonel Romero, Samantha Siedlecki

Profs Manning, Romero, and Siedlecki have received a $499,570 grant from the Long Island Sound Study Research Grant Program to investigate the drivers of oxygen depletion (hypoxia), and the duration and severity of low-oxygen conditions in western Long Island Sound using a combination of observational and modeling approaches.

Improved Mechanistic Understanding of Hypoxia Drivers in Western Long Island Sound Enabled with Data from a Wire-Following Profiler and Coupled Biogeochemical-Hydrodynamic Modeling

 

Professor Senjie Lin

Algae are both natural and industrial sources of renewable energy. Collaborating in a Columbia University-led multi-million-dollar project, Prof. Senjie Lin will lead his UConn team and contribute expertise on microalgae to advance the development of algae-based electricity-generating technologies.

ECO-SPARK: Enzymatic Conversion of Organic Carbon into Sustainable Power through Aquatic Reactors and Kinetics, DARPA $1,500,000

Publications: 

Prof. Rob Mason

Samples for measuring the concentrations of different forms of mercury in the Pacific Ocean waters were collected on a research expedition from Alaska to Tahiti and analyzed by our research group and those of our collaborators. Former student Yipeng He and Robert Mason participated in the cruise and were involved in the sample analysis.

Starr, L.D., He, Y., Mason, R.P., Hammerschmidt, C.R., Newell, S.E., Lamborg, C.H. 2025. Mercury distribution and speciation along the U.S. GEOTRACES GP15 Pacific Meridional Transect. JGR Oceans 130: Article # 130e2024JC021672.

He, Y., Inman, H., Kadko, D.C., Stephens, M.P, Hammond, D.E., Landing, W.M., Mason, R.P. 2025. Elevated methylmercury in Arctic rain and aerosol linked to air-sea exchange of dimethylmercury 
https://doi.org/10.1126/sciadv.adr3805.

Samples were collected on a research expedition in the Bering and Chukchi Seas off Alaska in the atmosphere and in the ocean waters to examine the factors effecting the inputs of various mercury (Hg) compounds to the ocean from the atmosphere and the loss of gaseous forms of Hg to the atmosphere, with a focus on the exchange of methylated Hg forms.

Zhou, C., Liu, M., Mason, R.P., Assavapanuvat, P., Zhang, N.H., Bianchi, T.S., Zhang, Q., Li, X. Sun, R., Chen, J., Wang, Raymond, P.A. 2025. Warming-induced retreat of West Antarctic glaciers weakened carbon sequestration ability but increased mercury enrichment. Nature Communications 16: Article # 1831.

The publication examined how the recent changes in climate is affecting the inputs of mercury (Hg) to the ocean waters off of Antarctica and the relative importance of inputs from the continent versus inputs from the atmosphere, and how these inputs differ for Hg compared to carbon. The study used information from ancient sediments to infer what will likely happen in the future in a changing climate.

 

Prof. Samantha Siedlecki

Carlson, A. J., Siedlecki, S. A., Granger, J., Veitch, J., Pitcher, G. C., Fearon, G., et al. (2025). Seasonal source water changes and winds contribute to the development of hypoxia in St Helena Bay within the southern Benguela upwelling system. Journal of Geophysical Research: Oceans, 130, e2024JC021702. https://doi.org/10.1029/2024JC021702

This work discusses oxygen dynamics in St. Helena Bay (SHB), a productive area in the southern Benguela Upwelling System off western South Africa severely impacted by low oxygen events through fish mortality events. Specifically, it highlights the seasonal cycle of oxygen, including periods of hypoxia and anoxia, and the role of winds and source water changes in driving these variations.

 

Professor Hannes Baumann 

Mosca, K.C., Savoy, T., R. Benway, J., Ingram, E.C., Schultz, E.T., and Baumann, H. (2025) Age structure and seasonal movement patterns of Atlantic sturgeon aggregating in eastern Long Island Sound and the Connecticut River. Fishery Bulletin 123:127-142

This study combined age analysis and telemetry to show that Atlantic sturgeon of all sizes frequently migrate into upper, freshwater portion of the Connecticut River

Jones, L.F., Schembri, S., Bouchard, C., and Baumann, H. (2025) Molecular identification of larval sand lance (Ammodytes spp.) caught in the Hudson Bay System 2010-2018. Environmental Biology of Fishes 108:305–316

PhD student Lucas Jones used genetics to find out what sand lance species inhabits the Hudson Bay in the Canadian Arctic.

 

Research Prof. Zofia Baumann

Hansen, G., Shumway, S. E., Mason, R. P., & Baumann, Z. (2025). Mercury distribution with size between the tissues of the northern quahog (= hard clam)(Mercenaria mercenaria). Environmental Pollution, 126287. https://doi.org/10.1016/j.envpol.2025.126287

This study examined the distribution of inorganic mercury (iHg) and methylmercury (MeHg) in the soft tissues of hard clams (quahogs) and found that muscular tissues contained a higher proportion of MeHg, while the viscera and mantle also harbored inorganic Hg.

Graduate student Eva Scrivner

Scrivner, E., Mladenov, N., Biggs, T., Grant, A., Piazza, E., Garcia, S., Lee, C.M., Ade, C., Tufillaro, N., Grötsch, P., Zurita, O., Holt, B., Sousa, D., 2025. Hyperspectral characterization of wastewater in the Tijuana River Estuary using laboratory, field, and EMIT satellite spectroscopy. Science of The Total Environment 981, 179598. https://doi.org/10.1016/j.scitotenv.2025.179598

The research links the chemical composition of effluent wastewater discharge in the Tijuana River Estuary with laboratory, field, and hyperspectral satellite spectroscopy. This work serves to inform real-time water quality monitoring in a heavily polluted coastal urban center.

At DMS phytoplankton are now on IFCB-TV

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The team of DMS researchers Dr. Zofia Baumann, Dr. Kate Randolph and Hazel Levine are happy to share that a major new instrument has begun its long anticipated work. The Imaging Flow Cytobot - or IFCB for short - is for now installed in the Rankin Seawater lab, after being purchased with a UConn-CLAS shared equipment grant nearly two years ago (Dierssen, Baumann et al.).

The instrument has the capacity to monitor and display in real time the breath-taking diversity of microscopic life in the ocean. Our IFCB focuses on the smaller size classes 5 - 150 um, which mostly represent single cell algae and small mixotrophs.

Leveraging additional NSF support, we were able to overcome challenges with operating the IFCB on a routine basis. The IFCB now accesses the intake line of the Rankin Lab (a very small fraction of it) and then photographs any particles and characteristic shapes. The compilation below shows a given size range to illustrate some of the diversity. The IFCB now records these images and displays them on a public-facing online Dashboard, which can be mesmerizing to watch.

 

Plankton-composite
The composition of some of the larger phytoplankton as captured by the IFCB on February 6th 2025.

The implementation of the IFCB in Rankin Lab was led by Kate Randolph and greatly supported by Hazel Levine, Bob Dziomba, Charlie Woods, Todd Fake, and Chris Mills! Thank you.

The next step is to develop an AI-based classification system for automatic species identification. This will still take time, but we are collaborating with other IFCB users, including its inventors, and are optimistic about the progress ahead.

We hope you enjoy the stunning images of phytoplankton on what we like to call

"IFCB TV" !

Kate IFCB
Dr. Randolph assembling the brand new IFCB in February of 2023. Photo credit: Dr. Zofia Baumann.

IFCB course
Some of the DMS researchers (Dr. Zofia Baumann, Bridget Holohan, and Dr. Kate Randolph) attending the IFCB training at McLane Labs in February of 2023. Photo credit: Dr. Paola Batta-Lona

Summary of Summer/Fall 2024 Departmental Achievements

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Awards: 

Professor Samantha Siedlecki 

Prof. Siedlecki was named as a 2024 – 2025 Fullbright Scholar for research in both Italy and South Africa, which has been featured at UConn Today 

 

Professor Hans Dam 

Professor Dam had the honor of giving the Maxilliped Lecture on “Copepods as Model Systems for the Study of the Response of the Biota to Global Change” during the 15th International Conference on Copepoda held in Hiroshima, Japan. 

 

Research Faculty Sandra Shumway 

Dr. Shumway was awarded the Distinguished Lifetime Achievement Award by the US Aquaculture Society and is the first female to receive the award. She was also appointed Fellow of the Marine Biological Association, FMBA. MBA Fellows are senior practitioners in marine biology who have contributed to the discipline at the highest level. The title of Fellow of the Marine Biological Association, FMBA, was first awarded in 2014, following granting of a Royal Charter to the Marine Biological Association. There are currently 50 MBA Fellows.   

 

Professor Senjie Lin 

Professor Lin has been awarded the 2024 UConn-AAUP Excellence Award in as well as the 2024 Alumni Faculty Excellence Award in Research and Creativity. 

 

Research Scientist Susan A. Smith (Mystic Aquarium):

Sue won first place in Animal Welfare Research for her presentation at the annual Association of Zoos and Aquariums conference in Calgary. Her work involved the use of non-invasive fecal samples to elucidate the microbiome and hormone profile of the African Penguin, along with the development of a genetic sexing test, which will soon be used to aid in the monitoring of endangered wild populations in South Africa.

 

PhD student Paxton Tomko 

Paxton was awarded a National Science Foundation Graduate Research Fellowship (NSF-GRFP) for research with Professor Pieter Visscher, which was featured at UConn Today 

 

PhD Candidate Halle Berger  

Halle was awarded the 2024 National Marine Fisheries-Sea Grant Fellowship by NOAA making her the first UConn student to ever receive the award. 

Grants: 

Professor Senjie Lin 

Prof Lin will collaborate with the University of Columbia and Yale University on a DARPA-funded multi-year (2024-2027) project that aims to utilize algal genomics to develop biosensors for various environmental stimuli  

MEBES: Modular engineered biosensors for environmental sensing 

 

Research Professor Paola Batta-Lona, Professor Hannes Baumann 

Led by UConn EEB professor Eric Schultz, co-PIs Batta-Lona and Baumann will collect and analyze novel data on short- and long-term changes in the trophic ecology of species of greatest conservation need.  

Bottoming Out? Testing Hypotheses on Why Long Island Sound Flatfishes Are Disappearing (Long Island Sound Study, $316,667).  

 

Professor Heidi Dierssen and Research Professor Paola Batta-Lona 

In collaboration with colleagues from URI, Dierssen and Batta-Lona will use eDNA to characterize biological communities in shallow seafloor, deep-sea seafloor, and offshore midwater acoustic soundscapes. Additionally remote sensing data and Distributed Sensing enabled Cabled Observatories (DiSCO’s) will be used for broader scale understanding of major ocean processes in these areas. 

Coastal and Offshore Biogeochemical Oceanographic Observatories Enabled with Distributed Sensing (NIUVT, $2,126,000) 

 

Research Scientist Zhuomin Chen 

Projecting future changes in the Gulf Stream warm-core rings and their impacts on the Northeast U.S. Large Marine Ecosystem in a changing climate using regional MOM6 simulations (NOAA $570,000) 

 

Research Scientist Tracy Romano (Mystic Aquarium) and Associate Professor in Residence Michael Finiguerra:

Drs Romano and Finiguerra were awarded an NSF grant to continue leading the Research Experience for Undergraduates (REU) program through an ongoing collaboration with Mystic Aquarium and the University of Connecticut Avery Point campus.  

Romano, T.A., Finiguerra, M. REU Site Mystic Aquarium: Collaborative Research: Plankton to Whales: Consequences of Global Change within Marine Ecosystems. National Science Foundation. $464,997.

Research Scientists Ebru Unal and Tracy Romano (Mystic Aquarium):
Drs Unal and Romano were awarded a North Pacific Research Board grant to further study the transcriptome of the beluga whale for the monitoring of wild populations, in an effort to isolate the health-related expression discrepancies between healthy and endangered populations.

Romano, T.A., Unal, E. The Beluga Skin Transcriptome as a Novel Tool for Monitoring Alaska’s Beluga Stocks. North Pacific Research Board. $244,601

Dr. Romano also received funding by the North Pacific Research Board to design and run a cultural exchange that allowed young Native Alaskans to visit Connecticut, where they met with local CT Native American youth, and together took part in educational and cultural workshops.

Romano, T.A., A Science Based Educational and Cultural Exchange Workshop at Mystic Aquarium for Alaska Native and Native American Youth. $20,000

Publications: 

Prof. Hans Dam 

Prof. Dam co-authored a study about the negative effects of marine heatwaves on copepods. The authors found that acclimation (“getting used to”) and parental effects (“the fate of the children depends on the experience of the parents”) mitigate the negative effects of heat waves on the fitness of two important copepod species.  

Sasaki, M.C, M. Finiguerra, H.G. Dam. 2024. Seasonally variable thermal performance curves prevent adverse effects of heatwaves. Journal of  Animal Ecology 2024;00:1–11. DOI: 10.1111/1365-2656.14221 

 

Graduate student Samantha Rush and Professor Penny Vlahos 

This study reports on how sea ice in the Arctic Ocean incorporates and stores boron as it forms, reducing the amount of boron from under ice waters. 

Rush, S., Vlahos, P., Lee, C.-H., Lee, K., Barrett, L. J. Boron to salinity ratios in the Fram Strait entering the Central Arctic: The role of sea ice formation and future predictions. Marine Chemistry. 267:104463. https://doi.org/10.1016/j.marchem.2024.104463 

 

DMS alumnus Max Zavell and Professor Hannes Baumann 

Zavell and Baumann show that the embryos and larvae of an abundant grouper species in Long Island Sound are unaffected by even very high CO2 levels in the water. 

Zavell, M.D. and Baumann, H. (2024) Resiliency of Black Sea Bass, Centropristis striata, early life stages to future high CO2 conditions. Environmental Biology of Fishes 107:677–691 

 

Research Prof. Paola Batta-Lona and Prof. Ann Bucklin 

This morphological and molecular analysis revealed the diet differences of 7 mesopelagic fish species, showing the importance of gelatinous prey.  

Bucklin, A., Batta-Lona, P.G., Questel, J., McMonagle, H., Wojcicki, M., Llopiz, J.K., Glancy, S., Caiger, P.E., Francolini, R., Govindarajan, A., Thorrold, S.R., Jech, M., Wiebe, P.H. (2024). Metabarcoding and morphological analysis of diets of mesopelagic fishes in the NW Atlantic Slope water. Front Mar Sci. 11:1411996. https://doi.org/10.3389/fmars.2024.1411996 

Batta-Lona also published a study on the diet diversity of three salp species, which showed a wide variety of prey, broadening our understanding of trophic pathways in the mesopelagic food web. 

Batta-Lona, P.G., Gardner, K., Questel, J.M., Thorrold, S.R., Llopiz, J.L., Wiebe, P.H., Bucklin, A. (2024). Salps in the NW Atlantic Slope Water: metabarcoding and compound-specific stable isotope analysis of diet diversity and trophic interactions. Mar Biol 171, 233. https://doi.org/10.1007/s00227-024-04535-x 

Batta-Lona further published a study that identified parrot fish larvae via morphology and DNA sequences.  

Morales‐Pulido, J. M., Galindo‐Sánchez, C. E., Jiménez‐Rosenberg, S. P. A., Batta‐Lona, P. G., Herzka, S. Z., Arteaga, M. C. (2024). A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny. Journal of Fish Biology 1-10 https://doi.org/10.1111/jfb.15921 

 Batta-Lona was also involved in the MetaZooGene Atlas and Database (MZGdb) provides DNA sequences for multiple genes, with unique capacity for searches by ocean region.  

O'Brien, T., Blanco-Bercial, L., Questel, J.M., Batta-Lona, P.G., Bucklin, A. (2024). MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems. Methods in molecular biology 2744: 475-489. https://doi.org/10.1007/978-1-0716-3581-0_28 

 

Prof. Peter Auster 

Prof. Auster used diver surveys of reef fish off Florida to map predation risk to coral eating fishes. 

Auster, P.J. and M.E. Cullerton. 2024. Can variation in fish predator density and the Landscape of Fear facilitate coral restoration success?  Reef Encounter 39:48-50. 

 In another study, Prof. Auster and colleagues argue that the term "destructive fishing" is used in international agreements and guidance without agreement on what this term means.   

McCarthy, A.H., D. Steadman, H. Richardson, J. Murphy, S. Benbow, J.I. Brian, H. Brooks, G. Costa-Domingo, C. Hazin, C. McOwen, J. Walker, D. Willer, M. Abdi, P.J. Auster, ..., N. Mukherjee. 2024. Destructive fishing: An expert‐driven definition and exploration of this quasi‐concept. Conservation Letters, e13015. https://doi.org/10.1111/conl.13015

 

Post-doctoral researcher Danielle Freeman 

Dr. Freeman published an article together with colleagues at WHOI that forecasts the effects of sunlight-driven chemistry during oil spills.  

Freeman, D. H.; Nelson, R. K.; Pate, K.; Reddy, C. M.; Ward, C. P. (2024) Forecasting Photo-Dissolution for Future Oil Spills at Sea: Effects of Oil Properties and Composition. Environ Sci Technol. 58: 15236-15245 https://doi.org/10.1021/acs.est.4c05169 

 

Research Scientist Ebru Unal (Mystic Aquarium):
Dr. Unal showed that skin samples can reveal relevant differences between endangered and stable beluga whale populations.

Unal, E., V. Singh, R. Suydam, C.E. Goertz, and T.A. Romano. (2024). Comparative skin transcriptome analysis as a potential tool to investigate intra- and inter-population differences in belugas. Frontiers in Marine Science: Marine Conservation and Sustainability. 11:1282210

Research Scientist Tracy A. Romano (Mystic Aquarium):

Aerial photogrammetry and lipid analyses can be used to describe the body condition of wild endangered St. Lawrence Estuary beluga whales.

Sherill, M., A. Bernier-Graveline, J. Ewald, Z. Pang, M. Moisan, M. Marzeliere, M. Muzzy, T.A. Romano, R. Michaud, and J. Verreault. (2024). Scaled mass index derived from aerial photogrammetry associated with predicted metabolic pathway disruptions in free ranging St. Lawrence Estuary belugas Frontiers in Marine Science. 11:1360374.

Danielle A. Lavoie (Mystic Aquarium):

This study provided insight into the detection of the invasive nematode parasite A. crassus using identification monitorting methods that allow for the survival of the host A. rostrata (the American eel).

Lavoie, D.L., Oliveira, K. (2024). Non-Lethal Detection of the Invasive American Eel Parasite Anguillicoloides crassus. Diseases of Aquatic Organisms.

A delayed spring bloom along the West Antarctica Peninsula 

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By Samantha Rush.

If you think about the holiday season, it is easy to grasp the trend that Christmas festivities that used to begin traditionally after Thanksgiving in the US appear much earlier. In recent years, the timeline has shifted and many Christmas and holiday themed advertisements, decorations, and events appear even sooner than before. Of course, this notable shift has traceable causes and is known (consciously or subconsciously) to be driven by retail strategies, commercialization, consumer behavior, social media influences, and cultural shifts.  

The changes in the timelines of global phenomena also extend to marine environments. In fact, the polar regions are some of the most rapidly changing locations on the planet due to human induced climate change. In the West Antarctic Peninsula (Figure 1), a combination of warming and sea ice loss have altered the timing of recurring seasonal events, the study of which is known as phenology. While most predictions have suggested that these changes in the environment would cause an earlier spring bloom, or ocean biology to kick start, lead author and postdoctoral researcher Jessie Turner found exactly the opposite in a recent study of the ice-associated waters west of the Antarctic Peninsula.  

turner fig1
Figure 1: Study area

Using satellite ocean color data from 1997 to 2022, researchers from the University of Connecticut and five other collaborating institutions and laboratories discovered that spring blooms were shifting later in ice zones and on continental shelf regions west of the Antarctic Peninsula (Figure 2). By using satellite derived chlorophyll-a concentrations as a proxy for phytoplankton biomass, researchers were able to track the concentration and timing of the elevated concentration corresponding to the date when heightened biological activity begins.  

turner-fig2

After investigating a handful of environmental variables to better ascertain the potential mechanisms for the seasonal shift, the authors found that wind speed was the most likely mechanism for the observed change in the spring bloom start date. Other variables such as light and temperature did not explain the trends. However, there was a long-term increase in wind mixing, which likely decreases the stability of the water column in the early spring season and suppresses phytoplankton accumulation until later in the season (Figure 3).  

While phytoplankton are small single cell plants, the timing of the phytoplankton spring bloom affects the entire marine food web. Higher trophic level organisms may experience feeding, migration, and breeding impacts. In fact, phenology changes at the base of the Antarctic food web are likely to disrupt the life history of key species such as Adélie penguins. Other, widespread impacts also include potential changes to the timing and magnitude of carbon dioxide absorption by the ocean in these locations.

Jessie Turner
Dr. Jessie Turner

turner fig3
Figure 3

Next, the researchers plan to investigate specific phytoplankton species and employ the use of new generation hyperspectral satellite missions to further study long-term trends in polar regions. Rapidly developing technology combined with field measurements will allow for better examinations of the changes rapidly occurring in this polar region in studies to come. 

Jessica S. Turner, J.S., Dierssen, H., Kim, H.H., Stammerjohn, S., Munro, D.R., and Kavanaugh, M. (2024). Changing phytoplankton phenology in the marginal ice zone west of the Antarctic peninsula. Marine Ecology Progress Series 734: 1–21

Heat tolerance changes across environments and populations

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March 27th 2023 - By Ewaldo Leitao.

Climate change is a threat to species persistence. Increasing temperatures affect species differently depending on their habitats, such as land or the ocean. However, species often consist of different populations (groups of individuals that reproduce together) that experience different temperature conditions. And if populations live in these areas long enough, they can genetically adapt to their local conditions. What does that mean? If the same species has a population in an area where it is constantly warm, like the tropics, and another population that lives in colder regions, like Connecticut, then we’d expect the tropical population to handle high temperatures better compared to the population living in colder regions. This kind of diversity within species affects how we think about the vulnerability of the species as a whole. To add another layer, if variation differs for terrestrial vs. oceanic species, we might be missing important information about where climate change will have the strongest effects on the planet.

sasaki-sample
Matt Sasaki looking at a water sample with a handheld microscope at Lake Okeechobee, FL.

That is what Dr. Matt Sasaki and collaborators investigated in a paper recently published in Nature Climate Change. Their main goal was to assess the heat tolerance (the highest survivable temperature) of populations in many different species, from different realms – terrestrial, freshwater, marine and intertidal. They assessed the vulnerability of species by surveying in the literature from the whole world that measured individual heat tolerance. They compiled and then conducted a meta-analysis of these published data, thereby assessing how the heat tolerance is related to the thermal environment these populations live in.

“This paper came out of the ‘Evolution in Changing Seas’ Research Coordination Network (RCN). Back in 2019 they brought some of us together at Shoal’s Marine Lab for a synthesis workshop and essentially told us to think about questions at the intersection of evolutionary biology and marine science”, said Matthew Sasaki, about the seed of the idea.

"I really enjoyed the collaborative aspect of this project, even though I’ve met most of the co-authors in person only once (or not at all!)"

By measuring how heat tolerance changes between populations of the same species, they found that marine and intertidal species show a decrease of heat tolerance between populations as the environment gets colder, but that was not observed in terrestrial and freshwater populations. This was an interesting result, because since the ocean is largely connected, they expected that there would be a smaller differentiation in the ocean compared to land, where geographical barriers can create physical separations, allowing difference in heat tolerance to build up among populations within a species.

Behavior may play a role in the observed patterns. In the terrestrial realm, many organisms can moderate body temperature by seeking shade and forested areas to find refuges from the heat. Even plants can exploit micro-climates. This decreases the amount of evolutionary pressure on terrestrial organisms, when compared to other realms.

sasaki-fig1
Data surveyed to analyze global patterns of heat tolerance. The histogram on the left side shows the higher proportion of studies in the northern hemisphere (Modified after Sasaki et al. 2022).

This study highlights the importance of accounting for evolutionary processes in the context of climate change and species persistence and extinction risk. Larger differentiation of heat tolerance within species may suggest a potential for evolutionary rescue. That is, populations with genes that allow them to be “warm adapted” may rescue populations that are more susceptible to increasing warming.

We asked what was the coolest part about the execution and findings of the project. “This wasn’t a project someone could do alone, and it was really cool to be part of such a big collaborative effort. The findings themselves were also really exciting for us. We expected there to be pretty clear differences between marine and terrestrial taxa, but we were surprised to see that local adaptation seems to be stronger in marine species and not terrestrial species. This goes against some of the traditional paradigms (that marine species’ are more often homogenized by larval dispersal, for example), and hints at a cool role of behavioral thermoregulation in shaping patterns in evolutionary adaptation.”

“This was definitely a pandemic pet project. I won’t say the pandemic helped us make progress though. This ended up being something we worked on a little bit each week for a couple years. Maybe that helped us put together a more robust product (slow and steady wins the race?). I really enjoyed the collaborative aspect of this project, even though I’ve met most of the co-authors in person only once (or not at all!). Having to do everything virtually definitely changed the nature of the collaboration (more written exchanges, less whiteboard brainstorming) but I think we made it work. We’ve just started working together on a couple new projects that build from this initial work, so it must not have been too terrible.”, said Matt.

DMS Kayla Mladinich shows that bivalves can reject microplastics

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8 November 2022. DMS is happy to share the latest publication by PhD student Kayla Mladinich, showing the surprising but good news that blue mussels and oysters appear not to ingest all microplastic particles floating in the water.

By Kayla Mladinich.

Oysters and mussels are filter feeders that draw particles in from the surrounding water to be eaten. These animals can select which particles are eaten or rejected depending on factors such as particle size and surface properties. This study was performed to determine what kinds of microplastics will be consumed or rejected by oysters and mussels. Both species rejected larger microplastics more than smaller microplastics and did not differentiate between different types of plastic polymers. The results suggest that oysters and mussels will not ingest all microplastics that they are exposed to in the natural environment!

Kayla_lab
Kayla changing water and replenishing food for the animals.

Kayla_oyster
An oyster being exposed to microplastics in the laboratory. Microplastics are gently pipetted over the inhalant aperture (where oysters draw particles in) which allows the oysters to choose between drawing the particles in or not (Photo: Kayla Mladinich).

KaylaGraphicAbstract-R4
Mladinich et al. ES&T (2022) Graphical abstract

The Arctic is not so Boron!

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Professor Penny Vlahos investigates what happens with the ocean chemistry at the marginal ice zones in her recent publication

By Ewaldo Leitao.

The Arctic Ocean is undergoing rapid changes due to climate change. Increasing temperatures result in decreasing sea-ice extent, constant decreasing and thinning of permanent sea-ice caps. Some projections even show a completely ice-free Summer by 2050!

Another consequence of climate change is ocean acidification due to increasing atmospheric CO2. That leads to the decrease in water pH and changes in carbon chemistry dynamics. The Arctic may be a small ocean (3% of total oceans area) but it has an important contribution to carbon uptake (10%). Therefore, it is necessary to understand the impact of these changes across the oceans, including the Arctic, in order to be prepared for it.

Some chemical elements, such as boron, contribute to the ocean’s capacity to resist changes in pH, that is ocean’s alkalinity. Boron, in combination with salinity, has been used as a universal rule in the open ocean (boron to salinity ratio) in order to understand the contribution of boron to alkalinity, and therefore ocean carbon chemistry. But how does that change in the less saline areas, such as the marginal ice zones of the Arctic?

In the recent paper published in Nature Communications, Prof. Penny Vlahos and graduate student Lauren Barrett observed that, when measured in low salinity areas (marginal ice zones), the boron to salinity ratio deviates from the expected in open oceans. In a cruise that took place in May of 2021 (you can read more about the cruise here), researchers were surprised to find significant deviations in the boron to salinity ratios in ice and brine samples. Lower water temperature and lower salinity alters the exchange between boric acid and borate, which is used to determine the contribution of boron to sea water alkalinity (capacity of water to resist changes in pH and acidification), driving this deviation of the boron to salinity ratio compared to open ocean waters.

group-ice
Prof. Penny Vlahos (right) with graduate students Lauren Barrett (left) and Emma Shipley (middle) on board the RV Sikuliaq

Boron-concentration
Stations sampled on the RV Sikuliaq between May 20th to June 14th, 2021.

The unique microenvironment of the marginal ice zones creates a very dynamic system. As seawater freezes, salts are rejected, but there is still a liquid region between ice crystals, called brine channels. These channels allow boron to undergo inorganic changes that may result in the variations observed in some of the samples, increasing the variability of boron to salinity ratio observed in these Arctic areas.

Prior to boarding the research vessel, researchers had to quarantine for two weeks. But this was a valuable time to Lauren Barrett. “Over quarantine I spent a lot of time reading about the various uncertainties that other authors encountered in accurately and precisely constraining the carbonate system in this highly heterogeneous environment. The boron to salinity ratios that we present here warn against applying universal ratios constrained in the open ocean to marginal ice zones and ice environments.” says Lauren.

Penny Vlahos Arctic
Lauren making a snowman at one of the stations that was ice covered, with the RV Sikuliaq on the back.

Lauren also shared a little bit about her experience: “I am very grateful for the opportunity to work with our international coauthors. The collaborative and interdisciplinary nature of marine science is one of my favorite aspects of working in this field. This research cruise was a great experience both personally and professionally, and I continue to be grateful to work in a field where cruising and getting to see polar bears is all in a day's work.”

The Arctic is an important sink of carbon and yet highly susceptible to climate change. Therefore, understanding detailed information of this system, instead of applying universal ratios, is necessary in order to better understand the carbon chemistry of the Arctic and be prepared for the consequences of climate change.

Vlahos, P., Lee, K., Lee, CH., Barrett, L, and Juranek, L. (2022) Non-conservative nature of boron in Arctic marginal ice zones. Nature Communications Earth & Environment 3, 214