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.
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.”
Energy companies Ørsted and Eversource are partnering with the University of Connecticut’s Department of Marine Sciences to research the impact of offshore wind farms on marine ecosystems. Link to UConn Today article.
Caption: Graphical abstract depicting that a multi-study analysis of raw 16S gut microbiome data collected from blue mussels revealed that depuration strongly influences the recovered microbial community.
Everybody poops, even mussels! And it turns out that whether a mussels has pooped matters a lot when you sample its gut microbiome. New research published in Environmental Microbiology by the Ward lab and lead author Tyler Griffin reveals that fecal egestion (or depuration) status of mussels is a critically important factor for determining the microbial community composition in the mussel gut. By performing a multistudy re-analysis of microbiome data from several projects conducted by the Ward lab over seven years, they were able to broaden the understanding of gut microbial dynamics of these foundational invertebrates in Long Island Sound. Link to the article.
A group of researchers at DMS joined together under Sandra Shumway and Evan Ward, critically reviewed 750+ publications on microplastics and molluscs in the field and laboratory. This incredible effort has resulted in a thoughtful review of the cluttered scientific literature. Many studies on suspension feeding molluscs and microplastics have perpetuated inaccurate findings based on inappropriate methodologies, poor animal husbandry, and misinterpreted results. All of these false conclusions have caused a damaging narrative for the shellfish industry, raising concerns about the safety of eating shellfish. While microplastics are ingested by shellfish, microplastics in molluscs are extremely low globally as these animals are capable of selective capture, ingestion, and egestion of particles. In reality, the number of microplastics inhaled and consumed by humans in everyday life far outweighs the number of microplastics found in shellfish. Recommendations were provided for future studies in both the field and laboratory that will prevent researchers from falling into the pitfalls discussed in this review. This review is presented from the perspective of experts on shellfish physiology and represents the opinions of, and assessments made by, the authors. The authors hope this review can be used as a starting point for those interested in furthering this field of research with thoughtful experimental questions. Link to the article.
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.
DMS Ph.D. Candidates Kayla Mladinich-Poole and Lauren Barrett have been selected as finalists in the 2024 cohort of the NOAA John A. Knauss Marine Policy Fellowship. Kayla will join the executive branch and Lauren will join the legislative branch. https://seagrant.noaa.gov/2024-knauss-finalists-announcement/
Our PhD student Anagha Payyambally was featured in UConn Today to celebrate her achievement of receiving the Quad Fellowship. Anagha is one of only 100 recipients out of over 3000 applicants to receive this fellowship to her graduate studies. This new fellowship program supports exceptional students who are citizens of the United States, Australia, India, and Japan to support their graduate studies in the United States and build collaboration among scientists and technologists.
Read the story here with quotes from Anagha and her advisor Dr. Manning. Congratulations, Anagha!
On 24 August, 2023, 10 community science organizations, the Connecticut Department of Energy and Environmental Protection (CT-DEEP) and the University of Connecticut collaborated to simultaneously sample total alkalinity in the embayments and rivers bordering Long Island Sound (LIS). Led by DMS PhD Candidate Lauren Barrett, the event was a regional repeat of the 2019 effort led across New England by the Northeast Coastal Acidification Network (NECAN, http://necan.org/ShellDay).
The participating groups sampled for total alkalinity (TA) and hydrographic variables such as salinity and temperature during low, mid-, and high tides, meaning the spatial variation in alkalinity across the Sound. Seawater alkalinity requires high precision, expensive instrumentation and a skilled analyst, and thus typical observations of TA in LIS conducted by a single or a few researchers require that spatially separate samples also have a temporal difference. However, TA varies across diel and tidal cycles, so the spatial and temporal difference is important to parse. The collaborative effort of Shell Day allowed for a spatial identification of TA trends in LIS without the confounding temporal variation.
Shell Day 2023 was a successful event. Despite some mild rain in the afternoon, community scientists weathered the storm and still provided high-quality samples, which are currently undergoing TA analysis at UConn. The results of this work will be interpreted in the context of open LIS data (available through the Vlahos lab at UConn) and the data collected during Shell Day 2019. This work will be presented to the LIS Science Technical and Advisory Committee (STAC) this fall as well as to the participating organizations at a meeting which is to be determined.
Ann Bucklin, Professor Emeritus of Marine Sciences, has been appointed U.S. Academic Delegate to the International Council for the Exploration of the Sea (ICES https://www.ices.dk). This appointment, made by the Department of State on August 17, 2023, authorizes Prof. Bucklin to serve as one of the two U.S. representatives on the ICES Council, which is the decision and policy-making body in ICES. The U.S. Academic Delegate is focused on encouraging and coordinating ICES-related research and activities in the academic community.
What is ICES and its mission?
ICES is a leading multidisciplinary scientific forum for exchanging information and ideas on all aspects of marine sciences, including environmental, scientific, fisheries, wildlife, and conservation affairs, pertaining to the North Atlantic Ocean, including the Baltic Sea and North Sea. Principal functions of ICES, since it was established in 1902 and continuing to the present time, are to: 1) promote, encourage, develop, and coordinate marine research; 2) publish and otherwise disseminate results of research; and 3) provide non-biased, non-political scientific advice. The ICES mission and goals are guided by a Strategic Plan, which identifies and addresses critical themes in science, collaboration, advice, data, communication, and service support. See: https://www.ices.dk/about-ICES/how-we-work/Pages/Our-strategy.aspx
How is ICES organized?
The principal decision- and policy-making body of ICES is the Council, which consists of a president and two delegates from each of 20 member nations across Europe and North America. One of the U.S. delegates is a federal employee and the other represents the academic community. The mission of ICES is accomplished by various committees and working groups. The Advisory Committee (ACOM) provides advice on fisheries and marine ecosystem issues. The Science Committee (SCICOM) oversees all aspects of the scientific work. Steering Groups coordinate more than 100 expert groups covering most aspects of the marine ecosystem that work under them. The scientific work of ICES is done by a community of more than 1,600 marine scientists from research institutes and universities in member and affiliate nations collaborating in expert working and study groups.
What’s the focus of your research and its relevance to your appointment as U.S. Academic Delegate?
My research focus is molecular analysis of biogeography and biodiversity of marine zooplankton, including population genetics of important species (especially copepods and euphausiids), local-to-global patterns of species diversity, and analysis of pelagic food webs based on DNA barcoding and metabarcoding. An important focus is time-series analysis of marine zooplankton species biodiversity, with applications for ecosystem monitoring and fisheries management on the NW Atlantic continental shelf. I have been a member of the ICES Working Group of Zooplankton Ecology (WGZE) and Working Group on Integrative Morphological and Molecular Taxonomy (WGIMT) since 2007; I served as Chair of WGIMT during 2014-2017. I am a grateful recipient of an ICES Service Award (2018) and an ICES Outstanding Achievement Award (2019). See: https://marinesciences.uconn.edu/person/ann-bucklin/ and https://en.wikipedia.org/wiki/Ann_Bucklin
What are your thoughts about being appointed the U.S. Academic Delegate?
I have participated in ICES activities for many years. The ICES Annual Science Conference (ASC) is a valuable forum for the exchange of research results and exploration of important applications for ecosystem assessment and fisheries management. I am honored to have been appointed as the U.S. Academic Delegate and look forward to contributing to the ICES organization. A primary goal is to encourage broader participation from the U.S. academic community, including active researchers, Early Career Scientists, and students.
