Research

“Just keep swimming: challenges in PhD research”

The ole adage holds true for DMS graduate student Emma Siegfried’s first experiments on a new species of sand lance

 

By Samantha Rush and Hannes Baumann

In 1984, the late Alphonse Smigielski and colleagues published a research paper that showed how American sand lance (Ammodytes americanus) could be successfully spawned and reared in the laboratory. Now, DMS PhD student Emma Siegfried is working to continue experimental research on this species, finding that revisiting the 40 year old study is not without challenges.

Sand lances are so called forage fish, meaning that their role in the ecosystem is to eat tiny planktonic organisms while being important food themselves for higher trophic animals such as other fish, seabirds, and marine mammals. Despite their importance, there is insufficient information about how this species will cope to climate change, particularly during the most sensitive larval and embryo stages. To fill this knowledge gap, Emma’s work focuses on exploring how increasing water temperatures and carbon dioxide (CO2) levels affect sand lance embryos and larvae.

Previous research conducted in Prof. Hannes Baumann’s Evolutionary Fish Ecology lab discovered that embryos of the closely related Northern sand lance (Ammodytes dubius) are extremely sensitive to elevated CO2 levels, as they are projected to occur in future oceans. However, whether American sand lance are equally CO2 sensitive is not known.

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On October 2nd 2024, Emma Siegfried looks at the beach seine stretched across the sand at low tide in Wells Harbor

American sand lance collected in Wells, ME, are being transported in a cooler to the Rankin lab at UConn Avery Point

Emma’s thesis research began in 2024 by first trying to find a reliable and easy to access location, where the species could be found and collected. In the harbor of the Wells National Estuarine Research Reserve in Wells, Maine, she found what she needed, because her fish occurred in high numbers there and could be sampled at low tide easily via beach seine. Now Emma’s goal was to catch the fish as close as possible prior to their spawning season, which in the case of sand lance starts with the beginning of winter.

In late August and early October 2024, Emma and her lab mates successfully collected sand lance and transported them live to the Rankin Seawater at Avery Point. There, however, sand lance proved challenging to care for, as they prefer spending days to weeks burrowed in sand (hence their name), making it difficult to monitor their health and development. Subsequent sampling efforts in November and early December brought a new set back, because the previously accessible population in Wells Harbor had evidently moved into slightly deeper waters and thereby out of reach for the beach seine. Unfazed, Emma proceeded to rear the fish she already had in the lab, hoping that they would ripen and eventually produce embryos for a CO2-sensitivity experiment.

At first, this looked like another failure. Sand lance use the declining temperature as a cue to ripen, but the waters of eastern Long Island Sound that flow through the Rankin lab remained unseasonably warm well into December. Eventually, however, on 23 December 2024, water temperatures crossed the critical 7°C threshold, and 3 days later, Emma and her lab mates indeed succeeded in strip-spawning a few ripened up females! The fertilized embryos were then placed in the Automatic Larval Fish Rearing System (ALFiRiS) that allows computer-controlled exposure of organisms to different temperature and CO2 conditions.

On 26 December 2024, Hannes Baumann, Emma Siegfried, and Lucas Jones lift a bowl of sand out of the big circle tank to look for buried sand lance.

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25 days old embryos of American sand lance developing slowly at 8 degrees celsius

Unfortunately, more experimental setbacks followed. Less than 1% of the embryos actually developed to hatch, the CO2-induced acidification did not produce the desired target pH levels, and a system malfunction remained undetected long enough to raise water temperatures to unnatural levels. Emma remains positive, however, and looks at her trials and tribulations as well as the preliminary data as a valuable exercise in gathering experience with this new, non-model species.

“Even though it didn’t go the way we expected, [we] still learned a lot.” she says.

She added that science is by definition challenging, but she is eager to apply what she has learned and move forward. More generally, her thesis research aims to answer the question whether CO2-sensitivity is a shared trait among sand lance species. To that end, she is applying for a grant to collaborate with researchers in Bergen, Norway who have experience with another, closely related sand lance species (Lesser sand eel, Ammodytes marinus). She hopes to secure funding to travel and conduct research there from December 2025 through March 2026.

DMS sophomore to study if tiny algae grow calcium carbonate crystals

A supply grant from UConn's Office of Undergraduate Research (OUR) will test whether cyanobacteria could assist with removing carbon dioxide

Evelyn Lewis glances at the well plates full of colorful slime in Prof. Visscher’s lab and smiles. The life thriving in there is invisible to the naked eye, but she knows how to keep the microscopic critters happy. For almost a year now, she has helped taking care of them, and this has helped others in the lab with their research projects.

But now, Evelyn is starting a project of her own. Her soft voice betrays the nascent excitement, as she examines a well plate full of what looks like crusty, white dust.

“These are calcium carbonate crystals, and they look so beautiful under the microscope”, she says.

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On February 12, Evelyn Lewis examines test plates of CaCO3 precipitates in the lab

Thanks to a new supply grant from UConn’s Office for Undergraduate research, she will now have the opportunity to look at many more of these crystals. Evelyn’s research will focus on some of the smallest photosynthetic organisms in world, cyanobacteria. When they bloom they often coat themselves in slime that they can chemically manipulate. The conditions in this extracellular slime might then become favorable to bind carbon dioxide (CO2) in form of calcium carbonate (CaCO3), ultimately removing it from the atmosphere. In other words, cyanobacteria may be tiny but mighty as a natural tool for combating the increase of heat-trapping CO2 in the atmosphere.

“These natural options of using microbial slime for CO2 removal remain surprisingly underexplored”, explains Visscher. “The slime binds calcium and when it sinks to the bottom, it supports CaCO3 formation in sediments for thousands of years. This recently discovered mechanism provides novel insights into the global carbon cycle.”

So over the course of the next months, Evelyn will culture cyanobacteria again – but this time for her project. In small well plates, she will measure their CaCO3 production for about two weeks in relation to differing amounts of calcium. Yet the arguably coolest part will come after that, when the collected crystals will be examined using scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS).

Ultimately, the gathered data will allow testing the overarching hypothesis that the presence of cyanobacteria increases CaCO3 precipitation.

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SEM photograph of rhomboid CaCO3 crystals formed in the presence of a large amount of calcium (lots of slime)

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Needle-shaped carbonate crystals form when a smaller amount of calcium, or less slime, is present (note the difference in scale).

At DMS phytoplankton are now on IFCB-TV

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.

 

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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" !

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

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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