Scientists have developed a revolutionary imaging technique that uncovers the intricate internal architecture of plankton, the ocean's microscopic powerhouses. Using ultrastructure expansion microscopy, researchers visualized over 200 marine species for the first time, mapping evolutionary patterns in their cellular skeletons. This work, stemming from a pandemic-era collaboration, launches a global atlas of plankton diversity.
Plankton, which produce a large share of the planet's oxygen and form the base of the ocean food chain, include tens of thousands of diverse species, many yet to be discovered. Protists, tiny single-celled organisms with significant evolutionary roles, were previously studied mainly through genetic data due to imaging limitations on their complex internal structures.
The breakthrough began during the COVID-19 pandemic when EMBL Group Leader Gautam Dey received a Zoom call from collaborator Omaya Dudin, then at EPFL. Dudin had adapted expansion microscopy to penetrate the tough cell walls of Ichthyosporea, a marine protist related to animals and fungi. Originally developed at MIT, the technique was refined into ultrastructure expansion microscopy (U-ExM) by Paul Guichard and Virginie Hamel at the University of Geneva, making cell walls permeable for clear observation.
This success spurred a three-year collaboration among Dey, Dudin, Guichard, and Hamel. Tied to the EMBL-led Traversing European Coastlines (TREC) expedition, their research, published in Cell on November 1, 2025 (DOI: 10.1016/j.cell.2025.09.027), examined over 200 plankton species, focusing on eukaryotes.
Sampling occurred at Roscoff, France's Station Biologique de Roscoff, where the team accessed more than 200 species, and in Bilbao, Spain. "We spent three days and nights just fixing those samples. This was a treasure trove we could not let go of," said co-first author Felix Mikus, now a postdoc in Dudin's University of Geneva lab.
Expansion microscopy embeds samples in a gel that expands up to 16 times while preserving structures, bypassing light microscopy's resolution limits. "When combined with regular light microscopy methods, expansion microscopy allows scientists to bypass the standard wavelength barriers which limit how small a structure can be resolved using light microscopy," said Guichard and Hamel.
The study mapped the cytoskeleton, including microtubules and centrins, across eukaryotic groups. "We were able to map features of microtubule and centrin organization across many different eukaryotic groups," explained co-first author Hiral Shah, an EIPOD Postdoctoral Fellow at EMBL. This enables evolutionary predictions, such as in dinoflagellates.
"U-ExM is transforming how we explore protist ultrastructure," said co-first author Armando Rubio Ramos of the University of Geneva. The findings bridge molecular data and physical organization, hinting at how cellular complexity evolved.
With a CHF 2 million grant from the Moore Foundation and Thomas Richards from Oxford University, the team advances PlanExM. "Our adventures with expansion microscopy are only beginning," said Dey. "The next step is to selectively look deeper into certain species... such as understanding how mitosis and multicellularity evolved," added Dudin.