Plankton are the unseen drivers of life on Earth. These microscopic organisms produce a large share of the planet’s oxygen and form the base of the ocean food chain. They are also astonishingly diverse, with tens of thousands of species already identified and many more waiting to be discovered. Among them, protists – tiny, single-celled organisms – are especially remarkable for their evolutionary significance. For many years, scientists could study them only through genetic data because existing imaging techniques were unable to reveal their complex internal structures.

A Pandemic Collaboration Sparks Discovery

During the COVID-19 pandemic, EMBL Group Leader Gautam Dey received a Zoom call from collaborator Omaya Dudin, then leading a research group at EPFL. Dudin had just succeeded in adapting a new imaging method to visualize the inner organization of Ichthyosporea (a marine protist closely related to animals and fungi). This breakthrough overcame a long-standing obstacle: the species’ tough cell walls.

The technique, known as expansion microscopy, was originally developed at MIT and later refined into ultrastructure expansion microscopy (U-ExM) by Paul Guichard and Virginie Hamel at the University of Geneva. Their improvements made the protist’s cell walls permeable, allowing scientists to clearly observe its inner architecture for the first time.

Motivated by this success, Dudin, Dey, Guichard, and Hamel began a long-term collaboration. Three years later, their partnership has produced an unprecedented body of knowledge about hundreds of protist species and laid the groundwork for a “planetary atlas” of plankton.

The EMBL-led Traversing European Coastlines (TREC) expedition offered an ideal opportunity to explore these marine organisms further. Recently published in Cell, the team’s findings provide detailed insight into the cellular structures of more than 200 plankton species, especially eukaryotes (organisms whose cells contain a membrane-bound nucleus). This research marks the beginning of PlanExM, a TREC project designed to map the hidden structural diversity of plankton using expansion microscopy.

Exploring Marine Microbes in Unprecedented Detail

At Roscoff, France – one of the first TREC expedition sampling sites – the Station Biologique maintains one of Europe’s most comprehensive collections of marine microorganisms. Expecting only a few dozen samples, the team asked manager Ian Probert for material to test their technique. Instead, they gained access to over 200 species.

“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, who completed his PhD in the Dey Group and is now a postdoc in Dudin’s laboratory at the University of Geneva.

How Expansion Microscopy Works

Expansion microscopy, which marks its 10th anniversary this year, physically enlarges biological samples. A sample – containing cells, tissues, or single-celled organisms – is embedded in a transparent gel that absorbs water and expands. Remarkably, the cell’s internal structures remain intact and stretch proportionally, allowing researchers to enlarge the specimen up to 16 times without using high-powered lenses.

“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.

Mapping the Cellular Skeleton of Life

Using samples from Roscoff and a second collection in Bilbao, Spain, the team conducted one of the most comprehensive studies ever of the cytoskeleton – the filament network that supports and organizes eukaryotic cells. They focused on microtubules (hollow filaments that help cells maintain shape, divide, and move) and centrins (proteins involved in organizing microtubules).

“We were able to map features of microtubule and centrin organization across many different eukaryotic groups,” explained Hiral Shah, EIPOD Postdoctoral Fellow in EMBL’s Dey and Schwab groups and co-first author of the study. “The scale of the study, with many species characterized in each group, opens up the possibility to make evolutionary predictions. For instance, dinoflagellates, one of the most diverse groups found in oceans across the planet, are well-represented in our study. We were able to map the presence of tubulin and centrin structures associated with the cell cortex or the flagella in these species.”

Revealing Evolutionary Patterns Through Microscopy

“U-ExM is transforming how we explore protist ultrastructure,” said co-first author Armando Rubio Ramos, a Postdoctoral Fellow at the University of Geneva. “By combining this technique with high-throughput imaging and comparative analyses, we can begin to decode how cellular architecture has diversified across evolution. It’s a bridge between molecular data and the physical organization of life at the microscopic scale.”

The results not only illuminate how eukaryotic cells are organized but also offer clues about the evolutionary development of their internal structures. The research highlights expansion microscopy’s power as a tool for studying even complex environmental samples collected directly from the ocean.

Toward a Planetary Atlas of Microscopic Life

“Our adventures with expansion microscopy are only beginning,” said Dey. “This is perhaps the first high-resolution microscopy technique that has the potential to match the scale and ambition of large biodiversity genomics projects, enabling us in the near future to associate new multiomics data with cellular physiology at scale across the tree of life.”

With Thomas Richards from Oxford University joining the collaboration, Dey and Dudin secured a CHF 2 million Moore Foundation Grant to continue expanding their research.

“The next step is to selectively look deeper into certain species within this broad collection to answer specific questions, such as understanding how mitosis and multicellularity evolved and the phenotypic diversity that underlie major evolutionary transitions,” Dudin said.