Researchers from UNIGE and EMBL reveal the internal structure of over hundreds of plankton species, paving the way for a global cellular atlas.
Plankton are essential for life on Earth: they underpin life in the oceans and influence climate. Despite their importance and immense diversity, detailed three-dimensional nanoscale architecture of these microscopic organisms has remained largely unexplored, limiting our understanding of their cellular structures and biological complexity. Researchers at the University of Geneva (UNIGE) and at the European Molecular Biology Laboratory (EMBL) have succeeded in visualising the internal structure of more than 200 eukaryotic microbial species, including plankton species, using an innovative technique, Ultrastructure Expansion Microscopy (U-ExM). Published in Cell, this work opens the door to a planetary atlas of eukaryotic cellular diversity.
Plankton, a diverse community of microscopic organisms, that includes marine microbial eukaryotes (cells with a nucleus), are the unseen engines driving Earth's life-support systems – producing oxygen and forming the base of the oceanic food chain. They are also incredibly diverse, with tens of thousands of species described so far, and many more waiting to be discovered.
We spent three days and nights just fixing those samples. It was a treasure trove we could not let go of!
A technique that expands biological boundaries
In a collaborative effort, the groups of Omaya Dudin, Paul Guichard and Virginie Hamel at UNIGE, and Gautam Dey at EMBL, used high-resolution microscopy to study marine plankton. Expansion microscopy allows biological samples to be physically enlarged to reveal their internal architecture. Optimised into Ultrastructure Expansion Microscopy (U-ExM), the method enables researchers to explore sub-cellular ultrastructure and overcome the problem of cell wall permeability, allowing the internal structures to be clearly visualised and studied.
From European coastlines to the microscopic world
The study was carried out within the Traversing European Coastlines (TREC) expedition led by EMBL, which aimed to explore coastal biodiversity. Sampling campaigns at Roscoff (France) gave the researchers access to extensive culture collections of marine microorganisms. "We spent three days and nights just fixing those samples. It was a treasure trove we could not let go of," recalls Felix Mikus, co-first author of the study, who completed his PhD in the Dey group and is now a postdoctoral researcher in the Dudin laboratory at UNIGE.
Expansion microscopy works by embedding biological samples in a transparent gel that expands when it absorbs water. The sample's structures enlarge proportionally, enabling researchers to observe subcellular details between four and sixteen times their original size of the biological samples. "When combined with conventional light microscopy, this approach overcomes the standard resolution limits of light, offering a new window into cellular architecture," explains Armando Rubio Ramos, co-first author and postdoctoral fellow in the Guichard and Hamel group at UNIGE.
Mapping the evolution of cellular architecture
By analysing samples from hundreds of species, the researchers carried out one of the most extensive studies of cytoskeletal diversity in microbial eukaryotes to date. They focused particularly on microtubules and centrins, key components of the cellular scaffold that govern cell shape, movement, and division. This allowed them to map features of microtubule and centrin organisation across many different eukaryotic groups. "This scale of analysis opens up the possibility of making evolutionary predictions about how cellular structures have diversified" notes Hiral Shah, EMBL postdoctoral fellow and co-first author.
This collaborative research not only advances the understanding of the principles governing eukaryotic cell organisation, but also highlights the potential of expansion microscopy for studying complex natural samples collected directly from marine environments. The work marks an important step towards large-scale, high-resolution exploration of biodiversity, bridging the gap between genomic data and cellular physiology.
