A brand new microscopy breakthrough is revealing the oceans’ invisible life

A Pandemic Collaboration Sparks Discovery

During the COVID-19 pandemic, EMBL Group Leader Gautam Dey acquired a Zoom name from collaborator Omaya Dudin, then main a analysis group at EPFL. Dudin had simply succeeded in adapting a brand new imaging technique to visualise the internal group of Ichthyosporea (a marine protist carefully associated to animals and fungi). This breakthrough overcame a long-standing impediment: the species’ robust cell partitions.

The method, often known as growth microscopy, was initially developed at MIT and later refined into ultrastructure growth microscopy (U-ExM) by Paul Guichard and Virginie Hamel on the University of Geneva. Their enhancements made the protist’s cell partitions permeable, permitting scientists to obviously observe its internal structure for the primary time.

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

The EMBL-led Traversing European Coastlines (TREC) expedition provided an excellent alternative to discover these marine organisms additional. Recently revealed in Cell, the staff’s findings present detailed perception into the mobile constructions of greater than 200 plankton species, particularly eukaryotes (organisms whose cells include a membrane-bound nucleus). This analysis marks the start of PlanExM, a TREC undertaking designed to map the hidden structural range of plankton utilizing growth microscopy.

Exploring Marine Microbes in Unprecedented Detail

At Roscoff, France — one of many first TREC expedition sampling websites — the Station Biologique maintains one among Europe’s most complete collections of marine microorganisms. Expecting just a few dozen samples, the staff requested supervisor Ian Probert for materials to check their method. Instead, they gained entry 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,” mentioned co-first creator Felix Mikus, who accomplished his PhD within the Dey Group and is now a postdoc in Dudin’s laboratory on the University of Geneva.

How Expansion Microscopy Works

Expansion microscopy, which marks its tenth anniversary this 12 months, bodily enlarges organic samples. A pattern — containing cells, tissues, or single-celled organisms — is embedded in a clear gel that absorbs water and expands. Remarkably, the cell’s inner constructions stay intact and stretch proportionally, permitting researchers to enlarge the specimen as much as 16 instances with out utilizing 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,” mentioned Guichard and Hamel.

Mapping the Cellular Skeleton of Life

Using samples from Roscoff and a second assortment in Bilbao, Spain, the staff performed some of the complete research ever of the cytoskeleton — the filament community that helps and organizes eukaryotic cells. They targeted on microtubules (hole filaments that assist cells preserve form, divide, and transfer) and centrins (proteins concerned in organizing microtubules).

“We were able to map features of microtubule and centrin organization across many different eukaryotic groups,” defined Hiral Shah, EIPOD Postdoctoral Fellow in EMBL’s Dey and Schwab teams and co-first creator of the examine. “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,” mentioned co-first creator Armando Rubio Ramos, a Postdoctoral Fellow on 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 outcomes not solely illuminate how eukaryotic cells are organized but additionally provide clues in regards to the evolutionary improvement of their inner constructions. The analysis highlights growth microscopy’s energy as a instrument for finding out even advanced environmental samples collected immediately from the ocean.

Toward a Planetary Atlas of Microscopic Life

“Our adventures with expansion microscopy are only beginning,” mentioned 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 becoming a member of the collaboration, Dey and Dudin secured a CHF 2 million Moore Foundation Grant to proceed increasing their analysis.

“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 mentioned.