Felix Mikus, Armando Rubio-Ramos, Hiral Shah, Jonas Hellgoth, Marine Olivetta, Susanne Borgers, Clémence Saint-Donat, Margarida Araújo, Chandni Bhickta, Paulina Cherek, Jone Bilbao, Estibalitz Txurruka, Yana Eglit, Nikolaus Leisch, Yannick Schwab, Filip Husník, Sergio Seoane, Ian Probert, Paul Guichard, Virginie Hamel, G.K. Dey, Omaya Dudin
Microbial eukaryotes remain understudied despite their critical ecological importance, with the exception of a few established models. They are often small, difficult to culture, and resistant to standard labeling and imaging techniques. Here, we use ultrastructure expansion microscopy (U-ExM) to carry out high-resolution volumetric imaging of over 200 cultured planktonic eukaryotes across major lineages. By combining U-ExM with pan- and specific immuno-labeling, we reveal microtubule and centrin-containing elements and assign molecular identities to enigmatic cytoskeletal structures observed previously only by electron microscopy. This comprehensive resource provides a basis for understanding cytoskeletal diversity, phenotypic plasticity, and evolutionary dynamics. Moreover, our approach extends to mixed environmental samples, paving the way for environmental cell biology at ultrastructural resolution-a crucial step toward understanding and protecting ecosystems in the face of accelerating biodiversity loss.