The diversity of microbial eukaryotic communities, revealed by worldwide metagenomic sampling, is under ecological stress. To date, the cellular physiology of these eukaryotes and the impact of climate change on their ecology remain largely unknown. Here, we collaborate with the EMBL TREC expedition to explore the ultrastructural biodiversity of the plankton using U-ExM and cryo-expansion microscopy (Cryo-ExM). This project, called PlanExM (for Planetary Expansion Microscopy), is part of a collective effort with several groups including the groups of Omaya Dudin (EPFL), Gautam Dey (EMBL), and Yannick Schwab (EMBL). By using expansion microscopy on environmental samples, we aim to create an atlas of native eukaryotic cellular biodiversity with unprecedented 3D spatial resolution, with a long-term view to assess the repercussions of climate change.