Diatom ultrastructural diversity across controlled and natural environments

Diatoms are ubiquitous aquatic microalgae critical to our planet, that were amongst the pioneer model organisms in cell biology for their large and transparent cell structure. However, their robust silica cell wall renders diatoms impermeable to many dyes and antibodies, and complicates the intracellular delivery of gene editing tools - driving in part the eventual decline of diatoms as mainstream model species despite their unique cellular physiology and remarkable ecological success. Here, we demonstrate that cryo-fixation combined with ultrastructural expansion microscopy (cryo-ExM) can overcome the silica barrier across diverse diatom species spanning over 80 million years of evolutionary time. We illustrate the potential of cryo-ExM to provide scalable, cost-effective volumetric imaging of diatom ultrastructure in laboratory cultures, as well as field-collected samples from the pan-European TREC expedition. We first reveal striking similarities in interphase microtubule organization across diverse diatom species by characterizing cytoskeletal arrangements throughout cell cycles and populations, uniting both pennate and centric morphologies under shared principles. We further unveil diatom photosynthetic diversity through qualitative and quantitative comparative analysis of chloroplast and pyrenoid morphologies, demonstrating that each diatom species architects unique photosynthetic machinery. Using cryo-ExM on environmental samples further exposes intricate diatom symbioses, revealing tight spatial organisation of ecological interactions. This methodology makes diatoms more accessible for modern and comparative cell biology research, providing new opportunities to investigate the cellular mechanisms of one of Earth’s most successful photosynthetic groups.