Comprehensive protocol for preparing diatom cell samples and associated bacterial consortia for scanning electron microscopy Meticulous sample preparation and strict adherence to preservation procedures are essential for electron microscopy investigations, which enable accurate capture of organisms' morphology, size, and potential interactions within the sample. Here, we present a protocol for preserving cells of the model diatom Phaeodactylum tricornutum and its native bacterial community. We describe steps for diatom fixation and coverslip preparation and washing. We then detail procedures for dehydrating, drying, and metallizing samples followed by observation using scanning electron microscopy.