Volume electron microscopy reveals bacterial endosymbiosis within host mitochondria

Bacterial endosymbionts can inhabit certain eukaryotic compartments, yet their direct associations with mitochondria have remained poorly understood. Using a multiscale volumetric electron microscopy (vEM) framework spanning whole-cell reconstructions to subnanometer-scale electron tomography, we investigated mitochondria of two phylogenetically distinct eukaryotes: the tick Ixodes ricinus and the marine protist Diplonema japonicum. We show that Midichloria mitochondrii, the maternally-transmitted symbiont of I. ricinus, penetrates into the intracristal space of host mitochondria, inducing ≥60-fold expansion of mitochondrial cristae, with individual cristae exceeding 1 µm in width. In D. japonicum, we observed staged endosymbiotic interactions with the host mitochondrion, including cases of complete engulfment by both mitochondrial membranes. To describe the phenomenon of bacterial residency within mitochondria or in tight association with mitochondria, we introduce the term mitobiosis. Together, these findings establish mitochondria as niches for endosymbiotic bacteria and highlight vEM as a powerful tool for uncovering hidden organelle-microbe interactions.