Cryogenic Electron Tomography by the Numbers: Charting Underexplored Lineages in Structural Cell Biology

Abstract Imaging of cells and their interactions across the whole biosphere, with molecular-scale resolution, is key for understanding structure-function relations. Cryogenic electron tomography (cryo-ET) is a powerful method for obtaining this critical information. However, cryo-ET studies are challenging and often limited to a small number of cell types per study. Here, we bring together cryo-ET data from hundreds of cells and tissues across the biosphere to (i) identify emerging methodological trends, (ii) reduce imaging time and costs, (iii) quantitively compare methods for cell freezing and sectioning and (iv) census cryo-ET species coverage across all domains of life. Comparison of the fraction of cellular material within lamellae across all domains of life reveals an order of magnitude difference between bacteria (9%) and archaea (15%) compared to eukaryotes (1%). We calculate the fraction of cellular material which can be imaged using distinct sectioning methods on multicellular communities and tissues - identifying serial lift-out as a powerful new approach for obtaining more complete cellular depictions. Finally, we show that the biodiversity of current cryo-ET studies is 2-3 order of magnitude lower than in sequence libraries and 4-5 lower than the total predicted on Earth. Our analyses reveal major evolutionary lineages which remain critically understudied and where future cryo-ET research would be most impactful. Significance Statement Cryogenic electron tomography (cryo-ET) is a powerful method for imaging inside cells, but it is challenging and typically limited to a few cells per study. We consolidate and quantify data from hundreds of cellular cryo-ET studies across the biosphere. The methodological trends we identify will enhance cryo-ET throughput and heighten biological insight from underexplored lineages of life on Earth.