In the 1960s, electron microscopes were opening a new window in biology, allowing scientists to look not just at cells, but into them. This revealed a rich world of ultrastructures too small to resolve with light microscopes, including organelles inside eukaryotic cells. To share this new vista with scientists and medical students who did not have microscopes to look for themselves, authors like Don Fawcett  and John Dodge  created atlases of electron microscopy images that remain valuable resources for biological and medical novices, as well as experts.
More than fifty years later, we are once again enjoying an expanded view of biology, thanks to another great advance in electron microscopy. The development of cryogenic electron microscopy, or cryo-EM, allows us to look inside cells in their native state. This has opened up even the smallest cells for examination, and revealed some surprising things. In particular, bacteria and archaea, orders of magnitude smaller than eukaryotic cells and lacking prominent organelles, previously seemed to be relatively unstructured bags of nucleic acids and protein. In the last decade, cryo-EM has challenged this idea, revealing a startling degree of structure in these tiny cells. Understanding this intricate molecular machinery might enable us to engineer new biological tools in the future. And so, inspired by the atlases of eukaryotic cell structure from the 1960s, here we offer an atlas of bacterial and archaeal cell structure, highlighting many of the molecular machines we have discovered so far. We hope it will be a useful tool for microbiology courses, serving as a quick introduction to the cells and what they contain before students go on to study aspects of biochemistry or medical importance.
Just as the technology of electron microscopy has advanced in the intervening decades, the technology of sharing information has similarly evolved. Taking advantage of a digital medium, we can share not just two-dimensional slices through cells, but full three-dimensional volumes with movies and animations. This medium also allows you to tailor your experience. If you want a brief overview, simply follow the main narrative. If you want to go into more depth on a topic, use the “Learn More” buttons to see additional examples and details. If you are interested in a particular species, navigate from the Phylogenetic Tree. If you are interested in a particular structure, try out the Feature Index. The digital format also lends itself to frequent updates so the textbook can better reflect an active field of research. To see what has been added in each new edition, check out About this Book.
If you are new to cryo-EM, we suggest starting with Chapter 1, which describes the methods used in structural biology, particularly cryo-EM. If you are already an expert, or pressed for time, go straight to the cells in Chapter 2. Before you do, though, please watch this short introductory video.
As Charles Darwin wrote in 1837, “I shall always feel respect for every one who has written a book, let it be what it may, for I had no idea of the trouble which trying to write common English could cost one” . The task was made immeasurably easier for us by the help of many minds and hands. See acknowledgments below ⇩.