CHAPTER 2

Observing the Microbial Cell

A scanning electron tomograph of Salmonella infecting a human cell. — Scanning electron tomography, with focused ion beam tomography, reveals *Salmonella* bacteria infecting a human cell. The 3D image shows bacteria (cyan) inside ruptured cell vesicles (yellow). Large vesicles (orange) take up extracellular material by pinocytosis. *Salmonella* bacteria resist the cell’s defenses and multiply within the vesicles, thus evading the host immune system. J. FREDLUND ET AL. 2018. *CELL MICROBIOL*. 20 (4)

Chapter Sections		Learning Objectives
2.1 Observing Microbes	»	Explain the distinction between detection and resolution, and summarize the use of microscopy across many scales of microbial size and shape.
2.2 Optics and Properties of Light	»	Define the different ways that light interacts with an object.
2.3 Bright-Field Microscopy and Phase-Contrast Microscopy	»	Explain the function of bright-field microscopy and phase-contrast microscopy, and the factors that influence them.
2.4 Fixation and Staining for Bright-Field Microscopy	»	Describe the use of fixation and staining in bright-field microscopy.
2.5 Fluorescence Microscopy, FISH, and Chemical Imaging Microscopy	»	Describe the use of fluorescence microscopy, fluorescence in situ hybridization (FISH), and chemical imaging microscopy.
Special Topic 2 Biogeography of a Gut Pathogen
2.6 Electron Microscopy, Scanning Probe Microscopy, and X-Ray Crystallography	»	Explain the use of transmission and scanning electron microscopy, and identify advanced methods of imaging cells and molecules.
eResearch Activity 2 How Do Bacteria Make a Magnet Chain?

One definition of a microbe is an organism that requires a microscope to see. Microscopy reveals the vast realm of life that is invisible to the unaided eye. A microscope enables us to count the number of microbes in the human bloodstream or in natural environments such as the open ocean. It shows us how microbes swim and respond to signals such as a new food source. Microscopes reveal entire communities, such as the microbes that colonize the root of a tree or those that form plaque on the surface of our teeth.

More powerful microscopes reveal the parts of our cells and their function in real time. Fluorescence microscopy captures single molecules within a living cell. The fluorophores can label specific kinds of DNA or proteins. At higher resolution, electron microscopy explores the cell’s interior. Cryo-electron microscopy reveals the cell in three dimensions and models the shape of viruses such as coronaviruses, including their spike proteins that lead to deadly infections.

Chapter 2 begins with light microscopy, the essential tool for every student and professional in the field or clinic. We then explore fluorescence and super-resolution imaging, electron microscopy, and scanning probe microscopy, which push ever farther the frontiers of our ability to observe the microbial world. And we continue to invent new kinds of microscopy, such as chemical imaging microscopy, to reveal microbial metabolism at work.