This article contains a small extract from Chapter 7 of “Atomic Force Microscopy”. Chapter 7 contains descriptions of applications of AFM in materials science, chemistry and physics, biology and the life sciences, nanotechnology, and in industry. This short section describes some examples of applications of AFM in bacteriology. References lists, and the second figure can be found in the full book.
AFM is a highly suitable tool to examine bacteria, and has been widely applied to their study. Bacteria are commonly studied by optical microscopy, which can give an overall idea about gross cell morphology (via a two-dimensional projection), and is also useful for cell-counting studies. In comparison, AFM is slower, and thus is less useful for quantitative cell-counting, but allows measurement of a variety of other cellular properties, particularly by nanoindentation and force spectroscopy experiments . In addition, the greatly increased resolution of AFM allows for the imaging of finer details of cell morphology and sub-cellular features such as pili and fimbriae . The three dimensional information from AFM can also be useful in differentiating morphologies which would look the same in optical microscopy . Various other micro-organisms have been studied by AFM such as spores [178, 613–615], fungi [616, 617], including yeasts [171, 618], viruses [287, 619], and others  but here we concentrate on bacteria for the sake of brevity.
Fig. 7.20. Studies of bacterial morphology. Top left: Streptococcus, showing typical linear clusters. Top right: large clusters of Staphylococcus aureus. Bottom left: Salmonella biofilm showing pili-like fimbrial structures. Bottom right: E. coli. All these images were measured in air. Reproduced with permission from  (top left) and  (bottom left). Right hand images the author's own work.