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The scientific literature is replete with reported observations of bacteria on rocks, in rocks, around rocks, precipitating rocks, and dissolving rocks in both ancient and modern systems, and this is an active and growing area of research. Many of these studies rely on scanning electron microscopy (SEM) to image mineral surfaces and to show a link between the presence of microorganisms and a particular geochemical process such as weathering or mineral precipitation. The ability of a researcher to show this link, however, will be governed by the quality and interpretation of the image, and the recognition of imaging artifacts and the shortcomings of using SEM as a sole method of investigation.

The purpose of this chapter is to provide basic guidelines and procedures for collecting, preserving and processing mineral samples for SEM imaging, and the use of biomass determination and fluorescence in situ hybridization (FISH) analysis of microorganisms attached to rocks to augment SEM image analysis. This is not a review of the existing literature, rather it is a report of the methods that we have found useful in characterizing microbes on rocks. For basic SEM technique, general texts are available (e.g., Goldstein et al., 1992). We have similarly not included a discussion of transmission electron microscopy (TEM) methods, which is another tool that can be used to examine microbe-mineral interactions at very high magnification.

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