This Volume presents key microscopy and imaging methods for revealing the structure and ultrastructure of environmental and experimental samples, of microbial communities and cultures, and of individual cells.
Introduction.- Electron microscopy protocols for the study of hydrocarbon-producing and -decomposing microbes: classical and advanced methods.- Protocol for laser scanning microscopy of microorganisms on hydrocarbons.- Fluorescence microscopy for microbiology.- Imaging bacterial cells and biofilms adhering to hydrophobic organic compounds-water interfaces.- Bacteria-mineral colloid interactions in biofilms - an ultrastructural and microanalytical approach.- Identification of microorganisms in hydrocarbon contaminated aquifer samples by fluorescence in-situ hybridization (CARD-FISH).- Studies of the ecophysiology of single cells in microbial communities by (quantitative) microautoradiography and fluorescence in situ hybridization (MAR-FISH).- Protocol for in situ detection of functional genes of microorganisms by Two-pass TSA-FISH.- Three-dimensional visualization and quantification of lipids in microalgae using confocal laser scanning microscopy.- A Correlative Light-Electron Microscopy (CLEM) protocol for the identification of bacteria in animal tissue, exemplified by methanotrophic symbionts of deep-sea mussels.