Microorganisms play a fundamental role in the cycle of nutrients and energy on our planet. The characterization of microorganisms in their natural environment is the objective and the greatest challenge of microbial ecologists. Single-cell techniques havewww.lw20.com become an integral part in the environmental microbiologist’s toolbox. One of these methods, Fluorescence in situ Hybridization (FISH), is a phylogenetic staining using labeled nucleotide probes to target ribosomal RNA of microbial cells in fixed samples.