A CAMECA IMS-3f SIMS ion microscope instrument capable of 500 nm spatial resolution was used for imaging single bacterial cells in the soil treated with C-13-labeled phenol in desired treatments. After formaldehyde fixation, the soil samples containing bacterial cells were smeared on the silicon substrate. The O-2(+) primary ion beam was used for the detection of negative secondary ions. Images of individual bacterial cells were recorded on a CCD camera in masses 24, 25, 26, and 27 signals. The respective mass images represented contributions from the molecular ions of interest, for example (24)(C-12(2)) , (25)((CC)-C-13-C-12) , (26)((CN)-C-12-N-14) , (27)((CN)-C-13-N-14) , as well as interfering mass species associated with a particular mass. However, in cells treated with C-13-labeled phenol the enhancement of signals in masses 25 and 27 images due to increased signals of (25)((CC)-C-13-C-12) and (27)((CN)-C-13-N-14) , respectively, unequivocally indicated the presence of C-13-labeled phenol in bacterial cells in direct comparison to the samples treated only with unlabeled phenol. The ratio images of masses 25/24 and 27/26 from individual cells revealed a cell-to-cell heterogeneity in the labeling with C-13-phenol. This study indicates that the ion microscope can be applied effectively for studies of labeled molecules in microbiology and biogeochemistry. (c) 2008 Elsevier B.V. All rights reserved.