Evaluation of fluorochromes for imaging bacteria in soil

The distribution of inoculated Escherichia coli cells and indigenous bacteria in a silt loam soil and a sandy soil was studied using fluorescence microscopy techniques. Ethidium bromide stained inoculated cells against the soil and resin background. Satisfactory results were also obtained with epifluorescence microscopy of samples stained with calcofluor white M2R (CFW) and 4′,6-diamidino-2-phenylindole (DAPI). Indigenous soil bacteria were visualized in soil thin sections, after staining with ethidium bromide, using fluorescence microscopy. The density of these bacteria was estimated to be 107–108 cells/cm3. Inoculated E. coli cells, stained with one of the green fluorochromes (fluorescein isothiocyanate (FITC), 5-(4,6-dichlorotriazinyl)aminofluorescein, or eosin Y), could be clearly distinguished in sandy soil thin sections. Confocal laser scanning microscopy with 3D image reconstruction was also successfully applied to characterize distribution of E. coli introduced to soil. The fate of introduced bacteria and the location of indigenous bacteria in soil can be confirmed using the microscopic techniques described in this paper.