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Updated: May 29, 2026

Fluorescence Microscopy Methods for Determining the Viability of Bacteria in Association with Mammalian Cells
Published on: September 5, 2013
The fluorescent dyes TO-PRO-3 and TOTO-3 iodide allow detection of microbial cells in soil samples without
Ruth Henneberger1, Debra Birch, Peter Bergquist
1Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Abstract:
Visualization of microorganisms in soils and sediments using fluorescent dyes is a common method in microbial ecology studies, but is often hampered by strong nonspecific background fluorescence that can mask genuine cellular signals. The cyanine nucleic acid binding dyes TO-PRO-3 and TOTO-3 iodide enabled a clear detection of microbial cells in a mineral soil, while nonspecific background was greatly reduced compared with commonly used dyes. When used as counterstains for fluorescence in situ hybridization (FISH), both cyanine dyes allowed identification of microbial cells despite strong background from nonspecifically bound probes. TO-PRO-3 and TOTO-3 are easy to use and represent superior alternatives for detecting microorganisms in soil environments.
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