9. Fluorescence In Situ Hybridization (FISH)

9.1 Summary of FISH

Fluorescence in situ hybridization (FISH) is a molecular biology method used to visualize and enumerate specific types of microorganisms or groups of microorganisms in an environmental sample. The method does not require isolation or cultivation of microorganisms and allows for examination of microorganisms in complex environmental samples with minimal disruption of the natural microbial communityThe microorganisms present in a particular sample.. Since its introduction in the late 1980’s, FISH has been used in medical and developmental biology and environmental bacteriology (Amann et al. 1995). Today, FISH is considered to be a powerful tool for phylogenetic, ecological, diagnostic, and environmental microbiology studies.

9.2 Applications

The results of FISH analysis of environmental samples are typically used in combination with a suite of analytical methods and field observations to generate a lines-of-evidence argument regarding biological degradation of contaminants. For example, FISH was recently used to provide evidence of intrinsic remediation or natural attenuation of PAH compounds in the coal-tar impacted aquifer underlying the Cherokee former manufactured gas plant (FMGP) site in Northwestern Iowa, in combination with analysis of redox indicators and groundwater contaminant concentrations (Rogers, Ong, and Moorman 2007). In soils, FISH has been used to evaluate the PAH associated microbial community in soils from a former coal gasification plant in Denmark (Uyttebroek et al. 2006) and the atrazine transforming community colonized on BioSep® beads in atrazine exposed soils (Ghosh et al. 2009). Examples of several diverse applications of FISH studies are provided in Table 9-1. This table is followed by a brief explanation of several key studies and major findings.

9.3 Data Interpretation

The application, analysis, and interpretation of microbiology-based EMD methods differ from typical soil and groundwater geochemical measurement in a number of ways. For example, microbial biomarkers cannot easily be preserved, and sample handling and processing requires special care. The analysis of microbial parameters requires specific data quality considerations for sampling plans, sample collection and handling, quality control and laboratory procedures, and these are discussed in Section 10. Included below is a brief introduction to how FISH data are typically reported and some specific examples of how the data would be interpreted in answering the questions presented in Table 2-3. 

9.3.1 How are the data typically reported?

9.3.2 How are the data interpreted?


9.3.3 Practical considerations

9.4 Additional Information

Example FISH probes and cellular stains used for environmental remediation studies or activities are also included in the FISH Fact Sheet. Further reading specific to FISH methods is provided in Appendix F.

9.4.1 How does it work?

9.4.2 Variations or Newer Methods Becoming Available

Publication Date: April 2013

Permission is granted to refer to or quote from this publication with the customary acknowledgment of the source (see suggested citation and disclaimer).


This web site is owned by ITRC.

1250 H Street, NW • Suite 850 • Washington, DC 20005

(202) 266-4933 • Email: itrc@itrcweb.org

Terms of Service, Privacy Policy, and Usage Policy


ITRC is sponsored by the Environmental Council of the States.