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8 - Whole Cell Identification of Microorganisms in Their Natural Environment with Fluorescence in situ Hybridization (FISH)

from Part III - Imaging Techniques

Published online by Cambridge University Press:  06 July 2019

By
Natuschka M. Lee
Edited by
Janice P. L. Kenney ,
Harish Veeramani  and
Daniel S. Alessi
Janice P. L. Kenney
Affiliation:
MacEwan University, Edmonton
Harish Veeramani
Affiliation:
Carleton University, Ottawa
Daniel S. Alessi
Affiliation:
University of Alberta
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Summary

One of the main goals in biogeochemistry is to explore the global relationships between organisms and chemical elements in different ecosystems. A diversity of analytical techniques based on chemical-physical or molecular biological procedures are available to explore different organisms and their abiotic and biotic interactions in a variety of ecosystems. Even though many of these modern analytical techniques are irreplaceable in today´s research, most of them can only provide indirect results because they are built on a “black-box” approach, where the biological species in an ecosystem or a geological environment are disrupted for extraction of nucleic acids, proteins, etc. Essential biological information, such as the morphology of specific species, their location, distribution, association with other organisms in their natural environment, and individual activities and functions, is therefore lost. Fluorescence in situ hybridization (FISH) helps retrieve this information without either cultivation or extraction of cell components, and can therefore provide a quick and useful complement to different “black-box”-based approaches. FISH is based on fluorescently labeled gene probes with a unique nucleotide composition designed to match specific genes in different cellular species. Thus, different biological species can be identified simultaneously with different gene probes labeled with different fluorochromes in their natural environment. The technique has undergone extensive development with around 30 variations for different applications. FISH is evaluated either by microscopy (e.g., fluorescence microscopy, Raman micro spectroscopy, Nano-SIMS), or by nonmicroscope-based methods, such as flow cytometry, microarray technology, or molecular biological methods such as proteomics. This chapter will serve as a guide for sample preparation, selection of appropriate FISH protocols, evaluation and design of gene probes, and evaluation of FISH experiments.

Type
Chapter
Information
Analytical Geomicrobiology
A Handbook of Instrumental Techniques
 , pp. 187 - 212
Publisher: Cambridge University Press
Print publication year: 2019

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References

8.10 References

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