Extraction of Microbial Cells from Environmental Samples for FISH Approaches

Jennifer Pratscher

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review


Fluorescent in situ hybridization (FISH) on environmental samples has become a standard technique to identify and enumerate microbial populations. However, visualization and quantification of cells in environmental samples with complex matrices is often challenging to impossible, and downstream protocols might also require the absence of organic and inorganic particles for analysis. Therefore, quite often microbial cells have to be detached and extracted from the sample matrix prior to use in FISH. Here, details are given for a routine protocol to extract intact microbial cells from environmental samples using density gradient centrifugation. This protocol is suitable and adaptable for a wide range of environmental samples.

Original languageEnglish
Title of host publicationFluorescence In-Situ Hybridization (FISH) for Microbial Cells
EditorsNuno F. Azevedo, Carina Almeida
PublisherHumana Press
Number of pages9
ISBN (Electronic)9781071611159
ISBN (Print)9781071611142
Publication statusPublished - 2021

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Cell extraction
  • Environmental samples
  • FISH
  • Microbial cells
  • Microbial ecology

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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