Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH)

  • Marta Nierychlo
  • Jeppe Lund Nielsen
  • Per Halkjær NielsenEmail author
Part of the Springer Protocols Handbooks book series (SPH)


Microautoradiography (MAR) in combination with fluorescence in situ hybridization (FISH) is a powerful method of obtaining information about the ecophysiology of probe-defined single cells in mixed microbial communities. The incorporation of radiolabelled substrates can be quantified by automated image analysis (MARQuant). Quantification of MAR signals can answer more specific questions regarding metabolic activity and function of the microbes. Here, we give an overview of how to use MAR-FISH in various ecosystems and provide a detailed protocol for MAR-FISH, including sampling, incubation with radiotracers, the MAR procedure in combination with FISH and other staining techniques, microscopy, and troubleshooting. A description of the MARQuant image analysis tool, including examples of its application, is also provided.


Ecophysiology FISH Microautoradiography Microbial communities Radiotracers 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Marta Nierychlo
    • 1
  • Jeppe Lund Nielsen
    • 1
  • Per Halkjær Nielsen
    • 1
    Email author
  1. 1.Department of Chemistry and BioscienceCenter for Microbial Communities, Aalborg UniversityAalborgDenmark

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