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

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Book cover Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

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.

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Author information

Authors and Affiliations

  1. Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark

    Marta Nierychlo, Jeppe Lund Nielsen & Per Halkjær Nielsen

Authors
  1. Marta Nierychlo
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  2. Jeppe Lund Nielsen
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  3. Per Halkjær Nielsen
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Corresponding author

Correspondence to Per Halkjær Nielsen .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Essex, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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Nierychlo, M., Nielsen, J.L., Nielsen, P.H. (2015). Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH). In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols. Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_66

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  • DOI: https://doi.org/10.1007/8623_2015_66

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-49132-4

  • Online ISBN: 978-3-662-49134-8

  • eBook Packages: Springer Protocols

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