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Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics

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Stable Isotope Probing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2046))

Abstract

Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.

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Author information

Authors and Affiliations

  1. Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Landscape Research, Müncheberg, Germany

    Eileen Kröber

  2. School of Biological and Chemical Sciences, Queen Mary University of London, London, UK

    Özge Eyice

Authors
  1. Eileen Kröber
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  2. Özge Eyice
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Corresponding author

Correspondence to Özge Eyice .

Editor information

Editors and Affiliations

  1. School of Biological Sciences, University of Southampton, Southampton, UK

    Marc G. Dumont

  2. School of Biological Sciences, University of Southampton, Southampton, UK

    Marcela Hernández García

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Kröber, E., Eyice, Ö. (2019). Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics. In: Dumont, M., Hernández García, M. (eds) Stable Isotope Probing. Methods in Molecular Biology, vol 2046. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9721-3_12

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  • DOI: https://doi.org/10.1007/978-1-4939-9721-3_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9720-6

  • Online ISBN: 978-1-4939-9721-3

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