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Stable Isotope Probing

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Marc G. Dumont

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

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    You can also search for this editor in PubMed   Google Scholar

  2. Marcela Hernández García

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

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

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

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Experimental Setup and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era

    • Roey Angel
    Pages 1-15

  3. DNA-Based Stable Isotope Probing

    • Zhongjun Jia, Weiwei Cao, Marcela Hernández García
    Pages 17-29

  4. RNA Stable Isotope Probing (RNA-SIP)

    • Noor-Ul-Huda Ghori, Benjamin Moreira-Grez, Paton Vuong, Ian Waite, Tim Morald, Michael Wise et al.
    Pages 31-44

  5. Stable Isotope Probing of Microbial Phospholipid Fatty Acids in Environmental Samples

    • Andrea Watzinger, Rebecca Hood-Nowotny
    Pages 45-55

  6. SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity

    • Martin Taubert
    Pages 57-69

  7. Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS

    • Xavier Mayali, Peter K. Weber, Erin Nuccio, Jory Lietard, Mark Somoza, Steven J. Blazewicz et al.
    Pages 71-87

  8. Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures

    • Quan Yuan
    Pages 89-94

  9. Stable Isotope-Labeled Single-Cell Raman Spectroscopy Revealing Function and Activity of Environmental Microbes

    • Li Cui, Kai Yang, Yong-Guan Zhu
    Pages 95-107

  10. Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP

    • Samuel E. Barnett, Nicholas D. Youngblut, Daniel H. Buckley
    Pages 109-128

  11. Stable Isotope Probing of Microorganisms in Environmental Samples with H218O

    • Egbert Schwartz, Michaela Hayer, Bruce A. Hungate, Rebecca L. Mau
    Pages 129-136

  12. Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing

    • Brianna K. Finley, Michaela Hayer, Rebecca L. Mau, Alicia M. Purcell, Benjamin J. Koch, Natasja C. van Gestel et al.
    Pages 137-149

  13. Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics

    • Eileen Kröber, Özge Eyice
    Pages 151-161

  14. Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing

    • Ang Hu, Yahai Lu, Marcela Hernández García, Marc G. Dumont
    Pages 163-174

  15. Stable Isotope Probing Techniques and Methodological Considerations Using 15N

    • Roey Angel
    Pages 175-187

  16. DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea

    • Xiuran Yin, Ajinkya C. Kulkarni, Michael W. Friedrich
    Pages 189-206

  17. Method Development for DNA and Proteome SIP Analysis of Activated Sludge for Anaerobic Dichloromethane Biodegradation

    • Miao Hu, Matthew Lee, Ling Zhong, Michael J. Manefield
    Pages 207-219

  18. RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment

    • Severin Weis, Sylvia Schnell, Markus Egert
    Pages 221-231

  19. Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere

    • Wafa Achouak, Feth el Zahar Haichar
    Pages 233-243

  20. Back Matter

    Pages 245-247
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Keywords

About this book

This book provides definitive methods to perform stable isotope probing (SIP) experiments, covering a wide spectrum of stable isotope techniques used in microbial ecology, such as methods to target and analyze labeled DNA, rRNA, mRNA, protein, and PLFA. Protocols to study stable isotope fractionation by microbial pathways, the analysis of labeled communities with Raman microscopy, Chip-SIM, as well as quantitative SIP (qSIP) and high-resolution SIP (HR-SIP) are also featured. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, Stable Isotope Probing: Methods and Protocols provides readers with up-to-date protocols ranging from basic to the most sophisticated applications of SIP and will benefit anyone pursuing this exciting area of study.

Editors and Affiliations

  • School of Biological Sciences, University of Southampton, Southampton, UK

    Marc G. Dumont, Marcela Hernández García

Bibliographic Information

  • Book Title: Stable Isotope Probing

  • Book Subtitle: Methods and Protocols

  • Editors: Marc G. Dumont, Marcela Hernández García

  • Series Title: Methods in Molecular Biology

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

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9720-6Published: 13 August 2019

  • Softcover ISBN: 978-1-4939-9723-7Published: 13 August 2020

  • eBook ISBN: 978-1-4939-9721-3Published: 12 August 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 247

  • Number of Illustrations: 8 b/w illustrations, 35 illustrations in colour

  • Topics: Microbiology, Microbial Genetics and Genomics

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