Stable Isotope Probing
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Stable Isotope Probing : Methods and Protocols

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Description

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.
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Product details

  • Hardback | 247 pages
  • 178 x 254 x 19.05mm | 723g
  • Totowa, NJ, United States
  • English
  • 1st ed. 2019
  • 35 Illustrations, color; 8 Illustrations, black and white; XI, 247 p. 43 illus., 35 illus. in color.
  • 1493997203
  • 9781493997206
  • 1,460,860

Back cover copy

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.
show more

Table of contents

1. Experimental Set Up and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era



Roey Angel







2. DNA-Based Stable Isotope Probing



Zhongjun Jia, Weiwei Cao, and Marcela Hernandez Garcia







3. RNA Stable Isotope Probing (RNA-SIP)



Noor-Ul-Huda Ghori, Benjamin Moreira-Grez, Paton Vuong, Ian Waite, Tim Morald, Michael Wise, and Andrew S. Whiteley







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



Andrea Watzinger and Rebecca Hood-Nowotny







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



Martin Taubert







6. 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, and Jennifer Pett-Ridge







7. Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures



Quan Yuan







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



Li Cui, Kai Yang, and Yong-Guan Zhu







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



Samuel E. Barnett, Nicholas D. Youngblut, and Daniel H. Buckley







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



Egbert Schwartz, Michaela Hayer, Bruce A. Hungate, and Rebecca L. Mau







11. 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 van Gestel, Egbert Schwartz, and Bruce A. Hungate







12. Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics



Eileen Kroeber and OEzge Eyice







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



Ang Hu, Yahai Lu, Marcela Hernandez Garcia, and Marc G. Dumont







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



Roey Angel







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



Xiuran Yin, Ajinkya C. Kulkarni, and Michael W. Friedrich







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



Miao Hu, Matthew Lee, Ling Zhong, and Michael J. Manefield







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



Severin Weis, Sylvia Schnell, and Markus Egert







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



Wafa Achouak and Feth el Zahar Haichar
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