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Stable Isotope Probing: Methods and Protocols

✍ Scribed by Marc G. Dumont, Marcela Hernández García

Publisher
Springer New York;Humana
Year
2019
Tongue
English
Leaves
247
Series
Methods in Molecular Biology 2046
Edition
1st ed. 2019
Category
Library
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✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xi
Experimental Setup and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era (Roey Angel)....Pages 1-15
DNA-Based Stable Isotope Probing (Zhongjun Jia, Weiwei Cao, Marcela Hernández García)....Pages 17-29
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
Stable Isotope Probing of Microbial Phospholipid Fatty Acids in Environmental Samples (Andrea Watzinger, Rebecca Hood-Nowotny)....Pages 45-55
SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity (Martin Taubert)....Pages 57-69
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
Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures (Quan Yuan)....Pages 89-94
Stable Isotope-Labeled Single-Cell Raman Spectroscopy Revealing Function and Activity of Environmental Microbes (Li Cui, Kai Yang, Yong-Guan Zhu)....Pages 95-107
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
Stable Isotope Probing of Microorganisms in Environmental Samples with H218O (Egbert Schwartz, Michaela Hayer, Bruce A. Hungate, Rebecca L. Mau)....Pages 129-136
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
Profiling of Active Microorganisms by Stable Isotope Probing—Metagenomics (Eileen Kröber, Özge Eyice)....Pages 151-161
Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing (Ang Hu, Yahai Lu, Marcela Hernández García, Marc G. Dumont)....Pages 163-174
Stable Isotope Probing Techniques and Methodological Considerations Using 15N (Roey Angel)....Pages 175-187
DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea (Xiuran Yin, Ajinkya C. Kulkarni, Michael W. Friedrich)....Pages 189-206
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
RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment (Severin Weis, Sylvia Schnell, Markus Egert)....Pages 221-231
Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere (Wafa Achouak, Feth el Zahar Haichar)....Pages 233-243
Back Matter ....Pages 245-247

✦ Subjects

Life Sciences; Microbiology; Microbial Genetics and Genomics

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