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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.
List of contents
Experimental Set Up and Data Analysis Considerations for DNA- and RNA-SIP Experiments in the Omics Era.- DNA-Based Stable Isotope Probing.- RNA Stable Isotope Probing (RNA-SIP).- Stable Isotope Probing of Microbial Phospholipid Fatty Acids in Environmental Samples.- SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity.- Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS.- Quantification of Methanogenic Pathways Using Stable Carbon Isotopic Signatures.- Stable Isotope-Labeled Single-Cell Raman Spectroscopy Revealing Function and Activity of Environmental Microbes.- Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High Resolution SIP.- Stable Isotope Probing of Microorganisms in Environmental Samples with H218O.- Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.- Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.- Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing.- Stable Isotope Probing Techniques and Methodological Considerations Using 15N.- DNA and RNA Stable Isotope Probing of Methylotrophic Methanogenic Archaea.- Method Development for DNA and Proteome SIP Analysis of Activated Sludge for Anaerobic Dichloromethane Biodegradation.- RNA-Based Stable Isotope Probing (RNA-SIP) in the Gut Environment.- Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere.
Summary
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.
