Stable Isotope Probing: Methods and Protocols

ISBN-13: 9781493997237 / Angielski / Miękka / 2020 / 247 str.

Marc G. Dumont;Marcela Hernandez Garcia

Opis

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.

Spis treści

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 Hernández García

 

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 Kröber and Özge Eyice

 

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

            Ang Hu, Yahai Lu, Marcela Hernández García, 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