Stable Isotope Probing: Methods and Protocols

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