Metagenomics: Methods and Protocols

ISBN-13: 9781493966899 / Angielski / Twarda / 2016 / 303 str.

Wolfgang Streit; Rolf Daniel

Spis treści

Preface...
Table of Contents...
Contributing Authors...

1. Construction of Small-Insert and Large-Insert Metagenomic Libraries
Carola Simon and Rolf Daniel

2. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies
Dominik Schneider, Franziska Wemheuer, Birgit Pfeiffer, and Bernd Wemheuer

3. Construction and Screening Marine Metagenomic Large Insert Libraries
Nancy Weiland-Bräuer, Daniela Langfeldt, and Ruth A. Schmitz

4. Constructing and Screening a Metagenomic Library of a Cold and Alkaline Extreme Environment
Mikkel A. Glaring, Jan K. Vester, and Peter Stougaard

5. DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J. Colin Murrell, Josh D. Neufeld, and Marc G. Dumont

6. Assessing Bacterial and Fungal Diversity in the Plant’s Endosphere
Bernd Wemheuer and Franziska Wemheuer

7. Shotgun Metagenomic Sequencing analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities
James Doonan, Sandra Denman, James E. McDonald, and Peter M. Golyshin

8. Cloning and Expression of Metagenomic DNA in Streptomyces lividans and its Subsequent Fermentation for Optimized Production
Yuriy Rebets, Jan Kormanec, Andriy Lutzhetskyy, Kristel Bernaerts, and Jozef Anné

9. Degradation Network Reconstruction Guided by Metagenomic Data
Rafael Bargiela and Manuel Ferrer

10. Novel Tools for the Functional Expression of Metagenomics DNA
Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, and Karl-Erick Jaeger

11. A Microtiter Plate-Based Assay to Screen for Active and Stereoselective Hydrolytic Enzymes in Enzyme Libraries
Dominique Böttcher, Patrick Zägel, Marlen Schmidt, and Uwe T. Bornscheuer

12. Screening for Cellulase Encoding Clones in Metagenomics Libraries
Nele Ilmberger and Wolfgang R. Streit

13. Liquid Phase Multiplex High-Throughput Screening of Metagenomic Libraries using p-Nitrophenyl-Linked Substrates for Accessory Lignocellulosic Enzymes
Mariette Smart, Robert J. Huddy, Don A. Cowan, and Marla Trindade

14. Screening Glycosyltransferases for Polyphenol Modifications
Nele Ilmberger and Ulrich Rabausch

15. Methods for the Isolation of Genes Encoding Novel PHA Matabolism Enzymes from Complex Microbial Communities

Jiujun Cheng, Ricardo Nordeste, Maria A. Trainer, and Trevor C. Charles

16. Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity
Genis A. Castillo Villamizar, Heiko Nacke, and Rolf Daniel

17. Activity-Based Screening of Metagenomics Libraries for Hydrogenase Enzymes
Nicole Adam and Mirjam Perner

18. Screening for N-AHSL-Based-Signaling Interfering Enzymes
Stéphane Uroz and Phil M. Oger

19. Mining Microbial Signals for Enhanced Biodiscovery of Secondary Metabolites
F. Jerry Reen, Jose A. Gutiérrez-Barranquero, and Fergal O‘Gara

Blurb

This second edition explores up-to-date tools in various function-based technologies currently used in metagenomics. The chapters in this book discuss all of the working steps involved in these technologies, such as: DNA isolation from soils and marine samples followed by the construction and screening of libraries for diverse enzymes and biomolecules; current methods used to isolate DNA and construct large- and small-insert libraries from terrestrial and marine habitats; methods for establishing metagenome libraries in none-E.coli hosts; new molecular tools used for function-driven mining of metagenomic DNA; and screening protocols for a wide array of different genes encoding enzymes with relevance to biotechnology and ecology. Metagenomics: Methods and Protocols, Second Edition also provides detailed screening protocols for phosphatases, poly-hydroxyalkanoate, metabolism-related enzymes, stereoselective hydrolases, and microbial signals for the discovery of secondary metabolites. Written in the highly successful Methods in Molecular Biology series format, 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.

Comprehensive and cutting-edge, Metagenomics: Methods and Protocols, Second Edition is a collection of up-to-date metagenome protocols and tools for the recovery of numerous major types of biocatalysts, and allows researchers to easily setup these screens in any microbiology laboratory.