Metagenomics

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.

Construction of Small-Insert and Large-Insert Metagenomic Libraries.- Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.- Construction and Screening Marine Metagenomic Large Insert Libraries.- Constructing and Screening a Metagenomic Library of a Cold and Alkaline Extreme Environment.- DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.- Assessing Bacterial and Fungal Diversity in the Plant's Endosphere.- Shotgun Metagenomic Sequencing analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities.- Cloning and Expression of Metagenomic DNA in Streptomyces lividans and its Subsequent Fermentation for Optimized Production.- Degradation Network Reconstruction Guided by Metagenomic Data.- Novel Tools for the Functional Expression of Metagenomics DNA.- A Microtiter Plate-Based Assay to Screen for Active and Stereoselective Hydrolytic Enzymes in Enzyme Libraries.- Screening for Cellulase Encoding Clones in Metagenomics Libraries.- Liquid Phase Multiplex High-Throughput Screening of Metagenomic Libraries using p-Nitrophenyl-Linked Substrates for Accessory Lignocellulosic Enzymes.- Screening Glycosyltransferases for Polyphenol Modifications.- Methods for the Isolation of Genes Encoding Novel PHA Matabolism Enzymes from Complex Microbial Communities.- Function-Based Metagenomic Library Screening and Heterologous Expression Strategy for Genes Encoding Phosphatase Activity.- Activity-Based Screening of Metagenomics Libraries for Hydrogenase Enzymes.- Screening for N-AHSL-Based-Signaling Interfering Enzymes.- Mining Microbial Signals for Enhanced Biodiscovery of Secondary Metabolites.