Hydrocarbon and Lipid Microbiology Protocols Genetic Genomic and System Analyses of Communities 1st Edition by Terry J Mcgenity, Kenneth N Timmis, Balbina Nogales ISBN 3662570629 978-3662570623

Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System Analyses of Communities 1st Edition by Terry J. Mcgenity, Kenneth N. Timmis, Balbina Nogales – Ebook PDF Instant Download/Delivery: 3662570629, 978-3662570623

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ISBN 10: 3662570629 

ISBN 13: 978-3662570623

Author: Terry J. Mcgenity, Kenneth N. Timmis, Balbina Nogales

 This Volume presents protocols for investigating the genetic, metabolic and ecological potential and functional analysis of microbial communities. Methods are described for the creation and bioinformatic assessment of metagenomic and metatranscriptomic libraries, and for metaproteomic analyses, which provide important insights into the metabolic potential and interactions of community members. These in turn lead to specific hypotheses concerning the functional contributions of individual populations in the community, which may be investigated by the stable isotope probing approaches described in this Volume, making it possible to identify those community members primarily responsible for particular functions. Methods for the direct extraction of proteins from environmental samples for sequencing and activity tests are presented, providing a broad overview of prevailing metabolic activities and of the types of microbe involved in them. Protocols for the analysis of nutrient flow through microbial communities and for the modelling of dynamic physiological interactions in communities are also provided. Lastly, the book presents a protocol for the quantitative assessment of permissiveness for the transfer of conjugative plasmids, important agents of physiological change and evolution in microbial communities.
Hydrocarbon and Lipid Microbiology ProtocolsThere are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.

Table of contents: 

1. Introduction to Genetic, Genomic and System Analyses of Pure Cultures

2. Broadening the SEVA Plasmid Repertoire to Facilitate Genomic Editing of Gram-Negative Bacteria

3. Protocols on Regulation of Gene Expression

4. Genetic, Genomic, and System Analyses for Pure Cultures and Communities: Protocol – Ultra-High-Throughput Transposon Scanning of Bacterial Genomes

5. Knock-In-Leave-Behind (KILB): Genetic Grafting of Protease-Cleaving Sequences into Permissive Sites of Proteins with a Tn5-Based Transposition System

6. Deep Sequencing to Study Microbial Transcriptomic Responses to Hydrocarbon Degradation/Production/Stress

7. Shotgun Proteomics for Hydrocarbon Microbiology

8. Interatomic Characterization of Protein–Protein Interactions in Membrane-Associated Mega-complexes

9. Lipidomic Analysis of Bacteria by Thin-Layer Chromatography and Liquid Chromatography/Mass Spectrometry

10. Accurate Microbial Genome Annotation Using an Integrated and User-Friendly Environment for Community Expertise of Gene Functions: The MicroScope Platform

11. Approaches for Displaying Complete Transcriptomes of Environmental Bacteria

12. A Practical Protocol for Genome-Scale Metabolic Reconstructions

13. GC-MS-Based Determination of Mass Isotopomer Distributions for 13C-Based Metabolic Flux Analysis

14. Analysis of the Hierarchical and Metabolic Regulation of Flux Through Metabolic Pathways

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Tags: Terry J Mcgenity, Kenneth N Timmis, Balbina Nogales, Hydrocarbon, Lipid Microbiology Protocols, Genetic, Genomic, System Analyses