Skip to main content
SpringerLink
Log in
Book cover

Hydrocarbon and Lipid Microbiology Protocols

Genetic, Genomic and System Analyses of Communities

  • Book
  • © 2017

Overview

Editors:
  1. Terry J. McGenity

    1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, United Kingdom

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Kenneth N. Timmis

    1. Braunschweig, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  3. Balbina Nogales

    1. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Offers readily-reproducible step-by-step laboratory methods
  • Provides helpful tips and tricks supporting the protocols
  • Includes troubleshooting advice
  • Contains practical laboratory guidance to promote successful results

Part of the book series: Springer Protocols Handbooks (SPH)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (14 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Introduction to Genetic, Genomic, and System Analyses for Communities

    • Jack A. Gilbert, Nicole M. Scott
    Pages 1-4

  3. Genomic Analysis of Pure Cultures and Communities

    • Stepan V. Toshchakov, Ilya V. Kublanov, Enzo Messina, Michail M. Yakimov, Peter N. Golyshin
    Pages 5-27

  4. Protocols for Metagenomic Library Generation and Analysis in Petroleum Hydrocarbon Microbe Systems

    • Stephanie M. Moormann, Jarrad T. Hampton-Marcell, Sarah M. Owens, Jack A. Gilbert
    Pages 29-49

  5. Preparation and Analysis of Metatranscriptomic Libraries in Petroleum Hydrocarbon Microbe Systems

    • Jarrad T. Hampton-Marcell, Angel Frazier, Stephanie M. Moormann, Sarah M. Owens, Jack A. Gilbert
    Pages 51-67

  6. Prokaryotic Metatranscriptomics

    • Danilo Pérez-Pantoja, Javier Tamames
    Pages 69-98

  7. Defining a Pipeline for Metaproteomic Analyses

    • Joseph A. Christie-Oleza, Despoina Sousoni, Jean Armengaud, Elizabeth M. Wellington, Alexandra M. E. Jones
    Pages 99-110

  8. Metabolic Profiling and Metabolomic Procedures for Investigating the Biodegradation of Hydrocarbons

    • Vincent Bonifay, Egemen Aydin, Deniz F. Aktas, Jan Sunner, Joseph M. Suflita
    Pages 111-161

  9. Generating Enriched Metagenomes from Active Microorganisms with DNA Stable Isotope Probing

    • Carolina Grob, Martin Taubert, Alexandra M. Howat, Oliver J. Burns, Yin Chen, Josh D. Neufeld et al.
    Pages 163-180

  10. DNA- and RNA-Based Stable Isotope Probing of Hydrocarbon Degraders

    • Tillmann Lueders
    Pages 181-197

  11. Protocol for Performing Protein Stable Isotope Probing (Protein-SIP) Experiments

    • Nico Jehmlich, Martin von Bergen
    Pages 199-214

  12. Protein Extraction from Contaminated Soils and Sediments

    • Mercedes V. Del Pozo, Mónica Martínez-Martínez, Manuel Ferrer
    Pages 215-231

  13. Analysis of the Regulation of the Rate of Hydrocarbon and Nutrient Flow Through Microbial Communities

    • Wilfred F. M. Röling, Lucas Fillinger, Ulisses Nunes da Rocha
    Pages 233-246

  14. Constructing and Analyzing Metabolic Flux Models of Microbial Communities

    • José P. Faria, Tahmineh Khazaei, Janaka N. Edirisinghe, Pamela Weisenhorn, Samuel M. D. Seaver, Neal Conrad et al.
    Pages 247-273

  15. Protocol for Evaluating the Permissiveness of Bacterial Communities Toward Conjugal Plasmids by Quantification and Isolation of Transconjugants

    • Uli Klümper, Arnaud Dechesne, Barth F. Smets
    Pages 275-288
Back to top

Keywords

About this book

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 Protocols
There 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.





Editors and Affiliations

  • Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, United Kingdom

    Terry J. McGenity

  • Braunschweig, Germany

    Kenneth N. Timmis

  • Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

Bibliographic Information

  • Book Title: Hydrocarbon and Lipid Microbiology Protocols

  • Book Subtitle: Genetic, Genomic and System Analyses of Communities

  • Editors: Terry J. McGenity, Kenneth N. Timmis, Balbina Nogales

  • Series Title: Springer Protocols Handbooks

  • DOI: https://doi.org/10.1007/978-3-662-50450-5

  • Publisher: Springer Berlin, Heidelberg

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer-Verlag Berlin Heidelberg 2017

  • Hardcover ISBN: 978-3-662-50449-9Published: 06 January 2017

  • Softcover ISBN: 978-3-662-57062-3Published: 30 April 2018

  • eBook ISBN: 978-3-662-50450-5Published: 26 December 2016

  • Series ISSN: 1949-2448

  • Series E-ISSN: 1949-2456

  • Edition Number: 1

  • Number of Pages: X, 288

  • Number of Illustrations: 20 b/w illustrations, 30 illustrations in colour

  • Topics: Microbiology, Biochemical Engineering

Publish with us

Policies and ethics

Back to top

Search

Navigation