© 2017

Hydrocarbon and Lipid Microbiology Protocols

Genetic, Genomic and System Analyses of Communities

  • Terry J. McGenity
  • Kenneth N. Timmis
  • Balbina Nogales
  • 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 Springer Protocols Handbooks book series (SPH)

Table of contents

  1. Front Matter
    Pages i-x
  2. Stepan V. Toshchakov, Ilya V. Kublanov, Enzo Messina, Michail M. Yakimov, Peter N. Golyshin
    Pages 5-27
  3. Stephanie M. Moormann, Jarrad T. Hampton-Marcell, Sarah M. Owens, Jack A. Gilbert
    Pages 29-49
  4. Jarrad T. Hampton-Marcell, Angel Frazier, Stephanie M. Moormann, Sarah M. Owens, Jack A. Gilbert
    Pages 51-67
  5. Danilo Pérez-Pantoja, Javier Tamames
    Pages 69-98
  6. Joseph A. Christie-Oleza, Despoina Sousoni, Jean Armengaud, Elizabeth M. Wellington, Alexandra M. E. Jones
    Pages 99-110
  7. Vincent Bonifay, Egemen Aydin, Deniz F. Aktas, Jan Sunner, Joseph M. Suflita
    Pages 111-161
  8. Carolina Grob, Martin Taubert, Alexandra M. Howat, Oliver J. Burns, Yin Chen, Josh D. Neufeld et al.
    Pages 163-180
  9. Mercedes V. Del Pozo, Mónica Martínez-Martínez, Manuel Ferrer
    Pages 215-231
  10. Wilfred F. M. Röling, Lucas Fillinger, Ulisses Nunes da Rocha
    Pages 233-246
  11. José P. Faria, Tahmineh Khazaei, Janaka N. Edirisinghe, Pamela Weisenhorn, Samuel M. D. Seaver, Neal Conrad et al.
    Pages 247-273

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.


Metatranscriptomics Metagenomic library generation Metaproteomic analyses Protein stable isotope probing (Protein-SIP) Hydrocarbon degraders

Editors and affiliations

  • Terry J. McGenity
    • 1
  • Kenneth N. Timmis
    • 2
  • Balbina Nogales
    • 3
  1. 1.Dept. Biological SciencesUniversity of Essex Dept. Biological SciencesColchesterUnited Kingdom
  2. 2.BraunschweigGermany
  3. 3.Department of BiologyUniversity of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC)Palma de MallorcaSpain

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
  • Series Abbreviated Title Springer Protocols Handbooks
  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2017
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-3-662-50449-9
  • Softcover ISBN 978-3-662-57062-3
  • eBook ISBN 978-3-662-50450-5
  • 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
  • Buy this book on publisher's site
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