© 2016

Hydrocarbon and Lipid Microbiology Protocols

Statistics, Data Analysis, Bioinformatics and Modelling

  • Terry J. McGenity
  • Kenneth N. Timmis
  • Balbina Nogales Fernández


  • Offers readily reproducible, step-by-step laboratory methods

  • Provides helpful tips and tricks to complement the protocols

  • Includes troubleshooting advice

  • Features practical laboratory guidelines to promote successful results


Part of the Springer Protocols Handbooks book series (SPH)

Table of contents

  1. Front Matter
    Pages i-xii
  2. Zhanshan (Sam) Ma, Chengchen Zhang, Qingpeng Zhang, Jie Li, Lianwei Li, Linyi Qi et al.
    Pages 7-39
  3. Sean M. Gibbons
    Pages 41-57
  4. Luke K. Ursell, Adam Robbins-Pianka, Nicole Scott, Antonio Gonzalez, Dan Knights, Jai Ram Rideout et al.
    Pages 89-113
  5. Florencio Pazos, Víctor de Lorenzo
    Pages 115-124
  6. Florencio Pazos, David de Juan
    Pages 125-134
  7. Jeremy Meulemans, Tonya Ward, Dan Knights
    Pages 135-154

About this book


This Volume covers protocols for in-silico approaches to hydrocarbon microbiology, including the selection and use of appropriate statistical tools for experimental design replication, data analysis, and computer-assisted approaches to data storage, management and utilisation. The application of algorithms to analyse the composition and function of microbial communities is presented, as are prediction tools for biodegradation and protein interactions. The basics of a major open-source programming language, Python, are explained. Protocols for calculating reaction kinetics and thermodynamics are presented, and modelling the environmental fate of hydrocarbons during bioremediation is explained. With the exception of molecular biology studies of molecular interactions, the use of statistics is absolutely essential for both experimental design and data analysis in microbiological research, and indeed in the biomedical sciences in general. Moreover, studies of highly varying systems call for the modelling and/or application of theoretical frameworks. Thus, while two protocols in this Volume are specific to hydrocarbon microbiology, the others are generic, and as such will be of use to researchers investigating a broad range of topics in microbiology and the biomedical sciences in general.

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.


Biodegradation Hydrocarbon bioremediation Analysis of microbial communities Ecological network theory Python, open-source programming language Calculating reaction kinetics and thermodynamics

Editors and affiliations

  • Terry J. McGenity
    • 1
  • Kenneth N. Timmis
    • 2
  • Balbina Nogales Fernández
    • 3
  1. 1.Dept. Biological SciencesUniversity of Essex Dept. Biological SciencesColchesterUnited Kingdom
  2. 2.BraunschweigGermany
  3. 3.University of the Balearic Islands Palma de MallorcaSpain

Bibliographic information

  • Book Title Hydrocarbon and Lipid Microbiology Protocols
  • Book Subtitle Statistics, Data Analysis, Bioinformatics and Modelling
  • Editors Terry J. McGenity
    Kenneth N. Timmis
    Balbina Nogales Fernández
  • Series Title Springer Protocols Handbooks
  • Series Abbreviated Title Springer Protocols Handbooks
  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2016
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-3-662-49309-0
  • Softcover ISBN 978-3-662-57000-5
  • eBook ISBN 978-3-662-49310-6
  • Series ISSN 1949-2448
  • Series E-ISSN 1949-2456
  • Edition Number 1
  • Number of Pages XII, 180
  • Number of Illustrations 0 b/w illustrations, 0 illustrations in colour
  • Topics Microbiology
    Biochemical Engineering
  • Buy this book on publisher's site
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