© 2016

Hydrocarbon and Lipid Microbiology Protocols

Ultrastructure and Imaging

  • Terry J. McGenity
  • Kenneth N. Timmis
  • Balbina Nogales
  • 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-x
  2. Manfred Auer
    Pages 1-3
  3. Gabriella Molinari
    Pages 49-69
  4. Alexis Canette, Priscilla Branchu, Régis Grimaud, Murielle Naïtali
    Pages 71-83
  5. Narin Chansawang, Boguslaw Obara, Richard J. Geider, Pierre Philippe Laissue
    Pages 145-161

About this book


This Volume presents key microscopy and imaging methods for revealing the structure and ultrastructure of environmental and experimental samples, of microbial communities and cultures, and of individual cells. Method adaptations that specifically address problems concerning the hydrophobic components of samples are highlighted and discussed. The methods described range from electron microscopy and light and fluorescence microscopy, to confocal laser-scanning microscopy, and include experimental set-ups for the analysis of interfacial processes like microbial growth and activities at hydrocarbon:water interfaces, biofilms and microbe:mineral interfaces. Three forms of fluorescence in situ hybridization - CARD-FISH, MAR-FISH and Two-pass TSA-FISH - are described for the ecophysiological analysis of functionally active microbes in samples. The methods presented will enable readers to obtain an ultrastructural picture of, and identify the key functional microbes in, samples under investigation. This in turn will constitute a key framework for the interpretation of information from other experimental approaches, such as physicochemical analyses and genomic investigations.

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.


Confocal microscopy Electron microscopy Fluorescence imaging Fluorescence in situ hybridization Microbial community analysis

Editors and affiliations

  • Terry J. McGenity
    • 1
  • Kenneth N. Timmis
    • 2
  • Balbina Nogales
    • 3
  1. 1.School of Biological SciencesUniversity of EssexColchesterUnited Kingdom
  2. 2.Institute of MicrobiologyTechnical University BraunschweigBraunschweigGermany
  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 Ultrastructure and Imaging
  • 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 2016
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-3-662-49132-4
  • Softcover ISBN 978-3-662-56983-2
  • eBook ISBN 978-3-662-49134-8
  • Series ISSN 1949-2448
  • Series E-ISSN 1949-2456
  • Edition Number 1
  • Number of Pages X, 174
  • 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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