© 2016

Hydrocarbon and Lipid Microbiology Protocols

Single-Cell and Single-Molecule Methods

  • 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. Sattar Taheri-Araghi, Suckjoon Jun
    Pages 5-16
  3. Paul Scott, Alan W. Walker
    Pages 29-41
  4. Daniel Read, Wei E. Huang, Andrew S. Whiteley
    Pages 65-76
  5. Yun Wang, Yizhi Song, Ian P. Thompson, Jian Xu, Wei E. Huang
    Pages 77-90
  6. Peiran Zhang, Yizhi Song, Ian P. Thompson, Bo Ma, Jian Xu, Wei E. Huang
    Pages 119-131
  7. Tingting Wang, Yuetong Ji, Yun Wang, Yuehui He, Jing Jia, Qiang Hu et al.
    Pages 133-144

About this book


This Volume presents relevant single-cell and single-molecule approaches in the study of microbes producing and utilizing hydrocarbons and lipids. While generically applicable for all microorganisms, the approaches described are, wherever possible, adapted to the field of study of hydrocarbon and lipid microbiology. The methods include basic procedures for isolating single cells by means of microfluidics and flow cytometry, and their cultivation in arrays as pure clones; for isolating, amplifying and sequencing single-cell genomes and transcriptomes; and for analysing single-cell metabolomes by means of Raman spectroscopy. Single-molecule approaches include the use of protein:fluorescent dye fusions for protein localization and methods for the production of cell division protostructures and lipid monolayers. Methods for the functional analysis of single cells include detection of metabolically active (protein-synthesizing) cells in environmental samples by bioorthogonal non-canonical amino acid tagging, Raman spectroscopy combined with stable isotope labelling and fluorescent in situ hybridisation, and visualization of single cells participating in gene transfer activity. Lastly, protocols are presented for single-cell biotechnological applications, including biofuel production.

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.


Bioreporters Functional flow cytometry Metabolomics Protein localisation with GFP fusions Proteomics Single-cell genomics Single-molecule science

Editors and affiliations

  • Terry J. McGenity
    • 1
  • Kenneth N. Timmis
    • 2
  • Balbina Nogales
    • 3
  1. 1.School of Biological SciencesUniversity of EssexColchesterUK
  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 Single-Cell and Single-Molecule Methods
  • Editors Terry J. McGenity
    Kenneth N. Timmis
    Balbina Nogales
  • Series Title Springer Protocols Handbooks
  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2016
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-3-662-49129-4
  • Softcover ISBN 978-3-662-56982-5
  • eBook ISBN 978-3-662-49131-7
  • Series ISSN 1949-2448
  • Series E-ISSN 1949-2456
  • Edition Number 1
  • Number of Pages X, 204
  • Number of Illustrations 20 b/w illustrations, 20 illustrations in colour
  • Topics Microbiology
    Biochemical Engineering
  • Buy this book on publisher's site
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