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Hydrocarbon and Lipid Microbiology Protocols

Single-Cell and Single-Molecule Methods

  • Book
  • © 2016

Overview

Editors:
  1. Terry J. McGenity

    1. School of Biological Sciences, University of Essex, Colchester, UK

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  2. Kenneth N. Timmis

    1. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

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  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

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  • 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 book series: Springer Protocols Handbooks (SPH)

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Table of contents (15 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Introduction to Single-Cell and Single-Molecule Methods

    • Wei E. Huang
    Pages 1-3

  3. Single-Cell Cultivation in Microfluidic Devices

    • Sattar Taheri-Araghi, Suckjoon Jun
    Pages 5-16

  4. Single-Cell Bacterial Bioreporter Assays to Measure Hydrocarbons

    • Robin Tecon
    Pages 17-28

  5. Whole Genome Amplification of Single Bacterial Cells

    • Paul Scott, Alan W. Walker
    Pages 29-41

  6. Detection of Specific mRNA Molecules in Hydrocarbon-Degrading Bacteria

    • Juhyun Kim, Víctor de Lorenzo
    Pages 43-50

  7. Localization of Proteins Within Intact Bacterial Cells Using Fluorescent Protein Fusions

    • Veronica Wells Rowlett, William Margolin
    Pages 51-63

  8. Single Cell Microbial Ecophysiology with Raman-FISH

    • Daniel Read, Wei E. Huang, Andrew S. Whiteley
    Pages 65-76

  9. Single-Cell Metabolomics

    • Yun Wang, Yizhi Song, Ian P. Thompson, Jian Xu, Wei E. Huang
    Pages 77-90

  10. Marrying Single Molecules to Single Cells: Protocols for the Study of the Bacterial Proto-ring Components Essential for Division

    • A. Sánchez-Gorostiaga, A. I. Rico, P. Natale, M. Krupka, M. Vicente
    Pages 91-118

  11. Single-Cell Biotechnology for Uncultured Microorganisms

    • Peiran Zhang, Yizhi Song, Ian P. Thompson, Bo Ma, Jian Xu, Wei E. Huang
    Pages 119-131

  12. Single-Cell and Systems Biology Tools for Biofuel Production

    • Tingting Wang, Yuetong Ji, Yun Wang, Yuehui He, Jing Jia, Qiang Hu et al.
    Pages 133-144

  13. Detection of Protein-Synthesizing Microorganisms in the Environment via Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT)

    • Roland Hatzenpichler, Victoria J. Orphan
    Pages 145-157

  14. Flow Cytometric Determination of Microbial Abundances and Its Use to Obtain Indices of Community Structure and Relative Activity

    • Josep M. Gasol, Xosé Anxelu G. Morán
    Pages 159-187

  15. Protocols for Visualizing Horizontal Gene Transfer in Gram-Negative Bacteria Through Natural Competence

    • Melanie Blokesch
    Pages 189-204

  16. Correction to: Marrying Single Molecules to Single Cells: Protocols for the Study of the Bacterial Proto-ring Components Essential for Division

    • A. Sánchez-Gorostiaga, A. I. Rico, P. Natale, M. Krupka, M. Vicente
    Pages C1-C1
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Keywords

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.








Editors and Affiliations

  • School of Biological Sciences, University of Essex, Colchester, UK

    Terry J. McGenity

  • Institute of Microbiology, Technical University Braunschweig, 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: Single-Cell and Single-Molecule Methods

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

  • Series Title: Springer Protocols Handbooks

  • DOI: https://doi.org/10.1007/978-3-662-49131-7

  • Publisher: Springer Berlin, Heidelberg

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer-Verlag Berlin Heidelberg 2016

  • Hardcover ISBN: 978-3-662-49129-4Published: 22 April 2016

  • Softcover ISBN: 978-3-662-56982-5Published: 22 April 2018

  • eBook ISBN: 978-3-662-49131-7Published: 13 April 2016

  • 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

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