Single Cell Microbial Ecophysiology with Raman-FISH

  • Daniel Read
  • Wei E. Huang
  • Andrew S. Whiteley
Part of the Springer Protocols Handbooks book series (SPH)


The ability to identify and characterise the roles that bacteria perform in their natural environment is a central prerequisite for understanding how ecosystems function. Traditional methods of culturing and identification are not always suitable due to the inability to grow most bacteria in pure cultures, the so-called great plate count anomaly. Recent developments in culture-independent molecular methods, coupled to microscopy-based ecophysiological analyses, are gaining increasing interest due to their ability to circumvent culture-based biases and allow physiological/phylogenetic analysis within ecological communities. Here we describe the application of Raman microspectroscopy and fluorescence in situ hybridisation (FISH) in combination with stable isotope labelling to help determine bacterial identity and function.


FISH Fluorescent in situ hybridisation Raman spectroscopy Stable isotope probing 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Daniel Read
    • 1
  • Wei E. Huang
    • 2
  • Andrew S. Whiteley
    • 3
  1. 1.Centre for Ecology & HydrologyWallingfordUK
  2. 2.Department of Engineering ScienceUniversity of OxfordOxfordUK
  3. 3.School of Earth and Environment, The University of Western AustraliaCrawleyAustralia

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