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Environmental Science and Pollution Research

, Volume 22, Issue 24, pp 19317–19325 | Cite as

Classification and identification of pigmented cocci bacteria relevant to the soil environment via Raman spectroscopy

  • Vinay Kumar
  • Bernd Kampe
  • Petra Rösch
  • Jürgen Popp
Alteration and element mobility at the microbe-mineral interface

Abstract

A soil habitat consists of a significant number of bacteria that cannot be cultivated by conventional means, thereby posing obvious difficulties in their classification and identification. This difficulty necessitates the need for advanced techniques wherein a well-compiled biomolecular database consisting of the already cultivable bacteria can be used as a reference in an attempt to link the noncultivable bacteria to their closest phylogenetic groups. Raman spectroscopy has been successfully applied to taxonomic studies of many systems like bacteria, fungi, and plants relying on spectral differences contributed by the variation in their overall biomolecular composition. However, these spectral differences can be obscured due to Raman signatures from photosensitive microbial pigments like carotenoids that show enormous variation in signal intensity hindering taxonomic investigations. In this study, we have applied laser-induced photobleaching to expel the carotenoid signatures from pigmented cocci bacteria. Using this method, we have investigated 12 species of pigmented bacteria abundant in soil habitats belonging to three genera mainly Micrococcus, Deinococcus, and Kocuria based on their Raman spectra with the assistance of a chemometric tool known as the radial kernel support vector machine (SVM). Our results demonstrate the potential of Raman spectroscopy as a minimally invasive taxonomic tool to identify pigmented cocci soil bacteria at a single-cell level.

Keywords

Raman spectroscopy Pigmented soil bacteria Carotenoids Photobleaching Bacterial identification and classification Radial kernel SVM 

Notes

Acknowledgments

This work is financially supported by the German Research Foundation (DFG) under the grant GRK 1257/2: “Alteration and element mobility at the microbe-mineral interface.”

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Vinay Kumar
    • 1
    • 3
  • Bernd Kampe
    • 1
    • 3
  • Petra Rösch
    • 1
    • 3
  • Jürgen Popp
    • 1
    • 2
    • 3
  1. 1.Institute of Physical Chemistry and Abbe Center of PhotonicsFriedrich Schiller University JenaJenaGermany
  2. 2.Leibniz Institute of Photonic TechnologyJenaGermany
  3. 3.InfectoGnostics, Forschungscampus JenaJenaGermany

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