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

  • Alteration and element mobility at the microbe-mineral interface
  • Published:
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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.

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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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Authors and Affiliations

  1. Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743, Jena, Germany

    Vinay Kumar, Bernd Kampe, Petra Rösch & Jürgen Popp

  2. Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745, Jena, Germany

    Jürgen Popp

  3. InfectoGnostics, Forschungscampus Jena, Philosophenweg 7, D-07743, Jena, Germany

    Vinay Kumar, Bernd Kampe, Petra Rösch & Jürgen Popp

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  1. Vinay Kumar
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  2. Bernd Kampe
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  3. Petra Rösch
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  4. Jürgen Popp
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Correspondence to Jürgen Popp.

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Responsible editor: Philippe Garrigues

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Kumar, V., Kampe, B., Rösch, P. et al. Classification and identification of pigmented cocci bacteria relevant to the soil environment via Raman spectroscopy. Environ Sci Pollut Res 22, 19317–19325 (2015). https://doi.org/10.1007/s11356-015-4593-5

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  • DOI: https://doi.org/10.1007/s11356-015-4593-5

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