Stable Isotope-Labeled Single-Cell Raman Spectroscopy Revealing Function and Activity of Environmental Microbes

  • Li CuiEmail author
  • Kai Yang
  • Yong-Guan Zhu
Part of the Methods in Molecular Biology book series (MIMB, volume 2046)


Microorganisms play a key role in driving the global element (C, N, H, P, and S) cycling. However, the function and activity of environmental microbes remain largely elusive because the vast majority of them are yet uncultured. Recent achievements in single cell stable isotope-labeled Raman spectroscopy enable direct investigation of function and activity of individual microbes in complex environmental communities. Here, this protocol describes a workflow to investigate environmental microbes in soil and water by combining 15N, 2D, and 13C stable isotope labeling with different single-cell Raman techniques, including normal Raman, resonance Raman (RR), and surface-enhanced Raman spectroscopy (SERS). Their applications in investigating functional bacteria driving the N and C cycles, and metabolically active cells are described.

Key words

Single-cell Raman spectroscopy Surface-enhanced Raman spectroscopy (SERS), 15N, 13C, 2D stable isotope probing Function Activity N2-fixing bacteria Metabolically active bacteria Microbial communities 



This work was supported by Natural Science Foundation of China (21777154 and 91851101), National Key Research and Development Program of China (2017YFD0200201), Strategic Priority Research Program of Chinese Academy of Sciences (XDB15020302, XDB15020402), and the K.C. Wong Education Foundation.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Key Lab of Urban Environment and HealthInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina

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