In situ identification of environmental microorganisms with Raman spectroscopy

Dongyu Cui; Lingchao Kong; Yi Wang; Yuanqing Zhu; Chuanlun Zhang

doi:10.1016/j.ese.2022.100187

In situ identification of environmental microorganisms with Raman spectroscopy

Environ Sci Ecotechnol. 2022 May 21:11:100187. doi: 10.1016/j.ese.2022.100187. eCollection 2022 Jul.

Authors

Dongyu Cui^{1

2}, Lingchao Kong³, Yi Wang^{1

2}, Yuanqing Zhu^{2

4}, Chuanlun Zhang^{1

2

5

4}

Affiliations

¹ Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
² Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
³ State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
⁴ Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China.
⁵ Shenzhen Key Laboratory of Marine Archaea Geo-Omics, University of Southern University of Science and Technology, Shenzhen, 518055, China.

Abstract

Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.

Keywords: Environmental microorganisms; Metabolic activities; Raman spectroscopy; Single cells.

Publication types

Review