Classification and identification of archaea using single-cell raman ejection and artificial intelligence: implications for investigating uncultivated microorganisms

Wang, Y., Xu, J. , Cui, D., Kong, L., Chen, S., Xie, W. and Zhang, C. (2021) Classification and identification of archaea using single-cell raman ejection and artificial intelligence: implications for investigating uncultivated microorganisms. Analytical Chemistry, 93(51), pp. 17012-17019. (doi: 10.1021/acs.analchem.1c03495) (PMID:34910467)

Abstract

Archaea can produce special cellular components such as polyhydroxyalkanoates, carotenoids, rhodopsin, and ether lipids, which have valuable applications in medicine and green energy production. Most of the archaeal species are uncultivated, posing challenges to investigating their biomarker components and biochemical properties. In this study, we applied Raman spectroscopy to examine the biological characteristics of nine archaeal isolates, including halophilic archaea (Haloferax larsenii, Haloarcula argentinensis, Haloferax mediterranei, Halomicrobium mukohataei, Halomicrobium salinus, Halorussus sp., Natrinema gari), thermophilic archaea (Sulfolobus acidocaldarius), and marine group I (MGI) archaea (Nitrosopumilus maritimus). Linear discriminant analysis of the Raman spectra allowed visualization of significant separations among the nine archaeal isolates. Machine-learning classification models based on support vector machine achieved accuracies of 88–100% when classifying the nine archaeal species. The predicted results were validated by DNA sequencing analysis of cells isolated from the mixture by Raman-activated cell sorting. Raman spectra of uncultured archaea (MGII) were also obtained based on Raman spectroscopy and fluorescence in situ hybridization. The results combining multiple Raman-based techniques indicated that MGII may have the ability to produce lipids distinct from other archaeal species. Our study provides a valuable approach for investigating and classifying archaea, especially uncultured species, at the single-cell level.

• Item Type: Articles
• Additional Information: This work was financially supported by the National Natural Science Foundation of China (91851210, 42141003), the State Key R&D project of China grant (No. 2018YFA0605800), the Stable Support Plan Program of Shenzhen Natural Science Fund (20200925173954005), the Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology (ZDSYS201802081843490), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (No. K19313901), and the financial support from China Postdoctoral Science Foundation (2020M682769).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Xu, Dr Jiabao
• Authors: Wang, Y., Xu, J., Cui, D., Kong, L., Chen, S., Xie, W., and Zhang, C.
• College/School: College of Science and Engineering > School of Engineering > Biomedical Engineering
• Journal Name: Analytical Chemistry
• Publisher: American Chemical Society
• ISSN: 0003-2700
• ISSN (Online): 1520-6882
• Published Online: 15 December 2021