Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis

Abstract

In this study, we aimed at developing a rapid and non‐destructive method to predict the genus‐level taxonomic affiliation of phenotypically similar halophilic archaea of Halobacteria Class. For this purpose, representatives of three widespread and frequently isolated haloarchaeal genera (Halobacterium sp., Haloferax sp. and Halorubrum sp.) were investigated by means of Raman spectroscopy. The most relevant Raman bands exhibited at 1505, 1150 and 1000 cm−1, respectively, were ascribed to the bacterioruberin carotenoid found in haloarchaea. Due to the similar spectral profiles, a robust chemometric approach based on fuzzy principal component analysis and linear discriminant analysis for the classification of the three halophilic strains was employed, and the high‐accuracy grouping of spectral data corresponding to those strains was achieved. Copyright © 2017 John Wiley & Sons, Ltd.

Haloterrigena sp. Strain SGH1, a Bacterioruberin-Rich, Perchlorate-Tolerant Halophilic Archaeon Isolated From Halite Microbial Communities, Atacama Desert, Chile

“…C-50 carotenoid identification from strain Haloterrigena sp. SGH1 was conducted by data analyses of Raman spectroscopy, chromatographic migrations, UV-Vis spectra, spectral fine structure and MS fragmentation patterns (Fong et al, 2001;Mandelli et al, 2012;Jehlička et al, 2014;De la Vega et al, 2016;Dina et al, 2017).…”

Recent advances in linear and nonlinear Raman spectroscopy. Part XII

“…They aimed at developing a rapid and nondestructive method to predict the genus‐level taxonomic affiliation of phenotypically similar halophilic Archaea of Halobacteria class. A robust chemometric approach based on fuzzy Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) for the classification of the three halophilic strains was employed, and a high‐accuracy grouping of spectral data, corresponding to those strains, was achieved . Lee et al performed SERS analysis of selectively captured exosomes using an integrin‐specific peptide ligand.…”

“…A robust chemometric approach based on fuzzy Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) for the classification of the three halophilic strains was employed, and a high-accuracy grouping of spectral data, corresponding to those strains, was achieved. [54] Lee et al performed SERS analysis of selectively captured exosomes using an integrin-specific peptide ligand. Their study shows the potential of developing a target-specific SERS detection approach for characterizing exosomes from a heterogeneous mixture in body fluid for early-stage disease diagnostics.…”

Small Sample Stress: Probing Oxygen-Deprived Ammonia-Oxidizing Bacteria with Raman Spectroscopy In Vivo

“…In contrast, confocal Raman microscopy is a powerful tool for the analysis of microbial cells and communities in vivo and in situ, even providing optical access to the proteome [24][25][26]. In combination with multivariate data analysis [27][28][29], it has proven suitable for the in vivo discrimination of microbial species at the cell level. For example, Maquelin et al used confocal Raman microscopy with 830 nm excitation to discriminate several strains of Acinetobacter in dried samples [30], while Dina et al used confocal Raman microscopy with 785 nm excitation and fuzzy principal component analysis to discriminate three halo-archaeal genera in vivo [29].…”

“…In combination with multivariate data analysis [27][28][29], it has proven suitable for the in vivo discrimination of microbial species at the cell level. For example, Maquelin et al used confocal Raman microscopy with 830 nm excitation to discriminate several strains of Acinetobacter in dried samples [30], while Dina et al used confocal Raman microscopy with 785 nm excitation and fuzzy principal component analysis to discriminate three halo-archaeal genera in vivo [29]. Incidentally, we used confocal Raman microscopy with cytochrome-c-resonant excitation at 532 nm and hierarchical cluster analysis for the in vivo discrimination and identification of several species of purple non-sulfur bacteria and AOB in planktonic cultures, as well as associated in microbial wastewater biofilms [28,31,32].…”