Raman imaging in geomicrobiology: endolithic phototrophic microorganisms in gypsum from the extreme sun irradiation area in the Atacama Desert

Abstract

The Raman imaging method was successfully applied for mapping the distribution of biomolecules (e.g., pigments) associated with cryptoendolithic and hypoendolithic microorganisms, as well as the inorganic host mineral matrix that forms the habitat for the biota. To the best of our knowledge, this is the first comprehensive study in the field of geomicrobiology based on this technique. The studied microbial ecosystem was located nearly 3000 m above sea level within the driest desert on Earth, the Atacama in Chile. Enhancement of carotenoid Raman signal intensity close to the surface was registered at different areas of endolithic colonization dominated by algae, with cyanobacteria present as well. This is interpreted as an adaptation mechanism to the excessive solar irradiation. On the other hand, cyanobacteria synthesize scytonemin as a passive UV-screening pigment (found at both the hypoendolithic and cryptoendolithic positions). The distribution of the scytonemin Raman signal was mapped simultaneously with the surrounding mineral matrix. Thus, mapping was done of the phototrophic microorganisms in their original microhabitat together with the host rock environment. Important information which was resolved from the Raman imaging dataset of the host rock is about the hydration state of Ca-sulfate, demonstrated on the presence of gypsum (CaSO4·2H2O) and the absence of both anhydrite (CaSO4) and bassanite (CaSO4·1/2H2O). Obtaining combined "in situ" simultaneous information from the geological matrix (inorganic) together with the microbial biomolecules (organic) is discussed and concluded as an important advantage of this technique. We discuss how selection of the laser wavelength (785 and 514.5-nm) influences the Raman imaging results.

Fundamental drivers for endolithic microbial community assemblies in the hyperarid Atacama Desert

“…A). The colonization zone within gypsum was mostly cryptoendolithic, close to the compact gypsum surface layer, and two characteristic pigment layers, orange for carotenoids and green for chlorophylls, were organized with depth (Wierzchos et al ., ; Vítek et al ., ) (Fig. B, Table ).…”

“…For example, the presence of cracks and fractures and large pores in the gypsum allow water to penetrate easily in the substrate where it is further retained by sepiolite, a magnesium silicate clay with high efficiency for water absorption and retention (Caturla et al ., ). Indeed, the microarchitectural structure we observed in close proximity of the cells may act as a sponge, enhancing the moisture content within the gypsum rocks (Wierzchos et al ., ; Vítek et al ., ). In the calcite, a chasmoendolithic habitat, water penetrating cracks and fissures connected to the rock surface will infiltrate deeper within the rocks and be less susceptible to evaporation (DiRuggiero et al ., ).…”

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

“…The spectral region selected for the discussion of the Raman bands is the range 800–1632 cm −1 . The Raman fingerprint can be properly discussed on four divided sections: between 1600 and 1500 cm −1 , the C═C stretches region, between 1450 and 1250 cm −1 the CCH in‐plane deformation, the 1250–1150 cm −1 region corresponding to the C―C stretches, and between 700 and 1000 cm −1 the hydrogen out‐of‐plane deformation vibrations . The first section is dominated by the intense C═C (υ 1 ) stretching mode, at 1505 cm −1 , due to the carotenoid structure.…”

“…Moreover, its obliviousness to water, so intrinsic for biological samples, and its specificity in terms of molecular structure acquired information are the main characteristics considered when selecting this spectroscopic investigation method. Recently, several studies were focused on the Raman detection of biomarkers (especially pigments) that are produced by microbial communities found in extreme habitats and demonstrated the successful on‐site use of Raman spectroscopy for this purpose …”

Application of Raman spectroscopy to analyse lignin/cellulose ratio in Norway spruce tree rings

“…In contrast to infrared spectroscopy, which is limited to dry samples due to the strong infrared absorption of water, Raman scattering of water is weak, thus allowing for this technique to be applied to fresh plant material (Gierlinger and Schwanninger 2007). Raman micro-spectroscopy enables analysis of biological tissues from the leaf level Baranska 2007, Vítek et al 2017) down to the cellular or subcellular level (Kaczor and Pilarczyk 2014, Prats-Mateu et al 2014, Vítek et al 2016. It has been established as a non-invasive analytical tool for chemical and structural analyses of wood (Agarwal and Ralph 1997), including for imaging analysis of cell wall structure (Gierlinger and Schwanninger 2007, Gierlinger et al 2012, 2013.…”