Raman imaging allows one to obtain spatially resolved chemical information in a nondestructive manner. Herein, we present analytical aspects of effective in situ and in vivo Raman imaging of algae and cyanobacteria from within their native rock habitats. Specifically, gypsum and halite inhabited by endolithic communities from the hyperarid Atacama Desert were analyzed. Raman imaging of these phototrophic colonization reveals a pigment composition within the aggregates that helps in understanding some of their adaptation strategies to survive in this harsh polyextreme environment. The study is focused on methodical aspects of Raman imaging acquisition and subsequent data processing. Point imaging is compared with line imaging in terms of their image quality, spatial resolution, spectral signal-to-noise ratio, time requirements, and risk of laser-induced sample alteration. The roles of excitation wavelength, exposure time, and step size of the imaging grid on successful Raman imaging results are also discussed. Graphical abstract.

• Klíčová slova
• Astrobiology, Bioimage, Geobiology, Image analysis, Raman mapping, Scytonemin,
• MeSH
• biologické pigmenty analýza   MeSH
• ekosystém MeSH
• pouštní klima MeSH
• půdní mikrobiologie * MeSH
• Ramanova spektroskopie * metody   MeSH
• sinice chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biologické pigmenty MeSH

The Black Sea is a permanently anoxic, marine basin serving as model system for the deposition of organic-rich sediments in a highly stratified ocean. In such systems, archaeal lipids are widely used as paleoceanographic and biogeochemical proxies; however, the diverse planktonic and benthic sources as well as their potentially distinct diagenetic fate may complicate their application. To track the flux of archaeal lipids and to constrain their sources and turnover, we quantitatively examined the distributions and stable carbon isotopic compositions (δ13 C) of intact polar lipids (IPLs) and core lipids (CLs) from the upper oxic water column into the underlying sediments, reaching deposits from the last glacial. The distribution of IPLs responded more sensitively to the geochemical zonation than the CLs, with the latter being governed by the deposition from the chemocline. The isotopic composition of archaeal lipids indicates CLs and IPLs in the deep anoxic water column have negligible influence on the sedimentary pool. Archaeol substitutes tetraether lipids as the most abundant IPL in the deep anoxic water column and the lacustrine methanic zone. Its elevated IPL/CL ratios and negative δ13 C values indicate active methane metabolism. Sedimentary CL- and IPL-crenarchaeol were exclusively derived from the water column, as indicated by non-variable δ13 C values that are identical to those in the chemocline and by the low BIT (branched isoprenoid tetraether index). By contrast, in situ production accounts on average for 22% of the sedimentary IPL-GDGT-0 (glycerol dibiphytanyl glycerol tetraether) based on isotopic mass balance using the fermentation product lactate as an endmember for the dissolved substrate pool. Despite the structural similarity, glycosidic crenarchaeol appears to be more recalcitrant in comparison to its non-cycloalkylated counterpart GDGT-0, as indicated by its consistently higher IPL/CL ratio in sediments. The higher TEX86 , CCaT, and GDGT-2/-3 values in glacial sediments could plausibly result from selective turnover of archaeal lipids and/or an archaeal ecology shift during the transition from the glacial lacustrine to the Holocene marine setting. Our in-depth molecular-isotopic examination of archaeal core and intact polar lipids provided new constraints on the sources and fate of archaeal lipids and their applicability in paleoceanographic and biogeochemical studies.

• Klíčová slova
• archaea, core lipids, intact polar lipids, lipid sources, lipid turnover, lipidomics, stable carbon isotope,
• MeSH
• Archaea * chemie   MeSH
• geologické sedimenty chemie   MeSH
• glycerol MeSH
• glycerylethery * MeSH
• lipidy chemie   MeSH
• mořská voda chemie   MeSH
• voda * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Černé moře MeSH
• Názvy látek
• crenarchaeol MeSH Prohlížeč
• glycerol MeSH
• glycerylethery * MeSH
• lipidy MeSH
• voda * MeSH

Coccolith dissolution together with post-mortem morphological features are immensely important phenomena that can affect assemblage compositions, complicate taxonomic identification as well as provide valuable palaeoenvironmental insights. This study summarizes the effects of pH oscillations on post-mortem coccolith morphologies and the abundances and compositions of calcareous nannoplankton assemblages in three distinct types of material-(i) Cretaceous chalk, (ii) Miocene marls, and (iii) late Holocene calcareous ooze. Two independent experimental runs within a semi-enclosed system setting were realized to observe assemblage alterations. One experiment was realized with the presence of bacteria and, in contrast, the second one inhibited their potential effect on the studied system. The pH was gradually decreased within the range of 8.3-6.4 using a reaction of CO2 with H2 O forming weak carbonic acid (H2 CO3 ), thereby affecting [ CO 3 2 - ]. Further, a subsequent overgrowth study was carried out during spontaneous degassing accompanied by a gradual pH rise. The experiment revealed that the process and intensity of coccolith corrosion and subsequent overgrowth build-ups are influenced by a plethora of different factors such as (i) pH and associated seawater chemistry, (ii) mineral composition of the sediment, (iii) the presence of coccoliths within a protective substrate (faecal pellets, pores, pits), and (iv) the presence/absence of bacteria. Nannoplankton assemblages with corroded coccoliths or with coccoliths with overgrowth build-ups showed that the observed relative abundances of taxa experienced alteration from the original compositions. Additionally, extreme pH oscillations may result in enhanced morphological changes that make coccoliths unidentifiable structures, and might even evoke the absence of coccoliths in the fossil record.

• Klíčová slova
• coccolith abundance, coccolith corrosion, coccolith overgrowths, dissolution-resistant taxa, pH fluctuations,
• MeSH
• Haptophyta * MeSH
• mořská voda chemie   MeSH
• rozpustnost MeSH
• uhličitan vápenatý * chemie   MeSH
• zkameněliny MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• uhličitan vápenatý * MeSH

We report the results of simple experiments which support the hypothesis that changes in ocean chemistry beginning in the Mesozoic Era resulted in an increase in the nutritional quality per mole of C and per cell of planktonic algal biomass compared to earlier phytoplankton. We cultured a cyanobacterium, a diatom, a dinoflagellate, and a green alga in media mimicking aspects of the chemistry of Palaeozoic and Mesozoic-Cenozoic oceans. Substantial differences emerged in the quality of algal biomass between the Palaeozoic and Mesozoic-Cenozoic growth regimes; these differences were strongly affected by interspecific interactions (i.e., the co-existence of different species alters responses to the chemistry of the medium). The change was in the direction of a Mesozoic-Cenozoic biomass enriched in protein per mole C, although cells contained less carbon overall. This would lead to a lower C:N ratio. On the assumption that Mesozoic-Cenozoic grazers' assimilation of total C was similar to that of their earlier counterparts, their diet would be stoichiometrically closer to their C:N requirement. This, along with an increase in mean cell size among continental shelf phytoplankton, could have helped to facilitate observed evolutionary changes in the Mesozoic marine fauna. In turn, increased grazing pressure would have operated as a selective force for the radiation of phytoplankton clades better equipped with antigrazing capabilities (sensu lato), as found widely in phytoplankton with biomineralization. Our results emphasize potential links between changing seawater chemistry, increased predation pressure and the rise to ecological dominance of chlorophyll a+c algae in Mesozoic oceans. The experiments also suggest a potential role for ocean chemistry in changes of marine trophic structure from the Palaeozoic to the later Mesozoic Era.

• Klíčová slova
• CO 2, FTIR, Mesozoic, Palaeozoic, biomass quality, interspecific communication, organic composition, phytoplankton evolution,
• MeSH
• biomasa * MeSH
• chlorofyl a metabolismus   MeSH
• chlorofyl metabolismus   MeSH
• fytoplankton metabolismus   MeSH
• oceány a moře MeSH
• spektroskopie infračervená s Fourierovou transformací MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Geografické názvy
• oceány a moře MeSH
• Názvy látek
• chlorofyl a MeSH
• chlorofyl MeSH
• chlorophyll c MeSH Prohlížeč

In this paper, it is demonstrated how Raman spectroscopy can be used to detect different carotenoids as possible biomarkers in various groups of microorganisms. The question which arose from previous studies concerns the level of unambiguity of discriminating carotenoids using common Raman microspectrometers. A series of laboratory-grown microorganisms of different taxonomic affiliation was investigated, such as halophilic heterotrophic bacteria, cyanobacteria, the anoxygenic phototrophs, the non-halophilic heterotrophs as well as eukaryotes (Ochrophyta, Rhodophyta and Chlorophyta). The data presented show that Raman spectroscopy is a suitable tool to assess the presence of carotenoids of these organisms in cultures. Comparison is made with the high-performance liquid chromatography approach of analysing pigments in extracts. Direct measurements on cultures provide fast and reliable identification of the pigments. Some of the carotenoids studied are proposed as tracers for halophiles, in contrast with others which can be considered as biomarkers of other genera. The limits of application of Raman spectroscopy are discussed for a few cases where the current Raman spectroscopic approach does not allow discriminating structurally very similar carotenoids. The database reported can be used for applications in geobiology and exobiology for the detection of pigment signals in natural settings.

• Klíčová slova
• Raman spectroscopy, algae, bacteria, cyanobacteria, detecting carotenoids, high-performance liquid chromatography,
• Publikační typ
• časopisecké články MeSH

The vaporization plane, a narrow zone of subsurface evaporation often present in porous rocks, separates the region where water flows due to capillary forces from the dry zone where moisture moves in gas phase only. The knowledge of its depth and geometry is critical for estimating water flux in rock-atmosphere interphase, for understanding moisture distribution and for localization of damaging salt crystallization. Yet, an easy-to-use method applicable in the exterior has been missing. This strongly limits interpretation of moisture-related measurements as moisture content differences in the above-mentioned zones are often immeasurable by currently used field techniques. We have introduced a new micro-destructive method to measure the vaporization plane depth using an instrument consisting of a rod, adhesive, and dye powder, reacting with moisture, that is inserted into porous materials in 2 mm diameter holes. We tested different rods, adhesives, and dyes, and the best combination of these has been used in >500 experiments to determine the vaporization plane depth in porous rocks and building materials. The knowledge of vaporization plane depth enables more reliably to interpret the moisture and suction data obtained from numerous existing techniques. This new uranine-probe method should be thus of interest to many scientific disciplines: evaporation, unsaturated hydrology, weathering, or geobiology.

• Klíčová slova
• Dry surface layer, Evaporation front, Fluorescein, Uranine, Vaporization plane, Weathering,
• Publikační typ
• časopisecké články MeSH

This study utilized X-ray micro-computed tomography (micro-CT) to investigate weathered gypsum rocks which can or do serve as a rock substrate for endolithic organisms, focusing on their internal pore-fracture microstructure, estimating porosity, and quantitative comparison between various samples. Examining sections and reconstructed 3D models provides a more detailed insight into the overall structural conditions within rock fragments and the interconnectivity in pore networks, surpassing the limitations of analyzing individual 2D images. Results revealed diverse gypsum forms, cavities, fractures, and secondary features influenced by weathering. Using deep learning segmentation based on the U-Net models within the Dragonfly software enabled to identify and visualize the porous systems and determinate void space which was used to calculate porosity. This approach allowed to describe what type of microstructures and cavities is responsible for the porous spaces in different gypsum samples. A set of quantitative analysis of the detected void and modeled networks provided a needed information about the development of the pore system, connectivity, and pore size distribution. Comparison with mercury intrusion porosimetry showed that both methods consider different populations of pores. In our case, micro-CT typically detects larger pores (> 10 μm) which is related to the effective resolution of the scanned images. Still, micro-CT demonstrated to be an efficient tool in examining the internal microstructures of weathered gypsum rocks, with promising implications particularly in geobiology and microbiology for the characterization of lithic habitats.

• Klíčová slova
• Deep learning, Gypsum, Micro-CT, Porosity, Segmentation, U-net, Weathering,
• Publikační typ
• časopisecké články MeSH

Organic minerals occur rather rarely in some types of peat bogs, sedimentary geological environments, and hydrothermal veins. Commonly, calcium oxalates are produced by several plants, terpenoids are often associated with conifers. Because of the organic precursor, these minerals, from the smallest group of the mineralogical system, are sometimes considered as biomarkers. Potential detection of these compounds has high relevance in the fields of exobiology or geobiology. Here we show the potential of four portable Raman spectrometers, using different excitation wavelengths and technologies (operating at 532, 785, and 1064nm together with an advanced spectrometer using the sequentially shifted excitation (SSE) technology), for the rapid and non-destructive identification of these phases. For the organic minerals investigated here, the most intense Raman bands are generally detected at the expected wavenumber positions ±1-4cm-1 in the region 100-2000cm-1 in the spectra obtained from all spectrometers. Additionally, two spectrometers (the 532nm instrument and the SSE) are capable of detecting Raman bands in the higher wavenumber shift region of 2000-3500cm-1, allowing the more detailed characterization and differentiation of the related phases. From this work, and on the basis of the experimental data obtained, it is clear that the longer laser excitation wavelengths are more preferable for organic minerals identification due to the better mitigation of fluorescence emission. In contrast, the Raman spectrometer equipped with the shortest excitation wavelength (532nm) gives a significantly higher spectral resolution and a more detailed discrimination of the Raman bands, provided that the conditions of general lower level of fluorescence emission are met. The results presented in the current study complement the knowledge on minerals and biomarkers of relevance for Martian environments which have been measured with mobile Raman spectrometers. The outcome creates a solid base towards the use of lightweight mobile Raman systems that can be used outdoors and on terrestrial outcrops. Moreover, these results and conclusions are of use for the further development of dedicated spectrometers destined for the instrumental suites on planetary rovers, in the frame of the forthcoming exobiology focused missions to Mars to be launched by NASA and ESA.

• Klíčová slova
• Dispersive 1064nm Raman spectrometer, Exobiology, Organic minerals, Portable Raman spectroscopy, Sequentially shifted excitation,
• Publikační typ
• časopisecké články MeSH

The development of miniaturized Raman instrumentation is in demand for applications relevant to forensic, pharmaceutical and art analyses, as well as geosciences, and planetary exploration. In this study we report on evaluation of a portable dispersive Raman spectrometer equipped with 1064 nm laser excitation. Selected samples from geological, geobiological and forensic areas of interest have been studied from which the advantages, disadvantages and the analytical potential of the instrument are assessed based on a comparison with bench instrumentation and other portable Raman spectrometers using 785 nm excitation. It is demonstrated that the instrument operating with 1064 nm excitation has potential for expanding the number and types of samples that can be measured by miniaturized Raman spectroscopy without interfering fluorescence background emission. It includes inorganic and organic minerals, biomolecules within living lichen and endolithic cyanobacteria as well as drugs of abuse and explosives.

• MeSH
• benzoáty analýza   MeSH
• benzofurany analýza   MeSH
• beta-karoten analýza   MeSH
• geologie metody   MeSH
• jantar analýza   MeSH
• minerály analýza   MeSH
• polystyreny analýza   MeSH
• Ramanova spektroskopie přístrojové vybavení   MeSH
• sloučeniny rtuti analýza   MeSH
• soudní vědy metody   MeSH
• šťavelan vápenatý analýza   MeSH
• výbušné látky analýza   MeSH
• zakázané drogy analýza   MeSH
• zkameněliny MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Názvy látek
• benzoáty MeSH
• benzofurany MeSH
• beta-karoten MeSH
• cinnabar MeSH Prohlížeč
• jantar MeSH
• mellitic acid MeSH Prohlížeč
• minerály MeSH
• polystyreny MeSH
• sloučeniny rtuti MeSH
• šťavelan vápenatý MeSH
• usnic acid MeSH Prohlížeč
• výbušné látky MeSH
• whewellite MeSH Prohlížeč
• zakázané drogy MeSH

This study is primarily focused on proving the potential of miniaturized Raman systems to detect any biomolecular and mineral signal in natural geobiological samples that are relevant for future application of the technique within astrobiologically aimed missions on Mars. A series of evaporites of varying composition and origin from two extremely dry deserts were studied, namely Atacama and Mojave. The samples represent both dry evaporitic deposits and recent evaporitic efflorescences from hypersaline brines. The samples comprise halite and different types of sulfates and carbonates. The samples were analysed in two different ways: (i) directly as untreated rocks and (ii) as homogenized powders. Two excitation wavelengths of miniaturized Raman spectrometers were compared: 532 and 785 nm. The potential to detect carotenoids as biomarkers on Mars compared with the potential detection of carbonaceous matter using miniaturized instrumentation is discussed.

• Klíčová slova
• algae, cyanobacteria, halophile, pigments, portable Raman, salt,
• Publikační typ
• časopisecké články MeSH