Biomarkers and their Raman spectroscopic signatures: a spectral challenge for analytical astrobiology

Evaluating Pigments as a Biosignature: Abiotic/Prebiotic Synthesis of Pigments and Pigment Mimics in Planetary Environments

Pigments serve a multitude of functions in biology including light harvesting for photosynthesis, radiation protection, membrane support, and defense. The ubiquity of pigments-especially within extremophiles found in high-radiation, high-salinity, and dry environments-and their detectability via mission-ready techniques have elevated these molecules as promising targets in the search for evidence of life elsewhere. Moreover, the detection of pigments has been proposed as a "smoking gun" for extraterrestrial life as it has been suggested that these molecules cannot be generated abiotically. However, while pigments may hold promise as a biosignature, current understanding of their possible prebiotic origins remains understudied and uncertain. Better understanding of the abiotic synthesis of pigments is critical for evaluating the biogenicity of any pigment detected during missions, including by the Mars Perseverance rover or from returned samples. Compounding this uncertainty is the broad definition of pigment as it includes any compound capable of absorbing visible light and by itself does not specify a particular chemical motif. While not experimentally verified, there are promising prebiotic routes for generating pigments including hemes, chlorophylls, and carotenoids. Herein, we review the biochemistry of pigments, the inherent assumptions made when searching for these molecules in the field, their abiotic synthesis in industry and prebiotic reactions, prebiotically relevant molecules that can mimic their spectral signatures, and implications/recommendations for future work.

Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition

In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.

Scytonin in gypsum endolithic colonisation: First Raman spectroscopic detection of a new spectral biosignature for terrestrial astrobiological analogues and for exobiological mission database extension

Microbial colonisations of gypsum from Eastern Poland (Badenian, Middle Miocene age) were investigated by Raman microspectrometry with a rarely used excitation 445 nm excitation. Zones of microbial colonisation in selenitic gypsum endolithic outcrops comprise algae and cyanobacteria, which commonly contain the photosynthetic and protective pigments carotenoids, scytonemin and gloeocapsin. Diagnostic bands differing from those of scytonemin have been identified in black colonies in gypsum outcrops at Chotel Czierwony (Poland). Raman spectral signatures of scytonin are reported here for the first time in two endolithic specimens identified by the band wavenumbers predicted from DFT calculations. The strong or medium strong intensity Raman bands observed at 1603, 1585, 1559, 1435, and 1424 cm^-1. Other weaker bands were located at 1676 (sh), 1660 (sh), 1649, 1399, 1362, 1342, 1320, 1294, 1272, 1259, and 1052 cm^-1. The first observation of the Raman spectrum of scytonin in the cyanobacterial colonisation of gypsum facilitates the inclusion of this new biomolecular signature in the library of unique Raman spectra of biological pigments invaluable for detection of traces of life in frame of the planetary missions.

Fast outdoor screening and discrimination of carotenoids of halophilic microorganisms using miniaturized Raman spectrometers

Eight miniaturized Raman spectrometers were used to perform a fast outdoor screening and discrimination of carotenoids of a series of halophilic and non-halophilic microorganisms on a set of eight lyophilized samples, each containing high concentrations of a specific dominant carotenoid pigment. Raman spectra were acquired using different excitations (532, 785, sequentially shifted excitation of 785 and 853, and 1064 nm), based on the model of each Raman spectrometer, in order to ascertain the feasibility of individual wavelengths. The wavenumber positions of diagnostic Raman bands of carotenoids were observed for the different carotenoid species. Characteristic carotenoid Raman bands of the pigment bacterioruberin were reported (using the 532 nm excitation) at 1504-1509 cm^-1, salinixanthin at 1510-1513 cm^-1, spirilloxanthin at 1509-1513 cm^-1, decaprenoxanthin at 1519 cm^-1, β-carotene at 1526 cm^-1, and sarcinaxanthin at 1526-1528 cm^-1. A 532 nm excitation consistently provided best results due to the significant resonance signal enhancement (both quantitative and qualitative carotenoid detection). Good results were also obtained using the sequentially shifted excitation combining two lasers in the near infrared spectral region, and similarly good results were acquired using a standard 1064 nm excitation. The least suitable was a 785 nm excitation, with the carotenoid Raman signal almost always weaker compared to major fluorescence signal arising from other types of pigments or biomolecules in the samples. A thorough light shielding was essential in order to acquire good quality data. This study shows that miniaturized Raman spectrometers, some even equipped with longer wavelength excitation, are able to detect different carotenoid pigments under non-laboratory conditions in a fast way, and discriminate between them, to a certain degree. The implications of this type of research are especially useful in astrobiology, where the searching, detection and discrimination of biomarkers such as carotenoids is receiving significant attention.

Raman spectroscopic peculiarities of Icelandic poorly crystalline minerals and their implications for Mars exploration

In this work, we have analyzed natural samples collected at three hydrothermal areas of Iceland by Raman spectroscopy. The studied high-latitude regions are considered environmentally and mineralogically appropriate Martian analogues since they are rich in weathered basalts that have been altered by hydrothermalism to mineral phases such as silica, clay minerals, sulfates, oxides, and sulfur. The main objective of this work was to assess the relation of the spectroscopic signatures of alteration to hydrothermal processes and biomediation, considering previous studies focused on the detection of lipid biomarkers in the same samples. The recorded Raman spectra, taken with optical parameters similar to the ExoMars 2022 Raman spectrometer, showed structural modifications in all secondary minerals in the form of peak shifts (in the case of sulfur and clay minerals), changes in the relative ratio intensity (in anatase) and/or shape broadening (in sulfates and hematite). These results reveal the suitability of Raman spectroscopy to examine areas rich in water-altered minerals, where a mixture of crystalline and amorphous phases can co-exist. The detection of silica is singularly interesting since, on the one hand, it can imply the past existence of hydrothermal hot springs rich in nutrient and redox gradients and, on the other hand, provides excellent matrix for biosignature preservation. The data can be helpful as an astrobiological database for the forthcoming missions to Mars, where potential upwelling groundwater systems could have altered the mineral phases in a similar way to that observed in this work.

Investigation of Raman Spectroscopic Signatures with Multivariate Statistics: An Approach for Cataloguing Microbial Biosignatures

Spectroscopic instruments are increasingly being implemented in the search for extraterrestrial life. However, microstructural spectral analyses of alien environments could prove difficult without knowledge on the molecular identification of individual spectral signatures. To bridge this gap, we introduce unsupervised K-means clustering as a statistical approach to discern spectral patterns of biosignatures without prior knowledge of spectral regions of biomolecules. Spectral profiles of bacterial isolates from analogous polar ice sheets were measured with Raman spectroscopy. Raman analysis identified carotenoid and violacein pigments, and key cellular features including saturated and unsaturated fats, triacylglycerols, and proteins. Principal component analysis and targeted spectra integration biplot analysis revealed that the clustering of bacterial isolates was attributed to spectral biosignatures influenced by carotenoid pigments and ratio of unsaturated/saturated fat peaks. Unsupervised K-means clustering highlighted the prevalence of the corresponding spectral peaks, while subsequent supervised permutational multivariate analysis of variance provided statistical validation for spectral differences associated with the identified cellular features. Establishing a validated catalog of spectral signatures of analogous biotic and abiotic materials, in combination with targeted supervised tools, could prove effective at identifying extant biosignatures.

Abiotic Formation of Calcium Oxalate under UV Irradiation and Implications for Biomarker Detection on Mars

A major objective in the exploration of Mars is to test the hypothesis that the planet has ever hosted life. Biogenic compounds, especially biominerals, are believed to serve as biomarkers in Raman-assisted remote sensing missions. However, the prerequisite for the development of these minerals as biomarkers is the uniqueness of their biogenesis. Herein, tetragonal bipyramidal weddellite, a type of calcium oxalate, is successfully achieved by UV-photolyzing pyruvic acid (PA). The as-prepared products are identified and characterized by micro-Raman spectroscopy and field emission scanning electron microscopy. Persistent mineralization of weddellite is observed with altering key experimental parameters, including pH, Ca²⁺ and PA concentrations. In particular, the initial concentration of PA can significantly influence the morphology of weddellite crystal. Oxalate acid is commonly of biological origin; thus calcium oxalate is considered to be a biomarker. However, our results reveal that calcium oxalate can be harvested by a UV photolysis pathway. Moreover, prebiotic sources of organics (e.g., PA, glycine, alanine, and aspartic acid) have been proven to be available through abiotic pathways. Therefore, our results may provide a new abiotic pathway of calcium oxalate formation. Considering that calcium oxalate minerals have been taken as biosignatures for the origin and early evolution of life on Earth and astrobiological investigations, its formation and accumulation by the photolysis of abiological organic compounds should be taken into account.

Spectroscopic characterization of samples from different environments in a Volcano-Glacial region in Iceland: Implications for in situ planetary exploration

Raman spectroscopy and laser induced breakdown spectroscopy (LIBS) are complementary techniques that together can provide a comprehensive characterization of geologic environments. For landed missions with constrained access to target materials on other planetary bodies, discerning signatures of life and habitability can be daunting, particularly where the preservation of organic compounds that contain the building blocks of life is limited. The main challenge facing any spectroscopy measurements of natural samples is the complicated spectra that often contain signatures for multiple components, particularly in rocks that are composed of several minerals with surfaces colonized by microbes. The goal of this study was to use the combination of Raman spectroscopy and LIBS to discern different environmental regimes based on the identification of minerals and biomolecules in rocks and sediments. Iceland is a terrestrial volcano-glacial location that offers a range of planetary analog environments, including volcanically active regions, extensive lava fields, geothermal springs, and large swaths of ice-covered terrain that are relevant to both rocky and icy planetary bodies. We combined portable VIS (532 nm) and NIR (785 nm) Raman spectroscopy, VIS micro-Raman spectroscopic mapping, and UV/VIS/NIR (200 - 1000 nm) and Mid-IR (5.6 - 10 μm, 1785 - 1000 cm^-1) laser induced breakdown spectroscopy (LIBS) to characterize the mineral assemblages, hydrated components, and biomolecules in rock and sediment samples collected from three main sites in the volcanically active Kverkfjöll-Vatnajökull region of Iceland: basalt and basalt-hosted carbonate rind from Hveragil geothermal stream, volcanic sediments from the base of Vatnajökull glacier at Kverkfjöll, and lava from the nearby Holuhraun lava field. With our combination of techniques, we were able to identify major mineral polytypes typical for each sample set, as well as a large diversity of biomolecules typical for lichen communities across all samples. The anatase we observed using micro-Raman spectroscopic mapping of the lava compared with the volcanic sediment suggested different formation pathways: lava anatase formed authigenically, sediment anatase could have formed in association with microbial weathering. Mn-oxide, only detected in the carbonate samples, seems to have two possible formation pathways, either by fluvial or microbial weathering or both. Even with our ability to detect a wide diversity of biomolecules and minerals in all of the samples, there was not enough variation between each set to distinguish different environments based on the limited measurements done for this study.

Validity and reliability of Raman spectroscopy for carotenoid assessment in cattle skin

Carotenoids are powerful antioxidants capable of helping to protect the skin from the damaging effects of exposure to sun by reducing the free radicals in skin produced by exposure to ultraviolet radiation, and they may also have a physical protective effect in human skin. Since carotenoids are lipophilic molecules which can be ingested with the diet, they can accumulate in significant quantities in the skin. Several studies on humans have been conducted to evaluate the protective function of carotenoids against various diseases, but there is very limited published information available to understand the mechanism of carotenoid bioavailability in animals. The current study was conducted to investigate the skin carotenoid level (SCL) in two cattle skin sets - weaners with an unknown feeding regime and New Generation Beef (NGB) cattle with monitored feed at three different ages. Rapid analytical and sensitive Raman spectroscopy has been shown to be of interest as a powerful technique for the detection of carotenoids in cattle skin due to the strong resonance enhancement with 532 nm laser excitation. The spectral difference of both types of skin were measured and quantified using univariate and linear discriminant analysis. SCL was higher in NGB cattle than weaners and there is a perfect classification accuracy between weaners and NGB cattle skin using carotenoid markers as a basis. Further work carried out on carotenoid rich NGB cattle skin of 8, 12 and 24 months of age identified an increasing trend in SCL with age. The present work validated the ability of Raman spectroscopy to determine the skin carotenoid level in cattle by comparing it with established HPLC methods. There is an excellent correlation of R2 = 0.96 between the two methods that could serve as a model for future application for larger population studies.

Detection of carbonate, phosphate minerals and cyanobacteria in rock from the Tomtor deposit, Russia, by Raman spectroscopy

Samples of rock from the Tomtor Nb - REE (rare-earth elements) deposit (Russia) have been investigated by Raman micro-spectroscopy using visible 532 nm wavelength excitation. Raman spectra of different samples of this rock confirm their composition as calcites and other carbonates such as rhodochrosite, and mixed solid solution phases (Ca, Mn, Fe, Mg, Ba, Sr, REE)(CO₃). An association between cyanobacteria and the apatite crystals has been noted Cyanobacteria exhibited Raman modes at 1520-1517 cm^-1 located in the double bonds of the central part of the polyene chain of carotenoids. A slight shift of this mode in the apatite-containing samples are dependent upon the compositions of carotenoids, the ratio of the rare earth elements adsorbed by cyanobacteria as well as their interaction with the environment. Laser-induced photoluminescence of REE and Mn⁺², obtained as an analytical artifact in the Raman spectra, has been observed in most cases with significant spectral intensity. The luminescence emission of Mn ²⁺, Sm³⁺, Eu ³⁺, Pr³⁺, Ho³⁺, Er ³⁺ in the spectra of the apatite-containing samples obtained with 532 nm excitation can be attributed both to apatite and to other mineral phases with a low concentration which contain these elemental ions. The results obtained in this study allowed us to confirm that the biogenic presence of the cyanobacterial mat had a significant impact on the formation of the unique Nb-REE Tomtor deposit.

Raman spectroscopic detection of carotenoids in cattle skin

Carotenoids, powerful anti-oxidants, play a significant role in protecting the skin from oxidation and help in balancing the redox status of skin. This study was aimed at investigating cattle skin to identify carotenoids in the lower epidermis (grain) and dermis (corium) layers for classification using Raman spectroscopy which is a powerful technique for the detection of carotenoids in cattle skin due to the strong resonance enhancement with 532 nm laser excitation. The spectral differences identified between these two layers were quantified by the univariate analysis of Raman peak heights and partial least squares (PLS) analysis. We compared the performance of the Raman spectroscopy method with the standard method, high performance liquid chromatography. The univariate analysis results demonstrated that the lower epidermis of the skin has a higher concentration of carotenoid than dermis using the carotenoid Raman peaks at 1151 cm⁻¹ and 1518 cm⁻¹. The carotenoid Raman intensity was linearly correlated with the total carotenoid concentration determined by standard HPLC methods. Partial Least Squares Regression analysis gives excellent results with R² = 0.99. Our results indicate that Raman spectroscopy is a potential tool to determine carotenoids in cattle skin with high precision.

The lower epidermis and dermis of cattle skin was investigated for the detection of carotenoids using Raman spectroscopy.

On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets

Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX) project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets.

Accurate Differentiation of Carotenoid Pigments Using Flight Representative Raman Spectrometers

Raman spectrometers will be utilized on two Mars rover missions, ExoMars and Mars 2020, in the near future, to search for evidence of life and habitable geological niches on Mars. Carotenoid pigments are recognized target biomarkers, and as they are highly active in Raman spectroscopy, they can be readily used to characterize the capabilities of space representative instrumentation. As part of the preparatory work being performed for the ExoMars mission, a gypsum crust colonized by microorganisms was interrogated with commercial portable Raman instruments and a flight representative Raman laser spectrometer. Four separate layers, each exhibiting different coloration resulting from specific halophilic microorganism activities within the gypsum crust, were studied by using two excitation wavelengths: 532 and 785 nm. Raman or fluorescence data were readily obtained during the present study. Gypsum, the main constituent of the crust, was detected with both excitation wavelengths, while the resonance Raman signal associated with carotenoid pigments was only detected with a 532 nm excitation wavelength. The fluorescence originating from bacteriochlorophyll a was found to overwhelm the Raman signal for the layer colonized by sulfur bacteria when interrogated with a 785 nm excitation wavelength. Finally, it was demonstrated that portable instruments and the prototype were capable of detecting a statistically significant difference in band positions of carotenoid signals between the sample layers. Key Words: Gypsum-Raman spectrometers-Carotenoids-ExoMars-Mars exploration-Band position shift. Astrobiology 17, 351-362.

Colonization of Snow by Microorganisms as Revealed Using Miniature Raman Spectrometers-Possibilities for Detecting Carotenoids of Psychrophiles on Mars?

We tested the potential of a miniaturized Raman spectrometer for use in field detection of snow algae pigments. A miniature Raman spectrometer, equipped with an excitation laser at 532 nm, allowed for the detection of carotenoids in cells of Chloromonas nivalis and Chlamydomonas nivalis at different stages of their life cycle. Astaxanthin, the major photoprotective pigment, was detected in algal blooms originating in snows at two alpine European sites that differed in altitude (Krkonoše Mts., Czech Republic, 1502 m a.s.l., and Ötztal Alps, Austria, 2790 m a.s.l.). Comparison is made with a common microalga exclusively producing astaxanthin (Haematococcus pluvialis). The handheld Raman spectrometer is a useful tool for fast and direct field estimations of the presence of carotenoids (mainly astaxanthin) within blooms of snow algae. Application of miniature Raman instruments as well as flight prototypes in areas where microbes are surviving under extreme conditions is an important stage in preparation for successful deployment of this kind of instrumentation in the framework of forthcoming astrobiological missions to Mars. Key Words: Snow algae-Chloromonas nivalis-Chlamydomonas nivalis-On-site field detection-Raman spectroscopy-Astaxanthin. Astrobiology 16, 913-924.

Raman Spectroscopic Techniques for Planetary Exploration: Detecting Microorganisms through Minerals

Raman spectroscopy can provide highly specific chemical fingerprints of inorganic and organic materials and is therefore expected to play a significant role in interplanetary missions, especially for the search for life elsewhere in our solar system. A major challenge will be the unambiguous detection of low levels of biomarkers on a mineral background. In addition, these biomarkers may not be present at the surface but rather inside or underneath minerals. Strong scattering may prevent focusing deeper into the sample. In this paper, we report the detection of carotenoid-containing microorganisms behind mineral layers using time-resolved Raman spectroscopy (TRRS). Two extremophiles, the bacterium Deinococcus radiodurans and the cyanobacterium Chroococcidiopsis, were detected through translucent and transparent minerals using 440 nm excitation under resonance conditions to selectively enhance the detection of carotenoids. Using 3 ps laser pulses and a 250 ps gated intensified CCD camera provided depth selectivity for the subsurface microorganisms over the mineral surface layer and in addition lowered the contribution of the fluorescent background. Raman spectra of both organisms could be detected through 5 mm of translucent calcite or 20 mm of transparent halite. Multilayered mineral samples were used to further test the applied method. A separate tunable laser setup for resonance Raman and a commercial confocal Raman microscope, both with continuous (non-gated) detection, were used for comparison. This study demonstrates the capabilities of TRRS for the depth-selective analysis through scattering samples, which could be used in future planetary exploration to detect microorganisms or biomarkers within or behind minerals.

Selection of Portable Spectrometers for Planetary Exploration: A Comparison of 532 nm and 785 nm Raman Spectroscopy of Reduced Carbon in Archean Cherts

Knowledge and understanding of the martian environment has advanced greatly over the past two decades, beginning with NASA's return to the surface of Mars with the Pathfinder mission and its rover Sojourner in 1997 and continuing today with data being returned by the Curiosity rover. Reduced carbon, however, is yet to be detected on the martian surface, despite its abundance in meteorites originating from the planet. If carbon is detected on Mars, it could be a remnant of extinct life, although an abiotic source is much more likely. If the latter is the case, environmental carbonaceous material would still provide a source of carbon that could be utilized by microbial life for biochemical synthesis and could therefore act as a marker for potential habitats, indicating regions that should be investigated further. For this reason, the detection and characterization of reduced or organic carbon is a top priority for both the ESA/Roscosmos ExoMars rover, currently due for launch in 2018, and for NASA's Mars 2020 mission. Here, we present a Raman spectroscopic study of Archean chert Mars analog samples from the Pilbara Craton, Western Australia. Raman spectra were acquired with a flight-representative 532 nm instrument and a 785 nm instrument with similar operating parameters. Reduced carbon was successfully detected with both instruments; however, its Raman bands were detected more readily with 785 nm excitation, and the corresponding spectra exhibited superior signal-to-noise ratios and reduced background levels.

Potential and limits of Raman spectroscopy for carotenoid detection in microorganisms: implications for astrobiology

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.