The potential of Raman spectroscopy for the analysis of diagenetically transformed carotenoids

Searching for Life in Hot Spring Carbonate Systems: Investigating Raman Spectra of Carotenoid-Bearing Organic Carbonaceous Inclusions from Travertines of Italy

Carotenoid pigments provide some of the most common exclusively biogenic markers on Earth, and these organic pigments may be present in extraterrestrial life. Raman spectroscopy can be used to identify carotenoids quickly and accurately through the inelastic scattering of laser light. In this study, we show that Raman spectra of organic matter found in hot spring bacterial assemblages exhibit "spectral overprinting" of the carotenoid spectrum by the carbon spectrum as the organic matter progressively breaks down. Here, we present how, with increasing thermal maturity, the relative intensity of the carotenoid spectrum increases, and as maturity increases a low-intensity carbon spectrum forms in the same region as the carotenoid spectrum. This carbon spectrum increases in intensity as the thermal maturity increases further, progressively obscuring the carotenoid spectrum until only the carbon spectrum can be observed. This means key carotenoid biogenic signatures in hot spring deposits may be hidden within carbon spectra. A detailed study of the transition from carotenoid to carbon, Raman spectra may help develop deconvolution processes that assist in positively identifying biogenic carbon over abiogenic carbon. Our results are relevant for the data analysis from the Raman spectroscopy instruments on the Perseverance (National Aeronautics and Space Administration [NASA]) and Rosalind Franklin (European Space Agency [ESA]) rovers.

Production of partially hydrogenated soybean oil with low trans-fatty acids using surface dielectric barrier discharge cold plasma

This study examined the feasibility of applying surface dielectric barrier discharge cold plasma (SDBDCP) to partially hydrogenate crude soybean oil. The oil sample was treated for 13 h using SDBDCP at 15 kV with 100% hydrogen gas under room temperature and atmospheric pressure. Fatty acid composition, iodine value, refractive index, carotenoid content, melting point, peroxide value, and free fatty acids content (FFA) were investigated during SDBDCP treatment. Analysis of fatty acid composition demonstrated an increase in the content of saturated and monounsaturated fatty acids (from 41.32% to 55.3%) and a decrease in the content of polyunsaturated fatty acids (from 58.62% to 40.98%), which resulted in a reduction of the iodine value to 98.49 over the treatment time. Also, the fatty acid profile indicated that the total detected level of trans-fatty acids was very low (0.79%). After a 13-h treatment, the samples showed a refractive index of 1.4637, melting point of 10°C, peroxide value of 4.1 meq/kg, and FFA content of 0.8%. In addition, the results revealed a 71% decline in the carotenoid content of the oil sample due to the saturation of their double bonds. Therefore, these findings suggest that SDBDCP can be effectively used for hydrogenation along with bleaching oil.

Raman imaging monitors the time-resolved response of A. thaliana to the artificial inhibition of PSII

The short-term (0-96 h) response of A. thaliana to the oxidative stress induced by PSII inhibitor metribuzin was examined using Raman spectroscopy. Whole leaves of wildtype (WT, Col-0) and ros1 mutant were scanned and changes in carotenoids were examined. Strong differences in Raman intensity distributions between WT and ros1 were observed. A stronger decrease of carotenoid v₁(C=C) band intensity across the leaf was observed in ros1 after 48 h of exposure to metribuzin. It can be assumed that higher sensitivity to oxidative stress in ros1 mutant results in significantly faster degradation of carotenoids.

A massive bloom of Karenia species (Dinophyceae) off the Kamchatka coast, Russia, in the fall of 2020

In the fall of 2020, a long-lasting and massive harmful algal bloom (HAB) with extensive fields of yellow sea foam was observed in relatively cold waters (7-13 °C) off the coasts of the Kamchatka Peninsula, Russia. According to the estimates based on bio-optical parameters in satellite imagery, the Kamchatka bloom 2020 lasted for two months and covered a vast area of more than 300 × 100 km. An abundance of dead fish and invertebrates, including sea urchins, sea anemones, chitons, cephalopods, bivalves were found on shore during the bloom. Animals suffered almost 100% mortality within a depth range between 5 and 20 m. To identify the causative microalgal species, light and scanning electron microscopy, Raman spectroscopy, and molecular phylogenetic approaches were used. The HAB area was estimated by the spectral analysis of satellite-derived imagery. The causative organisms were unarmored dinoflagellates of Karenia species. Their density and biomass reached 100-620 cells·mL^-1 and 1300-7700 mg·m^-3, respectively, which accounted for 31-99% of the total cell density and 82-99% of the total phytoplankton biomass in late September to mid-October. The dominant species was Karenia selliformis, and the other co-occurring kareniacean species were K. cf. cristata, K. mikimotoi, K. papilionacea, K. longicanalis, and two unidentified morphotypes of Karenia spp. The molecular phylogeny inferred from LSU rDNA and ITS region showed that K. selliformis from Kamchatka in 2020 belonged to the cold-water group I and was identical to K. selliformis strains from Hokkaido, Japan, identified in 2021. This is the first HAB event caused by K. selliformis recorded from Russian coastal waters.

Correlation Study between the Organic Compounds and Ripening Stages of Oil Palm Fruitlets Based on the Raman Spectra

The degree of maturity of oil palm fresh fruit bunches (FFB) at the time of harvest heavily affects oil production, which is expressed in the oil extraction rate (OER). Oil palm harvests must be harvested at their optimum maturity to maximize oil yield if a rapid, non-intrusive, and accurate method is available to determine their level of maturity. This study demonstrates the potential of implementing Raman spectroscopy for determining the maturity of oil palm fruitlets. A ripeness classification algorithm has been developed utilizing machine learning by classifying the components of organic compounds such as β-carotene, amino acid, etc. as parameters to distinguish the ripeness of fruits. In this study, 47 oil palm fruitlets spectra from three different ripeness levels-under ripe, ripe, and over ripe-were examined. To classify the oil palm fruitlets into three maturity categories, the extracted features were put to the test using 31 machine learning models. It was discovered that the Medium, Weighted KNN, and Trilayered Neural Network classifier has a maximum overall accuracy of 90.9% by using four significant features extracted from the peaks as the predictors. To conclude, the Raman spectroscopy method may offer a precise and efficient means to evaluate the maturity level of oil palm fruitlets.

Classification of oil palm fresh fruit maturity based on carotene content from Raman spectra

The oil yield, measured in oil extraction rate per hectare in the palm oil industry, is directly affected by the ripening levels of the oil palm fresh fruit bunches at the point of harvesting. A rapid, non-invasive and reliable method in assessing the maturity level of oil palm harvests will enable harvesting at an optimum time to increase oil yield. This study shows the potential of using Raman spectroscopy to assess the ripeness level of oil palm fruitlets. By characterizing the carotene components as useful ripeness features, an automated ripeness classification model has been created using machine learning. A total of 46 oil palm fruit spectra consisting of 3 ripeness categories; under ripe, ripe, and over ripe, were analyzed in this work. The extracted features were tested with 19 classification techniques to classify the oil palm fruits into the three ripeness categories. The Raman peak averaging at 1515 cm⁻¹ is shown to be a significant molecular fingerprint for carotene levels, which can serve as a ripeness indicator in oil palm fruits. Further signal analysis on the Raman peak reveals 4 significant sub bands found to be lycopene (ν1a), β-carotene (ν1b), lutein (ν1c) and neoxanthin (ν1d) which originate from the C=C stretching vibration of carotenoid molecules found in the peel of the oil palm fruit. The fine KNN classifier is found to provide the highest overall accuracy of 100%. The classifier employs 6 features: peak intensities of bands ν1a to ν1d and peak positions of bands ν1c and ν1d as predictors. In conclusion, the Raman spectroscopy method has the potential to provide an accurate and effective way in determining the ripeness of oil palm fresh fruits.

The Diversity of Linear Conjugated Polyenes and Colours in Nature: Raman Spectroscopy as a Diagnostic Tool

This review is centered on the linear conjugated polyenes, which encompasses chromatic biomolecules, such as carotenoids, polyunsaturated aldehydes and polyolefinic fatty acids. The linear extension of the conjugated double bonds in these molecules is the main feature that determines the spectroscopic properties as light-absorbing. These classes of compounds are responsible for the yellow, orange, red and purple colors which are observed in their parent flora and fauna in nature. Raman spectroscopy has been used as analytical tool for the characterization of these molecules, mainly due to the strong light scattering produced by the delocalized pi electrons in the carbon chain. In addition, conjugated polyenes are one of the main target molecular species for astrobiology, and we also present a brief discussion of the use of Raman spectroscopy as one of the main analytical tools for the detection of polyenes extra-terrestrially.

Continuous organic synthesis in water around micro-orifices after flows

Water flows through micro-orifices are important because they occur in various fields, such as biology, medical science, chemistry, and engineering. We have reported in previous work that organic matter was generated in micro-orifices after water flowed through the orifice, and we proposed that the organic matter was synthesized from nonorganic materials, including CO2 and N2 dissolved in water from air, and water via the action of hydroxyl radicals produced by the flow through the micro-orifice. In the present study, we examined whether organic materials are produced in the water outside of the orifices in addition to that in the orifice. We used the decrease in water volume to measure the organic synthesis because water should be consumed during the synthesis, and thus the decrease in water volume should reflect the organic synthesis. We let ultrapure water containing dissolved air flow through a micro-orifice as a pre-flow, we stopped the flow, and then we measured the volume of water enclosed in the mount in which the micro-orifice was set over more than 100 h. The volume of water decreased gradually and substantially over time. We used Raman and infrared spectroscopy to analyze the residue obtained by evaporating the water present around the orifice. The residue contained organic matter, including carotenoids, amides, esters, and sugars, which were similar to those found in the membranes generated in the orifice in our previous paper, suggesting that the organic matter was synthesized in a wide region of water around the orifice as well as in the orifice. These results may be relevant to the origins of life and biology, and may lead to the development of a technology for reducing CO2 in air, as well as applications in many scientific and engineering fields.

Fluoridation of a lizard bone embedded in Dominican amber suggests open-system behavior

Vertebrate fossils embedded in amber represent a particularly valuable paleobiological record as amber is supposed to be a barrier to the environment, precluding significant alteration of the animals' body over geological time. The mode and processes of amber preservation are still under debate, and it is questionable to what extent original material may be preserved. Due to their high value, vertebrates in amber have never been examined with analytical methods, which means that the composition of bone tissue in amber is unknown. Here, we report our results of a study on a left forelimb from a fossil Anolis sp. indet. (Squamata) that was fully embedded in Miocene Dominican amber. Our results show a transformation of the bioapatite to fluorapatite associated with a severe alteration of the collagen phase and the formation of an unidentified carbonate. These findings argue for a poor survival potential of macromolecules in Dominican amber fossils.

Recent advances in amniote palaeocolour reconstruction and a framework for future research

Preserved melanin pigments have been discovered in fossilised integumentary appendages of several amniote lineages (fishes, frogs, snakes, marine reptiles, non-avialan dinosaurs, birds, and mammals) excavated from lagerstätten across the globe. Melanisation is a leading factor in organic integument preservation in these fossils. Melanin in extant vertebrates is typically stored in rod- to sphere-shaped, lysosome-derived, membrane-bound vesicles called melanosomes. Black, dark brown, and grey colours are produced by eumelanin, and reddish-brown colours are produced by phaeomelanin. Specific morphotypes and nanostructural arrangements of melanosomes and their relation to the keratin matrix in integumentary appendages create the so-called 'structural colours'. Reconstruction of colour patterns in ancient animals has opened an exciting new avenue for studying their life, behaviour and ecology. Modern relationships between the shape, arrangement, and size of avian melanosomes, melanin chemistry, and feather colour have been applied to reconstruct the hues and colour patterns of isolated feathers and plumages of the dinosaurs Anchiornis, Sinosauropteryx, and Microraptor in seminal papers that initiated the field of palaeocolour reconstruction. Since then, further research has identified countershading camouflage patterns, and informed subsequent predictions on the ecology and behaviour of these extinct animals. However, palaeocolour reconstruction remains a nascent field, and current approaches have considerable potential for further refinement, standardisation, and expansion. This includes detailed study of non-melanic pigments that might be preserved in fossilised integuments. A common issue among existing palaeocolour studies is the lack of contextualisation of different lines of evidence and the wide variety of techniques currently employed. To that end, this review focused on fossil amniotes: (i) produces an overarching framework that appropriately reconstructs palaeocolour by accounting for the chemical signatures of various pigments, morphology and local arrangement of pigment-bearing vesicles, pigment concentration, macroscopic colour patterns, and taphonomy; (ii) provides background context for the evolution of colour-producing mechanisms; and (iii) encourages future efforts in palaeocolour reconstructions particularly of less-studied groups such as non-dinosaur archosaurs and non-archosaur amniotes.

Preparation and characterisation of novel water-soluble β-carotene-chitooligosaccharides complexes

β-carotene and chitooligosaccharides are bioactive compounds that find their application in the food industry as well in biomedical fields. However, the application of β-carotene is limited due to its very low water solubility, as well as its air, light and temperature sensitivity. The preparation of β-carotene-chitooligosaccharides complexes by mechanochemical methods was presented. Their physical and chemical properties including solubility, size, zeta potential and radical scavenging activity were investigated. The interaction of the two components was shown by NMR, FT-IR, and Raman spectroscopy. The complexes were analysed by scanning and transmission electron microscopy. Chitooligosaccharides could serve as a carrier for β-carotene delivery. The complexation did not cause the loss of the radical scavenging activity of β-carotene and guaranteed its water solubility.

Raman investigation of the pigment families in recent and fossil brachiopod shells

Shells of the three subphyla of extant and extinct representatives of the phylum Brachiopoda display coloured patterns with diverse shapes and at different degrees. These colourations are readily visible in natural light but are best revealed under UV light for the fossils concerned. To identify these pigments, Raman spectroscopy has been used for the first time on brachiopod shells. The widespread identified pigments belong to the carotenoid family, best represented in all the animal kingdom, the second one concerns the melanin/melanin-like pigments and, surprisingly, additional molecules of the cytochrome family are revealed for the first time in one of the brachiopod shells studied. The putative functions of shell pigmentation, still under debate, are discussed.

Thermal carbonization in nanoscale reactors: controlled formation of carbon nanodots inside porous CaCO3 microparticles

Synthesis of carbon nanodots (CNDs) in confined geometry via incorporation of dextran sulphate into pores of CaCO3 microparticles is demonstrated. The preparation process included three steps: co-precipitation of solutions of inorganic salts and carbon source, thermal treatment and CaCO3 matrix removal. We show that geometric constraints can be used to precisely control the amount of source material and to avoid formation of large carbon particles. Analysis of TEM data shows particle size of ~3.7 nm with narrow size distribution. Furthermore, we found that variation in pore morphology has a clear effect on CNDs structure and optical properties. CNDs with graphene oxide like structure were obtained in the nanoporous outer shell layer of CaCO3 microparticles, while less ordered CNDs with the evidence of complex disordered carbons were extracted from the inner microcavity. These results suggest that confined volume synthesis route in CaCO3 nanopores can be used to precisely control the structure and optical properties of CNDs.

Butyl Rubber Nanocomposites with Monolayer MoS₂ Additives: Structural Characteristics, Enhanced Mechanical, and Gas Barrier Properties

Emerging two-dimensional (2D) materialsm, such as molybdenum disulfide (MoS₂), offer opportunities to tailor the mechanical and gas barrier properties of polymeric materials. In this study, MoS₂ was exfoliated to monolayers by modification with ethanethiol and nonanethiol. The thicknesses of resulting MoS₂ monolayers were 0.7 nm for MoS₂-ethanethiol and 1.1 nm for MoS₂-nonanethiol. MoS₂ monolayers were added to chlorobutyl rubber to prepare MoS₂-butyl rubber nanocomposites at concentrations of 0.5, 1, 3, and 5 phr. The tensile stress showed a maximum enhancement of about 30.7% for MoS₂-ethanethiol-butyl rubber and 34.8% for MoS₂-nonanethiol-butyl rubber when compared to pure chlorobutyl rubber. In addition, the gas barrier properties were increased by 53.5% in MoS₂-ethanethiol-butyl rubber and 49.6% in MoS₂-nonanethiol-butyl rubber. MoS₂ nanosheets thus enhanced the mechanical and gas barrier properties of chlorobutyl rubber. The nanocomposites that are presented here may be used to manufacture pharmaceutical stoppers with high mechanical and gas barrier properties.

On the Habitability of Desert Varnish: A Combined Study by Micro-Raman Spectroscopy, X-ray Diffraction, and Methylated Pyrolysis-Gas Chromatography-Mass Spectrometry

In 2020, the ESA ExoMars and NASA Mars 2020 missions will be launched to Mars to search for evidence of past and present life. In preparation for these missions, terrestrial analog samples of rock formations on Mars are studied in detail in order to optimize the scientific information that the analytical instrumentation will return. Desert varnishes are thin mineral coatings found on rocks in arid and semi-arid environments on Earth that are recognized as analog samples. During the formation of desert varnishes (which takes many hundreds of years), organic matter is incorporated, and microorganisms may also play an active role in the formation process. During this study, four complementary analytical techniques proposed for Mars missions (X-ray diffraction [XRD], Raman spectroscopy, elemental analysis, and pyrolysis-gas chromatography-mass spectrometry [Py-GC-MS]) were used to interrogate samples of desert varnish and describe their capacity to sustain life under extreme scenarios. For the first time, both the geochemistry and the organic compounds associated with desert varnish are described with the use of identical sets of samples. XRD and Raman spectroscopy measurements were used to nondestructively interrogate the mineralogy of the samples. In addition, the use of Raman spectroscopy instruments enabled the detection of β-carotene, a highly Raman-active biomarker. The content and the nature of the organic material in the samples were further investigated with elemental analysis and methylated Py-GC-MS, and a bacterial origin was determined to be likely. In the context of planetary exploration, we describe the habitable nature of desert varnish based on the biogeochemical composition of the samples. Possible interference of the geological substrate on the detectability of pyrolysis products is also suggested. Key Words: Desert varnish-Habitability-Raman spectroscopy-Py-GC-MS-XRD-ExoMars-Planetary science. Astrobiology 17, 1123-1137.

Organic compounds generated after the flow of water through micro-orifices: Were they synthesized?

Micro-fluid mechanics is an important area of research in modern fluid mechanics because of its many potential industrial and biological applications. However, the field is not fully understood yet. In previous work, when passing ultrapure water (UPW) in which air was dissolved (UPW*) through micro-orifices, we found that the flow velocity decreased and stopped over time, and membranes were frequently formed in the orifice when the flow stopped. The membrane came from the dissolved air in UPW*, and membrane formation was closely related to electric charges generated in orifices by the flow. In the present paper, we clarified the components of the membrane and suggested a mechanism for membrane formation. We examined the effect of contaminants on the membrane formation and confirmed our previous results. We identified the chemical components of the membrane and those present in the UPW* itself by using an electron probe microanalyzer and found that the proportion of each element differed between the membrane and UPW*. Raman and infrared (IR) spectroscopy showed that the membrane consisted of organic substances such as carotenoids, amides, esters, and sugars. We irradiated UPW* with ultraviolet light to cut organic chains that may be left in UPW* as contaminants. We found a similar membrane and organic compounds as in nonirradiated UPW*. Furthermore, although the UPW that was kept from contact with air after it was supplied from the UPW maker (UPW₀) and bubbled with Ar gas (UPW₀ bubbled with Ar) formed no membrane, the UPW₀ bubbled with CO₂ formed thin membranes, and Raman and IR analysis showed that this membrane contained carboxylic acid salts, carotenoids, or a mixture of both. We found that electric grounding of the orifice reduces the probability of membrane formation and that the jets issuing from an aperture bear negative charges, and we assumed that the micro-orifices possess positive charges generated by flows. Consequently, we suggest that organic compounds are synthesized from nonorganic matter in air or CO₂ dissolved in water by the action of hydroxyl radicals generated by flows through micro-orifices.

Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry

A new method to measure growth rates of individual photoautotrophic cells by combining stable isotope probing (SIP) and single-cell resonance Raman microspectrometry is introduced. This report explores optimal experimental design and the theoretical underpinnings for quantitative responses of Raman spectra to cellular isotopic composition. Resonance Raman spectra of isogenic cultures of the cyanobacterium, Synechococcus sp., grown in ¹³C-bicarbonate revealed linear covariance between wavenumber (cm⁻¹) shifts in dominant carotenoid Raman peaks and a broad range of cellular ¹³C fractional isotopic abundance. Single-cell growth rates were calculated from spectra-derived isotopic content and empirical relationships. Growth rates among any 25 cells in a sample varied considerably; mean coefficient of variation, CV, was 29 ± 3% (σ/x¯), of which only ~2% was propagated analytical error. Instantaneous population growth rates measured independently by in vivo fluorescence also varied daily (CV ≈ 53%) and were statistically indistinguishable from single-cell growth rates at all but the lowest levels of cell labeling. SCRR censuses of mixtures prepared from Synechococcus sp. and T. pseudonana (a diatom) populations with varying ¹³C-content and growth rates closely approximated predicted spectral responses and fractional labeling of cells added to the sample. This approach enables direct microspectrometric interrogation of isotopically- and phylogenetically-labeled cells and detects as little as 3% changes in cellular fractional labeling. This is the first description of a non-destructive technique to measure single-cell photoautotrophic growth rates based on Raman spectroscopy and well-constrained assumptions, while requiring few ancillary measurements.

Raman imaging of macrophages incubated with triglyceride-enriched oxLDL visualizes translocation of lipids between endocytic vesicles and lipid droplets

Raman spectroscopic imaging was used to investigate the uptake of oxidized LDLs (oxLDLs) by human macrophages. To better understand the endocytic pathway and the intracellular fate of modified lipoproteins is of foremost interest with regard to the development of atherosclerotic plaques. To obtain information on the storage process of lipids caused by oxLDL uptake, Raman spectroscopic imaging was used because of its unique chemical specificity, especially for lipids. For the present study, a protocol was established to incorporate deuterated tripalmitate into oxLDL. Subsequently, human THP-1 macrophages were incubated for different time points and their chemical composition was analyzed using Raman spectroscopic imaging. β-Carotene was found to be a reliable marker molecule for the uptake of lipoproteins into macrophages. In addition, lipoprotein administration led to small endocytic vesicles with different concentrations of deuterated lipids within the cells. For the first time, the translocation of deuterated lipids from endocytic vesicles into lipid droplets over time is reported in mature human THP-1 macrophages.

Thermus and the Pink Discoloration Defect in Cheese

A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses. Prompted by this finding and data confirming the pink discoloration to be associated with the presence of a carotenoid, a culture-based approach was employed, and Thermus thermophilus was successfully cultured from defect-containing cheeses. The link between Thermus and the pinking phenomenon was then established through the cheese defect equivalent of Koch's postulates when the defect was recreated by the reintroduction of a T. thermophilus isolate to a test cheese during the manufacturing process. IMPORTANCE Pink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In this study, a combined 16S rRNA, whole-genome sequencing, and quantitative PCR approach was taken. This resulted in the identification of Thermus, a carotenoid-producing thermophile, in defect-associated cheeses and the recreation of the problem in cheeses to which Thermus was added. This finding has the potential to lead to new strategies to eliminate this defect, and our method represents an approach that can be employed to investigate the role of microbes in other food defects of unknown origin.

Preservation of Biomarkers from Cyanobacteria Mixed with Mars-Like Regolith Under Simulated Martian Atmosphere and UV Flux

The space mission EXPOSE-R2 launched on the 24th of July 2014 to the International Space Station is carrying the BIOMEX (BIOlogy and Mars EXperiment) experiment aimed at investigating the endurance of extremophiles and stability of biomolecules under space and Mars-like conditions. In order to prepare the analyses of the returned samples, ground-based simulations were carried out in Planetary and Space Simulation facilities. During the ground-based simulations, Chroococcidiopsis cells mixed with two Martian mineral analogues (phyllosilicatic and sulfatic Mars regolith simulants) were exposed to a Martian simulated atmosphere combined or not with UV irradiation corresponding to the dose received during a 1-year-exposure in low Earth orbit (or half a Martian year on Mars). Cell survival and preservation of potential biomarkers such as photosynthetic and photoprotective pigments or DNA were assessed by colony forming ability assays, confocal laser scanning microscopy, Raman spectroscopy and PCR-based assays. DNA and photoprotective pigments (carotenoids) were detectable after simulations of the space mission (570 MJ/m(2) of UV 200-400 nm irradiation and Martian simulated atmosphere), even though signals were attenuated by the treatment. The fluorescence signal from photosynthetic pigments was differently preserved after UV irradiation, depending on the thickness of the samples. UV irradiation caused a high background fluorescence of the Martian mineral analogues, as revealed by Raman spectroscopy. Further investigation will be needed to ensure unambiguous identification and operations of future Mars missions. However, a 3-month exposure to a Martian simulated atmosphere showed no significant damaging effect on the tested cyanobacterial biosignatures, pointing out the relevance of the latter for future investigations after the EXPOSE-R2 mission. Data gathered during the ground-based simulations will contribute to interpret results from space experiments and guide our search for life on Mars.

Melanosomes and ancient coloration re-examined: A response to Vinther 2015 (DOI 10.1002/bies.201500018)

Round to elongate microbodies associated with fossil vertebrate soft tissues were interpreted as microbial traces until 2008, when they were re-described as remnant melanosomes - intracellular, pigment-containing eukaryotic organelles. Since then, multiple claims for melanosome preservation and inferences of organismal color, behavior, and physiology have been advanced, based upon the shape and size of these microstructures. Here, we re-examine evidence for ancient melanosomes in light of information reviewed in Vinther (2015), and literature regarding the preservation potential of microorganisms and their exopolymeric secretions. We: (i) address statements in Vinther's recent (2015) review that are incorrect or which misrepresent published data; (ii) discuss the need for caution in interpreting "voids" and microbodies associated with degraded fossil soft tissues; (iii) present evidence that microorganisms are in many cases an equally parsimonious source for these "voids" as are remnant melanosomes; and (iv) suggest methods/criteria for differentiating melanosomes from microbial traces in the fossil record.

Raman Characterization of the UV-Protective Pigment Gloeocapsin and Its Role in the Survival of Cyanobacteria

Extracellular UV-screening pigments gloeocapsin and scytonemin present in the exopolysaccharide (EPS) envelopes of extremophilic cyanobacteria of freshwater and marine environments were studied by Raman spectroscopy and compared to their intracellular photosynthetic pigments. This Raman spectral analysis of the extracellular pigment gloeocapsin showed that it shared Raman spectral signatures with parietin, a radiation-protective pigment known in lichens. The UV-light spectra also show similarities. Gloeocapsin occurs in some cyanobacterial species, mostly with exclusion of scytonemin, indicating that these pigments have evolved in cyanobacteria as separate protective strategies. Both gloeocapsin and scytonemin are widely and species-specifically distributed in different cyanobacterial genera and families. The widespread occurrence of these pigments may suggest an early origin, while their detection by Raman spectroscopy makes them potential biosignatures for cyanobacteria in the fossil record and demonstrates the usefulness of nondestructive Raman spectroscopy analyses for the search for complex organics, including possible photosynthetic pigments, if preservable in early Earth and extraterrestrial samples.

Conjugated polyenes as chemical probes of life signature: use of Raman spectroscopy to differentiate polyenic pigments

Polyenes, which are represented by carotenes, carotenoids and conjugated polyenals, are some of the most important targets for astrobiology, because they can provide strong evidence of the presence of organic compounds in the most extreme environments, such as on Mars. Raman spectroscopy has been used as the main analytical tool in the identification of such compounds, for the greatest variety of living species, from microorganisms to animals and plants. However, using only the position of the characteristic Raman bands can lead to errors in tentatively identifying chemicals. In this work, we present a series of observations that can provide a more complete and robust way to analyse the Raman spectrum of a polyenal, in which the position, the intensity, the use of various laser lines for excitation, and the combination of more than one pigment can be considered in the complete analysis.

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

The remote robotic exploration of extraterrestrial scenarios for evidence of biological colonization in 'search for life' missions using Raman spectroscopy is critically dependent on two major factors: firstly, the Raman spectral recognition of characteristic biochemical spectral signatures in the presence of mineral matrix features; and secondly, the positive unambiguous identification of molecular biomaterials which are indicative of extinct or extant life. Both of these factors are considered here: the most important criterion is the clear definition of which biochemicals truly represent biomarkers, whose presence in the planetary geological record from an analytical astrobiological standpoint will unambiguously be indicative of life as recognized from its remote instrumental interrogation. Also discussed in this paper are chemical compounds which are associated with living systems, including biominerals, which may not in themselves be definitive signatures of life processes and origins but whose presence provides an indicator of potential life-bearing matrices.

Mobile Raman spectroscopy in astrobiology research

Raman spectroscopy has proved to be a very useful technique in astrobiology research. Especially, working with mobile instrumentation during fieldwork can provide useful experiences in this field. In this work, we provide an overview of some important aspects of this research and, apart from defining different types of mobile Raman spectrometers, we highlight different reasons for this research. These include gathering experience and testing of mobile instruments, the selection of target molecules and to develop optimal data processing techniques for the identification of the spectra. We also identify the analytical techniques that it would be most appropriate to combine with Raman spectroscopy to maximize the obtained information and the synergy that exists with Raman spectroscopy research in other research areas, such as archaeometry and forensics.

Estimation of bacterioruberin by Raman spectroscopy during the growth of halophilic archaeon Haloarcula marismortui

Halophilic archaea are interesting microorganisms that produce low biomass and metabolites, complicating their quantification. Raman spectroscopy (RS) is a powerful technique, which requires small samples, attractive for using in archaeal research. The objective of this work was the estimation of bacterioruberin content along with Haloarcula marismortui growth and their correlation with biomass concentration. RS was used to detect characteristic bands of bacterioruberin (vibrational modes C═CH, C─C, and C═C) in H. marismortui culture samples. The intensity of Raman spectra in bacterioruberin and the biomass concentration were adequately correlated. The highest production of bacterioruberin occurred at 60 h. RS is revealed as a reliable technique for the estimation of bacterioruberin in the biomass of H. marismortui, which could be considered as a promising qualitative and quantitative technique to assay metabolites in cell cultures.

Organic and mineral imprints in fossil photosynthetic mats of an East Antarctic lake

Lacustrine microbial mats in Antarctic ice-free oases are considered modern analogues of early microbial ecosystems as their primary production is generally dominated by cyanobacteria, the heterotrophic food chain typically truncated due to extreme environmental conditions, and they are geographically isolated. To better understand early fossilization and mineralization processes in this context, we studied the microstructure and chemistry of organo-mineral associations in a suite of sediments 50-4530 cal. years old from a lake in Skarvsnes, Lützow Holm Bay, East Antarctica. First, we report an exceptional preservation of fossil autotrophs and their biomolecules on millennial timescales. The pigment scytonemin is preserved inside cyanobacterial sheaths. As non-pigmented sheaths are also preserved, scytonemin likely played little role in the preservation of sheath polysaccharides, which have been cross-linked by ether bonds. Coccoids preserved thylakoids and autofluorescence of pigments such as carotenoids. This exceptional preservation of autotrophs in the fossil mats argues for limited biodegradation during and after deposition. Moreover, cell-shaped aggregates preserved sulfur-rich nanoglobules, supporting fossilization of instable intracellular byproducts of chemotrophic or phototrophic S-oxidizers. Second, we report a diversity of micro- to nanostructured CaCO3 precipitates intimately associated with extracellular polymeric substances, cyanobacteria, and/or other prokaryotes. Micro-peloids Type 1 display features that distinguish them from known carbonates crystallized in inorganic conditions: (i) Type 1A are often filled with globular nanocarbonates and/or surrounded by a fibrous fringe, (ii) Type 1B are empty and display ovoid to wrinkled fringes of nanocrystallites that can be radially oriented (fibrous or triangular) or multilayered, and (iii) all show small-size variations. Type 2 rounded carbonates 1-2 μm in diameter occurring inside autofluorescent spheres interpreted as coccoidal bacteria may represent fossils of intracellular calcification. These organo-mineral associations support organically driven nanocarbonate crystallization and stabilization, hence providing potential markers for microbial calcification in ancient rocks.

Real-time monitoring of lycopene content in tomato-derived products during processing: implementation of a novel double-slit Raman spectrometer

Lycopene is a very attractive antioxidant associated with cancer prevention in humans. Therefore, it is important to develop new analytical methods that allow for differentiation of food production streams that contain various antioxidant concentrations. The lycopene content in tomato juice, an intermediate between raw tomatoes and the final tomato paste product, was monitored on-line for 46 days at a production plant with a novel, patented double-channel Raman setup. The setup comprises a double-channel mini spectrometer placed in a fixed optical setup, and for each measurement there are two slightly shifted Raman spectra on the x-axis that opens up for additional data processing. The prototype was constructed specifically for 532 nm excitation with no moving parts, and it was designed to optimize each part for the rest of the system. That was the first step toward an integrated optical in-line process analytical solution for industry. As proof of concept, the developed prototype was able to perform a real-time differentiation of the normal and medium to high lycopene content in tomato juice. A correlation factor for double-channel measurements was compared with a correlation factor for background-corrected single-channel measurements by correlating with high performance liquid chromatography reference measurements (1-20 mg of lycopene per 100 g of wet sample). The latter gave a slightly better correlation for the specific application (R(2) = 0.76), acceptable for proof of concept. Real-time information is extremely valuable for the tomato processing plant, mainly because it can be used for improved differentiation of high lycopene content tomato paste to ensure a higher product price. In addition, the developed process analytical technology solution allows for differentiated payment of the tomato farmers based on the lycopene content in their crops.

Mineral evolution and processes of ferruginous microbialite accretion - an example from the Middle Eocene stromatolitic and ooidal ironstones of the Bahariya Depression, Western Desert, Egypt

Peritidal ferruginous microbialites form the main bulk of the Middle Eocene ironstone deposits of the Bahariya Depression, Western Desert, Egypt. They include ferruginous stromatolites and microbially coated grains (ferruginous oncoids and ooids). Their internal structures reveal repeated cycles of microbial and Fe oxyhydroxide laminae. The microbial laminae consist of fossilised neutrophilic filamentous iron-oxidising bacteria. These bacteria oxidised the Fe(II)-rich acidic groundwater upon meeting the marine water at an approximately neutral pH. The iron oxyhydroxide laminae were initially precipitated as amorphous iron oxhydroxides and subsequently recrystallised into nanocrystalline goethite during early diagenesis. Organic remains such as proteinaceous compounds, lipids, carbohydrates and carotenoids are preserved and can be identified by Raman spectroscopy. The ferruginous microbialites were subjected to post-depositional subaerial weathering associated with sea-level retreat and subsurface alteration by continued ascent of the Fe(II)-rich acidic groundwater. At this stage, another iron-oxidising bacterial generation prevailed in the acidic environment. The acidity of the groundwater was caused by oxidation of pyrite in the underlying Cenomanian Bahariya formation. The positive iron isotopic ratios and presence of ferrous and ferric iron sulphates may result from partial iron oxidation along the redox boundary in an oxygen-depleted environment.

Remote Raman spectroscopy for planetary exploration: a review

In this review, we discuss the current state of standoff Raman spectroscopy as it applies to remote planetary applications, including standoff instrumentation, the technique's ability to identify biologically and geologically important analytes, and the feasibility to make standoff Raman measurements under various planetary conditions. This is not intended to be an exhaustive review of standoff Raman and many excellent papers are not mentioned. Rather it is intended to give the reader a quick review of the types of standoff Raman systems that are being developed and that might be suitable for astrospectroscopy, a look at specific analytes that are of interest for planetary applications, planetary measurement opportunities and challenges that need to be solved, and a brief discussion of the feasibility of making surface and plume planetary Raman measurements from an orbiting spacecraft.

Feasibility of Raman microspectroscopic identification of biomarkers through gypsum crystals

The miniaturized Raman spectrometer is considered to be a candidate instrument for the Pasteur payload (the ExoMars mission scheduled for 2018). This mission will, for the first time, combine mobility and access to subsurface locations where organic molecules might be well preserved. Evaporitic crystals are among the potential protected habitats that have been postulated. Various concentrations of biomarkers (beta-carotene, glycine and phthalic acid) dispersed in a gypsum matrix were analyzed through transparent mineral (gypsum) plates of different thicknesses. By doing so, conditions were simulated in which biomarkers were trapped within evaporitic crystals. Using a long-working distance objective, all studied concentrations of biomarkers mixed in gypsum powder were detected. The characteristic Raman bands were easily observable for a 10% mixture of all chosen biomarkers not only through a 3.3 mm plate and but even through a 5.2 mm plate. It was possible to detect key Raman bands of 1% phthalic acid/gypsum mixture and 1% beta-carotene/gypsum mixture even through a 5.2 mm gypsum plate. The 1% beta-carotene/gypsum mixture was still clearly distinguishable through an 8.5mm gypsum crystal due to the known resonance Raman effect of the molecule.