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Vibrational spectroscopy of fossils
Abstract
Over the last two decades, there has an been increasing interest in applying vibrational spectroscopy in palaeontological research. For example, this chemical analytical technique has been used to elucidate the chemical composition of a wide variety of fossils, including Archaean putative microfossils, stromatolites, chitinozoans, acritarchs, fossil algae, fossil plant cuticles, putative fossil arthropods, conodonts, scolecodonts and dinosaur bones. The insights provided by these data have been equally far ranging: to taxonomically identify a fossil, to determine biogenicity of a putative fossil, to identify preserved biologically synthesized compounds and to elucidate the preservational mechanisms of fossil material. Vibrational spectroscopy has clearly been a useful tool for investigating various palaeontological problems. However, it is also a tool that has been misapplied and misinterpreted, and thus, this review is dedicated to providing a palaeontologist who is new to vibrational spectroscopy with a basic understanding of these techniques, and the types of chemical information that can be obtained. Two example applications of these techniques are discussed in detail, one looking into fossil palynomorph taxonomy and other into the enigmatic Burgess Shale-type preservation.
... The latest advent of geochemical profiles through calcium carbonate records is often applied as a method of reconstructing environmental conditions in geological history (Cavazza and Ingersoll 2005;Do Campo et al. 2010;Gomez Peral et al. 2011;Varela et al. 2013;Rexfort and Mutterlose 2006). Among the various geochemical characterization methods, Fourier-transform infrared spectroscopy (FTIR) is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid, or gas and is efficiently used for geochemical characterization (Yuvarani et al. 2009;Olcott and Marshall 2014). This technique uses a polychromatic beam of light with a wide range of continuous frequencies simultaneously, therefore allows a much higher speed of scanning versus the conventional monochromatic dispersive spectroscopy (Niu et al. 2019) and gives a higher signal-to-noise ratio by allowing more light to enter the spectrometer (Shaltout et al. 2011;Jacob et al. 2017). ...
... The electromagnetic radiation induces the vibration of molecules due to the characteristics of a particular chemical functional group, which aid in the identification of substances and molecular structure (Madejova 2003;Olcott and Marshall 2014;Manoli et al. 2002). The frequencies incurred are dependent upon the mass, strength, length, and geometry of the bonded atoms. ...
... The frequencies incurred are dependent upon the mass, strength, length, and geometry of the bonded atoms. Vibration spectroscopy has been applied to a wide range of paleontological studies, while FTIR and Raman spectroscopy can resolve paleontological assessment (Olcott and Marshall 2014;Shaltout et al. 2011). Infrared spectroscopy is concerned with the study of absorption of infrared radiation, which causes a vibrational transition in the molecule. ...
About 135 million years before, a form of marine animal called belemnites existed during the geological period of the Jurassic and Cretaceous. The Cauvery Basin is a pericratonic basin that lies along the southeast coast of India. The belemnites fossil used in the present study is collected from Karai East, Ariyalur District, Tamil Nadu. The inner and outer parts of the cross-section differ in the size of calcite forms and building up in the fossil. Geochemical characterization of rostrum and alveolus in the fossil was done to determine the mineral constitutions and assemblages. The elements were characterized by Fourier Transform Infrared (FTIR), Micro Raman, X-ray Powder Diffractometry (XRD) and X-ray fluorescence (XRF) analyses. A strong calcite mineral deposition was observed in the central part of the rostrum together with kaolinite and orthoclase feldspar as minor components. The peak observed in 3421, 2926 and 3436, 2924 cm-1 are the characteristic peaks of kaolinite in the rostrum and the alveolus respectively. The peaks were observed at 1038 cm-1 are the characteristic peak of orthoclase feldspar. The advent methodology directly and non-invasively affords spatially resolved assessments of organic matter preservation and microscale chemical diversity within any geologically preserved terrestrial sedimentary sample in technological applications.
... Micropaleontologists have widely used vibrational spectroscopy (e.g. Raman spectroscopy and Fourier-transform infrared spectroscopy (FTIR); Olcott Marshall and Marshall, 2015) to detect (thermally altered) OM, which is used for validating biogenicity of putative microfossils (e.g. Schopf et al., 2002Schopf et al., , 2005; but see also Marshall et al., 2010). ...
... In this study, we measured the variation of RSCM and estimated its paleotemperature for different sites within a fossil locality and among different types of fossil eggshells. In addition, we tested the presence of thermally altered OM in fossil eggshells using FTIR spectroscopy since it provides complementary results to Raman spectroscopy (Olcott Marshall and Marshall, 2015). Finally, qualitative and quantitative traits of calcite twinning in the eggshells were investigated because they are influenced by the maximum paleotemperature (Burkhard, 1993;Ferrill et al., 2004). ...
... Fig. 6C) because there might be OM, which is inactive in Raman spectroscopy. For this, FTIR is demonstrated to be an effective alternative because some molecular vibrations may be inactive in Raman spectroscopy but active in FTIR, and vice versa (Marshall et al., 2005;Olcott Marshall and Marshall, 2015). The FTIR results showed that all fossil materials show OM signal (Fig. 8). ...
Raman spectroscopic analyses of thermally altered organic materials can be used to assess the paleothermometry of the sedimentary deposits. Although this technique has been widely applied to diverse microfossils, macroscopic vertebrate fossils have been neglected. In this paper, we show that fossil eggshells can be used for this purpose by demonstrating the paleothermometric potential of diverse amniotic eggshells from the Wido Volcanics (Upper Cretaceous, South Korea) that contain thermally altered organic material. We estimate the maximum paleotemperature recorded in the eggshells using Raman spectroscopic data and the spectrum deconvolution technique, which was invented and developed by organic geochemists. The results show that the same type of eggshells record different paleotemperature gradients depending on their spatial distribution in the fossil locality, whereas different types of eggshells from similar locations show similar paleotemperature gradients (except for one specimen with a peculiar microstructure). These findings are further supported by Fourier transform infrared spectroscopic results, which focus on thermally altered organic materials, and electron backscatter diffraction data, which focus on calcite twinning. This study suggests that fossil eggshells are useful and reliable materials for paleothermometry because thermally altered organic materials and calcites of eggshells provide independent opportunities to assess paleothermometry. We propose that fossil eggshells may be useful for evaluating the thermal evolution of sedimentary basins.
... Nevertheless, this approach requires rather complicated preparation steps and laboratory resources (see electronic appendix of Schweitzer et al. 2005) that are not easily available to most paleontologists. In this respect, Raman spectroscopy used in Wie mann et al. (2018) and Yang et al. (2018) to detect preserved cuticle (an outermost proteinous layer of an eggshell) or pigments in the fossil eggshell is a promising technique because it is nondestructive and provides high spatial and spectral resolution without complicated preparation steps (Smith and Clark 2004;Schweitzer et al. 2008;Olcott Marshall and Marshall 2015). ...
... Numerous studies have shown that the peak shape and the relative intensities of G and D bands depend on thermal maturity of preserved carbonaceous matter (e.g. Schopf et al. 2005;Schiffbauer et al. 2012;Hartkopf -Fröder et al. 2015;McNeil et al. 2015;Olcott Marshall and Marshall 2015;Schito et al. 2017;Henry et al. 2019a,b). The spectral information, therefore, can be used for reconstructing the thermal history of the fossil materials (Schopf et al. 2005). ...
... Alternatively, some pristine organic matter (i.e. not thermally matured ones) may be present here as suggested inMarzola et al. (2015) that may be detected by Fourier -transform infrared spectroscopy (FTIR), useful to detect ６７ ` functional groups of pristine organic matter (OlcottMarshall and Marshall 2015). Potential pristine organic matter may cause the dark tint present in modern crocodyliform eggshells, but testing this hypothesis was out of scope of the present study.4.6.1.3 ...
Eggshells are biominerals that provide reproductive information of vertebrates. In paleontology, fossil eggshells offer a unique chance to investigate the reproductive
paleobiology of extinct taxa because diverse information inscribed in fossil eggshells are
unavailable from other types of fossils such as fossil bone and trace fossi ls. In addition,
geologic information has been added to once-purely-biogenic-biomineral because fossil
eggshells have experienced fossilization process . Being a discipline with biogenic calcite,
compared to other fields of vertebrate paleontology, fossil eggshell research can share
diverse methodologies with other fields of geology and biology, which are based on
analytical approaches (e.g. mineralogy) . Hence, it can have broad implications to diverse
fields including, but not limited to, paleontology per se, neontology, and sedimentology. In
this dissertation, firstly, I focused on the microstructure and crystallography of fossil and
modern eggshells using a device called Electron Backscatter Diffraction (EBSD), which has been a powerful tool in materials science and structural geology. The results can be
summarized in the four points. First, the crystallographies of gekkotan and archosaur
eggshells were completely different from each other, meaning that calcified eggshells of
those clades are independent and homoplastic in their origin. Secondly, the presence of the external zone and squamatic zone in maniraptoran eggshells can be identified by comparing the linearity of grain boundaries of the two zones. In addition, the two different
misorientation distribution pattern could be found between them. Thirdly, the crystallography of "geckoid‟ eggshells from Upper Cretaceous deposits in Europe confirmed that they are, in fact, maniraptoran dinosaur eggshells. Fourthly, the microstructural and crystallographic evolution of modern paleognath eggshells were investigated, which can be helpful to understand the evolution of eggshells in modern maniraptoran clades. Moreover, the dark color of fossil eggshells from the Korean Peninsula is mainly attributable to the presence of amorphous carbon, which can be detected by Raman spectroscopy. The amorphous carbon signal of Raman spectrum records the maximum paleotemperature that the fossil material experienced. The deconvolution approach of amorphous carbon in Raman spectrum developed by organic geochemist was adopted in this study, which allows estimating the maximum paleotemperature of fossil locality. These studies clearly show that EBSD can provide more objective results on the microstructure and crystallography of diverse amniotic
eggshells than conventional techniques do. They are not only useful for correct identification and classification for fossil eggshells but also helpful to read latent paleobiological information. Notably, crystallographic data might be related to the ethological feature of Maniraptora because the strength of eggshells might be related to the microstructure and crystallography of eggshells. Raman spectroscopic results imply that fossil eggshells might be a useful material to infer the maximum paleotemperature of terrestrial basins. It is because the spectroscopic analysis has been usually focused on marine microfossils and kerogen organic materials rather than terrestrial macrofossils. If the same logic works in the biocarbonate of amniotic eggshells, fossil eggshells can be used as invaluable materials to infer the sedimentological and taphonomic setting of the terrestrial fossil-bearing deposits. In short, EBSD and Raman spectroscopy are essential tools to get novel information from eggshells that we had never acquired before. Along with this new technology, future research should be focused on combining statistical and analytical methods to correctly interpret hidden information from fossil and modern eggshells.
... In this respect, Raman spectroscopy used in Wiemann et al. (2018) and to detect preserved cuticle (an outermost proteinous layer of an eggshell) or pigments in the fossil eggshell is a promising technique because it is nondestructive and provides high spatial and spectral resolution without complicated preparation steps (Smith and Clark, 2004;Schweitzer et al., 2008;Olcott Marshall and Marshall, 2015). In addition, Raman spectroscopy is useful in appraising the thermal maturity of preserved organic materials (or at least carbonaceous material) in fossils (Hartkopf-Fröder et al., 2015;Olcott Marshall and Marshall, 2015 and references therein). ...
... In this respect, Raman spectroscopy used in Wiemann et al. (2018) and to detect preserved cuticle (an outermost proteinous layer of an eggshell) or pigments in the fossil eggshell is a promising technique because it is nondestructive and provides high spatial and spectral resolution without complicated preparation steps (Smith and Clark, 2004;Schweitzer et al., 2008;Olcott Marshall and Marshall, 2015). In addition, Raman spectroscopy is useful in appraising the thermal maturity of preserved organic materials (or at least carbonaceous material) in fossils (Hartkopf-Fröder et al., 2015;Olcott Marshall and Marshall, 2015 and references therein). By using the parameters derived from the Raman spectra of thermally matured carbonaceous materials, the preserved carbonaceous matter in metasedimentary rock samples (Beyssac et al., 2002;Rahl et al., 2005;Lahfid et al., 2010) or fossil fuels (Schito et al., 2017;Henry et al., 2019a) could be used as a 'thermometer' because the parameters are affected mainly by heat, but little affected by other variables such as pressure at least in higher metamorphic grade (T > 350 • C) (Lahfid et al., 2010). ...
... It means that the dark band at the inner end of the modern crocodylian eggshell is not caused by the amorphous carbon unlike A. vesicularis. Alternatively, some pristine organic matter (i.e., not thermally matured ones) may be present here as suggested in Marzola et al. (2015) that may be detected by Fourier-transform infrared spectroscopy (FTIR), useful to detect functional groups of pristine organic matter (Olcott Marshall and Marshall, 2015). Potential pristine organic matter may cause the dark tint present in modern crocodyliform eggshells, but testing this hypothesis was out of scope of the present study. ...
Raman spectroscopy has been widely used in micropaleontology and organic geochemistry to identify carbonaceous materials and evaluate their thermal maturity in fossils or metasedimentary rocks. Meanwhile, fossil egg researches have mostly focused on biomineralized calcite, but preserved carbonaceous (or possibly organic) materials inside the eggshells have been usually neglected until recently. Here we report an enigmatic egg from the Wido Volcanics (Upper Cretaceous) of South Korea that was analyzed using diverse methods including polarized light microscope, scanning electron microscope, electron probe microanalyzer, electron backscatter diffraction, and Raman spectroscopy. The eggshell not only shows the crystallography of archosaurian eggshells but also contains peculiar dark bands, which were previously known as the trait of fossil and modern Crocodyliformes eggshells. Raman spectroscopic analysis showed that the dark bands are mainly due to amorphous carbon, as evidenced by the clear graphite (G) and disordered (D) bands. The deconvolution of amorphous carbon peaks and resultant parameters made it possible to infer the paleotemperature inscribed in the eggshell. The result suggests that preserved amorphous carbon in the fossil eggshells can be identified using Raman spectroscopy and Raman parameters may make it possible to compare the thermal maturity of spatiotemporally diverse fossil eggshells. The biogenicity of the dark band is not clear because Raman spectroscopic analysis is not sufficient to confirm biogenicity. However, overall distribution of the dark band may imply the biogenic origin. It is apparent that the material of this study is not a dinosaur egg but might belong to a crocodyliform or choristoderan egg, and even other non-dinosaur archosaur can be a candidate as well.
... 55-65 wt %), organic materials (approx. [25][26][27][28][29][30][31][32][33][34][35] wt %) and about 10 wt % water [1][2][3][4]. The mineral component of the bones is best described as carbonated hydroxyapatite particles embedded in an organic matrix, in particular in a mixture of collagen and non-collagenous proteins [1][2][3][4]. ...
... Correct classification rates of 96% and 81% were obtained for the classification of skull bone samples according to avian and mammalian, respectively. Overall, a 91% correct classification rate was obtained for the classification of skull samples according to the class (mammalian and avian) which is equivalent or better to the classification rates reported in similar studies [23][24][25][26][27][28]. ...
... The classification results obtained in this study infer that differences in the chemical composition of the bones might be responsible for the observed differences in the NIR spectra and thus in the classification results obtained. Differences in metabolism, nutrition, and environment effects (sunlight degradation, season) might explain the observed differences between the skull bones from different families and species [23][24][25][26][27][28]. Unfortunately, this information was not available in the set of samples analysed. ...
Near infrared (NIR) reflectance spectroscopy coupled with chemometric analysis was evaluated as a non-destructive tool to discriminate skull bone samples from different animal species. In total 70 skull bones from animals of three classes (mammalians, avian and reptiles) were scanned in the wavelength range between 950 to 1650 nm. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to analyse the NIR spectra of the skull samples. Correct classification rates of 96% and 81% were obtained for the classification of skull bone samples according to avian and mammalian classes, respectively. Overall, a 91% correct classification rate was obtained for the classification of skull samples according to the class (mammalian and avian). This study demonstrates the potential of NIR spectroscopy coupled with chemometric as data processing, as a means of a rapid, non-destructive classification technique for skull bone samples.
... Fossil plant cuticles, pollen, and spores are among the most resistant materials in the geological record and with multiple applications for science. The cuticle morphology, i.e. cell and stomata patterns are used for taxonomical identification and palaeoclimatology as a CO 2 proxy (McElwain et al., 2009;Steinthorsdottir and Vajda, 2015;Steinthorsdottir et al., 2016Steinthorsdottir et al., , 2019Slodownik et al., 2021), but the cuticles also comprise chemical compounds used for chemical analyses such as chemotaxonomy (e.g., Holloway, 1982;Tegelaar et al., 1991;van Bergen et al., 1994;Lyons et al., 1995;Olcott Marshall and Marshall, 2015;Vajda et al., 2017Vajda et al., , 2021Lafuente Diaz et al., 2020;Slodownik et al., 2021;among others), to assess the thermal alteration (Lis et al., 2005;Pšenička et al., 2005;Qu et al., 2019) and also palaeoclimatic activities (Chaloner and Mcelwain, 1997;Blokker et al., 2006). ...
... As FTIR spectroscopy is sensitive to changes within the vibrational groups' environment (Mayo et al., 2003;Heredia-Guerrero et al., 2014;Olcott Marshall and Marshall, 2015), it can also be used to address possible alterations inflicted by the processing steps previously mentioned. Moreover, for a better analysis of such alterations, the evaluation of the changes in the sample can be done by using the IR spectra to calculate the difference spectra. ...
... Rather than excluding the quantitative analysis of fossil sporomorph data a priori, we advocate for a more open and inquiry-driven approach, including generating data from additional PTB sections to compare with, and validate the results from our study, and extending these analyses to other proposed UV-B perturbations such as the end-Devonian mass extinction (12). We also note that, at present, micro-FTIR provides the only practical means of generating UAC datasets from fossil specimens, given the large sample sizes needed for gas chromatography-mass spectrometry-based analyses (13) and the challenges with applying Raman spectroscopy to isolated sporopollenin and related bio/geopolymers, because of strong autofluorescence (14,15). Naturally, we encourage the development of other approaches for generating UAC data from FTIR spectra, but to date, the peak height-based approach used in our paper is the only one that has been developed and tested on a range of extant, subfossil, and fossil material (2)(3)(4)(5)(6). ...
Seddon and Zimmermann have raised questions about the evidence for increased UV-B flux across the end-Permian mass extinction (EPME) that was presented in our recent study, specifically regarding the measurement of UV-B-absorbing compound (UAC) levels in fossil pollen. We respond to these points, arguing that the comparison of FTIR spectra of >250 million-year-old Permian fossil pollen with ~700-year-old subfossil pollen is not valid and that negligible nonrandom interference derived from water vapor fluctuations during data generation cannot coincidentally produce a substantial UAC peak during the EPME. Furthermore, we refute the suggestion that the measured aromatic peak at 1600 cm-1 could have been influenced by diagenetic products from other organic constituents of pollen. The most productive route forward will be to generate sporomorph geochemical data from additional Permian-Triassic boundary sections to test the results put forward in our study.
... Raman spectroscopy allows non-destructive compositional fingerprinting of complex biological and geological materials [1][2][3][4][5][6][7][8][9][10] . Rapidly generated in situ spectra yield information on covalent, ionic, and noncovalent bioinorganic interactions enabling a comparative search for informative heterogeneities across a diversity of samples 1 , such as modern organismal tissues and their fossilization products. ...
Raman spectroscopy is a popular tool for characterizing complex biological materials and their geological remains ¹⁻¹⁰ . Ordination methods, such as Principal Component Analysis (PCA), rely on spectral variance to create a compositional space ¹ , the ChemoSpace, grouping samples based on spectroscopic manifestations that reflect different biological properties or geological processes ¹⁻⁷ . PCA allows to reduce the dimensionality of complex spectroscopic data and facilitates the extraction of relevant informative features into data formats suitable for downstream statistical analyses, thus representing an essential first step in the development of diagnostic biosignatures. However, there is presently no systematic survey of the impact of sample, instrument, and spectral processing on the occupation of the ChemoSpace. Here the influence of sample count, signal–to–noise ratios, spectrometer decalibration, baseline subtraction routines, and spectral normalization on ChemoSpace grouping is investigated using synthetic spectra. Increase in sample size improves the dissociation of sample groups in the ChemoSpace, however, a stable pattern in occupation can be achieved with less than 10 samples per group. Systemic noise of different amplitude and frequency, features that can be introduced by instrument or sample 11,12 , are eliminated by PCA even when spectra of differing signal–to–noise ratios are compared. Routine offsets (± 1 cm ⁻¹ ) in spectrometer calibration contribute to less than 0.1% of the total spectral variance captured in the ChemoSpace, and do not obscure biological information. Standard adaptive baselining, together with normalization, increase spectral comparability and facilitate the extraction of informative features. The ChemoSpace approach to biosignatures represents a powerful tool for exploring, denoising, and integrating molecular biological information from modern and ancient organismal samples.
... Spectroscopy and geochemistry offer another approach. Vibrational, infrared, and Raman spectroscopy, for example, allows the molecular compounds present in organic material and the thermal maturity of a fossil to be determined (Hickman-Lewis et al., 2016;Olcott Marshall and Marshall, 2015). Carbon isotope analysis (Rosing, 1999;Tashiro et al., 2017) of carbonaceous remains adds a strong component to help determine the biogenic character, or not, of a given relic. ...
Sediments from the 2.1- to 1.9-billion-year-old Francevillian Group in southeastern Gabon include centimeter-sized pyritized structures suggestive of colonial organisms (El Albani et al., 2010), some of which may have been motile (El Albani et al., 2019). However, these interpretations were largely based on morphological and geochemical characteristics that lack metabolic clues and/or can be explained by abiotic processes. To move this work forward, we describe other centimeter-sized specimens, loosely referred to as lenticular forms (LF), from the same area and apply a more holistic approach including morphology, mineralogy, and geochemistry. The objects are 0.2–4 cm in diameter, and most of them are endowed with a regular brim that scales proportionally to external diameter reminiscent of biological order, hence rendering the LF putative biogenic traces. The LF are perfectly delineated in every direction and deflect the sedimentary layers on which they rest. X-ray microtomography further demonstrates that the LF are syn-depositional features and not concretions, while lead isotope systematics indicate that the geochemical imprint of diagenesis is inconsequential. Low sulfur content is largely concentrated in the organic matrix, and scarcity of pyrite and its persistence as micron-sized crystals show that the role of sulfate reduction is minor. Most interestingly, the fillings of the LF cavities show large and correlated excesses of organic carbon and zinc, with the latter being distinctly enriched in its light isotopes. The geochemical anomalies of the fillings relative to the host rock, notably those associated with Zn, clearly were buried with the LF, and further imply biogenicity. In this regard, a ten-fold increase in LF size towards the top of the black shale series hosting the LF might be related to increasing Zn (nutrient) availability. Although we cannot conclude with any certainty what these remnant organisms were, their features all taken together are evocative of very large agglutinate protists that grazed on bacterial biomass either in the water column or as benthic mats.
... The phosphate ν1 band was also observed as a shoulder at ca. 960 cm -1 . The bands around 1450 cm -1 (A-type carbonated apatite) and 1417 cm -1 (B-type carbonated apatite) were assigned to a ν3 vibrational mode and the band at 872 cm -1 (B-type carbonated apatite) is due to the ν2 vibrational mode of carbonate ions (Elliot, 1985;Rey et al., 1991;Lebon et al., 2011;Marshall and Marshall, 2015). Fig. 3B shows the spectral changes of the average ATR-FTIR spectra of human bone remains from Hakemi Use as a function of temperature values (unburned-25°C, 300°C, 500°C, 700°C and 900°C). ...
Physical and chemical properties of skeletal bone undergo significant alterations during burning. The analysis of heat-induced changes in human skeletal remains has been providing important knowledge that has been applied to the research of burned bones from archaeological and forensic settings.
... Each type of chemical bond will absorb infrared (IR) waves in a distinct wave number range in the near-IR (12,500-4000 cm −1 ), mid-IR (4000-400 cm −1 ), or far-IR (400-10 cm −1 ) regions. Most of the important chemical signals that are indicative of functional groups will be present in the mid-IR range [43]. FTIR can be combined with light microscopy to identify the location of the detected functional groups in the sample. ...
This review provides an overview of organic compounds detected in non-avian dinosaur fossils to date. This was enabled by the development of sensitive analytical techniques. Non-destructive methods and procedures restricted to the sample surface, e.g., light and electron microscopy, infrared (IR) and Raman spectroscopy, as well as more invasive approaches including liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), time-of-flight secondary ion mass spectrometry, and immunological methods were employed. Organic compounds detected in samples of dinosaur fossils include pigments (heme, biliverdin, protoporphyrin IX, melanin), and proteins, such as collagens and keratins. The origin and nature of the observed protein signals is, however, in some cases, controversially discussed. Molecular taphonomy approaches can support the development of suitable analytical methods to confirm reported findings and to identify further organic compounds in dinosaur and other fossils in the future. The chemical properties of the various organic compounds detected in dinosaurs, and the techniques utilized for the identification and analysis of each of the compounds will be discussed.
... By the turn of the 21st century, advances in slice-based, computed-tomographic (CT) imaging, surface-based laser scanning, and photogrammetry have revolutionized fossil restoration. Newer methods, such as "vibrational spectroscopy," are adding to our understanding of the preservation and modification of fossilized tissues (Schopf et al., 2005;Gutiérez-Garcia et al., 2015;Marshall and Marshall, 2015). Digital images are obtained by increasingly refined scanning methods that capture both the external and internal morphology of fossils, which can then be manipulated digitally for graphical restoration, skeletal articulation, animation of joint excursion or movement, other biomechanical hypothesis testing in silico (e.g., examination of stress/strain through finite element analysis), and physical scalable reproduction (Lautenschlager, 2016a;Lautenschlager, 2016b;Lautenschlager, 2017;Kambic et al., 2017;Vidal et al., 2020). ...
Digital restoration of fossils based on computed tomographic (CT) imaging and other scanning technologies has become routine in paleontology. Digital restoration includes the retrodeformation and reconstruction of a fossil specimen. The former involves modification of the original 3D model to reverse post-mortem brittle and plastic deformation; and the latter involves the infilling of fractures, addition of missing pieces, and smoothing of the mesh surface. The restoration process often involves digital editing of the specimen in ways that are difficult to document and reproduce. To record all actions taken during the digital restoration of a fossil, we outline a workflow that generates both the restored bone and the sequence of steps involved in its retrodeformation and reconstruction. Our method can also generate an animation showing the transformation of the original digital model into its final form. We applied this method to a dorsal rib and frontal bone of a small-bodied Jurassic-age armored dinosaur from Africa, the digital restoration of which engaged all modalities of deformation (translation, rotation, scaling, distortion) and reconstruction (fracture infilling, adding missing bone, surface smoothing). Each bone was CT-scanned, segmented, and imported into Blender, an open-source 3D-graphics animation program. Blender has an animation tool called an “armature” that allows for precise control over portions of a surface mesh while keeping a record of manipulations. To retrodeform a fossil, an armature is created and then linked, or “rigged,” to the fossil in order to control the displacement and distortion of its fragments. After using the armature to perform retrodeformation, we use Blender to record the movement and distortion of each fragment and also record reconstructive modifications. By ensuring documentation and reproducibility in an open-source program, our workflow and output open a window onto the heretofore largely hidden process of digital restoration in paleontology.
... Beyond the present enamel Ca isotope data set, further investigation of dentine and bone, as initiated by Heuser et al. (2011), is desirable. Thomas et al. (2007) have shown that Raman spectroscopy was a non-destructive and rapid technique for determining significant changes in the microcrystalline structure of biogenic phosphates (bones and teeth) induced by burial and fossilization processes (Olcott Marshall and Marshall, 2015;Keenan, 2016). As with other techniques, using Fourier-transform infrared spectroscopy and X-ray diffraction, Pucéat et al. (2004) defined a new crystallinity index from the ratio of the FWHM of the intense peak of the PO 4 symmetric stretching mode in a biogenic apatite sample. ...
Reconstructing dinosaur trophic structure prior to the Cretaceous−Paleogene (K−Pg) boundary may provide information about ecosystem organization and evolution. Using calcium isotopes, we investigate preserved biogenic isotope compositions in a set of dinosaur teeth from three continental formations from Alberta, Canada, to assess latest Cretaceous food web structure. Tooth enamel δ44/42Ca values are presented for tyrannosaurids (n = 34) and potential large herbivorous prey (n = 42) in the upper Campanian Dinosaur Provincial Park Formation, uppermost Campanian−Maastrichtian Horseshoe Canyon Formation, and upper Maastrichtian−lower Paleocene Scollard Formation, spanning the last ∼10 m.y. of the Cretaceous. The influence of diagenesis is assessed in a subset sample through major and trace elemental concentrations and ultraviolet (UV) Raman spectra, which provides a framework for interpreting calcium isotope values. In the Dinosaur Park Formation, hadrosaurid δ44/42Ca values are systematically heavier than ceratopsid values, a difference that is interpreted to reflect niche partitioning among megaherbivores. Tyrannosaurid δ44/42Ca values are scattered but on average, they are 44Ca-depleted relative to herbivorous dinosaurs in all three formations. As interpreted from the Dinosaur Park data set, tyrannosaurids may have preferentially fed on hadrosaurids. These analyses offer possibilities for testing whether trophic structure among non-avian dinosaur ecosystems changed several millions of years prior to the K−Pg boundary.
... ATR-FT-IR spectrometer can be used for the identification of the thermally immature organic substance (Marshall & Marshall 2015). Fossil organic substance (kerogen) usually gives IR bands at following wavenumber regions: 3000-2800 cm −1 and 1500-1350 cm −1 (aliphatic C-H stretches and bends in the CH 3 and CH 2 ); 1200-1000 cm −1 (C-O stretches); 1700-1600 cm −1 (C-C stretches in the aromatic ring) (e.g. ...
The anatomy of a dorsal head shield of an agnathan fossil Kalanaspis delectabilis, belonging to class Osteostraci from the Aeronian (early Silurian) Kalana Lagerstätte of Estonia was studied using the X‐ray computer‐tomography. Scanning exposed shallow superficial relief on the dorsal surface of the head shield, which unmasked the internal anatomy of the specimen. The Kalanaspis fossil displays a mosaic of morphological characters: the overall shape of the cephalothoracic head shield and the main structures, like lateral fields, are typical for the group, but instead of the open pineal foramen, common to most osteostracans, the organs in the pineal region are concealed by the shield. A combination of characters that are common to osteostracans, along with unique features known among other early vertebrates, refer to the position of K. delectabilis within the stem group of Osteostraci. The carbonaceous mode of preservation of the head shield of the Kalanaspis fossil, previously undocumented among vertebrate fossils, contradicts the conventional fossilization pattern and refers to an unusual taphonomic history. This anomalous type of preservation appears to be the key to unlock its fossilization history and the complex taphonomic conditions of the whole Kalana Lagerstätte. The main processes for the atypical fossilization of the specimen of K. delectabilis are most likely related to the microbially controlled dissolution of apatitic bone tissues and replacement with microbial biofilms, possibly by the invasion of collagenolytic bacteria.
... These factors induce the displacement and decrease of the intensity of the peaks. 7,27 Furthermore, the samples fluoresced during data collection, causing the signal intensities to drop dramatically. For this reason, Raman spectra show a break between 1200 and 2000 cm −1 to minimize the interference caused by the fluorescence presented by the determined minerals as the working power varied. ...
... No manganese oxide peaks were found with the Raman analyses other than within the MS. The MS often display broad Raman peaks and sometimes fluorescence, consistent with an amorphous mineralogical composition as well as the presence of organic material and metal oxides (Olcott and Marshall 2015). This anisotropic nature of the MSs are confirmed by analyses using optical microscopy retardation plate (530 nm, Nobile et al. 2009) showing strong anisotropic colours of the MS, in contrast to the surrounding crystalline aragonite (Fig. 2c). ...
Micrometer sized stromatolitic structures called Frutexites are features observed in samples from the deep subsurface, and hot-spring environments. These structures are comprised of fine laminations, columnar morphology, and commonly consist of iron oxides, manganese oxides, and/or carbonates. Although a biological origin is commonly invoked, few reports have shown direct evidence of their association with microbial activity. Here, we report for the first time the occurrence of subsurface manganese-dominated Frutexites preserved within carbonate veins in ultramafic rocks. To determine the biogenicity of these putative biosignatures, we analyzed their chemical and isotopic composition using Raman spectroscopy and secondary ion mass spectroscopy (SIMS). These structures were found to contain macromolecular carbon signal and have a depleted 13C/12C carbon isotopic composition of – 35.4 ± 0.50‰ relative to the entombing carbonate matrix. These observations are consistent with a biological origin for the observed Frutexites structures.
... These geochemical-spectroscopic methods of determining the material composition have been applied in studies of both mineralized and organic fossils of Ediacaran and other ages and for distinguishing in-life from taphonomic mineralization (Schopf et al., 2005;Cai et al., 2012;Meyer et al., 2012Meyer et al., , 2014Moczydłowska et al., 2014;Schiffbauer et al., 2014;Tarhan et al., 2014;Muscente et al., 2015;Pruss et al., 2015Pruss et al., , 2018Shang et al., 2018). Laser-Raman spectroscopy is a nondestructive optical method that provides the information to identify the chemical composition of fossils and allows their mineral identification (Kudryavtsev et al., 2001;Schopf et al., 2002Schopf et al., , 2005Wacey, 2009;Olcott Marshall and Marshall, 2015). In the present case study, this method supports biomineralization, as does the petrography. ...
In this study, a new assemblage of Ediacaran metazoan fossils is reported from the basal Stáhpogieddi Formation on the Digermulen Peninsula of Arctic Norway, including Anulitubus n. gen. Moczydłowska in Moczydłowska et al., Anulitubus formosus n. gen. n. sp. Moczydłowska in Moczydłowska et al., Coniculus n. gen. Moczydłowska in Moczydłowska et al., Coniculus elegantis n. gen. n. sp. Moczydłowska in Moczydłowska et al., Fistula n. gen. Moczydłowska in Moczydłowska et al., and Fistula crenulata n. gen. n. sp. Moczydłowska in Moczydłowska et al. The specimens are three-dimensionally preserved and include tubular and conical skeletons that are morphologically distinguished by their body-wall constructions, radial symmetry, polarity, segmentation, and annulation. The skeletons are interpreted to be biomineralized by primary silica based on computed micro-tomographic, petrographic, geochemical, and spectroscopic evidence of originally rigid body wall with layers of constant thicknesses, composed of opal, microcrystalline quartz, and an admixture of carbonaceous material, which differ from the host sediment mineralogy and do not show replacement or encrustation. The fossil-bearing interval immediately overlies strata of Gaskiers age and can be bracketed within 580–541 Ma, but it is estimated to be ca. 575 Ma on the basis of averaged sedimentation rates and biostratigraphic correlations with Ediacaran biota found in up-section deposits of ca. 558–555 Ma. Future new findings of such fossils in different preservation modes and further multi-collector inductively coupled plasma mass spectrometry, which shows the silicon fractionation and traces its biogenic origin versus inorganic mineralization, may corroborate the interpretation of biogenic silicification of these earliest skeletal fossils.
UUID: https://zoobank.org/6bccada1-870e-47b0-b819-82685152ea54
... Techniques based on molecular and vibrational spectroscopy have been used over the past several decades to help unravel some of the uncertainties that exist with conventional laboratory methods. Fourier transform infrared (FTIR) and Raman spectroscopy are relatively non-destructive techniques that can directly and rapidly assess the dispersed organic and carbonaceous materials which are present in a range of sedimentary rocks [10,11]. Advances in FTIR spectroscopy over the past several decades have enabled the characterisation of organic matter in rocks obtained from a range of different geological settings and environments. ...
The chemical analysis of carbonaceous and organic materials in geological samples (i.e., rocks) is an important and necessary step of hydrocarbon resource development. Despite some significant advances in the last several decades, there still is a need for improved analytical techniques that deliver greater sensitivity and reliable information regarding source rock properties and characterisation. Infrared spectroscopy is a promising technique in terms of providing both qualitative and quantitative information on carbonaceous materials. However, the application of this method for routinely determining parameters relevant to the organic geochemistry of geological systems has not been widely accepted. Here, we compare infrared spectroscopy to standard methods for deriving the total organic carbon content, number of free/volatile hydrocarbons and the hydrocarbon generating potential in shale rocks. Two common methods for collecting infrared spectra, namely Attenuated Total Reflectance (ATR) and Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectroscopy, were evaluated to determine which one is most suitable for shale characterisation. It was revealed that the carbonate overtone band is largely responsible for causing quantitative interferences and errors. Although DRIFT was more sensitive, it was found that the ATR method is less prone to spectral interferences caused by the carbonate overtone band. Irrespective, both methods yielded reasonable correlations against established analytical techniques providing that the CH absorption band was corrected for variations in the carbonate content.
... All spectra exhibit common vibrational bands corresponding to organic and mineral components of bone/ bone remains [20][21][22][42][43][44][47][48][49][50]65,67,68]. ...
Examining diagenetic parameters such as the organic carbonate contents and the crystallinity of bone apatite quantify the post-mortem alteration of bone. Burial conditions are one of the factors that can influence the diagenesis process. We studied the changes to the organic and mineral components and crystallinity of human bone remains from five Medieval sites in Turkey: Hakemi Use, Komana, İznik, Oluz Höyük and Tasmasor using Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) and principal component analysis (PCA).
Analysis of spectral band ratios related to organic and mineral components of bone demonstrated differences in the molecular content in the skeletal remains from the five sites. In order to examine the degree of carbonation of a phosphate matrix, curve-fitting procedures were applied to the carbonate band. We found that the infrared crystallinity index appears to not be sensitive to carbonate content at room temperature for the bone remains studied here. The recrystallization process in bone remains behaved differently among the archaeological sites. The results demonstrate that the burial environments differently affect the organic and mineral components of archaeological bone remains.
... Recent effort has been devoted to the development of vibrational spectroscopic technologies based on Fourier transform infrared (FTIR) and Raman spectroscopy (Bonoldi et al., 2016;Pejcic et al., 2017;Wilkins et al., 2018). These are relatively non-destructive techniques that can directly and rapidly assess the dispersed organic and carbonaceous materials which are present in a range of sedimentary rocks (Chen et al., 2015;Olcott-Marshall and Marshall, 2015). However, very little has been reported on the combined application of FTIR and Raman spectroscopy for determining the organic geochemistry of shales. ...
Determining the amount and geochemistry of organic matter in rocks is an important and essential step of hydrocarbon resource development. Despite extensive publications there still is a need for improved analytical methods for source rock evaluation and characterisation. Techniques based on infrared and Raman spectroscopy are promising in terms of providing qualitative and quantitative information on carbonaceous materials. However, the application of these methods for routinely determining parameters relevant to the organic geochemistry of petroleum systems has not been thoroughly addressed. The objective of this research is to evaluate the reliability of vibrational spectroscopic techniques for understanding the organic composition and geochemistry of shale rocks. It has been shown that infrared and Raman spectroscopy can be used to derive a number of important parameters such as the hydrocarbon generating potential, thermal maturity and total organic carbon.
... Vibrational spectroscopic techniques such as Fourier transform infrared (FTIR) and Raman spectroscopy have also been used to analyse cuticle chemistry, because they have the advantages of being non-destructive, efficient and able to analyse very small sample quantities (Heredia-Guerrero et al. 2014;Olcott Marshall and Marshall 2014). These approaches have been employed in both modern and fossil settings, with the aims of understanding cuticle chemistry and its response to environmental change and ontogenetic development (Villena et al. 2000;Ribeiro da Luz 2006;Dominguez et al. 2012;Littlejohn et al. 2015;Innes et al. 2019;Liu et al. 2019), diagenesis/fossilisation processes and the characterisation of organic matter in the geological record (Lyons et al. 1995;Collinson et al. 1999;Zodrow et al. 2000Zodrow et al. , 2012aMastalerz 2002, 2009;D'Angelo 2006;D'Angelo et al. 2010D'Angelo et al. , 2011D'Angelo and Zodrow 2015), and the taxonomic identification of plants using their chemical signature (termed chemotaxonomy) Mastalerz 2001, 2002;D'Angelo 2006;D'Angelo et al. 2010;D'Angelo and Zodrow 2015;Vajda et al. 2017). ...
Cuticles have been a key part of palaeobotanical research since the mid-19th Century. Recently, cuticular research has moved beyond morphological traits to incorporate the chemical signature of modern and fossil cuticles, with the aim of using this as a taxonomic and classification tool. For this approach to work, cuticle chemistry would have to maintain a strong taxonomic signal, with a limited input from the ambient environment in which the plant grew. Here, we use attenuated total reflectance Fourier Transform infrared (ATR-FTIR) spectroscopy to analyse leaf cuticles from Ginkgo biloba plants grown in experimentally enhanced CO 2 conditions, to test for the impact of changing CO 2 regimes on cuticle chemistry. We find limited evidence for an impact of CO 2 on the chemical signature of Ginkgo cuticles, with more pronounced differences demonstrated between the abaxial (lower leaf surface) and adaxial (upper leaf surface) cuticles. These findings support the use of chemotaxonomy for plant cuticular remains across geological timescales, and the concomitant large-scale variations in CO 2 concentrations.
... Vibrational spectroscopic techniques such as Fourier transform infrared (FTIR) and Raman spectroscopy have also been used to analyse cuticle chemistry, because they have the advantages of being non-destructive, efficient and able to analyse very small sample quantities (Heredia-Guerrero et al. 2014;Olcott Marshall and Marshall 2014). These approaches have been employed in both modern and fossil settings, with the aims of understanding cuticle chemistry and its response to environmental change and ontogenetic development (Villena et al. 2000;Ribeiro da Luz 2006;Dominguez et al. 2012;Littlejohn et al. 2015;Innes et al. 2019;Liu et al. 2019), diagenesis/fossilisation processes and the characterisation of organic matter in the geological record (Lyons et al. 1995;Collinson et al. 1999;Zodrow et al. 2000Zodrow et al. , 2012aMastalerz 2002, 2009;D'Angelo 2006;D'Angelo et al. 2010D'Angelo et al. , 2011D'Angelo and Zodrow 2015), and the taxonomic identification of plants using their chemical signature (termed chemotaxonomy) Mastalerz 2001, 2002;D'Angelo 2006;D'Angelo et al. 2010;D'Angelo and Zodrow 2015;Vajda et al. 2017). ...
Cuticles have been a key part of palaeobotanical research since the mid-19th Century. Recently, cuticular research has moved beyond morphological traits to incorporate the chemical signature of modern and fossil cuticles, with the aim of using this as a taxonomic and classification tool. For this approach to work, cuticle chemistry would have to maintain a strong taxonomic signal, with a limited input from the ambient environment in which the plant grew. Here, we use attenuated total reflectance Fourier Transform infrared (ATR-FTIR) spectroscopy to analyse leaf cuticles from Ginkgo biloba plants grown in experimentally enhanced CO2 conditions, to test for the impact of changing CO2 regimes on cuticle chemistry. We find limited evidence for an impact of CO2 on the chemical signature of Ginkgo cuticles, with more pronounced differences demonstrated between the abaxial (lower leaf surface) and adaxial (upper leaf surface) cuticles. These findings support the use of chemotaxonomy for plant cuticular remains across geological timescales, and the concomitant large-scale variations in CO2 concentrations.
... Peak assignments are based on Larkin (2011) and on comparison with microfossil analyses in the literature (see Arouri et al., 1999;Coates, 2000;Marshall et al., 2005). The initial biopolymer composition of the living microorganisms can be altered by diagenesis (with possible aliphatization or sulfurization) and metamorphism (with possible aromatization) Marshall and Marshall, 2015). Consequently, comparison is made between analyses of microfossils with the same taphonomic history (same sample, different taxa), between identical taxa from different context (different taphonomy), and control of maturity with Raman spectroscopy. ...
Important biological and geological events occurred during the early to middle Neoproterozoic. Among diversifying eukaryotic assemblages, populations of Cerebrosphaera, a distinctive and robust organic-walled vesicular microfossil (acritarch), show restricted stratigraphic distribution in several late Tonian to early Cryogenian worldwide successions. Here, we report the first occurrence of this taxon in Africa, in the Bouenza Subgroup (Republic of the Congo), enlarging its paleogeographic distribution and biostratigraphic significance. We also attempt to determine its biological affinity, using a combined analytical approach on specimens from the Kanpa and Hussar formations, Australia, and from the Svanbergfjellet Formation, Spitsbergen. Morphological and quantitative analyses were performed using light microscopy and scanning electron microscopy. The analyses show fine-scale morphological details and a morphological continuum between the former species Cerebrosphaera ananguae and Cerebrosphaera buickii, confirming their synonymy as proposed by a recently revised taxonomy. These observations also highlighted the presence of a thin external envelope, previously reported but formerly described and illustrated here for the first time. The characteristics of this envelope, the large diameter range of the vesicles, and the absence of excystment structure, suggest that Cerebrosphaera was a metabolically active growing cell. Ultrastructural analyses performed with TEM revealed a complex multilayered wall ultrastructure. The molecular composition and thermal maturity of the organic walls were estimated using Infrared and Raman microspectroscopies. The wall of Cerebrosphaera has a highly aromatic composition with short/highly branched aliphatic chains. The complex morphology and wall ultrastructure, combined with the large size (not a criterion by itself) of Cerebrosphaera, confirm its eukaryotic nature. Comparison with strikingly similar modern analogues permits to suggest a possible affinity to stem metazoan eggs, based on morphology and ultrastructure, but the chemical composition is unlike known biopolymers. This hypothesis is also consistent with estimates from molecular clocks. If confirmed, our results would provide an older direct evidence for stem metazoans than the Cryogenian biomarker and Ediacaran body fossil records. Our study reveals that Cerebrosphaera populations are important for Neoproterozoic biostratigraphy, but also participated to the diversification of eukaryotes in worldwide connected oceans.
... Infrared (IR) spectroscopy, commonly referred to as Fourier transform infrared (FTIR) spectroscopy, has been widely used for several decades to understand the chemical properties and composition of a range of materials (rocks, cuttings, fossils and fluids) acquired from geological formations (Ganz and Kalkreuth, 1991;Chen et al., 2015;Olcott Marshall and Marshall, 2015). The IR spectrum is divided into three regions (i.e. ...
Shales are of significant interest as reservoirs, seals and overburden in petroleum exploration and production, geological storage of CO 2 and in the nuclear waste industry. Their properties and microstructure are difficult to measure and image and as such, there are still considerable gaps in our understanding of shale behaviour. The advent of more advanced and quantitative imaging methods along with novel sample preparation techniques including synchrotron imaging and K-edge subtraction with a contrast fluid, scanning (SEM) and transmission electron microscopy (TEM), have combined to allow the resolution of pores in the matrix and the organic matter in gas shales down to the nanometre scale. Textural quantification methods include neutron diffraction to quantify clay fabric alignment in siliciclastic shales as well as stress-dependent calcite c-axis orientation in carbonate-rich gas shales. The contents of the pores are also critical to the assessment of the preservation state of shales as well as the degree of water/gas saturation in resource shales. Combinations of dielectric analysis and 2 and 23 MHz nuclear magnetic resonance (NMR) measurements in siliciclastic and carbonate-rich gas shales can resolve not only the location of water, but also the interaction between water and mineral/organic surfaces in addition to the water and oil content. The organic content of shales is of particular interest in unconventional resources and this has driven application of Fourier transform infra-red (FTIR), to distinguish both mineral and organic maceral components in gas shales and Raman spectroscopy, which is increasingly used for organic matter characterisation in high maturity shales. Ultimately, shales are extremely complex nano-composite materials which require the application of multiple techniques to help determine their bulk physical and flow properties as well as factors controlling fabric and pore orientations and structure.
... Based on its capabilities and non-invasive, nondestructive nature, together with the minimal or no sample preparation requirements, confocal Raman spectroscopy is now widely used to investigate the chemical and molecular composition of liquid and solid materials in a wide range of research fields such as plant biology (e.g., Baranska et al., 2013), biomedical research (e.g., Kallaway et al., 2013), chemical kinetics (e.g., Ma et al., 2014), artpreservation and archaeology (Bouchard & Smith, 2003) and in geosciences and planetary exploration Olcott Marshall & Marshall, 2015). ...
Raman spectroscopy is a molecule-specific technique allowing the investigation of the chemical structure of organic and inorganic geological materials. Being a nobiostructures from the Barberton greenstone belt of South An-invasive analytical procedure, Raman spectroscopy is ideally suited to palaeontology. Raman spectroscopy is herein applied to the study of carbonaceous chert facies of the ~3.4 Ga old Buck Reef Chert of South Africa, which contains some of the oldest well-preserved evidence of early life. Laminated chert typically consists of microbands composed of microcrystalline quartz (chert) and an association of siderite and carbonaceous material (CM) in the form of mat-like laminations, simple carbonaceous grains, vein infills and diffuse CM. Using Raman spectroscopy, the structural characteristics of CM in mat-rich chert were investigated and compared with CM-rich grains from the same unit, which were deposited as layers that bear no evidence for mat construction. All CM retains a structural organisation consistent with the lower greenschist grade regional metamorphic imprint, however, a detailed study of the Raman signal of CM revealed some heterogeneity between different sedimentary facies, indicating the presence of different types of CM. Multiple CM precursors are indicated and may reflect different sources or different alteration chemistries of various microbial metabolic pathways. © 2010–2018 Italian Paleontological Society. All rights reserved.
... Turritellid septa were confirmed to be aragonitic using Raman spectroscopy, a nondestructive technique that can distinguish among aragonite, calcite, and vaterite (Frech et al. 1980;Urmos et al. 1991;Wehrmeister et al. 2010;Olcott Marshall and Marshall 2015; Supplementary Fig. S1). Spectra were acquired with a Renishaw InVia microRaman system housed at the Cornell Center for Materials Research using the 785 nm laser, with 10 s acquisition times, and between 5 and 10 accumulations to obtain good signalto-noise ratio. ...
Although generally considered rare in gastropods, septation has long been noted in turritellids, but functional hypotheses do not survive strong scrutiny. Here we outline a methodology for testing spandrel hypotheses and apply it to the problem of turritellid septa. We follow Gould in using “spandrel” as a term for all features that are nonadaptive sequelae of adaptive features of organisms, including those that are structurally necessary, those that are developmentally correlated, and nondeterministic by-products that are correlated to features under selection.
In turritellids, septa are constructed in microstructural continuity with secondary internal thickening of the shell, are highly variable features infraspecifically, and are strongly associated with degree of shell thickening. We therefore conclude that rather than being themselves adaptive, turritellid septa are spandrels of shell thickening. Turritellid septa are composed of crossed lamellar aragonite, which appears to be constructed by mantle epithelium over the visceral mass. Septation was also found in 22 of 24 gastropod families examined from a broad phylogenetic distribution. Septa thus appear to be a widespread feature of caenogastropods, in strong contrast to previous assertions that septa are less common in modern or high-spired shells.
... It is an effective method of extending the data available down to the molecular-structural level. Hence, there is an increasing interest in applying Raman spectroscopy to palaeontological studies, e.g. to elucidate the chemical composition of a wide variety of fossils (Igisu et al., 2014;Olcott Marshall and Marshall, 2015) and to ascertain the biogenicity of putative ancient microfossils (Schopf et al., 2002(Schopf et al., , 2005. Similarly, the disseminated organic matters in Doushantuo chert nodules were analyzed by Raman spectroscopy in Qu et al. (2017). ...
... Recently, in-situ analyses of Precambrian microfossils and carbonaceous matter preserved in thin sections have been used to obtain elemental, isotopic, and molecular compositions on nanometer-to-micrometer scales; these enable us to examine spatial relationships between their individual morphological structures and the surrounding minerals (e.g., Wacey et al., 2016). Micro-FTIR is one of the techniques used to characterize chemical components in microfossils, and has been used to examine biological affinities of Proterozoic organic-walled microfossils (e.g., Igisu et al., 2006;Olcott Marshall and Marshall, 2015). However, the spatial resolution of a conventional FTIR microspectrometer, which usually exceeds ~10 mm, is not tip. ...
Synchrotron radiation-based Fourier transform infrared microspectroscopy (SR micro-FTIR) was applied to ∼830 Ma prokaryotic fossils in a doubly polished thin section in order to examine the micrometer-scaled spatial distributions of organic components in the microfossils. Mapping analysis allowed us to locate aliphatic C-H bonds (∼2925 cm⁻¹ band and ∼2850 cm⁻¹ band) in two species of microfossils (a filament and a coccoid) with a ∼2 ×2 m² rectangular aperture. The distributions of the ∼2925 cm⁻¹ band and ∼2850 cm⁻¹ band agree with the morphology of the filament, and also seem to be partially distributed along the wall structure of the coccoid. These results suggest that the SR micro-FTIR can provide a few microscale distributions of organic/inorganic components in prokaryotic fossils in doubly polished thin sections. However, artifacts are sometimes generated when certain analytical models are used, and some caution must be exercised to avoid their generation.
... Infrared and Raman measurements offer information about the molecular structure from vibrational modes related to the chemical bonds, but, Raman spectroscopy is nondestructive analysis of the materials surface with no sample preparation. Another no sample preparation technique, energy dispersive spectroscopy (EDS), was used to furnish a rapid elemental (chemical) quantification of the samples [10,[12][13][14][15][16][17]. From these results, it was possible to infer aspects related to the feeding habits of the animals that have produced the coprolites originated from the two different sedimentary basins. ...
In this paper we performed the study of two coprolites (fossilized feces) collected from the exposed levels of the Pedra de Fogo Formation, Parnaiba Sedimentary Basin, and Rio do Rasto Formation, Paraná Sedimentary Basin, both of the Palaeozoic era (Permian age). They were characterized using X-ray diffractometry, infrared, Raman and energy dispersive spectroscopy techniques in order to aid our understanding of the processes of fossilization and to discuss issues related to the feeding habits of the animals which generated those coprolites, probably cartilaginous fishes. The results obtained using a multitechnique approach showed that although these coprolites are from different geological formations, 3000 km away from each other, they show the same major crystalline phases and elemental composition. The main phases found were hydroxyapatite, silica, calcite and hematite, which lead to infer that those coprolites were formed under similar conditions and produced by a similar group of carnivore or omnivore fishes.
Raman spectroscopy is a popular tool for characterizing complex biological materials and their geological remains. Ordination methods, such as principal component analysis (PCA), use spectral variance to create a compositional space, the ChemoSpace, grouping samples based on spectroscopic manifestations reflecting different biological properties or geological processes. PCA allows to reduce the dimensionality of complex spectroscopic data and facilitates the extraction of informative features into formats suitable for downstream statistical analyses, thus representing a first step in the development of diagnostic biosignatures from complex modern and fossil tissues. For such samples, however, there is presently no systematic and accessible survey of the impact of sample, instrument, and spectral processing on the occupation of the ChemoSpace. Here, the influence of sample count, unwanted signals and different signal‐to‐noise ratios, spectrometer decalibration, baseline subtraction, and spectral normalization on ChemoSpace grouping is investigated and exemplified using synthetic spectra. Increase in sample size improves the dissociation of groups in the ChemoSpace, and our sample yields a representative and mostly stable pattern in occupation with less than 10 samples per group. The impact of systemic interference of different amplitude and frequency, periodical or random features that can be introduced by instrument or sample, on compositional biological signatures is reduced by PCA and allows to extract biological information even when spectra of differing signal‐to‐noise ratios are compared. Routine offsets ( 1 cm ⁻¹ ) in spectrometer calibration contribute in our sample to less than 0.1% of the total spectral variance captured in the ChemoSpace and do not obscure biological information. Standard adaptive baselining, together with normalization, increases spectral comparability and facilitates the extraction of informative features. The ChemoSpace approach to biosignatures represents a powerful tool for exploring, denoising, and integrating molecular information from modern and ancient organismal samples.
The identification of preserved organic material within fossils is challenging. Well-established vibrational spectroscopy techniques, such as micro-FTIR (Fourier Transform Infra-Red spectroscopy), have been widely used to investigate organic fossils molecular composition. However, even when well-adapted to study objects several tens of micrometre across, they still suffer from limitations, notably regarding resolution and sample preparation requirements. Optical Photothermal Infrared Spectroscopy (O-PTIR), a recently developed technique, overcomes the challenges of bench-top FTIR spectroscopy. By combining an IR excitation laser with a 532 nm green probe laser, this technique allows molecular characterization at high spectral resolution (~2 cm-1) and with extremely fine spatial resolution (~500 nanometres). Additionally, problems linked with sample thickness, surface roughness and particle shape/size are mitigated when compared with FTIR or Atomic Force Microscopy-based nanoIR techniques. Here we show that O-PTIR can be used to easily and successfully map the molecular composition of small organic fossils preserved in silica matrix (chert) in petrographic thin sections. Our study reveals that O-PTIR resolves spatial heterogeneities in the preserved molecular composition of organic fossils (spores and plants) at a sub-micron scale, and that such heterogeneities occur in the cuticle in an early Devonian plant, where they suggest a structural organisation comparable to modern plants. These results on 400 million years old fossils, validate O-PTIR as a powerful and extremely promising new tool for nanoanalytical palaeontology.
Polyene pigments represent a major class of pigments in present-day organisms. Their occurrence in fossils has been frequently discussed, but to date no spectroscopic evidence has been found. Here, we use in situ Raman spec-troscopy to examine the chemistry of exceptionally well-preserved gastropod shells with colour preservation from the Middle Miocene of the Vienna Basin (Austria, Hungary). Raman signals indicative of the presence of intact (i.e. non-hydrogenated) polyene pigments were obtained from fossil shells with reddish colour patterns, thus revealing the first record of intact polyenes in fossils. The observed Raman values are in good agreement with those of unmethylated (non-carotenoid) polyenes. Fossil polyene pigments were detected in representatives of the superfamily Cerithioidea, but not in representatives of other gastropod families with colour preservation found at the same localities, demonstrating that the occurrence of polyene pigments is taxon-specific. Our results show that Raman spectroscopy represents a valuable tool for the non-destructive screening of rare fossils with colour preservation for the occurrence of polyene pigments.
Sporomorphs (pollen and spores) are a mainstay of research into past vegetation, and increasingly spor-omorph chemistry is being used as a palaeoecological tool. To make extant sporomorphs directly comparable to fossil specimens, fresh material is processed to remove labile compounds and isolate the sporopollenin wall. A range of processing approaches are currently in use, but the chemis-tries produced by these different techniques have not yet been compared across a range of taxa. It is therefore not clear how they compare in terms of efficiently isolating sporopollenin without changing its chemical structure, and what impact they have on relative chemical similarities and differences among taxa (i.e. whether more closely related species will always appear chemically more similar, regardless of how they have been processed). Here, we test this by applying five different processing approaches to sporomorphs from 15 taxa from across the vascular plant phylogeny. We show that each approach has its own idiosyncrasies in terms of impacts on sporomorph chemistry. For the most part a common pattern of among-taxon chemical variability is uncovered, and a phylogenetic signal within sporopollenin chemistry is supported. Working with spectral derivatives generally increases agreement among the different processing approaches, but decreases the strength of the phylogenetic signal. No one processing approach is ideal, and the choice of which to use is likely to depend on the goal of the study, the type and quantity of material being processed, and the laboratory facilities available for processing.
The affinities of extinct organisms are often difficult to resolve using morphological data alone. Chemical analysis of carbonaceous specimens can complement traditional approaches, but the search for taxon-specific signals in ancient, thermally altered organic matter is challenging and controversial, partly because suitable positive controls are lacking. Here, we show that non-destructive Fourier Transform Infrared Spectroscopy (FTIR) resolves in-situ molecular fingerprints in the famous 407 Ma Rhynie chert fossil assemblage of Aberdeenshire, Scotland, an important early terrestrial Lagerstätte. Remarkably, unsupervised clustering methods (principal components analysis and K-mean) separate the fossil spectra naturally into eukaryotes and prokaryotes (cyanobacteria). Additional multivariate statistics and machine-learning approaches also differentiate prokaryotes from eukaryotes, and discriminate eukaryotic tissue types, despite the overwhelming influence of silica. We find that these methods can clarify the affinities of morphologically ambiguous taxa; in the Rhynie chert for example, we show that the problematic “nematophytes” have a plant-like composition. Overall, we demonstrate that the famously exquisite preservation of cells, tissues and organisms in the Rhynie chert accompanies similarly impressive preservation of molecular information. These results provide a compelling positive control that validates the use of infrared spectroscopy to investigate the affinity of organic fossils in chert.
Fourier transform infrared spectroscopy (FTIR) provides a rapid non-destructive molecular characterization of organic and inorganic material in geological samples. Combination of qualitative and semi-quantitative approaches are routinely used in FTIR study of kerogen and coals. A diversity of descriptors provides straightforward tools to characterize kerogen type, composition and structure. However, only a few of these descriptors are applied in the chemical investigation of Precambrian organic-walled microfossils. Synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIR) permits high spatial resolution investigations of organic matter in a large range of applications in biology, geochemistry and cosmochemistry, but remains rarely applied in Precambrian microfossils studies. Here we show that SR-FTIR spectroscopy combined with an integrative approach of kerogen description is particularly relevant for the study of minute organic-walled microfossils of unknown biological origin. The analyses of five morphospecies from three different Proterozoic formations in northwestern Canada highlight kerogen signatures rich in aromatic, aliphatic and oxygenated moieties. This is evidenced by the combined use of spectrum qualitative descriptions (band assignments and positions) and the calculations of semi-quantitative parameters using intensities and integrated areas of absorption bands (CH2/CH3, R3/2, Al/C=C, C=O/C=C, A factor, C factor). Altogether, this study demonstrates the interest of an integrative approach when investigating the chemistry of organic-walled microfossils with FTIR spectroscopy.
UV light‐induced fluorescence is widely used as a key to reveal residual shell colour patterns of Neogene and Palaeogene molluscs. However, only few examples of fluorescent colour patterns are known from Mesozoic marine shells and little is known about the nature of fluorescence in fossils. Here, UV light‐induced fluorescence reveals previously unseen abundance and diversity in the colour patterns of the basal pectinid Pleuronectites laevigatus from the Middle Triassic Muschelkalk of Central Europe. In addition to known variations of radial bands, a multitude of zigzag and zigzag‐related patterns was found. The diversity of colour patterns is comparable to modern pectinids and is interpreted as colour pattern polymorphism. Raman spectra of the colour patterns indicated the preservation of residual organic pigments with aromatic moieties. The fluorescence properties of P. laevigatus and other basal pectinids from the Muschelkalk of Germany and France are described in detail, suggesting that colour pattern fluorescence is due to colourless diagenetic products of the pigments, not to the fossil pigments themselves. A remarkable feature of the colour patterns of P. laevigatus is the presence of different fluorescence colours. Because a gradual shift of the fluorescence colour from yellow to red with decreasing intensity to finally non‐fluorescent is observed, which correlates with the provenance of the specimens, the fluorescence properties are interpreted to reflect differences in diagenetic history. The results show that the fluorescence colour of fossil molluscs, especially of Mesozoic molluscs, may be affected by diagenesis and should only be used with caution for taxonomic purposes.
The “Search for life”, which may be extinct or extant on other planetary bodies is one of the major goals of NASA planetary exploration missions. Finding such evidence of biological residue in a vast planetary landscape is an enormous challenge. We have developed a highly sensitive instrument, the “Compact Color Biofinder”, which can locate minute amounts of biological material in a large area at video speed from a standoff distance. Here we demonstrate the efficacy of the Biofinder to detect fossils that still possess strong bio-fluorescence signals from a collection of samples. Fluorescence images taken by the Biofinder instrument show that all Knightia spp. fish fossils analysed from the Green River formation (Eocene, 56.0–33.9 Mya) still contain considerable amounts of biological residues. The biofluorescence images support the fact that organic matter has been well preserved in the Green River formation, and thus, not diagenetically replaced (replaced by minerals) over such a significant timescale. We further corroborated results from the Biofinder fluorescence imagery through Raman and attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopies, scanning electron microscopy, energy dispersive X-ray spectroscopy (SEM–EDS), and fluorescence lifetime imaging microscopy (FLIM). Our findings confirm once more that biological residues can survive millions of years, and that using biofluorescence imaging effectively detects these trace residues in real time. We anticipate that fluorescence imaging will be critical in future NASA missions to detect organics and the existence of life on other planetary bodies.
Chemical studies of fossil clam shrimps have taken relevance in the possibility of inferring about fossilization processes. Laser–induced Breakdown Spectroscopy (LIBS) is an attractive technique for geological analyses because the laser can ablate a few micrograms directly from a small area on the solid sample. On the other hand, RAMAN spectroscopy is a technique that allows rapid and non-destructive in situ detection of the components of the samples and has been used in micropalaeontology to identify carbonaceous materials. In this study, the aim was an analysis of the preservation of the clam shrimp Eosolimnadiopsis? Santacrucensis Gallego, 1994 from La Matilde Formation (Jurassic) using diverse methods including LIBS, RAMAN and X–ray fluorescence (XRF) techniques as well as surrounding rock. Afterwards LIBS results were evaluated using principal component analysis (PCA). According to XRF data, Si was the main element, indicating that the rock sample consists primarily of silicate minerals. Our results of LIBS and PCA analysis indicate chemical changes between the points from carapaces and rock matrix. Some areas of the carapace showed high peaks of Ca, Na, Mg and it was variable for Si, while in other parts of the carapace and rock matrix the Si remained at high intensity. Also, RAMAN spectroscopic analysis revealed the presence of amorphous carbon. This is the first report and evaluation on the LIBS and RAMAN techniques applied to fossil clam shrimps and contributes to obtaining a range of additional information to subsequently establish the different mechanisms involved in the taphonomic history of these organisms.
Limited taxonomic classification is possible for Archaean microbial mats and this is a fundamental limitation in constraining early ecosystems. Applying Fourier transform infrared spectroscopy (FTIR), a powerful tool for identifying vibrational motions attributable to specific functional groups, we characterized fossilized biopolymers in 3.5-3.3 Ga microbial mats from the Barberton greenstone belt (South Africa). Microbial mats from four Palaeoarchaean horizons exhibit significant differences in taxonomically informative aliphatic contents, despite high aromaticity. This reflects precursor biological heterogeneity since all horizons show equally exceptional preservation and underwent similar grades of metamorphism. Low methylene to end-methyl (CH 2 /CH 3) absorbance ratios in mats from the 3.472 Ga Middle Marker horizon signify short, highly branched n-alkanes interpreted as isoprenoid chains forming archaeal membranes. Mats from the 3.45 Ga Hooggenoeg Chert H5c, 3.334 Ga Footbridge Chert, and 3.33 Ga Josefsdal Chert exhibit higher CH 2 /CH 3 ratios suggesting mostly longer, unbranched fatty acids from bacterial lipid precursors. Absorbance ratios of end-methyl to methylene (CH 3 /CH 2) in Hooggenoeg, Josefsdal and Footbridge mats yield a range of values (0.20-0.80) suggesting mixed bacterial and archaeal architect communities based on comparison with modern examples. Higher (0.78-1.25) CH 3 / CH 2 ratios in the Middle Marker mats identify Archaea. This exceptional preservation reflects early, rapid silicification preventing the alteration of biogeochemical signals inherited from biomass. Since silicification commenced during the lifetime of the microbial mat, FTIR signals estimate the affinities of the architect community and may be used in the reconstruction of Archaean ecosystems. Together, these results show that Bacteria and Archaea flourished together in Earth's earliest ecosystems.
Studies of soft tissue, cells and original biomolecular constituents preserved in fossil
vertebrates have increased greatly in recent years. Here we report preservation of ‘skin’
with chemical and molecular characterization from a three-dimensionally preserved
caudal portion of an aspidorhynchid Cretaceous fish from the equatorial Barremian
of Colombia, increasing the number of localities for which exceptional preservation is
known. We applied several analytical techniques including SEM-EDS, FTIR and ToFSIMS to characterize the micromorphology and molecular and elemental composition
of this fossil. Here, we show that the fossilized ‘skin’ exhibits similarities with those from
extant fish, including the wrinkles after suffering compression stress and flexibility,
as well as architectural and tissue aspects of the two main layers (epidermis and
dermis). This similarity extends also to the molecular level, with the demonstrated
preservation of potential residues of original proteins not consistent with a bacterial
source. Our results show a potential preservation mechanism where scales may have
acted as an external barrier and together with an internal phosphate layer resulting
from the degradation of the dermis itself creating an encapsulated environment for the
integument.
SEM Observation of Non-Metallized Samples in Paleopalynology - Volume 26 Supplement - Mercedes di Pasquo, José Félix Vilá
The Perseverance rover (Mars 2020) is equipped with an instrumental and analytical payload capable of identifying a broad range of organic molecules in geological samples. To determine the efficacy of these analytical techniques in recognizing important ecological and environmental signals in the rock record, this study utilized analogous equipment, including gas chromatography/mass spectrometry, Raman spectroscopy, X-ray fluorescence (XRF), Fourier transform infrared spectroscopy, along with macroscopic and petrographic observations, to examine early-middle Cambrian microbialites from the Arrowie Basin, South Australia. Morphological and petrographic observations of these carbonate successions reveal evidence of hypersaline-restricted environments. Microbialites have undergone moderate diagenesis, as supported by XRF data that show mineral assemblages, including celestine and the illitization of smectite. Raman spectral data, carbon preference indices of ∼1, and the methylphenanthrene index place the samples in the prehnite/pumpellyite metamorphic facies. Pristane and phytane are the only biomarkers that were detected in the least thermally mature samples. This research demonstrates a multitechnique approach that can yield significant geological, depositional, paleobiological, and diagenetic information that has important implications for planning future astrobiological exploration.
Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of the biology of living organisms. These studies are limited with regard to extinct organisms, particularly those from the Mesozoic, because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, using the lens of the iconic non‐avian dinosaurs and their closest relatives, we discuss molecular methods that have been applied to Mesozoic fossils, and the challenges inherent in such studies. We address taphonomic processes resulting in the transition of a living organism from the biosphere to the fossil record, and their possible effects on downstream analyses, then consider the history of molecular studies applied to ancient remains. We evaluate these studies with respect to producing phylogenetically and/or evolutionarily significant data, address the limits and challenges on molecular studies in very old (>1 million years, Ma) material, and the complications of such analyses induced by molecular modifications and limits on comparative databases. Finally, we propose criteria for assessing the presence of endogenous biomolecules in ancient fossil remains as a starting framework for such studies, and conclude by discussing the power and potential of a molecular approach to Mesozoic fossils. This article is protected by copyright. All rights reserved
The Upper Carboniferous Sandstone at São Gonçalo do Gurgueia, Northeastern of the Brazil, is notable for its large number of preserved root-like structures. Among these structures it is found rhizoliths, fossils of a root system, containing the original cellular material and mineral impregnation and/or mineral replacement. Furthermore, the fossil can present characteristics of preserved anatomical features of the root. The present study shows the physico-chemical characterization results of the mineralized rhizolith (PIC 073.15) from Piauí Formation. This fossil was investigated through X-ray diffraction, X-ray fluorescence, Fourier transform infrared and Raman spectroscopy. The analysis showed that the SiO2 is the main component found in the sample, as demonstrated by the presence of quartz and clay minerals. However, there is also the presence of iron oxides (goethite and hematite) whose content increases from the inner to the outer part. The iron accumulation in PIC 073.15 suggests alternated oxidizing and reduction cycles, indicating humidity's variation of the Piauí Formation environment. The measurements suggest that the first mineralization of the rhizolith occurred through silification process followed by ferruginous precipitations (pos diagenetic process).
Stromatolites are laminated microbial deposits, normally composed of accretionary layers of cyanobacteria and other (often anoxic) bacteria which form on the sediment-water interface. Stromatolites represent one of the earliest records of life on Earth, dating back at least 3.7 billion years. Stromatolites became extremely diverse and very abundant throughout the Archean era 4-2.5 billion years ago, eventually causing increasing levels of atmospheric oxygen on Earth, as part of the Great Oxidation Event. The emergence and radiation of bilaterian animals and the development of new and more complex food webs during the early Cambrian coincided with a sharp decline in the abundance of stromatolites, yet they continued to exist in a range of Cambrian carbonate environments. The appearance, environment, and possibly the biogeochemistry, of Cambrian stromatolites appears to have been altered after the evolutionary development of epifaunal grazing bilaterians. Stromatolites were sampled from a wide spectrum of carbonate facies in the lower Cambrian Hawker Group in the Flinders Ranges, South Australia. The appearance, construction, distribution, and biogeochemistry of stromatolites from different depositional environments, including phosphatic hardgrounds, intertidal shoals and shelf/ramp settings is being described as part of an investigation into their morphological variation and ecological association, aiding the clarification of specific stromatolitic biofacies, and taxonomic associations. There has been little previous research on the morphology, architecture, growth, and biogeochemistry of Cambrian stromatolites in the Arrowie Basin. This study is designed to provide novel data about stromatolite evolution and ecology during a period dominated by the radiation of complex animals.
Microbialites are organo-sedimentary deposits, sometimes composed of accumulations of cyanobacteria and other bacteria, which form at the sediment-water interface. Microbialites represent one of the earliest records of life on Earth, with stromatolites - laminated accretionary microbialites - dating back at least 3.7 Ga. Stromatolites became extremely diverse and abundant throughout the Archean era (4-2.5 Ga), causing increased atmospheric oxygen levels on Earth as part of the Great Oxidation Event. The early Cambrian bilaterian radiation coincided with a sharp decline in stromatolite abundance.
In this study, microbialites were sampled from lower and middle Cambrian carbonate facies in the Arrowie Basin, South Australia. The appearance, construction, and biogeochemistry of stromatolites from different depositional environments, is described to investigate morphological variation and ecological associations which, may have been altered after the evolution of epifaunal grazing bilaterians. Few research projects have investigated stromatolites in the Arrowie Basin. This project investigates morphological variations in microbialites through petrographic observations, attempting to resolve previously unanswered biogeochemical questions using multi-disciplinary techniques: field relationships, hand and thin section observations, gas chromatography-mass spectrometry, Raman spectroscopy, fourier transform infrared spectroscopy, and X-ray fluorescence. The samples are highly thermally mature. Microbialites are not found in association with any fossils preserved in life position. Depositional environments ranging from shallow supratidal to low-energy subtidal are consistent with previous regional interpretations.
Large acritarchs were recovered from the Awaynat Wanin II Formation in the A1–69 borehole, western Libya at 394.4 m. This sample has been dated by acritarchs and spores as Givetian (Middle Devonian). Two species of acanthomorph acritarchs were recovered that are unusually large for the Paleozoic. The first type, represented by a single specimen, is a new occurrence of a previously described but unnamed form from the Middle Devonian of the Sahara. The second type, which is more abundant, is named as Vanguestainidium cucurbitulum gen. et sp. nov. Biogeochemical analysis using infrared microspectroscopy shows that the wall composition of this new taxon is close to algaenans isolated from the green alga Botryococcus braunii Kützing 1849 although these forms are not morphologically similar. The presence of well‐preserved fragile palynomorphs, abundant terrestrially‐derived palynomorphs including large megaspores, and rare marine palynomorphs suggests deposition in a low‐energy nearshore environment such as a coastal swamp.
Plumage colours bestowed by carotenoid pigments can be important for visual communication and likely
have a long evolutionary history within Aves. Discovering plumage carotenoids in fossil feathers could
provide insight into the ecology of ancient birds and non-avian dinosaurs. With reference to a modern
feather, we sought chemical evidence of carotenoids in six feathers preserved in amber (Miocene to
mid-Cretaceous) and in a feather preserved as a compression fossil (Eocene). Evidence of melanin
pigmentation and microstructure preservation was evaluated with scanning electron and light microscopies. We observed fine microstructural details including evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands did not confirm the presence of carotenoids in them. Carotenoids may have been originally absent from these feathers or the pigments may have degraded during burial; the preservation of microstructure may suggest the former. Significantly, we show that carotenoid plumage pigments can be detected without sample destruction through an amber matrix using confocal Raman spectroscopy.
Understanding the taphonomy of organic matter of sponges will be helpful in reconstructing a more exhaustive picture of the evolutionary history of these organisms from fossil records. The so-called ‘round sponge fossils’ (RSF) from the Burgess Shale-type (BST) Chengjiang Lagerstätte predominantly yield explicit organic remains, which seem more durable than the carbonaceous components of other fossils in the same Lagerstätte. In order to characterize these carbonaceous remains with Raman spectroscopy, a quick and non-destructive technique with the ability of analyzing the molecular composition and crystal structure in high resolution, 5 RSF specimens were examined in this study. Another Cambrian sponge fossil from the Xiaoyanxi Formation and a few algal remains from the Ediacaran Wenghui Biota were
also measured for comparison. The resulting Raman spectra of the macroscopic fossils confirmed previous observations on microfossils by Bower et al. (2013) that carbonaceous material with compositionally complex precursor material and low diagenetic thermal affection will plot in a certain region in a ΓD over R1 diagram. The results also successfully differentiated the sponge material from the algal material, as well as the fossil-derived signal from the background. However, it is still uncertain whether the different clustering of the RSF data and the algal data reflects the variance of precursor material or only the
diagenetic and geological history. The variance within the RSF data appears to be larger than that within the algal data. Considering the similar diagenetic history of the RSF, this is possibly reflecting the difference in precursor material. Nonetheless, further measurements on other fossil algal and poriferan material must be involved in the future, in order to improve and testify the current interpretation. Despite the properties revealed by Raman spectroscopy, the taphonomy of carbonaceous material in RSF has not been investigated. According to our observation, as well as the phenomenon described in previous studies, the preservation of the carbonaceous material in RSF does not show obvious taxonomical preferences. Because the RSF are polyphylogenetic and currently lack evidence to indicate that they represent any special development stage of sponges, we infer that this unusual carbonaceous preservation is due to diagenetic bias relating to their specific morphology, which in turn is possibly controlled by similar living environments. Again, to test these inferences, more detailed taxonomical and paleoecological studies are necessary.
Arpylorus antiquus, erected by Calandra in 1964, was isolated from upper Silurian sedimentary rocks from the Mechiguig 1 borehole in southern Tunisia, with other palynomorphs. The folded vesicle and the quadrangular form of the aperture break down into platelike fragments, resembling the tabulation of dinoflagellates. The presence of these elements has been used to interpret A. antiquus as a dinoflagellate cyst. The morphology and affinity of A. antiquus is reinterpreted herein based on investigation of larger sets of samples, including material from the type locality, together with material of Algeria, Saudi Arabia, and Brazil. More complete specimens than those previously described have been observed using gentle laboratory techniques, showing a large development of a fine membrane at the periphery of vesicles. This element was destroyed using classical palynological treatments, implying that the holotype is an incomplete specimen. The membrane at the periphery of vesicles and dorsoventral differentiation of these vesicles suggest that A. antiquus is a part of a more complex biological structure. We suggest a possible relationship with eurypterids, arthropods related to phyllocarids, represented by abundant fragments in the assemblages. Arpylorus antiquus is possibly a structure of storage. The chemical composition of A. antiquus using a Fourier transform infrared FTIR microspectroscopy analysis, reveals a wall composed of biopolymer that is not consistent with dinosporin. We conclude that Arpylorus antiquus is definitively not a dinoflagellate cyst. Although dinoflagellates may have older Paleozoic or even Proterozoic ancestors as the biomarker record may suggest, the dinoflagellate tabulation evolved only in the early Mesozoic.
Geochemical analyses of specimens of Reduviasporonites suggests that it is most likely of algal, rather than fungal origin. As a probable alga, Reduviasporonites is unlikely to be integral to the process of mass extinction occurring at or near the Permian‐Triassic boundary, as suggested by Visscher and other workers because it cannot have acted as a saprophytic metaboliser of dead vegetation resulting from that event. Moreover, it ranges outside the postulated time of mass extinction by at least 10 million years. Optical and electron microscopy of topotype material confirms that Reduviasporonites Wilson 1962 is the senior synonym of Chordecystia Foster 1979, and Tympanicysta Balme 1980. Moreover the type species of the last two genera, assigned in 1999 to Reduviasporonites by Elsik as R. chalastus (Foster) and R. stoschianus (Balme), are conspecific. The type species, R. catenulatus Wilson 1962, differs from R. chalastus in that its constituent cells are significantly smaller, more rounded, and have less well developed connecting areas (terminal rims) between cells. Brazilea helbyi forma gregata Foster 1979, recorded only from the type material of R. chalastus, is likely to be a junior synonym of that taxon.The stratigraphic occurrences of the species of Reduvia‐sporonites suggest that R. catenulatus is most common in the Wordian (Kazanian) of Oklahoma, though specimens of the size range associated with R. catenulatus are present very rarely in the Early Triassic Mazzin Member of the Werfen Formation, Austria. R. chalastus is present in Capitanian to Griesbachian rocks spanning at least 10 million years, and outside the more narrow age span of the Permian—Triassic boundary. The size of the constituent cells present in R. chalastus appears to be related to paleolatitude with large examples occurring in the paleotemperate Permian of China, Russia, and Australia (Moura) and smaller specimens occurring in the paleotropical and paleoequatorial Permian of northern Australia, Saudi Arabia, United Kingdom and Austria.
New types of carbonaceous filamentous microstructures have been identified in silica veins at two new localities in the ∼3.5 Ga North Pole area of Western Australia. Their carbon isotopic compositions were measured in situ by secondary-ion mass spectrometry. The carbonaceous filaments are ∼1μm wide, 10 to 100 μm long, and are permineralized in a fine-grained (∼1 μm) silica matrix. They are morphologically divided into three types (i.e., spiral, threadlike, and branched filaments). Their sizes and morphologies resemble modern and previously reported fossil bacteria. These similarities and their complex three-dimensional geometry suggest that they may represent morphologically preserved fossil bacteria. δC values of the carbonaceous filaments range from −42 to −32‰, which strongly suggest that they are composed of biologically fixed organic compounds, possibly via the reductive acetyl-CoA pathway or the Calvin cycle. This is consistent with the hypothesis that autotrophs already existed on the Archean Earth.
Organic geochemical methods for conodont analysis have been developed. Coniform elements of the conodont genus Drepanodus from the Ordovician Emanuel Formation and pectiniform elements of the conodont genus Polygnathus from the Devonian Napier Formation both from the Canning Basin, Australia have been shown to contain different organic matter. Both conodont samples have been artificially matured and the structure of organic matter present related to the conodont alteration index (CAI) and maturation temperature (TM). The carbon 1s X-ray photoelectron spectra (XPS) acquired from both sample sets contain six peaks. These peaks are assigned to highly ordered graphitic like carbon (282.9 eV), sp3 hybridised carbon bonded to only carbon or hydrogen (284.7 eV), ether (286.1 eV), alcohol (287.0 eV), carbonyl (287.6 eV) and carboxyl (289.0 eV) functional groups. Alkene and aromatic carbon is also probably present but is difficult to delineate. During artificial maturation, XPS analysis monitors the main chemical modifications expressed by the carbon–oxygen functional groups. The first stage of maturation begins with the removal of carboxyl and alcohol groups before a CAI of 2 (TM 450 °C). Between a CAI of 3–6 (TM 450–800 °C) an increase of sp3 hybridised carbon bonded to only carbon or hydrogen is found, which is accompanied by a decrease in ether and carbonyl functional groups. From a CAI of 6–7 (TM 800–950 °C), sp3 hybridised carbon bonded to hydrogen or carbon and carbonyl decreases while the development of highly ordered graphitic like carbon is observed. The first order laser Raman spectra recorded for both sample sets show a low degree of structural order from a CAI of 2–3, and from CAI 4–6 show a progressive increase in structural disorder of conodont organic matter. The D/G band (band at approximately 1345–1365/band at 1610 cm−1) line width ratio correlates with CAI. Conodont colour during artificial maturation occurs by migration of compounds to the surface. As the nitrogen compounds are volatilised from the surface, colour disappears.
Discovery of a fossil (30-35 million-year-old) urolith from Early Oligocene deposits in northeastern Colorado provides the earliest evidence for the antiquity of bladder stones. These are spherical objects with a layered phosphatic structure and a hollow center. Each layer is composed of parallel crystals oriented perpendicular to the surface. Macroscopic and microscopic examination and X-ray diffraction analysis, along with comparison with 1,000 contemporary uroliths, were used as evidence in the confirmation of this diagnosis. Raman microspectroscopy verified the presence of organic material between layers, confirming its biologic origin.
The samples comprise the foliage of four pteridosperm-medullosalean plant fossil species of differing preservation states and one of a cordaitean species from two Canadian Maritime sub-basins of Carboniferous age (300 Ma; Sydney and Stellarton coalfields, Nova Scotia, respectively). Included in the sample set were some coal samples from Sydney Coalfield, along with published data for coal macerals for comparison. By applying Schulze’s maceration process to the fossil foliage to obtain the cuticles, five sample forms evolved, viz. compressions, cuticles and fossilized cuticles, and acidic and alkaline solutions from Schulze’s process, to which was added the Sydney coal samples as the sixth form. Area integration of the absorbance spectra from solid and liquid state Fourier transform infrared (FTIR) spectroscopy, produced functional chemical parameters which were organized into a data matrix of eight variables and 62 samples (8 × 62 matrix). Since we were interested in grouping the sample forms as a function of phytochemistry (functional groups) to assess primarily the palaeophytotaxonomic potential as a general approach to Carboniferous taxonomy, principal components were extracted from the matrix, and a subset of 4 × 33 samples in order to refine the grouping results from the initial component analysis. In each case, a two component model resulted, accounting for least 80% of the cumulative variance.
Large acritarchs were recovered from the Awaynat Wanin II Formation in the A1–69 borehole, western Libya at 394.4 m. This sample has been dated by acritarchs and spores as Givetian (Middle Devonian). Two species of acanthomorph acritarchs were recovered that are unusually large for the Paleozoic. The first type, represented by a single specimen, is a new occurrence of a previously described but unnamed form from the Middle Devonian of the Sahara. The second type, which is more abundant, is named as Vanguestainidium cucurbitulum gen. et sp. nov. Biogeochemical analysis using infrared microspectroscopy shows that the wall composition of this new taxon is close to algaenans isolated from the green alga Botryococcus braunii Kützing 1849 although these forms are not morphologically similar. The presence of well‐preserved fragile palynomorphs, abundant terrestrially‐derived palynomorphs including large megaspores, and rare marine palynomorphs suggests deposition in a low‐energy nearshore environment such as a coastal swamp.
Organic-walled dinoflagellate cysts, produced as a result of sexual reproduction, are important tools for studies on recent and past environments. Additionally, the organic-walled cysts can be used as proxies for understanding the composition and chemical transformations of marine kerogen, the largest global organic carbon pool. However, any usage of dinoflagellate cysts in this manner is predicated on an understanding of the composition and transformations of this potential proxy. Dinoflagellate cyst walls are composed of “dinosporin”, a refractory biomacromolecule that probably represents a suite of chemically distinct biopolymers. In order to investigate both the nature of dinosporin and the extent to which the composition of this biomacromolecule may differ between dinoflagellate cyst taxa, we analyzed cyst species from the genus Apectodinium. The species defined within this genus are visually similar with several seeming to represent end-members along a continuum of morphological variation. Micro-Fourier transform infrared (FTIR) analysis was performed on three of these morphospecies (identified visually as A. paniculatum, A. parvum and A. augustum) from two regionally distinct samples. The analyses showed consistent patterns with clear differences between the species. The dinosporin of A. paniculatum closely resembles cellulose and is rich in ether bonds (Csingle bondO), while the dinosporin of A. augustum contains more carboxyl (COOH) groups. A. parvum appears intermediate in many respects, despite representing an end-member in terms of morphology. These differences are consistent regardless of the regional setting or post-depositional conditions, and strongly suggest that the original cyst wall composition of the species differed when the cysts were formed. These data are the first to clearly show differences in cyst wall composition between species of the same genus and indicate that the chemical diversity of dinosporins is greater than previously thought.
In this study, biometric and structural engineering tool have been used to examine a possible relationship within Chuaria–Tawuia complex and micro-FTIR (Fourier Transform Infrared Spectroscopy) analyses to understand the biological affinity of Chuaria circularis Walcott, collected from the Mesoproterozoic Suket Shales of the Vindhyan Supergroup and the Neoproterozoic Halkal Shales of the Bhima Group of peninsular India. Biometric analyses of well preserved carbonized specimens show wide variation in morphology and uni-modal distribution. We believe and demonstrate to a reasonable extent that C. circularis most likely was a part of Tawuia-like cylindrical body of algal origin. Specimens with notch/cleft and overlapping preservation, mostly recorded in the size range of 3–5 mm, are of special interest. Five different models proposed earlier on the life cycle of C. circularis are discussed. A new model, termed as ‘Hybrid model’ based on present multidisciplinary study assessing cylindrical and spherical shapes suggesting variable cell wall strength and algal affinity is proposed. This model discusses and demonstrates varied geometrical morphologies assumed by Chuaria and Tawuia, and also shows the inter-relationship of Chuaria–Tawuia complex.
IntroductionApplication of Raman SpectroscopyConclusions
DisclaimerReferences
Geochemical analyses of specimens of Reduviasporonites suggests that it is most likely of algal, rather than fungal origin. As probable alga, Reduviasporonites is unlikely to be integral to the process of mass extinction occurring at or near the Permian Triassic boundary, as suggested
by Visscher and other workers because it cannot have acted as a saprophytic metaboliser of dead vegetation resulting from
that event. Moreover, it ranges outside the postulated time of mass extinction by at least 10 million years Optical and electron
microscopy of topotype material confirms that Reduviasporonites Wilson 1962 is the senior synonym of Chordecystia Foster 1979, and Tympanicysta Balme 1980. More over the type species of the last two genera, assigned in 1999 to Reduviasporonites by Elsik as R. chalastus (Foster) and R stoschianus (Balme), are conspecific. The type species, R catenulatus Wilson 1962, differs from R. chalastus in that its constituent cells are significantly smaller, more rounded, and have less well developed connecting areas (terminal
rims) between cells. Brazilea helbyi forma gregata Foster 1979, recorded only from the type material of R. chalastus, is likely to be a junior synonym of that taxon.
The stratigraphic occurrences of the species of Reduviasporonites suggest that R. catenulatus is most common in the Wordian (Kazanian) of Oklahoma, though specimens of the size range associated with R. catenulatus are present very rarely in the Early Triassic Mazzin Member of the Werfen Formation, Austria. R chalastus is present in Capitanian to Griesbachian rocks spanning at least 10 million years, and outside the more narrow age span of
the Permian–Triassic boundary. The size of the constituent cells present in R. chalastus appears to be related to paleolatitude with large examples occurring in the paleotemperate Permian of China, Russia, and
Australia (Moura) and smaller specimens occurring in the paleotropical and paleoequatorial Permian of northern Australia,
Saudi Arabia, United Kingdom and Austria.
Conodonts and scolecodonts are common Paleozoic microfossils that are often used to determine the geothermometry of Paleozoic sequences. The two fossils, which can be difficult morphologically to distinguish one from the other, undergo a different thermal alteration pathway. In this study, Fourier transform infrared (FTIR) spectroscopy of scolecodont and conodont microfossils from the Woodford Shale of southern Oklahoma, United States, confirmed they have different chemical compositions. Infrared (IR) spectra acquired from conodonts show a predominance of an inorganic carbonated hydroxylapatite (CO(3)OHAp) with a minor organic composition of aliphatic hydrocarbon, containing carbonyl substituent functional groups. In contrast, IR spectra acquired from scolecodonts show no inorganic mineralogy but instead confirm that these microfossils are composed of organic material consisting of an aliphatic and aromatic hydrocarbon network with ether linkages and carbonyl substituent functional groups. These data reveal that scolecodont elements can easily be distinguished from conodont elements with FTIR microspectroscopy due to their different chemical compositions. This study provides future fossil workers with a viable method to independently identify enigmatic toothlike microfossils that cannot confidently be assigned to either scolecodont or conodont groups by morphology alone.
Study of the Burgess Shale-type deposits of the Cambrian has greatly enhanced scientific understanding of early animal evolution, but as the mechanisms by which these deposits formed are still unclear, here we outline and present data from the application of a new analytical approach, Raman spectroscopy, that can be used to characterize fossils from these deposits. Although these deposits present exceptional views into a diverse, nonbiomineralized to lightly biomineralized biota, this taphonomic regime mostly disappears from the fossil record after the Cambrian, with a few notable exceptions. Numerous detailed taphonomic and chemical studies have provided significant insight hito modes of fossil preservation in these deposits, although there is still significant debate regarding the preservational and diagenetic mechanisms that may be involved. Compared to previous electron microscopy-based elemental mapping approaches, which have identified the elemental components of similar fossils, Raman spectroscopy allows a determination of the chemical phases and specific mineralogy at the molecular level, as well as the thermal maturity, of these fossils. This approach therefore provides new types of data, such as hematite phase, that may prove helpful for elucidating some of the mechanisms responsible for the exceptional types of preservation found in these deposits, and potentially helps to resolve the existing taphonomic debates.
Fossil remains of the most ancient, minute forms of life on Earth and
other planets are hard to recognize. Schopf et al. claim to have
identified the biological remnant material known as kerogen in
microscopic entities in rock by using Raman spectroscopic analysis. On
the basis of a substantial body of published evidence, however, we
contend that the Raman spectra of Schopf et al. indicate that these are
disordered carbonaceous materials of indeterminate origin. We maintain
that Raman spectroscopy cannot be used to identify microfossils
unambiguously, although it is a useful technique for pinpointing
promising microscopic entities for further investigation.
Ediacara-type fossils are found in a diverse array of preservational styles, implying that multiple taphonomic mechanisms might have been responsible for their preservational expression. For many Ediacara fossils, the ''death mask'' model has been invoked as the primary taphonomic pathway. The key to this preservational regime is the replication or sealing of sediments around the degrading organisms by microbially induced precipitation of authigenic pyrite, leading toward fossil preservation along bedding planes. Nama-style preservation, on the other hand, captures Ediacaran organisms as molds and three-dimensional casts within coarse-grained mass flow beds, and has been previously regarded as showing little or no evidence of a microbial preservational influence. To further understand these two seemingly distinct taphonomic pathways, we investigated the three-dimensionally preserved Ediacaran fossil Pteridinium simplex from mass flow deposits of the upper Kliphoek Member, Dabis Formation, Kuibis Subgroup, southern Namibia. Our analysis, using a combination of petrographic and micro-analytical methods, shows that Pteridinium simplex vanes are replicated with minor pyrite, but are most often represented by open voids that can be filled with secondary carbonate material; clay minerals are also found in association with the vanes, but their origin remains unresolved. The scarcity of pyrite and the development of voids are likely related to oxidative weathering and it is possible that microbial activities and authigenic pyrite may have contributed to the preservation of Pteridinium simplex; however, any microbes growing on P. simplex vanes within mass flow deposits were unlikely to have formed thick mats as envisioned in the death mask model. Differential weathering of replicating minerals and precipitation of secondary minerals greatly facilitate fossil collection and morphological characterization by allowing Pteridinium simplex vanes to be parted from the massive hosting sandstone. INTRODUCTION
The Pilbara Craton in Western Australia contains the best-preserved and most complete record of Archean rocks in the world. As such, they are some of the most studied rocks in the world; paleontologists, isotopic geochemists, geologists and geobiologists have all investigated these rocks for clues about the early biosphere and atmosphere. Here we show using high-resolution transmission electron microscopy that the carbonaceous material found in the Apex chert, and potentially in other associated units, was formed by multiple processes such as abiotic catalytic synthesis and/or biological synthesis. We use these data as well as the geological history of the craton to demonstrate that when the rocks of the Pilbara Craton experienced a high degree of post-depositional hydrothermal alteration, carbonaceous material could have been remobilized and redeposited. As the carbonaceous material within the Apex chert samples was formed over nearly a billion years, bulk chemistry, even at the micron level, will be unable to unambiguously delineate the presence of life in these ancient rocks, although nanoscale observations may provide a way forward in the search for ancient life.
Abstract Initially, Raman spectroscopy was a specialized technique used by vibrational spectroscopists; however, due to rapid advancements in instrumentation and imaging techniques over the last few decades, Raman spectrometers are widely available at many institutions, allowing Raman spectroscopy to become a widespread analytical tool in mineralogy and other geological sciences. Hyperspectral imaging, in particular, has become popular due to the fact that Raman spectroscopy can quickly delineate crystallographic and compositional differences in 2-D and 3-D at the micron scale. Although this rapid growth of applications to the Earth sciences has provided great insight across the geological sciences, the ease of application as the instruments become increasingly automated combined with nonspecialists using this techique has resulted in the propagation of errors and misunderstandings throughout the field. For example, the literature now includes misassigned vibration modes, inappropriate spectral processing techniques, confocal depth of laser penetration incorrectly estimated into opaque crystalline solids, and a misconstrued understanding of the anisotropic nature of sp(2) carbons. Key Words: Raman spectroscopy-Raman imaging-Confocal Raman spectroscopy-Disordered sp(2) carbons-Hematite-Microfossils. Astrobiology 13, xxx-xxx.
Micro Fourier-Transform Infrared (FT–IR) spectroscopy in combination with transmitted and reflected light microspectrophotometry relates the chemical and physical properties of sporopollenin during thermal maturation; the physical properties measured being colour, as the chromaticity coordinates a*, b* and L*, (luminance) and the reflectance (Rsp) of the sporinite wall layers in the polished section. During maturation, sporopollenin exhibits a wide range of colours before there are any significant changes in Rsp. The immature phase is characterised by subtle colour changes through a series of progressively darkening yellows. This coincides with a reduction in the relative proportion of >CO groups and an increase in the relative proportion of aliphatic –CH2 and –CH3 groups. During the mature phase, functional groups within spores and pollen are thermally cracked to generate hydrocarbons. Their colours change rapidly through orange and brown and the FT–IR data indicate the loss of a considerable portion of the aliphatic groups and increases in the CC content associated with aromatic rings. Significant structural reorganisation during the spore ‘oil-window’ results in the formation of isolated aromatic rings. A further increase in maturity yields little change in colour but a rapid increase in reflectivity. This is caused by the formation of multi-ring aromatic units from isolated aromatic units. The size of these polyaromatic units increases with rank. Investigation of artificially matured samples of Lycopodium clavatum spores indicates considerable chemical differences in >CO, CC and aromatic skeletal structure, in comparison to fossil palynomorphs, although they progress through a similar series of colours. Only the behaviour of the aliphatic CH2, CH3 groups, in artificially heated samples replicates that seen in samples matured naturally, under geological conditions.
Raman analyses are reported of μm-sized areas of 103 individual carbonaceous presolar grains (“graphite grains”) from three different density fractions of the Murchison meteorite. Few of the grains (2 or 3 of each density fraction) have Raman spectra typical for non-crystalline sp2-bonded carbon (i.e., “organic carbon”) with extremely wide 1st-order and no (or very subdued) 2nd-order peaks, similar to the ones found for terrestrial kerogens. Based on depth profiles of isotopic ratios measured with the NanoSIMS, it is unlikely that such kerogen-type Raman signatures are caused by contamination of the presolar grains with insoluble organic material from the Murchison matrix that stuck to the surfaces of the grains. Rather, the kerogen-type grains are considered to be a new type of presolar carbon grains, which are made up of organic (PAH-like) sp2-bonded carbon. However, most of the other studied presolar carbon grains (95 of 103) have spectra with very narrow 1st-order peaks (called D and G peaks) and very strong 2nd-order peaks typical for inorganic sp2-bonded carbon. Based on their D/G intensity ratios, those grains were grouped into the following Raman types: (fairly well ordered) “graphite” (D/G < 0.5), “disordered graphite” (0.5 < D/G < 1.1), “glassy carbon” (D/G > 1.1), and “unusual sp2-bonded graphitic carbon” (with extremely intense 2nd-order peaks relative to the 1st-order peaks). Grains from the low-density fraction KFA1 (2.05–2.10 g/cm3) have predominantly “cauliflower” morphology and Raman spectra characteristic of either very disordered graphite or “glassy carbon” (i.e., the latter is amorphous from the Raman spectroscopic perspective), whereas most grains from the high-density fraction KFC1 (2.15–2.20 g/cm3) have “onion” morphology and Raman spectra characteristic of well-crystalline graphite. The KFB1 grains with intermediate density (2.10–2.15 g/cm3) are mixed, both in terms of their morphology and their Raman spectra but are closer to KFC1 than to KFA1 grains. The correlation of the Raman results with both morphology and isotopic data show that presolar sp2-bonded carbon grains from different stellar sources differ in their crystalline structure. Grains that dominate the high density fractions and whose isotopic ratios indicate an origin in AGB stars consist of well crystallized graphite, whereas grains that dominate the low-density fraction and whose isotopic ratios indicate a supernova origin consist of very disordered graphite or even of amorphous “glassy carbon”.
Abstract Raman spectrometers are being miniaturized for future life-detection missions on Mars. Field-portable Raman spectrometers, which have similar spectral parameters to the instruments being developed for Mars rovers, have been used to examine extant biosignatures, but they have not yet been used to examine ancient biosignatures. Here, a portable Raman spectrometer was used to analyze an Ordovician stromatolite at the outcrop, revealing both its mineralogy and the presence of sp(2) carbonaceous material. As stromatolites are often used as proof of the presence of life in Archean rocks and are searched for on Mars, the ability to analyze them in the field with no sample preparation has important ramifications for future Mars missions. However, these results also reveal that a 785 nm excitation source, rather than the 532 nm excitation source planned for future missions, might be a better choice in the search for fossil biosignatures. Key Words: Raman spectroscopy-Portable/miniaturized Raman instruments-Stromatolites-Carbonaceous material-Life detection. Astrobiology 13, xxx-xxx.
A reflectance FT-infrared microscope spectrometer has been employed to study the chemical structures of individual macerals including vitrinite, resinite, cutinite and alginite (Botryococcus braunii and Tasmanites), which are then used to infer the petroleum generation characteristics of the macerals. The optical microscope was modified so that it is equipped with fluorescent illumination, and it serves as a sampling accessory attached to the infrared spectrometer. The system is capable of measuring infrared spectra of individual macerals with cross sectional areas as small as 20 × 20 microns. At similar maturities, alginite and cutinite are shown to contain the highest concentrations of aliphatic C—Hx, whereas vitrinite contains the most aromatic C=C. A closer look at the stretching vibrations of the aliphatic C—Hx region reveals further structural difference. Maximum likelihood spectral restoration of the stretching vibrations of the aliphatic C—Hx bands is employed to calculate the intensities of individual C—Hx bands. It is found that vitrinite and resinite have significantly higher terminal CH3 relative to methylene CH2 in comparison to alginite and cutinite. A lower CH2/CH3 ratio signifies shorter and more branched aliphatic chains, which can reduce the bond dissociation energies of a kerogen. This may be able to explain the “low-rank” gas/condensate generation characteristics which are exhibited by resinite and vitrinite macerals contained in source rocks of the Mackenzie and Mahakam Deltas. The oil- versus gas/condensate-proneness of a kerogen can also be assessed by using the CH2/CH3 ratio.
Chemical data are given on the remains of nine fossil genera ranging from Precambrian to Carboniferous in age (Chuaria, Sporangites, Taeniocrada, Orestovia, Parka, Protosalvinia, Spongiophyton, Solenites, Botryococcus). It is suggested that such chemical data are useful additional criteria in making taxonomic assignments in palaeontology. Analyses indicate a high level of organic chemical diversity, although the original composition has evidently been altered by temperature and pressure over a long period of time. The labile chemical constituents are retained within a more chemically inert carbon matrix, which shows a progressive alteration of the ratios of C, N, O and H with respect relative age, similar to that seen in the coalification process.The chemical composition of Sporangites specimens is more suggestive of an animal rather than a plant affinity; it is here suggested that this genus represents in part the remains of some animal egg test. Hydrolytic products of Solenites and Taeniocrada indicate the presence of aliphatic hydroxy acids suggesting the presence of cutin and suberin. The chemical compositions of Orestovia, Parka, Protosalvinia, Spongiophyton and Botryococcus are interpreted as being consistent with an algal rather than a vascular plant affinity. Evidence for extreme diagenesis of the acritarch-like Chuaria greatly limits chemotaxonomic consideration. The possible role of thermal and biotic-thermal degradation patterns seen in palaeochemistry is discussed.
IR spectroscopy in combination with chemometric techniques is an effective tool for the detection of adulteration of high economic value food products such as wine, dietary supplements and olive oil. It provides practical and quick alternative to other commonly used analytical methods.
Preservation of soft-bodied fossil biotas (Konservat-Lagerstäten) that preserve traces of volatile nonmineralized tissues (readily degraded by bacteria) are not evenly spaced through geologic time. When compared to outcrop area, exceptional faunas appear to be over-represented in the Cambrian and Jurassic. These concentrations in time correspond to particular environments, indicating that controls on the distribution of exceptional faunas may have operated on a global scale. The reduction in the number of exceptional faunas after the Cambrian may reflect the evolution and diversification of deep bio- turbators. Specific conditions favoring stagnation and episodic burial were required to ensure preservation in younger rocks.
The splendid preservation of the Middle Cambrian Burgess Shale fauna, a fauna of exceptional importance for our understanding of the evolution of life, has not been adequately explained. Preservation of diagenetically altered remnants of the original organic tissues and formation of chlorite/illite coatings and cuticle replacements, both documented in the Burgess Shale fossils though not necessarily occurring together, can be understood as products of the same mechanism of fossilization of soft tissues. It is argued here that this mechanism consists of the following steps:1) adsorption on structural biopolymers such as chitin, cellulose, and collagens of Fe2+ ions released during the oxidation of organic matter by iron(Ill)reducing bacteria, (2) inhibition by the adsorbed Fe2+ ions of further bacterial decomposition of these biopolymers, which enables them to persist and later become kerogens; (3) in some microenvironments, nucleation of crystals of an iron(II)-rich clay mineral, a berthierine or a ferroan saponite, on the Fe2+ ions adsorbed on the preserved biopolymers and growth of such clay-mineral crystals to form a coating on the organic remains and/or to replace parts of the organism. The critical factors in the Burgess Shale-type preservation of Early and Middle Cambrian soft-bodied and lightly armored animals were probably: (1) rapid transport of live or freshly killed organisms into suboxic water, (2) extensive suboxic diagenesis in a sediment of high iron(III)/ (organic carbon) ratio, and (3) curtailment of the supply of sulfate ions shortly after the onset of pyritization. The proposed model of early diagenesis that results in Burgess Shale-type fossil preservation critically depends on the availability of steady suboxic depositional environments in open oceanic settings at depths of the order of 100 m in which iron(HI)-rich fine-grained sediments, rapidly deposited with the entrained animals by turbidity currents, could accumulate without being disturbed by storm waves and deep currents. Evidence discussed in the present paper suggests that such conditions were common in the Early and Middle Cambrian. Adsorption of Fe2+ ions on structural biopolymers as a means of protecting organic fossil remains from decomposition by bacterial enzymes is a novel suggestion and needs to be demonstrated by direct experimentation. It is based on the following considerations. First, Fe2+ ions are strongly adsorbed on chitin under experimental conditions comparable to those in pore waters of suboxic iron-rich sediments, and while data on Fe2+ ion adsorption on collagen and cellulose seem to be lacking, other heavy metal ions are strongly adsorbed on these biopolymers under appropriate conditions. Second, Fe2+ ions bonded with functional groups of chitin, collagen, or cellulose would prevent the very specific configuration and bonding which a biopolymer strand has to achieve within the active-site cleft of the appropriate bacterial enzyme to make enzymatic hydrolysis possible. Close examination of two other mechanisms recently proposed for Burgess Shale-type preservation of soft tissues shows that they are implausible: preservation by inactivation of extracellular enzymes on clay minerals would require a maladaptive reliance of tissue-decomposing bacteria on free extracellular enzymes, and preservation by attachment of pre-existing clay-mineral particles would require a sequence of physically improbable events. It is argued here that adsorption of Fe2+ ions on structural biopolymers was the first step not only in Burgess Shale-type preservation of soft-bodied and lightly armored fossils but also in the preservation of such fossils by pyritization in Beecher's Trilobite Bed in the Upper Ordovician Frankfort Shale in upstate New York and in the Lower Devonian Hunsrfick Slate in Rhineland-Palatinate and in the preservation of such fossils within siderite concretions in various localities. It was probably the first step in the preservation (obscured by alunitic weathering) of soft-bodied and lightly armored fossils in the Soom Shale of the Cape Province, South Africa, and in the preservation of Ediacaran soft-bodied fossils in the classical localities of the Ediacaran Range of Australia and Mistaken Point, Newfoundland.
The chemical composition of well-preserved naraoiids from the Chengjiang, Kaili, and Burgess Shale biotas is compared. Gut diverticulae in samples from all three biotas contain C, P, and Fe, indicating a primary composition of organic carbonaceous material, and the presence of apatite and pyrite as the result of authigenic mineralization in association with decay and early diagenetic processes. Gut traces from Burgess Shale specimens retain apatite and pyrite, as well as clay minerals, reflecting a history involving greenschist-grade metamorphism. Kaili specimens have been subjected to lower-grade metamorphism and, or thermal alteration, but alteration of pyrite pseudomorphs in the gut traces to limonite indicates the effect of weathering. Loss of sulfur and calcium, oxidation of pyrite, and the light color of the Chengjiang samples are the result of a greater degree of weathering than in specimens from the other two localities. As demonstrated here, Kaili samples serve as an important baseline for interpreting specimens from the Burgess Shale (high-grade metamorphism) and the Chengjiang (intense chemical weathering) deposits. Our study shows for the first time that the conservation of organic carbon is the common primary mode of soft-part preservation in naraoiid arthropods from these three signature Burgess Shale-type localities. Differences among these major deposits are a product of later diagenesis and weathering of the authigenic mineralization associated with the preservation of labile structures. Among the major constituents formed during diagenesis—carbonaceous material, calcium phosphate (e.g., apatite), and iron sulfide (e.g., pyrite)—the minerals are more susceptible to chemical weathering via hydrolysis.
In a paper read to the Society at a former meeting, the Doctor announced some observations which seemed to indicate that there are two sorts of rays proceeding from the sun; the one the calorific rays, which are luminous and refrangible into a variegated spectrum; and the other the invisible rays, which produce no illumination, but create a sensible degree of heat, and appear to have a greater range of refrangibility than the colorific rays. To the latter he assigns the name of radiant heat . Having lately had some favourable opportunities to prosecute this investigation, he here delivers an account of the series of experiments he made on the subject, which seem to him to confirm the above conjecture. The mode of conducting these experiments was simply this:— On a horizontal tablet covered with white paper, and divided into squares, for the conveniency of measurement, a part of the extreme colour of a prismatic spectrum was suffered to fall, the remainder of the coloured rays passing by the edge of the tablet, so as not to interfere with the experiment.
In that section of my former paper which treats of radiant heat, it was hinted, though from imperfect experiments, that the range of its refrangibility is probably more extensive than that of the prismatic colours; but, having lately had some favourable sunshine, and obtained a sufficient confirmation of the same, it will be proper to add the following experiments to those which have been given. I provided a small stand, with four short legs, and covered it with white paper. On this I drew five lines, parallel to one end of the stand, at half an inch distance from each other, but so that the first of the lines might only be ¼ of an inch from the edge. These lines I intersected at right angles with three others; the 2d and 3d whereof were, respectively, at 2½ and at 4 inches from the first.
The present paper deals with the chemistry and ultrastructure of the cell wall of Tasmanites punctatus Newton, Tasmanites erraticus Eisenack and undetermined species of Leiosphaeridia Eisenack. Infra-red microspectrometry has revealed absorption bands interpreted as being due to the presence of COOH, CH2 and CH3 groups. Ultrastructural differences are shown between T. punctatus, T. erraticus and Leiosphaeridia.
Naturally macerated cuticles (NMC) and one synangium, representing medullosalean and marattialean tree-fern species, from two Carboniferous coalfields in Nova Scotia, Canada, are investigated. The samples were analyzed by infrared spectroscopy (FTIR), and by pyrolysis-gas chromatograph/mass spectrometry (py-Gc/Ms) techniques in search for chemical signatures that would help in developing a chemotaxonomic classification of Carboniferous fern species, assuming genetically dependent make-up of cuticles. FTIR-derived CH2/CH3 ratios, in conjunction with contributions from carboxyl groups, demonstrated a better potential for discriminating between medullosalean genera and species than molecular signatures obtained by py-Gc/Ms. However, the latter provided better data for differentiating medullosalean from marattialean tree ferns as a group. Changes in the chemical make-up of naturally macerated cuticles due to sample preparation are discussed.
Micro-Raman spectra were acquired from a series of individual chitinozoans of low (Rch 0.6%) to high thermal maturity (Rch 5.1%). This provides information on their molecular and structural characteristics. All spectra show two broad bands on a fluorescent background at ∼ 1600 and 1355 cm−1. With increasing rank there is a significant decrease in the line-width of the 1600 cm−1 band, assigned to the out of phase coupling of an in-plane C-C stretching vibration. The rate of change for the reduction in the line-width is most pronounced within the lower rank material as the sample matures through the “oil window”. These data suggest that Raman spectroscopy of chitinozoan maceral, in particular monitoring of the half-width of the 1600 cm−1 band, shows potential as a maturation indicator in sedimentary rocks. Significantly, it offers a link between optical methods of thermal maturity determination and the underlying changes in the physical and chemical structure of the organic material.
Chemical analyses of the hydrocarbon, amino acid, and carbohydrate constituents of the fossil remains of Parka suggest the genus is referable to the Chlorophyta. Gas chromatograms of the reproductive and vegetative areas of thalli show a smooth distribution of normal, saturated acids with maxima at C16 and C12, respectively. Esters of organic-soluble compounds isolated from reproductive areas are characteristically longer in their carbon chain-lengths and show higher maxima. Mass spectra of acid mixtures (before esterification) reveal various series of phenyl- and naphthylaromatic acids, phenols, and dicarboxylic acids. Acid hydrolysis indicated the presence of various polysaccharides rich in mannose and glucose, while enzymatic catalysis with α- and β-amylases and cellulase/chitinase mixtures indicate the presence of α-(1 → 4) and β-(1 → 4) glucopyranose linkages suggesting the presence of starch and cellulose, respectively. Gas chromatographic analysis coupled to mass spectroscopy reveal the presence of sterane derivatives (stigmatane and ergostane) associated with representative genera of the Chlorophyta.
Silicified and carbonized axes of Prototaxites are chemically analyzed by means of X-ray and organic-extraction techniques. The isolation and identification of cutin and suberin derivatives, i.e., ω-hydroxymonocarboxylic acids, suggest that Prototaxites may have been a terrestrial plant or an aquatic plant showing chemical adaptation to periods of desiccation. Normal saturated acids showing no odd or even carbon-number predominance, phenyl and naphthyl aromatic acids, and normal and aromatic dicarboxylic acids isolated from fossil material, are considered inconsistent with an algal biochemistry. The normal saturated fatty acids isolated from Parka, Pachytheca, Spongiophyton, Protosalvinia, Orestovia and Taeniocrada are compared with Prototaxites. Parka, Pachytheca, Spongiophyton and Orestovia, parallel one another in their organic chemical constituents, while Protosalvinia, Taeniocrada and Prototaxites appear to have paralleled one another in their adaptation to a terrestrial habit.
Sphenopterid specimens from the Late Pennsylvanian of Sydney Coalfield, Canada, are investigated by FTIR and py-GC-MS techniques as part of an on-going research project into the biochemistry and chemotaxonomy of Pennsylvanian-age pteridophylls. Included in the investigation are samples of the true-fern species Oligocarpia brongniartii and Zeilleria delicatula that are preserved as naturally macerated cuticles (NMC), and the seed-fern Eusphenopteris neuropteroides that is also preserved as a compression/impression. FTIR spectra of NMC seed-fern E. neuropteroides, and fern sphenopterid O. brongniartii are very similar, except that the latter does not have aromatic bands in the 700–900 cm−1 out-of-plane region. py-GC-MS show more aromatic compounds for the seed fern than for the two true-fern sphenopterids. Another difference between seed-fern and true-fern sphenopterids is a lower ratio of CH2 to CH3 in chemically treated specimens (CTC) for the seed fern. These observations suggest slightly higher aromaticity for the seed ferns, perhaps related to some chemotaxonomic differences. Comparison of FTIR and py-GC-MS characteristics of sphenopterids and other plant groups shows that these two techniques have potential to identifying chemotaxonomic signals from Carboniferous pteridophylls in general, although more data are needed to confirm this.
Well-preserved cuticles were isolated from Cordaites principalis�Germar.Geinitz leaf compressions, i.e., foliage from extinct gymnosperm trees Coniferophyta: Order Cordaitales. The specimens were collected from the Sydney, Stellarton and Bay St. George subbasins of the once extensive Carboniferous Maritimes Basin of Atlantic Canada. Fourier transformation of infrared spectra (�FTIR) and elemental analyses indicate that the ca. 300–306-million-year-old fossil cuticles share many of the functional groups observed in modern cuticles. The similarities of the functional groups in each of the three cuticular morphotypes studied support the inclusion into a single cordaite-leaf taxon, i.e., C. principalis� (Germar), confirming previous morphological investigations. Vitrinite reflectance measurements on coal seams in close proximity to the fossil-bearing sediments reveal that the Bay St. George sample site has the lowest thermal maturity, whereas the sites in Sydney and Stellarton are more mature. IR absorption and elemental analyses of the cordaite compressions corroborate this trend, which suggests that the coalified mesophyll in the leaves follows a maturation path similar to that of vitrinite. Comparison of functional groups of the cordaite cuticles with those from certain pteridosperms previously studied from the Sydney Subbasin shows that in the cordaite cuticles highly conjugated C–O �1632 cmy1 bands dominate over carbonyl stretch that characterizes the pteridosperm cuticles. The differences demonstrate the potential of chemotaxonomy as a valuable tool to assist distinguishing between Carboniferous plant–fossil groups.
Raman spectra are reported from single crystals of graphite and other graphite materials. Single crystals of graphite show one single line at 1575 cm−1. For the other materials like stress‐annealed pyrolitic graphite, commercial graphites, activated charcoal, lampblack, and vitreous carbon another line is detected at 1355 cm−1. The Raman intensity of this band is inversely proportional to the crystallite size and is caused by a breakdown of the k‐selection rule. The intensity of this band allows an estimate of the crystallite size in the surface layer of any carbon sample. Two in‐plane force constants are calculated from the frequencies.