What can infrared spectroscopy do for characterizing organic remnant in fossils?

An evaluation of the effect of hydrofluoric acid (HF) treatment on keratins

Hydrofluoric acid (HF) is commonly used in geological and paleontological research to extract organic fossils for morphological and chemical studies. However, during HF treatment, organic matter can also be altered, which raises concerns that HF-treated organic matter may not be representative of the original organic matter. To provide reference data for protein studies on fossils, herein, we use Fourier transform infrared (FTIR) spectroscopy to investigate the effect of HF (21.3 M) treatment on keratins, with treatment durations ranging from 2 to 48 h. Results show that the FTIR spectra of HF-treated samples are overall similar to that of the untreated sample, while curve fitting shows that HF treatment has led to alteration of the secondary structure in all the HF-treated samples and the effect is time-dependent. The 2- and 4-h treatment mainly reduced the content of the random coils, α-helix, and intermolecular β-sheet. From 8h onwards, the content of random coils greatly increased at the expense of other structures. Our results imply that for protein detection in fossils using FTIR spectroscopy, the negative effect of HF treatment is not substantial, as the bands characteristic of proteins, that is, amide A, amide B, amide I, amide II, and amide III, are still present after the 48-h treatment. If the target is a secondary structure, the effect of HF treatment should be considered. When HF treatment is necessary, limiting the treatment duration to less than 4h may be a choice.

Morphological and organic spectroscopic studies of a 44-million-year-old leaf beetle (Coleoptera: Chrysomelidae) in amber with endogenous remains of chitin

This study details the quality of preservation of amber deposits in the Eocene. Through Baltic amber crack-out studies using Synchrotron Micro-Computed Tomography and Scanning Electron Microscopy it was found that the cuticle of a specimen of leaf beetle (Crepidodera tertiotertiaria (Alticini: Galerucinae: Chrysomelidae)) is exceptionally well preserved. Spectroscopic analysis using Synchrotron Fourier Transform Infrared Spectroscopy suggests presence of degraded [Formula: see text]-chitin in multiple areas of the cuticle, and Energy Dispersive Spectroscopy supports the presence of organic preservation. This remarkable preservation is likely the result of several factors such as the favourable antimicrobial and physical shielding properties of Baltic amber as compared to other depositional media, coupled to rapid dehydration of the beetle early in its taphonomic process. We provide evidence that crack-out studies of amber inclusions, although inherently destructive of fossils, are an underutilised method for probing exceptional preservation in deep time.

Biofinder detects biological remains in Green River fish fossils from Eocene epoch at video speed

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.

Effect of organic matrix alteration on strain rate dependent mechanical behaviour of cortical bone

The organic matrix phase of bone plays important role in its mechanical performance, especially in the post-yield regime. Also, the organic phase influences loading rate-dependent behaviour of bone which is relevant during the high-speed loading events. Many diseases, as well as aging, affect the matrix phase of bone which causes compromised mechanical properties. Improved understanding of alterations in the organic matrix phase on mechanical response of bone will be helpful in the mitigation of fractures associated with inferior matrix quality. In the present work, effect of alteration in organic matrix of cortical bone on its strain-rate dependent behaviour was investigated. To produce different amounts of collagen denaturation, bovine cortical bones were heated at the temperature of 180 °C and 240 °C. Further, compression testing was performed at quasi-static strain rates of 10^-4 s^-1 to 10^-2 s^-1 using a conventional testing machine whereas a modified Split Hopkinson Pressure Bar (SHPB) was used for high strain rate (∼10³) testing. Thermal treatment-induced changes in the mineral and organic phases of bone were assessed using X-ray diffraction (XRD) and Fourier-transform infrared-attenuated total reflection (FTIR-ATR) techniques respectively. Compression test results show that thermal treatment of bone up to 180 °C did not affect mechanical properties significantly whereas treating at 240 °C significantly reduced elastic modulus, failure stress and failure strain. Also, thermal denaturation of collagen reduced the strain rate sensitivity of cortical bone at high strain rates. Similar to the compression test observations, nanoindentation results show a significant reduction in elastic modulus and hardness of denatured samples. Further, FTIR results revealed that with the heat treatment of bone, collagen structure undergoes conformational changes at the molecular level. The initial helix structure breakdowns into unordered/random coil structures which subsequently reduced the mechanical competence of bone. The present study provides insight into the effect of organic matrix modification on mechanical behaviour of cortical bone which could be helpful in understanding bone disorders associated with organic matrix phase and development of therapeutic interventions.

Mars Rover Techniques and Lower/Middle Cambrian Microbialites from South Australia: Construction, Biofacies, and Biogeochemistry

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 identification of fungi microfossils in a Neoproterozoic shale rock

Precambrian fossils of fungi are sparse, and the knowledge of their early evolution and the role they played in the colonization of land surface are limited. Here, we report the discovery of fungi fossils in a 810 to 715 million year old dolomitic shale from the Mbuji-Mayi Supergroup, Democratic Republic of Congo. Syngenetically preserved in a transitional, subaerially exposed paleoenvironment, these carbonaceous filaments of ~5 μm in width exhibit low-frequency septation (pseudosepta) and high-angle branching that can form dense interconnected mycelium-like structures. Using an array of microscopic (SEM, TEM, and confocal laser scanning fluorescence microscopy) and spectroscopic techniques (Raman, FTIR, and XANES), we demonstrated the presence of vestigial chitin in these fossil filaments and document the eukaryotic nature of their precursor. Based on those combined evidences, these fossil filaments and mycelium-like structures are identified as remnants of fungal networks and represent the oldest, molecularly identified remains of Fungi.

Applications of chemical imaging techniques in paleontology

Chemical imaging techniques, based on a combination of microscopy and spectroscopy, are designed to analyse the composition and spatial distribution of heterogeneous chemical complexes within a sample. Over the last few decades, it has become an increasingly popular tool for characterizing trace elements, isotopic information and organic biomarkers (molecular biosignatures) found in fossils. Here, we introduce the analytical principle of each technique and the interpretation of the chemical signals, followed by a review of the main applications of these techniques in paleontology. We also demonstrate that each technique is associated with pros and cons, and the current limitations and obstacles associated with the use of each specific technique should be taken into account before being applied to fossil samples. Finally, we propose that, due to the rapid advances in the available technology and overall trends towards more multi-disciplinary studies in paleontology, chemical imaging techniques can be expected to have broader applications in paleontology in the near future.

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, 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, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs- and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

Organic molecular heterogeneities can withstand diagenesis

Reconstructing the original biogeochemistry of organic fossils requires quantifying the extent of the chemical transformations that they underwent during burial-induced maturation processes. Here, we performed laboratory experiments on chemically different organic materials in order to simulate the thermal maturation processes that occur during diagenesis. Starting organic materials were microorganisms and organic aerosols. Scanning transmission X-ray microscopy (STXM) was used to collect X-ray absorption near edge spectroscopy (XANES) data of the organic residues. Results indicate that even after having been submitted to 250 °C and 250 bars for 100 days, the molecular signatures of microorganisms and aerosols remain different in terms of nitrogen-to-carbon atomic ratio and carbon and nitrogen speciation. These observations suggest that burial-induced thermal degradation processes may not completely obliterate the chemical and molecular signatures of organic molecules. In other words, the present study suggests that organic molecular heterogeneities can withstand diagenesis and be recognized in the fossil record.