Organic molecular heterogeneities can withstand diagenesis

X-ray Raman Scattering: A Hard X-ray Probe of Complex Organic Systems

This paper provides a review of the characterization of organic systems via X-ray Raman scattering (XRS) and a step-by-step guidance for its application. We present the fundamentals of XRS required to use the technique and discuss the main parameters of the experimental set-ups to optimize spectral and spatial resolution while maximizing signal-to-background ratio. We review applications that target the analysis of mixtures of organic compounds, the identification of minor spectral features, and the spatial discrimination in heterogeneous systems. We discuss the recent development of the direct tomography technique, which utilizes the XRS process as a contrast mechanism for assessing the three-dimensional spatially resolved carbon chemistry of complex organic materials. We conclude by exposing the current limitations and provide an outlook on how to overcome some of the existing challenges and advance future developments and applications of this powerful technique for complex organic systems.

Disentangling the chemistry of Australian plant exudates from a unique historical collection

Significance For millennia, Aboriginal Australian peoples have used the extraordinary physicochemical properties of plant exudates from practical applications to cultural expression. We employ state-of-the-art spectroscopy to characterize the molecular compositions of well-preserved, native Australian plant exudates (Xanthorrhoea, Callitris, Eucalyptus, and Acacia) from a historic collection assembled over a century ago. This work demonstrates the benefits of X-ray Raman spectroscopy for the analysis of these complex natural systems. It provides key information for a broader understanding of their terpenoid, aromatic, phenolic, and polysaccharide composition and subsequent chemical classification. It complements Fourier-transform infrared and pyrolysis-gas chromatography-mass spectrometry by allowing bulk-sensitive analysis in a fully noninvasive manner and probes molecular features which remain silent in these commonly employed analyses.

Comparative soft-tissue preservation in Holocene-age capelin concretions

Determining how soft tissues are preserved and persist through geologic time are continuing challenge because decay begins immediately after senescence while diagenetic transformations generally progress over days to millions of years. However, in recent years, carbonate concretions containing partially-to-fully decayed macroorganisms have proven to be remarkable windows into the diagenetic continuum revealing insights into the fossilization process. This is because most concretions are the result of biologically induced mineral precipitation caused by the localized decay of organic matter, which oftentimes preserves a greater biological signal relative to their host sediment. Here we present a comparative lipid biomarker study investigating processes associated with soft-tissue preservation within Holocene-age carbonate concretions that have encapsulated modern capelin (Mallotus villosus). We focus on samples collected from two depositional settings that have produced highly contrasting preservation end-members: (1) Kangerlussuaq, Greenland: a marine environment, which, due to isostatic rebound, has exposed strata containing concretions exhibiting exceptional soft-tissue preservation (6-7 kya), and (2) Greens Creek, Ottawa, Canada: a paleo brackish-to-freshwater marine excursion containing concretions exhibiting skeletal remains (~11 kya). Lipid biomarker analysis reveals endogenous capelin tissues and productive waters at Kangerlussuaq that are in sharp contrast to Greens Creek concretions, which lack appreciable capelin and environmental signals. Comparable distributions of bacterial fatty acids and statistical analyses suggest soft-tissue preservation within concretions is agnostic to specific heterotrophic decay communities. We, therefore, interpret preservation within carbonate concretions may represent a race between microbially induced authigenic precipitation and decay. Namely, factors resulting in exceptional preservation within concretions likely include: (1) organic matter input, (2) rate of decay, (3) carbonate saturation, (4) porewater velocity, and (5) rate of authigenic (carbonate) precipitation resulting in arrested decay/bacterial respiration due to cementing pore spaces limiting the diffusion of electron acceptors into the decay foci.

Fast and pervasive diagenetic isotope exchange in foraminifera tests is species-dependent

Oxygen isotope compositions of fossil foraminifera tests are commonly used proxies for ocean paleotemperatures, with reconstructions spanning the last 112 million years. However, the isotopic composition of these calcitic tests can be substantially altered during diagenesis without discernible textural changes. Here, we investigate fluid-mediated isotopic exchange in pristine tests of three modern benthic foraminifera species (Ammonia sp., Haynesina germanica, and Amphistegina lessonii) following immersion into an ¹⁸O-enriched artificial seawater at 90 °C for hours to days. Reacted tests remain texturally pristine but their bulk oxygen isotope compositions reveal rapid and species-dependent isotopic exchange with the water. NanoSIMS imaging reveals the 3-dimensional intra-test distributions of ¹⁸O-enrichment that correlates with test ultra-structure and associated organic matter. Image analysis is used to quantify species level differences in test ultrastructure, which explains the observed species-dependent rates of isotopic exchange. Consequently, even tests considered texturally pristine for paleo-climatic reconstruction purposes may have experienced substantial isotopic exchange; critical paleo-temperature record re-examination is warranted.

Paleoclimate reconstructions commonly use oxygen isotope compositions from fossil foraminifera tests as proxies. Here, the authors show that these tests exchange O-isotopes with surrounding fluids, with implications for paleotemperature records.

Raman spectroscopy is a powerful tool in molecular paleobiology: An analytical response to Alleon et al. (https://doi.org/10.1002/bies.202000295)

A recent article argued that signals from conventional Raman spectroscopy of organic materials are overwhelmed by edge filter and fluorescence artefacts. The article targeted a subset of Raman spectroscopic investigations of fossil and modern organisms and has implications for the utility of conventional Raman spectroscopy in comparative tissue analytics. The inferences were based on circular reasoning centered around the unconventional analysis of spectra from just two samples, one modern, and one fossil. We validated the disputed signals with in situ Fourier-Transform Infrared (FT-IR) Spectroscopy and through replication with different lasers, filters, and operators in independent laboratories. Our Raman system employs a holographic notch filter which is not affected by edge filter or other artefacts. Multiple lines of evidence confirm that conventional Raman spectra of fossils contain biologically and geologically meaningful information. Statistical analyses of large Raman and FT-IR spectral data sets reveal patterns in fossil composition and yield valuable insights into the history of life.

Structural and chemical heterogeneity of Proterozoic organic microfossils of the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada

Organic microfossils in Meso- and Neoproterozoic rocks are of key importance to track the emergence and evolution of eukaryotic life. An increasing number of studies combine Raman spectroscopy with synchrotron-based methods to characterize these microfossils. A recurring observation is that Raman spectra of organic microfossils show negligible variation on a sample scale and that variation between different samples can be explained by differences in thermal maturation or in the biologic origin of organic precursor material. There is a paucity of work, however, that explores the extent to which the petrographic framework and diagenetic processes might influence the chemical structure of organic materials. We present a detailed Raman spectroscopy-based study of a complex organic microfossil assemblage in the ca. 1 Ga old Angmaat Formation, Baffin Island, Canada. This formation contains abundant early diagenetic chert that preserves silicified microbial mats with numerous, readily identifiable organic microfossils. Individual chert beds show petrographic differences with discrete episodes of cementation and recrystallization. Raman spectroscopy reveals measurable variation of organic maturity between samples and between neighboring organic microfossils of the same taxonomy and taphonomic state. Scanning transmission X-ray microscopy performed on taphonomically similar coccoidal microfossils from the same thin section shows distinct chemical compositions, with varying ratios of aromatic compounds to ketones and phenols. Such observations imply that geochemical variation of organic matter is not necessarily coupled to thermal alteration or organic precursor material. Variation of the Raman signal across single samples is most likely linked to the diagenetic state of analyzed materials and implies an association between organic preservation and access to diagenetic fluids. Variation in the maturity of individual microfossils may be a natural outcome of local diagenetic processes and potentially exceeds differences derived from precursor organic material. These observations stress the importance of detailed in situ characterization by Raman spectroscopy to identify target specimens for further chemical analysis.

Chemical signatures of soft tissues distinguish between vertebrates and invertebrates from the Carboniferous Mazon Creek Lagerstätte of Illinois

The chemical composition of fossil soft tissues is a potentially powerful and yet underutilized tool for elucidating the affinity of problematic fossil organisms. In some cases, it has proven difficult to assign a problematic fossil even to the invertebrates or vertebrates (more generally chordates) based on often incompletely preserved morphology alone, and chemical composition may help to resolve such questions. Here, we use in situ Raman microspectroscopy to investigate the chemistry of a diverse array of invertebrate and vertebrate fossils from the Pennsylvanian Mazon Creek Lagerstätte of Illinois, and we generate a ChemoSpace through principal component analysis (PCA) of the in situ Raman spectra. Invertebrate soft tissues characterized by chitin (polysaccharide) fossilization products and vertebrate soft tissues characterized by protein fossilization products plot in completely separate, non-overlapping regions of the ChemoSpace, demonstrating the utility of certain soft tissue molecular signatures as biomarkers for the original soft tissue composition of fossil organisms. The controversial problematicum Tullimonstrum, known as the Tully Monster, groups with the vertebrates, providing strong evidence of a vertebrate rather than invertebrate affinity.

Phylogenetic and physiological signals in metazoan fossil biomolecules

Proteins, lipids, and sugars establish animal form and function. However, the preservation of biological signals in fossil organic matter is poorly understood. Here, we used high-resolution in situ Raman microspectroscopy to analyze the molecular compositions of 113 Phanerozoic metazoan fossils and sediments. Proteins, lipids, and sugars converge in composition during fossilization through lipoxidation and glycoxidation to form endogenous N-, O-, and S-heterocyclic polymers. Nonetheless, multivariate spectral analysis reveals molecular heterogeneities: The relative abundance of glycoxidation and lipoxidation products distinguishes different tissue types. Preserved chelating ligands are diagnostic of different modes of biomineralization. Amino acid-specific fossilization products retain phylogenetic information and capture higher-rank metazoan relationships. Molecular signals survive in deep time and provide a powerful tool for reconstructing the evolutionary history of animals.

Formation and Preservation of Microbial Palisade Fabric in Silica Deposits from El Tatio, Chile

Palisade fabric is a ubiquitous texture of silica sinter found in low temperature (<40°C) regimes of hot spring environments, and it is formed when populations of filamentous microorganisms act as templates for silica polymerization. Although it is known that postdepositional processes such as biological degradation and dewatering can strongly affect preservation of these fabrics, the impact of extreme aridity has so far not been studied in detail. Here, we report a detailed analysis of recently silicified palisade fabrics from a geyser in El Tatio, Chile, tracing the progressive degradation of microorganisms within the silica matrix. This is complemented by heating experiments of natural sinter samples to assess the role of diagenesis. Sheathed cyanobacteria, identified as Leptolyngbya sp., were found to be incorporated into silica sinter by irregular cycles of wetting, evaporation, and mineral precipitation. Transmission electron microscopy analyses revealed that nanometer-sized silica particles are filling the pore space within individual cyanobacterial sheaths, giving rise to their structural rigidity to sustain a palisade fabric framework. Diagenesis experiments further show that the sheaths of the filaments are preferentially preserved relative to the trichomes, and that the amount of water present within the sinter is an important factor for overall preservation during burial. This study confirms that palisade fabrics are efficiently generated in a highly evaporative geothermal field, and that these biosignatures can be most effectively preserved under dry diagenetic conditions.

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.

The degradation of organic compounds impacts the crystallization of clay minerals and vice versa

Expanding our capabilities to unambiguously identify ancient traces of life in ancient rocks requires laboratory experiments to better constrain the evolution of biomolecules during advanced fossilization processes. Here, we submitted RNA to hydrothermal conditions in the presence of a gel of Al-smectite stoichiometry at 200 °C for 20 days. NMR and STXM-XANES investigations revealed that the organic fraction of the residues is no longer RNA, nor the quite homogeneous aromatic-rich residue obtained in the absence of clays, but rather consists of particles of various chemical composition including amide-rich compounds. Rather than the pure clays obtained in the absence of RNA, electron microscopy (SEM and TEM) and diffraction (XRD) data showed that the mineralogy of the experimental residues includes amorphous silica and aluminosilicates mixed together with nanoscales phosphates and clay minerals. In addition to the influence of clay minerals on the degradation of organic compounds, these results evidence the influence of the presence of organic compounds on the nature of the mineral assemblage, highlighting the importance of fine-scale mineralogical investigations when discussing the nature/origin of organo-mineral microstructures found in ancient rocks.

Organo-mineral associations in chert of the 3.5 Ga Mount Ada Basalt raise questions about the origin of organic matter in Paleoarchean hydrothermally influenced sediments

Hydrothermal and metamorphic processes could have abiotically produced organo-mineral associations displaying morphological and isotopic characteristics similar to those of fossilized microorganisms in ancient rocks, thereby leaving false-positive evidence for early life in the geological record. Recent studies revealed that geologically-induced alteration processes do not always completely obliterate all molecular information about the original organic precursors of ancient microfossils. Here, we report the molecular, geochemical, and mineralogical composition of organo-mineral associations in a chert sample from the ca. 3.47 billion-year-old (Ga) Mount Ada Basalt, in the Pilbara Craton, Western Australia. Our observations indicate that the molecular characteristics of carbonaceous matter are consistent with hydrothermally altered biological organics, although significantly distinct from that of organic microfossils discovered in a chert sample from the ca. 3.43 Ga Strelley Pool Formation in the same area. Alternatively, the presence of native metal alloys in the chert, previously believed to be unstable in such hydrothermally influenced environments, indicates strongly reducing conditions that were favorable for the abiotic formation of organic matter. Drawing definitive conclusions about the origin of most Paleoarchean organo-mineral associations therefore requires further characterization of a range of natural samples together with experimental simulations to constrain the molecular composition and geological fate of hydrothermally-generated condensed organics.

Challenges in evidencing the earliest traces of life

Earth has been habitable for 4.3 billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4 billion years ago-and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond.

Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers

Vertebrate hard tissues consist of mineral crystallites within a proteinaceous scaffold that normally degrades post-mortem. Here we show, however, that decalcification of Mesozoic hard tissues preserved in oxidative settings releases brownish stained extracellular matrix, cells, blood vessels, and nerve projections. Raman Microspectroscopy shows that these fossil soft tissues are a product of diagenetic transformation to Advanced Glycoxidation and Lipoxidation End Products, a class of N-heterocyclic polymers generated via oxidative crosslinking of proteinaceous scaffolds. Hard tissues in reducing environments, in contrast, lack soft tissue preservation. Comparison of fossil soft tissues with modern and experimentally matured samples reveals how proteinaceous tissues undergo diagenesis and explains biases in their preservation in the rock record. This provides a target, focused on oxidative depositional environments, for finding cellular-to-subcellular soft tissue morphology in fossils and validates its use in phylogenetic and other evolutionary studies.

Changes of aliphatic C-H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy

Aliphatic C-H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C-H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250-450°C. Changes in the infrared (IR) signals were monitored by micro-Fourier transform infrared (FTIR) spectroscopy. Micro-FTIR shows that absorbances at 2,925 cm^-1 band (aliphatic CH₂ ) and 2,960 cm^-1 band (aliphatic CH₃ ) decrease during heating, indicating loss of the C-H bonds, which was delayed by the presence of silica. A theoretical approach using solid-state kinetics indicates that the most probable process for the aliphatic C-H decrease is three-dimensional diffusion of alteration products under both non-embedded and silica-embedded conditions. The extrapolation of the experimental results obtained at 250-450°C to lower temperatures implies that the rate constant for CH₃ (k_CH3 ) is similar to or lower than that for CH₂ (k_CH2 ; i.e., CH₃ decreases at a similar rate or more slowly than CH₂ ). The peak height ratio of 2,960 cm^-1 band (CH₃ )/2,925 cm^-1 band (CH₂ ; R_3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C-H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R_3/2 values. Meanwhile, studies of microfossils suggest that the R_3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R_3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R_3/2 values, might have occurred during fossilization.

Experimental maturation of Archaea encrusted by Fe-phosphates

Burial is generally detrimental to the preservation of biological signals. It has often been assumed that (bio)mineral-encrusted microorganisms are more resistant to burial-induced degradation than non-encrusted ones over geological timescales. For the present study, we submitted Sulfolobus acidocaldarius experimentally encrusted by amorphous Fe phosphates to constrained temperature conditions (150 °C) under pressure for 1 to 5 days, thereby simulating burial-induced processes. We document the molecular and mineralogical evolution of these assemblages down to the sub-micrometer scale using X-ray diffraction, scanning and transmission electron microscopies and synchrotron-based X-ray absorption near edge structure spectroscopy at the carbon K-edge. The present results demonstrate that the presence of Fe-phosphates enhances the chemical degradation of microbial organic matter. While Fe-phosphates remained amorphous in abiotic controls, crystalline lipscombite (FeIIxFeIII3-x(PO4)2(OH)3-x) entrapping organic matter formed in the presence of S. acidocaldarius cells. Lipscombite textures (framboidal vs. bipyramidal) appeared only controlled by the initial level of encrustation of the cells, suggesting that the initial organic matter to mineral ratio influences the competition between nucleation and crystal growth. Altogether these results highlight the important interplay between minerals and organic matter during fossilization, which should be taken into account when interpreting the fossil record.