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MRW was funded by a NERC PhD studentship at the University of Manchester. PLM thanks STFC for their support (ST/M001814/1). We are grateful to SSRL for continued support for imaging at beamline 6-2 at SLAC. We are also grateful to the Manchester X-Ray Imaging Facility, which was funded in part by the EPSRC (grants EP/F007906/1, EP/F001452/1 and EP/I02249X/1). Ancient stromatolites can provide key insights into the early evolution of life on Earth. Neoarchean fenestrate stromatolites from the ∼2520 Ma Upper Nauga Formation (Transvaal Supergroup, South Africa) preserve cuspate morphologies. They possess clearly delineated support and drape structures interpreted as dolomitized microbial mat material. Petrographic observations show that the biogenic structures are composed of planar-s to non-planar ferroan dolomite, encased in ferroan calcite, including herringbone calcite textures. The cuspate stromatolites were analyzed using Synchrotron Rapid Scanning X-Ray Fluorescence (SRS-XRF) and more conventional techniques to determine: (i) whether element distributions could be distinguished in ancient stromatolites at both cm to dm scales, (ii) whether element distributions show variation between biogenic and abiogenic textures, and (iii) the sample’s paragenesis. The distributions of Ca, Fe, Mn, Pb, Cu, As, Br, Al, Si, P, and S directly correspond to dolomitized stromatolitic structures and show trace element distributions are principally controlled by calcite and dolomite occurrence. Dolomite formation was mainly driven by seawater-derived fluids given the high concentrations of Fe and retention of marine shale-normalized rare earth element and yttrium (REYSN) patterns, however the spatial association of dolomite to stromatolite structures may reflect microbially-influenced mineral nucleation. Given the complexity of this sample’s paragenetic evolution, trace metal distributions cannot be conclusively tied to specific metabolic pathways, bioaccumulation or passive binding, however, the results show SRS-XRF can be used for quantifiable, spatial, in-situ investigation of ancient microbialites. Postprint

Attempts to extend methods for dating archaeological bones beyond that of radiocarbon dating, such as amino acid racemization, have met with limited success owing to the dependence on multiple environmental factors and controls. Despite facing similar challenges, deamidation of glutamine has recently been investigated as a potential indicator of ‘thermal age’ in archaeological bones, as well as a measure of their preservation quality. Here, we analysed bones from different Middle Palaeolithic layers from Grotte Mandrin (France), as well as undertook a series of simulated diagenetic experiments, to investigate whether deamidation can be used as a tool for the relative dating of bones.

International audience; Myriapods were, together with arachnids, the earliest animals to occupy terrestrial ecosystems, by at least the Silurian. The origin of myriapods and their land colonization have long remained puzzling until euthycarcinoids, an extinct group of aquatic arthropods considered amphibious, were shown to be stem-group myriapods, extending the lineage to the Cambrian and evidencing a marine-to-terrestrial transition. Although possible respiratory structures comparable to the air-breathing tracheal system of myriapods are visible in several euthycarcinoids, little is known about the mechanism by which they respired. Here, we describe a new euthycarcinoid from Upper Devonian alluvio-lagoonal deposits of Belgium. Synchrotron-based elemental X-ray analyses were used to extract all available information from the only known specimen. Sulfur X-ray fluorescence (XRF) mapping and spectroscopy unveil sulfate evaporation stains, spread over the entire slab, suggestive of a very shallow-water to the terrestrial environment prior to burial consistent with an amphibious lifestyle. Trace metal XRF mapping reveals a pair of ventral spherical cavities or chambers on the second post-abdominal segment that do not compare to any known feature in aquatic arthropods, but might well play a part in air-breathing. Our data provide additional support for amphibious lifestyle in euthycarcinoids and show that different respiratory strategies were used during the marine-to-terrestrial transition in the myriapod lineage.

Not just settling What controls the distribution of microplastics on the deep seafloor? Kane et al. show that the answer to that question is more complicated than particles simply settling from where they are found on the sea surface (see the Perspective by Mohrig). Using data that they collected off the coast of Corsica, the authors show that thermohaline-driven currents can control the distribution of microplastics by creating hotspots of accumulation, analogous to their role in causing focused areas of seafloor sediment deposition. Such currents also supply oxygen and nutrients to deep-sea benthos, so deepsea biodiversity hotspots are also likely to be microplastic hotspots. Science , this issue p. 1140 ; see also p. 1055

Mass transport by aqueous fluids is a dynamic process in shallow crustal systems, redistributing nutrients as well as contaminants. Rock matrix diffusion into fractures (void space) within crystalline rock has been postulated to play an important role in the transient storage of solutes. The reacted volume of host rock involved, however, will be controlled by fluid-rock reactions. Here we present the results of a study which focusses on defining the length scale over which rock matrix diffusion operates within crystalline rock over timescales that are relevant to safety assessment of radioactive and other long-lived wastes. Through detailed chemical and structural analysis of natural specimens sampled at depth from an active system (Toki Granite, Japan), we show that, contrary to commonly proposed models, the length scale of rock matrix diffusion may be extremely small, on the order of centimetres, even over timescales of millions of years. This implies that in many cases the importance of rock matrix diffusion will be minimal. Additional analyses of a contrasting crystalline rock system (Carnmenellis Granite, UK) corroborate these results.

Significance Jawless, boneless, and virtually without fossil record, hagfish have long escaped systematists’ grip on their place among other fish. Yet their systematic resolution is critical to define vertebrates as a clade. Here we report an unequivocal fossil hagfish from the Cretaceous Mediterranean. Using this fossil to calibrate the evolutionary history of the group, our analysis supports hagfish and lampreys as sister groups, which likely diverged from one another in early Paleozoic times. As a result, vertebrates have a deep dichotomy, where some fossil jawless vertebrates sit closer to hagfish and lampreys than to jawed vertebrates. We showed that morphology-based analysis converged onto molecular inferences when characters are coded nonindependently, providing a case study for morphological–molecular conflicts in animal phylogeny., Hagfish depart so much from other fishes anatomically that they were sometimes considered not fully vertebrate. They may represent: (i) an anatomically primitive outgroup of vertebrates (the morphology-based craniate hypothesis); or (ii) an anatomically degenerate vertebrate lineage sister to lampreys (the molecular-based cyclostome hypothesis). This systematic conundrum has become a prominent case of conflict between morphology- and molecular-based phylogenies. To date, the fossil record has offered few insights to this long-branch problem or the evolutionary history of hagfish in general, because unequivocal fossil members of the group are unknown. Here, we report an unequivocal fossil hagfish from the early Late Cretaceous of Lebanon. The soft tissue anatomy includes key attributes of living hagfish: cartilages of barbels, postcranial position of branchial apparatus, and chemical traces of slime glands. This indicates that the suite of characters unique to living hagfish appeared well before Cretaceous times. This new hagfish prompted a reevaluation of morphological characters for interrelationships among jawless vertebrates. By addressing nonindependence of characters, our phylogenetic analyses recovered hagfish and lampreys in a clade of cyclostomes (congruent with the cyclostome hypothesis) using only morphological data. This new phylogeny places the fossil taxon within the hagfish crown group, and resolved other putative fossil cyclostomes to the stem of either hagfish or lamprey crown groups. These results potentially resolve the morphological–molecular conflict at the base of the Vertebrata. Thus, assessment of character nonindependence may help reconcile morphological and molecular inferences for other major discords in animal phylogeny.

Trace element inventories are known to correlate with specific histological structures in bone, reflecting organismal physiology and life histories. By studying trace elements in fossilised bone, particularly in individuals with cyclic bone growth (alternating fast/slow bone deposition), we can improve our understanding of the physiology of extinct organisms. In this study we present the first direct comparison between optical histology (bone tissue identification) and synchrotron-based chemical mapping, quantification, and characterisation of trace elements (biochemistry) within cyclic growth tissues, in this case within bones of a cave hyaena (Crocuta crocuta spelaea). Results show distributions of zinc, an element strongly associated with active ossification and bone growth, correlating with (1) fast-growing tissue of zonal bone (cyclic growth) in an extinct hyaena and (2) secondary osteons (remodelling) in both extant and extinct hyaena. Concentrations and coordination chemistry of zinc within the fossil sample are comparable to those seen in extant bone suggesting that zinc is endogenous to the sample and that the chemistry of bone growth has been preserved for 40 ka. These results demonstrate that the study of trace elements as part of the histochemistry has wide utility for reconstructing growth, diet and other lifestyle factors in archaeological and fossil bone.

Despite the increasing interest in geologic co-sequestration of CO2 and H2S, the long-term consequences of the chemical interactions involved in this process remain largely unknown on a reservoir scale. A Mississippian aged CO2-H2S reservoir in LaBarge Field, Wyoming, USA is an ideal study site to investigate mineral and fluid reactions related to gaseous H2S and CO2. We conducted two reaction path models based on mineralogical, fluid, gas, and stable isotope compositional data to discern the role of CO2 influx upon the generation of H2S through thermochemical sulphate reduction (TSR). We discriminate between two models-one in which TSR is triggered by temperature at a given burial depth and one where TSR is triggered by ingress of CO2. The reaction path model based upon burial-controlled TSR and later CO2 influx is consistent with mineralogical observations and stable isotope measurements from drill cores. The models show that CO2 influx leads to calcite precipitation which is only limited by the calcium concentration in the fluid. This modelling approach is useful in constraining the timing of fluid flux in the reservoir and gives further insight into the mineralogical consequences of the gas, water, and rock interactions occurring in the reservoir. In terms of geologic co-sequestration this implies that the addition of CO2 into a reducing carbonate system can result in calcite precipitation, instead of anhydrite as previously thought. Furthermore, it is only limited by the availability of Ca2+ and will therefore not diminish the amount of H2S in the system.

International audience

The complexity and heterogeneity of bone chemistry makes it difficult to discern information on physiological and taphonomic processes stored within the bone matrix. Analysis of archaeological and palaeontological bone becomes more difficult because in many cases the most pivotal specimens are too scientifically valuable for destructive analysis. This problem is further escalated by the fact that the heterogeneity of the bone may cause small “pockets” of preservation that can be missed during sampling. Therefore, a non-destructive technique that can spatially resolve such heterogeneity within the bone is needed. Here we use microfocus, non-destructive synchrotron-based X-Ray Fluorescence (XRF) imaging and X-ray Absorption Spectroscopy (XAS) to map the organic constituents within extant and fossil bovid bones. XAS analysis of sulfur allowed organic sulfur (within collagen as methionine) to be distinguished from inorganic sulfate (within bone apatite). Mapping and quantification of organic sulfur within the samples were made by setting the beam to the methionine resonance, allowing for the detection, distribution and quantification of collagen present by using organic sulfur as an internal marker. Results show organic sulfur to be distributed in small “pockets” throughout the bone matrix in both extant and fossil specimens. Significant loss of organic sulfur was seen in specimens between 100 ka and 650 ka with little organic sulfur preservation persisting after this date. Comparison of residual organic sulfur concentrations as a function of sample age revealed a second order rate law for organic sulfur oxidation (k ≈ 1 × 10−5 y−1) within bone. These results show that non-destructive, synchrotron-based XRF mapping of organic sulfur is a useful tool for not only calculating rates of collagen degradation through time, but also identifying areas of potential collagen preservation for other paleobiological applications such as proteomics and stable isotope analyses.

We have synthesized and analyzed by mid-infrared reflectance spectroscopy silicate glasses that are representative for the glasses on the surface of Mercury. The glass compositions are based on high-pressure laboratory experiments and the resulting compositions of the glass phase. The spectra are of interest for investigating the surface of Mercury using the MERTIS (Mercury Radiometer and Thermal Infrared Spectrometer) instrument on board of the ESA/JAXA BepiColombo mission.Both powdered fractions and polished blocks have been analyzed. Powdered size fractions of 0–25 μm, 25-63 μm, 63-125 μm, and 125–250 μm were measured in reflectance in the thermal infrared (2–20 μm). Spectra for powdered bulk glasses (1.6 wt% - 19.0 wt% MgO) show a single, dominating Reststrahlenband (RB, 9.3–9.8 μm), a Christiansen Feature (CF; 7.6 μm - 8.1 μm), and a size dependent Transparency Feature (TF; 11.6–11.9 μm). Micro-FTIR analyses of polished blocks of glasses (3.4–26.5 wt% MgO) have characteristic bands at 7.8–8.2 μm (CF), and 9.3–9.9 μm (RB). Only few olivine crystalline features were observed.Spectral features correlate with compositional characteristics, e.g. SiO2 content or SCFM (SiO2/(SiO2 + CaO + FeO + MgO) index. The strongest correlation between band features CF and the strong RB are with Mg/Si. No simple mixture of glass spectra from this study is able to reproduce the entire ground based spectrum of the surface of Mercury. However, Mg-rich glasses reproduce identified features at 8.5 μm, 9.9 μm and 12.4 μm.

Faunal remains from archaeological sites allow for the identification of animal species that enables the better understanding of the relationships between humans and animals, not only from their morphological information, but also from the ancient biomolecules (lipids, proteins, and DNA) preserved in these remains for thousands and even millions of years. However, due to the costs and efforts required for ancient biomolecular analysis, there has been considerable research into development of accurate and efficient screening approaches for archaeological remains. FTIR spectroscopy is one such approach that has been considered for screening of proteins, but its widespread use has been hindered by the fact that its predictive accuracy can vary widely depending on the extent of sample preservation and the instrument used. Further, screening methods for ancient DNA (aDNA) analysis are scarce. Here we present a new approach to vastly improve upon FTIR-based screening methods prior to ZooMS (Zooarchaeology by Mass Spectrometry) and aDNA analysis through the use of random forest-based machine learning. To do so, we use ATR-FTIR to examine three sets of archaeological bone assemblages and analyse them by ZooMS (for taxonomic identification). Two of these are from Palaeolithic contexts, dominated by terrestrial fauna and include specimens with a variety of preservational conditions. The third set consists of Holocene faunal remains, with variable levels of preservation and is dominated by cetaceans. Using the Holocene faunal remains, we were able to more consistently evaluate ATR-FTIR-based screening for mtDNA as well as ZooMS success. We report on the potential of machine learning in ATR-FTIR-based screening for ancient mtDNA analysis, and our machine learning models conclusively improve the accuracy prior to usage of ATR-FTIR-based screening for ZooMS by 20–40%. The results also suggest this approach potentially allows for a universal screening system, applicable across multiple sites and largely independent of the spectrometers used.

The ~492 Ma Shetland Ophiolite Complex contains an extensive mantle section, within which numerous podiform chromitite bodies formed during melt percolation in a supra-subduction zone setting. One of the Shetland ophiolite chromitite localities has an unusual style of platinum-group element (PGE) mineralization. Specifically, the Cliff chromitite suite has relatively high (>250 ppm) Pt plus Pd, compared to other chromitites in the Shetland Ophiolite Complex. In this study, we apply petrographic observation, mineral chemistry and novel X-ray microtomography data to elucidate the petrogenesis of PGE-bearing phases at Cliff. The combined datasets reveal that the PGE at Cliff have probably been fractionated by an As-rich fluid, concentrating Pt and Ir into visible (0.1–1 µm) platinum-group minerals (PGM) such as sperrylite and irarsite, respectively. The high (>1 ppm) bulk-rock concentrations of the other PGE (e.g. Os) in the Cliff chromitites suggests the presence of abundant fine-grained unidentified PGM in the serpentinized groundmass. The spatial association of arsenide phases and PGM with alteration rims on Cr-spinel grains suggests that the high Pt and Pd abundances at Cliff result from a late-stage low-temperature (e.g. 200–300°C) hydrothermal event. This conclusion highlights the potential effects that secondary alteration processes can have on modifying and upgrading the tenor of PGE deposits.

International audience; Carbon compounds are ubiquitous and occur in a diversity of chemical forms in many systems including ancient and historic materials ranging from cultural heritage to paleontology. Determining their speciation cannot only provide unique information on their origin but may also elucidate degradation processes. Synchrotron-based X-ray absorption near-edge structure (XANES) spectroscopy at the carbon K-edge (280−350 eV) is a very powerful method to probe carbon speciation. However, the short penetration depth of soft X-rays imposes stringent constraints on sample type, preparation, and analytical environment. A hard X-ray probe such as X-ray Raman scattering (XRS) can overcome many of these difficulties. Here we report the use of XRS at ∼6 keV incident energy to collect carbon K-edge XANES data and probe the speciation of organic carbon in several specimens relevant to cultural heritage and natural history. This methodology enables the measurement to be done in a nondestructive way, in air, and provides information that is not compromised by surface contamination by ensuring that the dominant signal contribution is from the bulk of the probed material. Using the backscattering geometry at large photon momentum transfer maximizes the XRS signal at the given X-ray energy and enhances nondipole contributions compared to conventional XANES, thereby augmenting the speciation sensitivity. The capabilities and limitations of the technique are discussed. We show that despite its small cross section, for a range of systems the XRS method can provide satisfactory signals at realistic experimental conditions. XRS constitutes a powerful complement to FT-IR, Raman, and conventional XANES spectroscopy, overcoming some of the limitations of these techniques.

The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more ‘crouched' in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil., Birds have a more crouched posture compared to their theropod dinosaur ancestors. Here, Jiang and colleagues describe a lower hindlimb of the Early Cretaceous bird Confuciusornis with soft tissues apparently preserved even as molecules, indicating a somewhat more modern posture in ancient birds.

Polarization-dependent grazing incidence X-ray absorption spectroscopy (XAS) measurements were completed on oriented single crystals of magnesite [MgCO3] and brucite [Mg(OH)2] reacted with aqueous uranyl chloride above and below the solubility boundaries of schoepite (500, 50, and 5 ppm) at pH 8.3 and at ambient (PCO2 = 10(-3.5)) or reduced partial pressures of carbon dioxide (PCO2 = 10(-4.5)). X-ray absorption near edge structure (XANES) spectra show a striking polarization dependence (χ = 0° and 90° relative to the polarization plane of the incident beam) and consistently demonstrated that the uranyl molecule was preferentially oriented with its Oaxial═U(VI)═Oaxial linkage at high angles (60-80°) to both magnesite (101̅4) and brucite (0001). Extended X-ray absorption fine structure (EXAFS) analysis shows that the "effective" number of U(VI) axial oxygens is the most strongly affected fitting parameter as a function of polarization. Furthermore, axial tilt in the surface thin films (thickness ∼ 21 Å) is correlated with surface roughness [σ]. Our results show that hydrated uranyl(-carbonate) complexes polymerize on all of our experimental surfaces and that this process is controlled by surface hydroxylation. These results provide new insights into the bonding configuration expected for uranyl complexes on the environmentally significant carbonate and hydroxide mineral surfaces.

Around the world large quantities of sludge wastes derived from nuclear energy production are currently kept in storage facilities. In the UK, the British government has marked sludge removal as a top priority as these facilities are nearing the end of their operational lifetimes. Therefore chemical understanding of uranium uptake in Mg-rich sludge is critical for successful remediation strategies. Previous studies have explored uranium uptake by the calcium carbonate minerals, calcite and aragonite, under conditions applicable to both natural and anthropogenically perturbed systems. However, studies of the uptake by Mg-rich minerals such as brucite [Mg(OH)2], nesquehonite [MgCO3·3H2O] and hydromagnesite [Mg5(CO3)4(OH)2·4H2O], have not been previously conducted. Such experiments will improve our understanding of the mobility of uranium and other actinides in natural lithologies as well as provide key information applicable to nuclear waste repository strategies involving Mg-rich phases. Experiments with mineral powders were used to determine the partition coefficients (Kd) and coordination of UO22+ during adsorption and co-precipitation with brucite, nesquehonite and hydromagnesite. The Kd values for the selected Mg-rich minerals were comparable or greater than those published for calcium carbonates. Extended X-ray absorption fine structure analysis results showed that the structure of the uranyl-triscarbonato [UO2(CO3)3] species was maintained after surface attachment and that uptake of uranyl ions took place mainly via mineral surface reactions.

An experimental technique has been developed and applied to the problem of determining effective diffusion coefficients and partition coefficients of Sr in low permeability geological materials. This technique, the micro-reactor simulated channel method (MRSC), allows rapid determination of contaminant transport parameters with resulting values comparable to those determined by more traditional methods and also creates product surfaces that are amenable for direct chemical analysis. An attempt to further constrain mass flux was completed by detailed ion beam analysis of polished tuff surfaces (tuff is a polycrystalline polyminerallic aggregate dominated by silicate phases) that had been reacted with Sr solutions at concentrations of 10−5, 10−3 and 10−1 mol l−1. Ion beam analysis was carried out using beams of both protons (using particle induced X-ray emission and elastic backscattering spectrometry or EBS) and alpha-particles (using Rutherford backscattering spectrometry). The ion beam analyses showed that increased solution concentrations resulted in increased surface concentrations and that in the highest concentration experiment, Sr penetrated to at least 4 μm below the primary interface. The Sr surface concentrations determined by EBS were 0.06 (±0.05), 0.87 (±0.30) and 2.40 (±1.0) atomic weight % in the experiments with starting solution concentrations of 10−5, 10−3, and 10−1 mol l−1, respectively.

Aspects of the (bio)geochemical cycling of metals (including Fe, Cu, Pb, Zn, Hg, As, Sb, U, Tc, Np) at or near the Earth's surface are discussed with reference to the recent work of the authors. Key stages of the breakdown of metalliferous minerals, transport of metals as solution complexes or colloidal precipitates, and interaction of metals in solution with the surfaces of minerals are considered. Emphasis is on molecular-scale observations using techniques such as scanning probe microscopy, photoelectron and (synchrotron) X-ray spectroscopies. The importance of the biological/mineralogical interface is also emphasized with reference to the bacterial colonization of mineral surfaces and formation of biofilms, and their influence on mineral surface reactivity and flow of fluids through rocks and sediments. Also noted is the importance of relating molecular and micro-scale observations to macroscopic phenomena. Molecular-scale understanding is central to attempts to model many processes of relevance in mineral exploration and exploitation, and in the containment of hazardous wastes and remediation of polluted areas. Mineralogists have a central role to play in the relevant environmental sciences and technologies.

Colour and pattern are key traits with important roles in camouflage, warning and attraction. Ideally, in order to begin to understand the evolution and ecology of colour in nature, it is important to identify and, where possible, fully characterise pigments using biochemical methods. The phylum Mollusca includes some of the most beautiful exemplars of biological pigmentation, with the vivid colours of sea shells particularly prized by collectors and scientists alike. Biochemical studies of molluscan shell colour were fairly common in the last century, but few of these studies have been confirmed using modern methods and very few shell pigments have been fully characterised. Here, we use modern chemical and multimodal spectroscopic techniques to identify two porphyrin pigments and eumelanin in the shell of marine snails Clanculus pharaonius and C margaritarius. The same porphyrins were also identified in coloured foot tissue of both species. We use high performance liquid chromatography (HPLC) to show definitively that these porphyrins are uroporphyrin I and uroporphyrin III. Evidence from confocal microscopy analyses shows that the distribution of porphyrin pigments corresponds to the striking pink-red of C. pharaonius shells, as well as pink-red dots and lines on the early whorls of C. margaritarius and yellow-brown colour of later whorls. Additional HPLC results suggest that eumelanin is likely responsible for black spots. We refer to the two differently coloured porphyrin pigments as trochopuniceus (pink-red) and trochoxouthos (yellow-brown) in order to distinguish between them. Trochopuniceus and trochoxouthos were not found in the shell of a third species of the same superfamily, Calliostoma zizyphinum, despite its superficially similar colouration, suggesting that this species has different shell pigments. These findings have important implications for the study of colour and pattern in molluscs specifically, but in other taxa more generally, since this study shows that homology of visible colour cannot be assumed without identification of pigments.