Heitt Mjölnir: a heated miniature triaxial apparatus for 4D synchrotron microtomography.

Third- and fourth-generation synchrotron light sources with high fluxes and beam energies enable the use of innovative X-ray translucent experimental apparatus. These experimental devices access geologically relevant conditions whilst enabling in situ characterization using the spatial and temporal resolutions accessible at imaging beamlines. Here, Heitt Mjölnir is introduced, a heated miniature triaxial rig based on the design of Mjölnir, but covering a wider temperature range and larger sample volume at similar pressure capacities. This device is designed to investigate coupled thermal, chemical, hydraulic and mechanical processes from grain to centimetre scales using cylindrical samples of 10 mm × 20 mm (diameter × length). Heitt Mjölnir can simultaneously reach confining (hydraulic) pressures of 30 MPa and 500 MPa of axial stress with independently controlled sample pore fluid pressure < 30 MPa. This internally heated apparatus operates to temperatures up to 573 K with a minimal vertical thermal gradient in the sample of <0.3 K mm-1. This new apparatus has been deployed in operando studies at the TOMCAT (Swiss Light Source), I12 JEEP (Diamond Light Source) and PSICHÉ (Synchrotron SOLEIL) beamlines for 4D X-ray microtomography with scan intervals of a few minutes. Heitt Mjölnir is portable and modular, allowing a wide range of 4D characterizations of low-grade metamorphism and deformational processes. It enables spatially and temporally resolved fluid-rock interaction studies at conditions of crustal reservoirs and is suitable for characterization of material properties in geothermal, carbonation or subsurface gas storage applications. Technical drawings and an operation guide are included in this publication.

Seismic events miss important kinematically governed grain scale mechanisms during shear failure of porous rock.

Catastrophic failure in brittle, porous materials initiates when smaller-scale fractures localise along an emergent fault zone in a transition from stable crack growth to dynamic rupture. Due to the rapid nature of this critical transition, the precise micro-mechanisms involved are poorly understood and difficult to image directly. Here, we observe these micro-mechanisms directly by controlling the microcracking rate to slow down the transition in a unique rock deformation experiment that combines acoustic monitoring (sound) with contemporaneous in-situ x-ray imaging (vision) of the microstructure. We find seismic amplitude is not always correlated with local imaged strain; large local strain often occurs with small acoustic emissions, and vice versa. Local strain is predominantly aseismic, explained in part by grain/crack rotation along an emergent shear zone, and the shear fracture energy calculated from local dilation and shear strain on the fault is half of that inferred from the bulk deformation.

Geological Hydrogen Storage: Geochemical Reactivity of Hydrogen with Sandstone Reservoirs.

The geological storage of hydrogen is necessary to enable the successful transition to a hydrogen economy and achieve net-zero emissions targets. Comprehensive investigations must be undertaken for each storage site to ensure their long-term suitability and functionality. As such, the systematic infrastructure and potential risks of large-scale hydrogen storage must be established. Herein, we conducted over 250 batch reaction experiments with different types of reservoir sandstones under conditions representative of the subsurface, reflecting expected time scales for geological hydrogen storage, to investigate potential reactions involving hydrogen. Each hydrogen experiment was paired with a hydrogen-free control under otherwise identical conditions to ensure that any observed reactions were due to the presence of hydrogen. The results conclusively reveal that there is no risk of hydrogen loss or reservoir integrity degradation due to abiotic geochemical reactions in sandstone reservoirs.

'Ear stones' in crocodylians: a cross-species comparative and ontogenetic survey of otolith structures.

The vestibular system of the inner ear is a crucial sensory organ, involved in the sensation of balance and equilibrium. It consists of three semicircular canals that sense angular rotations of the head and the vestibule that detects linear acceleration and gravity. The vestibule often contains structures, known as the otoliths or 'ear stones'. Otoliths are present in many vertebrates and are particularly well known from the fossil record of fish, but surprisingly have not been described in detail in most tetrapods, living or extinct. Here, we present for the first time a survey of the otoliths of a broad sample of extant crocodylian species, based on computed tomography scans. We find that otoliths are present in numerous crocodylian species of different growth stages, and they continue to increase in size during ontogeny, with positive allometry compared to skull length. Our results confirm that otoliths are a common component of the crocodylian vestibular system, and suggest they play an important role in sensory detection. Otoliths are likely common, but overlooked, constituents of the inner ear in tetrapods, and a broader study of their size, shape and distribution promises insight into sensory abilities.

A skeleton from the Middle Jurassic of Scotland illuminates an earlier origin of large pterosaurs.

Pterosaurs were the first vertebrates to evolve flight1,2 and include the largest flying animals in Earth history.3,4 While some of the last-surviving species were the size of airplanes, pterosaurs were long thought to be restricted to small body sizes (wingspans ca. <1.8-1.6 m) from their Triassic origins through the Jurassic, before increasing in size when derived long-skulled and short-tailed pterodactyloids lived alongside a diversity of birds in the Cretaceous.5 We report a new spectacularly preserved three-dimensional skeleton from the Middle Jurassic of Scotland, which we assign to a new genus and species: Dearc sgiathanach gen. et sp. nov. Its wingspan is estimated at >2.5 m, and bone histology shows it was a juvenile-subadult still actively growing when it died, making it the largest known Jurassic pterosaur represented by a well-preserved skeleton. A review of fragmentary specimens from the Middle Jurassic of England demonstrates that a diversity of pterosaurs was capable of reaching larger sizes at this time but have hitherto been concealed by a poor fossil record. Phylogenetic analysis places D. sgiathanach in a clade of basal long-tailed non-monofenestratan pterosaurs, in a subclade of larger-bodied species (Angustinaripterini) with elongate skulls convergent in some aspects with pterodactyloids.6 Far from a static prologue to the Cretaceous, the Middle Jurassic was a key interval in pterosaur evolution, in which some non-pterodactyloids diversified and experimented with larger sizes, concurrent with or perhaps earlier than the origin of birds. VIDEO ABSTRACT.

Ontogenetic variation in the crocodylian vestibular system.

Crocodylians today live in tropical to subtropical environments, occupying mostly shallow waters. Their body size changes drastically during ontogeny, as do their skull dimensions and bite forces, which are associated with changes in prey preferences. Endocranial neurosensory structures have also shown to change ontogenetically, but less is known about the vestibular system of the inner ear. Here we use 30 high-resolution computed tomography (CT) scans and three-dimensional geometric morphometrics to investigate the size and shape changes of crocodylian endosseous labyrinths throughout ontogeny, across four stages (hatchling, juvenile, subadult and adult). We find two major patterns of ontogenetic change. First, the labyrinth increases in size during ontogeny, with negative allometry in relation to skull size. Second, labyrinth shape changes significantly, with hatchlings having shorter semicircular canal radii, with thicker diameters and an overall dorsoventrally shorter labyrinth than those of more mature individuals. We argue that the modification of the labyrinth during crocodylian ontogeny is related to constraints imposed by skull growth, due to fundamental changes in the crocodylian braincase during ontogeny (e.g. verticalisation of the basicranium), rather than changes in locomotion, diet, or other biological functions or behaviours.

Triple iron isotope constraints on the role of ocean iron sinks in early atmospheric oxygenation.

The role that iron played in the oxygenation of Earth's surface is equivocal. Iron could have consumed molecular oxygen when Fe3+-oxyhydroxides formed in the oceans, or it could have promoted atmospheric oxidation by means of pyrite burial. Through high-precision iron isotopic measurements of Archean-Paleoproterozoic sediments and laboratory grown pyrites, we show that the triple iron isotopic composition of Neoarchean-Paleoproterozoic pyrites requires both extensive marine iron oxidation and sulfide-limited pyritization. Using an isotopic fractionation model informed by these data, we constrain the relative sizes of sedimentary Fe3+-oxyhydroxide and pyrite sinks for Neoarchean marine iron. We show that pyrite burial could have resulted in molecular oxygen export exceeding local Fe2+ oxidation sinks, thereby contributing to early episodes of transient oxygenation of Archean surface environments.

Neurosensory and Sinus Evolution as Tyrannosauroid Dinosaurs Developed Giant Size: Insight from the Endocranial Anatomy of Bistahieversor sealeyi.

Tyrannosaurus rex and other tyrannosaurid dinosaurs were apex predators during the latest Cretaceous, which combined giant size and advanced neurosensory systems. Computed tomography (CT) data have shown that tyrannosaurids had a trademark system of a large brain, large olfactory bulbs, elongate cochlear ducts, and expansive endocranial sinuses surrounding the brain and sense organs. Older, smaller tyrannosauroid relatives of tyrannosaurids developed some, but not all, of these features, raising the hypothesis that tyrannosaurid-style brains evolved before the enlarged tyrannosaurid-style sinuses, which might have developed only with large body size. This has been difficult to test, however, because little is known about the brains and sinuses of the first large-bodied tyrannosauroids, which evolved prior to Tyrannosauridae. We here present the first CT data for one of these species, Bistahieversor sealeyi from New Mexico. Bistahieversor had a nearly identical brain and sinus system as tyrannosaurids like Tyrannosaurus, including a large brain, large olfactory bulbs, reduced cerebral hemispheres, and optic lobes, a small tab-like flocculus, long and straight cochlear ducts, and voluminous sinuses that include a supraocciptal recess, subcondyar sinus, and an anterior tympanic recess that exits the braincase via a prootic fossa. When characters are plotted onto tyrannosauroid phylogeny, there is a two-stage sequence in which features of the tyrannosaurid-style brain evolved first (in smaller, nontyrannosaurid species like Timurlengia), followed by features of the tyrannosaurid-style sinuses (in the first large-bodied nontyrannosaurid tyrannosauroids like Bistahieversor). This suggests that the signature tyrannosaurid sinus system evolved in concert with large size, whereas the brain did not. Anat Rec, 303:1043-1059, 2020. © 2020 American Association for Anatomy.

Virtual endocranial and inner ear endocasts of the Paleocene 'condylarth' Chriacus: new insight into the neurosensory system and evolution of early placental mammals.

The end-Cretaceous mass extinction allowed placental mammals to diversify ecologically and taxonomically as they filled ecological niches once occupied by non-avian dinosaurs and more basal mammals. Little is known, however, about how the neurosensory systems of mammals changed after the extinction, and what role these systems played in mammalian diversification. We here use high-resolution computed tomography (CT) scanning to describe the endocranial and inner ear endocasts of two species, Chriacus pelvidens and Chriacus baldwini, which belong to a cluster of 'archaic' placental mammals called 'arctocyonid condylarths' that thrived during the ca. 10 million years after the extinction (the Paleocene Epoch), but whose relationships to extant placentals are poorly understood. The endocasts provide new insight into the paleobiology of the long-mysterious 'arctocyonids', and suggest that Chriacus was an animal with an encephalization quotient (EQ) range of 0.12-0.41, which probably relied more on its sense of smell than vision, because the olfactory bulbs are proportionally large but the neocortex and petrosal lobules are less developed. Agility scores, estimated from the dimensions of the semicircular canals of the inner ear, indicate that Chriacus was slow to moderately agile, and its hearing capabilities, estimated from cochlear dimensions, suggest similarities with the extant aardvark. Chriacus shares many brain features with other Paleocene mammals, such as a small lissencephalic brain, large olfactory bulbs and small petrosal lobules, which are likely plesiomorphic for Placentalia. The inner ear of Chriacus also shares derived characteristics of the elliptical and spherical recesses with extinct species that belong to Euungulata, the extant placental group that includes artiodactyls and perissodactyls. This lends key evidence to the hypothesized close relationship between Chriacus and the extant ungulate groups, and demonstrates that neurosensory features can provide important insight into both the paleobiology and relationships of early placental mammals.

An X-ray computed micro-tomography dataset for oil removal from carbonate porous media.

This study reveals the pore-scale details of oil mobilisation and recovery from a carbonate rock upon injection of aqueous nanoparticle (NP) suspensions. X-ray computed micro-tomography (µCT), which is a non-destructive imaging technique, was used to acquire a dataset which includes: (i) 3D images of the sample collected at the end of fluid injection steps, and (ii) 2D radiogram series collected during fluid injections. The latter allows monitoring fluid flow dynamics at time resolutions down to a few seconds using a laboratory-based µCT scanner. By making this dataset publicly available we enable (i) new image reconstruction algorithms to be tested on large images, (ii) further development of image segmentation algorithms based on machine learning, and (iii) new models for multi-phase fluid displacements in porous media to be evaluated using images of a dynamic process in a naturally occurring and complex material. This dataset is comprehensive in that it offers a series of images that were captured before/during/and after the immiscible fluid injections.

The Dynamics of Nanoparticle-enhanced Fluid Displacement in Porous Media - A Pore-scale Study.

This work provides new insights into the dynamics of silica nanoparticle-based removal of organic fluids (here oil) from naturally occurring porous media. We have used 4D (time-resolved 3D) imaging at pore-scale using X-ray computed micro-tomography (µCT) technique. The captured 3D tomographic time-series data reveal the dynamics of immiscible oil displacement from a carbonate rock upon injection of nanoparticle (NP) suspensions (0.06 and 0.12 wt% SiO2 in deionised water). Our analysis shows significant pore-scale remobilisation of initially trapped oil upon injection of the NP suspensions, specifically, at higher concentration. Our data shows that oil clusters become significantly smaller with larger fluid/fluid interface as a result of the higher concentration NP injection. This paper demonstrates that use of 2D radiograms collected during fluid injections allows monitoring flow dynamics at time resolutions down to a few seconds using conventional laboratory-based µCT scanners. Here, as an underlying mechanism for oil remobilisation, we present the first 4D evidence of in-situ formation of an oil in water emulsion induced by nanoparticles.

New tyrannosaur from the mid-Cretaceous of Uzbekistan clarifies evolution of giant body sizes and advanced senses in tyrant dinosaurs.

Tyrannosaurids--the familiar group of carnivorous dinosaurs including Tyrannosaurus and Albertosaurus--were the apex predators in continental ecosystems in Asia and North America during the latest Cretaceous (ca. 80-66 million years ago). Their colossal sizes and keen senses are considered key to their evolutionary and ecological success, but little is known about how these features developed as tyrannosaurids evolved from smaller basal tyrannosauroids that first appeared in the fossil record in the Middle Jurassic (ca. 170 million years ago). This is largely because of a frustrating 20+ million-year gap in the mid-Cretaceous fossil record, when tyrannosauroids transitioned from small-bodied hunters to gigantic apex predators but from which no diagnostic specimens are known. We describe the first distinct tyrannosauroid species from this gap, based on a highly derived braincase and a variety of other skeletal elements from the Turonian (ca. 90-92 million years ago) of Uzbekistan. This taxon is phylogenetically intermediate between the oldest basal tyrannosauroids and the latest Cretaceous forms. It had yet to develop the giant size and extensive cranial pneumaticity of T. rex and kin but does possess the highly derived brain and inner ear characteristic of the latest Cretaceous species. Tyrannosauroids apparently developed huge size rapidly during the latest Cretaceous, and their success in the top predator role may have been enabled by their brain and keen senses that first evolved at smaller body size.

Droplet fragmentation: 3D imaging of a previously unidentified pore-scale process during multiphase flow in porous media.

Using X-ray computed microtomography, we have visualized and quantified the in situ structure of a trapped nonwetting phase (oil) in a highly heterogeneous carbonate rock after injecting a wetting phase (brine) at low and high capillary numbers. We imaged the process of capillary desaturation in 3D and demonstrated its impacts on the trapped nonwetting phase cluster size distribution. We have identified a previously unidentified pore-scale event during capillary desaturation. This pore-scale event, described as droplet fragmentation of the nonwetting phase, occurs in larger pores. It increases volumetric production of the nonwetting phase after capillary trapping and enlarges the fluid-fluid interface, which can enhance mass transfer between the phases. Droplet fragmentation therefore has implications for a range of multiphase flow processes in natural and engineered porous media with complex heterogeneous pore spaces.

Use of bioreporters and deletion mutants reveals ionic silver and ROS to be equally important in silver nanotoxicity.

The mechanism of antibacterial action of silver nanoparticles (AgNp) was investigated by employing a combination of microbiology and geochemical approaches to contribute to the realistic assessment of nanotoxicity. Our studies showed that suspending AgNp in media with different levels of chloride relevant to environmental conditions produced low levels of ionic silver thereby suggesting that dissolution of silver ions from nanoparticulate surface could not be the sole mechanism of toxicity. An Escherichia coli based bioreporter strain responsive to silver ions together with mutant strains of E. coli lacking specific protective systems were tested against AgNp. Deletion mutants lacking silver ion efflux systems and resistance mechanisms against oxidative stress showed an increased sensitivity to AgNp. However, the bioreporter did not respond to silver nanoparticles. Our results suggest that oxidative stress is a major toxicity mechanism and that this is at least partially associated with ionic silver, but that bulk dissolution of silver into the medium is not sufficient to account for the observed effects. Chloride ions do not appear to offer significant protection, indicating that chloride in receiving waters will not necessarily protect environmental bacteria from the toxic effects of nanoparticles in effluents.

A low-cost X-ray-transparent experimental cell for synchrotron-based X-ray microtomography studies under geological reservoir conditions.

A new modular X-ray-transparent experimental cell enables tomographic investigations of fluid rock interaction under natural reservoir conditions (confining pressure up to 20 MPa, pore fluid pressure up to 15 MPa, temperature ranging from 296 to 473 K). The portable cell can be used at synchrotron radiation sources that deliver a minimum X-ray flux density of 10(9) photons mm(-2) s(-1) in the energy range 30-100 keV to acquire tomographic datasets in less than 60 s. It has been successfully used in three experiments at the bending-magnet beamline 2BM at the Advanced Photon Source. The cell can be easily machined and assembled from off-the-shelf components at relatively low costs, and its modular design allows it to be adapted to a wide range of experiments and lower-energy X-ray sources.

Carbonate precipitation under pressure for bioengineering in the anaerobic subsurface via denitrification.

A number of bioengineering techniques are being developed using microbially catalyzed hydrolysis of urea to precipitate calcium carbonate for soil and sand strengthening in the subsurface. In this study, we evaluate denitrification as an alternative microbial metabolism to induce carbonate precipitation for bioengineering under anaerobic conditions and at high pressure. In anaerobic batch culture, the halophile Halomonas halodenitrificans is shown to be able to precipitate calcium carbonate at high salinity and at a pressure of 8 MPa, with results comparable to those observed when grown at ambient pressure. A larger scale proof-of-concept experiment shows that, as well as sand, coarse gravel can also be cemented with calcium carbonate using this technique. Possible practical applications in the subsurface are discussed, including sealing of improperly abandoned wells and remediation of hydraulic fracturing during shale gas extraction.

Inhibition of Sporosarcina pasteurii under anoxic conditions: implications for subsurface carbonate precipitation and remediation via ureolysis.

The use of Sporosarcina pasteurii to precipitate calcium carbonate in the anoxic subsurface via ureolysis has been proposed for reducing porosity and sealing fractures in rocks. Here we show that S. pasteurii is unable to grow anaerobically and that the ureolytic activity previously shown under anoxic conditions is a consequence of the urease enzyme already present in the cells of the aerobically grown inoculum. The implications are discussed, suggesting that de novo synthesis of urease under anoxic conditions is not possible and that ureolysis may decline over time without repeated injection of S. pasteurii as the urease enzyme degrades and/or becomes inhibited. Augmentation with a different ureolytic species that is able to grow anaerobically or stimulation of natural communities may be preferable for carbonate precipitation over the long term.

Abiotic pyrite formation produces a large Fe isotope fractionation.

The iron isotope composition of sedimentary pyrite has been proposed as a potential proxy to trace microbial metabolism and the redox evolution of the oceans. We demonstrate that Fe isotope fractionation accompanies abiotic pyrite formation in the absence of Fe(II) redox change. Combined fractionation factors between Fe(II)(aq), mackinawite, and pyrite permit the generation of pyrite with Fe isotope signatures that nearly encapsulate the full range of sedimentary δ(56)Fe(pyrite) recorded in Archean to modern sediments. We propose that Archean negative Fe isotope excursions reflect partial Fe(II)(aq) utilization during abiotic pyrite formation rather than microbial dissimilatory Fe(III) reduction. Late Proterozoic to modern sediments may reflect greater Fe(II)(aq) utilization and variations in source composition.