Optimizing electron backscatter diffraction of carbonate biominerals-resin type and carbon coating

Microstructure and crystallographic texture data in modern giant clam shells (Tridacna squamosa and Hippopus hippopus)

This article provides novel data on the microstructure and crystallographic texture of modern giant clam shells (Tridacna squamosa and Hippopus hippopus) from the Coral Triangle region of northeast Borneo. Giant clams have two aragonitic shell layers-the inner and outer shell layer. This dataset focuses on the inner shell layer as this is well preserved and not affected by diagenetic alteration. To prepare samples for analysis, shells were cut longitudinally at the axis of maximum growth and mounted onto thin sections. Data collection involved scanning electron microscopy (SEM) to determine microstructure and SEM based electron backscatter diffraction (EBSD) for quantitative measurement of crystallographic orientation and texture. Post-acquisition reanalysis of saved EBSD patterns to optimize data quality included changing the number of reflectors and band detection mode. We provide EBSD data as band contrast images and colour-coded orientation maps (inverse pole figure maps). Crystallographic co-orientation strength obtained with multiple of uniform density (MUD) values are derived from density distributed pole figures of indexed EBSD points. Raw EBSD data files are also given to ensure repeatability of the steps provided in this article and to allow extraction of further crystallographic properties for future researchers. Overall, this dataset provides 1. a better understanding of shell growth and biomineralization in giant clams and 2. important steps for optimizing data collection with EBSD analyses in biogenic carbonates.

Avian obligate brood parasitic lineages evolved variable complex polycrystalline structures to build tougher eggshells

Avian brood parasites and their hosts display varied egg-puncture behaviors, exerting asymmetric co-evolutionary selection pressures on eggshells' breaking strength. We investigated eggshell structural and textural characteristics that may improve its mechanical performance. Parasitic eggshell calcified layers showed complex ultra- and microstructural patterns. However, stronger parasitic eggshells are not due to lower textural severity (characterized by lower preferred crystallographic orientation, larger local grain misorientation and smaller Kearns factor), but rather to grain boundary (GB) microstructure characteristics within the eggshell outermost layer (palisade layer, PL). Accordingly, the thicker the PL and the more complex the GB pathways are, the tougher the parasitic eggshells will be. These characteristics, which we can identify as a "GB Engineering" driven co-evolutionary process, further improve eggshell breaking strength in those parasitic species that suffer relatively high frequencies of egg-puncturing by congeneric or hosts. Overall, plain textural patterns are not suitable predictors for comparing mechanical performance of bioceramic materials.

X-ray nanotomography and electron backscatter diffraction demonstrate the crystalline, heterogeneous and impermeable nature of conodont white matter

Conodont elements, microfossil remains of extinct primitive vertebrates, are commonly exploited as mineral archives of ocean chemistry, yielding fundamental insights into the palaeotemperature and chemical composition of past oceans. Geochemical assays have been traditionally focused on the so-called lamellar and white matter crown tissues; however, the porosity and crystallographic nature of the white matter and its inferred permeability are disputed, raising concerns over its suitability as a geochemical archive. Here, we constrain the characteristics of this tissue and address conflicting interpretations using ptychographic X-ray-computed tomography (PXCT), pore network analysis, synchrotron radiation X-ray tomographic microscopy (srXTM) and electron back-scatter diffraction (EBSD). PXCT and pore network analyses based on these data reveal that while white matter is extremely porous, the pores are unconnected, rendering this tissue closed to postmortem fluid percolation. EBSD analyses demonstrate that white matter is crystalline and comprised of a single crystal typically tens of micrometres in dimensions. Combined with evidence that conodont elements grow episodically, these data suggest that white matter, which comprises the denticles of conodont elements, grows syntactically, indicating that individual crystals are time heterogeneous. Together these data provide support for the interpretation of conodont white matter as a closed geochemical system and, therefore, its utility of the conodont fossil record as a historical archive of Palaeozoic and Early Mesozoic ocean chemistry.

Structure and Composition of the Eggshell of a Passerine Bird, Setophaga ruticilla (Linnaeus, 1758)

The mineral composition of eggshells is assumed to be a conserved phylogenetic feature. Avian eggshells are composed of calcite, whereas those of taxa within Chelonia are aragonitic. Yet, the eggshells of a passerine bird were reported to be made of aragonite. Here, we report a new study of the same bird eggshells using a combination of in situ microscopy and chemical techniques. A microstructural analysis finds a similar arrangement to other avian eggshells, despite their very thin and fragile nature. Fourier transform infrared spectrometry (FTIR) and electron backscatter diffraction (EBSD) results also confirm that the eggshells are entirely composed of calcite. Our findings demonstrate that passerine eggshells are not an exception and similar to other birds and reinforce the phylogenetic placement of this bird species.

The cono-dos and cono-dont's of phosphatic microfossil preparation and microanalysis

Scanning electron microscope (SEM) imaging of fossils allows unlocking ultrastructural information about their skeletal tissues, but sample preparation of biominerals forming their skeletons requires time, patience, and knowledge. SEM and associated analytical methods allow the observation of internal microstructure, shedding light on function, growth and chemistry. Sample preparation is the process by which material is fixed within a medium (e.g. epoxy resin), a transect created and surface defects removed. This step is arguably the most important in any SEM-based analysis, allowing for the acquisition of reliable, high quality data sets. When conducting any SEM-based technique, the presence of a flat surface is needed to collect consistent and reliable data. Surfaces with topography will both induce charging effects but will also compromise the reliability of data acquired. Techniques from material science are continuously adapted to palaeontological applications, in particular with respect to calcareous microfossils. However, similar studies have not been extensively conducted on bioapatite, owing in part to the difficulties faced in sample preparation alongside its susceptibility to electron beam damage. This case study focuses on conodonts, a marine vertebrate group ranging from the late Cambrian to the Late Triassic. They have been chosen as a model due to the abundance of material, complexity of internal tissues and previous work focused on histological features. With these phosphatic microfossils, we attempt to outline the process of sample preparation and provide information on how to avoid and overcome common pitfalls.

Selectively bred oysters can alter their biomineralization pathways, promoting resilience to environmental acidification

Commercial shellfish aquaculture is vulnerable to the impacts of ocean acidification driven by increasing carbon dioxide (CO₂ ) absorption by the ocean as well as to coastal acidification driven by land run off and rising sea level. These drivers of environmental acidification have deleterious effects on biomineralization. We investigated shell biomineralization of selectively bred and wild-type families of the Sydney rock oyster Saccostrea glomerata in a study of oysters being farmed in estuaries at aquaculture leases differing in environmental acidification. The contrasting estuarine pH regimes enabled us to determine the mechanisms of shell growth and the vulnerability of this species to contemporary environmental acidification. Determination of the source of carbon, the mechanism of carbon uptake and use of carbon in biomineral formation are key to understanding the vulnerability of shellfish aquaculture to contemporary and future environmental acidification. We, therefore, characterized the crystallography and carbon uptake in the shells of S. glomerata, resident in habitats subjected to coastal acidification, using high-resolution electron backscatter diffraction and carbon isotope analyses (as δ¹³ C). We show that oyster families selectively bred for fast growth and families selected for disease resistance can alter their mechanisms of calcite crystal biomineralization, promoting resilience to acidification. The responses of S. glomerata to acidification in their estuarine habitat provide key insights into mechanisms of mollusc shell growth under future climate change conditions. Importantly, we show that selective breeding in oysters is likely to be an important global mitigation strategy for sustainable shellfish aquaculture to withstand future climate-driven change to habitat acidification.

Calcium carbonate unit realignment under acidification: A potential compensatory mechanism in an edible estuarine oyster

Ocean acidification (OA) is well-known for impairing marine calcification; however, the end response of several essential species to this perturbation remains unknown. Decreased pH and saturation levels (Ω) of minerals under OA is projected to alter shell crystallography and thus to reduce shell mechanical properties. This study examined this hypothesis using a commercially important estuarine oyster Magallana hongkongensis. Although shell damage occurred on the outmost prismatic layer and the undying myostracum at decreased pH 7.6 and 7.3, the major foliated layer was relatively unharmed. Oysters maintained their shell hardness and stiffness through altered crystal unit orientation under pH 7.6 conditions. However, under the undersaturated conditions (Ω_Cal ~ 0.8) at pH 7.3, the realigned crystal units in foliated layer ultimately resulted in less stiff shells which indicated although estuarine oysters are mechanically resistant to unfavorable calcification conditions, extremely low pH condition is still a threat to this essential species.

Coastal acidification impacts on shell mineral structure of bivalve mollusks

Ocean acidification is occurring globally through increasing CO 2 absorption into the oceans creating particular concern for calcifying species. In addition to ocean acidification, near shore marine habitats are exposed to the deleterious effects of runoff from acid sulfate soils which also decreases environmental pH. This coastal acidification is being exacerbated by climate change-driven sea-level rise and catchment-driven flooding. In response to reduction in habitat pH by ocean and coastal acidification, mollusks are predicted to produce thinner shells of lower structural integrity and reduced mechanical properties threatening mollusk aquaculture. Here, we present the first study to examine oyster biomineralization under acid sulfate soil acidification in a region where growth of commercial bivalve species has declined in recent decades. Examination of the crystallography of the shells of the Sydney rock oyster, Saccostrea glomerata, by electron back scatter diffraction analyses revealed that the signal of environmental acidification is evident in the structure of the biomineral. Saccostrea glomerata, shows phenotypic plasticity, as evident in the disruption of crystallographic control over biomineralization in populations living in coastal acidification sites. Our results indicate that reduced sizes of these oysters for commercial sale may be due to the limited capacity of oysters to biomineralize under acidification conditions. As the impact of this catchment source acidification will continue to be exacerbated by climate change with likely effects on coastal aquaculture in many places across the globe, management strategies will be required to maintain the sustainable culture of these key resources.

The Application of Scanning Electron Microscopy with Energy-Dispersive X-Ray Spectroscopy (SEM-EDX) in Ancient Dental Calculus for the Reconstruction of Human Habits

The great potential of scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) is in detection of unusual chemical elements included in ancient human dental calculus to verify hypotheses about life and burial habits of historic populations and individuals. Elemental spectra were performed from archeological samples of three chosen individuals from different time periods. The unusual presence of magnesium, aluminum, and silicon in the first sample could confirm the hypothesis of high degree of dental abrasion caused by particles from grinding stones in flour. In the second sample, presence of copper could confirm that bronze jewelery could lie near the buried body. The elemental composition of the third sample with the presence of lead and copper confirms the origin of individual to Napoleonic Wars because the damage to his teeth could be explained by the systematic utilization of the teeth for the opening of paper cartridges (a charge with a dose of gunpowder and a bullet), which were used during the 18th and the 19th century AD. All these results contribute to the reconstruction of life (first and third individual) and burial (second individual) habits of historic populations and individuals.

Effects of ocean acidification on the shells of four Mediterranean gastropod species near a CO2 seep

Marine CO₂ seeps allow the study of the long-term effects of elevated pCO₂ (ocean acidification) on marine invertebrate biomineralization. We investigated the effects of ocean acidification on shell composition and structure in four ecologically important species of Mediterranean gastropods (two limpets, a top-shell snail, and a whelk). Individuals were sampled from three sites near a volcanic CO₂ seep off Vulcano Island, Italy. The three sites represented ambient (8.15pH), moderate (8.03pH) and low (7.73pH) seawater mean pH. Shell mineralogy, microstructure, and mechanical strength were examined in all four species. We found that the calcite/aragonite ratio could vary and increased significantly with reduced pH in shells of one of the two limpet species. Moreover, each of the four gastropods displayed reductions in either inner shell toughness or elasticity at the Low pH site. These results suggest that near-future ocean acidification could alter shell biomineralization and structure in these common gastropods.

Analogous biomineralization processes between the fossil coral Calceola sandalina (Rugosa, Devonian) and other Recent and fossil cnidarians

The current work represents a distinctive study about the biomineral properties of exceptionally good preserved skeletons of Calceola sandalina from the Middle Devonian of Couvin (Belgium), Smara (Morocco) and (Algeria) and their relation in the evolution of biomineralization of cnidarians. Structural and crystallographic analyses of the skeletons have been done by petrographic microscopy, electron scanning microscopy (SEM), atomic force microscopy (AFM), electron backscatter diffraction (EBSD), computer-integrated polarization microscopy (CIP) and electron microprobe analysis (EMPA). Calceola skeletons have many similarities with other cnidarians, mainly with other Palaeozoic corals as Syringoporicae: The microcrystals are composed of co-oriented nanocrystals that remind to mesocrystals, suggesting a biocrystallization process by particle attachment (CPA). The relationship between the nanocrystals and microcrystals suggest a growth mode similar to mineral bridges. A similar model was described for Syringoporicae corals (Tabulata) and it is similar to the coordinated-growth mode described in scleractinians and molluscs. Calceola skeletons show also a convergent structure with scleractinian forming Rapid Accretion Deposits (RAD), which share some structural and chemical properties. These evidences suggest analogous processes of biomineralization derived from a stem group of cnidarians. The results of this paper highlight the value of biomineralization studies in fossil organisms to understand the evolution of biomineralization mechanism through Phanerozoic.

Combined Use of Electron and Light Microscopy Techniques Reveals False Secondary Shell Units in Megaloolithidae Eggshells

Abnormalities in the histo- and ultrastructure of the amniote eggshell are often related to diverse factors, such as ambient stress during egg formation, pathologies altering the physiology of the egg-laying females, or evolutionarily selected modifications of the eggshell structure that vary the physical properties of the egg, for example increasing its strength so as to avoid fracture during incubation. When dealing with fossil materials, all the above hypotheses are plausible, but a detailed taphonomical study has to be performed to rule out the possibility that secondary processes of recrystallization have occurred during fossilization. Traditional analyses, such as optical microscopy inspection and cathodoluminescence, have proven not to be enough to understand the taphonomic story of some eggshells. Recently, electron backscatter diffraction has been used, in combination with other techniques, to better understand the alteration of fossil eggshells. Here we present a combined study using scanning electron microscopy, optical microscopy, cathodoluminescence and electron backscatter diffraction of eggshell fragments assigned to Megaloolithus cf. siruguei from the Upper Cretaceous outcrops of the Cameros Basin. We focus our study on the presence of secondary shell units that mimic most aspects of the ultrastructure of the eggshell mammillae, but grow far from the inner surface of the eggshell. We call these structures extra-spherulites, describe their crystal structure and demonstrate their secondary origin. Our study has important implications for the interpretation of secondary shell units as biological or pathological structures. Thus, electron backscatter diffraction complements other microscope techniques as a useful tool for understanding taphonomical alterations in fossil eggshells.

Microstructure, crystallography and diagenetic alteration in fossil ostrich eggshells from Upper Palaeolithic sites of Indian peninsular region

Biominerals studies are of importance as they provide an understanding of natural evolutionary processes. In this study we have investigated the fossil ostrich eggshells using Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD) and Electron Backscatter Diffraction (EBSD). SEM studies demonstrated the ultrastructure of fossil eggshells and formation of calcified cuticular layer. The presence of calcified cuticle layer in eggshell is the basis for ancient DNA studies as it contains preserved biomolecules. EBSD accentuates the crystallographic structure of the ostrich eggshells with sub-micrometer resolution. It is a non-destructive tool for evaluating the extent of diagenesis in a biomineral. EBSD analysis revealed the presence of dolomite in the eggshells. This research resulted in the complete recognition of the structure of ostrich eggshells as well as the nature and extent of diagenesis in these eggshells which is vital for genetic and paleoenvironmental studies.

Biomineral shell formation under ocean acidification: a shift from order to chaos

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO₂ leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO₂) compared to present day conditions (380 μatm pCO₂). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Comparison of the structure, crystallography and composition of eggshells of the guinea fowl and graylag goose

The structure and composition of the eggshells of two commercial species (guinea fowl and greylag goose) have been studied. Thin sections and scanning electron microcopy show the similarity of the overall structure, but the relative thickness of the layers differs in these two taxa. Atomic force microscopy shows that the different layers are composed of rounded, heterogeneous granules, the diameter of which is between 50 and 100 nm, with a thin cortex. Infrared data and thermogravimetric analyses show that both eggshells are made of calcite, but differing on the quality and quantity when the organic component is considered. Chemical maps show that chemical element distribution is not uniform within a sample, and differs between the species, but with low magnesium content. Electron back scattered diffraction confirms the eggshells are calcite, but the microtexture strongly differs between the two species. Based on the chemical-structural differences, a species-specific biological control on the biomineralization is found, despite the rapid formation of an eggshell. Overall results indicate that to estimate the quality of eggshells, such as resistance to breakage, is not a straightforward process because of the high complexity of avian eggshell biomineralization.

Ocean acidification impacts mussel control on biomineralisation

Ocean acidification is altering the oceanic carbonate saturation state and threatening the survival of marine calcifying organisms. Production of their calcium carbonate exoskeletons is dependent not only on the environmental seawater carbonate chemistry but also the ability to produce biominerals through proteins. We present shell growth and structural responses by the economically important marine calcifier Mytilus edulis to ocean acidification scenarios (380, 550, 750, 1000 µatm pCO2). After six months of incubation at 750 µatm pCO2, reduced carbonic anhydrase protein activity and shell growth occurs in M. edulis. Beyond that, at 1000 µatm pCO2, biomineralisation continued but with compensated metabolism of proteins and increased calcite growth. Mussel growth occurs at a cost to the structural integrity of the shell due to structural disorientation of calcite crystals. This loss of structural integrity could impact mussel shell strength and reduce protection from predators and changing environments.

Species-specific shells: Chitin synthases and cell mechanics in molluscs

The size, morphology and species-specific texture of mollusc shell biominerals is one of the unresolved questions in nature. In search of molecular control principles, chitin has been identified by Weiner and Traub (FEBS Lett. 1980, 111:311–316) as one of the organic compounds with a defined co-organization with mineral phases. Chitin fibers can be aligned with certain mineralogical axes of crystalline calcium carbonate in a species-specific manner. These original observations motivated the functional characterization of chitin forming enzymes in molluscs. The full-length cDNA cloning of mollusc chitin synthases identified unique myosin domains as part of the biological control system. The potential impact of molecular motors and other conserved domains of these complex transmembrane enzymes on the evolution of shell biomineralization is investigated and discussed in this article.