Academic literature on the topic 'Biomineral archive'

Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales. Understanding the role of templates in biomineral nucleation, and their importance in skeletal geochemistry requires an integrated, multiscale approach, which can place atom-scale observations of organic-mineral interfaces within a broader structural and geochemical context. Here we map the chemistry of an embedded organic template structure within a carbonate skeleton of the foraminifera Orbulina universa using both atom probe tomography (APT), a 3D chemical imaging technique with Ångström-level spatial resolution, and time-of-flight secondary ionization mass spectrometry (ToF-SIMS), a 2D chemical imaging technique with submicron resolution. We quantitatively link these observations, revealing that the organic template in O. universa is uniquely enriched in both Na and Mg, and contributes to intraskeletal chemical heterogeneity. Our APT analyses reveal the cation composition of the organic surface, offering evidence to suggest that cations other than Ca2+, previously considered passive spectator ions in biomineral templating, may be important in defining the energetics of carbonate nucleation on organic templates.

Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.

An optimized synchrotron-based X-ray diffraction method is described for the direct and efficient measurement of crystallite phase and orientation at micrometre resolution across textured polycrystalline samples of millimetre size (high scale dynamics) within a reasonable time frame. The method is demonstrated by application to biomineral fish otoliths. Otoliths are calcium carbonate accretions formed in the inner ears of vertebrates. Fish otoliths are essential biological archives, providing information for individual age estimation, the study of population dynamics and fish stock management, as well as past environmental and climatic conditions from archaeological specimens. Here, X-ray diffraction mapping is discussed as a means of describing the mineralogical structure and microtexture of otoliths. Texture maps could be generated with a fewa priorihypotheses on the aragonitic system. Full-section imaging allows quantitative intercomparison of crystal orientation coupled to microstructural description, across the zones of the otoliths that represent distinctive mineral organization. It reveals the extents of these regions and their internal textural structure. Characterization of structural and textural correlations across whole images is therefore proposed as a complementary approach to investigate and validate the local in-depth nanometre-scale study of biominerals. The estimation of crystallite size and orientational distribution points to diffracting domains intermediate in size between the otolith nanogranules and the crystalline units, in agreement with recently reported results.

Bivalve shells serve as powerful high-resolution paleoclimate archives. However, the number of reliable temperature proxies is limited. It has remained particularly difficult to extract temperature signals from shell Sr/Ca, although Sr is routinely employed in other biogenic aragonites. In bivalves, Sr/Ca is linked to the prevailing microstructure and is sometimes affected by kinetics. Here, the hypothesis is tested that temperature can be reconstructed from shell Sr/Ca once microstructure and/or growth-rate-related bias has been mathematically eliminated. Therefore, the relationship between Sr/Ca and increment width, as well as biomineral unit size, has been studied in three different shell portions of field-grown Arctica islandica specimens. Subsequently, microstructure and/or growth-rate-related variation was removed from Sr/Ca data and residuals compared to temperature. As demonstrated, the hypothesis could not be verified. Even after detrending, Sr/Ca remained positively correlated to water temperature, which contradicts thermodynamic expectations and findings from inorganic aragonite. Any temperature signal potentially recorded by shell Sr/Ca is overprinted by other environmental forcings. Unless these variables are identified, it will remain impossible to infer temperature from Sr/Ca. Given the coupling with the biomineral unit size, a detailed characterization of the microstructure should remain an integral part of subsequent attempts to reconstruct temperature from Sr/Ca.

Bivalve shells are increasingly used as archives for high-resolution paleoclimate analyses. However, there is still an urgent need for quantitative temperature proxies that work without knowledge of the water chemistry–as is required for δ18O-based paleothermometry–and can better withstand diagenetic overprint. Recently, microstructural properties have been identified as a potential candidate fulfilling these requirements. So far, only few different microstructure categories (nacreous, prismatic and crossed-lamellar) of some short-lived species have been studied in detail, and in all such studies, the size and/or shape of individual biomineral units was found to increase with water temperature. Here, we explore whether the same applies to properties of the crossed-acicular microstructure in the hinge plate of Arctica islandica, the microstructurally most uniform shell portion in this species. In order to focus solely on the effect of temperature on microstructural properties, this study uses bivalves that grew their shells under controlled temperature conditions (1, 3, 6, 9, 12 and 15°C) in the laboratory. With increasing temperature, the size of the largest individual biomineral units and the relative proportion of shell occupied by the crystalline phase increased. The size of the largest pores, a specific microstructural feature of A. islandica, whose potential role in biomineralization is discussed here, increased exponentially with culturing temperature. This study employs scanning electron microscopy in combination with automated image processing software, including an innovative machine learning–based image segmentation method. The new method greatly facilitates the recognition of microstructural entities and enables a faster and more reliable microstructural analysis than previously used techniques. Results of this study establish the new microstructural temperature proxy in the crossed-acicular microstructures of A. islandica and point to an overarching control mechanism of temperature on the micrometer-scale architecture of bivalve shells across species boundaries.

Abstract. Mollusks record valuable information in their hard parts that reflect ambient environmental conditions. For this reason, shells can serve as excellent archives to reconstruct past climate and environmental variability. However, animal physiology and biomineralization, which are often poorly understood, can make the decoding of environmental signals a challenging task. Many of the routinely used shell-based proxies are sensitive to multiple different environmental and physiological variables. Therefore, the identification and interpretation of individual environmental signals (e.g., water temperature) often is particularly difficult. Additional proxies not influenced by multiple environmental variables or animal physiology would be a great asset in the field of paleoclimatology. The aim of this study is to investigate the potential use of structural properties of Arctica islandica shells as an environmental proxy. A total of 11 specimens were analyzed to study if changes of the microstructural organization of this marine bivalve are related to environmental conditions. In order to limit the interference of multiple parameters, the samples were cultured under controlled conditions. Three specimens presented here were grown at two different water temperatures (10 and 15 °C) for multiple weeks and exposed only to ambient food conditions. An additional eight specimens were reared under three different dietary regimes. Shell material was analyzed with two techniques; (1) confocal Raman microscopy (CRM) was used to quantify changes of the orientation of microstructural units and pigment distribution, and (2) scanning electron microscopy (SEM) was used to detect changes in microstructural organization. Our results indicate that A. islandica microstructure is not sensitive to changes in the food source and, likely, shell pigment are not altered by diet. However, seawater temperature had a statistically significant effect on the orientation of the biomineral. Although additional work is required, the results presented here suggest that the crystallographic orientation of biomineral units of A. islandica may serve as an alternative and independent proxy for seawater temperature.

As one of the biominerals, hydroxyapatite (HAP) plays important roles in biology, and inspires researchers to investigate HAP-based materials for the applications in various biomedical fields. Among them, one-dimensional (1-D) micro-/nanostructured HAP materials have attracted great interest in the last decades. This review summarizes the preparation and applications of 1-D HAP materials, and discusses different aspects of 1-D HAP materials. Various synthetic methods have been developed to prepare 1-D HAP materials with different morphologies, sizes, surface properties and crystallinities. In addition, elements-substituted 1-D HAP materials and composites have also been prepared. Surfactants and additives are usually adopted to control the nucleation and growth of 1-D HAP materials, but the related mechanisms are not very clear yet. The applications of 1-D HAP materials have been widely investigated, and the biomedical applications show great prospect but still need further improvements. A new kind of highly flexible fire-resistant inorganic paper made of ultralong HAP nanowires has been developed and is a promising alternative of the traditional cellulose paper for valuable archives and important documents. Regardless of the advances, further studies should be made for preparing 1-D HAP materials with controlled structures, sizes and morphologies and for boosting their various applications.

Abstract. Carbonate biological hard tissues are valuable archives of environmental information. However, this information can be blurred or even completely lost as hard tissues undergo diagenetic alteration. This is more likely to occur in aragonitic skeletons because bioaragonite often transforms into calcite during diagenesis. For reliably using aragonitic skeletons as geochemical proxies, it is necessary to understand in depth the diagenetic alteration processes that they undergo. Several works have recently investigated the hydrothermal alteration of aragonitic hard tissues during short-term experiments at high temperatures (T > 160 ∘C). In this study, we conduct long-term (4 and 6 months) hydrothermal alteration experiments at 80 ∘C using burial-like fluids. We document and evaluate the changes undergone by the outer and inner layers of the shell of the bivalve Arctica islandica, the prismatic and nacreous layers of the hard tissue of the gastropod Haliotis ovina, and the skeleton of the coral Porites sp. combining a variety of analytical tools (X-ray diffraction, thermogravimetry analysis, laser confocal microscopy, scanning electron microscopy, electron backscatter diffraction and atomic force microscopy). We demonstrate that this approach is the most adequate to trace subtle, diagenetic-alteration-related changes in aragonitic biocarbonate structural hard materials. Furthermore, we unveil that the diagenetic alteration of aragonitic biological hard tissues is a complex multi-step process where major changes occur even at the low temperature used in this study, well before any aragonite into calcite transformation takes place. Alteration starts with biopolymer decomposition and concomitant generation of secondary porosity. These processes are followed by abiogenic aragonite precipitation that partially or totally obliterates the secondary porosity. Only subsequently does the transformation of the aragonite into calcite occur. The kinetics of the alteration process is highly dependent on primary microstructural features of the aragonitic biomineral. While the skeleton of Porites sp. remains virtually unaltered for the entire duration of the conducted experiments, Haliotis ovina nacre undergoes extensive abiogenic aragonite precipitation. The outer and inner shell layers of Arctica islandica are significantly affected by aragonite transformation into calcite. This transformation is extensive for the prismatic shell layer of Haliotis ovina. Our results suggest that the majority of aragonitic fossil archives are overprinted, even those free of clear diagenetic alteration signs. This finding may have major implications for the use of these archives as geochemical proxies.

Abstract. In the last few decades and in the near future CO2-induced ocean acidification is potentially a big threat to marine calcite-shelled animals (e.g. brachiopods, bivalves, corals and gastropods). Despite the great number of studies focusing on the effects of acidification on shell growth, metabolism, shell dissolution and shell repair, the consequences for biomineral formation remain poorly understood. Only a few studies have addressed the impact of ocean acidification on shell microstructure and geochemistry. In this study, a detailed microstructure and stable isotope geochemistry investigation was performed on nine adult brachiopod specimens of Magellania venosa (Dixon, 1789). These were grown in the natural environment as well as in controlled culturing experiments under different pH conditions (ranging from 7.35 to 8.15±0.05) over different time intervals (214 to 335 days). Details of shell microstructural features, such as thickness of the primary layer, density and size of endopunctae and morphology of the basic structural unit of the secondary layer were analysed using scanning electron microscopy. Stable isotope compositions (δ13C and δ18O) were tested from the secondary shell layer along shell ontogenetic increments in both dorsal and ventral valves. Based on our comprehensive dataset, we observed that, under low-pH conditions, M. venosa produced a more organic-rich shell with higher density of and larger endopunctae, and smaller secondary layer fibres. Also, increasingly negative δ13C and δ18O values are recorded by the shell produced during culturing and are related to the CO2 source in the culture set-up. Both the microstructural changes and the stable isotope results are similar to observations on brachiopods from the fossil record and strongly support the value of brachiopods as robust archives of proxies for studying ocean acidification events in the geologic past.

Biominerals are important archives of the presence of life and environmental processes in the geological record. However, ascribing a clear biogenic nature to minerals with nanometer-sized dimensions has proven challenging. Identifying hallmark features of biologically controlled mineralization is particularly important for the case of magnetite crystals, resembling those produced by magnetotactic bacteria (MTB), which have been used as evidence of early prokaryotic life on Earth and in meteorites. We show here that magnetite produced by MTB displays a clear coupled C–N signal that is absent in abiogenic and/or biomimetic (protein-mediated) nanometer-sized magnetite. We attribute the presence of this signal to intracrystalline organic components associated with proteins involved in magnetosome formation by MTB. These results demonstrate that we can assign a biogenic origin to nanometer-sized magnetite crystals, and potentially other biominerals of similar dimensions, using unique geochemical signatures directly measured at the nanoscale. This finding is significant for searching for the earliest presence of life in the Earth’s geological record and prokaryotic life on other planets.

Due to their high biodiversity and widespread distribution in the Phanerozoic oceans, brachiopods are very important tools for research in palaeontology and related fields in Earth Sciences to investigate the past and present global change. Their biominerals have been considered the best carbonate archives of proxies for extending climate and environmental records on a broad geographical scale over long periods of time. Their fidelity as archives is supported by the following: 1) they record the physical and chemical composition of the seawater in which they live without, or with very limited, vital effects; 2) they precipitate a low-Mg calcite shell, which withstands post-depositional alteration; and 3) they are low metabolic and physiologically unbuffered animals sensitive to change in the physicochemical composition of the ambient seawater. However, there is still insufficient knowledge of the microstructures of these biomineral archives and their biomineralization processes during the evolutionary history of the phylum. The aims of the present thesis, focused on solving these issues, are to: 1) examine the micro- and morpho- structural diversity of modern and fossil brachiopods, 2) assess the microstructure variation in different environmental conditions; and 3) reconstruct the evolutionary changes and fabric differentiation of the main brachiopod classes through geological time. A multidisciplinary approach was used for the microstructural analyses: 1) a comprehensive dataset was established based on detailed microstructural observations of modern and fossil brachiopods analysed by Scanning Electron Microscopy (SEM); 2) new measurement methods were developed based on SEM observations to quantitatively describe the morphology and size of the structural units (fibres) of the shell secondary layer, the thickness of the primary layer, and the density and size of endopunctae of modern brachiopod shells; 3) new measurement methods were developed to describe the structural units (laminae and fibres) of fossil brachiopod shells; 4) statistical analyses of the acquired data were performed, i.e. independent-sample t-tests, frequency distribution plots, principal component analysis, and symmetric and asymmetric variants analyses; 5) stable isotope compositions (δ13C and δ18O) were tested from the secondary shell layer along shell ontogenetic increments in both dorsal and ventral valves of modern brachiopod shells; and 6) Transmission Electron Microscope (TEM) and Electron Backscatter Diffraction (EBSD) were performed in collaboration with other researchers to investigate the micro- and nanoscale features of modern brachiopod shells. Through these approaches, details of microstructural patterns were described and compared of twenty-nine specimens of six recent brachiopod species [Notosaria nigricans (Sowerby, 1846), Liothyrella neozelanica (Thomson, 1918), Liothyrella uva (Broderip, 1833), Magasella sanguinea (Leach, 1814), Gryphus vitreus (Born, 1778), Calloria inconspicua (Sowerby, 1846)] from different environmental conditions. Based on the morphology and size of the shell secondary layer fibres, the following conclusions were reached: 1) There was no significant difference in the shape and size of the fibres between ventral and dorsal valves of the same specimen; 2) An ontogenetic trend in the morphology of the fibres was found, as they become larger, wider, and flatter with increasing age. This change in size and shape indicated that the animal produced a fibrous layer with a different organic content during the ontogeny. 3) The relationship between size and shape of fibres and environmental conditions was clear when comparing two species of the same genus (L. neozelanica, L. uva) living in seawater with different carbonate saturation state and temperature, i.e. the fibres of L. uva are narrower and rounder than those of L. neozelanica. This in turn indicated a higher shell organic content in L. uva. Additional investigations were performed on the species Magellania venosa (Dixon, 1789), grown in the natural environment and in controlled culturing experiments in different pH conditions (7.35 to 8.15 ±0.05), and led to following conclusions: 1) Under low pH conditions, M. venosa produced a more organic-rich shell with larger and higher density endopunctae, and smaller secondary layer fibres, when subjected to about one year of culturing. 2) Increasingly negative δ13C and δ18O values were recorded by the shell produced during culturing and are related to the CO2–source in the culture setup. 3) Both the microstructural changes and the stable isotope results supported the value of brachiopods as robust archives of proxies for studying ocean acidification events in the geologic past. Finally, the measurements made on the size of structural units (laminae/fibres) of Cambrian to Devonian fossil brachiopod shells coupled with very detailed qualitative micro-scale observations, allowed the following conclusion: 1) The fossil organocarbonate brachiopod shells produced two main secondary layer fabrics: a laminar fabric in the Strophomenata, and a fibrous fabric in the Rhynchonellata. The Strophomenata laminar fabric shells appeared to be more variable and complex in their structural organization, but the thickness of the laminae was rather uniform and much thinner than that of the fibres. The Rhynchonellata fibrous fabric was more simple and uniform in its organization, but the size of the fibres was much more variable and comparable to the fabric of modern brachiopods. 2) Brachiopods with a fibrous secondary layer were mostly associated with biconvex shells, whereas brachiopods with a laminar secondary layer are associated with a variety of shell shapes. 3) Detailed microstructural studies were shown to be a very useful tool to construct the phylogenetic tree of the Phylum Brachiopoda. For example, the recorded gradual change in thickness of laminae from Billingselloidea to Productida could be important evidence to support the hypothesis that taxa with laminar microstructure diverged from the Billingsellida. Microstructural observation on the Chonetidina suggested that their shells had already evolved a laminar fabric during the Devonian. In summary, this new multidisciplinary and quantitative approach to describe the microstructure of brachiopod shells is a powerful tool to interpret microstructural variations of brachiopod shells in different ontogenetic stages and environmental conditions. Moreover, using the microstructure of brachiopod shells as a biomineral archive is a very promising tool for studying climate and environmental change and reconstructing the state of the oceans over the long history of geological time, and may be used to constrain the evolutionary history of the Phylum Brachiopoda.