Combining µXANES and µXRD mapping to analyse the heterogeneity in calcium carbonate granules excreted by the earthworm Lumbricus terrestris

Earthworm granules: A model of non-classical biogenic calcium carbonate phase transformations

Different non-classical crystallization mechanisms have been invoked to explain structural and compositional properties of biocrystals. The identification of precursor amorphous nanoparticle aggregation as an onset process in the formation of numerous biominerals (crystallization via particle attachment) constituted a most important breakthrough for understanding biologically mediated mineralization. A comprehensive understanding about how the attached amorphous particles transform into more stable, crystalline grains has yet to be elucidated. Here, we document structural, biogeochemical, and crystallographic aspects of the formation as well as the further phase transformations of the amorphous calcium carbonate particles formed by cultured specimens of earthworm Lumbricus terrestris. In-situ observations evidence the formation of proto-vaterite after dehydration of earthworm-produced ACC, which is subsequently followed by proto-vaterite transformation into calcite through nanoparticle attachment within the organic framework. In culture medium spiked with trace amounts of Mn²⁺, the cauliflower-like proto-vaterite structures become longer-lived than in the absence of Mn²⁺. We propose that the formation of calcite crystals takes place through a non-classical recrystallization path that involves migration of proto-vaterite nanoparticles to the crystallization site, and then, their transformation into calcite via a dissolution-recrystallization reaction. The latter is complemented by ion-by-ion crystal growth and associated with impurity release. These observations are integrated into a new model of the biocrystallization of earthworm-produced carbonate granules which highlights the sensibility of this process to environmental chemical changes, its potential impact on the bioavailability of contaminants as well as the threat that chemical pollution poses to the normal development of its early stages. STATEMENT OF SIGNIFICANCE: Understanding the mechanisms of nucleation, stabilization and aggregation of amorphous calcium carbonate (ACC) and factors controlling its further transformation into crystalline phases is fundamental for elucidation of biogenic mineralization. Some species of earthworms are natural workbench to understand the biogenic ACC, stabilization and the transformation mechanisms, because they create millimeter-sized calcareous granules from amorphous calcium carbonate, which crystallize to a more stable mineral phase (mostly calcite). This study undergoes into the mechanisms of ACC stabilization by the incorporation of trace elements, as manganese, and the ulterior precipitation of calcareous granules by a coupled process of amorphous particle attachment and ion-by-ion growth. The study points to sensibility of this process to environmental chemical changes.

Characterisation of carapace composition in developing and adult ostracods (Skogsbergia lerneri) and its potential for biomaterials

The protective carapace of Skogsbergia lerneri, a marine ostracod, is scratch-resistant and transparent. The compositional and structural organisation of the carapace that underlies these properties is unknown. In this study, we aimed to quantify and determine the distribution of chemical elements and chitin within the carapace of adult ostracods, as well as at different stages of ostracod development, to gain insight into its composition. Elemental analyses included X-ray absorption near-edge structure, X-ray fluorescence and X-ray diffraction. Nonlinear microscopy and spectral imaging were performed to determine chitin distribution within the carapace. High levels of calcium (20.3%) and substantial levels of magnesium (1.89%) were identified throughout development. Amorphous calcium carbonate (ACC) was detected in carapaces of all developmental stages, with the polymorph, aragonite, identified in A-1 and adult carapaces. Novel chitin-derived second harmonic generation signals (430/5 nm) were detected. Quantification of relative chitin content within the developing and adult carapaces identified negligible differences in chitin content between developmental stages and adult carapaces, except for the lower chitin contribution in A-2 (66.8 ± 7.6%) compared to A-5 (85.5 ± 10%) (p = 0.03). Skogsbergia lerneri carapace calcium carbonate composition was distinct to other myodocopid ostracods. These calcium polymorphs and ACC are described in other biological transparent materials, and with the consistent chitin distribution throughout S. lerneri development, may imply a biological adaptation to preserve carapace physical properties. Realisation of S. lerneri carapace synthesis and structural organisation will enable exploitation to manufacture biomaterials and biomimetics with huge potential in industrial and military applications.

Calcite Nanocrystals Investigated Using X-ray Absorption Spectroscopy

For the present work, calcite nanocrystals were grown by annealing precursors at 500 °C. These precursors were obtained by three different thermal schemes. Among these schemes, two involve heating at 100 °C for 16 h and 16 + 24 h, respectively. In the third scheme, heating was performed at 100 °C for 16 h, followed by annealing at 300 °C for 24 h. X-ray diffraction studies, followed by Fourier transform infrared and Raman spectroscopic studies, exhibited the formation of calcite phase of calcium carbonate. Transmission electron microscopy showed that particle sizes of synthesized calcite nanocrystals were in the range of 25–40 nm. Onsets of shape change were also observed with different thermal schemes, using these measurements. X-ray absorption spectroscopy envisaged that the coordination numbers of Ca-O and Ca-Ca shell were not influenced by the thermal schemes; however, bond lengths of these shells were modified. This study in the near edge region evidenced the manifestation of a local electronic structure of calcite when kept in an open environment, depending upon different thermal schemes.

Mechanistic Insights of Dissolution and Mechanical Breakdown of FeCO3 Corrosion Films

Carbon steel is a universally used material in various transportation and construction industries. Research related to CO₂ corrosion environments agrees on the occurrence of siderite (FeCO₃) as a main product conforming corrosion films, suggested to impart protection to carbon steel. Identifying and understanding the presence of all corrosion products under certain conditions is of greatest importance to elucidate the behavior of corrosion films under operation conditions (e.g., flow, pH, temperature), but information regarding the nature and formation of other Fe corrosion products apart from FeCO₃ is lacking. Corrosion products in CO₂ environments typically consist of common Fe minerals that in nature have been demonstrated to undergo transformations, forming other Fe phases. This fact of nature has not been yet explored in the corrosion science field, which can help us to describe mechanisms associated with industrial processes. In this work, we present a multiscale and multidisciplinary approach to understand the mechanisms occurring on corrosion films under the key factors of flow and pH through the combination of molecular techniques with imaging. We report that certainly siderite (FeCO₃, cylindrical with trigonal-pyramidal caps) is the main product identified under the conditions used (representative of brine transport at 80 °C), but wustite (FeO) and magnetite (Fe₃O₄) minerals also form, likely from the de-carbonation of FeCO₃ → FeO → Fe₃O₄, depending on pH under the action of flow. These minerals exist across the corrosion films evidencing a more complex nature of the three-dimensional layer not currently accounted for in the mechanistic models. A relatively low flow velocity (1 m/s), as recognized for industrial operations, is enough to produce chemo-mechanical damage to the FeCO₃ crystals, causing breakage at low pH where dissolution of FeCO₃ occurs with a rapid crystal size reduction of the cylindrical FeCO₃ geometry of ∼80% in just 8 h, changing also the local chemical structure of Fe₃C under the film. Similarly, a flow velocity of 1 m/s is capable of inducing crystal removal at neutral pH, promoting further degradation of the steel, compromising the protectiveness assumption of FeCO₃ corrosion films. The chemo-mechanical damage and Fe phase transformations will affect the critical localized corrosion, and therefore, they need to be accounted for in mechanistic models aiming to find new avenues for control and mitigation of carbon steel corrosion.

Iron Calcium Carbonate Instability: Structural Modification of Siderite Corrosion Films

Corrosion research related to CO₂-containing environments has focused over the past few decades on siderite formation (FeCO₃) as a main corrosion product on carbon steel, yet the influence of Ca and other ions on its chemical and structural characteristics is not fully understood. Metal-localized corrosion is the biggest industrial challenge because of the unknown and unpredictable character of this phenomenon that frequently leads to failure. We report here the role of Ca and formation of iron-calcium carbonate (Fe_xCa_yCO₃) through a spiral growth model as in the calcite system and quantify the replacement of Fe²⁺ by Ca²⁺ ions in the structure of FeCO₃ to form Fe_xCa_yCO₃. The incorporation of Ca²⁺ inhibits the completion of spiral segments on the growth of the rhombohedral crystals of FeCO₃, promoting an enlargement of its structure along the c-axis. This leads to distortions in the chemical structure and morphology affecting the chemical and mechanical properties. Under flow conditions over time in an undersaturated environment, Ca is leached out from the expanded structure of Fe_xCa_yCO₃ increasing the solubility of the crystals, weakening the mechanical properties of the resulting corrosion films and stimulating localized corrosion.

Synchrotron radiation Ca K-edge 2D-XANES spectroscopy for studying the stratigraphic distribution of calcium-based consolidants applied in limestones

In Heritage Science, the evaluation of stone consolidation treatments by investigating the nature of in situ newly formed products and their penetration depth within the consolidated matrix is a grand challenge. A number of analytical methods have been proposed, but, currently, most of them are not able to supply a full overview of the spatial, structural and compositional information of the newly formed crystalline and amorphous phases with a submicrometric lateral resolution. Here, we examined, the capabilities of synchrotron radiation (SR)-based two-dimensional X-ray absorption near-edge structure (2D-XANES) spectroscopy at Ca K-edge for determining the structural and compositional properties of the compounds formed after the application of a calcium acetoacetate-based consolidant on a porous carbonatic stone (limestone) and for investigating their stratigraphic distribution at the submicrometric scale length. We evaluated advantages and drawbacks of three Ca K-edge 2D-XANES-based approaches: (i) transmission mode full-field-XANES (FF-XANES) imaging; (ii) micro-X-ray fluorescence (μ-XRF) mapping above the Ca K-edge combined with the acquisition of XRF mode μ-XANES spectra at a limited number of spots; (iii) full-spectral µ-XANES (FS µ-XANES) mapping in XRF mode and its variant called selectively induced X-ray emission spectroscopy (SIXES) mapping. Overall, Ca K-edge 2D-XANES spectroscopy provided accurate qualitative and semi-quantitative information on the newly formed calcium carbonates (i.e., amorphous calcium carbonate, vaterite and calcite) and their stratigraphic distribution at the submicrometric scale, thus opening a new scenario to study the carbonatation process of calcium-based consolidants in limestones.

The application of the vermicomposting process in the bioremediation of diesel contaminated soils

Polycyclic Aromatic Hydrocarbons (PAHs) are among the environmental pollutants that have very high carcinogenic and mutagenic activity. Among hundreds of different PAHs, 17 are considered priority pollutants and routinely monitored for regulatory purposes. Extended periods of exposure and expensive clean-up costs are typically associated with the vast majority of processes used for the remediation of areas contaminated with PAHs. The results of this study indicate that bioremediation via vermicomposting could be an effective method for remedying soils contaminated with toxic organic compounds, such as PAHs. This study was conducted over 90 days in the presence of various quantities of organic matter (cattle manure) to recover soils contaminated with PAHs. High-performance liquid chromatography (HPLC) was applied to identify PAHs. An evaluation of the toxicity of the final material and the transformation of the organic matter throughout the process was also conducted. The data presented here suggest a relationship between the molar mass of the PAHs and the ability of the vermicomposting process to promote biodegradation. These results suggest that vermicomposting has great potential to be utilized as a tool for the bioremediation of soils impacted by PAHs.

A versatile liquid-jet/sessile droplet system for operando studies of reactions in liquid dispersions and solutions by X-ray absorption spectroscopy

X-ray absorption spectroscopy for operando studies of liquid dispersions and solutions.

The Spectroscopy Village at Diamond Light Source

This manuscript presents the current status and technical details of the Spectroscopy Village at Diamond Light Source. The Village is formed of four beamlines: I18, B18, I20-Scanning and I20-EDE. The village provides the UK community with local access to a hard X-ray microprobe, a quick-scanning multi-purpose XAS beamline, a high-intensity beamline for X-ray absorption spectroscopy of dilute samples and X-ray emission spectroscopy, and an energy-dispersive extended X-ray absorption fine-structure beamline. The optics of B18, I20-scanning and I20-EDE are detailed; moreover, recent developments on the four beamlines, including new detector hardware and changes in acquisition software, are described.

Biomineralisation by earthworms - an investigation into the stability and distribution of amorphous calcium carbonate

BACKGROUND

Many biominerals form from amorphous calcium carbonate (ACC), but this phase is highly unstable when synthesised in its pure form inorganically. Several species of earthworm secrete calcium carbonate granules which contain highly stable ACC. We analysed the milky fluid from which granules form and solid granules for amino acid (by liquid chromatography) and functional group (by Fourier transform infrared (FTIR) spectroscopy) compositions. Granule elemental composition was determined using inductively coupled plasma-optical emission spectroscopy (ICP-OES) and electron microprobe analysis (EMPA). Mass of ACC present in solid granules was quantified using FTIR and compared to granule elemental and amino acid compositions. Bulk analysis of granules was of powdered bulk material. Spatially resolved analysis was of thin sections of granules using synchrotron-based μ-FTIR and EMPA electron microprobe analysis.

RESULTS

The milky fluid from which granules form is amino acid-rich (≤ 136 ± 3 nmol mg^-1 (n = 3; ± std dev) per individual amino acid); the CaCO₃ phase present is ACC. Even four years after production, granules contain ACC. No correlation exists between mass of ACC present and granule elemental composition. Granule amino acid concentrations correlate well with ACC content (r ≥ 0.7, p ≤ 0.05) consistent with a role for amino acids (or the proteins they make up) in ACC stabilisation. Intra-granule variation in ACC (RSD = 16%) and amino acid concentration (RSD = 22-35%) was high for granules produced by the same earthworm. Maps of ACC distribution produced using synchrotron-based μ-FTIR mapping of granule thin sections and the relative intensity of the ν₂: ν₄ peak ratio, cluster analysis and component regression using ACC and calcite standards showed similar spatial distributions of likely ACC-rich and calcite-rich areas. We could not identify organic peaks in the μ-FTIR spectra and thus could not determine whether ACC-rich domains also had relatively high amino acid concentrations. No correlation exists between ACC distribution and elemental concentrations determined by EMPA.

CONCLUSIONS

ACC present in earthworm CaCO₃ granules is highly stable. Our results suggest a role for amino acids (or proteins) in this stability. We see no evidence for stabilisation of ACC by incorporation of inorganic components. Graphical abstractSynchrotron-based μ-FTIR mapping was used to determine the spatial distribution of amorphous calcium carbonate in earthworm-produced CaCO₃ granules.