Nanometer-Scale Chemistry of a Calcite Biomineralization Template: Implications for Skeletal Composition and Nucleation

Abstract

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.

Keywords: biomineralization; foraminifera; geochemistry; paleoceanography; templating.

Fig. 1.

The spherical shell of O. universa is constructed around a POS and is chemically heterogeneous. (A) Light micrograph of O. universa with a newly calcified spherical chamber surrounded by calcite spines and cellular material. Bright points on the spines are symbiotic dinoflagellates. (B) SEM of a 1-d-old calcite sphere, broken to expose a wall cross-section and shell pore. The white arrow identifies the embedded POS, which is visible as a raised ridge in the cross-section. Calcite precipitation occurs on both sides of the POS. (C) TEM of the cross-section of an agar-mounted decalcified shell wall (paler, Right) and pore (darker, Left). The POS (green horizontal layer, white arrow) is visible within the decalcified shell. The pore has an organic lining (red), and “pore plate” (blue) contiguous with the POS. For a detailed discussion of these features, see ref. . The POS appears to be a complex, branched structure rather than a continuous sheet, with numerous electron-dense regions of similar structure to the POS extending ∼500 nm either side of the POS (light green). SEM and TEM images were generated following methods in ref. . (D and E) ToF-SIMS ⁴³Ca/⁴⁰Ca, ²⁴Mg/⁴⁰Ca, and ²³Na/⁴⁰Ca maps of cross-sections through a mature, 4-d-old shell wall. This foraminifera was moved between ⁴³Ca enriched seawater at night, and “natural” seawater during the day, resulting in three ⁴³Ca enriched bands on each side of the POS. The position of the POS (white arrows) is bracketed by these symmetric ⁴³Ca “labels” (numbered in D₁; SI Appendix, section 2.4), which identify the origin of calcification and constrain the location of the POS (white arrow). The region associated with the POS has elevated Na and Mg. E captures the base of a Na-rich calcite spine within the shell wall of a different specimen. The spines originate at the POS (18), further identifying the Na-rich band in D₃ as associated with the POS. Profiles in F₁ are extracted from white boxes in D, and enlargements in F₂ highlight the coincident Mg/Ca and Na/Ca maxima that are uniquely present at the POS. The double Mg maxima either side of the Na maximum in this specimen is present in ∼33% of specimens, and is caused by the POS being between two, close high-Mg bands. A more typical signal can be seen in SI Appendix, section 2.4.

Fig. 2.

Three-dimensional APT reconstruction of a planar organic-mineral templating surface within foraminiferal calcite. (A) The APT reconstruction captures the interface between calcite (Ca-rich) and an organic (Ca-poor) region. The structure of this predominantly planar interface is highlighted by a 50% Ca-concentration isosurface. (B) When viewed in plane with the interface, Na appears elevated at the interface. The symbols for Na have been enlarged 2× for emphasis. Note that whereas Na appears more abundant on the calcite side of the interface, this reflects the higher ionic yield from calcite than the organic layer, and by atomic fraction Na is more abundant in the organic layer, as highlighted in Fig 3.

Fig. 3.

Compositional profiles through the APT reconstruction reveal Na enrichment in the organic surface. (A) Chemical profiles (“proxygrams”) across the biomineral interface in Fig. 2 quantify sharp changes in major elements across an ∼2-nm interface, defining the transition between the calcite and organic layers (dashed line). Profiles are presented as percent of collected ions, with profile bins defined using a constant number of ions per bin. Shaded error envelope calculated based on counting statistics. (B) Both Na and Mg are elevated in the organic material relative to the calcite. This enrichment is not centered on the interface, but instead occurs within the first few nanometers on the organic side of the interface.

Fig. 4.

Observed POS-specific Na and Mg maxima in ToF-SIMS can be explained by APT measurements, suggesting that both techniques are imaging the same structure. ToF-SIMS and APT cannot be directly compared because of differences in spatial scale. Instead, the relative magnitude of the POS Na and Mg enrichment measured by ToF-SIMS (crosses) are compared with APT measurements of POS composition (solid lines) in the same specimen using a quantitative model. The shaded gray envelopes show the mean and SD of the POS-associated signal in 18 other ToF-SIMS specimens, and highlight a degree of variability in Na and Mg enrichment between individuals. Modeled intensities are based on APT measured compositions, a beam width of 312 nm, and a POS thickness of 130 nm. The double Mg peaks bracketing the POS can be explained by two Gaussians with 312-nm FWHM (dashed peaks), consistent with two narrow bands of higher-Mg calcite ∼300 nm either side of the POS. At this distance, the contribution of these peaks to the POS location is negligible. The combination of these Gaussian peaks and the modeled POS signal (solid black line) describe the POS-associated Mg maxima in this specimen (SI Appendix, section 4.5).