Nanoscale identification of organic pigments in biogenic calcite by atom probe tomography

Deep within the shells of sea creatures and the spines of sea urchins lies a world of intricate engineering that human eyes cannot see. These natural structures, known as biominerals, are not just simple rocks; they are complex composites where hard, inorganic crystals grow together with soft, organic molecules like proteins and pigments. For decades, scientists have understood that these organic components act as a sort of internal architecture, guiding how the crystals form and giving them their unique strength and color. However, a significant gap has remained in our knowledge: while we can see the large-scale structure of these materials, we have struggled to map exactly where the tiny organic molecules sit inside the crystal lattice at the nanometer scale. Without this three-dimensional map, the precise relationship between the living organism and the mineral it builds remains a mystery.

A team of researchers has now taken a major step toward filling this gap by using a powerful imaging tool called atom probe tomography to look inside the purple spines of a sea urchin. This species, known as Sphaerechinus granularis, has spines that are white at the tips but turn a deep purple at the base. That color comes from specific organic molecules called spinochromes, which get trapped inside the growing crystal. The scientists wanted to find out exactly how these pigment molecules are arranged inside the mineral and how they interact with the surrounding atoms. To do this, they had to overcome a major hurdle: when these organic molecules are subjected to the intense electric fields required to analyze them, they tend to break apart into tiny fragments, making it difficult to identify what the original molecule was.

To solve this puzzle, the researchers first created a controlled test environment. They grew synthetic crystals of calcium carbonate, the same material that makes up the sea urchin's spine, and deliberately added the purple pigment molecules to them. By analyzing these synthetic samples alongside the real sea urchin spines, they could compare the results and identify which signals came from the pigment and which came from the mineral itself. They discovered that the purple color in the sea urchin is indeed caused by a specific molecule called spinochrome A. When they analyzed the real spines, they found that this molecule is distributed evenly throughout the purple regions, rather than clumping together in isolated spots.

The most significant finding, however, concerns how these pigment molecules are held in place. The researchers found that the spinochrome A molecules are not just floating randomly inside the crystal; they are strongly associated with magnesium atoms, another element naturally present in the sea urchin's spine. Using a new method of data analysis that tracks ions detected at the same time and in close proximity to one another, the team showed that the fragments of the pigment molecule and the magnesium atoms appear together far more often than would happen by chance. This suggests that the pigment binds directly to the magnesium within the crystal structure. In contrast, other elements found in the spine, such as lithium, do not show this same connection and are actually found in different areas, mostly in the white, unpigmented tips of the spines.

This work demonstrates that it is possible to identify specific organic molecules inside a hard mineral and map their location in three dimensions, even when those molecules break apart during the analysis. By developing new ways to filter the data and look for patterns in how the fragments appear together, the researchers were able to reconstruct the presence of the pigment and its relationship to the mineral's building blocks. This approach offers a new way to understand how living things build their hard parts, revealing the hidden chemical conversations between organic molecules and inorganic crystals that shape the natural world.