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.

Occlusion of organic components in synthetic calcite crystals has been recently used as a model to understand the role of intra-crystalline organics in biominerals. However, the characterization of the distribution of both types of organics inside these calcite crystals is very challenging. Here, we discuss the potential of using the technique of atom probe tomography (APT) for such characterization, focusing on the analysis of chitin incorporation in single crystals. Additionally, APT has at least the same spatial resolution as TEM tomography, yet with the advantage of obtaining quantitative chemical data. Results show that chitin, either after degradation with yatalase or in the form of nanofibers, forms discrete clusters (2 to 5 nm) in association to water and hydronium molecules, rather than forming a 3D network inside crystals. Overall findings indicate that APT can be an ideal technique to characterize intra-crystalline organic components in abiogenic and biogenic carbonates to further advance our understanding of biomineralization.

Bivalve shells are extensively used as bioarchives for paleoclimate and paleoenvironmental reconstructions. Proxy calibrations in recent shells are the basis for sclerochronology and the applications of geochemistry data to fossils. Shell geochemical information, however, could be altered with the disappearance of intercrystalline organic matrix components, including those linked to shell growth increments, during early diagenesis. Thus, an evaluation of the chemistry of such organics is needed for the correct use of sclerochronological records in fossil shells. Here, we use atom probe tomography (APT) for in situ geochemical characterization of the insoluble organic matrix in shell growth increments in the Antarctic scallop, Adamussium colbecki. We confirm the presence of carboxylated S-rich proteoglycans, possibly involved in calcite nucleation and growth in these scallops, with significant concentrations of magnesium and calcium. Diagenetic modification of these organic components could impact proxy data based on Mg/Ca ratios, but more importantly the use of the δ¹⁵N proxy, since most of the shell nitrogen is likely bound to the amide groups of proteins. Overall, our findings reinforce the idea that shell organics need to be accounted for in the understanding of geochemical proxies.