Deep-branching magnetotactic bacteria form intracellular carbonates enriched in trace metals.

Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation. IMPORTANCE: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba²⁺ and Ni²⁺, and biologically essential Mg²⁺. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba²⁺ and Ni²⁺) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.