The Calcidiscus leptoporus genome reveals vitamin-mediated holobiont interactions.

Coccolithophores are major marine phytoplankton that contribute to ocean carbon cycling through both organic carbon fixation and calcium carbonate biomineralization, yet the functional basis of their interactions with phycosphere bacteria remains poorly resolved. Here, we present the nuclear genome of the haploid phase of the coccolithophore Calcidiscus leptoporus, a coccolithophore that calcifies in both life-cycle stages. We combined host genome analysis, genome-resolved characterization of associated bacteria, and a four-month vitamin-manipulation experiment to test how B-vitamin biosynthetic complementarity relates to host performance and phycosphere community assembly. Metabolic reconstructions indicate partitioned B-vitamin biosynthtic potential: the host encodes pathways for B2, B5, B6, and B9, including a rare fused B5 biosynthesis gene, but lacks complete pathways for B1, B3, B7, and B12. These missing functions were distributed among recurrent bacterial taxa, with no single bacterial MAG encoding the full set of host-missing vitamins. Across the experiment, bacterial community composition was structured primarily by the experimental phase, while vitamin treatments secondarily influenced which taxa became enriched at later stages. Consistent with genome-inferred auxotrophy, B-vitamin availability constrained long-term growth under the tested conditions, with B1 alone providing partial rescue and vitamin-replete treatments showing equal or stronger responses. Together, these data establish C. leptoporus as a genomic model for coccolithophore biology and holobiont interactions, while providing a testable framework linking vitamin economies to phycosphere assembly and host performance.