Trichodesmiumis a widespread, N2fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmiumubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmiumholobiont could influence the fate of fixed carbon and nitrogen. Metatranscriptome sequencing was performed on Trichodesmiumcolonies collected during high-frequency Lagrangian sampling in the North Pacific Subtropical Gyre (NPSG) to identify possible interactions between the Trichodesmiumhost and microbiome over day–night cycles. Here we show significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day–night periodicity. The functions of the co-expressed genes suggested a suite of interactions within the holobiont linked to key resources including nitrogen, carbon, and iron. Evidence of microbiome reliance on Trichodesmium-derived vitamin B12 was also detected in co-expression patterns, highlighting a dependency that could shape holobiont community structure. Collectively, these patterns of expression suggest that biotic interactions could influence colony cycling of resources like nitrogen and vitamin B12, and decouple activities, like N2fixation, from typical abiotic drivers of Trichodesmiumphysiological ecology.