Multifunctionally diverse alkaline phosphatases of Alteromonas drive the phosphorus cycle in the ocean.

Phosphorus is a critically limiting nutrient in marine ecosystems, with alkaline phosphatases (APases) playing a vital role in liberating phosphate from organic compounds. However, the dominant taxa and APase families driving the marine phosphorus cycle, particularly in the deep ocean, remain poorly understood. Equally enigmatic remains the (multi)functional diversity and mechanisms of action of different APases. To address these gaps, this study combines global multi-omic analyses, biochemical studies of purified recombinant proteins, and laboratory experiments with proteomics and enzymatic rate measurements. Here we show that multi-omics consistently identify Alteromonas as a primary contributor to APase expression and production, with PhoA as the dominant APase family, particularly in the deep ocean. Furthermore, all four major APase families (PhoA, PhoD, PhoX, PafA) exhibit multifunctionality, revealing distinct substrate preferences and regulatory mechanisms. Ultimately, this study expands the mechanistic understanding of the marine phosphorus cycle, while revealing the significance of enzyme multifunctionality in elemental cycles.