Marine microbial communities regulate global carbon storage, nutrient cycling, and oxygen availability, yet their diversity remains difficult to represent in Earth-system models. Most marine ecosystem models simplify this diversity as a set of independently prognosed plankton functional types. Although necessary for tractability, this architecture can become restrictive when community-level biogeochemical function depends on rapid physiological reorganization, functional redundancy, or metabolic strategies that cut across fixed taxonomic categories. Here, we develop a superorganism framework that represents total microbial biomass as a single prognostic state variable, while an environmentally regulated allocation vector partitions that biomass among photosynthetic, heterotrophic, nitrifying, and denitrifying pathways. The framework retains pathway-specific physiological, stoichiometric, and environmental constraints without requiring each pathway to evolve as an independent biomass compartment. In reduced ecological models, the superorganism recovers equilibria mapped from discrete functional-type models and preserves leading aggregate biogeochemical responses, while expressing transient adjustment through internal functional reallocation rather than explicit population turnover. This structure provides a natural representation of continuously varying mixotrophy and rapid metabolic succession. Implemented in a global MITgcm-Darwin configuration, the model reproduces major carbon-cycle patterns while retaining dynamically adjustable functional diversity. The superorganism framework therefore offers a testable alternative to taxon-resolved state variables for Earth-system applications focused on community-level biogeochemical function rather than the population dynamics of individual taxa.