Microorganisms mediate the biogeochemical cycles of the Earth system and the atmospheric fluxes of greenhouse gases. However, historically, microorganisms have been crudely represented in Earth system models in ways that have limited our understanding of global-scale microbial impacts and potential feedbacks to global change. As our understanding of microbial communities expands, how can their activity be more mechanistically represented at large scales? I will discuss new insights into nitrogen and carbon cycling in the ocean gained from describing microbial activity simply yet dynamically in marine ecosystem models, harnessing physical and chemical constraints to microbial growth. The broadly applicable strategy allows the presence or absence of microbial “metabolic functional types” to emerge from ecological interactions, providing more fundamental explanations for observed biogeochemical patterns and paving the way for improved prognostic capabilities.