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How metabolic activity is partitioned among individuals determines the scaling of cellular physiology to higher levels of biological organization. Yet the mechanisms that generate this heterogeneity and shape its distribution remain largely unresolved. We quantified single-cell metabolism in microbial communities spanning aquatic, terrestrial, and host-associated ecosystems. Across more than one million cells, metabolic activity followed a long-tailed distribution best described by a lognormal model, with a small subset of individuals contributing disproportionately to community metabolism. In some cases, the most active 20% of cells accounted for over 90% of metabolic output, but this pattern became less pronounced in more productive environments. To assess the consequences of metabolic inequality, we developed a stochastic simulation model linking single-cell activity to community respiration via enzyme kinetics. Because respiration responds nonlinearly to enzyme activity, variation among cells does not translate proportionally into ecosystem-level fluxes. As a result, ignoring metabolic heterogeneity can bias estimates of community respiration by up to 60%. Our findings reveal a general pattern of metabolic inequality in microbial communities that holds across a wide range of habitats. Accounting for this structure is critical for understanding how microorganisms regulate ecosystem processes and for improving predictions of large-scale biogeochemical dynamics. 

ABSTRACT Much of life on Earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources remain in a system based on the ratio of volume (V) to flow rate (Q). Shortτshould promote immigration but limit species establishment, while longτshould favour species that survive on limited resources. Theory suggests these opposing forces shape the abundance, diversity and function of flowing systems. We experimentally tested how residence time affects a lake microbial community by exposing chemostats to aτgradient spanning seven orders of magnitude. Microbial abundance, richness and evenness increased non‐linearly withτ, while functions like productivity and resource consumption declined. Taxa formed distinct clusters of short‐ and long‐τspecialists consistent with niche partitioning. Our findings demonstrate that residence time drives biodiversity and community function in flowing habitats that are commonly found in environmental, engineered and host‐associated ecosystems. 

ABSTRACT Much of life on Earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources stay within a system based on the ratio of volume (V) to flow rate (Q). Short residence times promote immigration but may prevent the establishment of species that cannot quickly reproduce, or resist being washed out. In contrast, long residence times reduce resource input, selecting for species that can survive on a low supply of energy and nutrients. Theory suggests that these opposing forces shape the abundance, diversity, and function of flowing systems. In this study, we subjected chemostats inoculated with a complex lake microbial community to a residence time gradient spanning seven orders of magnitude. Microbial abundance, richness, and evenness increased with residence time, while functions like productivity and resource consumption decreased along the gradient. Microbial taxa were non- randomly distributed, forming distinct clusters of short-τ and long-τ specialists, reflecting a pattern of niche partitioning. Consistent with theoretical predictions, we demonstrate that residence time shapes assembly processes with direct implications for biodiversity and community function. These insights are crucial for understanding and managing flowing environments, such as animal gut microbiomes, soil litter invertebrate communities, and plankton in freshwater and marine ecosystems.