Understanding the effects of individual organisms on material cycles and energy fluxes within ecosystems is central to predicting the impacts of human-caused changes on climate, land use, and biodiversity. Here we present a theory that integrates metabolic (organism-based bottom-up) and systems (ecosystem-based topdown) approaches to characterize how the metabolism of individuals affects the flows and stores of materials and energy in ecosystems. The theory predicts how the average residence time of carbon molecules, total system throughflow (TST), and amount of recycling vary with the body size and temperature of the organisms and with trophic organization. We evaluate the theory by comparing theoretical predictions with outputs of numerical models designed to simulate diverse ecosystem types and with empirical data for real ecosystems. Although residence times within different ecosystems vary by orders of magnitude-from weeks in warm pelagic oceans with minute phytoplankton producers to centuries in cold forests with large tree producers-as predicted, all ecosystems fall along a single line: residence time increases linearly with slope = 1.0 with the ratio of whole-ecosystem biomass to primary productivity (B/P). TST was affected predominantly by primary productivity and recycling by the transfer of energy from microbial decomposers to animal consumers. The theory provides a robust basis for estimating the flux and storage of energy, carbon, and other materials in terrestrial, marine, and freshwater ecosystems and for quantifying the roles of different kinds of organisms and environments at scales from local ecosystems to the biosphere. metabolic theory | systems ecology | total system throughflow | residence time | cycling I n most ecosystems, energy and materials flow through trophic networks comprised of plant primary producers, animal consumers, and microbial decomposers (Fig. 1). The individual organisms that make up these networks control the storage and flux of energy, carbon, and other materials. Consequently, a theoretical framework that can account for how different kinds of organisms and ecosystems affect fluxes and stores of energy and materials in ecosystems is central to understanding the carbon cycle of the biosphere and to predicting the impacts of humancaused changes in climate, land use, and biodiversity (1-3). Although it has long been recognized that different kinds of organisms play important roles in the processing of energy and materials in ecosystems, existing treatments are incomplete. Most studies have focused on particular trophic levels, such as primary producers or herbivores, specific ecosystem types, such as tropical forest or pelagic marine, or single species, such as top predators or ecosystem engineers (4-14). Still missing is a simple mechanistic theory that can make precise, quantitative predictions based on the mechanistic relationships between traits of the organisms in the different trophic levels and whole-ecosystem properties, such as carbon flux or recycling.Two main t...