Residence time structures microbial communities through niche partitioning

Abstract

Much of life on Earth is at the mercy of currents and flow. Residence time ({tau}) 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-{tau} and long-{tau} 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.