Spatial, Temporal, and Phylogenetic Scales of Microbial Ecology

Microbial communities play a major role in disease, biogeochemical cycling, agriculture, and bioremediation. However, identifying the ecological processes that govern microbial community assembly and disentangling the relative impacts of those processes has proven challenging. Here, we propose that this discord is due to microbial systems being studied at different spatial, temporal, and phylogenetic scales. We argue that different processes dominate at different scales, and that through a more explicit consideration of spatial, temporal, and phylogenetic grains and extents (the two components of scale) a more accurate, clear, and useful understanding of microbial community assembly can be developed. We demonstrate the value of applying ecological concepts of scale to microbiology, specifically examining their application to nestedness, legacy effects, and taxa–area relationships of microbial systems. These proposed considerations of scale will help resolve long-standing debates in microbial ecology regarding the processes determining the assembly of microbial communities, and provide organizing principles around which hypotheses and theories can be developed. Understanding the processes that shape microbial communities holds potential to provide important insights into ecology and evolutionary biology, and can enable forecasting and management of microbial ecosystem services.At least four fundamental processes (selection, dispersal limitation, neutral processes, mutation) may shape microbial communities, but determining their importance has proven challenging.Ecology has a long history of recognizing that numerous patterns and processes are dependent on spatial, temporal, and phylogenetic scales. Each scale is comprised of two fundamental components: grain and extent.Recognizing that different processes may dominate at different scales in microbial systems could be instrumental in resolving long-standing uncertainty about which processes are important in shaping microbial communities.