A microbiologist's field guide to community ecology

Many microbiological outcomes are shaped by the determinants of community composition, including the factors that allow pathogens to invade healthy microbiota and the processes that maintain the diversity that underpins soil function. Community ecology provides a rich conceptual toolset to investigate patterns of coexistence that can be adapted to explain and manage these outcomes. However, these concepts have complex histories of controversy and debate that must be considered when applying them to the microbial context. Microorganisms also have distinctive characteristics that must be accounted for when studied using ideas that were originally developed to describe macroscopic ecosystems. Here, we provide a concise overview for microbiologists to five key frameworks from community ecology: Niche theory, Trophic levels, Keystone species, Succession, and Metacommunities. We discuss the historical context and controversies surrounding each framework and outline existing and potential applications to microbial systems. This work therefore provides a practical guide for microbiologists who wish to use community ecology to understand and manipulate microbial community composition.