Adaptation in Natural Microbial Populations

Although their diversity greatly exceeds that of plants and animals, microbial organisms have historically received less attention in ecology and evolutionary biology research. This knowledge gap is rapidly closing, owing to recent technological advances and an increasing appreciation for the role microbes play in shaping ecosystems and human health. In this review, we examine when and how the process and patterns of bacterial adaptation might fundamentally differ from those of macrobes, highlight methods used to measure adaptation in natural microbial populations, and discuss the importance of examining bacterial adaptation across multiple scales. We emphasize the need to consider the scales of adaptation as continua, in which the genetic makeup of bacteria blur boundaries between populations, species, and communities and with them concepts of ecological and evolutionary time. Finally, we examine current directions of the field as we move beyond the stamp-collecting phase and toward a better understanding of microbial adaptation in nature.