Investigating bacterial evolution in nature with metagenomics

Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome’s response to environmental change.