Abstract
Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity1,2. These microorganisms and their traits directly impact ecosystems and human health3,4. As such, a focus on functional traits has become increasingly common in microbial ecology and these trait-based approaches have the potential to link microbial communities and their ecological function5,6. But what is missing is how, why, and in what order microorganisms acquired the traits we observe in the present day. These are important questions because they relate to the evolution, selective advantage, and trait similarity of extant organisms. Here, we reconstruct the evolutionary history of microbial traits using genomic data. We use the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Finally, we show that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many labile genes while specialist genomes comprise more highly conserved functional genes. Our results provide a framework for understanding the evolutionary history of extant microorganisms, and provide insights into the evolution, selective advantage, and phylogenetic patterns of microbial traits. We anticipate that our work will improve our understanding of microbial trait variation and help identify microbial functional groups. In doing so, the evolutionary history of microbial traits will shed new light on our understanding of microbial communities in environmental and human ecosystems.