The community structure of any microbial ecosystem results from a complex set of interactions between cells, viruses, and molecules, and these interactions are a result of constant, often rapid evolution. In wild microbial genomes, localized hypervariation (mediated by viruses and horizontal/lateral gene transfer) can generate massive genetic diversity, offering selective advantages by optimizing a variety of cellular and viral functions.Organisms in several environments (e.g., marine, soil, groundwater), and spanning most of the microbial tree of life, have recently been identified by our team with a capacity for rapid protein evolution. We have observed highly precise mutation occurring naturally in bacterial, archaeal, and viral genomes, directed by a class of retroelements that can select particular regions of target genes for rewriting. Moreover, our research has found that organisms are capable of recruiting these genetic tools to hypermutate a variety of genes on chromosomes and plasmids. Taken together, these recent discoveries constitute a natural system, which serves as a modular tool for targeted protein, pathway, and chassis engineering for any organism of interest. Such a toolset would be invaluable for the transformation and evolution of non-model microbes, for which no such tools exist.