CRISPR herd immunity against a transducing phage underlies adaptive homologous recombination in resting bacteria

Homologous recombination (HR) is ubiquitous across evolution, driving adaptation by reshuffling standing genetic variation. Although bacteria lack meiotic recombination, HR extensively shapes their genomes. However, the mechanisms and ecological conditions sustaining frequent HR in bacteria remain unclear. Using Escherichia coli, we reveal how frequent recombination emerges from herd immunity to a generalized transducing phage. Herd immunity-established here via CRISPR immunity-maintains genetic polymorphism and enables stable host-phage coexistence, thereby promoting genome-wide gene flow and accelerating adaptation through recombination up to two orders of magnitude relative to de novo mutations. Notably, we show that recombination occurs in stationary phase and is mediated by RecG, which has been previously reported to be regulated by the stringent response - a bacterial reaction to nutrient deprivation and other stress conditions. Bacterial herd immunity thus fulfills an unexpected role of promoting adaptation by HR. This mechanism helps explain the enigmatic high rates of HR across bacterial populations, clarifies how bacteria adapt as resources wane, and suggests a broader evolutionary role for bacterial immune systems beyond individual defense.