article epub_ahead yes Pavel Payne author 35F78294-F248-11E8-B48F-1D18A9856A870000-0002-2711-9453 Pavel Plevka author Jonathan P Bollback author 2C6FA9CC-F248-11E8-B48F-1D18A9856A870000-0002-4624-4612 Calin C Guet author 47F8433E-F248-11E8-B48F-1D18A9856A870000-0001-6220-2052 CaGu department Homologous recombination is ubiquitous across evolution, generating variation through genetic reshuffling. Although bacteria lack meiotic recombination, homologous recombination has been known to extensively shape their genomes. However, the mechanisms and ecological conditions sustaining frequent recombination in bacteria remain unclear. Using an Escherichia coli–P1 phage model system, we reveal how frequent recombination emerges from CRISPR-based herd immunity to a generalized transducing phage (DNA vector). Herd immunity maintains phage-susceptible donor bacteria, recipient immune bacteria, and transducing phage, which promotes chromosomal gene flow that exceeds spontaneous mutation by up to two orders of magnitude. Notably, recombination begins as bacterial cultures enter stationary phase, when canonical mutation supply through population growth and DNA replication is strongly reduced, and recombination can be reinitiated by brief fresh nutrient pulses. Genetic analysis showed that stationary-phase recombination requires recA, recB, and recG, connecting this process to a defined homologous recombination pathway, and suggests a plausible transcriptional regulatory link to transition to nutrient limitation. Bacterial herd immunity therefore has an unexpected evolutionary consequence: it can promote homologous recombination by turning phages into de facto pollinators. This mechanism can help explain how high rates of homologous recombination may be sustained across bacterial populations and suggests that bacterial immune systems can shape molecular evolution not only by blocking infection but also by regulating genetic exchange. Oxford University Press2026 eng homologous recombinationdefense systemsCRISPR-Casherd immunitystationary phasebacterial evolution 0737-4038 1537-1719 4282708010.1093/molbev/msag238 4310 P. Payne, P. Plevka, J. P. Bollback, and C. C. Guet, “Herd immunity underlies homologous recombination in stationary phase bacteria,” <i>Molecular Biology and Evolution</i>, vol. 43, no. 10. Oxford University Press, 2026. Payne, P., Plevka, P., Bollback, J. P., &#38; Guet, C. C. (2026). Herd immunity underlies homologous recombination in stationary phase bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href="https://doi.org/10.1093/molbev/msag238">https://doi.org/10.1093/molbev/msag238</a> Payne P, Plevka P, Bollback JP, Guet CC. Herd immunity underlies homologous recombination in stationary phase bacteria. <i>Molecular Biology and Evolution</i>. 2026;43(10). doi:<a href="https://doi.org/10.1093/molbev/msag238">10.1093/molbev/msag238</a> Payne, Pavel, et al. “Herd Immunity Underlies Homologous Recombination in Stationary Phase Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 43, no. 10, msag238, Oxford University Press, 2026, doi:<a href="https://doi.org/10.1093/molbev/msag238">10.1093/molbev/msag238</a>. Payne, Pavel, Pavel Plevka, Jonathan P Bollback, and Calin C Guet. “Herd Immunity Underlies Homologous Recombination in Stationary Phase Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2026. <a href="https://doi.org/10.1093/molbev/msag238">https://doi.org/10.1093/molbev/msag238</a>. P. Payne, P. Plevka, J.P. Bollback, C.C. Guet, Molecular Biology and Evolution 43 (2026). Payne P, Plevka P, Bollback JP, Guet CC. 2026. Herd immunity underlies homologous recombination in stationary phase bacteria. Molecular Biology and Evolution. 43(10), msag238. 230902026-10-11T22:02:04Z2026-10-12T10:51:54Z