Pervasive prophage recombination occurs during evolution of spore-forming 
Bacilli

Dragoš, A.; Priyadarshini, B.; Hasan, Z.; Strube, M. L.; Kempen, P. J.; Maróti, G.; Kaspar, C.; Bose, B.; Burton, B. M.; Bischofs, I. B.; Kovács Á, T.

doi:10.1038/s41396-020-00854-1

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Pervasive prophage recombination occurs during evolution of spore-forming Bacilli

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Kaspar, C.
Department-Independent Research Group Complex Adaptive Traits, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;
BioQuant Center of the University of Heidelberg;

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Bischofs, I. B.
Department-Independent Research Group Complex Adaptive Traits, Max Planck Institute for Terrestrial Microbiology, Max Planck Society;
BioQuant Center of the University of Heidelberg;

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https://doi.org/10.1038/s41396-020-00854-1
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Citation

Dragoš, A., Priyadarshini, B., Hasan, Z., Strube, M. L., Kempen, P. J., Maróti, G., et al. (2020). Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. The ISME Journal, 15(5), 1344-1358. doi:10.1038/s41396-020-00854-1.

Cite as: https://hdl.handle.net/21.11116/0000-000A-A433-3

Abstract

Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.