Competence repression by the SPβ prophage in Bacillus subtilis revealed by transcriptomics across culture conditions

Prophages are near-ubiquitous in bacterial genomes, yet their effects on host physiology are typically assayed under a narrow range of laboratory conditions, mostly involving DNA-damaging agents or physical and chemical stress. This leaves open the question of which ecological and physiological conditions trigger prophage-host interaction, and whether the outcome benefits the host or the prophage. Here, we used publicly available transcriptomic data to investigate conditions promoting prophage-host interaction in Bacillus subtilis. This analysis identified that competence strongly induces prophage gene expression. To further investigate the role of competence, we used two sets of B. subtilis strains: a natural SPβ lysogen strain and its cured counterpart, and a natural non-lysogenic strain and the same strain lysogenised with SPβ. Under competence-inducing conditions, both lysogen strains showed lower expression of the competence genes compared with their non-lysogenic counterparts. This result was corroborated by transformation assays that showed consistently lower transformation efficiency in the lysogen strains, and by fluorescence microscopy using a transcriptional reporter for the late competence gene. Because competence is a principal route for horizontal gene transfer in B. subtilis, prophage repression of the competence programme constrains host DNA uptake and evolvability. More broadly, these results show that mining public transcriptomes for condition effects can guide experimental effort towards prophage-host phenotypes that conventional laboratory conditions would miss.