Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales.

Prophages constitute a substantial portion of bacterial genomes, yet their effects on hosts remain poorly understood. We examine the abundance, distribution, and activity of prophages in Bacillus subtilis using computational and laboratory analyses. Genome sequences from the NCBI database and riverbank soil isolates reveal prophages primarily related to mobile genetic elements in laboratory strains. Distinct and previously unknown prophages in local isolates prompt an investigation into factors shaping prophage presence, with phylogenetic relatedness predicting the prophage repertoire slightly better than geographical origin. Data also show that prophages exhibit strong co-occurrence and exclusion patterns within genomes. Laboratory experiments indicate that most predicted prophages are cryptic, as they are not induced under DNA-damaging conditions. Importantly, stress responses increase with the number of predicted prophages, suggesting their influence on host physiology. This study highlights the diversity, integration patterns, and potential roles of prophages in B. subtilis, shedding light on bacterial genome evolution and phage-host dynamics.