Microdiversity is higher in temperate than in virulent bacteriophages from soil environments

Abstract Bacteriophages are not only the most ubiquitous biological entity on earth, they also display remarkable genetic diversity across and within populations. While macrodiversity has been extensively studied, the drivers of microdiversity (intra-species genetic diversity) remain poorly understood, particularly in relation to phage lifestyle. The distinguishing ability of temperate phages to integrate themselves into the host genome, thereby experiencing distinct evolutionary pressures, has an unknown influence on the microdiversity present in the viral genome. This difference in microdiversity could impact the coevolution of phages with their hosts or the resilience of phages to new environments or hosts. To identify a possible association between microdiversity and lifestyle, we used four existing metagenomics datasets focusing on bacteriophages from soil environments as input for a newly constructed pipeline calculating microdiversity and predicting phage lifestyles. These four datasets together consist of 11 073 viral genomes and span across environments. We found that temperate phages consistently exhibit significantly higher microdiversity than their virulent counterparts in three of four datasets, a pattern that held across multiple quality thresholds and lifestyle prediction methods. These findings suggest that lysogeny may promote or preserve genetic variation within phage populations, with potential implications for phage-host coevolution and environmental adaptability.