Unexplored diversity and ecological functions of transposable phages

Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.

Automated summary

Phages, including transposable phages (TBPs), are widely distributed and play important roles in diverse environments. We established a TBP genome dataset by mining microbial genomes and viromes, expanding the accessible TBP genomes 384-fold. TBPs are prevalent and genetically diverse, and can infect a wider range of hosts than non-TBPs. We identified diverse auxiliary metabolic genes (AMGs) in TBP genomes, including genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis. Our findings greatly expand the genetic diversity of TBPs and reveal their potential influences in various ecosystems.