Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements

Phage satellites are mobile genetic elements that propagate by parasitizing bacteriophage replication. We report here the discovery of abundant and diverse phage satellites that were packaged as concatemeric repeats within naturally occurring bacteriophage particles in seawater. These same phage-parasitizing mobile elements were found integrated in the genomes of dominant co-occurring bacterioplankton species. Like known phage satellites, many of the marine phage satellites encoded genes for integration, DNA replication, phage interference, and capsid assembly. Many also contained distinctive gene suites indicative of unique virus hijacking, phage interference and mobilization mechanisms. Marine phage satellite sequences were widespread in local and global oceanic virioplankton populations, reflecting their ubiquity, abundance, and temporal persistence in marine planktonic communities worldwide. Their gene content and putative life cycles suggest they may impact host-cell phage immunity and defense, lateral gene transfer, and bacteriophage-induced cell mortality and host and virus productivity. These previously unrecognized marine phage satellites therefore have potential to impact the ecology and evolution of bacteria and their bacteriophages in the ocean, and similar phage parasites likely thrive in many other microbial habitats as well. Significance statement Phage satellites are mobile genetic elements that parasitize bacteriophage, thereby exerting profound biological and ecological impacts. To date however, phage satellites have been found primarily in Gram-positive cocci and a few Gram-negative bacteria, many of which are human pathogens. Direct inspection of “wild” marine virus particles however, revealed that phage satellites are widely distributed in the sea, and that their genetic diversity, gene repertoires, and host ranges are much greater than previously supposed. Our analyses provide insight into their parasitic life cycles, potential satellite-helper-phage interactions, and reproductive strategies of these newly recognized phage-parasitizing mobile elements. Their properties, diversity and environmental distributions suggest they exert pervasive influence on marine plankton ecology and bacterial and virus evolution in the sea.