Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats

Abstract Horizontal gene transfer (HGT) is enabled in part through the movement of DNA within two broad groups of small (<0.2 µm), diffusible nanoparticles: extracellular vesicles (EVs) and virus-like particles (VLPs; including viruses, gene transfer agents, and phage satellites). These structures enclose a substantial portion of the HGT potential in planktonic ecosystems, but whether genes move preferentially through one type of nanoparticle versus another is unknown. Here we show that EVs and VLPs from the oligotrophic ocean differ in their DNA capacity and encoded functions. Both particle types are enriched in mobile genetic elements (MGEs), and we highlight how this property enables novel MGE discovery. Examining the Pelagibactermobilome reveals >7200 diverse chromosomal fragments and MGEs, many differentially partitioned between EVs and VLPs. Together these results suggest that distinctions in nanoparticle contents contribute to the mode and trajectory of microbial HGT networks and evolutionary dynamics in natural habitats.