Phage-plasmid hybrids are found throughout diverse environments and encode niche-specific functional traits

Phage-plasmids are unique mobile genetic elements that function as plasmids and temperate phages. While it has been observed that such elements often encode antibiotic resistance genes and defense system genes, little else is known about other functional traits they encode. Further, no study to date has documented their environmental distribution and prevalence. Here, we performed genome sequence mining of public databases of phages and plasmids utilizing a random forest classifier to identify phage-plasmids. We recovered 5,742 unique phage-plasmid genomes from a remarkable array of disparate environments, including human, animal, plant, fungi, soil, sediment, freshwater, wastewater, and saltwater environments. The resulting genomes were used in a comparative sequence analysis, revealing functional traits/accessory genes associated with specific environments. Host-associated elements contained the most defense systems (including CRISPR and anti-CRISPR systems) as well as antibiotic resistance genes, while other environments, such as freshwater and saltwater systems, tended to encode components of various biosynthetic pathways. Interestingly, we identified genes encoding for certain functional traits, including anti-CRISPR systems and specific antibiotic resistance genes, that were enriched in phage-plasmids relative to both plasmids and phages. Our results highlight that phage-plasmids are found across a wide-array of environments and likely play a role in shaping microbial ecology in a multitude of niches. IMPORTANCEPhage-plasmids are a novel, hybrid class of mobile genetic element which retain aspects of both phages and plasmids. However, whether phage-plasmids represent merely a rarity or are instead important players in horizontal gene transfer and other important ecological processes has remained a mystery. Here, we document that these hybrids are encountered across a broad range of distinct environments and encode niche-specific functional traits, including the carriage of antibiotic biosynthesis genes and both CRISPR and anti-CRISPR defense systems. These findings highlight phage-plasmids as an important class of mobile genetic element with diverse roles in multiple distinct ecological niches.