Activity and diversity of prophages harbored by wheat phyllosphere bacteria

Abstract

The plant microbiome harbors an enormous diversity of fungi, bacteria, and viruses, but little is known on the diversity and function of prophages harbored within plant-associated bacteria. Using VIP-Seq, a novel method based on supernatant sequencing, we identified and quantified the activity of 120 spontaneously induced prophages in a collection of 63 Erwinia and Pseudomonas strains isolated from wheat flag leaves collected from the same field. These bacterial strains exhibited high levels of spontaneous prophage induction, with some producing > 108 virions/mL in overnight culture. Significant induction in planta also occurred from a lysogenic Erwinia strain inoculated on wheat seedlings. The potential of these active prophages in bacterial warfare was exhibited by their widespread killing of rival bacterial strains. Evidence of transduction was observed, and the prophages were shown to contribute a majority of the non-core genome of E. aphidicola isolates. Many additional prophages were predicted by bioinformatic tools, and we found that the predicted prophages that were not spontaneously induced had a significantly higher number of IS elements. Our results suggest that spontaneous induction of prophages may represent an unknown but wide-spread competition mechanism involved in phyllosphere microbiome assembly and function. This may also have implications for the design and resilience of synthetic bacterial communities used as biocontrol for certain plant diseases.

Evidence for the key roles of thePseudomonas syringaemobilome in shaping biotic interactions

“…As part of the mobilome, prophages and viral satellites, among other types of genomic parasites, can act as carriers for the dispersal of genetic information between bacteria in a community. Often these genes offer the host an evolutionary advantage, referred to as lysogenic conversion (11), as these genes are involved in metabolic pathways, influence the outcome of biotic interactions within the community (12, 13), or shape the bacterium-host interaction (11). For example, several prophages are described that carry auxiliary metabolic genes, such as those involved in the carbohydrate metabolism and two-component transporter for the uptake of specific compounds (14), and direct microbial interactions can be modulated by prophage-encoded antimicrobial resistance genes (15).…”