Biology subjects

Dougherty, P. E.

Publications and source records attributed to Dougherty, P. E..

3 recordsLinked to original sources

bioRxiv2025

Persistent virulent phages exist in bacterial isolates

Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial cells through lysogeny. Virulent phages, characterized by their obligatory lytic cycle, are assumed to lack the ability to persist within bacterial colonies, and their infection is expected to decimate the host population under in-vitro conditions. Consequently, when bacterial isolates are cultured for sequencing, the resulting assemblies are not expected to contain virulent phage genomes. To test this assumption on a large scale, we analyzed over 267,000 publicly available Escherichia assemblies. Surprisingly, we identified 373 genomes corresponding to virulent phages within the bacterial genomes. These viral genomes are associated with specific phage groups and especially with jumbo phages with very large genomes (>200 kb). Chimallin was a core gene in two of these jumbo phage clusters, the major protein used by some jumbo phages to form a protective phage nucleus during infection. We found multiple lines of evidence suggesting that these virulent phage genomes in bacterial assemblies arise from persistent infections rather than contamination. Supporting this, we experimentally demonstrated the coexistence of non-temperate jumbo phages with their bacterial hosts. In a targeted follow-up search for three clades of persistent jumbo phages, we identified 285 additional jumbo phage genomes in bacterial taxa beyond Escherichia, highlighting that there are many more undiscovered persistent phages in bacterial assemblies. Our findings challenge the traditional virulent-temperate dichotomy, highlighting the overlooked diversity and prevalence of non-canonical phage lifestyles.

microbiology↗

bioRxiv2024

Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.

microbiology↗

bioRxiv2023

Activity and diversity of prophages harbored by wheat phyllosphere bacteria

1.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.

microbiology↗