Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages

Storey, Nathaniel; Rabiey, Mojgan; Neuman, Benjamin W.; Jackson, Robert W.; Mulley, Geraldine

doi:10.3390/v12111286

Cited by 5 publications

(1 citation statement)

References 127 publications

(94 reference statements)

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“…Storey et al. ( 2020 ) also saw a similar trend with variability in the resistance of Pseudomonas bacteria to future phages. One very promising observation from our study was that coevolved phages were more effective against wild‐type Pss than the original (ancestral) phages and that they appeared to reduce or prevent the emergence of resistance.…”

Section: Discussionmentioning

confidence: 72%

Coevolutionary analysis of Pseudomonas syringae–phage interactions to help with rational design of phage treatments

Rabiey,

Grace,

Pawlos

et al. 2024

Microbial Biotechnology

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Treating plant bacterial diseases is notoriously difficult because of the lack of available antimicrobials. Pseudomonas syringae pathovar syringae (Pss) is a major pathogen of cherry (Prunus avium) causing bacterial canker of the stem, leaf and fruit, impacting productivity and leading to a loss of trees. In an attempt to find a treatment for this disease, naturally occurring bacteriophage (phage) that specifically target Pss is being investigated as a biocontrol strategy. However, before using them as a biocontrol treatment, it is important to both understand their efficacy in reducing the bacterial population and determine if the bacterial pathogens can evolve resistance to evade phage infection. To investigate this, killing curve assays of five MR phages targeting Pss showed that phage resistance rapidly emerges in vitro, even when using a cocktail of the five phages together. To gain insight to the changes occurring, Pss colonies were collected three times during a 66‐h killing curve assay and separately, Pss and phage were also coevolved over 10 generations, enabling the measurement of genomic and fitness changes in bacterial populations. Pss evolved resistance to phages through modifications in lipopolysaccharide (LPS) synthesis pathways. Bacterial fitness (growth) and virulence were affected in only a few mutants. Deletion of LPS‐associated genes suggested that LPS was the main target receptor for all five MR phages. Later generations of coevolved phages from the coevolution experiment were more potent at reducing the bacterial density and when used with wild‐type phages could reduce the emergence of phage‐resistant mutants. This study shows that understanding the genetic mechanisms of bacterial pathogen resistance to phages is important for helping to design a more effective approach to kill the bacteria while minimizing the opportunity for phage resistance to manifest.

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Section: Discussionmentioning

confidence: 72%

Coevolutionary analysis of Pseudomonas syringae–phage interactions to help with rational design of phage treatments

Rabiey,

Grace,

Pawlos

et al. 2024

Microbial Biotechnology

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Bacterial community dynamics and metabolic functions prediction in white button mushroom (Agaricus bisporus) during storage

Hou

Song

et al. 2023

Food Research International

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

Dougherty,

Pedersen,

Forero-Junco

et al. 2024

Preprint

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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 phyllosphereErwiniaandPseudomonasstrains, 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 relatedPseudomonasphages 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 theErwiniajumbo-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.

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Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages

Cited by 5 publications

References 127 publications

Coevolutionary analysis of Pseudomonas syringae–phage interactions to help with rational design of phage treatments

Coevolutionary analysis of Pseudomonas syringae–phage interactions to help with rational design of phage treatments

Bacterial community dynamics and metabolic functions prediction in white button mushroom (Agaricus bisporus) during storage

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

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