Isolation and Characterization of a Novel Jumbo Phage from Leaf Litter Compost and Its Suppressive Effect on Rice Seedling Rot Diseases.

Ryota Sasaki,Shuhei Miyashita,Toshiyuki Fukuhara,Sugihiro Ando,Hideki Takahashi,Kumiko Ito

doi:10.3390/v13040591

Ryota Sasaki, Shuhei Miyashita + Show 4 more

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https://doi.org/10.3390/v13040591

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Abstract

Jumbo phages have DNA genomes larger than 200 kbp in large virions composed of an icosahedral head, tail, and other adsorption structures, and they are known to be abundant biological substances in nature. In this study, phages in leaf litter compost were screened for their potential to suppress rice seedling rot disease caused by the bacterium Burkholderia glumae, and a novel phage was identified in a filtrate-enriched suspension of leaf litter compost. The phage particles consisted of a rigid tailed icosahedral head and contained a DNA genome of 227,105 bp. The phage could lyse five strains of B. glumae and six strains of Burkholderia plantarii. The phage was named jumbo Burkholderia phage FLC6. Proteomic tree analysis revealed that phage FLC6 belongs to the same clade as two jumbo Ralstonia phages, namely RSF1 and RSL2, which are members of the genus Chiangmaivirus (family: Myoviridae; order: Caudovirales). Interestingly, FLC6 could also lyse two strains of Ralstonia pseudosolanacearum, the causal agent of bacterial wilt, suggesting that FLC6 has a broad host range that may make it especially advantageous as a bio-control agent for several bacterial diseases in economically important crops. The novel jumbo phage FLC6 may enable leaf litter compost to suppress several bacterial diseases and may itself be useful for controlling plant diseases in crop cultivation.

Highlights

Bacteriophages are viruses that infect bacteria and exploit the metabolic processes of the host to replicate their own genome
The jumbo Burkholderia phage FLC6 (Figure 1) was isolated from leaf litter compost, which is sometimes used in nursery soil for organic-farmed rice because it is known to suppress seedling rot
While organically farmed soils with a disease suppression effect have been shown to harbor more diverse and more robust bacterial structures than conventional commercial soils [37], polyvalent phages might contribute to maintaining a robust bacterial population, which can lead to the suppression of diseases

Summary

Introduction

Bacteriophages (phages) are viruses that infect bacteria and exploit the metabolic processes of the host to replicate their own genome. The host bacteria are generally lysed as a result of phage infection, thereby releasing the virions, while phages that convert to the lysogenic cycle do not lyse the host cells but instead become integrated into the host genome as prophages [1]. In Caudovirales, tailed phages with DNA genomes larger than 200 kbp are classified as “jumbo phages” [6]. The larger genomes of jumbo phages enable them to encode many more proteins than is possible for phages with smaller genomes, the functions of many jumbo phage genes remain to be elucidated. Some proteins encoded in the jumbo phage genome may compensate for the host proteins required for phage multiplication in the host bacteria, enabling jumbo phages to have a wider host range [6]. The wider host range of jumbo phages may make them especially advantageous as biocontrol agents against multiple bacterial diseases

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