Jumbo Bacteriophages Are Represented Within an Increasing Diversity of Environmental Viruses Infecting the Emerging Phytopathogen, Dickeya solani

Abstract

Dickeya species are economically important phytopathogens widespread in mainland Europe that can reduce crop yields by 25%. There are no effective environmentally-acceptable chemical systems available for diseases caused by Dickeya. Bacteriophages have been suggested for use in biocontrol of these pathogens in the field, and limited field trials have been conducted. To date the majority of bacteriophages capable of infecting Dickeya solani, one of the more aggressive species, are from the same family, the Ackermannviridae, many representatives of which have been shown to be unsuitable for use in the field due to their capacity for generalized transduction. Members of this family are also only capable of forming individual plaques on D. solani. Here we describe novel bacteriophages from environmental sources isolated on D. solani, including members of two other viral families; Myoviridae and Podoviridae, most of which are capable of forming plaques on multiple Dickeya species. Full genomic sequencing revealed that the Myoviridae family members form two novel clusters of jumbo bacteriophages with genomes over 250 kbp, with one cluster containing phages of another phytopathogen Erwinia amylovora. Transduction experiments showed that the majority of the new environmental bacteriophages are also capable of facilitating efficient horizontal gene transfer, however the single Podoviridae family member is not. This particular phage therefore has potential for use as a biocontrol agent against multiple species of Dickeya.

Isolation and characterization of bacteriophages against virulent Aeromonas hydrophila

“…In this study, TEM analyses indicated that N21, W3 and G65 virions resembled a novel virulent Myoviridae phage, AHP-1, recently identified [28], consisting of an icosahedral head, and a contractile tail with a base plate and six long fibers, but with no "stars" or "prongs" at the base of the tail [29]. Although the virions of Ackermannviridae and Herelleviridae have been also reported to be of myovirus morphology, the tail spikes are the morphological markers of the family Ackermannviridae [29,30] and the phages of the family Herelleviridae always infect members of the phylum Firmicutes [31]. Therefore, phages N21, W3 and G65 are actually more closely related to the family Myoviridae.…”

Pseudomonas Phage PaBG—A Jumbo Member of an Old Parasite Family

“…The genome with the greatest similarity (63%) belongs to the jumbo phage Lu11, infecting Pseudomonas putida [42]. Other phages found with OrthoANIu were cyanobacterial Trichodesmium phage NCTB (NCBI Accession number LT598654) [43] with ANI 59.0%, Achromobacter phage Motura (Accession number MN094788) and several phages infecting Dickeya (vB_DsoM_AD1-MH460463, vB_DsoM_JA13-MH460460, vB_DsoM_JA29-MH460461, vB_DsoM_JA11-MH389777, vB_DsoM_JA33-MH460462) [44] and Erwinia The GC content of the genome sequence is indicated by the internal purple or yellow histograms. Full annotations and the GenBank file can be found in Supplementary File S1 and Supplementary Table S2.…”

“…The genome with the greatest similarity (63%) belongs to the jumbo phage Lu11, infecting Pseudomonas putida [42]. Other phages found with OrthoANIu were cyanobacterial Trichodesmium phage NCTB (NCBI Accession number LT598654) [43] with ANI 59.0%, Achromobacter phage Motura (Accession number MN094788) and several phages infecting Dickeya (vB_DsoM_AD1-MH460463, vB_DsoM_JA13-MH460460, vB_DsoM_JA29-MH460461, vB_DsoM_JA11-MH389777, vB_DsoM_JA33-MH460462) [44] and Erwinia (vB_EamM_Y3-KY984068, vB_EamM_Yoloswag-KY448244, vB_EamM_Alexandra-MH248138) [45,46]. Achromobacter phage Motura was attributed to the Mieseafarmvirus genus, while the other phages belong to unclassified groups.…”

Structural Analysis of Jumbo Coliphage phAPEC6

“…Available capsid structures of jumbo phages usually show a canonical phage HK97 major capsid protein (MCP)-fold [8]. Additionally, large viruses can display specific structures like long, wavy and curly tail fibers, which have rarely been observed [9], and their large genomes encode DNA polymerases, RNA polymerases, endolysins, chitinases, glycoside hydrolases, lyases and many other genes with unknown functions [3]. As such, they are a distinct and diverse group of phages, but only roughly 100 different jumbo phages have been isolated since their discovery [10,11], and only a few have been structurally classified [8,12].…”