High genomic diversity of novel phages infecting the plant pathogen Ralstonia solanacearum, isolated in Mauritius and Reunion islands

Abstract

Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is among the most important plant diseases worldwide, severely affecting a high number of crops and ornamental plants in tropical regions. Only a limited number of phages infecting R. solanacearum have been isolated over the years, despite the importance of this bacterium and the associated plant disease. The antibacterial effect or morphological traits of these R. solanacearum viruses have been well studied, but not their genomic features, which need deeper consideration. This study reports the full genome of 23 new phages infecting RSSC isolated from agricultural samples collected in Mauritius and Reunion islands, particularly affected by this plant bacterial pathogen and considered biodiversity hotspots in the Southwest Indian Ocean. The complete genomic information and phylogenetic classification is provided, revealing high genetic diversity between them and weak similarities with previous related phages. The results support our proposal of 13 new species and seven new genera of R. solanacearum phages. Our findings highlight the wide prevalence of phages of RSSC in infected agricultural settings and the underlying genetic diversity. Discoveries of this kind lead more insight into the diversity of phages in general and to optimizing their use as biocontrol agents of bacterial diseases of plants in agriculture.

Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy Against the Phytopathogen<em> Ralstonia solanacearum</em>

“…The latter could be indicative of their common origin, R. solanacearum contaminated river water samples in Spain, although from three different regions geographically distant from each other, and different years of isolation. Their genomes exhibited low similarity to other phages infecting Ralstonia spp., mostly from Asia were the first Ralstonia phages were reported and also from Africa, in both cases mostly isolated against R. pseudosolanacearum, the species more prevalent under field conditions in these two continents [4,49,50], except for one Asian Ralstonia sp. phage, DU_RP_I and three African phages recently reported, RsoP1EGY, P-PSG-11 and P-PSG-11-1 [46,47].…”

“…2.5.3. Phylogenetic analysis Phylogenetic analysis was performed with the whole genomes of the three river water European phages and a selection of their 26 closest viruses belonging to Autographiviridae family (formerly Podoviridae) able to infect either R. solanacearum (three African phages [46,47], one American [48] and one Asian (accession number: MF979559) or the closely related species R. pseudosolanacearum (21 phages from diseased plants, soil or irrigation water isolated from Africa (14) [49] and Asia (7) [50][51][52]). A genome-based phylogeny was generated using VICTOR [53], intergenomic distances were calculated with the Genome BLAST Distance Phylogeny (GBDP) d0 formula for nucleotidic sequences.…”

“…The phylogenetic tree based on genomic distances of phages using VICTOR showed two clusters (Figure 6). In the upper cluster, all the African phages of R. pseudosolanacearum from plant, soil and water samples from Mauritius and Reunion islands [49] and the Asian phage RpY1 from Korean soil [52] were grouped. In the lower cluster, there were most of the Asian R. pseudosolanacearum phages and the only R. solanacearum American phage from Brazilian soil; in a subcluster, there were the three European R. solanacearum water phages (intergenomic similarity > 99%) together with the Egyptian R. solanacearum soil RsoP1EGY phage (intergenomic similarity ranging from 99 to 98.5%, depending on the phage), more distant were located the Asian Ralstonia sp.…”

Genomic Analysis of the First European Bacteriophages with Depolymerase Activity and Biocontrol Efficacy against the Phytopathogen Ralstonia solanacearum

“…Phylogenetic analysis was performed with the whole genomes of the three river water European phages and a selection of their 26 closest viruses belonging to the Autographiviridae family (formerly Podoviridae) able to infect either R. solanacearum (three African phages [46,47], one American [48] and one Asian (accession number: MF979559) or the closely related species R. pseudosolanacearum (21 phages from diseased plants, soil or irrigation water isolated from Africa (14) [49] and Asia (7) [50][51][52]).…”

“…The phylogenetic tree based on genomic distances of phages using VICTOR showed two clusters (Figure 6). In the upper cluster, all the African phages of R. pseudosolanacearum from plant, soil and water samples from Mauritius and Reunion islands [49] and the Asian phage RpY1 from Korean soil [52] were grouped. In the lower cluster were most of the Asian R. pseudosolanacearum phages and the only R. solanacearum American phage from Brazilian soil; in a subcluster were the three European R. solanacearum water phages (intergenomic similarity > 99%) together with the Egyptian R. solanacearum soil RsoP1EGY phage (intergenomic similarity ranging from 99 to 98.5%, depending on the phage), and more distant phages were located the Asian Ralstonia sp.…”