Taxonomy and Phylogenetic Research on Ralstonia solanacearum Species Complex: A Complex Pathogen with Extraordinary Economic Consequences

Abstract

The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separation of Ralstonia solanacearum into three genomic species. Frequent name changes occurred as methodology transitioned from phenotypic, biochemical, and molecular studies, to genomics and functional genomics. The diversity, wide host range, and geographical distribution of the bacterial wilt pathogen resulted in its division into three species as genomic analyses elucidated phylogenetic relationships among strains. Current advances in phylogenetics and functional genomics now open new avenues for research into epidemiology and control of the devastating bacterial wilt disease.

Keywords: Bugtok disease; Granville Wilt of tobacco; Ralstonia solanacearum species complex; bacterial wilt; brown rot of potato; moko disease of banana; phylogenomic; plant bacteria; taxonomy; tomato wilt.

Figure 1

Timeline highlighting the major events based on taxonomic and phylogenetic studies of the bacterial wilt pathogen now in the Ralstonia solanacearum species complex (RSSC). Events in red boxes with red fonts indicate major changes in taxonomy and nomenclature. Blue boxes with blue fonts indicate milestones in the DNA-based analyses of RSSC. Purple boxes with purple fonts represent genomic advancements in understanding the diversity of multiple strains of RSSC. Bold labels with grey backgrounds indicate landmark taxonomic and genomic events. Landmark publications associated with each date are provided in the text associated with the date.

Figure 2

Phylogenetic relationships in the Ralstonia solanacearum species complex. Minimum spanning tree V2 was generated from concatenated sequences of six chromosomal housekeeping genes (adk, dnaA, gap, gdh, gyrB and rplB) and two megaplasmid genes (hrpB and egl) using GrapeTree software [75]. The number of compartments within a circle indicates the number of strains in the group. The number between any two lines is the distance between two strains calculated using the same software. The same strains were used in the ClonalFrame analyses. The details of the strains are provided in Supplementary Table S1. Note that reference strain GMI1000 originally isolated from French Guyana is in Phylotype I and clusters with strains of Asian origin.

Figure 3

Circa plot showing the presence of predicted genomic islands in representative strains for each Phylotype of the RSSC. Track 1 (outer circle) shows the relative size of respective genomes: Phylotype I (GMI1000), Phylotype II (CFBP2957), Phylotype III (CMR15) and Phylotype IV (PSI07). The Ch tag stands for the chromosome and the mp tag stands for the megaplasmid. Approximate size of the replicons are: CMR15: ch—3.59 Mb, mp—2 Mb; CFBP2957: ch—3.42 Mb, mp—2.2 Mb; PSI07: ch—3.52 Mb, mp—2.09 Mb; GMI1000: ch—3.71 Mb, mp—2.1 Mb. Track 2 shows the relative positions of predicted genomic islands in their respective genomes. Track 3 is a scatter plot showing the GC content of the virulence gene coding sequences in the genome. Track 4 is a ribbon plot showing the links between the genomic islands in each genome. The image was generated using supplemental data of Remenant, et al. [86]; Island Viewer 4 software was used to predict genomic islands present in the GMI1000 genome retrieved from NCBI GenBank genome database. The Circa plot was created with Circa software (http://omgenomics.com/circa).

Figure 4

Graphviz network representing the genealogy of Ralstonia solanacearum species complex (RSSC) strains, representing geographically distinct phylotypes, generated using ClonalFrame v 1.0 [104]. Eight genes (adk, dnaA, gap, gdh, gyrB, rplB, hrpB and egl) were concatenated and aligned using progressive MAUVE alignment plugin [105]. The aligned sequences were used as input for ClonalFrame. The strain numbers inside each circle correspond to strains listed in Supplemental Table S1. Circles without numbers represent an unknown parental node for strains in that phylotype. The circle with the heavy black border is the theoretical ancestral node for all phylotypes. Plant host images adjacent to each circle represent the hosts from which the strains were isolated. Gene sequences for each strain were extracted from the NCBI GenBank database.

Figure 5

Taxonomic revision of Ralstonia solanacearum species complex phylotypes into three species: R. pseudosolanacearum (origin: Asia and Africa), R. solanacearum (origin: America) and R. syzygii (origin: Indonesia).