Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species

Abstract

BackgroundThe increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants.ResultsWe used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species.ConclusionsTogether, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2413-z) contains supplementary material, which is available to authorized users.

Técnicas para el aislamiento, identificación y caracterización molecular de cepas de Ralstonia solanacearum relacionadas a Moko del plátano

“…Existe una alta variabilidad dentro de la especie, por lo que R. solanacearum es considerada una "especie complejo", abreviado como RSSC por sus siglas en inglés "Ralstonia solanacearum species complex" (Safni et al, 2014;Prior et al, 2016). Una especie complejo es definida como un grupo de aislados relacionados cercanamente, cuyos miembros individuales pueden representar más de una especie (Fegan y Prior, 2005).…”

“…Una especie complejo es definida como un grupo de aislados relacionados cercanamente, cuyos miembros individuales pueden representar más de una especie (Fegan y Prior, 2005). R. solanacearum tiene una amplia distribución mundial y un alto número de plantas hospedantes, que incluye cientos de plantas de al menos 54 familias botánicas, tanto dicotiledóneas como monocotiledóneas (Prior et al, 2016). Muchas de las especies vegetales afectadas son cultivos agrícolas estratégicos which make evident that Multiplex can result in incorrect conclusions.…”

“…A species complex is defined as a group of closely-related isolations, the individual members of which can represent more than one species (Fegan and Prior, 2005). R. solanacearum has a wide global distribution and a high number of host plants, which include hundreds of plants from at least 54 botanical families, both dicotyledonous and monocotyledonous (Prior et al, 2016). Many of the plant species affected are strategic crops or important subsistence foods.…”

“…There is a high variability within the species, therefore R. solanacearum is considered a "species complex", abbreviated as RSSC, for "Ralstonia solanacearum species complex" (Safni et al, 2014;Prior et al, 2016). A species complex is defined as a group of closely-related isolations, the individual members of which can represent more than one species (Fegan and Prior, 2005).…”

“…Since R. solanacearum makes up a heterogenous group of strains with a high genetic and phenotypic diversity, its classification has been under constant reconsideration for 50 years (Hayward, 1964;Fegan and Prior, 2005;Safni et al, 2014;Prior et al, 2016). Classification into biovars does not reflect the genetic background of the strains, so a genetic classification scheme is currently used, hierachically organized into the categories of phylotypes and sequevars (Fegan and Prior, 2005;Prior et al, 2016 Hayward, 2001;Champoiseau et al, 2009).…”