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.
Highlights
The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity
Members of the Ralstonia solanacearum species complex (RSSC) can collectively infect over 250 hosts in 54 botanical families and include: R. solanacearum strains, which collectively infect a broad host range and are typically soil-borne; R. syzygii, a spittlebug-transmitted pathogen that causes Sumatra disease in cloves; and the Blood Disease Bacterium (BDB), an unclassified organism responsible for the pollinator-transmitted Blood Disease of bananas and plantains in the Philippines
Phenotypic diversity in the RSSC Safni et al, [21] analyzed the RSSC using phenotype microarrays and identified major variation in the core metabolisms both between and within phylotypes, which generally supported the idea that R. solanacearum can be divided into multiple species but no assay was able to provide clear distinction between the three proposed species
Summary
The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. 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. Thousands of genetically distinct strains within the Ralstonia solanacearum species complex (RSSC) cause bacterial wilt diseases in plants These bacteria colonize the xylem tissue of host plant vascular systems causing stunting, wilting, yield reduction, and death. The Sumatra disease pathogen, originally described as Pseudomonas syzygii, was placed in a separate species in the genus Ralstonia based on 16S sequences and DNA-DNA hybridization (DDH) data showing substantial divergence from R. solanacearum [8]. The DDH study that concluded R. syzygii should be placed in a separate species was based on a comparison with R. solanacearum K60T, a phylotype II strain that is quite phenotypically and genotypically divergent from R. syzygii, a member of phylotype IV
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
