title: Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Together, 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.
authors.affiliation: UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France. philippe.prior@cirad.fr.|Department of Plant Health and Environment (SPE), INRA, Paris, France. philippe.prior@cirad.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Prior
authors.affiliation: UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France. flt.ailloud@gmail.com.|Anses-Plant Health Laboratory (LSV), 7 chemin de l'IRAT, Saint-Pierre, La Réunion, France. flt.ailloud@gmail.com.
authors.forename: Florent
authors.initials: F
authors.lastname: Ailloud
authors.affiliation: Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA. bldalsing@wisc.edu.
authors.forename: Beth L
authors.initials: BL
authors.lastname: Dalsing
authors.affiliation: UMR PVBMT Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD, Saint Pierre, La Réunion, France. remenant.benoit@gmail.com.
authors.forename: Benoit
authors.initials: B
authors.lastname: Remenant
authors.affiliation: Department of Plant Health and Environment (SPE), INRA, Paris, France. borja.sanchez@uvigo.es.|Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain. borja.sanchez@uvigo.es.
authors.forename: Borja
authors.initials: B
authors.lastname: Sanchez
authors.affiliation: Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA. cza@plantpath.wisc.edu.
authors.forename: Caitilyn
authors.initials: C
authors.lastname: Allen
mesh_terms: D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D040901:Proteomics / Q000379:methods; D043368:Ralstonia solanacearum / Q000145:classification / Q000235:genetics* / Q000378:metabolism*
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