Comparison of 16S Ribosomal DNA Sequences of All Xanthomonas Species

Abstract

The phylogenetic relationships of all validly described species of the genus Xanthomonas and the type strain of Stenotrophomonas maltophilia were analyzed by sequencing and comparing 16s ribosomal DNAs (rDNAs). The two genera exhibited a mean sequence similarity value of 96.6%, corresponding to differences at 50 nucleotide positions on average. The species of the genus Xanthomonas exhibited relatively high levels of overall sequence similarity; the mean similarity value was 98.2%, which corresponds to an average of 14 mutual nucleotide differences. Within the genus Xanthomonas, a group containing Xanthomonas albilineans, Xanthomonas hyacinthi, Xanthornonas theicoh, and Xanthomonas translucens clustered apart from the main Xanthomonas core, whereas Xanthomonas sacchari formed a third phylogenetic lineage. Due to the very restricted variability in 16s rDNA sequences within the genusxanthomonas, rDNA signatures that have possible diagnostic value for differentiating the Xanthomonas species could not be determined with certainty. When sequence similarities were compared with DNA-DNA pairing data determined previously, there was only a limited correlation. This illustrates the different resolving powers of the techniques for determining phylogenetic hierarchies and for species delineation.The phytopathogenic specialization and the broad host range of members of the genus Xanthomonas (30) have made these microorganisms the subject of numerous taxonomic studies (for a review, see reference 59). Traditional methods used for the detection and identification of xanthomonads, such as biochemical (55), serological, and pathogenicity tests (3, 4, 5, 31, 45, 48), have been extended by molecular methods based on protein profiling (57, 60) and fatty acid analysis (7, 63).Currently, molecular approaches are being used increasingly in studies of the taxonomy and epidemiology of Xanthomonas species (15, 19). This has led to the development of different probes for detection and identification by hybridization or by PCR amplification (17, 18, 20, 21, 24, 25, 27, 32,40) and to analyses of the genetic structures of field populations (1,4,26, 28, 29).A polyphasic approach, such as the approach described by Vandamme et al. (54), could utilize all of these methods to contribute to the classification of the genus Xanthomonas. In practice, however, DNA reassociation, which provides a measure of the overall similarity of chromosomal genomes, is generally used for species delineation. This strategy has been used by Vauterin et al. (58), who recently reclassified the genus Xanthomonas and recognized and described 20 genomic species.Ideally, a comparison of the complete nucleotide sequences of genomes would probably be the most informative technique and thus the best method for determining the overall taxonomic relatedness of bacterial taxa. As sequencing entire genomes on a routine basis for taxonomy purposes is still impractical, techniques such as the sequencing of "molecular chronometers" like rRNA genes have been developed during the las...

Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences.

“…LeblondBourget et al (1996) analysed the 16S rDNA sequences Phylogenetic analysis of Xylella fastidiosa of 18 different species of Bifidobacterium and encountered a similarity level of 92-99 %. Similarly, a mean similarity value of 98n2 % was found within the genus Xanthomonas (Hauben et al, 1997). The high level of similarity to other strains of the 16S rDNA sequence of the pear strain (97n1-98n5 %) and the low DNA-DNA homology (below 20 %) found between the pear strain and a citrus strain obtained in this study resemble the results found for the genus Xanthomonas, in which some strains showing extremely low levels of DNA-DNA homology did not necessarily exhibit low levels of 16S rDNA similarity (Hauben et al, 1997).…”

“…Similarly, a mean similarity value of 98n2 % was found within the genus Xanthomonas (Hauben et al, 1997). The high level of similarity to other strains of the 16S rDNA sequence of the pear strain (97n1-98n5 %) and the low DNA-DNA homology (below 20 %) found between the pear strain and a citrus strain obtained in this study resemble the results found for the genus Xanthomonas, in which some strains showing extremely low levels of DNA-DNA homology did not necessarily exhibit low levels of 16S rDNA similarity (Hauben et al, 1997). A striking similarity of 95 % was found between the Xylella fastidiosa 16S rDNA sequence and that of Pseudomonas boreopolis, a bacterium isolated from the soil.…”

“…The 16S rDNA and 16S-23S spacer of Xylella fastidiosa strains sequenced in this study, as well as other Xylella fastidiosa sequences available in the GenBank database, were used for comparison. Sequences of Xanthomonas species representing the different cores obtained in the analysis of the 16S rDNA (Hauben et al, 1997) and 16S-23S spacer (E. R. Gonc: alves and Y. B.…”

Genetic diversity of Xanthomonas axonopodis pv. citri based on plasmid profile and pulsed field gel electrophoresis

“…Several molecular techniques have been used to study the population structure of different plant pathogens, including RAPD, Rep and Eric-PCR, RFLP, plasmid profile analysis, PCR amplification, SDS-PAGE, sequencing of the 16S rDNA, and pulsed field gel electrophoresis (Hartung and Civerolo, 1987;Lazo et al, 1987;Cooksey and Graham, 1989;Graham et al, 1990;Leach et al, 1990;Egel et al, 1991;Pruvost et al, 1992;Pooler et al, 1996;Hauben et al, 1997).…”

The effect of crop sequences on soil microbial, chemical and physical indicators and its relationship with soybean sudden death syndrome (complex of Fusarium species)

“…These primers amplify the intergenic transcribed spacer region (ITS) of ribosomal DNA and have been successfully used to amplify ascomycete and basidiomycete (White et al, 1990;Gardes & Bruns, 1993). For bacteria, a 5 pmol of PET-labelled 1087r (5'-CTC GTT GCG GGA CTT ACC CC-3') (Hauben et al, 1997), and 63f (5'-AGG CCT AAC ACA TGC AAG TC-3') (Marchesi et al, 1998) were used. These primers amplify the 16S ribosomal DNA and are widely used to characterize bacterial community structure.…”