The genus Xanthomonas currently comprises 27 species with validly published names that are important crop and horticultural pathogens. We have constructed a phylogram from alignment of gyrase B (gyrB) sequences for all xanthomonad species, both to indicate inter-species relatedness and as an aid for rapid and accurate species-level identification. The phylogeny indicated a monophyletic group, with X. albilineans and X. sacchari as the most ancestral species. Three species, X. hyacinthi, X. translucens and X. theicola, formed an early-branching group. Three clades were supported by high bootstrap values: group 1 comprised X. cucurbitae, X. cassavae and X. codiaei; group 2 comprised X. arboricola, X. campestris, X. populi, X. hortorum, X. gardneri and X. cynarae; group 3 contained the remaining species, within which two further clades, supported by a 100 % bootstrap value, were identified. Group 3A comprised X. axonopodis, X. euvesicatoria, X. perforans and X. melonis, together with X. alfalfae, X. citri and X. fuscans, whose names were recently validly published. Group 3B contained the monocot pathogens X. vasicola and X. oryzae. Two recently identified species, X. cynarae and X. gardneri, were poorly discriminated and were related closely to X. hortorum. Three species, X. perforans, X. euvesicatoria and X. alfalfae, had identical gyrB sequences. Partial sequencing of a further five genes from these species found only minor sequence differences that confirmed their close relatedness. Although branch lengths between species varied, indicating different degrees of genetic distinctiveness, the majority (n=21) were well-differentiated, indicating the utility of the method as an identification tool, and we now use this method for routine diagnosis of xanthomonad species.
The relationships of the genus Azotobacter, Azomonas macrocytogenes and the genus Pseudomonas were revealed by comparative analysis of partial 16S rRNA and atpD, carA and recA gene sequences and as concatenated nucleotide and peptide sequences. Sequence similarities of Azotobacter species and Azomonas macrocytogenes indicated that these may be considered to be synonyms at the molecular level. In addition, these species show an intimate relationship with species of Pseudomonas, especially P. aeruginosa (the type species of the genus). In terms of the current circumscription of the genus Pseudomonas, Azotobacter and Azomonas macrocytogenes should be considered for amalgamation with Pseudomonas. Azotobacter and Azomonas comprise nitrogen-fixing strains with large pleomorphic cells that form cysts, and peritrichous flagella insertion; characteristics not included in the current circumscription of Pseudomonas. The data are discussed in the light of whether lateral transfer of genes could be involved in the determination of significant morphological characteristics, thus leading to a problem that may be encountered more frequently: how to resolve classification of taxa based on conserved sequences with those based on their phenotype. More fundamentally, the results illuminate problems that will increasingly be encountered: by what criteria can taxa be delineated, what are the most appropriate methods for classification, and what are the proper assumptions of bacterial classification?