Differentiation of Pseudomonas solanacearum, Pseudomonas syzygii, Pseudomonas pickettii and blood disease bacterium by partial 16S rRNA sequencing: construction of oligonucleotide primers for sensitive detection by polymerase chain reaction.
The sequence of a 292 bp segment of the DNA encoding 16S rRNA (corresponding to positions 44-337 of the Escherichia coli 16S rRNA sequence) was determined for each of 40 P. solanacearum, 4 banana blood disease bacterium (Pseudomonas sp.) (BDB), 3 P. syzygii and 2 P. pickettii strains. Phylogenetic relationships derived from comparison of these sequences to each other, and to equivalent 16S rRNA gene sequences from other bacteria present in the EMBL databank, conformed well with those obtained previously by DNA-DNA/rDNA hybridization experiments. The 16S rRNA sequence of the BDB was identical over the 292 bp to 1 of the 4 sequence groups of P. solanacearum, suggesting that these pseudomonads are more closely related to each other than to P. syzygii or P. pickettii. Sequence data comparisons allowed construction of an oligonucleotide specific for P. solanacearum, P. syzygii and the BDB. Use of the specific oligonucleotide with a non-specific oligonucleotide in the polymerase chain reaction enabled 1-10 cells of bacteria in this group to be detected after 50 rounds of amplification by visualizing a 287-288 bp product on agarose gels.