Table 1.
Bacterial strains used in this study for biochemical characterization and pathogenicity tests.
Table 2.
LOPAT tests of eighteen local (Crete, Greece) P. viridiflava isolates along with P. viridiflava reference strain NCPPB1249 and other pseudomonads.
Table 3.
Comparison of P. viridiflava local isolates from different hosts found in the island of Crete and other fluorescent Pseudomonas species (Table 1) used in differential nutritional, biochemical and other tests.
Figure 1.
Agarose gel electrophoresis of BOX-PCR of 18 local P. viridiflava isolates.
Agarose gel electrophoresis of BOX-PCR amplification products from genomic DNA of 18 local P. viridiflava isolates. The molecular size marker is λ phage DNA digested with the restriction endonuclease PstI. The negative film filter was applied to the image of an ethidium bromide gel. Isolate codes are given over each lane.
Figure 2.
Phylogenetic trees of the local P. viridiflava isolates.
The construction of the dendrograms was based on A: BOX- and ERIC-PCR fingerprints (rep-PCR) and B: the combined gyrB, rpoD and rpoB gene sequences. The plant hosts are given next to the code number (PVXXX, see Table 1) of each isolate. The evolutionary history was inferred using the UPGMA method. The consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the isolates analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test is shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. All positions containing gaps and missing data were eliminated. There were a total of 2222 positions in the final dataset. Evolutionary analyses were conducted in MEGA5.
Table 4.
Local bacterial strains used in this study for gyrB, rpoD and rpoB phylogenetic analysis.
Figure 3.
P. viridiflava phylogenetic tree, utilizing gyrB sequences determined in this study along with sequences obtained from GenBank.
The evolutionary history was inferred using the Neighbor-Joining method. The bootstrap consensus tree inferred from 1500 replicates is taken to represent the evolutionary history of the taxa analyzed. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site. The analysis involved 52 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 740 positions in the final dataset. Evolutionary analyses were conducted in MEGA5. The host plant species is presented next to the code number (e.g. PVXXX) of each isolate.
Figure 4.
P. viridiflava phylogenetic trees, utilizing rpoD sequences along with sequences obtained from GenBank.
The evolutionary history was inferred using the Neighbor-Joining method. Tree construction and evolutionary distances were carried out as described in the Figure 2 legend. The analysis involved 32 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 513 positions in the final dataset. The methodology used for the evolutionary analysis, tree construction and other details are described in the Figure 3 legend.
Figure 5.
P. viridiflava phylogenetic trees, utilizing rpoB sequences along with sequences obtained from GenBank.
The evolutionary history was inferred using the Neighbor-Joining method. Tree construction and evolutionary distances were carried out as described in the Figure 2 legend. The analysis involved 27 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 741 positions in the final dataset. The methodology used for the evolutionary analysis, tree construction and other details are described in the Figure 3 legend.