Figure captions
Figure 1. Rarefaction curves showing a near saturation of
bacterial sampling.
Each curve represents the mean of 1000 replicates. Data of 95%
confidence intervals are displayed with discontinuous lines.
Figure 2. Phylogenetic relationships of sugar beet-associatedPseudomonas .
Isolates from Oxford and Auckland are differentiated by blue and red
colors, respectively. Six reference Pseudomonas species were
included in the analysis. Asterisks indicate the few Oxford isolates in
the Auckland cluster, and vice versa.
Figure 3. Comparative analysis of Pseudomonas isolated
from Oxford and Auckland
- Clonal frame output displayed as an unrooted network, indicating the
origination of isolation. Distance was calculated using the NJ method
with Kimura 2 correction. Sizes of the circles are proportional to the
number of isolates.
- Multi-dimensional scaling plot showing separation ofPseudomonas from Oxford (blue) and Auckland (green).
- Nucleotide and amino acid polymorphism of the concatenated sequences
by location.
- Simpson’s index of diversity (1-D) calculated on the basis of unique
STs and OTUs clustered at the level of 0.06. Error bars are 95% CIs.
Figure 4. Evidence of recombination and structure of the Oxford
and Auckland subpopulations.
- Recombination breakpoints were detected using the method of GARD.
Results of the Kishino-Hasegawa (KH) test are shown below the two
detected breakpoints.
- Distribution of the six “ancestral” genotypes revealed by STRUCTURE
analysis.
- Individual isolates sharing ancestry for the Oxford and Auckland
subpopulations.
Figure 5. Principal component analysis showing correlations
between genotypes and phenotypes.
Figure 6. Genotypic relatedness of carbon source utilization
(A) and the role of individual substrate in separating pseudomonads from
Oxford and Auckland (B).
- Canonical analysis of principal coordinates (CAP) based on a Euclidean
distance similarity matrix generated from the Biolog and MLSA data.
The six “ancestral” populations revealed by STRUCTURE analysis are
indicated as A to E, while X denotes the other ancestral types. Only
carbon substrates with r value larger than 0.8 are shown. A to
E denotes the six an
- Ratio of the mean value of bacterial growth
(A660 ) on each carbon source was calculated for
isolates from Oxford and Auckland. The carbon substrates are listed iny -axis in order of their location in the Biolog GN2 MicroPlate
from A2 to H12 labelled from number 1 to 95. Red circles denote the
eight carbon substrates of strong correlation with genotypes (Fig.
6B).
Figure 7. An unrooted phylogenetic tree showing the association
of urocanate utilization with genotypes.
The capability of bacterial growth on histidine (His) and urocanate
(Uro) are marked in four different colours. Number of isolates showing
the same phenotype is provided in a table below the tree, and percentage
of each phenotype in the Auckland, Oxford and total population is shown
in parenthesis.