ý.,,: V. ý ýý . - Nottingham eTheses - University of Nottingham

identification was made based on 153 bp of sequence and therefore the identification is
considered to be of low confidence. Isolate 583 showed a 94.7% similarity to an
unspeciated Psychrobacter sp. (AJ272303). Isolates 213 had a sequence similarity with
an unspeciated Halomonas sp. (AB016049) of 97.2% from a sequence length of 179bp.
Isolate 466 showed no close similarity to any sequence in the database for the 567bp
entered. Therefore, isolate 466 will require further investigation to provide an accurate
identification.
Growth media Isolate 302 Isolate 33
Fluorescens Agar +
-
CFC Agar + +
Table 5.2 -
Growth results for suspected pseudomonad species isolates on
pseudomonad selective agar and fluorescein selective agar.
5.2.3 -
Phylogenetic tree
16S rDNA sequences for each of the 19 AFP active bacterial isolates from this
study were aligned and analysed against the electropherograms from the sequencing
results (see chapter 2). The consensus sequences for each of the 19 isolates were then
compared against the Genbank nucleotide database and the nearest known phylogenetic
relatives for each isolate were determined (Table 5.3). Only 13 of the isolates had
sufficient sequence length for analysis, which was determined as being over 800 bp of
contiguous sequence. Therefore, isolates 494 (153bp), 213 (179bp), 492 (408bp), 466
(567bp) and 5ice3 (277bp) could not be included in the alignment. Also removed was
isolate 47 as although it comprised 1182bp of sequence, that sequence was not
contiguous, it included a 300bp `gap' in the middle and so was not of sufficient
contiguous length for alignment. An 887 bp consensus sequence for each of the
remaining 13 isolates were re-aligned with the sequences of the nearest known relatives
using PileUp (GCG package), which aligns the sequences using progressive pairwise
alignment. This was the shortest contiguous sequence length in the analysis. The same
887 bp region was used for all isolates to enable an accurate phylogeny to be calculated.
A total of 18 published species were aligned (Table 5.3) these included species that Nt ere
putatively related to the 6 isolates which could not be included in the alignment. Isolate
494 was identified as Sphingomonas sp, which is the only identification belonging to a
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