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

contain contaminants. If the profiles were contaminated they may show a closer
similarity to each other.
6.3.2.4.5. -
16S rRNA operon heterogeneity
Lastly, sequence heterogeneity within multiple 16S rRNA operons can lead to a
biased reflection of microbial diversity (van Wintzingerode et al., 1997). As
demonstrated by figures 6.1 and 6.2, most of the AFP active species studied as pure
culture DGGE profiles demonstrate more than one copy of the rRNA gene. Multiple rrn
copies have been identified in many bacterial species (Condon et al., 1995, Fancily et al..
1995; Nübel et al., 1996; Afseth & Mallavia, 1997; Lin & Tseng, 1997, Fegatella et al.,
1998; Ueda et al., 1999; Klappenbach et al., 2000; Klappenbach et al., 2001: Moreno ct
al., 2002). Farrelly et al. (1995) showed that genomic properties such as genome size and
rrn gene copy number can have an effect on PCR amplification efficiencies. Nicolaisen
and Ramsing (2002) have suggested that it is important to evaluate any gene used in
DGGE analysis for the presence of multiple copies of that gene before it can be used
effectively in community fingerprinting. The number of rRNA operons varies
significantly between taxa, for example the pathogenic bacteria Rickettsia prowa: keii
only has one copy, whereas the Escherichia coli has seven copies and Clostridium
paradoxum possess 15 copies (Klappenbach et al., 2001). It is generally assumed that
multiple copies of rRNA operons in prokaryotes are indicative of high growth rates
(Farrelly et al., 1995), however, inactivation of operons in multiple copy number species
shows marginal impact on growth rates, and species with a single copy still have short
doubling rates (Condon et al., 1995, Klappenbach et al.. 2001). It has been suggested
that the number of rRNA operons may indicate the ability of a bacterium to adapt to
favourable changes in growth conditions by the rapid synthesis of ribosomes (Condon et
al., 1995). Klappenbach et al. (2000) demonstrated this, showing direct correlation
between the rates at which a variety of phylogenetically diverse bacterial species respond
to changes in resource availability and the number of rRNA genes in the genome,
suggesting that the number of rRNA operons in a bacterial genome represents an adaptive
strategy to changing resource availability. It was therefore considered that Antarctic
bacterial species should contain multiple copies of the 16S rRNA gene as the`, have to
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