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LIST OF FIGURES
FIGURE 2.1 Schematic diagram of the PCR reaction
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(http://people.uwec.edu/piercech/tox/Techniques.htm). ............................. 47
FIGURE 2.2 Schematic diagram of PCR-DGGE showing steps in the procedure from: (i)
DNA extraction to (ii) PCR of rRNA genes to (iii) the separation of DNA
fragments with a GC clamp in a denaturing gel (Crump, 2005). ................ 56
FIGURE 3.1 A PCA biplot (standardised and centred data) of sites and soil variables for
subsamples of fields with various land uses at Baynesfield Estate. ............ 76
FIGURE 3.2 Plot of samples (classified by land use) and selected soil variables along the
first two axes of a CCA of the effect of soils on bacterial composition (band
presence) at Baynesfield. ............................................................................ 77
FIGURE 3.3 Non-metric multidimensional scaling (NMS) site plot (rotated by PCA) of
bacterial populations (presence/absence of bands) at Baynesfield. NMS
stress = 0.07963. ......................................................................................... 81
FIGURE 3.4 Plot of bands in the NMS ordination, generated by DGGE of soil bacterial
communities (Figure 3.3) at Baynesfield. ................................................... 82
FIGURE 3.5 Plot of samples and soil variables along the first two axes of a standardised
and centred PCA of different land treatments at Mount Edgecombe. ........ 86
FIGURE 3.6 Plot of samples (classified by land treatment) and soil variables along the
first two axes of a CCA of the effect of selected soil variables on bacterial
composition (band presence) at Mount Edgecombe. .................................. 87
FIGURE 3.7 NMS two-dimensional plot (rotated by PCA) of bacterial communities
(presence or absence of bands) under four land treatments at Mount
Edgecombe. NMS stress = 0.00049. ........................................................... 90
FIGURE 4.1 Schematic representation of annealing sites of PCR primers in the region
coding for fungal SSU rDNA. The relative positions of the primers and
their direction of extension are indicated by arrows (after Vainio and
Hantula, 2000). .......................................................................................... 106
FIGURE 4.2 Quantity One diagram of DGGE gel (Plate 4.2) of Baynesfield soil fungal
18S rDNA banding patterns produced with primer pair FR1GC/NS1. ..... 111
FIGURE 4.3 Quantity One diagram of DGGE gel (Plate 4.3) showing bands not visible