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xiv LIST OF TABLES PAGE soil fungal communities at Baynesfield .................................................... 115 TABLE 4.4 ANOVA of soil fungal species richness (number of bands) and land treatment means at Mount Edgecombe ..................................................... 117 TABLE 5.1 Means (± sd) for selected physicochemical properties of soils collected at 0–5 cm depth from different land uses at Baynesfield Estate ................... 135 TABLE 5.2 Identity of 18S rRNA gene sequences from excised DGGE bands of soil fungal communities from different land uses at Baynesfield .................... 142 TABLE 5.3 ANOVA of species richness (number of bands produced using primer pair FR1GC/FF390) and land use means in the fungal communities at Baynesfield ............................................................................................... 144 TABLE 5.4 ANOVA and land use means of soil fungal species evenness (J) at Baynesfield Estate ..................................................................................... 145 TABLE 5.5 ANOVA and land use means of soil fungal species diversity (H′) at Baynesfield Estate ..................................................................................... 146 TABLE 5.6 Means (± sd) for selected chemical properties of soils collected at 0–5 cm depth from different land management practices at Mount Edgecombe... 149 TABLE 5.7 Identity of 18S rRNA gene sequences from excised DGGE bands of soil fungal communities from different land management practices at Mount Edgecombe ................................................................................................ 154 TABLE 5.8 ANOVA and land management means of soil fungal species richness (S) at Mount Edgecombe .................................................................................... 156 TABLE 6.1 Mean soil moisture content (%) of soils (0-5cm depth) under the different land uses at Baynesfield Estate ................................................................. 178 TABLE 6.2 Mean soil moisture content (%) of soils (0–5cm depth) under the different land management practices at Mount Edgecombe .................................... 185 TABLE 6.3 A non-parametric one-way analysis (Kruskal-Wallis test) of variation in catabolic richness under different treatments at Mount Edgecombe ........ 189 TABLE 7.1 A non-parametric one-way analysis (Kruskal-Wallis test) of variation in catabolic evenness (J) (turbidity distribution) of soil fungal communities
xv LIST OF TABLES PAGE under different land uses at Baynesfield Estate ........................................ 212 TABLE 7.2 A non-parametric one-way analysis (Kruskal-Wallis test) of variation in catabolic diversity (H′) of soil fungal communities (a composite of substrate richness and evenness) under different land uses at Baynesfield Estate ......................................................................................................... 212 TABLE A1 ANOVA of bacterial community species evenness and land use means at Baynesfield ............................................................................................... 279 TABLE A2 ANOVA and land treatment means (± sd) of the effects of sugarcane trash management on soil bacterial species richness, evenness and diversity at Mount Edgecombe .................................................................................... 279 TABLE B1 ANOVA of fungal community species evenness and land use means at Baynesfield ............................................................................................... 280 TABLE B2 ANOVA of soil fungal community species diversity and land use means at Baynesfield using the Shannon Weaver Diversity Index (H′) .................. 280 TABLE C1 Summary of the results of a Monte Carlo permutation test of CCA data on the effects of land use on the soil fungal communities at Baynesfield ..... 281 TABLE C2 Summary of the results of a Monte Carlo permutation test of CCA data on the effects of land management at Mount Edgecombe ............................. 281 TABLE D1 The substrates in the wells of a BIOLOG EcoPlate replicated three times across the plate (BIOLOG, 2008) ............................................................. 282 TABLE D2 MRPP of log-transformed data from Baynesfield bacterial functional diversity PCA (Figure 6.2) ........................................................................ 283 TABLE D3 Non-parametric one-way analysis (Kruskal-Wallis test) of catabolic richness (S) of soil bacterial communities (number of substrates utilized) under different land uses at Baynesfield Estate ........................................ 284 TABLE D4 Non-parametric one-way analysis (Kruskal-Wallis test) of catabolic evenness (J) (colour distribution) of soil bacterial communities under different land uses at Baynesfield Estate .................................................. 284 TABLE D5 Non-parametric one-way analysis (Kruskal-Wallis test) of catabolic functional diversity (H′) of soil bacterial communities (a composite of
Page 1 and 2: The Effects of Land Use and Managem
Page 3 and 4: i ABSTRACT The environmental impact
Page 5 and 6: iii communities from those under th
Page 7 and 8: v DECLARATION I hereby certify that
Page 9 and 10: vii TABLE OF CONTENTS PAGE Abstract
Page 11 and 12: ix TABLE OF CONTENTS PAGE 3.2.1 Sit
Page 13 and 14: xi TABLE OF CONTENTS 5.4.2 Effects
Page 15: xiii LIST OF TABLES PAGE TABLE 3.1
Page 19 and 20: xvii LIST OF TABLES PAGE evenness u
Page 21 and 22: xix LIST OF FIGURES PAGE in the pho
Page 23 and 24: xxi LIST OF FIGURES PAGE the differ
Page 25 and 26: xxiii LIST OF PLATES PAGE PLATE 3.1
Page 27 and 28: LSU Large subunit xxv mcrA Methyl-c
Page 29 and 30: Chapter 1 GENERAL INTRODUCTION Biod
Page 31 and 32: within ecosystem boundaries, to sus
Page 33 and 34: 2.1 INTRODUCTION Chapter 2 LITERATU
Page 35 and 36: Species interactions at the communi
Page 37 and 38: conditions in relatively few microh
Page 39 and 40: patches into a relatively homogeneo
Page 41 and 42: processes in soil because other mic
Page 43 and 44: communities can have the same index
Page 45 and 46: the Shannon index described below t
Page 47 and 48: of the plant community critically d
Page 49 and 50: such as season, year and field site
Page 51 and 52: Research evidence suggests that the
Page 53 and 54: mulch applications might result in
Page 55 and 56: Galdos et al. (2009), also working
Page 57 and 58: Levels of actinobacteria increased
Page 59 and 60: 2002b). In terrestrial ecosystems,
Page 61 and 62: Avrahami et al. (2002) studied the
Page 63 and 64: using both a macroscale and a micro
Page 65 and 66: 2.3.3.3 Pesticides The influence of
Page 67 and 68:
microbial storage products, they ca
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Prokaryote community analysis and e
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2.4.2 Molecular techniques Molecula
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assessed the efficiency of isolatio
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FIGURE 2.1 Schematic diagram of the
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within the V9 region could be used
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environmental samples containing hi
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2.4.2.2.3 Reverse transcription (RT
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that contain a linearly increasing
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methanotrophic communities in an ag
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2.4.2.2.7 Single strand conformatio
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level of resolution. It is a quanti
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these concepts has largely been mad
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Soil organic matter status and micr
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(Farmingham series) (Soil Classific
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3.2.5 PCR amplification of 16S rDNA
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(Bio-Rad Quantity One Instruction M
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evenness (J') (a measure of the equ
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Overall dissimilarities among the s
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CCA was used to show the effects of
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concur with those of other workers
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Axis 2 1.5 1.0 0.5 0.0 -0.5 -1.0 SA
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Analysis of evenness (J) at this si
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MRPP of Mount Edgecombe soils, whic
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CCA analysis showed the effects of
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treatments across the gels were mor
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TABLE 3.12 Two-way ANOVA of the mai
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They suggested that the bright band
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eduction in genetic diversity, whic
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the land use types at this site. Re
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assessment of the DGGE gels indicat
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organic matter under long-term suga
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Chapter 4 EFFECTS OF LAND USE AND M
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4.2 MATERIALS AND METHODS Methods w
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everse primer and 0.5 µM of NS1 fo
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4.3.2 PCR-DGGE analysis of fungal c
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FIGURE 4.2 Quantity One diagram of
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TABLE 4.3 ANOVA of species richness
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TABLE 4.4 ANOVA of soil fungal spec
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Hantula, 2000). The approach used i
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18-43% suggested by Vainio and Hant
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decomposers of dead organic matter
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and of the whole community. Diversi
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Chapter 5 DNA-DERIVED ASSESSMENTS O
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Subsamples for DNA extraction and C
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cycles comprising a denaturing (95
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The eluted DNA was used for PCR amp
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TABLE 5.1 Means (± sd) for selecte
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5.3.2 PCR-DGGE analysis of fungal c
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PLATE 5.3 DGGE gel (denaturing grad
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Page 171 and 172:
Soil fungal community composition u
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TABLE 5.4 ANOVA and land use means
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CCA 2 (30.4%) 3.0 2.0 1.0 0.0 -1.0
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TABLE 5.6 Means (± sd) for selecte
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PC2 (16.0%) 0.6 0.4 0.2 0.0 -0.2 -0
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A DGGE gel (denaturing gradient 35-
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closely clustered of all the treatm
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effects and 11.2% of total variance
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a resurgence in interest, particula
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sequencing studies. This was regard
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soils (see below). This was possibl
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plant species, which may affect mic
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little is known of the effects of a
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significantly affected soil fungal
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and mixed DNA templates among the s
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Graham (2003) used BIOLOG GN microp
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A method adapted from Govaerts et a
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6.2.6 Statistical analysis BIOLOG s
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6.3.2 Bacterial catabolic (function
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Testing by MRPP of the PCA data of
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RDA 2 (27.5%) 1.0 0.8 0.6 0.4 0.2 0
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TABLE 6.2 Mean soil moisture conten
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PC2 (17.3%) 1.0 0.8 0.6 0.4 0.2 0.0
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TABLE 6.3 A non-parametric one-way
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0.8 0.6 0.4 0.2 0.0 -0.2 -0.4 -0.6
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populations. This was confirmed by
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observed in pine soil. Less litter
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and evenness. In this study, the re
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more closely clustered together tha
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soil organic C content. In the pres
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Chapter 7 EFFECTS OF LAND USE AND M
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7.2.2 Chemical analysis Chemical an
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obtained from the substrate-contain
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AWCD at OD650 0.40 0.35 0.30 0.25 0
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1.0 0.5 0.0 -0.5 -1.0 10A 6G 8F 12G
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RDA results, showing the relationsh
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7.3.3 Analyses of soils at the Moun
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Log [X+1]-transformed PCA data (Fig
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RDA2 (35.8%) FIGURE 7.9 RDA ordinat
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7.4 DISCUSSION It is important to t
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nutrients, which could account for
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sugarcane soils were more acidic (p
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7.4.2 Fungal catabolic (functional)
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the conditions prevailing under a s
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(which affected the pH and the leve
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Notwithstanding the generally accep
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ECEC and P, with exchange acidity a
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8.3 CRITICAL EVALUATION OF THE RESE
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8.3.2 Evaluation of the PCR-DGGE pr
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8.4.1 Baynesfield Estate The benefi
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This would help reduce the soil deg
Page 273 and 274:
REFERENCES Aboim, M.C.R., Coutinho,
Page 275 and 276:
Benckiser, G., Schnell, S., 2007. B
Page 277 and 278:
Carrera, L.M., Buyer, J.S., Vinyard
Page 279 and 280:
Dilly, O., Bloem, J., Vos, A., Munc
Page 281 and 282:
Garbeva, P., van Veen, J.A., van El
Page 283 and 284:
Graham, M.H., Haynes, R.J., Meyer,
Page 285 and 286:
Heuer, H., Kroppenstedt, R.M., Lott
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and diversity of microorganisms in
Page 289 and 290:
sequencing, in silico- and microarr
Page 291 and 292:
Maharning, A.R., Mills, A.A.S., Adl
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Mitchell, J.I., Zuccaro, A., 2006.
Page 295 and 296:
for phosphorus efficiency in the ac
Page 297 and 298:
Poll, C., Thiede, A., Wermbter, N.,
Page 299 and 300:
Ros, G.H., Hanegraaf, M.C., Hofflan
Page 301 and 302:
Smalla, K., Wachtendorf, U., Heuer,
Page 303 and 304:
Torsvik, V., Salte, K., Sørheim, R
Page 305 and 306:
Wang, G., Liu, J., Qi, X., Jin, J.,
Page 307 and 308:
BAYNESFIELD ESTATE APPENDIX A TABLE
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BAYNESFIELD ESTATE APPENDIX C TABLE
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BAYNESFIELD ESTATE 1.5 1.0 0.5 0.0
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TABLE D5 Non-parametric one-way ana
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TABLE D8 Non-parametric one-way ana
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APPENDIX E TABLE E1 The substrates
Page 319 and 320:
TABLE E3 Non-parametric one-way ana
Page 321 and 322:
TABLE E6 Non-parametric one-way ana
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