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x TABLE OF CONTENTS PAGE 4.3.2 PCR-DGGE analysis of fungal communities ............................................ 109 4.3.3 Statistical analysis of fungal communities at Baynesfield Estate (site 1) . 113 4.3.4 Statistical analysis of fungal communities at Mount Edgecombe (site 2) 115 4.4 DISCUSSION ........................................................................................................ 117 4.4.1 Effects of different land uses and management practices on soil fungal community structure at the experimental sites .......................................... 121 4.4.1.1 Baynesfield Estate (site 1) ........................................................ 121 4.4.1.2 Mount Edgecombe (site 2) ........................................................ 124 4.4.2 Overall assessment of the DGGE analysis of the soil fungal communities from both sites ........................................................................................... 125 4.5 CONCLUSIONS .................................................................................................... 125 Chapter 5: DNA-DERIVED ASSESSMENTS OF FUNGAL COMMUNITY COMPOSITION IN SOILS UNDER DIFFERENT LAND USES AND MANAGEMENT PRACTICES ........................................................................ 127 5.1 INTRODUCTION ................................................................................................. 127 5.2 MATERIALS AND METHODS ........................................................................... 128 5.2.1 Study sites and soil sampling .................................................................... 128 5.2.2 Chemical analysis ..................................................................................... 129 5.2.3 DNA extraction, purification and quantification....................................... 129 5.2.4 PCR amplification of fungal 18S rDNA fragments .................................. 130 5.2.5 Community fingerprinting by DGGE ....................................................... 131 5.2.6 Data analysis ............................................................................................. 132 5.2.7 Statistical analysis ..................................................................................... 132 5.2.8 DNA sequencing analysis of DGGE bands .............................................. 132 5.3 RESULTS .............................................................................................................. 134 5.3.1 Analyses of soils at the Baynesfield experimental site (site 1) ................. 134 5.3.2 PCR-DGGE analysis of fungal communities ............................................ 137 5.3.3 Soil fungal community structure at Baynesfield Estate (site 1) ................ 138 5.3.4 Analyses of soils at the Mount Edgecombe site (site 2) ........................... 148 5.3.5 Soil fungal community structure at Mount Edgecombe (site 2) ............... 151 5.4 DISCUSSION ........................................................................................................ 158 5.4.1 Effects of different land uses on soil fungal community structure at Baynesfield Estate ..................................................................................... 161
xi TABLE OF CONTENTS 5.4.2 Effects of different management practices on soil fungal community PAGE structure at the Mount Edgecombe experimental site ............................... 167 5.5 CONCLUSIONS .................................................................................................... 170 Chapter 6: EFFECTS OF LAND USE AND MANAGEMENT ON SOIL BACTERIAL CATABOLIC DIVERSITY ............................................................................... 172 6.1 INTRODUCTION ................................................................................................. 172 6.2 MATERIALS AND METHODS ........................................................................... 174 6.2.1 Study sites and soil sampling .................................................................... 174 6.2.2 Chemical analysis ..................................................................................... 174 6.2.3 Soil moisture ............................................................................................. 174 6.2.4 CLPP using BIOLOG microplates ............................................................ 174 6.2.5 Data analysis ............................................................................................. 176 6.2.6 Statistical analysis ..................................................................................... 177 6.3 RESULTS .............................................................................................................. 178 6.3.1 Analyses of soils at the Baynesfield experimental site ............................. 178 6.3.2 Bacterial catabolic (functional) diversity at Baynesfield .......................... 179 6.3.3 Analyses of soils at the Mount Edgecombe site ........................................ 184 6.3.4 Bacterial catabolic (functional) diversity at Mount Edgecombe ............... 185 6.4 DISCUSSION ........................................................................................................ 191 6.4.1 Bacterial catabolic (functional) diversity at Baynesfield Estate ............... 192 6.4.2 Bacterial catabolic (functional) diversity at Mount Edgecombe ............... 197 6.5 CONCLUSIONS .................................................................................................... 201 Chapter 7: EFFECTS OF LAND USE AND MANAGEMENT ON SOIL FUNGAL CATABOLIC DIVERSITY ............................................................................... 203 7.1 INTRODUCTION ................................................................................................. 203 7.2 MATERIALS AND METHODS ........................................................................... 204 7.2.1 Study sites and soil sampling .................................................................... 204 7.2.2 Chemical analysis ..................................................................................... 205 7.2.3 Soil moisture ............................................................................................. 205 7.2.4 CLPP using BIOLOG microplates ............................................................ 205 7.2.5 Data analysis ............................................................................................. 206 7.2.6 Statistical analysis ..................................................................................... 207 7.3 RESULTS .............................................................................................................. 208
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: ix TABLE OF CONTENTS PAGE 3.2.1 Sit
Page 15 and 16: xiii LIST OF TABLES PAGE TABLE 3.1
Page 17 and 18: xv LIST OF TABLES PAGE under differ
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
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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
Page 141 and 142:
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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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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
Page 213 and 214:
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
Page 265 and 266:
8.3 CRITICAL EVALUATION OF THE RESE
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8.3.2 Evaluation of the PCR-DGGE pr
Page 269 and 270:
8.4.1 Baynesfield Estate The benefi
Page 271 and 272:
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
Page 287 and 288:
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
Page 293 and 294:
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
Page 317 and 318:
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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