The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface

The Rhizosphere: Biochemistry and Organic Substances at the Soil-Plant Interface, Second Edition......Page 8
Preface to the First Edition......Page 10
Preface to the Second Edition......Page 12
The Editors......Page 13
Contributors......Page 14
Table of Contents......Page 16
I. INTRODUCTION......Page 18
II. ROOT GROWTH, THE RHIZOSPHERE, AND ROOT PRODUCTS......Page 21
III. AMOUNTS RELEASED......Page 23
IV. TYPES OF ROOT PRODUCTS: SECRETIONS AND THEIR ROLES......Page 25
V. THE RIGHT SET OF CIRCUMSTANCES......Page 30
VI. CONCLUSIONS......Page 31
REFERENCES......Page 32
CONTENTS......Page 39
I. INTRODUCTION......Page 40
A. COLLECTION TECHNIQUES WITH TRAP SOLUTIONS......Page 41
B. LOCALIZED SAMPLING TECHNIQUES IN SOLUTION AND SOIL CULTURE SYSTEMS......Page 42
2. Soil Culture Systems......Page 43
1. Microbial Activity......Page 44
4. Root Injury......Page 46
A. DIFFUSION......Page 47
D. OTHER TRANSPORT MECHANISMS......Page 48
1. Role of Carboxylate Exudation for P Mobilization in Soils......Page 49
a. Biosynthesis of Carboxylates......Page 52
b. Reduced Turnover of Carboxylates......Page 55
c. Mechanisms of P-Deficiency-Induced Carboxylate Exudation......Page 56
4. Root-Secretory Phosphohydrolases......Page 57
3. Potassium Nutrition......Page 59
1. Strategy I Plants......Page 60
2. Strategy II Plants......Page 62
2. Role of Carboxylates, Rhizosphere pH, and Redox State......Page 65
b. Zinc......Page 66
V. ALUMINUM TOXICITY......Page 67
A. DROUGHT......Page 70
X. FUTURE RESEARCH PERSPECTIVES AND PROSPECTS FOR RHIZOSPHERE MANAGEMENT......Page 71
REFERENCES......Page 73
CONTENTS......Page 89
A. THE RHIZOSPHERE : A DEFINITION......Page 90
C. CARBON RHIZODEPOSITION: CURRENT ESTIMATES......Page 91
F. THE STUDY OF SOIL?PLANT?MICROBE INTERACTIONS......Page 92
G. THE INFLUENCE OF PLANT AND MICROBIAL FACTORS......Page 94
2. Plant Age and Stage of Development......Page 95
II. MICROBIAL INTERACTIONS IN THE RHIZOSPHERE......Page 96
A. COLONIZATION OF THE RHIZOSPHERE......Page 97
b. Mycorrhizae......Page 98
c. Biocontrol......Page 99
a. Plant Pathogens......Page 102
A. MICROORGANISMS ASSOCIATED WITH GERMINATING SEEDS AND YOUNG ROOTS......Page 103
B. MICROORGANISMS ASSOCIATED WITH MATURE ROOTS......Page 104
1. Temperature......Page 106
3. Oxygen Deficit......Page 107
4. pH and Availability of Nutrient Ions......Page 108
B. STRUCTURAL FACTORS......Page 109
D. BIOTIC FACTORS......Page 110
V. APPLICATION......Page 111
VI. FUTURE DIRECTIONS......Page 113
REFERENCES......Page 114
I. INTRODUCTION......Page 126
A. DIFFERENT COMPONENTS OF SOIL RESPIRATION AND QUANTIFICATION OF RHIZODEPOSITIONS......Page 127
B. DEGRADATION OF ROOT EXUDATES AND CHANGE IN THE COMPOSITION OF MICROBIAL COMMUNITIES......Page 130
C. EFFECTS OF ELEVATED CO2 ATMOSPHERIC CONCENTRATION ON MICROBIAL PROCESSES OF RHIZOSPHERE SOIL......Page 131
A. NITROGEN UPTAKE BY PLANTS......Page 133
B. THE ROLE OF MICROFAUNA IN THE N MINERALIZATION PROCESS......Page 135
A. CONCEPTS, MEANING OF MEASUREMENTS, AND ROLE OF PHOSPHATASES......Page 137
C. LINKING ENZYME ACTIVITY TO GENE EXPRESSION AND PROTEOMICS APPROACH......Page 139
VI. SOME NEW APPROACHES AND TECHNIQUES FOR STUDYING RHIZOSPHERE PROCESSES......Page 140
REFERENCES......Page 142
I. INTRODUCTION......Page 149
A. SIGNALS......Page 150
1. Lateral Roots......Page 151
2. Root Hairs......Page 152
III. SENSING......Page 154
A. AUXIN......Page 155
B. CYTOKININS......Page 156
A. TRANSCRIPTION FACTORS......Page 157
C. CHROMATIN REMODELING AND PROTEIN?PROTEIN INTERACTIONS......Page 158
D. INTERORGAN COMMUNICATION......Page 159
REFERENCES......Page 160
I . INTRODUCTION......Page 165
A. S TRUCTURE......Page 166
1. Energization of Nutrient Transport......Page 167
2. Nutrient Acquisition through Rhizosphere Acidification......Page 169
3. Response to Abiotic Stress......Page 170
b. Plant Growth Promoting Rhizobacteria......Page 171
A. ANION CARRIERS......Page 172
B. CATION CARRIERS......Page 176
A. CATION CHANNELS......Page 178
C. PORINLIKE CHANNELS......Page 179
V. CONCLUDING REMARKS AND FUTURE PERSPECTIVES......Page 180
REFERENCES......Page 181
I. INTRODUCTION......Page 187
II. SIDEROPHORES AND IRON OXIDE DISSOLUTION......Page 188
III. IRON SPECIATION AND LIGAND EXCHANGE REACTIONS IN SOLUTION......Page 189
A. PLANT IRON UPTAKE MECHANISMS......Page 193
V. PLANT MICROBIAL INTERACTIONS......Page 195
A. TYPES OF SIDEROPHORES PRODUCED......Page 196
B. MICROSITE DIFFERENCES IN SIDEROPHORE PRODUCTION......Page 199
B. ANALYSIS OF FE STRESS EFFECTS ON MICROBIAL COMMUNITY STRUCTURES IN THE RHIZOSPHERE OF BARLEY......Page 201
VIII. FUNCTIONS OF SIDEROPHORES IN RHIZOSPHERE COMPETENCE......Page 203
IX. ROLE OF SIDEROPHORES IN BIOCONTROL OF PLANT PATHOGENS......Page 204
X. FUNCTION OF SIDEROPHORES IN NITROGEN FIXATION......Page 206
XI. SUMMARY......Page 207
REFERENCES......Page 208
I. INTRODUCTION......Page 215
II. MYCORRHIZAL FUNGI ARE GENETICALLY DIVERSE......Page 216
A. RHIZOSPHERIC SIGNALS......Page 219
B. CHEMODIFFERENTIATION AT THE ROOT SURFACE......Page 220
C. FUNGAL PHYTOHORMONES ARE PRODUCED IN THE RHIZOSPHERE......Page 222
IV. MYCORRHIZAL FUNGI DEVELOP STRUCTURES OUTSIDE AND INSIDE THE ROOTS......Page 223
A. AT THE PLANT?FUNGUS INTERFACE: STRUCTURE, ROLE, AND BIOGENESIS OF A NEW COMPARTMENT......Page 227
B. THE GENETIC BASIS OF FUNGAL COLONIZATION......Page 229
C. ECTOMYCORRHIZA DEVELOPMENT: A COORDINATED EXPRESSION OF GENE NETWORKS......Page 230
V. THE ROLE OF MYCORRHIZAL FUNGI IN NUTRIENT CYCLING AT THE SOIL?ROOT INTERFACE......Page 232
A. NITROGEN ACQUISITION IN MYCORRHIZAL FUNGI......Page 233
2. Uptake of NO3- and NH4+......Page 234
B. UTILIZATION OF SOIL CARBON COMPOUNDS BY MYCORRHIZAL FUNGI......Page 235
2. Pi Uptake by AM Fungi......Page 236
D. THE WOOD-WIDE WEB CONCEPT......Page 237
VI. DO MYCORRHIZAL FUNGI PROTECT THEIR HOST FROM ELEMENTAL POLLUTANTS?......Page 238
VII. BACTERIA AND MYCORRHIZAL FUNGI IN THE RHIZOSPHERE......Page 239
VIII. CONCLUSIONS......Page 241
REFERENCES......Page 242
I. INTRODUCTION......Page 251
II. THE ECOLOGY OF RHIZOBIA AND LEGUMES......Page 252
A. FLAVONOID -DEPENDENT SIGNALING......Page 255
B. OTHER COMPONENTS OF COMMUNICATION: CYCLIC GLUCANS, EPS, AND LPS......Page 258
IV. NOD FACTOR SIGNALING AND RELATED PROCESSES......Page 262
V. INFECTION AND NODULE COMPARTMENTATION DEVELOPMENT......Page 266
VI. SOIL STRESS FACTORS AFFECTING THE SYMBIOSIS......Page 269
VIII. CONCLUSIONS......Page 272
REFERENCES......Page 273
I. INTRODUCTION TO BIOCONTROL-RELATED PHENOMENA IN THE RHIZOSPHERE......Page 281
II. RHIZOSPHERE COMPETENCE......Page 283
A. ANTIBIOSIS......Page 285
E. INDUCTION OF SYSTEMIC RESISTANCE......Page 286
F. COMPETITION FOR NUTRIENTS AND NICHES......Page 288
H. OTHER REMARKS ON THE MECHANISMS OF BIOCONTROL......Page 289
IV. BIOREPORTERS AND BIOCONTROL......Page 290
V. NATURAL ROLES OF SMALL MOLECULES IN THE RHIZOSPHERE......Page 292
VI. ENHANCING OF BIOCONTROL EFFICACY BY MANIPULATION......Page 294
VIII. VISUALIZATION OF BIOCONTROL......Page 295
X. COMMERCIALIZATION OF BIOCONTROL......Page 297
REFERENCES......Page 298
I. INTRODUCTION......Page 311
A. CHEMICAL SIGNALING AS BELOWGROUND COMMUNICATION......Page 312
B. CHEMICAL SIGNALS IN THE RHIZOSPHERE......Page 313
C. SIGNAL MOBILITY, PERSISTENCE, AND ACTIVITY IN THE RHIZOSPHERE......Page 314
A. ALLELOPATHY......Page 315
B. AUTOINHIBITION......Page 319
C. HOST?PARASITIC PLANT INTERACTIONS......Page 320
A. PLANT ANTIMICROBIAL SIGNALS AND RESISTANCE TO SOIL PATHOGENS......Page 323
B. MICROBIAL SIGNALS AND INDUCED PLANT DISEASE RESPONSES......Page 326
A. HERBIVORE RESISTANCE......Page 327
B. ROOT DETECTION AND NAVIGATION......Page 328
V. POSITIVE ROOT?MICROBE COMMUNICATION......Page 329
A. EXTRACELLULAR PLANT GROWTH-PROMOTING RHIZOBACTERIA......Page 330
B. RHIZOBIA?LEGUME INTERACTIONS......Page 332
C. FRANKIA?ACTINORHIZAL INTERACTIONS......Page 333
E. MYCORRHIZAL FUNGI......Page 334
REFERENCES......Page 336
I. INTRODUCTION......Page 345
II. MODELING SHORT-RANGE TRANSPORT AND UPTAKE IN SOILS......Page 347
A. DIFFUSION OF SOLUTES......Page 348
D. TRANSFERS BETWEEN AVAILABLE AND UNAVAILABLE FORMS......Page 350
E. ROOT BOUNDARY CONDITIONS......Page 352
3. Outer-Boundary Condition......Page 353
4. Interroot Competition......Page 354
1. Numerical Approximation......Page 355
2. Analytical Solution......Page 357
3. Other Analytical Approximations......Page 361
G. VALIDATION OF THE LOCAL-SCALE MODEL OF NUTRIENT UPTAKE......Page 362
III. MODELING THE DYNAMICS OF MICROBIAL POPULATIONS AROUND THE ROOT......Page 363
IV. MODELING UPTAKE AT THE PLANT SCALE......Page 366
A. THE ASSUMPTION OF CONSTANT ROOT RADIUS......Page 367
B. THE ASSUMPTION OF EXPONENTIAL ROOT GROWTH WITH A CONSTANT COEFFICIENT......Page 371
V. PLANT UPTAKE IN HETEROGENEOUS ENVIRONMENTS......Page 374
VI. WATER AND NUTRIENT UPTAKE......Page 377
VII. FUTURE PROSPECTS......Page 379
REFERENCES......Page 380
I. INTRODUCTION......Page 385
II. METHODS FOR THE STUDY OF RHIZOSPHERE CARBON FLOW IN ARTIFICIAL MEDIA......Page 386
III. MEASUREMENT OF RHIZODEPOSITION IN SOIL......Page 387
A. 14CO2-LABELING TECHNIQUES FOR CARBON FLOW STUDIES......Page 388
B. 13CO2-LABELING TECHNIQUES FOR CARBON FLOW STUDIES......Page 390
IV. ANALYSIS OF CARBON FLOW COMPOSITION......Page 391
A. CULTURE-DEPENDENT TECHNOLOGIES......Page 394
B. CULTURE-INDEPENDENT TECHNOLOGIES......Page 396
1. Nucleotide-Based Biomarkers......Page 397
2. Other Biomarkers......Page 399
C. ANALYSIS OF MICROBIAL RESPONSES TO CARBON FLOW......Page 400
REFERENCES......Page 403
CONTENTS......Page 414
A. TRANSDUCTION IN BACTERIA AND REGULATION......Page 415
2. Types of Transduction......Page 416
2. Bacteria and Phage Physiological State and Interactions......Page 417
C. METHODS AND PREDICTIONS OF TRANSDUCTION GENE TRANSFER IN SOIL......Page 418
1. Natural Transformation Determinants......Page 419
2. Natural Transformation Gene Transfer Regulation: The Obstacle Race of the Penetrating Extracellular DNA......Page 420
1. Persistence of Extracellular DNA in Soil......Page 421
1. Methods to Investigate Natural Transformation-Mediated Gene Transfer in Soil......Page 422
2. Natural Transformation Gene Transfer in the Rhizosphere......Page 423
1. Conjugative Plasmids......Page 424
1. Cell Density and Physiological Status of Bacterial Cells......Page 425
2. Conjugative Transfer in the Rhizosphere......Page 426
V. GENE TRANSFER FROM GENETICALLY MODIFIED PLANTS TO RHIZOSPHERIC BACTERIA......Page 427
REFERENCES......Page 429