Molecular Ecology of Rhizosphere Microorganisms: Biotechnology and the Release of GMOs

Molecular Ecology of Rhizosphere Microorganisms......Page 2
Content......Page 12
Preface......Page 8
List of Contributors......Page 10
1.1 Introduction and Definitions......Page 18
1.2 Relationship of Root Colonization to Biocontrol and Growth Promotion......Page 19
1.3 The Process of Colonization......Page 20
1.4 Effect of Biotic and Abiotic Factors......Page 21
1.5 Bacterial Traits Contributing to Rhizosphere Competence......Page 22
1.6 Population Dynamics of PGPR in the Field......Page 24
1.7 Release of Genetically Engineered Rhizobacteria......Page 25
1.8 Mechanisms of Biological Control by PGPR......Page 26
1.9 Inconsistant Performance of PGPR......Page 28
1.10 Improving Root Colonizing and Biological Control......Page 29
1.12 References......Page 30
2.1 Introduction......Page 36
2.2.3 Sample Preparation and Surface Sterilization......Page 37
2.2.6 Strain Identification......Page 38
2.3.1 Population Dynamics......Page 39
2.3.2 Bacterial Identification......Page 40
2.4 Discussion......Page 41
2.5 References......Page 44
3.1 Introduction......Page 46
3.2.1 Spontaneous Antibiotic Resistance......Page 47
3.2.2 Marker Genes......Page 48
3.2.2.1 New metabolic capability......Page 49
3.2.2.5 Transposons carrying antibiotic resistance......Page 50
3.2.3 DNA Probes......Page 52
3.2.4.2 Enrichment......Page 54
3.3 Case Study: \"Tracking LacZY-labelled Pseudomonus corrugata in the Field......Page 55
3.3.1 Pre-release Testing......Page 56
3.3.2 Field Release......Page 57
3.4.2 Reduced Fitness......Page 58
3.5 Conclusions......Page 59
3.6 References......Page 61
4.1 Introduction......Page 66
4.2 A Most Probable Number (MPN) Recovery Technique......Page 67
4.3 The Need for an Eco-Physiological Index (EPI)......Page 68
4.4 Conclusions......Page 70
4.5 References......Page 71
5.1 Introduction......Page 74
5.2 Siderophore-Mediated Competitive Exclusion of Phytopathogens......Page 75
5.3 Exploiting Antifungal Metabolites to Enhance Biological Control......Page 77
5.4 Stability of Introduced Genes and Biological Containment Systems for GMO\'s......Page 78
5.5 Conclusion......Page 80
5.6 References......Page 81
6.1 Introduction......Page 84
6.2.1 Chemical Identification of Extracellular Metabolites......Page 85
6.2.2 Genetic Manipulation of Strain CHA0......Page 87
6.2.3 Gnotobiotic System......Page 90
6.2.4 Mutations Affecting Biocontrol Efficacy, Regulation of Secondary Metabolism, and some Caveats......Page 92
6.2.5 Induced Systemic Resistance in Plants......Page 94
6.2.6 Genetic Instability of Strain CHA0: Effects on Secondary Metabolism and Biological Control......Page 95
6.3 Environmental Impact of Bacterial Inoculants......Page 96
6.3.2 Microcosms......Page 97
6.4 Potential Applications......Page 98
6.5 Conclusion......Page 99
6.6 References......Page 100
7.2 Mini-Transposons as Genetic Tools......Page 108
7.2.2 A Universal Suicide Delivery System......Page 109
7.2.3 Alternative Selection Markers......Page 111
7.3.1 Selecting an Adequate Level of Transcription......Page 112
7.3.2 Post-Transcriptional Bottlenecks......Page 113
7.4 Engineering Alkyl- and Halo-aromatic Responsive Phenotypes......Page 114
7.5 Outlook......Page 116
7.6 References......Page 117
8.1 Introduction......Page 120
8.2.1 Southern Blot and Hybridization......Page 121
8.2.3 Ribotyping of Bacterial Strains......Page 122
8.2.4 Fingerprinting by Arbitrarily Primed PCR......Page 123
8.2.5 Fingerprinting by tRNA Consensus Primed PCR......Page 124
8.3 Outlook......Page 126
8.4 References......Page 128
9.2 System with Biotinylated and Mercurated Subtracter DNA......Page 130
9.3 Combined Subtraction Hybridization and PCR Amplification Procedure......Page 131
9.3.1 Technical details......Page 132
9.3.1.2 Synthesis of oligonucleotides and preparation of linkers......Page 133
9.3.1.6 Isolation of probe strain DNA sequences from the subtraction mixture......Page 134
9.5 Conclusions......Page 135
9.6 References......Page 136
10.1 Introduction......Page 138
10.2.1 DNA-DNA hybridization data......Page 139
10.2.2 Sequencing of 16S rDNA genes......Page 140
10.3.1 Conventional Techniques......Page 142
10.3.2.1 Intergenic Spacers......Page 143
10.3.2.2 PCR/RFLP......Page 144
10.4.1 Detection of Frankia in Actinorhizae......Page 145
10.4.2 Direct Detection of Frankia Present in the Soil......Page 146
10.6 References......Page 147
11.1 Introduction......Page 150
11.2 Life-cycle of Streptomycetes in Soil......Page 151
11.2.1 Spore Germination and Mycelial Development in Soil......Page 152
11.2.2 Molecular Monitoring of Differentiation in Soil......Page 153
11.3 Potential for Genetic Interactions between Actinomycetes in Soil......Page 155
11.3.1 Conjugative Interactions between Streptomycetes in Soil......Page 156
11.3.2 Gene Exchange between Actinomycetes and Other Bacteria......Page 157
11.3.3 Interactions between Streptomycetes and Actinophages in Soil......Page 158
11.4 Detection and Expression of Specific Genes in Soil......Page 159
11.4.1 Antibiotic Resistance Genes and Expression of Antibiotic Production Genes in Soil......Page 160
11.4.2 Detection of Amplified Genes in Soil......Page 161
11.5 Conclusions......Page 162
11.7 References......Page 163
12.1 Introduction......Page 168
12.2 Soil and Rhizosphere as Habitats for Bacteria......Page 169
12.3.1 Transformation......Page 170
12.3.2 Transduction......Page 172
12.3.3 Conjugation......Page 174
12.4 Concluding Remarks......Page 176
12.5 References......Page 178
13.1 Introduction......Page 182
13.2 The International Regulatory Framework......Page 184
13.3 The European Community Regulation......Page 185
13.4 Biosafety Results of Field Tests of GMOs......Page 186
13.6 References......Page 188
Index......Page 192