Beneficial plant-bacterial interactions

Description

Preface Acknowledgements Contents 1: Introduction to Plant Growth-Promoting Bacteria 1.1 The Problem 1.2 Possible Solutions 1.3 Plant Growth-Promoting Bacteria 1.3.1 Organisms in Soil 1.3.2 Root Exudation 1.3.3 Effect of PGPB on Plants 1.4 PGPB Mechanisms 1.5 Screening for New PGPB 1.6 Commercial Inoculants 1.6.1 Commercial Considerations 1.6.2 Inoculation Methods 1.6.3 Large-Scale Growth of PGPB 1.6.4 Commercialized Inoculant Examples Bibliography 2: Microbiomes and Endophytes 2.1 Microbiomes 2.1.1 Root Microbiome 2.1.2 Seed Microbiome 2.1.3 Synthetic Microbiomes 2.2 Endophytes 2.2.1 Endophytic Genes 2.2.2 Isolating Endophytes 2.2.3 Endophytes and Flowers 2.2.4 Endophytic Fungi Bibliography 3: Some Techniques Used to Elaborate Plant-Microbe Interactions 3.1 Next-Generation DNA Sequencing 3.1.1 DNA Sequences of Complete Bacterial Genomes 3.2 The Polymerase Chain Reaction 3.2.1 Real-Time PCR 3.3 Transcriptomics 3.3.1 DNA Microarray Technology 3.4 Proteomics 3.5 Metabolomics 3.6 CRISPR 3.7 Imaging 3.7.1 High-Resolution Scanning 3.7.2 Labeling PGPB 3.8 Microencapsulation Bibliography 4: Resource Acquisition 4.1 Nitrogen Fixation 4.1.1 Cyanobacteria 4.1.2 Rhizobia 4.1.3 Free-Living Bacteria 4.1.4 Nitrogenase 4.1.5 Nodulation 4.1.6 Hydrogenase 4.2 Sequestering Iron 4.2.1 Siderophore Structure 4.2.2 Siderophore Biosynthesis Genes 4.2.3 Regulation of Iron Uptake 4.2.4 Siderophores in the Rhizosphere 4.3 Solubilizing Phosphorus Bibliography 5: Modulating Phytohormone Levels 5.1 Auxin 5.1.1 Biosynthetic Pathways 5.1.1.1 The IAM Pathway 5.1.1.2 The IPA Pathway 5.1.1.3 The IAN Pathway 5.1.1.4 Multiple Pathways 5.1.2 Regulation 5.1.2.1 Gene Localization 5.1.2.2 IAA Conjugation 5.1.2.3 Stationary Phase Control 5.1.2.4 Regulatory Sequences 5.1.3 Effects on PGPB Survival 5.2 Cytokinin 5.3 Gibberellin 5.4 Ethylene 5.4.1 Ethylene Biosynthesis and Mode of Action 5.4.2 ACC Deaminase 5.4.2.1 Enzyme Assays 5.4.2.2 Transcriptional Regulation 5.4.3 Ethylene and Nodulation 5.4.4 Ethylene and Plant Transformation 5.5 Volatile Organic Compounds Bibliography 6: Biocontrol of Bacteria and Fungi 6.1 Phytopathogens 6.2 Allelochemicals Including Antibiotics and HCN 6.3 Siderophores 6.4 Cell Wall-Degrading Enzymes 6.5 Phytohormones 6.6 Competition 6.7 Volatile Compounds 6.8 Lowering Ethylene 6.9 Systemic Resistance 6.9.1 Effects on Plant Gene Expression 6.10 Bacteriophages 6.11 Quorum Sensing and Quorum Quenching Bibliography 7: Biocontrol of Insects and Nematodes 7.1 Insects 7.1.1 Bacillus thuringiensis 7.1.1.1 Producing B. thuringiensis Cry Protein During Vegetative Growth 7.1.1.2 Transferring Cry Genes 7.1.1.3 Preventing the Development of Insect Resistance 7.1.2 Antifeeding Prophage 7.1.3 PGPB-Mediated Insect Killing 7.1.4 Brevibacillus laterosporus 7.2 Nematodes 7.2.1 PGPB as Nematode Biocontrol Agents 7.2.1.1 Pine Wilt Disease 7.2.1.2 Endophytic Fungi and Bacteria Bibliography 8: Environmental Interactions 8.1 Overview of Stress 8.2 Salt and Drought 8.2.1 IAA 8.2.2 Ethylene 8.2.3 Trehalose 8.2.4 Cytokinin 8.2.5 Exopolysaccharides 8.2.6 Gibberellins 8.2.7 Volatile Organic Compounds 8.2.8 Trace Element Deficiency 8.3 Flooding and Anoxia 8.4 Natural Selection 8.4.1 Monitoring ACC Deaminase in Soil 8.5 Cold Temperature 8.5.1 Antifreeze Proteins 8.5.2 Chilling Stress 8.6 Bacterial Cooperation 8.7 Diazotrophic Endophytes 8.8 Methane and Global Warming 8.9 Changing Plant Gene Expression Bibliography 9: Mycorrhizal-Plant Interactions 9.1 Overview of Mycorrhizae 9.1.1 Selecting New Arbuscular Mycorrhizae 9.1.2 Growing and Formulating Mycorrhizae 9.2 Phytohormones 9.3 Mycorrhizae and Bacteria 9.4 Mycorrhizae and Stress 9.4.1 Mycorrhizae and Viruses Bibliography 10: Phytoremediation 10.1 Problem Overview 10.2 Metals 10.2.1 Siderophores 10.2.2 IAA 10.2.3 ACC Deaminase 10.2.4 Nitrogen Fixation 10.2.5 Biosurfactants 10.2.6 Consortia 10.3 Arsenic 10.4 Organics 10.5 Endophytes 10.6 Phytoremediation and OMICS 10.6.1 Changes to Plants 10.6.2 Changes to PGPB 10.6.2.1 Bacterial Changes Caused by Plants 10.6.2.2 Bacterial Changes Caused by Environmental Contaminants Bibliography 11: Issues Regarding the Use of PGPB 11.1 PGPB in the Environment 11.1.1 Environmental Concerns 11.1.1.1 Transfer of Genes to Other Organisms 11.1.1.2 Monitoring PGPB 11.1.1.3 Some Environmental Hazards 11.1.1.4 Nonreplicating Transgenic Bacteria 11.1.1.5 Releasing Transgenic Rhizobia 11.2 Metabolic Load 11.3 Patenting 11.3.1 Patenting in Different Countries 11.3.2 Patenting DNA Sequences 11.3.3 Patenting Multicellular Organisms 11.3.4 Patenting the Plant Microbiome 11.3.5 Patenting and Fundamental Research Bibliography