Beneficial plant-bacterial interactions

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