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Phytomicrobiome Interactions and Sustainable Agriculture. Edition No. 1

  • Book

  • 320 Pages
  • February 2021
  • John Wiley and Sons Ltd
  • ID: 5841883
A guide to the role microbes play in the enhanced production and productivity of agriculture to feed our growing population

Phytomicrobiome Interactions and Sustainable Agriculture offers an essential guide to the importance of ‘Phytomicrobiome’ and explores its various components. The authors - noted experts on the topic - explore the key benefits of plant development such as nutrient availability, amelioration of stress and defense to plant disease. Throughout the book, the authors introduce and classify the corresponding Phytomicrobiome components and then present a detailed discussion related to its effect on plant development: controlling factors of this biome, its behaviour under the prevailing climate change condition and beneficial effects.

The book covers the newly emerging technical concept of Phytomicrobiome engineering, which is an advanced concept to sustain agricultural productivity in recent climatic scenario. The text is filled with comprehensive, cutting edge data, making it possible to access this ever-growing wealth of information. This important book:

- Offers a one-stop resource on phytomicrobiome concepts - Provides a better understanding of the topic and how it can be employed for understanding plant development - Contains a guide to sustaining agriculture using phytomicrobiome engineering - Presents information that can lead to enhanced production and productivity to feed our growing population

Written for students, researchers and policy makers of plant biology, Phytomicrobiome Interactions and Sustainable Agriculture offers a clear understanding of the importance of microbes in overall plant growth and development.

Table of Contents

List of Contributors xii

Preface xvi

About the Editors xviii

1 Plant Root Exudate Analysis: Recent Advances and Applications 1
Shulbhi Verma and Amit Verma

1.1 Introduction 1

1.2 Root Exudates Composition: Collection and Analysis 3

1.3 Role of Root Exudates in Shaping Rhizospheric Microbiomes 5

1.4 Applications of Root Exudation 6

1.5 Conclusion and Future Prospects 7

References 10

2 Phytoproteomics: A New Approach to Decipher Phytomicrobiome Relationships 15
Prachie Sharma and Kapila Kumar

2.1 Introduction 15

2.2 Phytomicrobiome 16

2.3 Phytomicrobiome: The Communication via Signaling 18

2.4 Proteomics 19

2.4.1 Gel-Based Protein Separation Techniques 21

2.4.2 Non-Gel Protein Separation Techniques 21

2.5 Analysis of Phytomicrobial Interactions Using Proteomics Approaches 22

2.6 Conclusion and Future Prospects 26

References 28

3 Metagenomics: An Approach to Unravel the Plant Microbiome and Its Function 32
Ravindra Soni, Deep Chandra Suyal, Balram Sahu, and Suresh Chandra Phulara

3.1 Introduction 32

3.2 Metagenomics 33

3.3 Metagenomics of Plant Rhizosphere 33

3.4 Metagenomics of Plant Phyllosphere 35

3.5 Metagenomics of Plant Endosphere 36

3.6 In-silico Tools for Metagenome Analysis 37

3.6.1 Mothur 37

3.6.2 Quantitative Insights into Microbial Ecology (QIIME) 37

3.6.3 MEta Genome Analyzer (MEGAN) 38

3.7 Recent Progress in Metagenomic Studies of Plant Microbiome 38

3.8 Conclusion and Future Prospects 38

References 38

4 Combating the Abiotic Stress Through Phytomicrobiome Studies 45
Hemant S. Maheshwari, Abhishek Bharti, Richa Agnihotri, Ajinath Dukare, B. Jeberlin Prabina, Saurabh Gangola, and Mahaveer P. Sharma

4.1 Introduction 45

4.1.1 Abiotic Stress and Phytomicrobiome 45

4.1.2 Role of Signaling in Phytomicrobiome Interactions 46

4.2 Phytomicrobiome Signaling Compounds 47

4.2.1 Root Exudates and Plant Volatiles Compounds 47

4.2.2 Microbial Volatile Organic Compounds 47

4.2.3 Quorum Sensing 48

4.2.4 Underground Phytomicrobiome Signaling 48

4.3 Mechanisms of Phytomicrobiome Associated with Abiotic Stress Tolerance 49

4.3.1 Drought Stress Alleviation 50

4.3.2 Salinity Stress Mitigation 53

4.3.3 Heavy Metal Toxicity 55

4.3.4 Low-Temperature Stress 56

4.3.5 Nutrient Deficiency 56

4.3.6 Flooding or Water Submergence 56

4.4 Importance of Phytomicrobiome Engineering for Crop Stress Alleviation 57

4.5 Omics Strategies in Phytomicrobiome Studies 58

4.6 Conclusion and Future Prospects 59

Acknowledgments 59

References 60

5 Microbial Diversity of Phyllosphere: Exploring the Unexplored 66
Rakhi Dhankhar, Aparajita Mohanty, and Pooja Gulati

5.1 Introduction 66

5.2 Origin of Phyllosphere Microflora 67

5.3 Tools to Study Phyllomicrobiome 68

5.3.1 Conventional Methods 69

5.3.2 Microscopic Techniques 69

5.3.3 First-Generation Molecular Techniques 70

5.3.4 Next-Generation Sequencing Methods 70

5.3.5 Omics and Bioinformatics Approaches 76

5.3.6 Other Molecular Methods 77

5.4 Biodiversity of Phyllosphere 77

5.5 Microbial Adaptation to Phyllosphere 78

5.5.1 Adaptation to Abiotic Stresses 79

5.5.2 Adaptation to Biotic Stresses 80

5.5.3 Adaptation to Nutrient Scarcity 81

5.6 Interaction of Phyllomicrobiota with Plants 81

5.6.1 Positive Interactions 82

5.6.2 Negative Interactions 83

5.7 Significance of Phyllomicrobiome Studies 83

5.8 Conclusion and Future Prospects 84

References 85

6 Rhizosphere Engineering: An Effective Approach for Sustainable Modern Agriculture 91
Reema Mishra, Tripti Grover, Pooja Gulati, and Aparajita Mohanty

6.1 Introduction 91

6.2 Natural Plant-Microbe Interactions in Rhizosphere 92

6.3 Molecular Mechanisms in Plant-Microbe Interactions in Rhizosphere 93

6.4 Biochemical Components in Rhizosphere Signaling 94

6.5 Tools and Techniques in Rhizosphere Engineering 96

6.5.1 Stable Isotope Probing (SIP) 96

6.5.2 DNA Arrays 97

6.5.3 Fluorescence In Situ Hybridization (FISH) 97

6.5.4 Bioreporters 97

6.5.5 Genomics 98

6.5.6 Transcriptomics 98

6.5.7 Proteomics 99

6.5.8 Metabolomics 99

6.6 Rhizosphere Components Amenable to Engineering 100

6.6.1 Soil Modification 100

6.6.2 Plant Amendment 100

6.6.2.1 Root Exudate Modification 100

6.6.2.2 Root Architecture Modification 101

6.6.2.3 Enhancing Abiotic Stress Tolerance in Plants 101

6.6.2.4 Enhancing Biotic Stress Tolerance in Plants 103

6.6.2.5 Engineering Metabolic Pathways in Plants 105

6.6.3 Engineering Microbial Populations 107

6.7 Conclusion and Future Prospects 107

Acknowledgment 108

References 108

7 Plant Communication with Associated: Its Components, Composition and Role in Maintaining Plant Homeostasis 118
Dibyajit Lahiri, Moupriya Nag, Sayantani Garai, Bandita Dutta, and Rina Rani Ray

7.1 Introduction 118

7.2 Biofilm and Rhizospheric Interactions 119

7.3 Biofilm Formation at the Root Rhizosphere 120

7.3.1 The Components of Biofilm Matrix 121

7.3.2 Bacterial Quorum Sensing 122

7.4 Genetic Features Responsible for Bacterial Cell Adhesion to Plant System 125

7.4.1 Chemotaxis Motility 125

7.4.2 Substrate Utilization and Transport 125

7.4.3 Lipopolysaccharide and Membrane Proteins 126

7.4.4 Plant Cell Wall Modification 127

7.4.5 Adhesion and Biofilm Formation 128

7.4.6 Stress Protection 128

7.4.7 Bacterial Secretion System 129

7.4.8 Transcriptional Regulators and Sensor Proteins 130

7.5 Nutrient Interactions 138

7.5.1 Release and Activation of Minerals 138

7.5.2 Nutrient Recycling 138

7.5.3 Nitrogen Dynamics 138

7.5.4 Ionic Modification 139

7.6 Biotic Interaction 140

7.6.1 Symbiosis 140

7.6.2 Synergy 140

7.6.3 Competition 140

7.6.4 Antagonism 141

7.6.5 Pathogenesis 142

7.7 Conclusion and Future Prospects 142

References 143

8 Phytomicrobiome: Synergistic Relationship in Bioremediation of Soil for Sustainable Agriculture 150
Nimmy Srivastava

8.1 Introduction 150

8.2 Phytoremediation 151

8.2.1 Process of Phytoremediation 151

8.2.2 Strategies for Phytoremediation 151

8.3 Phytomicrobe Interactions and Rhizomediation 152

8.3.1 Principle of Phytomicrobiome Interaction During Rhizomediation 152

8.3.2 Removal of Inorganic Contaminants 154

8.3.3 Removal of Organic Pollutants 154

8.3.4 Factors Affecting Rhizomediation 157

8.4 Conclusion and Future Prospects 157

References 158

9 Rhizospheric Biology: Alternate Tactics for Enhancing Sustainable Agriculture 164
Kalpana Bhatt and Pankaj Bhatt

9.1 Introduction 164

9.2 Engineering the Rhizosphere 165

9.2.1 Rhizosphere and Rhizobia 165

9.2.2 Root Exudates: Chemical Nature and Types 167

9.2.3 Factors Affecting Root Exudate 168

9.3 Engineering Soil Microbial Populations and Plant-Microbe Interactions 169

9.3.1 Microorganisms in Soil 169

9.3.2 Soil Modification: Altering Microbial Populations 170

9.4 Plant Growth-Promoting Rhizobacteria: Mechanisms, Potential, and Usages 170

9.4.1 Direct Mechanisms 171

9.4.1.1 Biological N2 Fixation 171

9.4.1.2 Phosphate Solubilization 173

9.4.1.3 Zinc Solubilization 174

9.4.1.4 Siderophore Production 174

9.4.1.5 Production of Phytohormones 174

9.4.1.6 ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity 175

9.4.2 Indirect Mechanisms 175

9.5 Plant-Microbe Interaction 176

9.6 Biofertilizers and its Applications 177

9.7 Plant Genetic Engineering 177

9.8 Conclusion and Future Prospects 178

Acknowledgments 178

References 179

10 Application of Inorganic Amendments to Improve Soil Fertility 187
Sunita Chauhan and Shweta Kulshreshtha

10.1 Introduction 187

10.2 Impact of Bhoochetna Movement in Southern India 188

10.3 Sustainable Agriculture 188

10.3.1 Healthy Soil and Soil Quality 189

10.3.2 Soil Quality 189

10.3.3 Soil Quality Indicator 190

10.3.4 Soil Quality Index 191

10.4 Factors to Be Considered While Selecting a Soil Amendment 192

10.5 Advantages of Soil Amendments 194

10.6 Land Modeling 194

10.7 Major Applications of Soil Amendments 195

10.7.1 Phyto-Stabilization in Polluted or Contaminated Soils 195

10.7.2 Restoration of Soil 196

10.7.2.1 Soil Acidity/pH Soil Amendments 196

10.7.2.2 Mineral Soil Amendments and Conditioners 196

10.7.2.3 Different Types of Inorganic Amendments 197

10.8 Combination Strategy for Soil Quality Improvement 202

10.9 Conclusion and Future Prospects 203

References 203

11 Improved Plant Resistance by Phytomicrobiome Community Towards Biotic and Abiotic Stresses 207
Neha Trivedi

11.1 Introduction 207

11.2 Microbes and Plants 207

11.2.1 Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants 208

11.2.2 Microbial-Induced Response to Stresses 208

11.3 Response of Abiotic Response on Plant 209

11.3.1 Induced Systemic Tolerance (IST) 209

11.3.2 Metabolic Changes in Plants Induced by Microbes During Stress 209

11.3.2.1 Metabolic Cross-Talk in Plants After Stress Induction 210

11.3.2.2 Activation of Antioxidant Mechanism 210

11.3.2.3 Activation of Systemically Induced Resistance 210

11.4 Role of Phytohormones in Increasing Abiotic and Biotic Stress Tolerance 211

11.5 Gene Transfer in Plants 212

11.6 Conclusion and Future Prospects 212

References 212

12 Bioprospecting: At the Interface of Plant and Microbial Communities 217
Madan L. Verma, Varsha Rani, Reena Kumari, Deepka Sharma, Sanjeev Kumar, and Rekha Kushwaha

12.1 Introduction 217

12.2 Plant-Associated Microbial Communities 218

12.3 Beneficial Effects of Plant-Associated Microbial Communities 222

12.3.1 Rhizoremediation 223

12.3.2 Plant Growth-Promoting Rhizobacteria (PGPR) 223

12.3.3 Biotic and Abiotic Stress Resistance 224

12.3.4 Signalomics 226

12.4 Role of Microbial Processing (Signals) in Facilitating Plant Growth 226

12.5 Conclusion and Future Prospects 230

Acknowledgments 230

References 231

13 Advances in Omics and Bioinformatics Tools for Phyllosphere Studies 240
Hina Bansal

13.1 Introduction 240

13.2 Recent Trends and Approaches 241

13.3 Computing for Biology 243

13.4 Bioinformatics in Microbial Research 243

13.5 Phyllosphere Microbiome Studies Based on Genome-Wide Association 245

13.6 Omics Strategies and Their Integration 246

13.6.1 Metagenomics 246

13.6.2 Metatranscriptomics 246

13.6.3 Metabolomics 247

13.6.4 Proteomics 247

13.7 Conclusion and Future Prospects 248

References 248

14 Microbial Mediated Zinc Solubilization in Legumes for Sustainable Agriculture 254
Pawan Saini, Sharon Nagpal, Pooja Saini, Arun Kumar, and Mudasir Gani

14.1 Introduction 254

14.2 Chronological Events of Zinc Biology 255

14.3 Role of Zinc in Living System 256

14.3.1 Essentiality of Zinc in Humans 256

14.3.2 Essentiality of Zinc in Plants 257

14.4 Zinc Deficiency vs. Zinc Toxicity in Crop Plants 259

14.5 Availability of Zinc in Soil Environment 260

14.6 Factors Affecting Zinc Availability to Plants 261

14.7 Response of Legume Crops to Zinc 262

14.8 Microbial Mediated Zinc Solubilization in Legume Crops 263

14.8.1 Zinc-Solubilizing Bacteria (ZnSB) 264

14.8.2 Zinc-Solubilizing Fungi (ZnSF) 265

14.9 Conclusion and Future Prospects 266

References 266

15 Composition and Interconnections in Phyllomicrobiome 277
Meghmala Waghmode, Aparna Gunjal, Neha Patil, and Sonali Shinde

15.1 Introduction 277

15.2 Significance of Phyllospheremicrobiota 279

15.3 Phyllosphere Microorganisms as Plant Growth Regulator 280

15.3.1 Plant Growth Hormones Production by Phyllosphere Microorganisms 280

15.3.2 Phosphorus Solubilization by Phyllosphere Microorganisms 280

15.3.3 Siderophores Production by Phyllosphere Microorganisms 280

15.3.4 Phyllosphere Microorganisms as Biocontrol Agents Against the Phytopathogens 280

15.3.5 Phyllosphere Microorganisms to Reduce Biotic and Abiotic Stress 281

15.3.6 Synthesis of 1-Aminocyclopropane-1-Carboxylate Deaminase (ACC) 282

15.3.7 Phyllosphere Microorganisms in Nitrogen-Fixation 282

15.3.8 Frost Injury and Frost Control by Altering the Phyllosphere Microbiota 282

15.3.9 Remediation of Toxic Pollutants 283

15.3.10 Plant Probiotics 283

15.3.11 Role of Phyllosphere Microorganisms in Climate Change 284

15.3.12 Phyllosphere Microorganisms in Nutrient Yield and Increase of Plant Growth 284

15.3.13 Plant Hormones as Colonization Mediators of the Plant Leaves 284

15.4 Plant-Pathogen Interactions Mediated by Phyllosphere Microbiome 285

15.4.1 Interaction Dependent on the Ionome 285

15.4.2 Role of Secretory Systems and Secretory Products 285

15.4.3 Quorum Sensing 286

15.5 Conclusion and Future Prospects 286

References 286

Authors

Amit Verma Jitendra Kumar Saini Harikesh Bahadur Singh Abd El-Latif Hesham