<p>List of Contributors xii</p> <p>Preface xvi</p> <p>About the Editors xviii</p> <p><b>1 Plant Root Exudate Analysis: Recent Advances and Applications </b><b>1<br /></b><i>Shulbhi Verma and Amit Verma</i></p> <p>1.1 Introduction 1</p> <p>1.2 Root Exudates Composition: Collection and Analysis 3</p> <p>1.3 Role of Root Exudates in Shaping Rhizospheric Microbiomes 5</p> <p>1.4 Applications of Root Exudation 6</p> <p>1.5 Conclusion and Future Prospects 7</p> <p>References 10</p> <p><b>2 Phytoproteomics: A New Approach to Decipher Phytomicrobiome Relationships </b><b>15<br /></b><i>Prachie Sharma and Kapila Kumar</i></p> <p>2.1 Introduction 15</p> <p>2.2 Phytomicrobiome 16</p> <p>2.3 Phytomicrobiome: The Communication via Signaling 18</p> <p>2.4 Proteomics 19</p> <p>2.4.1 Gel-Based Protein Separation Techniques 21</p> <p>2.4.2 Non-Gel Protein Separation Techniques 21</p> <p>2.5 Analysis of Phytomicrobial Interactions Using Proteomics Approaches 22</p> <p>2.6 Conclusion and Future Prospects 26</p> <p>References 28</p> <p><b>3 Metagenomics: An Approach to Unravel the Plant Microbiome and Its Function </b><b>32<br /></b><i>Ravindra Soni, Deep Chandra Suyal, Balram Sahu, and Suresh Chandra Phulara</i></p> <p>3.1 Introduction 32</p> <p>3.2 Metagenomics 33</p> <p>3.3 Metagenomics of Plant Rhizosphere 33</p> <p>3.4 Metagenomics of Plant Phyllosphere 35</p> <p>3.5 Metagenomics of Plant Endosphere 36</p> <p>3.6 <i>In-silico </i>Tools for Metagenome Analysis 37</p> <p>3.6.1 Mothur 37</p> <p>3.6.2 Quantitative Insights into Microbial Ecology (QIIME) 37</p> <p>3.6.3 MEta Genome Analyzer (MEGAN) 38</p> <p>3.7 Recent Progress in Metagenomic Studies of Plant Microbiome 38</p> <p>3.8 Conclusion and Future Prospects 38</p> <p>References 38</p> <p><b>4 Combating the Abiotic Stress Through Phytomicrobiome Studies </b><b>45<br /></b><i>Hemant S. Maheshwari, Abhishek Bharti, Richa Agnihotri, Ajinath Dukare, B. Jeberlin Prabina, Saurabh Gangola, and Mahaveer P. Sharma</i></p> <p>4.1 Introduction 45</p> <p>4.1.1 Abiotic Stress and Phytomicrobiome 45</p> <p>4.1.2 Role of Signaling in Phytomicrobiome Interactions 46</p> <p>4.2 Phytomicrobiome Signaling Compounds 47</p> <p>4.2.1 Root Exudates and Plant Volatiles Compounds 47</p> <p>4.2.2 Microbial Volatile Organic Compounds 47</p> <p>4.2.3 Quorum Sensing 48</p> <p>4.2.4 Underground Phytomicrobiome Signaling 48</p> <p>4.3 Mechanisms of Phytomicrobiome Associated with Abiotic Stress Tolerance 49</p> <p>4.3.1 Drought Stress Alleviation 50</p> <p>4.3.2 Salinity Stress Mitigation 53</p> <p>4.3.3 Heavy Metal Toxicity 55</p> <p>4.3.4 Low-Temperature Stress 56</p> <p>4.3.5 Nutrient Deficiency 56</p> <p>4.3.6 Flooding or Water Submergence 56</p> <p>4.4 Importance of Phytomicrobiome Engineering for Crop Stress Alleviation 57</p> <p>4.5 Omics Strategies in Phytomicrobiome Studies 58</p> <p>4.6 Conclusion and Future Prospects 59</p> <p>Acknowledgments 59</p> <p>References 60</p> <p><b>5 Microbial Diversity of Phyllosphere: Exploring the Unexplored </b><b>66<br /></b><i>Rakhi Dhankhar, Aparajita Mohanty, and Pooja Gulati</i></p> <p>5.1 Introduction 66</p> <p>5.2 Origin of Phyllosphere Microflora 67</p> <p>5.3 Tools to Study Phyllomicrobiome 68</p> <p>5.3.1 Conventional Methods 69</p> <p>5.3.2 Microscopic Techniques 69</p> <p>5.3.3 First-Generation Molecular Techniques 70</p> <p>5.3.4 Next-Generation Sequencing Methods 70</p> <p>5.3.5 Omics and Bioinformatics Approaches 76</p> <p>5.3.6 Other Molecular Methods 77</p> <p>5.4 Biodiversity of Phyllosphere 77</p> <p>5.5 Microbial Adaptation to Phyllosphere 78</p> <p>5.5.1 Adaptation to Abiotic Stresses 79</p> <p>5.5.2 Adaptation to Biotic Stresses 80</p> <p>5.5.3 Adaptation to Nutrient Scarcity 81</p> <p>5.6 Interaction of Phyllomicrobiota with Plants 81</p> <p>5.6.1 Positive Interactions 82</p> <p>5.6.2 Negative Interactions 83</p> <p>5.7 Significance of Phyllomicrobiome Studies 83</p> <p>5.8 Conclusion and Future Prospects 84</p> <p>References 85</p> <p><b>6 Rhizosphere Engineering: An Effective Approach for Sustainable Modern Agriculture </b><b>91<br /></b><i>Reema Mishra, Tripti Grover, Pooja Gulati, and Aparajita Mohanty</i></p> <p>6.1 Introduction 91</p> <p>6.2 Natural Plant–Microbe Interactions in Rhizosphere 92</p> <p>6.3 Molecular Mechanisms in Plant–Microbe Interactions in Rhizosphere 93</p> <p>6.4 Biochemical Components in Rhizosphere Signaling 94</p> <p>6.5 Tools and Techniques in Rhizosphere Engineering 96</p> <p>6.5.1 Stable Isotope Probing (SIP) 96</p> <p>6.5.2 DNA Arrays 97</p> <p>6.5.3 Fluorescence In Situ Hybridization (FISH) 97</p> <p>6.5.4 Bioreporters 97</p> <p>6.5.5 Genomics 98</p> <p>6.5.6 Transcriptomics 98</p> <p>6.5.7 Proteomics 99</p> <p>6.5.8 Metabolomics 99</p> <p>6.6 Rhizosphere Components Amenable to Engineering 100</p> <p>6.6.1 Soil Modification 100</p> <p>6.6.2 Plant Amendment 100</p> <p>6.6.2.1 Root Exudate Modification 100</p> <p>6.6.2.2 Root Architecture Modification 101</p> <p>6.6.2.3 Enhancing Abiotic Stress Tolerance in Plants 101</p> <p>6.6.2.4 Enhancing Biotic Stress Tolerance in Plants 103</p> <p>6.6.2.5 Engineering Metabolic Pathways in Plants 105</p> <p>6.6.3 Engineering Microbial Populations 107</p> <p>6.7 Conclusion and Future Prospects 107</p> <p>Acknowledgment 108</p> <p>References 108</p> <p><b>7 Plant Communication with Associated: Its Components, Composition and Role in Maintaining Plant Homeostasis </b><b>118<br /></b><i>Dibyajit Lahiri, Moupriya Nag, Sayantani Garai, Bandita Dutta, and Rina Rani Ray</i></p> <p>7.1 Introduction 118</p> <p>7.2 Biofilm and Rhizospheric Interactions 119</p> <p>7.3 Biofilm Formation at the Root Rhizosphere 120</p> <p>7.3.1 The Components of Biofilm Matrix 121</p> <p>7.3.2 Bacterial Quorum Sensing 122</p> <p>7.4 Genetic Features Responsible for Bacterial Cell Adhesion to Plant System 125</p> <p>7.4.1 Chemotaxis Motility 125</p> <p>7.4.2 Substrate Utilization and Transport 125</p> <p>7.4.3 Lipopolysaccharide and Membrane Proteins 126</p> <p>7.4.4 Plant Cell Wall Modification 127</p> <p>7.4.5 Adhesion and Biofilm Formation 128</p> <p>7.4.6 Stress Protection 128</p> <p>7.4.7 Bacterial Secretion System 129</p> <p>7.4.8 Transcriptional Regulators and Sensor Proteins 130</p> <p>7.5 Nutrient Interactions 138</p> <p>7.5.1 Release and Activation of Minerals 138</p> <p>7.5.2 Nutrient Recycling 138</p> <p>7.5.3 Nitrogen Dynamics 138</p> <p>7.5.4 Ionic Modification 139</p> <p>7.6 Biotic Interaction 140</p> <p>7.6.1 Symbiosis 140</p> <p>7.6.2 Synergy 140</p> <p>7.6.3 Competition 140</p> <p>7.6.4 Antagonism 141</p> <p>7.6.5 Pathogenesis 142</p> <p>7.7 Conclusion and Future Prospects 142</p> <p>References 143</p> <p><b>8 Phytomicrobiome: Synergistic Relationship in Bioremediation of Soil for Sustainable Agriculture </b><b>150<br /></b><i>Nimmy Srivastava</i></p> <p>8.1 Introduction 150</p> <p>8.2 Phytoremediation 151</p> <p>8.2.1 Process of Phytoremediation 151</p> <p>8.2.2 Strategies for Phytoremediation 151</p> <p>8.3 Phytomicrobe Interactions and Rhizomediation 152</p> <p>8.3.1 Principle of Phytomicrobiome Interaction During Rhizomediation 152</p> <p>8.3.2 Removal of Inorganic Contaminants 154</p> <p>8.3.3 Removal of Organic Pollutants 154</p> <p>8.3.4 Factors Affecting Rhizomediation 157</p> <p>8.4 Conclusion and Future Prospects 157</p> <p>References 158</p> <p><b>9 Rhizospheric Biology: Alternate Tactics for Enhancing Sustainable Agriculture </b><b>164<br /></b><i>Kalpana Bhatt and Pankaj Bhatt</i></p> <p>9.1 Introduction 164</p> <p>9.2 Engineering the Rhizosphere 165</p> <p>9.2.1 Rhizosphere and Rhizobia 165</p> <p>9.2.2 Root Exudates: Chemical Nature and Types 167</p> <p>9.2.3 Factors Affecting Root Exudate 168</p> <p>9.3 Engineering Soil Microbial Populations and Plant–Microbe Interactions 169</p> <p>9.3.1 Microorganisms in Soil 169</p> <p>9.3.2 Soil Modification: Altering Microbial Populations 170</p> <p>9.4 Plant Growth-Promoting Rhizobacteria: Mechanisms, Potential, and Usages 170</p> <p>9.4.1 Direct Mechanisms 171</p> <p>9.4.1.1 Biological N2 Fixation 171</p> <p>9.4.1.2 Phosphate Solubilization 173</p> <p>9.4.1.3 Zinc Solubilization 174</p> <p>9.4.1.4 Siderophore Production 174</p> <p>9.4.1.5 Production of Phytohormones 174</p> <p>9.4.1.6 ACC (1-Aminocyclopropane-1-Carboxylate) Deaminase Activity 175</p> <p>9.4.2 Indirect Mechanisms 175</p> <p>9.5 Plant–Microbe Interaction 176</p> <p>9.6 Biofertilizers and its Applications 177</p> <p>9.7 Plant Genetic Engineering 177</p> <p>9.8 Conclusion and Future Prospects 178</p> <p>Acknowledgments 178</p> <p>References 179</p> <p><b>10 Application of Inorganic Amendments to Improve Soil Fertility </b><b>187<br /></b><i>Sunita Chauhan and Shweta Kulshreshtha</i></p> <p>10.1 Introduction 187</p> <p>10.2 Impact of Bhoochetna Movement in Southern India 188</p> <p>10.3 Sustainable Agriculture 188</p> <p>10.3.1 Healthy Soil and Soil Quality 189</p> <p>10.3.2 Soil Quality 189</p> <p>10.3.3 Soil Quality Indicator 190</p> <p>10.3.4 Soil Quality Index 191</p> <p>10.4 Factors to Be Considered While Selecting a Soil Amendment 192</p> <p>10.5 Advantages of Soil Amendments 194</p> <p>10.6 Land Modeling 194</p> <p>10.7 Major Applications of Soil Amendments 195</p> <p>10.7.1 Phyto-Stabilization in Polluted or Contaminated Soils 195</p> <p>10.7.2 Restoration of Soil 196</p> <p>10.7.2.1 Soil Acidity/pH Soil Amendments 196</p> <p>10.7.2.2 Mineral Soil Amendments and Conditioners 196</p> <p>10.7.2.3 Different Types of Inorganic Amendments 197</p> <p>10.8 Combination Strategy for Soil Quality Improvement 202</p> <p>10.9 Conclusion and Future Prospects 203</p> <p>References 203</p> <p><b>11 Improved Plant Resistance by Phytomicrobiome Community Towards Biotic and Abiotic Stresses </b><b>207<br /></b><i>Neha Trivedi</i></p> <p>11.1 Introduction 207</p> <p>11.2 Microbes and Plants 207</p> <p>11.2.1 Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants 208</p> <p>11.2.2 Microbial-Induced Response to Stresses 208</p> <p>11.3 Response of Abiotic Response on Plant 209</p> <p>11.3.1 Induced Systemic Tolerance (IST) 209</p> <p>11.3.2 Metabolic Changes in Plants Induced by Microbes During Stress 209</p> <p>11.3.2.1 Metabolic Cross-Talk in Plants After Stress Induction 210</p> <p>11.3.2.2 Activation of Antioxidant Mechanism 210</p> <p>11.3.2.3 Activation of Systemically Induced Resistance 210</p> <p>11.4 Role of Phytohormones in Increasing Abiotic and Biotic Stress Tolerance 211</p> <p>11.5 Gene Transfer in Plants 212</p> <p>11.6 Conclusion and Future Prospects 212</p> <p>References 212</p> <p><b>12 Bioprospecting: At the Interface of Plant and Microbial Communities </b><b>217<br /></b><i>Madan L. Verma, Varsha Rani, Reena Kumari, Deepka Sharma, Sanjeev Kumar, and Rekha Kushwaha</i></p> <p>12.1 Introduction 217</p> <p>12.2 Plant-Associated Microbial Communities 218</p> <p>12.3 Beneficial Effects of Plant-Associated Microbial Communities 222</p> <p>12.3.1 Rhizoremediation 223</p> <p>12.3.2 Plant Growth–Promoting Rhizobacteria (PGPR) 223</p> <p>12.3.3 Biotic and Abiotic Stress Resistance 224</p> <p>12.3.4 Signalomics 226</p> <p>12.4 Role of Microbial Processing (Signals) in Facilitating Plant Growth 226</p> <p>12.5 Conclusion and Future Prospects 230</p> <p>Acknowledgments 230</p> <p>References 231</p> <p><b>13 Advances in Omics and Bioinformatics Tools for Phyllosphere Studies </b><b>240<br /></b><i>Hina Bansal</i></p> <p>13.1 Introduction 240</p> <p>13.2 Recent Trends and Approaches 241</p> <p>13.3 Computing for Biology 243</p> <p>13.4 Bioinformatics in Microbial Research 243</p> <p>13.5 Phyllosphere Microbiome Studies Based on Genome-Wide Association 245</p> <p>13.6 Omics Strategies and Their Integration 246</p> <p>13.6.1 Metagenomics 246</p> <p>13.6.2 Metatranscriptomics 246</p> <p>13.6.3 Metabolomics 247</p> <p>13.6.4 Proteomics 247</p> <p>13.7 Conclusion and Future Prospects 248</p> <p>References 248</p> <p><b>14 Microbial Mediated Zinc Solubilization in Legumes for Sustainable Agriculture </b><b>254<br /></b><i>Pawan Saini, Sharon Nagpal, Pooja Saini, Arun Kumar, and Mudasir Gani</i></p> <p>14.1 Introduction 254</p> <p>14.2 Chronological Events of Zinc Biology 255</p> <p>14.3 Role of Zinc in Living System 256</p> <p>14.3.1 Essentiality of Zinc in Humans 256</p> <p>14.3.2 Essentiality of Zinc in Plants 257</p> <p>14.4 Zinc Deficiency vs. Zinc Toxicity in Crop Plants 259</p> <p>14.5 Availability of Zinc in Soil Environment 260</p> <p>14.6 Factors Affecting Zinc Availability to Plants 261</p> <p>14.7 Response of Legume Crops to Zinc 262</p> <p>14.8 Microbial Mediated Zinc Solubilization in Legume Crops 263</p> <p>14.8.1 Zinc-Solubilizing Bacteria (ZnSB) 264</p> <p>14.8.2 Zinc-Solubilizing Fungi (ZnSF) 265</p> <p>14.9 Conclusion and Future Prospects 266</p> <p>References 266</p> <p><b>15 Composition and Interconnections in Phyllomicrobiome </b><b>277<br /></b><i>Meghmala Waghmode, Aparna Gunjal, Neha Patil, and Sonali Shinde</i></p> <p>15.1 Introduction 277</p> <p>15.2 Significance of Phyllospheremicrobiota 279</p> <p>15.3 Phyllosphere Microorganisms as Plant Growth Regulator 280</p> <p>15.3.1 Plant Growth Hormones Production by Phyllosphere Microorganisms 280</p> <p>15.3.2 Phosphorus Solubilization by Phyllosphere Microorganisms 280</p> <p>15.3.3 Siderophores Production by Phyllosphere Microorganisms 280</p> <p>15.3.4 Phyllosphere Microorganisms as Biocontrol Agents Against the Phytopathogens 280</p> <p>15.3.5 Phyllosphere Microorganisms to Reduce Biotic and Abiotic Stress 281</p> <p>15.3.6 Synthesis of 1-Aminocyclopropane-1-Carboxylate Deaminase (ACC) 282</p> <p>15.3.7 Phyllosphere Microorganisms in Nitrogen-Fixation 282</p> <p>15.3.8 Frost Injury and Frost Control by Altering the Phyllosphere Microbiota 282</p> <p>15.3.9 Remediation of Toxic Pollutants 283</p> <p>15.3.10 Plant Probiotics 283</p> <p>15.3.11 Role of Phyllosphere Microorganisms in Climate Change 284</p> <p>15.3.12 Phyllosphere Microorganisms in Nutrient Yield and Increase of Plant Growth 284</p> <p>15.3.13 Plant Hormones as Colonization Mediators of the Plant Leaves 284</p> <p>15.4 Plant–Pathogen Interactions Mediated by Phyllosphere Microbiome 285</p> <p>15.4.1 Interaction Dependent on the Ionome 285</p> <p>15.4.2 Role of Secretory Systems and Secretory Products 285</p> <p>15.4.3 Quorum Sensing 286</p> <p>15.5 Conclusion and Future Prospects 286</p> <p>References 286</p>