Microbiome Stimulants for Crops

Description

Microbiome Stimulants for Crops: Mechanisms and Applications provides the latest developments in the real-world development and application of these crop management alternatives in a cost-effective, yield protective way. Sections address questions of research, development and application, with insights into recent legislative efforts in Europe and the United States. The book includes valuable information regarding mechanisms and the practical information needed to support the growing microbial inoculant and biostimulant industry, thus helping focus scientific research in new directions.

Provides methods for finding and testing endophytic and growth promotional microbes
Explains the mechanisms of microbes and other biostimulant function in promoting plant growth
Evaluates methods for treatments of plants with microbes and microbiome stimulants
Identifies areas for new research

Front Cover 2
Microbiome Stimulants for Crops 5
Copyright Page 6
Contents 7
List of contributors 15
Introduction 19
- References 20
1 Microbial endophytes: evolution, diversity, community functions, and regulation 21
- 1.2 Endophytism, rhizophagy cycle, and plant development 21
- 1.1 Evolution of endophytism 21
- 1.3 The clavicipitalean model for the evolution of endophytism 22
  - 1.3.2 Epichloë endophytes as fungi trapped in host plants 23
  - 1.3.1 Life cycle variations 23
  - 1.3.3 Significance of meristem colonization 24
- 1.5 Plant and fungal diversity 24

Front Cover 2
Microbiome Stimulants for Crops 5
Copyright Page 6
Contents 7
List of contributors 15
Introduction 19
- References 20
1 Microbial endophytes: evolution, diversity, community functions, and regulation 21
- 1.2 Endophytism, rhizophagy cycle, and plant development 21
- 1.1 Evolution of endophytism 21
- 1.3 The clavicipitalean model for the evolution of endophytism 22
  - 1.3.2 Epichloë endophytes as fungi trapped in host plants 23
  - 1.3.1 Life cycle variations 23
  - 1.3.3 Significance of meristem colonization 24
- 1.5 Plant and fungal diversity 24
- 1.4 Geographic patterns 24
- 1.6 Species and community regulation in clavicipitalean endophytes 25
- 1.7 Plant-microbe talking: signaling and sensing 26
  - 1.7.1 Fungal quorum signaling and inhibiting metabolites 27
  - 1.7.2 Plant-produced reactive oxygen and quorum inhibitors of pathogenicity 28
- 1.8 Future challenges 29
- References 30
- Acknowledgment 30
- Conflicts for interest 30
2 Friends in low places: Soil derived microbial inoculants for biostimulation and biocontrol in crop production 35
- 2.1 Terrestrial plants evolved with the help of soil microbes 35
- 2.2 Targeting soils for bioprospection of microbial inoculants 37
- 2.3 Plant growth-promoting soil microbes 38
- 2.4 Soil microbes helping plants resist abiotic stress 39
  - 2.4.1 Aiding in plant nutrition 39
  - 2.4.2 Helping plants cope with soil salinity and drought stress 40
  - 2.4.3 Rhizosphere microbes helping with soil phytoremediation 41
  - 2.4.4 Soil microbes can bioharden, bioprime, and biotize plantlets to reduce transplant shock 42
- 2.5 Using soil microbes for biocontrol of plant pathogens 42
- 2.6 Soil microbes can help plants establish symbiosis with other rhizosphere dwellers 44
- 2.7 Conclusions 44
- References 45
3 The roles of endophytes in modulating crop plant development 53
- 3.1 Introduction 53
- 3.2 Endophytes and plant growth promotion 54
  - 3.2.2 Modulation of plant development through nutrient mobilization 54
  - 3.2.1 Modulation of plant development through phytohormones production 54
- 3.3 Endophytes and protection of plant from abiotic stresses 56
- 3.5 Conclusion 57
- 3.4 Endophytes and protection of crop plant from diseases 57
- Acknowledgment 58
- References 58
4 Epichloë endophytes stimulate grass development and physiological state in China 61
- 4.1 Introduction 61
- 4.2 Salt stress 62
- 4.3 Disease resistance 63
- 4.5 Drought stress 66
- 4.4 Cold stress 66
- 4.6 Nitrogen stress 67
- 4.8 Insect 68
- 4.7 Heavy metal stress 68
- 4.10 Root-associated microorganism communities 69
- 4.9 Breeding 69
- 4.11 Conclusion and future prospects 73
- References 73
5 Endophytic microbes promote plant growth and alter host secondary metabolites 79
- 5.1 Introduction 79
- 5.2 Endophytes versus epiphytes and mycorrhizae 79
- 5.3 Entrance, establishment, and transmission of endophytes within plants 80
  - 5.3.1 Endophytic microbes in plant growth enhancement 81
  - 5.3.2 Endophytic microbes in plant protection 82
- 5.4 Microbial endophytes altering host secondary metabolites 85
  - 5.4.2 Endophytes colonization induces host metabolite production 85
  - 5.4.1 Partial or total production of host-derived metabolites by endophytes 85
  - 5.4.3 Biotransformation of host origin compounds by endophytes 86
- Acknowledgment 87
- References 87
- 5.5 Conclusion 87
- Further reading 92
6 The dynamic mechanisms underpinning symbiotic Epichloë–grass interactions: implications for sustainable and resilient agr... 93
- 6.1 Introduction 93
- 6.2 Epichloë life cycle 94
- 6.3 Epichloë secondary metabolites 97
- 6.4 Host and endophyte metabolome changes in response to endophyte infection 100
  - 6.4.3 Benefits of Epichloë under nutrient deficient and/or polluted environmental conditions 101
  - 6.4.1 Specific endophyte-induced changes on the host metabolome 101
  - 6.4.2 Host-induced changes to fungal secondary metabolism 101
  - 6.4.4 Environmental effects on alkaloid production 102
- 6.5 Interactions between Epichloë and other microorganisms 102
- 6.6 Role of the Epichloë reactive NADPH oxidase complex in symbiosis 104
- 6.7 Regulation of iron homeostasis in Epichloë–ryegrass symbioses 106
- 6.8 Mechanisms of host responses—transcriptomics studies 108
- 6.9 Plant hormones and Epichloë fungal endophytes of grasses 111
  - 6.9.2 Plant growth-promoting and stress hormones associated with Epichloë endophytes 113
  - 6.9.1 Plant defense hormones associated with Epichloë endophytes 113
  - 6.9.3 Conclusions and future experiments 114
- 6.10 Applications in agriculture and economic importance 114
- 6.11 Final perspectives 117
- References 118
7 Potential application of plant growth promoting bacteria in bioenergy crop production 129
- 7.1 Introduction 129
- 7.2 Microbiome research in bioenergy crops 129
- 7.3 Growth promotion for bioenergy crops 131
  - 7.3.1 Switchgrass 131
  - 7.3.2 Miscanthus 131
  - 7.3.3 Poplar 132
- 7.4 Stress tolerance 132
  - 7.4.2 Abiotic stress - salt stress 133
  - 7.4.3 Biotic stress control - switchgrass and Miscanthus 133
  - 7.4.1 Abiotic stress - drought 133
- 7.5 Bioremediation 134
- 7.6 Mechanisms 135
  - 7.6.1 Nitrogen fixation 135
  - 7.6.2 Plant hormone regulation 136
  - 7.6.3 Phosphate solubilization 136
  - 7.6.4 Biocontrol of pathogens 136
  - 7.6.5 Abiotic stress tolerance 137
  - 7.6.6 Molecular mechanisms 137
- 7.7 Perspectives and challenges 137
  - 7.7.3 Seed endophytes and vertical transmission 138
  - 7.7.1 Growth promoting efficiency in the field 138
  - 7.7.4 Consortia and superior plant growth promoting bacteria 138
  - 7.7.2 Plant growth promoting bacteria genotype-specific effects 138
  - 7.7.5 Engineering plant growth promoting bacteria with genes of interest 139
- References 139
8 Soil microbiome to maximize the benefits to crop plants—a special reference to rhizosphere microbiome 145
- 8.1 Introduction 145
- 8.2 Soil microbiome and rhizosphere microbiome 147
- 8.3 Microbiome-mediated abiotic stress management and plant growth 147
- 8.4 Physiological and molecular mechanisms mediated abiotic stress management in plants by plant growth-promoting rhizobacteria 149
- 8.5 Microbiome-mediated biotic stress management and plant growth 149
- 8.6 Mechanisms exerted by plant growth-promoting rhizobacteria to combat biotic stress management and plant growth 152
- 8.7 Conclusion 153
- References 153
9 Belowground dialogue between plant roots and beneficial microbes 161
- 9.1 Introduction 161
- 9.3 Plant growth-promoting microbes and their ways out to enhance plant growth 162
  - 9.3.1 Phytohormone production 162
  - 9.3.2 Mineral nutrient assimilation (N2 fixation) and solubilization of insoluble minerals (P, K, Zn, and Si) 165
  - 9.3.3 1-Aminocyclopropane-1-carboxylic acid deaminase activity 166
  - 9.3.4 Volatile organic compounds production for stimulation of plant growth 166
  - 9.3.5 Siderophore and hydrogen cyanide production 167
- 9.2 Crosstalk between plant root system and microorganisms 162
- 9.4 Role of plant growth promoting rhizobacteria in abiotic and biotic stress management 167
  - 9.4.1 Abiotic stresses 167
    - 9.4.1.1 Salinity stress 168
    - 9.4.1.2 Drought stress 168
    - 9.4.1.3 Heavy metals stress 168
  - 9.4.2 Biotic stress management 171
- Acknowledgment 172
- 9.5 Conclusion and future directions 172
- References 173
10 The microbial role in the control of phytopathogens—an alternative to agrochemicals 179
- 10.1 Introduction 179
- 10.2 Antibiosis 180
  - 10.2.1 Antibiosis by Gram-negative bacteria 180
  - 10.2.2 Antibiosis by Gram-positive bacteria 181
  - 10.2.3 Antibiosis by fungi 182
- 10.3 Induction of systemic resistance 182
  - 10.3.1 Plant defenses 182
  - 10.3.2 Inducing systemic resistance mechanisms 183
- 10.4 Interference in the quorum sensing signal by N-acyl homoserine lactones-degrading 184
- 10.5 Control of phytopathogenic agents by mycoparasitism 185
- 10.6 Competition: an indirect interaction with pathogens 185
- 10.7 Licensed products for biological control 187
- References 191
11 Microbial biocontrol formulations for commercial applications 199
- 11.1 Introduction 199
- 11.2 Biocontrol agents 199
- 11.3 Mechanism of action of BCAs 200
  - 11.3.1 Induced resistance 201
  - 11.3.2 Antibiosis 201
  - 11.3.5 Combined modes of action 202
  - 11.3.3 Hyperparasitism (mycoparasitism) 202
  - 11.3.4 Competition 202
- 11.4 Commercialized microbial BCAs 203
- 11.5 Types and modes of application of BCAs 204
  - 11.5.1 Types of BCA 204
    - 11.5.1.1 Bacterial BCAs 204
    - 11.5.1.2 Fungal BCAs 204
    - 11.5.1.3 Yeast BCAs 207
  - 11.5.2 Modes of application of BCAs 207
    - 11.5.2.1 Soil inoculation 207
    - 11.5.2.2 Seed inoculation 208
    - 11.5.2.3 Vegetative part inoculation 208
  - 11.5.3 Formulations 208
    - 11.5.3.5 Nanoparticle based formulations 208
    - 11.5.3.3 Alginate bead-based formulation (encapsulation method) 208
    - 11.5.3.1 Talc-based formulations 208
    - 11.5.3.4 Oil based formulations 208
    - 11.5.3.2 Coffee husk-based formulations 208
  - 11.6 Challenges with microbial BCAs 208
  - 11.8 Conclusions 209
  - 11.7 Future aspects 209
  - References 210
- 12 Potential effect of microbial biostimulants in sustainable vegetable production 213
  - 12.1 Introduction 213
  - 12.2 Microbial biostimulants and action mechanisms 214
    - 12.2.1 Plant growth promoting rhizobacterias as microbial biostimulants and their mechanisms 214
    - 12.2.2 Arbuscular mycorrhizal fungi and its mechanisms as microbial biostimulants 218
  - 12.3 Effects of plant growth promoting rhizobacterias on nutrient uptake in vegetable crops 223
    - 12.3.1 Solanaceae 223
    - 12.3.2 Cucurbitaceae 225
    - 12.3.3 Brassicaceae 227
    - 12.3.4 Other vegetables 228
  - 12.4 Effects of arbuscular mycorrhizal fungi on nutrient uptake in vegetable crops 230
    - 12.4.1 Solanaceae 230
    - 12.4.2 Cucurbitaceae 230
    - 12.4.3 Other vegetables 235
  - 12.5 Conclusions and prospects 238
  - References 239
- 13 Microbes as biostimulants: tissue culture prospective 259
  - 13.1 Introduction 259
  - 13.2 Agriculturally important microorganisms 260
  - 13.3 Mechanism of action 262
  - 13.4 Scope in micropropagation 262
  - References 266
  - 13.5 Conclusions 266
- 14 Biostimulant applications in crops under abiotic stress conditions 273
  - 14.1 Introduction 273
  - 14.2 Impact of abiotic environmental stressors on plants 274
    - 14.2.2 Salinity 274
    - 14.2.1 Drought 274
    - 14.2.3 Heavy metal/metalloid stress 275
    - 14.2.4 Temperature stress 275
  - 14.3 Role of biostimulants in management of abiotic environmental stresses 275
    - 14.3.1 Biostimulants potential in management of drought 276
    - 14.3.2 Biostimulants potential in management of salinity 278
    - 14.3.3 Potential of biostimulants in management of heavy metal stress 279
    - 14.3.4 Biostimulants potential in management of temperature stress 279
    - 14.3.5 Mechanism of action of biostimulants fostering tolerance against environmental stresses 280
  - 14.4 Conclusion and future recommendations 281
  - References 282
- 15 Actinomycetes as biostimulants and their application in agricultural practices 287
  - 15.1 Introduction 287
    - 15.1.1 General characteristics distribution and diversity 287
    - 15.1.2 Functional role of actinobacteria in sustainable agriculture 288
    - 15.1.3 Actinomyces as plant defense mediators 288
    - 15.1.4 Ecological relevance of actinobacteria 289
  - 15.2 Isolation, identification, and characterization of actinomycetes 289
    - 15.2.1 Isolation sources 289
    - 15.2.2 Morphological, biochemical, molecular, and physiological characterization of actinobacteria 290
  - 15.3 Function role of actinobacteria in plant growth and soil ecosystem 291
    - 15.3.1 Actinobacteria as plant growth-promoting rhizobacteria 291
    - 15.3.2 Role of actinomycetes in soil health and benefits 292
  - 15.4 Actinomycetes: defense mediators against plant pathogens and control of plant diseases 293
  - 15.5 Role of actinomycetes in management and resilience toward abiotic stresses 294
  - 15.6 Recent advances in actinomycetes research 295
  - Acknowledgments 296
  - References 296
  - Conflict of interest statement 296
  - 15.7 Conclusion 296
  - Author contributions 296
- 16 An insight on potential role of microbial volatiles as an aromatic tool in management of crop productivity 303
  - 16.1 Introduction 303
  - 16.2 Chemical nature and diversity of microbial volatiles 303
  - 16.3 Role of microbial volatiles in plant–microbe interaction and signaling 304
  - 16.4 Role of microbial volatiles in stress tolerance 305
  - 16.7 Microbial volatiles as semiochemicals 306
  - 16.5 Microbial volatiles in pollination by insects 306
  - 16.6 Inhibitory potential of microbial volatiles against soilborne pathogens 306
  - 16.9 Environmental factors controlling the emission of microbial volatiles 307
  - 16.8 Microbial volatiles as indicators of growth promotion 307
  - 16.10 Microbial volatiles and climate changes 308
  - 16.11 Conclusions and future perspectives 308
  - References 309
- 17 Microbial consortia: approaches in crop production and yield enhancement 313
  - 17.1 Introduction 313
  - 17.2 Classification of microbial consortia on the basis of functions 314
    - 17.2.2 Nutrient exchange consortium 314
    - 17.2.3 Substrate facilitator consortium 314
    - 17.2.1 Environment maintenance consortium 314
    - 17.2.4 Signal exchange consortium 314
  - 17.3 Microbial consortia aspects in plant growth promotion 316
    - 17.3.1 Stimulation of phytohormone production 316
      - 17.3.1.1 Auxins 316
      - 17.3.1.2 Cytokinins and gibberellins 317
      - 17.3.1.3 Ethylene 317
    - 17.3.2 Solubilization of mineral nutrients 317
      - 17.3.2.3 Uptake of other nutrients 317
      - 17.3.2.1 Phosphate solubilization 317
      - 17.3.2.2 Potassium solubilization 317
    - 17.3.3 Nitrogen fixation 318
    - 17.3.4 Siderophore production 318
  - 17.4 Applications of microbial consortia in plant growth promotion 318
  - 17.5 Selection of microbes in the consortium 318
  - 17.6 Advantages of a microbial consortium 319
  - 17.7 Disadvantages of a microbial consortium 319
  - 17.8 Conclusion and future prospective 319
  - References 320
- 18 Fungi, fungal enzymes and their potential application as biostimulants 325
  - 18.2 Biostimulants 325
    - 18.2.1 Types of plant-based biostimulants 325
      - 18.2.1.1 Chitosan 326
      - 18.2.1.4 Phosphites (Phi) and silicon 326
      - 18.2.1.2 Humic substances 326
      - 18.2.1.5 Seaweed extracts 326
      - 18.2.1.3 Protein hydrolysates 326
    - 18.3 Types of plant growth-promoting fungi 327
      - 18.3.1 Endophytic fungi in agriculture 327
      - 18.3.2 Mycorrhizal fungi in agriculture 328
    - 18.2.2 Types of microbial biostimulants 327
      - 18.2.2.1 Plant growth-promoting rhizobacteria 327
      - 18.2.2.2 Fungi as biostimulants 327
    - 18.4 Role of soil enzymes in agriculture 328
    - 18.5 Fungal enzymes as biostimulants 328
      - 18.5.1 Biocontrol 328
        
        18.5.1.1 Fungal chitinases 328
        
        18.5.1.2 Fungal cellulases 329
  - 18.1 Introduction 325

Mechanisms and Applications

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