This book includes 25 contributions from vastly experienced, global experts in PGPR research in a comprehensive and influential manner, with the most recent facts and extended case studies. Also, the chapters address the current global issues in biopesticide research.

• Advances in PGPR Research
• Copyright
• Contents
• Contributors
• Foreword
• Preface
• 1 Mechanisms of Growth Promotion by Members of the Rhizosphere Fungal Genus Trichoderma
  • 1.1 Introduction
  • 1.2 Trichoderma Plant Growth Promotion: Direct Mechanisms
    • 1.2.1 Nutrient acquisition
      • Phosphate solubilization
      • Siderophores
      • Synthesis of secondary metabolites
  • 1.3 Trichoderma Plant Growth Promotion: Indirect Mechanisms
    • 1.3.1 Biocontrol of plant disease
      • Induced systemic resistance
      • Mycoparasitism
      • Antibiosis
      • Competition
    • 1.3.2 Abiotic Stress Tolerance
  • 1.4 The ‘Omics’ of Trichoderma
    • 1.4.1 Trichoderma –plant interaction transcriptomics
    • 1.4.2 Proteomics
  • 1.5 Conclusion
  • Acknowledgments
  • References
• 2 Physiological and Molecular Mechanisms of Bacterial Phytostimulation
  • 2.1 Introduction
  • 2.2 Chemical Recognition between Plants and Bacteria
    • 2.2.1 Plant developmental and genetic responses to PGPR
    • 2.2.2 Plant molecular responses to PGPR
  • 2.3 Bacterial Signals Regulate Root Morphogenesis
    • 2.3.1 N-acyl-L-homoserine lactones
    • 2.3.2 Cyclodipeptides
    • 2.3.3 Volatile compounds
    • 2.3.4 Virulence factors
  • 2.4 Molecular Responses of Bacteria to Root Exudates
    • 2.4.1 Exudate-induced changes in PGPR gene expression
    • 2.4.2 Exudates modulate the protein profile
  • 2.5 Conclusion
  • References
• 3 Real-time PCR as a Tool towards Understanding Microbial Community Dynamics in Rhizosphere
  • 3.1 Introduction
  • 3.2 Extraction of Metagenomic Nucleic Acid from Environment
    • 3.2.1 Cell lysis
    • 3.2.2 Purification of nucleic acid
    • 3.2.3 Extraction of RNA from soil
  • 3.3 Real-time PCR
    • 3.3.1 q-PCR: Setting up the reaction
    • 3.3.2 Primer designing
    • 3.3.3 Optimizing real-time PCR conditions
    • 3.3.4 Standards for quantification, calibration curve generation and normalization
  • 3.4 Microbial Gene Abundance and Expression Studies in Rhizosphere Biology
    • 3.4.1 16S rRNA as a molecular chronometer for total bacteria
    • 3.4.2 Quantification of specific microbial taxa
    • 3.4.3 Functional genes as markers
  • 3.5 Conclusion
  • Acknowledgement
  • References
• 4 Biosafety Evaluation: A Necessary Process Ensuring the Equitable Beneficial Effects of PGPR
  • 4.1 Biosafety of PGPR in Soil
    • 4.1.1 Risk groups and biosafety levels
    • 4.1.2 Ecological interactions
      • Soil indigenous populations
      • Soil essential populations: the beneficial organisms
    • 4.1.3 Hidden dangers in the use of PGPR
    • 4.1.4 Economic impact of inattentive application
  • 4.2 Mechanisms Involved
    • 4.2.1 Antigenic substances
    • 4.2.2 Biological control agents
    • 4.2.3 Competence
    • 4.2.4 Virulence
    • 4.2.5 Alteration of plant-associated mechanisms
  • 4.3 Determining the Biosafety of PGPR
    • 4.3.1 In vitro bioassays
    • 4.3.2 Environmental and human safety (EHSI) index as a new biosafety tool
  • 4.4 Conclusions and Future Prospects of Biosafety Screening
  • References
• 5 Role of Plant Growth-Promoting Microorganisms in Sustainable Agriculture and Environmental Remediation
  • 5.1 Introduction: Plant Growth- Promoting Rhizobacteria (PGPR)
  • 5.2 Role of Plant Growth-Promoting Bacteria (PGPR) and Fungi (PGPF) in Sustainable Agriculture
    • 5.2.1 Fixation, solubilization and mineralization of nutrients
      • Biological nitrogen fixation
      • Phosphate solubilization
      • Potassium solubilization
      • Fe sequestration
    • 5.2.2 Phytostimulation by production of hormones
    • 5.2.3 Enhanced resistance against abiotic stresses
    • 5.2.4 Role of PGPR and PGPF in disease control
      • Antagonism against phytopathogenic microbes
      • PGPR-mediated breakdown of pathogen communication
      • PGPR-mediated ISR and change in root exudation
      • Non-pathogen: production of lipopeptides as ISR agents
      • Plant-driven recruitment of PGPR for defence
    • 5.2.5 Enhancing the nutritional quality and yield of agricultural produce
    • 5.2.6 Beneficial microbiome management and recruitment in the rhizosphere
  • 5.3 Importance of PGPR and PGPF in Phyto/Bioremediation
    • 5.3.1 Heavy metals
    • 5.3.2 Organic contaminants
  • 5.4 Role of PGPR and PGPF in Biomass and Biofuel Production
  • 5.5 Role of PGPR and PGPF in Wasteland and Degraded Land Reclamation
  • 5.6 Role of Plant Growth-Promoting Microorganisms in Carbon Sequestration under Warming Climate
  • 5.7 Strategies for Enhancing the Performance of Plant Growth-Promoting Microorganisms
    • 5.7.1 Agronomic practices
    • 5.7.2 Rhizospheric engineering
    • 5.7.3 Molecular approach
  • 5.8 Challenges and Future Research Perspectives
  • Acknowledgements
  • References
• 6 Pseudomonas Communities in Soil Agroecosystems
  • 6.1 Introduction
  • 6.2 Tillage Managements and Sustainable Agriculture Systems
  • 6.3 Application of Agrochemicals
  • 6.4 Crop Species
  • 6.5 Suppressive Soils and Pseudomonas : a Close Relationship
  • 6.6 Perspectives and Future Directions
  • References
• 7 Management of Soilborne Plant Pathogens with Beneficial Root-Colonizing Pseudomonas
  • 7.1 Introduction
  • 7.2 Rhizosphere Pseudomonads and Natural Suppression of Soilborne Plant Pathogens
    • 7.2.1 Take-all decline
    • 7.2.2 Rhizoctonia -suppressive soils
    • 7.2.3 Soils suppressive to Thielaviopsis basicola and Fusarium oxysporum
  • 7.3 The emerging Role of Rhizodeposits in the Establishment and Performance of Pseudomonas Spp. in Suppressive Soils
  • 7.4 Biocontrol Pseudomonas spp. as a Model for Climate-Driven Selection of Beneficial Microbiome
  • 7.5 Conclusion
  • References
• 8 Rhizosphere, Mycorrhizosphere and Hyphosphere as Unique Niches for Soil-Inhabiting Bacteria and Micromycetes
  • 8.1 Introduction
  • 8.2 Historical Aspects of Rhizosphere, Mycorhizospere and Hyphosphere Study and Modern Research Approaches
    • 8.2.1 The terms: brief background
    • 8.2.2 Research approaches: some recent advances and classical techniques
  • 8.3 Rhizosphere, the Niche Influenced by Plant Roots
    • 8.3.1 Bacteria in rhizosphere
    • 8.3.2 Micromycetes in rhizosphere
  • 8.4 Mycorrhizosphere, the Niche Influenced both by Roots and ­Associated Mycobionts
    • 8.4.1 Bacteria in mycorrhizosphere
    • 8.4.2 Micromycetes in mycorrhizosphere
  • 8.5 Hyphosphere, the Niche Influenced By Fungi
    • 8.5.1 Bacteria in hyphosphere
    • 8.5.2 Micromycetes in hyphosphere
  • 8.6 Conclusion
  • 8.7 Future Trends and Perspectives
  • Acknowledgements
  • References
• 9 The Rhizospheres of Arid and Semi-arid Ecosystems are a Source of Microorganisms with Growth-Promoting Potential
  • 9.1 Introduction
  • 9.2 Extremophile Microorganisms
    • 9.2.1 Thermophiles
    • 9.2.2 Psychrophiles
    • 9.2.3 Halophiles
    • 9.2.4 Alkaliphiles
    • 9.2.5 Acidophiles
  • 9.3 Concluding Remarks
  • References
• 10 Rhizosphere Colonization by Plant-Beneficial Pseudomonas spp.: Thriving in a Heterogeneous and Challenging Environment
  • 10.1 Introduction
  • 10.2 The Rhizosphere: a Heterogeneous Environment Shaped by Plant Rhizodeposition
    • 10.2.1 Root exudation
      • Composition
      • Mechanisms
      • Localization
    • 10.2.2 Senescence of root outer cells
    • 10.2.3 Contributions of the rhizodeposition mechanisms
  • 10.3 Beneficial Pseudomonas spp. Colonization of the Rhizosphere and Their Influence on the Plant Physiology
    • 10.3.1 Rhizosphere colonization
    • 10.3.2 Pseudomonas spp. toolbox to impact the plant
      • Disruption of plant hormone signalling
      • Alteration of root exudation
      • Type III secretion system
  • 10.4 Competitiveness-Enhancing Traits Involved in Pseudomonas spp. Rhizosphere Colonization
    • 10.4.1 Root exudates utilization
    • 10.4.2 Siderophore production and uptake
    • 10.4.3 Nitrogen dissimilation
    • 10.4.4 Phase variation
    • 10.4.5 Phenazine production
  • 10.5 Conclusions and Future Prospects
  • References
• 11 Endophytomicrobiont: A Multifaceted Beneficial Interaction
  • 11.1 Introduction
  • 11.2 Endophytic Classification
  • 11.3 Recognition of Endophytic Status In Planta
  • 11.4 Plant Colonization by Endophytic Bacteria: the Complete Process
    • 11.4.1 Chemotaxis
    • 11.4.2 Biofilm formation: the basis of endophytism
    • 11.4.3 Tissue invasion for endophytic entry
    • 11.4.4 Plant defence genes involved in endophytic colonization
    • 11.4.5 Entry and localization within plant tissues
  • 11.5 Multifaceted Benefits of Endophytic Bacteria
    • 11.5.1 Plant growth promotion
    • 11.5.2 Remediators of oxidative stress
    • 11.5.3 Bioremediation
    • 11.5.4 Antibiotic production
  • 11.6 Endophytes as Parasites
  • 11.7 Conclusion and Future Prospects
  • Acknowledgements
  • References
• 12 Contribution of Plant Growth-Promoting Bacteria to the Maize Yield
  • 12.1 Introduction
  • 12.2 Bacteria and Maize
    • 12.2.1 Endophytic bacteria
    • 12.2.2 Rhizospheric bacteria
    • 12.2.3 Plant growth-promoting bacteria
  • 12.3 Bacterial Mechanism of Plant Growth Promotion
    • 12.3.1 Biological nitrogen fixation
    • 12.3.2 Phosphate solubilization
    • 12.3.3 Siderophore production
    • 12.3.4 Indole acetic acid production
    • 12.3.5 ACC-deaminase
  • 12.4 Maize Yield Improved by Bacteria in Field Trial
    • 12.4.1 Azospirillum
      • Study 1 (Fulchieri and Frioni, 1994)
      • Study 2 (Swędrzyńska and Sawicka, 2000)
      • Study 3 (Hungria et al., 2010)
      • Study 4 (Ferreira et al., 2013)
      • Study 5 (Morais et al., 2016)
      • Study 6 (Müller et al., 2016)
      • Study 7 (Fukami et al., 2016)
    • 12.4.2 Pseudomonas
      • Study 1 (Shaharoona et al., 2006)
      • Study 2 (Hameeda et al., 2008)
      • Study 3 (Viruel et al., 2014)
    • 12.4.3 Azotobacter
      • Study 1 (Hussain et al., 1987)
      • Study 2 (Pandey et al., 1998)
      • Study 3 (Hajnal-Jafari et al., 2012)
    • 12.4.4 Serratia
      • (Hameeda et al., 2008)
    • 12.4.5 Rhanella
      • (Montañez and Sicardi, 2013)
    • 12.4.6 Herbaspirillum
      • (Alves et al., 2015)
  • 12.5 Conclusion
  • Reference
• 13 The Potential of Mycorrhiza Helper Bacteria as PGPR
  • 13.1 Introduction
  • 13.2 Early Findings
  • 13.3 Proposed Helper Mechanisms
    • 13.3.1 Promoted germination of fungal propagules
    • 13.3.2 Promoted mycelial growth
    • 13.3.3 Modification of the mycorrhizosphere soil
    • 13.3.4 Host recognition and modifications in root system architecture
    • 13.3.5 Receptivity of the roots
  • 13.4 Genomic Approaches
  • 13.5 Potential use of MHB as PGPR
  • 13.6 Future Challenges in MHB Research
  • References
• 14 Methods for Evaluating Plant Growth-Promoting Rhizobacteria Traits
  • 14.1 Introduction
    • 14.1.1 Plant growth-promoting rhizobacteria
    • 14.1.2 Types of PGPR
    • 14.1.3 Mechanisms of action
    • 14.1.4 The need for PGPR utilization in agricultural practice
  • 14.2 Determination of PGPR Properties
    • 14.2.1 Nitrogen fixation
      • Growth in solid N-free media
      • Growth in semisolid N-free media
      • Acetylene (C 2 H 2)-dependent ethylene (C 2 H 4) production (acetylene reduction activity (ARA) assay
      • PCR amplification of nif genes
    • 14.2.2 Phosphate solubilization
      • Qualitative assay
      • Quantitative assay
    • 14.2.3 Siderophores production
      • Qualitative assay
      • Quantitative assay
    • 14.2.4 Indole acetic acid production
      • Quantitative assay of intrinsic IAA and IAA-related compounds
      • Quantitative determination of potential IAA and IAA-related compounds
    • 14.2.5 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity
      • Qualitative assay
      • Quantitative assay
    • 14.2.6 PGPR as biocontrol agent
      • Antagonism
      • Antibiosis
      • Hydrogen cyanide production
      • Exo-polysaccharides production
      • Lytic enzyme production
  • 14.3 Conclusion
  • Acknowledgements
  • References
• 15 The Rhizosphere Microbial Community and Methods of its Analysis
  • 15.1 Introduction
  • 15.2 Rhizospheric Microbial Communities
  • 15.3 Methods for Microbial Community Analysis
    • 15.3.1 Culture-dependent methods
      • Dilution plating and culturing methods
      • Community-level physiological profiles
    • 15.3.2 Culture-independent techniques
      • Fatty acid methyl ester analysis (FAME)
      • Phospholipid fatty acids (PLFAs)
      • Fluorescent in situ hybridization (FISH)
      • Flow cytometry (FCM)
      • Automated ribosomal intergenic spacer analysis (ARISA)
      • 16S rRNA amplicon pyrosequencing
      • Denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE)
      • Restriction fragment length polymorphism (RFLP)/amplified ribosomal DNA restriction analysis (ARDRA)
      • Terminal restriction fragment length polymorphism (T-RFLP)
      • Single-strand conformation polymorphism (SSCP)
      • Amplicon length-heterogeneity PCR (LH-PCR)
      • Random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) technique
      • DNA-Microarray
      • Metagenomic approaches
  • 15.4 Conclusions and Future Perspectives
  • References
• 16 Improving Crop Performance under Heat Stress using Thermotolerant Agriculturally Important Microorganisms
  • 16.1 Introduction
  • 16.2 What is Heat Stress?
  • 16.3 Effects of High Temperature on Plants
    • 16.3.1 Seed germination and emergence
    • 16.3.2 Growth and morphology
    • 16.3.3 Physiological effects
    • 16.3.4 Photosynthesis
    • 16.3.5 Water relations
    • 16.3.6 Dry matter partitioning
    • 16.3.7 Reproductive development
    • 16.3.8 Yield
  • 16.4 Heat Stress Tolerance in Plants
  • 16.5 Role of Microorganisms to Improve Crop Performance under Stress
    • 16.5.1 Adaptation of microorganisms as a response to abiotic stress
    • 16.5.2 PGPR-mediated alleviation of abiotic stress
  • 16.6 Conclusion
  • Acknowledgement
  • References
• 17 Phytoremediation and the Key Role of PGPR
  • 17.1 Phytoremediation
    • 17.1.1 Phytoremediation mechanisms
    • 17.1.2 Focus on bioavailability
  • 17.2 Significance of PGPR for an Effective Phytoremediation
  • 17.3 PGPR Effect on Metals Phytoextraction
  • 17.4 Rhizoremediation of Organic Contaminants
  • References
• 18 Role of Plant Growth-Promoting Rhizobacteria (PGPR) in Degradation of Xenobiotic Compounds and Allelochemicals
  • 18.1 Xenobiotic Compounds and Allelochemicals – Major Inhibitors of Plant Growth and Productivity
    • 18.1.1 Xenobiotic compounds as priority environmental pollutants
    • 18.1.2 Effects of xenobiotic compounds on plant growth and productivity
    • 18.1.3 Approaches for decontamination of niches contaminated with xenobiotic compounds
    • 18.1.4 Biological approaches for degradation of xenobiotic compounds
    • 18.1.5 Plant associated microorganisms for degradation of xenobiotic compounds
    • 18.1.6 Allelochemicals as potential inhibitors of normal plant growth
    • 18.1.7 Structural and functional diversity of allelochemicals and their mode of actions
    • 18.1.8 Role of allelochemicals in ecological success of invasive plants and weeds
    • 18.1.9 Invasive plants with allelopathy potential
    • 18.1.10 Environmental fate of allelochemicals – natural factors and microbial metabolism
  • 18.2 Microbial Degradation of Xenobiotic Compounds and Allelochemicals
    • 18.2.1 Microbial degradation of xenobiotic compounds
    • 18.2.2 Degradation of xenobiotic compounds by plant-associated microorganism (endophytes and PGPRs)
    • 18.2.3 Degradation of xenobiotic compounds by rhizospheric bacteria and PGPR
    • 18.2.4 Degradation of xenobiotic compounds via rhizosphere engineering
    • 18.2.5 Genetically modified rhizospheric bacteria/PGPR for degradation of xenobiotic compounds
    • 18.2.6 Microbial degradation of allelochemicals
    • 18.2.7 Degradation of allelochemicals by rhizospheric bacteria/PGPR
  • 18.3 Conclusion and Future Perspective
  • References
• 19 Harnessing Bio-priming for Integrated Resource Management under Changing Climate
  • 19.1 Introduction
  • 19.2 Bio-priming
  • 19.3 Advantages of Bio-priming with Reference to Stress Moderation
  • 19.4 Mechanisms Used by Microorganisms for Improved Plant Nutrition
  • 19.5 Effect of Bio-priming in Different Crop Species
  • 19.6 Proteomic Analysis Induced by Bio-Priming
  • 19.7 Conclusion
  • Acknowledgement
  • References
• 20 Unravelling the Dual Applications of  Trichoderma spp. as Biopesticide and Biofertilizer
  • 20.1 Introduction
  • 20.2 Commercial Biocontrol Agents
  • 20.3 Trichoderma Biodiversity
  • 20.4 Trichoderma spp. Identification
  • 20.5 Trichoderma spp. as Biopesticide
    • 20.5.1 Mycoparasitism
    • 20.5.2 Antibiosis
    • 20.5.3 Competition
  • 20.6 Trichoderma spp. as Biofertilizers
  • 20.7 Commercial Formulations of  Trichoderma spp.
  • 20.8 Conclusion and Future Prospects
  • Acknowledgments
  • References
• 21 Genome Insights into Plant Growth-Promoting Rhizobacteria, an Important Component of Rhizosphere Microbiome
  • 21.1 Introduction
  • 21.2 Bacterial Rhizobiome
  • 21.3 Mechanisms of PGPR
  • 21.4 NGS Technologies and Genome Assembly
  • 21.5 Genome-based Taxonomy and Phylogenomics
  • 21.6 Genome Mining of Plant Beneficial Genes in PGPR
  • 21.7 Comparative Genomic Analyses
  • 21.8 Conclusion and Future Prospects
  • References
• 22 Plant Growth-Promoting Rhizobacteria (PGPR): Mechanism, Role in Crop Improvement and Sustainable Agriculture
  • 22.1 Introduction
  • 22.2 History
  • 22.3 Plant Growth-Promoting Rhizobacteria (PGPR)
  • 22.4 Role of PGPR in soil
  • 22.5 PGPR and their Interaction with Plants
  • 22.6 Mechanism of PGPR
    • 22.6.1 Direct antagonism
      • Hyperparasitism
      • Nitrogen fixation
      • Phosphate solubilization
      • Potassium solubilization
      • Phytohormone production
    • 22.6.2 Indirect mechanisms
      • Antibiosis
      • Siderophore production
      • Burkholderia phytofirmans
      • Role of Burkholderia phytofirmans as PGPR
      • Microbe–microbe signalling in the rhizosphere
  • 22.7 Future Prospective
  • 22.8 Conclusion
  • Acknowledgements
  • References
• 23 PGPR: A Good Step to Control Several of Plant Pathogens
  • 23.1 Introduction
  • 23.2 Biocontrol of Plant Virus
  • 23.3 Biocontrol of Plant Bacteria
  • 23.4 Biocontrol of Plant Fungi
  • 23.5 Biocontrol of Plant Nematode
  • 23.6 Biocontrol of Plant Parasite
  • 23.7 Biocontrol of Phytoplasma
  • 23.8 Conclusion
  • References
• 24 Role of Trichoderma Secondary Metabolites in Plant Growth Promotion and Biological Control
  • 24.1 Introduction
  • 24.2 Trichoderma : An Overview
  • 24.3 Secondary Metabolites
  • 24.4 Secondary Metabolites of Trichoderma
  • 24.5 Adequacy of Secondary Metabolites Inferred from Trichoderma
  • 24.6 Conclusion
  • Acknowledgment
  • References
• 25 PGPR-Mediated Defence Responses in Plants under Biotic and Abiotic Stresses
  • 25.1 Introduction
  • 25.2 PGPR in Abiotic Stress Management
  • 25.3 PGPR in Biotic Stress Management
  • 25.4 Conclusion
  • References
• Index