Rhizosphere Engineering

Front Cover
Rhizosphere Engineering
Copyright
Dedication
Contents
Contributors
Preface
Chapter 1 Plant growth promotion by rhizosphere dwelling microbes
1.1 Introduction
1.2 Plant growth promoting rhizobacteria (PGPR)
1.2.1 Pseudomonads
1.2.2 Bacillus and Paenibacillus
1.2.3 Streptomyces
1.3 Plant growth-promoting fungi (PGPF)
1.3.1 Piriformospora
1.3.2 Trichoderma
1.3.3 Fusarium
1.3.4 Penicillium
1.4 Plant growth-promoting protozoa
1.5 Conclusions
References
Chapter 2 Indigenous nitrogen fixing microbes engineer rhizosphere and enhance nutrient availability and plant growth
2.1 Introduction
2.2 Nitrogen-fixing microbes
2.3 Mechanism of biological nitrogen fixation
2.3.1 Symbiotic nitrogen fixation
2.3.2 Nonsymbiotic nitrogen fixation
2.4 Rhizosphere engineering by N2-fixing microbes
2.5 Role of nitrogen-fixing microbes in plant growth enhancement and nutrient uptake
2.6 Nitrogen-fixing microbes as biofertilizer for sustainable agriculture
2.7 Conclusions
References
Chapter 3 Rhizospheric bacteria as soil health engineer promoting plant growth
3.1 Introduction
3.2 Mechanisms involved in plant growth promotion by rhizobacteria
3.2.1 Availability of soil phosphorus and phosphate solubilization
3.2.2 Phytohormone production
3.2.3 1-Aminocyclopropane-1-carboxylate (ACC)-deaminase activity
3.2.4 Production of siderophores
3.2.5 Production of antifungal metabolites
3.3 Stress tolerance in PGPR
3.4 Rhizosphere competence of PGPR
3.5 Effect of PGPR on plant growth
References
Chapter 4 Role of Bacillus species in soil fertility with reference to rhizosphere engineering
4.1 Introduction
4.2 Characters and diversity of Bacillus species
4.3 Bioefficacy of B. subtilis
4.4 Induction of systemic resistance (ISR) by B. subtilis isolates for growth promotion
4.5 Peroxidise activity
4.6 Polyphenol oxidase activity
4.7 Phenylalanine ammonia-lyase activity
4.8 Formulation, shelf-life, and compatibility of B. subtilis with fungicides
4.9 Conclusions
Acknowledgment
References
Chapter 5 Rhizobium as soil health engineer
5.1 Introduction
5.2 Classification and history of Rhizobium
5.3 Importance of Rhizobium in governing soil health and crop productivity
5.3.1 Soil physical condition and reactions
5.3.1.1 Soil pH (acidity and alkalinity)
5.3.1.2 Saline soil
5.3.1.3 Chemical residue in soil
5.3.2 Nitrogen enrichment
5.3.3 BNF mechanism
5.3.4 Siderophore as chelating agent
5.3.5 Rhizobium as biocontrol agent
5.3.6 Removal of heavy metals and other pollutants
5.3.6.1 Rhizoremediation
5.3.6.2 Factors affecting rhizoremediation
5.3.7 Needs for rhizobial inoculates
5.3.8 In hill agrosystem
5.4 Factors affecting the Rhizobium in soil
5.4.1 Mineral nutrition
5.4.2 Abiotic and biotic factors
5.5 Conclusion
References
Chapter 6 Azotobacter —A potential symbiotic rhizosphere engineer
6.1 Introduction
6.2 Azotobacter —A beneficial bacterium
6.3 PGPR activities of Azotobacter
6.3.1 Vitamins and amino acids
6.3.2 Plant growth hormones (IAA, GA)
6.3.3 Phosphate solubilization
6.3.4 Anti-mycotic compounds
6.3.5 HCN and siderophore production
6.3.6 Nitrogen fixation
6.4 Impact of pesticides on soil ecosystem
6.5 Effect of pesticides on Azotobacter
6.6 Biodegradation of pesticides
6.7 Benefits of Azotobacter in agriculture
6.8 Conclusions
Acknowledgment
References
Chapter 7 Application of cyanobacteria in soil health and rhizospheric engineering
7.1 Introduction
7.2 Cyanobacteria in the improvement of soil health
7.2.1 Biofertilizers
7.2.2 Cyanobacteria as biocontrol agents
7.2.2.1 Mechanism of action
7.2.3 Cyanobacteria: Bioremediation of waste material and reclamation of wasteland
7.2.4 Cyanobacteria in carbon dioxide sequestration and reduction of climatic changes
7.3 Cyanobacteria in rhizospheric engineering
7.4 Conclusions
References
Chapter 8 Bacterial inoculants for rhizosphere engineering: Applications, current aspects, and challenges
8.1 Introduction
8.2 Microbes associated with plants
8.2.1 Above-ground microbiome
8.2.2 Below-ground microbiome
8.3 Rhizosphere engineering
8.4 Why microbial inoculants?
8.5 Microbial inoculants
8.6 Types of microbial inoculants
8.7 Bacterial biofertilizers
8.7.1 Nitrogen-fixing bacteria
8.7.1.1 Rhizobium
8.7.1.2 Azospirillum
8.7.1.3 Azotobacter
8.7.1.4 Blue green algae (Cyanobacteria) and Azolla
8.7.1.5 Nitrogen-fixing endophytes
8.7.2 Phosphate solubilizing microorganisms
8.7.2.1 Mechanism of P solubilization
8.7.3 Plant growth-promoting rhizobacteria
8.7.4 Consortium or composite inoculants
8.8 Applications of microbial inoculants
8.8.1 Phytohormones
8.8.2 ACC deaminase activity
8.8.3 Siderophore production
8.8.4 Microbial antagonism
8.9 Challenges in bacterial inoculant application
8.9.1 Technological constraints
8.9.1.1 Strains for production
8.9.1.2 Technical personnel
8.9.1.3 Quality of production units
8.9.1.4 Quality of carrier material
8.9.1.5 Quality of inoculants
8.9.1.6 Shelf-life of inoculants
8.9.2 Financial constraints
8.9.3 Physical and environmental constraints
8.9.3.1 Seasonal demand for biofertilizers
8.9.3.2 Cropping operations
8.9.3.3 Soil characteristics
8.9.3.4 Regulation
8.10 Solutions to constraints
8.10.1 Use of native strains
8.10.2 Choice of carrier material
8.10.3 Screening mechanisms
8.10.4 Marketing
8.11 Conclusions
References
Chapter 9 Microbial inoculants in agriculture and its effects on plant microbiome
9.1 Introduction
9.2 Plant microbiomes
9.3 Bioinoculants in agriculture
9.4 Direct effect of bioinoculant on plants
9.5 Effect of bioinoculants on the structure of the bacteriome with benefits for plants
9.6 How does the bioinoculants change the structure of the bacteriome?
9.7 Conclusion and future perspectives
References
Chapter 10 Arbuscular mycorrhiza—A health engineer for abiotic stress alleviation
10.1 Introduction
10.2 Role of AM fungi in plant growth promotion
10.2.1 Mycorrhizosphere
10.3 Salinity stress
10.3.1 The present scenario
10.3.2 Mechanism of salinity tolerance by mycorrhizal plants
10.3.2.1 Ionic balance
10.3.2.2 Biosynthesis of osmoprotectants, polyamines, and antioxidant enzymes under salt stress
10.3.3 Plant growth
10.3.4 Soil aggregation and stability
10.4 Drought stress
10.4.1 Manifold protection of AM fungi against drought
10.4.2 Role of AM fungi in drought tolerance
10.4.3 Mechanism of drought tolerance by mycorrhizal plants
10.5 Heavy metal (HM) stress
10.5.1 AM fungi in overcoming HM toxicity
10.5.2 Mycorrhizoremediation-AM-mediated phytoremediation
10.5.2.1 AMF-mediated phytoextraction process
10.5.2.2 AMF-mediated phytostabilization process
10.5.3 Success of AM fungi-plant association in reducing heavy metal toxicity
10.6 Conclusions
References
Chapter 11 Potassium solubilizing microorganisms as soil health engineers: An insight into molecular mechanism
11.1 Introduction
11.2 Need of potassium solubilizing bacteria in K nutrition
11.3 Mechanism of potassium solubilization and mobilization
11.4 Characterization of potassium solubilizing bacteria
11.4.1 Morphological characterization
11.4.2 Biochemical characterization
11.4.3 Molecular characterization
11.5 Determination of PGPR attributes of KSB strains
11.6 Hydrolytic enzymes
11.7 Molecular mechanisms of KSB in solubilizing K
11.8 Biology of potassium transporter genes in potassium solubilizing microorganisms
11.9 Conclusions and future perspectives
References
Chapter 12 Zinc solubilizing rhizobacteria as soil health engineer managing zinc deficiency in plants
12.1 Introduction
12.2 Present status of soil fertility
12.3 Possible causes of Zn scarcity in crop plants
12.4 Possible Zn-deficient plant symptoms and effect of Zn deficiency on plant metabolism
12.5 Importance of Zn micronutrient in the plant system
12.6 Chemical fertilizer: Dilemma between necessity and sustainability
12.7 ZSB: The alternative way
12.8 Diversity of ZSB associated with plant
12.9 Mechanism of Zn solubilization by ZSB
12.9.1 Chelating mechanism of Zn
12.9.2 Production of organic acid and proton extrusion
12.9.3 Amendment in root architecture
12.9.4 Effects of ZSB on Zn-transporters
12.10 Genetics of Zn solubilization and uptake
12.11 Prospect of ZSB in nanofertilizer
12.12 Conclusions
References
Chapter 13 Rhizosphere engineering through pesticides-degrading beneficial bacteria
13.1 Introduction
13.2 Pesticides
13.2.1 Chemical classes of pesticides
13.3 Beneficial bacteria
13.3.1 Phytomicrobiome
13.4 Effect of pesticides on beneficial bacteria
13.5 Adverse effect of pesticides on humans
13.6 Mechanism of microbial degradation of pesticide
13.6.1 Pesticide degradation based on microbial enzymes
13.6.1.1 Microbial enzymes
Hydrolase
Phosphotriesterases
Esterases
Oxidoreductases
13.7 Engineering the rhizobia
13.8 Conclusions
References
Chapter 14 Enzymes in rhizosphere engineering
14.1 Introduction
14.2 Soil indicators—A measurable parameter
14.2.1 Types of soil indicators
14.3 Rhizozymes
14.3.1 Dehydrogenase
14.3.2 Glucosidases and glactosidases
14.3.3 Cellulase
14.3.4 Xylanase
14.3.5 Invertase
14.3.6 Urease
14.3.7 Arylsulfatase
14.3.8 Phosphatase
14.3.8.1 Factors affecting phosphatase activity
14.4 Rhizozyme—Categorization based on location
14.4.1 Factors affecting soil enzyme
14.4.2 Functions of rhizozymes
14.4.2.1 As a plant defense system
14.4.2.2 Elimination of soil pollutants
14.4.2.3 Metabolic and ecological balance
14.5 Microbiome of rhizosphere
14.6 Conclusions
References
Chapter 15 Actinobacterial enzymes—An approach for engineering the rhizosphere microorganisms as plant growth promotors
15.1 Introduction
15.2 Actinobacteria—Enzyme reservoirs
15.3 PGPR and actinobacterial communities in rhizosphere
15.4 Rhizosphere enzymes and its importance
15.5 Rhizosphere—Actinobacteria and carbon sequestration
15.6 Rhizosphere engineering
15.7 Conclusions
Acknowledgments
References
Chapter 16 Reactive oxygen species and oxidative stress in higher plants, and role of rhizosphere in soil remediation
16.1 Introduction
16.2 Abiotic stresses
16.2.1 Drought
16.2.2 Temperature
16.2.3 Salinity
16.2.4 Metal toxicity
16.2.5 High light
16.3 ROS formation under high light
16.3.1 ROS by excitation energy transfer
16.3.1.1 PSII antenna complexes
16.3.1.2 PSII reaction center
16.3.1.3 Triplet excited carbonyls
16.3.2 ROS by electron transport
16.3.2.1 PSII electron acceptor side
16.3.2.2 PSII electron donor side
16.4 Conclusions
References
Chapter 17 Nanotechnology for rhizosphere engineering
17.1 Introduction
17.1.1 Synthesis of nanomaterials
17.1.2 Classification of nanomaterials
17.1.3 Applications of nanomaterials
17.2 Rhizosphere engineering
17.3 Applications of nanotechnology for rhizosphere engineering
17.3.1 Smart delivery system for precision farming
17.3.1.1 Slow release fertilizers
17.3.1.2 Nanofertilizers
17.3.1.3 Coated/controlled release fertilizers
17.3.1.4 Nanoenabled plant growth regulator
17.3.1.5 Immobilized/encapsulated hybrid fertilizers
17.3.1.6 Nanopesticides and nanoweedicides
17.4 NPs for soil microbial community functioning and stress alleviation
17.5 Nanosensors for precision agriculture
17.6 Nanomaterials for rhizosphere remediation
17.7 Nanotechnology for plant modification
17.8 Nanotechnology for drought recovery and water conservation in rhizosphere
17.9 Nanotechnology for improving heat tolerance in plants
17.10 Conclusions
References
Chapter 18 Rhizospheric health management through nanofertilizers
18.1 Introduction
18.2 Nanofertilizers
18.2.1 Zeolite nanofertilizer for sustainable agriculture
18.2.2 Zinc/zinc oxide nanoparticles in fertilizers
18.2.3 Iron oxide nanoparticles in fertilizers
18.2.4 Copper and copper oxide nanoparticles in fertilizers
18.2.5 Titanium dioxide nanoparticles in fertilizer
18.2.6 Cerium oxide nanoparticles in fertilizers
18.2.7 Novel metal nanoparticles
18.2.7.1 Silver nanoparticles
18.2.7.2 Gold nanoparticles in fertilizers
18.2.7.3 Platinum nanoparticles in fertilizers
18.2.8 Selenium nanoparticles in fertilizers
18.2.9 Carbon-based nanomaterials in fertilizers
18.2.10 Silicon dioxide nanoparticles in fertilizers
18.3 Demerits of nanoparticles for rhizosphere
18.3.1 Metal nanoparticles interaction
18.3.2 Silver nanoparticles
18.3.3 Gold nanoparticles
18.3.4 Iron and iron oxides nanoparticles
18.3.5 Zinc, zinc oxide nanoparticles
18.3.6 Titanium oxide nanoparticles
18.3.7 Copper and copper oxides nanoparticles
18.3.8 Cerium nanoparticles
18.3.9 Aluminum oxide nanoparticles
18.4 Conclusions
References
Chapter 19 Quorum sensing in rhizosphere engineering
19.1 Introduction
19.2 Plant rhizosphere as a hot spot for microbial activity
19.3 Plant growth-promoting rhizobacteria
19.4 Bacterial quorum sensing
19.5 Quorum sensing in plant growth-promoting rhizobacteria
19.5.1 Involvement of QS systems in nitrogen fixation process
19.5.2 Involvement of QS system in phosphate solubilization by rhizobacteria
19.5.3 Involvement of QS system in phytohormone production
19.5.4 Involvement of QS system in siderophore production
19.5.5 Involvement of QS system in ACC deaminase activity of rhizobacteria
19.5.6 Involvement of QS in root colonization by rhizobacteria
19.5.7 Involvement of QS systems in biological control activity of rhizobacteria
19.5.8 Quorum sensing in the induction of plant systemic resistance
19.6 Prospects for using QS mechanisms to improve plant growth and development
19.7 Conclusions
References
Chapter 20 Quorum sensing in rhizosphere microbiome: Minding some serious business
20.1 Introduction
20.2 AHL-mediated intraspecies interaction in Gram-negative bacteria
20.3 Autoinducing peptides-mediated intraspecies interaction in Gram-positive bacteria
20.4 Bacterial quorum-sensing systems in rhizosphere
20.4.1 TraI/TraR signaling system in Agrobacterium tumefaciens
20.4.2 ExpI/ExpR-CarI/CarR-coupled quorum-sensing system in Erwania carotovora
20.4.3 LasI/LasR-RhlI/RhlR serial overlapping system in Pseudomonas aeruginosa
20.4.4 PlcR-PapR quorum-sensing system in Bacillus cereus
20.4.5 ComP/ComA quorum-sensing system in Bacillus subtilis
20.5 Conclusions
Acknowledgments
References
Chapter 21 Metagenomics for rhizosphere engineering
21.1 Introduction
21.2 Key components of rhizosphere
21.3 Need for rhizosphere engineering
21.4 Metagenomics as a tool for rhizosphere engineering
21.5 Experimental strategies in metagenomics
21.5.1 Metagenomic DNA extraction
21.5.2 Construction and sequencing of metagenome DNA library
21.5.3 Metagenomic data analysis
21.6 Rhizosphere prospective of metagenomics
21.6.1 Characterization of unculturable microbes
21.6.2 Revealing the structure and function of core plant microbiome
21.6.3 Elucidation of nutrient recycling
21.6.4 Description of novel genes and gene products
21.6.5 Manipulating the rhizosphere signaling network
21.6.6 Plants disease amelioration
21.6.7 Pollutant degradation
21.6.8 Induction of abiotic stress tolerance
21.7 Challenges in rhizosphere engineering
21.8 Conclusions
References
Chapter 22 Rhizosphere engineering for crop improvement
22.1 Introduction
22.2 Plant-microbe interaction
22.2.1 Beneficial plant-microbe interaction
22.2.1.1 Plant growth-promoting rhizobacteria
22.2.1.2 Plant growth-promoting fungi
22.2.1.3 Biocontrol agents
22.2.2 Harmful plant-microbe interaction
22.3 Understanding the science behind plant-microbe interaction
22.3.1 Factors governing composition of rhizospheric microbiome
22.3.2 The interplay between root exudates and the microbial community
22.3.3 Profiling of plant microbiome
22.4 Approaches for rhizosphere engineering
22.4.1 Use of wild PGPM formulation
22.4.2 Genetic modification in PGPM and/or its host plant
22.4.2.1 Engineering PGPM
22.4.2.2 Engineering the plants
22.5 Modern tools for plant engineering
22.5.1 RNA interference
22.5.2 Genome editing
22.5.2.1 Zinc-finger nucleases
22.5.2.2 Transcription activator-like effector molecules
22.5.2.3 Clustered regularly interspaced short palindromic repeats (CRISPR)
22.6 Conclusions and future prospect
References
Chapter 23 Bacterial induced alleviation of cadmium and arsenic toxicity stress in plants: Mechanisms and future prospects
23.1 Introduction
23.2 Plant-associated PGPB
23.3 Cd and As resistance mechanisms in PGPB
23.4 Mechanisms of decreased accumulation of Cd and As in plant tissues by PGPB
23.5 Mechanisms of palliation of Cd and As toxicity in plants by PGPB
23.6 Conclusions and future prospects
Acknowledgment
References
Chapter 24 Microbial community in soil-plant systems: Role in heavy metal(loid) detoxification and sustainable agriculture
24.1 Introduction
24.2 Diversity in plant-microbe interface
24.2.1 Plant growth-promoting rhizobacteria (PGPR)
24.2.2 Endophytes
24.2.3 Nitrogen-fixing microbes
24.2.4 Mycorrhiza
24.3 Intercommunication between plants-microbes in rhizosphere
24.3.1 Volatile organic compounds (VOCs)
24.3.2 Quorum sensing
24.3.3 Plant-induced signaling
24.4 Functional attributes of plant-microbe interactions in agriculture
24.4.1 Plant growth improvement and nutrient availability
24.4.2 Siderophore production
24.4.3 Phytohormone production
24.4.4 Biological nitrogen fixation (BNF)
24.4.5 Production of metabolites/enzymes
24.4.6 Improvement of soil attributes
24.5 Microbe-assisted remediation of soils contaminated with metal(loid)s: A promising approach for sustainable agricultu ...
24.5.1 Rhizoremediation
24.5.1.1 Rhizoremediation of metals by plant growth-promoting rhizobacteria (PGPR)
24.5.1.2 Rhizoremediation by endophytic microorganisms
24.5.1.3 Mycorrhizoremediation
24.5.2 Bioremediation by microbes
24.5.2.1 Immobilization techniques
24.5.2.2 Mobilization
24.6 Conclusions and future prospects
References
Chapter 25 Rhizosphere microbe-mediated alleviation of aluminum and iron toxicity in acidic soils
25.1 Introduction
25.2 Cultivation challenges in acidic soils
25.2.1 Distribution of acid soils
25.2.2 Formation of acid soils
25.2.3 Toxic effects of acid soils
25.2.4 Management of acid soils
25.3 Metal toxicity—A major concern in acidic soil
25.3.1 Impact of Al toxicity in plants
25.3.1.1 Disturbance of plant architecture
25.3.1.2 Interference with plant physiological processes
25.3.1.3 Aluminum-induced changes in gene expression
25.3.2 Excessive iron for plants
25.3.2.1 Occurrence of iron toxicity
25.3.2.2 Contributing factors for iron toxicity
25.3.2.3 Manifestations of iron toxicity
25.4 Metal–microbe interactive technology
25.4.1 Microbial adoption of diverse defense machinery
25.4.2 Rhizosphere microbiota—The smart agents for metal detoxification
25.4.3 Dual mechanisms of metal tolerance and plant growth promotion in microorganisms
25.5 Conclusion
References
Index
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