Rhizosphere Engineering

Rhizosphere Engineering is a guide to applying environmentally sound agronomic practices to improve crop yield while also protecting soil resources. Focusing on the potential and positive impacts of appropriate practices, the book includes the use of beneficial microbes, nanotechnology and metagenomics. Developing and applying techniques that not only enhance yield, but also restore the quality of soil and water using beneficial microbes such as Bacillus, Pseudomonas, vesicular-arbuscular mycorrhiza (VAM) fungi and others are covered, along with new information on utilizing nanotechnology, quorum sensing and other technologies to further advance the science. Designed to fill the gap between research and application, this book is written for advanced students, researchers and those seeking real-world insights for improving agricultural production. Explores the potential benefits of optimized rhizosphere Includes metagenomics and their emerging importance Presents insights into the use of biosurfactants 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 Back Cover