Rhizomicrobiome in Sustainable Agriculture and Environment

1st Edition - October 18, 2024
Editors: Joginder Singh Panwar, Vikas Sharma
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 3 6 9 1 - 4
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 3 6 9 2 - 1

Rhizomicrobiome in Sustainable Agriculture and Environment explores the important potential of biocontrol agents in the reduction of overexploitation of synthetic pesticide… Read more

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Rhizomicrobiome in Sustainable Agriculture and Environment explores the important potential of biocontrol agents in the reduction of overexploitation of synthetic pesticides, enhancing crop production, and maintaining the natural texture and health of agricultural soils. As concerns about sustainable production challenge current practices, this book presents opportunities for utilizing biological systems as part of the solution. Written by a team of global experts, sections explore the full range of rhizomicrobiome topics, including sustainable agriculture, food security, and environmental management. This will be a valuable resource for researchers, academics, and advanced students.

Rhizomicrobiome is a significant part of plant biological system which impacts the plant growth and survival in different physiological conditions. Its composition includes different microbial networks whose presence is mainly impacted by the root exudates. Archaea, bacteria, protozoa, fungi, oomycetes, nematodes, microarthropods etc. are the significant parts of the rhizomicrobiome. Rhizomicrobiome could be that novel ecosystem housing the bioinoculants that can help create sustainable, productive growth environments.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Contributors
Chapter 1. Rhizomicrobiome: Biodiversity and functional annotation for agricultural sustainability
Introduction
Biodiversity of rhizomicrobiome
Mechanisms of plant growth promotion
Rhizomicrobiome as biofertilizers
Nitrogen fixation
Phosphate solubilization
Potassium solubilization
Zinc solubilization
Manganese solubilization
Rhizomicrobiome as biocontrol agents
Siderophores production
Hydrolytic enzymes production
Hydrogen cyanide production
Ammonia production
Antibiotics production
Rhizomicrobiome as phytostimulators
Auxins production
Cytokinins production
Gibberellins production
Rhizomicrobiome as stress alleviators
Osmolytes
1-aminocyclopropane-1-carboxylate deaminase
Antioxidants
Effect of inoculating rhizomicrobiome in crops
Conclusions
Chapter 2. Rhizomicrobiome interactions fluxes and its various significance
Introduction
Interkingdom signaling in plant-rhizomicrobiome interactions
Conclusions
Chapter 3. Rhizomicrobiome – characterization and potential applications
Introduction
Factors affecting the composition and dynamics of RM
Plant-factors
Soil factors
Characterization of RM
Conventional/culture dependent methods
Microbial count analysis
Carbon source utilization profiling (CSUP)
Fluorescence microscopy (FM)
Fatty acid methyl esters (FAMEs)
Advanced/culture independent methods
PCR-independent approaches
PCR-dependent approaches
Functional genomics
Metagenomics (MG)
Meta-transcriptomics (MT)
Meta-proteomics (MP)
Applications of RM research in basic- and applied-sciences
Basic sciences
The structure, function and dynamics of the microbiome
Microbial ecology and evolution studies
Microbial interaction studies
Host-microbe coevolution studies
The development of research tools and methods
Improving crop yields
Soil health and restoration
Understanding the plant-host defense system
Biocontrol of plant pathogens
Ecological restoration
Applied sciences
Informed plant breeding
Sustainable agriculture
Bioremediation
Phytoremediation
Biofertilizers and microbial inoculants
Biotechnology and bio prospecting
Conclusions
Chapter 4. Tools and technique to explore rhizomicrobiomes
Background
Rhizosphere: narrow region expanding microbial activity
Bacteria in rhizosphere
Abundance and diversity
Colonization and competence
Distribution along the rhizosphere microsites
Classical molecular techniques in the study of bacteria in the rhizosphere
Fingerprinting techniques
Quantitative PCR (qPCR) and gene expression
Microarray and transcriptome
Biosensors
Proteomics
Post‒genomic techniques in the study of bacteria in the rhizosphere
Metagenomics
Metagenomics
Metatranscriptomics
Conclusions and perspectives
Chapter 5. Rhizomicrobiome interactions: Fundamentals and recent advances
Introduction
Root-soil interactions mediated by soil-microorganisms
Rhizomicrobiome: Microbial complexity and interactions
Intercommunications among rhizomicrobiome
Plant microbe signaling and hormonal communications
Chemical messengers released by the host plants
Advantageous rhizomicrobiome strategies: Symbiotic development through signal mediation
Mycorrhizal symbiotic development
Legume-rhizobial symbiosis
Interplay between the host with phytopathogens
Improvement of rhizomicrobiome interactions
Application of PGPR
Growth of living multch
Conclusions and challenges
Chapter 6. Biodiversity and biotechnological applications of rhizomicrobiome for agricultural, environmental and industrial sustainability
Introduction
Functional diversity of rhizomicrobiomes
Nitrogen fixers
Phosphorus solubilizers
Potassium solubilizers
Zinc solubilizers
Siderophore producers
Phytohormone producers
Auxins
Cytokinins
Gibberellins
Lytic enzyme producers
Chitinase
Proteases
Cellulases
Glucanses
Ammonia producers
Biotechnological applications of rhizomicrobiomes
Agricultural applications
Biofertilizers
Biopesticides
Stress mitigators
Environmental applications
Bioremediation
Industrial applications
Conclusion
Chapter 7. Sustainable use of rhizomicrobiome in managing abiotic stress
Introduction
Role of rhizomicrobiome in plant growth and yield
Role of rhizomicrobiome in drought stress
Role of rhizomicrobiome in salt stress
Rhizomicrobiome aid – Plants survival in extreme temperatures
Role of rhizomicrobiome during heavy metal stress
Role of rhizomicrobial VOC's (volatile organic compounds) in plants
Enhanced photosynthetic efficiency via rhizomicrobial VOC's
Adequate nutrient acquirement via rhizomicrobial VOC's
Modulated phytohormonal communication pathways
Solubilization of available nutrients via rhizomicrobiome
Rhizomicrobiome as biocontrol agents
Role of rhizomicrobiome in agricultural allied sectors
Conclusion and future perspectives
Chapter 8. Biocontrol of weeds and their impacts on rhizomicrobiome
Introduction
Concept of biocontrol of weeds and sustainable agricultural growth
Control of weeds
Importance of rhizomicrobiome on plant growth, nutrient uptake and disease suppression
Plant growth
Nutrient uptake
Disease suppression
Biocontrol of weeds
Use of insects, pathogens and other natural enemies
Advantages of biocontrol against traditional chemical herbicides
Importance of integrating different control strategies for effective weed management
The rhizomicrobiome
The rhizomicrobiome and its components including bacteria, fungi, archaea and viruses
Indirect effects of biocontrol on rhizomicrobiome
Biocontrol agents indirectly influence the rhizomicrobiome through their impact on weed communities
Competition for resources (water, nutrients, and space) between weeds and desirable plants and how biocontrol agents can alleviate this competition
Positive effects of reduced weed competition on the growth and activity of beneficial rhizomicrobes
Direct effects of biocontrol on rhizomicrobiome
Biocontrol agents, particularly microbial organisms, can establish themselves in the rhizosphere and interact with resident microorganisms
Potential mechanisms of interaction, such as nutrient competition, production of antimicrobial compounds, and induction of systemic resistance in plants
Disruption of weed-microbe interactions
Specific interactions between weeds and rhizomicrobes that influence weed growth and competitiveness
Biocontrol agents can disrupt these interactions, leading to changes in the composition and activity of the rhizomicrobiome
Potential consequences of disrupted weed-microbe interactions on plant health, nutrient availability, and ecosystem dynamics
Case studies and experimental evidence
Case studies and experimental evidence that investigate the impact of biocontrol of weeds on the rhizomicrobiome
Findings, including changes in rhizomicrobiome composition, microbial diversity, and functional dynamics
Highlight the importance of considering specific biocontrol agents, target weeds, and environmental conditions when assessing the impact on the rhizomicrobiome
Future perspectives and challenges
Outlook on the future of biocontrol of weeds and its impact on the rhizomicrobiome
Need for further research to fully understand the mechanisms and long-term effects of biocontrol on the rhizomicrobiome
Highlight the importance of developing integrated approaches that optimize biocontrol strategies while minimizing unintended consequences
Conclusion
Emphasize the importance of considering the impact of biocontrol of weeds on the rhizomicrobiome for sustainable weed management practices
Call for continued research and collaboration to enhance our understanding of these complex interactions
Chapter 9. Involvement of soil parameters and rhizosphere microbiome in sustainable crop productivity
Introduction
Microbial role in soil-crop quality enhancement
Role of PGPR
Phosphate solubilization
Nitrogen fixation
Siderophore production
HCN generation
Phytohormone production
Vitamins
ACC deaminase
Antibiotics
Extracellular enzymes
Mycorrhizal role in crop health promotion
Mechanism
Role of algae in crop production
Benefits
Biofertilisers
Prevent soil erosion and act as soil conditioners
Plant hormone mimicking compounds
Against pests
Heavy metal removal
Other benefits
Mechanism
Role of other beneficial fungi in crop production
Microbial associations with nodule-forming plants
Conclusion
Chapter 10. Role of rhizomicrobiome in in-situ and ex-situ conservation of plant community
Introduction
Rhizomicrobiome and its importance for plant community
Role of rhizomicrobiome in the conservation of plants
In-situ conservation of plant community
Enhancement of nutrient availability
Growth-promoting activities
Mitigation of abiotic stress
Mitigation of biotic stress
Decontamination of the toxic soil environment
Ex situ conservation of plant community
Conclusions
Chapter 11. Role of rhizomicrobiome in plant disease management
Introduction
Rhizomicrobiome: unveiling its potential
Reprograming of plant physiology by rhizomicrobiome
Role in biotic stress mitigation
Role in the management of plant diseases
Competition
Antagonism
Hyperparasitism
Different mechanisms of action of the beneficial rhizomicrobiome for plant disease management
Role in the management of insect pests
Commercial formulations of rhizobiota
Formulations of rhizomicrobiome
Talc-based formulations
Peat-based formulations
Vermiculite-based formulations
Commercialization of rhizomicrobiome formulations
Commercial formulations for plant disease management
Challenges and opportunities
Future prospects
Conflict of interest
Chapter 12. Rhizomicrobiome as a potential reservoir of heavy metal resistant microorganisms
Introduction
Toxic effects of HMs
On aquatic environment
On humans
On plants
Sources of HMS
HM-resistant microbes
Effects of HMS on the environment
Arsenic
Cadmium
Lead
Mercury
Chromium
Mechanism involved in HMs tolerance
Metal exclusion by permeability barrier
Active transport of the metal away from the microorganism
Intracellular sequestration of metals by protein binding
Extracellular sequestration
Enzymatic detoxification of a metal to a less toxic form
Reduction in metal sensitivity of cellular targets
Precipitation
Oxidation/reduction
Methylation/demethylation
Application of HMs resistant microbes
Discussion
Conclusion
Chapter 13. Rhizomicrobiome: Role in management of heavy metal stress in plants
Introduction
Rhizosphere and microbial association
Mechanisms of rhizospheric microbes assisted phytoremediation
EPS production and metal immobilization and remediation
Siderophore producing rhizobacteria mediated bioremediation
Metallothionein-assisted phytoremediation
Metal remediation by crop plants by crop plants
Mycorrhizae and other fungus-associated phytoremediation
Conclusions
Abbreviations
Chapter 14. Applications of rhizomicrobiome in bioremediation and assisted phytoremediation
Introduction to rhizomicrobiome and bioremediation
Understanding the role of rhizomicrobes in bioremediation processes
Harnessing the power of rhizomicrobiome for environmental cleanup
Enhanced biodegradation and biostimulation
Rhizofiltration and phytoremediation
Enhanced phytoextraction
Microbial communities for enhanced remediation
Case studies: successful applications of rhizomicrobiome in bioremediation
Enhancing phytoremediation with rhizomicrobiome assistance
Enhanced biodegradation of contaminants
Phytostimulation for improved plant health
Enhanced metal uptake and immobilization
Bioaccumulation and rhizoaccumulation
Mechanisms of rhizomicrobiome-assisted phytoremediation
Enhanced contaminant biodegradation
Improved nutrient uptake and plant health
Facilitated metal uptake and immobilization
Rhizoaccumulation and bioaccumulation
Synergistic approaches: integrating rhizomicrobiome with plant genetics
Plant selection and engineering for enhanced rhizomicrobiome interactions
Engineering plant traits for enhanced phytoremediation
Optimizing microbial consortia for plant-microbe interactions
Targeted enhancement of plant stress tolerance
Challenges and limitations of rhizomicrobiome-based bioremediation strategies
Rhizomicrobiome variability and complexity
Limited understanding of rhizomicrobiome function
Inconsistent performance
Limited application to specific contaminants
Potential ecological risks
Future prospects and emerging technologies in rhizomicrobiome bioremediation
Precision engineering of rhizomicrobiomes
Omics technologies for rhizomicrobiome analysis
Synthetic biology approaches
Engineered microbial biofilms
Multifunctional plant-microbe partnerships
Chapter 15. Rhizomicrobiome as a potential source of microbial inoculants for use in in vitro biotization mediated acclimatization of micropropagated plants
Introduction
Role of microbial interactions in addressing acclimatization challenges
The rhizomicrobiome: understanding plant-microbe interactions
Composition of the rhizomicrobiome
Exploration of symbiotic and mutualistic relationships
Significance of symbiosis and mutualism in plant health
Microbial inoculants for in vitro biotization
Identification and isolation methods for beneficial rhizomicrobes with potential application in micropropagated plant acclimatization
Considerations for microbial diversity and strain specificity in the inoculant formulation
Mechanisms of rhizomicrobiome-mediated plant acclimatization
Application of rhizomicrobiome inoculants in vitro biotization
Techniques for inoculant application
Evaluation methods for assessing the effectiveness of rhizomicrobiome-based inoculants on plant acclimatization
Future perspectives and challenges
Overcoming challenges through research and innovation
Chapter 16. Rhizomicrobiome: Applications of secondary metabolite/bioactive of industrial importance
Introduction
Secondary metabolites
Secondary metabolites isolated from rhizomicrobiomes
Plant microbiome: source for active compounds
Kakadumicins
Javanicin
Aminoglycoside
Aristeromycin
Cervinomycin
Friulimicins
Pyrrolnitrin
Streptotricin
β-hydroxybutyrate
β-lactams
Elaboration of root exudates from rhizobacterial activities
Pseudomonas spp.
Bacillus spp.
Conclusions
Chapter 17. Applications and importance of metagenomic studies for exploring rhizomicrobiome dynamics
Introduction
Plant-microbe interactions in rhizosphere microenvironment
Metagenomics and multi-omics technologies
Rhizomicrobiome metagenomics studies on different plants
Metagenomics of rhizosphere: Challenges and constraints
Conclusion or future prospective
Chapter 18. Computational approaches to understand rhizomicrobiome community and its future implications
Introduction
Computational approaches in rhizomicrobiome analysis
Databases and resources for microbial interaction data
Data preprocessing
Taxonomic profiling
Functional profiling
Differential abundance analysis
Network analysis to explore microbial interactions
Metagenome assembly
Machine learning techniques for predictive modeling
Random forest
Support vector machines (SVM)
Gradient boosting
Neural networks
K-nearest neighbors (K-NN)
Regularized regression (e.g., lasso, ridge)
Feature selection techniques
Integrative approaches to combine multi-omics data
Data integration
Pathway analysis and enrichment
Multiomics clustering
Canonical correlation analysis (CCA)
Joint dimensionality reduction
Bayesian approaches
Statistical analysis
Visualization
Ethics and safety considerations in manipulating the rhizomicrobiome
Future implications of rhizomicrobiome research
Chapter 19. Role of modern techniques for revealing chemical signatures of rhizomicrobiome
Introduction
Rhizospheric signaling
Rhizosphere engineering
Plant based engineering
Rhizomicrobiome based engineering
Genome-wide association
Quantitative trait locus
CRISPR-Cas technology
Horizontal gene transfer method
Recombinant Inbred lines
Inoculation of consortia
Microbiome transplantation
Transcriptomics, metagenomics and omics approaches
Soil based engineering
Soil amemdments by organic farming
Soil amendments by nanotechnology
Significance of chemical signatures of rhizomicrobiome
Conclusion and future prospects
Chapter 20. Role of rhizobiome in biosynthesis of secondary metabolites of industrial importance
Introduction
Classification of SM
Alkaloids
Terpenoids
Phenolics
Limitations to produce secondary metabolites
Enhancing secondary metabolite production
Secondary metabolite production enhancement via rhizomicrobiome
Rhizospheric microbiome
Phyllospheric microbiome
Endospheric microbiome
Impact of environmental variables on plant microbiome
Plant microbiomes contribute to the productions of PSMs
Conclusion
Chapter 21. Rhizomicrobiome as potential agents used against polyaromatic hydrocarbons contaminated soils for plants
Introduction
Phytotoxicity of petroleum hydrocarbons on plants and soil
The impact of PAHs contamination on the soil properties
Toxic impacts of PHs on plants
Impacts on seed germination
Impacts on growth, yield, and biochemical properties
Adsorption, absorption and accumulation of PAHs by plants
Adsorption
Absorption
Accumulation
Detoxification of PAHs by plants
Rhizomicrobiome bioremediation of polycyclic aromatic hydrocarbons (PAHs)
Plant root exudates
Enzymes degrading-hydrocarbon
Microbiome-driven rhizoremediation for hydrocarbon cleanup
Bioaugmentation (in-situ strategy)
Bioventing (in-situ strategy)
Biostimulation (ex-situ strategy)
Factors affecting the bioremediation mechanism of PAHs by microorganisms
Structure and physicochemical properties of PAHs
Environmental factors
Conclusions
Chapter 22. Rhizomicrobiome diversity and role in treating infectious disease
Introduction
Intercommunication among rhizomicrobiome
Quorum sensing and performance of bacterial communities
Quenching of quorum-sensing signaling
Plant-microbe signaling
Chapter 23. Synergistic interplay: unraveling the significance of the rhizomicrobiome in mitigating heavy metal stress in plants
Introduction
Heavy metals (HMs)
Heavy metal toxicity
Microorganisms
Relationship between plant and microbes in the rhizosphere and mitigation of heavy metal stress
Plants with heavy metal signaling and tolerance
Microbial strategies for heavy metal (HM) remediation
Biosorption
Biomining (bioleaching and bio-oxidation)
Extracellular and intracellular sequestration
Biotransformation
Volatilization
Extracellular polymeric substances (EPS)
Sidephores and biosurfactants
Microbial enzymatic reduction
Plant microbial remediation
Conclusion
Chapter 24. Rooting for resilience: Harnessing the rhizomicrobiome for abiotic stress survival in plants
Introduction
Plants, microbes interaction in rhizosphere
Classification of soil rhizomicrobiome
Soil bacteria
Soil fungi
Mycorrhizae
Nematodes
Protozoa
Rhizomicrobiome induced systematic tolerance (IST) under abiotic stress
Drought stress
Role of rhizomicrobiome in drought stress alleviation
Salinity stress
Role of rhizomicrobiome in salt stress alleviation
Heavy metal stress
Alleviation of heavy metal stress by rhizomicrobiome
Heat/cold stress increased synthesis
Alleviation of heat/cold stress by rhizomicrobiome
Conclusion and future perspective
Index

Joginder Singh Panwar

Prof. Joginder Singh is a Professor at the Department of Botany, Nagaland University, Lumami, Nagaland, India. Previously, he worked as a Professor in the School of Bioengineering and Biosciences, Lovely Professional University and also as a Young Scientist at Microbial Biotechnology and Biofertilizer Laboratory, Department of Botany, Jai Narain Vyas University on a research project funded by the Department of Science and Technology, Government of India. He is an active member of various scientific societies and organizations, including the Association of Microbiologists of India, the Indian Society of Salinity Research Scientists, the Indian Society for Radiation Biology, and the European Federation of Biotechnology. He has published extensively with Elsevier and Springer both in journals and books. He serves as a reviewer for many prestigious journals, including Current Research in Engineering, Science and Technology; Journal of Cleaner Production; Science of the Total Environment; Environmental Monitoring and Assessment; Pedosphere; Soil and Sediment Contamination; Symbiosis; International Journal of Phytoremediation; Ecotoxicology and Environmental Safety; Annals of Agricultural Sciences; and Annals of the Brazilian Academy of Sciences.

Affiliations and expertise

Professor, Department of Botany, Nagaland University, Nagaland, India

Vikas Sharma

Dr. Vikas Sharma is currently working as Associate Professor in School of Bioengineering and Biosciences, Lovely Professional University, Phagwara-Jalandhar. He has published research, review articles and book chapters in leading International and National journals or books. He has wide area of research experience, especially in the field of Plant-Microbe Interactions, in vitro plant propagation and assay development for screening of beneficial plant microbe interactions related with the medicinal plants. Dr Sharma also serves as a member of editorial board of Plant cell biotechnology & molecular Biology. Dr. Sharma has attended several International and National Seminars, Symposia, Conferences and chaired technical sessions and presented papers in them. He has also organised funded National level conferences and workshops.

Affiliations and expertise

Associate Professor, Molecular biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara-Jalandhar, India

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