Оглавление
Группа авторов. Core Microbiome
Core Microbiome. Improving Crop Quality and Productivity
Contents
List of Illustrations
List of Tables
Guide
Pages
List of Contributors
Preface
1 A Review of Endophytic Microbiota of Medicinal Plants and Their Antimicrobial Properties
1.1 Introduction
1.2 Antimicrobial Properties of Medicinal Plants with Particular Reference to Neem (Azadirachtaindica)
1.3 Current Trends on Bioactive Metabolites from Endophytic Microbiota of Medicinal Plants
1.4 Plant Growth-Promoting Rhizobacteria (PGPR): Biological Management of Plant Pathogens
1.5 Conclusion
References
2 Plant Microbiome A Key to Managing Plant Diseases
2.1 Introduction
2.2 Plant–Microbe Interaction in the Rhizosphere
2.2.1 Microbial Population in the Rhizosphere
2.2.2 Biocontrol Mechanism in the Rhizosphere
2.2.2.1 Competition
2.2.2.2 Parasitism
2.2.2.3 Antagonism
2.2.2.4 Induced Systemic Resistance (ISR)
2.2.3 Plant Disease Management
2.3 Plant–Microbe Interaction in the Endosphere
2.3.1 Microbial Population in the Endosphere
2.3.2 Biocontrol Mechanism in the Endosphere
2.3.2.1 Competition
2.3.2.2 Parasitism
2.3.2.3 Antagonism
2.3.2.4 Induced Systemic Resistance
2.3.3 Plant Disease Management
2.4 Plant–Microbe Interaction in the Phyllosphere
2.4.1 Microbial Population in the Phyllosphere
2.4.2 Biocontrol Mechanism in the Phyllosphere
2.4.2.1 Competition
2.4.2.2 Parasitism
2.4.2.3 Antagonism
2.4.2.4 Induced Systemic Resistance
2.4.3 Plant Disease Management
2.5 Conclusion and Prospects
References
3 Impact of Microbiomes to Counter Abiotic Stresses in Medicinal Plants- A Review
3.1 Introduction
3.2 Structure and Function of Microbiota
3.3 Physiological and Molecular Response of Plant and Microbiota against Stress
3.3.1 Effect of Plant Genotype on Rhizosphere Microbiome Assembly
3.4 Microbe-Mediated Mitigation of Abiotic Stresses
3.5 Plant Root Exudates and the Recruitment of Beneficial Microbes
3.5.1 Multi-omics Approaches Used to Mitigate Abiotic Stresses in Medicinal Plants
3.5.1.1 Genomics
3.5.1.2 Phytochemical Genomics in Medicinal Plants
3.5.2 Proteomics
3.6 Medicinal Plants: Plant- and Microbe-Derived Ingredients
3.7 Biological Control and Plant Improvement
3.8 Management Strategies to Alleviate Abiotic Stress in Medicinal Plants
3.9 Conclusion and Future Consensus
References
4 Uses of Compost in Agriculture and Bioremediation – A Review
4.1 Introduction
4.2 Applications of Compost. 4.2.1 Compost Use for Soil Amendment and as Conditioner
4.2.2 Compost to Alleviate Soil Compaction
4.2.3 Control of Erosion by the Addition of Compost
4.2.4 Bioremediation of Organic Contaminants, Heavy Metals, and Pesticides in Soils
4.2.5 Compost in Horticulture as the Supply of Minerals to Crops and Other Plants
4.3 Use of Compost in Mulching
4.4 Perspectives
4.5 Conclusion
References
5 Metagenomics and Microbiome Engineering Identification of Core Microbiome and Improvement of Rhizosphere
5.1 Introduction
5.2 Definitions of Genome, Metagenome, Genomics, and Metagenomics. 5.2.1 Genome
5.2.2 Genomics
5.2.3 Metagenome
5.2.4 Metagenomics
5.3 Basis of Metagenomics
5.4 Steps Involved in the Metagenomics Study. 5.4.1 Sampling
5.4.2 DNA Extraction and Purification
5.4.3 Preparation and Screening in Metagenomics Libraries
5.4.4 Sequencing Methods
5.4.5 Bioinformatics Analysis
5.5 Metagenomics Applications
5.6 Metagenomics: a Way to Study Soil Biodiversity
5.7 Methods Used in Metagenomics
5.7.1 Denaturing Gradient Gel Electrophoresis
5.8 Comparison of DGGE and PLFA Performance in Soil Microbial Diversity Assessment
5.9 Factors Affecting Soil Microbiome
5.10 Plant Growth-Affecting Bacteria
5.11 How Bacteria Move Toward Plants
5.12 Soil Improvement to Increase Microbiome
5.13 Conclusion
Abbreviations
References
6 Core Microbiome Plant Growth and Development
6.1 Introduction
6.2 Types of Microbiome. 6.2.1 Root Microbiome
6.2.2 Leaf Microbiome
6.3 Hormone Interactions with Microbiota
6.4 Enhancement of Plant Growth
6.5 Nitrogen Fixation and the Possible Role of Core Microbiota
6.5.1 Non-symbiotic Nitrogen Fixation
6.5.2 Symbiotic Fixation in Diazotrophs
6.6 Biochemistry of Nitrogen Fixation
6.7 Pathway of Nitrogen Fixation in Root Nodules
6.8 Plant Genes for Nodule Development
6.9 Role of Biofertilizers
6.10 Conclusion
References
7 Microbiome Engineering and Biotechnology The Real Finenesses of a Robust Rhizosphere
7.1 Agriculture and Microorganisms
7.2 Microbiome
7.2.1 Rhizosphere Microbiome: Active Microbial Hotspot
7.2.2 Significance of Rhizospheric Microbiome
7.2.3 Why Do We Modify the Rhizosphere Microbiome?
7.3 Microbiome Engineering
7.3.1 Conventional Microbiome Engineering. 7.3.1.1 Soil Amendments
7.3.1.2 Organic Additives
7.3.2 Contemporary Rhizospheric Microbiome Engineering. 7.3.2.1 Phytomicrobiome Targeting
7.3.2.2 Artificial Consortia of Microbes
7.3.2.3 Microbiome Breeding and Transplantation
7.3.2.4 Host-Mediated Selection and Manipulation
7.4 Advance Rhizosphere Microbiome Engineering
7.4.1 Bottom-Up Approach
7.4.1.1 Phage Integrase System
7.4.1.2 Integrative and Conjugative Elements System
7.4.1.3 Chassis-independent Recombinase-assisted Genome Engineering System
7.4.2 Top-Down Approach
7.4.2.1 Mobile Genetic Elements
7.4.2.2 Phages
7.5 Rhizospheric Biotechnological Approaches
7.5.1 Fingerprinting Methods Based on Polymerase Chain Reaction
7.5.1.1 Denaturing Gradient Gel Electrophoresis/Temperature Gradient Gel Electrophoresis
7.5.1.2 Terminal Restriction Fragment Length Polymorphism Fingerprinting
7.5.1.3 Single-strand Conformation Polymorphism
7.5.1.4 Automated Ribosomal Intergenic Spacer Analysis
7.5.1.5 Random Amplified Polymorphic DNA
7.5.1.6 Amplified Ribosomal DNA Restriction Analysis
7.6 Non-PCR Methods. 7.6.1 Phospholipid Fatty Acid Analysis
7.6.2 Stable-Isotope Probing
7.6.3 DNA Arrays
7.6.4 Fluorescence In Situ Hybridization
7.6.5 High-Throughput Sequencing Technologies
7.6.6 Illumina Genome Analyzer
7.6.7 Ion PGM (Personal Genome Machine)
7.6.8 Helioscope Single-Molecule Sequencer
7.6.9 Quorum Sensing in Defense of Abiotic Stress
7.7 Metagenomics: the Rhizosphere as a Basis of Genes
7.7.1 Metabolic Engineering
7.8 Conclusion and Future Perspectives
References
8 Role of Rhizospheric Microbiome in Enhancing Plant Attributes and Soil Health for Sustainable Agriculture
8.1 Introduction
8.2 Beneficial Effects of Plant Growth-Promoting Rhizobacteria
8.3 Improvement of Soil Health and Agricultural Production in Sustainable Agriculture
8.4 Microbial Mechanism for Plant Growth Attributing Characteristics
8.5 Direct Mechanism. 8.5.1 Biological Nitrogen Fixation
8.5.2 Phytohormone Production
8.5.3 Phosphate Solubilization
8.5.4 Siderophore Production
8.5.5 ACC Deaminase Activity
8.5.6 Antagonistic Activities, Extracellular Polymeric Substances, and Antioxidant Enzymes for Managing Biotic and Abiotic Stresses
8.6 Mycorrhizae
8.7 Application of Microbial Inoculants and Future Prospects
8.8 Conclusion
References
9 Toxic Effects of Some Herbicides on the Fatty Acid Profile of Wheat Varieties A Phytomicrobiome Study
9.1 Introduction
9.2 Herbicides
9.2.1 Uptake and Transport of Herbicides
9.2.2 Oxidative Stress and Antioxidative Defense System of Herbicides on Plants
9.2.3 The Effect of Herbicides on Cereals Growth and Yield
9.3 Phytoremediation
9.4 Phytoremediation Techniques
9.4.1 Phytoextraction (Herbal Extraction)
9.4.2 Phytodegradation (Vegetal Degradation)
9.4.3 Phytostabilization (Root Fixing)
9.4.4 Phytovolatilization (Herbal Evaporation)
9.4.5 Rhizodegradation (Root Degradation)
9.4.6 Rhizofiltration (Root Filtration)
9.4.7 Hydraulic Control
9.4.8 Vegetative Cover Systems
9.4.9 Coastal Buffer Strips
9.5 Evaluation of Ideal Plants and Harvested Plants for Phytoremediation
9.6 Conclusion
References
10 Microbial Prospects in Sediment Denitrification of Eutrophic Wetland Ecosystems
10.1 Introduction
10.2 Macrophyte Rhizosphere for Habitat Structuring of Microorganisms
10.3 Influence of Macrophyte Rhizosphere on the Removal of Excessive Nitrogen in the Aquatic Ecosystem
10.3.1 Future Prospects and Conclusion
Acknowledgments
References
11 Role of Plant Microbiome in Carbon Sequestration for Sustainable Agriculture
11.1 Introduction
11.2 Importance of Carbon Sequestration
11.3 Prokaryotic Microbes in Carbon Sequestration
11.4 Eukaryotic Microbes in Carbon Sequestration
11.5 Agricultural Practices and Carbon Sequestration
11.6 Impact of Agricultural Practices on Soil Microbes and Carbon Sequestration
11.7 Carbon Capture by Plant Microbiome
11.8 Plant–Microbe Interaction in an Elevated CO 2 Ecosystem
11.9 Conclusion
References
12 Functions and Emerging Trends of the Microbial Community in Heavy Metals Bioremediation A Review
12.1 Introduction
12.2 Heavy Metals Toxicity: A Threat to the Biosphere
12.3 Factors Affecting Microbial Bioremediation
12.4 Different Microorganisms and Related Pollutants
12.5 Conclusion
References
13 Microbiomics and Sustainable Agriculture New Frontiers
13.1 Introduction
13.2 Concepts and Development of Studies on Plant Microbiomes
13.3 Valuable Microorganisms for Crop Plants. 13.3.1 Plant Growth-Promoting Bacteria
13.3.2 Plant Growth-Promoting Fungi
13.3.3 Biocontrol Agents
13.4 Influences of the Community Compositions of Rhizosphere, Phyllosphere, and Endosphere Microbiota on Growth and Performance of Crop Plants
13.5 Applications of Individual Microbes for Improvement of Crop Performance and Soil Ameliorations
13.6 Root and Shoot Microbiome
References
14 Role of Nanotechnology in Soil Microbiome and Agricultural Development
14.1 Introduction
14.2 Ancient Agricultural Concepts and Techniques
14.3 Synthesis of Nanoparticles
14.3.1 Chemical Methods
14.3.2 Physical Methods
14.3.3 Biological Methods
14.3.4 Role of Nanotechnology in Agriculture
14.4 Application of Nanotechnology in Plant Growth
14.5 Role of Nanotechnology in Soil Microbiome Development
14.6 Conclusions
References
15 Microbial Biofilms Optimal Genetic Material Exchange in a Microbiome Environment
15.1 Introduction
15.2 Role of Extracellular DNA (eDNA) in Bacterial Biofilms
15.3 Horizontal Gene Transfer and Bacterial Biofilm Interconnection
15.4 Different Modes of HGT in Biofilms. 15.4.1 Conjugative Transfer of Genetic Material in Bacterial Biofilms
15.4.2 Transformation in Biofilms
15.4.3 Transduction in Biofilms
15.4.4 Membrane Vesicles-Mediated HGT in Biofilms
15.5 Methods for Studying HGT in Biofilms
15.6 Conclusion and Future Challenges
References
16 Rhizosphere Improvement Role of Biotechnology and Microbioengineering
16.1 Introduction
16.2 Rhizosphere Improvement
16.3 Role of Microbiome Engineering in Rhizosphere Improvement
16.4 Role of Biotechnology in Rhizosphere Improvement
16.5 Molecular Approach
16.6 Conclusion
Acknowledgments
References
17 Exploring Biological Agents and Core Microbiomes as a Tool for Reclamation of Abandoned Mines
17.1 Introduction
17.1.1 Bioremediation Types
17.2 Abandoned Mines and Bioremediation: Problems and Solutions
17.2.1 Impacts on Water Resources
17.2.2 Erosion of Soil and Mine Wastes into Surface Water
17.2.3 Mine Dewatering and Its Impact
17.2.4 Mine Projects and Air Quality
17.2.5 Public Health
17.2.6 Climate Change
17.3 Organisms that Can Help Transform Abandoned Mine Sites
17.3.1 Fungi
17.3.2 Sunflower
17.3.3 Bivalves
17.3.4 Bonfire Moss
17.3.5 Alpine Pennycress
17.3.6 Tobacco
17.3.7 Wave Moth Caterpillars
17.3.8 Earthworms
17.3.9 Microorganisms
17.4 Core Microbiomes as Tools for Abandoned Mine Reclamation
17.5 The Future of Bioremediation
References
18 Mycorrhizal Strategy for the Management of Hazardous Chromium Contaminants
18.1 Introduction
18.2 Impact of Heavy Metals
18.3 Mechanism to Ameliorate Metal Toxicity
18.4 Amelioration of Cr Toxicity by AMF
18.5 Chromium-Tolerance Mechanism
18.6 Cr Stress Amelioration with AMF Symbioses
18.7 Growth, Cr Absorption, and Photosynthate Impact on AMF: Cr Toxicity and Its Effect on the Physiology of Plants with AMF
18.8 Plant Cr Absorption and Partitioning as a Result of AMF Symbiosis
18.9 Factors Affecting AMF Functioning in Relation to Plant Cr Uptake and Tolerance
18.10 Effects of AMF on Cr Translocation by Roots
References
Index
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