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BENEFICIAL MICROBES IN AGRO-ECOLOGY
BENEFICIAL MICROBES IN AGRO-ECOLOGY
Copyright
Contents
Contributors
Preface
I - Bacteria
1 - Arthrobacter
1. Introduction
2. Taxonomy
3. Isolation and identification of Arthrobacter genus
4. Arthrobacter as a plant growth-promoting rhizobacteria
5. Siderophore production and metal solubilization by Arthrobacter
6. Role of Arthrobacter in bioremediation
7. Future prospects
8. Conclusion
References
2 - Alcaligenes
1. Taxonomy
2. Isolation of A. faecalis No. 4
3. Identification of A. faecalis No. 4
4. Beneficial properties of A. faecalis No. 4
4.1 In vitro test of A. faecalis No. 4 against plant pathogens
4.2 Product analysis and denitrification by A. faecalis No. 4
4.2.1 Growth and products of A. faecalis No. 4
4.2.2 Aerobic denitrification by A. faecalis No. 4
4.2.3 In vitro tests of the products
4.2.4 Production of a nonhydroxylamine-producing mutant of A. faecalis No. 4 and in vitro tests
4.3 Plant test using A. faecalis No. 4 and nonhydroxylamine-producing mutant, A. faecalis No. 4-1
4.4 Effect of hydroxylamine solution on plant disease
4.5 Additional experiment
4.6 Harvesting of massive numbers of A. faecalis No. 4 from wastewater treatment
5. Conclusion
References
3 - Serratia
1. Introduction
2. Taxonomy of the genus Serratia
3. Isolation of the genus
4. Characterization and identification of the genus
5. Plant growth-promoting attributes of Serratia spp.
5.1 Biological control potential
6. Phytoremediation
6.1 Other plant growth-promoting activities
Acknowledgment
References
4 - Rhizobium
1. Introduction
2. Diversity and taxonomy of rhizobia
3. Physiologic aspects of rhizobia
4. Beneficial effect of rhizobia
4.1 Nitrogen fixation.
4.2 Abiotic stress tolerance
4.3 Growth regulators
4.3.1 Indole-3-acetic acid
4.3.2 Gibberellins
4.3.3 Cytokinins
4.4 Abscisic acid
4.5 Phosphate solubilization
4.6 Siderophore production
4.7 Biocontrol abilities of rhizobia
5. Conclusion
References
5 - Streptomyces
1. Introduction
2. Taxonomy of Streptomyces
3. Isolation of Streptomyces
4. Identification of Streptomyces
5. Beneficial role of Streptomyces in ago-ecology: in vitro PGP and biocontrol traits of the Streptomyces
6. In vitro physiologic traits of the Streptomyces
7. In planta PGP traits of the Streptomyces
8. In planta biocontrol traits of the Streptomyces
9. Secondary metabolite production traits of the Streptomyces
10. Streptomyces research at ICRISAT
11. Conclusion
Acknowledgments
References
6 - Azospirillum
1. Taxonomy of Azospirillum
2. Isolation of Azospirillum
3. Biochemical and genetic methods for the identification of Azospirillum
4. Beneficial role of the genus Azospirillum in agroecology
4.1 Plant growth-promoting properties
4.2 Biofilm production and colonization of plant roots
4.3 Use as biofertilizer
4.4 Abiotic stress tolerance induction: salinity and water stress
4.5 Bioremediation
4.6 Biofortification
4.7 Biocontrol
5. Concluding remarks
References
7 - Bacillus
1. Taxonomy of Bacillus
1.1 Bacillus taxonomy based on 16S rRNA gene
1.2 Bacillus taxonomy based on core genomes
2. Isolation of different Bacillus species
2.1 History
2.1.1 Description of Bacillus subtilis by Ferdinand Cohn
2.1.2 Isolation of Bacillus anthracis (anthrax) by Robert Koch: the first pure culture of a bacterium
2.1.3 Isolation of Bacillus thuringiensis by Ernst Berliner
2.2 Enrichment cultures of different species
2.2.1 Soil and seawater.
2.2.2 Rhizosphere
2.2.3 Plant inner tissues (endophytes)
2.2.4 Enrichment from extreme environments
3. Morphology and simple biochemical and molecular methods for identification of different Bacillus species
3.1 Gram staining, morphology, and spore formation
3.1.1 Gram staining procedure
3.1.2 Spore staining procedure
3.2 Motility and growth
3.2.1 Motility
3.2.2 Growth in presence of sodium chloride
3.2.3 Growth at different temperatures
3.2.4 Growth in presence of 0.001% lysozyme
3.3 Early steps of differentiation: catalase, lecithinase, citrate utilization, and anaerobic growth
3.3.1 Yellow egg (lecithinase) reaction
3.3.2 Citrate and propionate utilization
3.3.3 Anaerobic growth
3.4 Biochemical tests
3.4.1 Voges-Proskauer
3.4.1.1 Voges-Proskauer broth
3.4.2 Nitrate reduction
3.4.3 Indole formation
3.4.4 Hydrolysis of macromolecules (starch, casein, gelatin)
3.4.5 Hydrolysis of tyrosin
3.4.6 Phenylalanine deamination
3.5 Acid formation from carbohydrates and organic acids
3.6 Appendix: Useful Bacillus media for cultivation, enrichment, and phenotypic characterization
3.6.1 Standard media
3.6.1.1 Nutrient agar
3.6.1.2 Glucose mineral base agar
3.6.1.3 Trypticase soy agar (TSA)
3.6.2 Enrichment media
3.6.2.1 Soil extract agar (Claus, 1965)
3.6.2.2 Schaeffer's sporulation agar
3.6.3 Cultivation and phenotypic cultivation
3.6.3.1 glucose mineral base agar
3.6.3.2 Anaerobic culture agar
3.6.3.3 Citrate and propionate utilization medium
4. Beneficial role of bacilli in agroecology
4.1 Plant and microbiota as a holobiont
4.2 Plant growth promotion (biofertilizer function)
4.3 Suppression of plant pathogens (biocontrol function)
4.4 Resistance of plants against abiotic and biotic stress.
4.5 Positive effects on plant microbiome by beneficial bacilli
References
8 - Pseudomonas
1. Introduction
2. Historical perspective of Pseudomonas and their classification
3. Role of Pseudomonas as PGPR in agriculture
3.1 Direct mechanisms
3.1.1 Nutrient mobilization
3.1.2 Production of plant growth regulators
3.2 Indirect mechanisms
3.2.1 Role of Pseudomonas as biocontrol agent
3.2.2 Antibiotics production
3.2.3 Synthesis of mycolytic enzymes
3.2.4 Induced systemic resistance in host plant
4. Role of Pseudomonas in biodegradation of pesticides
5. Conclusion
References
9 - Brevibacillus
1. Taxonomy of the genus Brevibacillus
1.1 Historical developments
1.2 Taxonomic structure
2. Isolation of the genus Brevibacillus
2.1 Underlying principle of enrichment and isolation
2.2 Selective media
3. Biochemical methods for identification of the genus Brevibacillus
3.1 Identification of the genus Brevibacillus
3.2 Polyphasic identification
4. Beneficial role of the genus Brevibacillus in agroecology
4.1 Plant growth-promoting properties
4.2 Biocontrol agent
4.3 Bioremediation
References
10 - Exiguobacterium
1. Introduction/taxonomy
1.1 The genomes of Exiguobacterium
2. Isolation of the Exiguobacterium genus
3. Identification of the Exiguobacterium genus
3.1 Physiology and metabolism
3.1.1 Degradation of complex substances
3.1.2 Heavy metal resistance
4. Beneficial properties of Exiguobacterium
4.1 Role of Exiguobacterium as plant growth enhancer
4.1.1 Interaction of bacteria with plant root
4.1.2 Nutrient acquisition
4.1.3 Phosphate solubilization
4.1.4 Production of plant hormones
4.1.5 Siderophore production
4.1.6 Exopolysaccharide production
4.2 Improvement of plant growth under stressful conditions.
4.2.1 Rhizoremediation
4.2.2 Enhancement of plant antioxidant system
4.2.3 Biocontrol
4.3 Strategies for improving PGPRs as inoculants
5. Future prospects
6. Concluding remarks
Acknowledgments
References
11 - Frankia
1. Introduction/taxonomy
1.1 Frankia
1.2 Taxonomy of Frankia
1.3 Genetics of Frankia
2. Isolation of the Frankia spp.
2.1 Morphologic characteristics of Frankia spp.
2.2 Hyphae
2.3 Sporangia
2.4 Vesicles
2.5 Physiology of Frankia
2.6 Biochemical properties of Frankia
2.7 Serology of Frankia
2.8 Ecology of Frankia
2.9 Isolation and cultivation of Frankia
2.10 Isolation on solid medium
2.11 Isolation on liquid medium
3. Characterization of Frankia
3.1 Microscopic characterization
3.1.1 Light microscopy
3.1.2 Scanning electron microscopy
3.1.3 Casuarina
3.1.4 Taxonomy of Casuarina
3.1.5 Morphologic features of Casuarina
3.1.6 Propagation of Casuarina
3.1.7 Distribution of Casuarina
3.1.8 Benefits of Casuarina
3.1.9 Hydroponic system of C. equisetifolia
3.1.9.1 Seedlings adapted with BDN medium
3.1.9.2 Hydropony of seedlings
3.1.9.3 Determination of Frankia symbiotic ability in hydropony
3.2 Morphologic study of root nodules
3.2.1 Structure of root nodules using phase contrast microscope
3.2.2 Hydroponic conditions for root nodulation kinetics
3.2.3 Symbiotic ability of Frankia isolates
3.2.4 Structure of root nodules
3.3 Screening of phytohormone production from Frankia spp.
3.3.1 Screening of IAA
3.3.2 Screening of siderophore production
3.3.3 Screening phosphate solubilization
3.4 Analysis of plant growth promoting substances by using analytical techniques
3.4.1 Quantification of IAA
3.4.2 Quantification of siderophore
3.5 Phytohormone production
3.5.1 IAA.
3.5.2 Quantification of IAA.
BENEFICIAL MICROBES IN AGRO-ECOLOGY
BENEFICIAL MICROBES IN AGRO-ECOLOGY
Copyright
Contents
Contributors
Preface
I - Bacteria
1 - Arthrobacter
1. Introduction
2. Taxonomy
3. Isolation and identification of Arthrobacter genus
4. Arthrobacter as a plant growth-promoting rhizobacteria
5. Siderophore production and metal solubilization by Arthrobacter
6. Role of Arthrobacter in bioremediation
7. Future prospects
8. Conclusion
References
2 - Alcaligenes
1. Taxonomy
2. Isolation of A. faecalis No. 4
3. Identification of A. faecalis No. 4
4. Beneficial properties of A. faecalis No. 4
4.1 In vitro test of A. faecalis No. 4 against plant pathogens
4.2 Product analysis and denitrification by A. faecalis No. 4
4.2.1 Growth and products of A. faecalis No. 4
4.2.2 Aerobic denitrification by A. faecalis No. 4
4.2.3 In vitro tests of the products
4.2.4 Production of a nonhydroxylamine-producing mutant of A. faecalis No. 4 and in vitro tests
4.3 Plant test using A. faecalis No. 4 and nonhydroxylamine-producing mutant, A. faecalis No. 4-1
4.4 Effect of hydroxylamine solution on plant disease
4.5 Additional experiment
4.6 Harvesting of massive numbers of A. faecalis No. 4 from wastewater treatment
5. Conclusion
References
3 - Serratia
1. Introduction
2. Taxonomy of the genus Serratia
3. Isolation of the genus
4. Characterization and identification of the genus
5. Plant growth-promoting attributes of Serratia spp.
5.1 Biological control potential
6. Phytoremediation
6.1 Other plant growth-promoting activities
Acknowledgment
References
4 - Rhizobium
1. Introduction
2. Diversity and taxonomy of rhizobia
3. Physiologic aspects of rhizobia
4. Beneficial effect of rhizobia
4.1 Nitrogen fixation.
4.2 Abiotic stress tolerance
4.3 Growth regulators
4.3.1 Indole-3-acetic acid
4.3.2 Gibberellins
4.3.3 Cytokinins
4.4 Abscisic acid
4.5 Phosphate solubilization
4.6 Siderophore production
4.7 Biocontrol abilities of rhizobia
5. Conclusion
References
5 - Streptomyces
1. Introduction
2. Taxonomy of Streptomyces
3. Isolation of Streptomyces
4. Identification of Streptomyces
5. Beneficial role of Streptomyces in ago-ecology: in vitro PGP and biocontrol traits of the Streptomyces
6. In vitro physiologic traits of the Streptomyces
7. In planta PGP traits of the Streptomyces
8. In planta biocontrol traits of the Streptomyces
9. Secondary metabolite production traits of the Streptomyces
10. Streptomyces research at ICRISAT
11. Conclusion
Acknowledgments
References
6 - Azospirillum
1. Taxonomy of Azospirillum
2. Isolation of Azospirillum
3. Biochemical and genetic methods for the identification of Azospirillum
4. Beneficial role of the genus Azospirillum in agroecology
4.1 Plant growth-promoting properties
4.2 Biofilm production and colonization of plant roots
4.3 Use as biofertilizer
4.4 Abiotic stress tolerance induction: salinity and water stress
4.5 Bioremediation
4.6 Biofortification
4.7 Biocontrol
5. Concluding remarks
References
7 - Bacillus
1. Taxonomy of Bacillus
1.1 Bacillus taxonomy based on 16S rRNA gene
1.2 Bacillus taxonomy based on core genomes
2. Isolation of different Bacillus species
2.1 History
2.1.1 Description of Bacillus subtilis by Ferdinand Cohn
2.1.2 Isolation of Bacillus anthracis (anthrax) by Robert Koch: the first pure culture of a bacterium
2.1.3 Isolation of Bacillus thuringiensis by Ernst Berliner
2.2 Enrichment cultures of different species
2.2.1 Soil and seawater.
2.2.2 Rhizosphere
2.2.3 Plant inner tissues (endophytes)
2.2.4 Enrichment from extreme environments
3. Morphology and simple biochemical and molecular methods for identification of different Bacillus species
3.1 Gram staining, morphology, and spore formation
3.1.1 Gram staining procedure
3.1.2 Spore staining procedure
3.2 Motility and growth
3.2.1 Motility
3.2.2 Growth in presence of sodium chloride
3.2.3 Growth at different temperatures
3.2.4 Growth in presence of 0.001% lysozyme
3.3 Early steps of differentiation: catalase, lecithinase, citrate utilization, and anaerobic growth
3.3.1 Yellow egg (lecithinase) reaction
3.3.2 Citrate and propionate utilization
3.3.3 Anaerobic growth
3.4 Biochemical tests
3.4.1 Voges-Proskauer
3.4.1.1 Voges-Proskauer broth
3.4.2 Nitrate reduction
3.4.3 Indole formation
3.4.4 Hydrolysis of macromolecules (starch, casein, gelatin)
3.4.5 Hydrolysis of tyrosin
3.4.6 Phenylalanine deamination
3.5 Acid formation from carbohydrates and organic acids
3.6 Appendix: Useful Bacillus media for cultivation, enrichment, and phenotypic characterization
3.6.1 Standard media
3.6.1.1 Nutrient agar
3.6.1.2 Glucose mineral base agar
3.6.1.3 Trypticase soy agar (TSA)
3.6.2 Enrichment media
3.6.2.1 Soil extract agar (Claus, 1965)
3.6.2.2 Schaeffer's sporulation agar
3.6.3 Cultivation and phenotypic cultivation
3.6.3.1 glucose mineral base agar
3.6.3.2 Anaerobic culture agar
3.6.3.3 Citrate and propionate utilization medium
4. Beneficial role of bacilli in agroecology
4.1 Plant and microbiota as a holobiont
4.2 Plant growth promotion (biofertilizer function)
4.3 Suppression of plant pathogens (biocontrol function)
4.4 Resistance of plants against abiotic and biotic stress.
4.5 Positive effects on plant microbiome by beneficial bacilli
References
8 - Pseudomonas
1. Introduction
2. Historical perspective of Pseudomonas and their classification
3. Role of Pseudomonas as PGPR in agriculture
3.1 Direct mechanisms
3.1.1 Nutrient mobilization
3.1.2 Production of plant growth regulators
3.2 Indirect mechanisms
3.2.1 Role of Pseudomonas as biocontrol agent
3.2.2 Antibiotics production
3.2.3 Synthesis of mycolytic enzymes
3.2.4 Induced systemic resistance in host plant
4. Role of Pseudomonas in biodegradation of pesticides
5. Conclusion
References
9 - Brevibacillus
1. Taxonomy of the genus Brevibacillus
1.1 Historical developments
1.2 Taxonomic structure
2. Isolation of the genus Brevibacillus
2.1 Underlying principle of enrichment and isolation
2.2 Selective media
3. Biochemical methods for identification of the genus Brevibacillus
3.1 Identification of the genus Brevibacillus
3.2 Polyphasic identification
4. Beneficial role of the genus Brevibacillus in agroecology
4.1 Plant growth-promoting properties
4.2 Biocontrol agent
4.3 Bioremediation
References
10 - Exiguobacterium
1. Introduction/taxonomy
1.1 The genomes of Exiguobacterium
2. Isolation of the Exiguobacterium genus
3. Identification of the Exiguobacterium genus
3.1 Physiology and metabolism
3.1.1 Degradation of complex substances
3.1.2 Heavy metal resistance
4. Beneficial properties of Exiguobacterium
4.1 Role of Exiguobacterium as plant growth enhancer
4.1.1 Interaction of bacteria with plant root
4.1.2 Nutrient acquisition
4.1.3 Phosphate solubilization
4.1.4 Production of plant hormones
4.1.5 Siderophore production
4.1.6 Exopolysaccharide production
4.2 Improvement of plant growth under stressful conditions.
4.2.1 Rhizoremediation
4.2.2 Enhancement of plant antioxidant system
4.2.3 Biocontrol
4.3 Strategies for improving PGPRs as inoculants
5. Future prospects
6. Concluding remarks
Acknowledgments
References
11 - Frankia
1. Introduction/taxonomy
1.1 Frankia
1.2 Taxonomy of Frankia
1.3 Genetics of Frankia
2. Isolation of the Frankia spp.
2.1 Morphologic characteristics of Frankia spp.
2.2 Hyphae
2.3 Sporangia
2.4 Vesicles
2.5 Physiology of Frankia
2.6 Biochemical properties of Frankia
2.7 Serology of Frankia
2.8 Ecology of Frankia
2.9 Isolation and cultivation of Frankia
2.10 Isolation on solid medium
2.11 Isolation on liquid medium
3. Characterization of Frankia
3.1 Microscopic characterization
3.1.1 Light microscopy
3.1.2 Scanning electron microscopy
3.1.3 Casuarina
3.1.4 Taxonomy of Casuarina
3.1.5 Morphologic features of Casuarina
3.1.6 Propagation of Casuarina
3.1.7 Distribution of Casuarina
3.1.8 Benefits of Casuarina
3.1.9 Hydroponic system of C. equisetifolia
3.1.9.1 Seedlings adapted with BDN medium
3.1.9.2 Hydropony of seedlings
3.1.9.3 Determination of Frankia symbiotic ability in hydropony
3.2 Morphologic study of root nodules
3.2.1 Structure of root nodules using phase contrast microscope
3.2.2 Hydroponic conditions for root nodulation kinetics
3.2.3 Symbiotic ability of Frankia isolates
3.2.4 Structure of root nodules
3.3 Screening of phytohormone production from Frankia spp.
3.3.1 Screening of IAA
3.3.2 Screening of siderophore production
3.3.3 Screening phosphate solubilization
3.4 Analysis of plant growth promoting substances by using analytical techniques
3.4.1 Quantification of IAA
3.4.2 Quantification of siderophore
3.5 Phytohormone production
3.5.1 IAA.
3.5.2 Quantification of IAA.