Dr Neeta Sharma is a senior faculty member in the Department of Botany at the University of Lucknow, India.

• Preface xviiList of Contributors xixAcknowledgments xxiii1 Biologicals: Green Alternatives for Plant Disease Management 1Neeta Sharma1.1 Introduction 11.2 Food supply on a collision course 21.3 The enormity of the problem 31.3.1 Overpopulation 31.3.2 Effective land usage 31.3.3 Water use 41.3.4 Energy use 41.4 Preventing food losses 41.5 Hazards from synthetic pesticides 51.6 A way out of this crisis 61.7 Types of biopesticides 61.7.1 Microbial pesticides 61.7.2 Plant-derived products 91.7.3 Semiochemicals 101.8 Strategies of biological control 101.9 Biopesticides: advantages and limitations 161.10 Major constraints 171.10.1 Agronomic aspects 171.10.2 The commercial perspective 181.10.3 Public anxiety over BCAs 191.10.4 Technical issues 201.10.5 Virulence and efficacy 201.11 Conclusion and future prospects 23References 242 Postharvest Damages of Mandarin (Citrus reticulata Blanco) and Its Management 27N. Chakraborty, N. S. Gupta, S. K. Basu, and K. Acharya2.1 Introduction 272.2 Diseases and disorders in mandarins 282.2.1 Postharvest diseases of mandarins 282.2.2 Physiological disorders in mandarins 292.2.3 Postharvest loss of mandarins 302.3 Strategies for postharvest management 312.3.1 Physical methods 312.3.2 Chemical methods 322.3.3 Biological methods 322.4 Naturally occurring antifungal compounds for biocontrol 342.5 Induced resistance 342.6 Conclusion and future prospects 35References 363 Yeasts: Bio-Bullets for Postharvest Diseases of Horticultural Perishables 41Neeta Sharma and Richa Tiwari3.1 Introduction 413.2 Presence of an antagonist 443.3 Introduction of the yeast antagonist in the postharvest system of horticultural perishables 443.3.1 Yeast as a natural antagonist 443.3.2 Yeast as an artificially introduced antagonist 453.3.3 Application methods of yeast antagonist for biosuppression of the pathogen 453.4 Commercial production 493.4.1 Properties of an ideal antagonist suitable for commercialization 493.4.2 Characteristics required for commercial production 503.4.3 Biocontrol yeast products 513.5 Problems in product development and registration 523.6 Enhancement of the bioactivity of the yeast antagonist 553.6.1 Mixed cultures with antagonistic yeast 553.6.2 Low levels of fungicides with a yeast antagonist 563.6.3 Exogenous substances with a yeast antagonist 573.6.4 Physical treatment with a yeast antagonist 583.7 Conclusion and future prospects 59References 604 Dissecting the Mechanisms of Action of Biocontrol Agents to Control Postharvest Diseases of Fruit 69Davide Spadaro4.1 Introduction 694.2 Studying the mechanism of action 704.3 Competition 714.4 The role of biofilm formation 724.5 Production of diffusible and volatile antimicrobial compounds 734.6 Parasitism and release of hydrolases 754.7 Induction of resistance 774.8 The role of oxidative stress 794.9 Conclusion and future prospects 80Acknowledgements 81References 815 Potential of PGPR Bacteria in Plant Disease Management 87Madhu Prakash Srivastava and Swati Sharma5.1 Introduction 875.2 Beneficial bacteria in soil 885.3 Rhizobacteria 895.3.1 Gram-positive bacteria as antagonists 895.3.2 Gram-negative bacteria 935.4 Bacterial parasites of nematodes 935.4.1 Pasteuria 935.5 Mechanisms involved in biocontrol 955.5.1 Structural mechanisms 955.5.2 Biochemical mechanisms 965.5.3 Competition for niche and nutrients 1035.5.4 Molecular mechanisms 1065.6 Conclusion and future prospects 106References 1086 Entophytic Microbes and Biocontrol of Plant Diseases 117Shradha Srivastava, Arpita Tripathi, and Rakesh Pandey6.1 Introduction 1176.2 How entophytes affect plants 1196.3 Entophytes in plant protection 1206.4 Entophytes’ interactions with fungi 1206.5 Interactions with viruses and bacteria 1226.6 Entophytes’ interactions with nematodes 1226.7 Entomopathogenic entophytes 1236.8 Entophytes in postharvest management of diseases 1246.9 Endophytic microorganisms with the potential to improve phytoremediation 1246.10 Mechanisms of entophytic protection 1256.10.1 Direct mechanisms 1256.10.2 Indirect mechanisms 1286.10.3 Ecological mechanisms 1296.11 Bioprospecting entophytes 1296.12 Conclusion and future prospects 130References 1317 AM Fungi: A Natural Bio-Protectant against Soil Pathogens 139Avantina S. Bhandari7.1 Introduction 1397.2 The rhizosphere 1407.3 Mycorrhiza 1417.3.1 Types of mycorrhizal associations 1427.4 Soil microbes and AMF dynamics 1437.5 The bio-communications of microbes and mycorrhizae 1437.5.1 Beneficial bio-communications 1447.5.2 The role of AMF in plant growth promotion (PGP) 1447.5.3 The antagonistic bio-communication 1457.6 The role of AMF in plant protection 1467.7 AMF as a potential natural bio-protectant 1467.8 AMF biocontrol efficacy and mechanisms 1487.8.1 Direct mechanisms 1487.8.2 Indirect mechanisms 1517.9 The genetic interpretation of induction 1547.9.1 The signalling pathways involved 1557.10 Conclusion and future prospects 155References 1578 Potential of Entomopathogenic Fungi in Bio-Management of Insect Pests 163Musarrat Haseeb and Ritu Srivastava8.1 Introduction 1638.2 Storage pests 1648.3 Insecticide resistance in storage pests 1648.4 The urgent need 1658.5 Entomopathogenic fungi 1668.5.1 Advantages 1678.5.2 Disadvantages 1688.6 Efficacy of entomopathogenic fungi 1688.7 Mode of infection 1708.8 Mode of action 1728.8.1 Oviposition deterrence activity 1728.8.2 Chitin inhibitor 1728.8.3 Bacterial septicaemia 1728.9 Virulence and viability 1738.10 Effect of temperature and relative humidity 1738.11 Compatibility of entomopathogens with botanicals 1748.12 Compatibility of entomopathogens with chemicals 1748.13 Production of entomopathogens 1758.14 Constraints on the production and commercialization of entomopathogens 1768.15 Conclusion and future prospects 177References 1779 The Multifaceted Role of the Trichoderma System in Biocontrol 183Richa Tiwari and Abhishek Tripathi9.1 Introduction 1839.2 Why Trichoderma? 1849.3 Mechanisms used by Trichoderma spp. 1849.3.1 Direct action 1859.3.2 Antibiotic activity and production of secondary metabolites 1869.3.3 Competition with soil microsphere 1899.3.4 Indirect action of the biocontrol agents 1899.4 Compatibility of the Trichoderma system with other microorganisms 1939.4.1 With mycorrhiza 1939.5 Other applications 1949.5.1 As a nematicide 1949.5.2 Against insects 1949.5.3 As a weedicide 1949.5.4 Diseases of fruits and vegetables 1959.6 Pesticide susceptibility 1959.7 Mass multiplication of Trichoderma 1959.8 Methods of mass multiplication 1969.8.1 Micropropagules 1969.9 Commercial use of Trichoderma 1979.10 Basic components of biocontrol systems 1999.10.1 Biocontrol strain 1999.10.2 Compatibility testing of Trichoderma 2009.10.3 Commercial potential 2009.10.4 Constraints on the commercialization of Trichoderma spp. BCAs 2039.11 Conclusion and future prospects 203References 20410 Ladybirds: Potential Bioagents against Plant Pests and Vectors 211Omkar and Geetanjali Mishra10.1 Insects and humans 21110.2 The rise of crop pests and their management 21110.3 Biocontrol rediscovered 21210.3.1 Types of biocontrol 21310.3.2 Shift from classical biocontrol 21410.4 Ladybirds: potential bioagents 21410.5 Pre-release studies 21610.5.1 Food: identification of target prey and optimization for mass production 21610.5.2 Predator interactions 21910.5.3 Temperature 22210.5.4 Light 22310.5.5 Age 22510.5.6 Mating and reproduction 22610.6 Mass production and release techniques 22710.7 Success stories 22710.8 The urgent need 229References 22911 Biomanagement of Phytonematodes 241Nupur Srivastava and Akhtar Haseeb11.1 Introduction 24111.2 Ecologically safe methods/products 24211.2.1 Mixed cropping/intercropping 24311.2.2 Crop rotation 24411.2.3 Soil amendment using natural products 24411.2.4 Chitin 25011.3 Antagonists of plant-parasitic nematodes 25011.3.1 Antagonistic bacteria 25211.3.2 Opportunistic parasitic bacteria 25311.3.3 Rhizobacteria 25511.3.4 Cry protein-forming bacteria 25611.4 Endophytic bacteria 25711.5 Nematophagous fungi 25711.6 Predacious nematodes 25811.7 Invertebrates 25811.8 Proposed mechanisms behind the antagonism 25911.8.1 Common by-products of decomposition 26011.8.2 Plant-specific toxins 26111.8.3 Stimulation of natural enemies of nematodes 26211.8.4 The Linford hypothesis 26211.8.5 The chitin hypothesis 26311.8.6 Plant tolerance 26311.8.7 Habitat modification 26411.9 Conclusion and future prospects 264References 26612 The Effect of Essential Oils on the Development of Phytopathogenic Fungi 273Jasenka ´ Cosi´c, Karolina Vrandeˇci´c, and Drazenka Jurkovic12.1 Introduction 27312.2 Essential oils and their effects 27412.3 Bioactivities of essential oils 27912.4 Antifungal effects 28112.5 Results 28212.6 Application of essential oils 28612.7 Conclusion and future prospects 28713 Chitosan: A Potential Antifungal Compound to Control Anthracnose Disease in Papaya 293Ilmi Hewajulge, Shanthi Wilson Wijeratnam, and Takeo Shiina13.1 Introduction 29313.2 Papaya (Carica papaya L.) 29513.2.1 Status of the papaya industry in the world 29613.2.2 Harvest maturity and postharvest handling 29713.2.3 Chemical constituents of papaya 29813.3 Major postharvest diseases of papaya 29913.3.1 Anthracnose disease in papaya 30013.3.2 Methods of control of postharvest pathogens 30213.3.3 Chitosan (poly (1–4) β, D-glucosamine) 30413.3.4 Chitosan as an elicitor response mechanism in plants 30713.3.5 Effect of chitosan on postharvest disease control and quality retention of horticultural commodities 30713.3.6 Effect of γ-irradiation on the antifungal properties of chitosan 30813.3.7 Effect of chitosan on anthracnose disease control of papaya 308References 31114 Induction of Defence Responses for Biological Control of Plant Diseases 321Shalini Srivastava and Vivek Prasad14.1 Introduction 32114.2 Plant protein-induced systemic resistance 32214.3 Ribosome-inactivating proteins 32514.4 Plant growth-promoting rhizobacteria 32614.5 Systemic acquired resistance 32914.6 Induction of SAR and role of PR-proteins and salicylic acid 33114.7 Conclusion and future prospects 332References 33315 Molecular Markers and Phytopathology 341Ayman M.H. Esh15.1 Introduction 34115.2 Types of molecular markers 34315.3 Hybridization-based markers 34515.3.1 Restriction fragment length polymorphism (RFLP) 34515.3.2 Microarrays 34615.4 PCR-based markers 34815.4.1 Random amplified polymorphic DNA (RAPD-PCR) 34815.4.2 Short simple repeats (SSRs) 35015.4.3 Inter-sequence simple repeats (ISSRs) 35115.4.4 PCR-RFLP 35215.4.5 Amplified fragment length polymorphism (AFLP) 35315.4.6 cDNA amplified fragment length polymorphism (cDNA-AFLP) 35715.5 Sequencing-based markers 35815.5.1 Internal transcribed sequence (ITS) and the intergenic spacer region (IGS) 35915.5.2 Single nucleotide polymorphism (SNP) 36015.6 Applications of molecular markers in plant pathogen genomic analysis 36215.6.1 Mapping and tagging of genes 36215.6.2 Plant pathogen species or strain detection, identification and polymorphism and genetic diversity 363References 36616 Deciphering the Pathogenic Behaviour of Phyto-Pathogens Using Molecular Tools 377H.B. Singh, Akansha Jain, Amrita Saxena, Akanksha Singh,Chetan Keswani, Birinchi Kumar Sarma, and Sandhya Mishra16.1 Introduction 37716.2 Bacteria 37916.2.1 Detection methods: past vs present 37916.2.2 Pulsed field gel electrophoresis (PFGE) 38016.2.3 Nucleic acid-based techniques 38116.2.4 Polymerase chain reaction 38116.2.5 Real-time PCR (RT-PCR) 38216.2.6 The loop-mediated isothermal amplification technique (LAMP) 38216.2.7 DNA array technology 38316.2.8 Biosensors 38416.3 Fungi 38516.3.1 Nucleic acid-based approaches 38616.3.2 PCR 38716.3.3 Fingerprinting approaches 38916.3.4 DNA hybridization technologies 38916.3.5 Immunological techniques 39016.4 Nematodes 39116.4.1 Non-polymerase chain reaction methods 39216.4.2 Restriction fragment length polymorphism (RFLP) analysis 39216.4.3 Polymerase chain reaction-based approaches 39216.5 Viruses 39516.5.1 Serological techniques 39516.5.2 Molecular-based detection techniques 39616.5.3 Polymerase chain reaction (PCR) 39616.5.4 Microarray 39716.6 Conclusion and future prospects 398References 39817 Is PCR-DGGE an Innovative Molecular Tool for the Detection of Microbial Plant Pathogens? 409Aly Farag El Sheikha and Ramesh Chandra Ray17.1 Detection methods of plant pathogens from the past to the present 40917.2 Molecular detection techniques of plant pathogens 41117.2.1 Detection of plant-pathogenic bacteria and viruses 41217.2.2 Molecular diagnostics of fungal plant pathogens 41617.3 Microbial plant pathogens: what we know and how can we benefit? 41817.4 PCR-DGGE: novel microbial pathogens detection tool…but how? 41917.4.1 What does PCR-DGGE do? 41917.4.2 Identifying microbial communities isolated from plant samples by PCR-DGGE 42017.4.3 PCR-DGGE: benefits and biases 42117.5 Conclusion and future prospects 424References 425Index 435

Dr Neeta Sharma is a senior faculty member in the Department of Botany at the University of Lucknow, India.

• Preface xviiList of Contributors xixAcknowledgments xxiii1 Biologicals: Green Alternatives for Plant Disease Management 1Neeta Sharma1.1 Introduction 11.2 Food supply on a collision course 21.3 The enormity of the problem 31.3.1 Overpopulation 31.3.2 Effective land usage 31.3.3 Water use 41.3.4 Energy use 41.4 Preventing food losses 41.5 Hazards from synthetic pesticides 51.6 A way out of this crisis 61.7 Types of biopesticides 61.7.1 Microbial pesticides 61.7.2 Plant-derived products 91.7.3 Semiochemicals 101.8 Strategies of biological control 101.9 Biopesticides: advantages and limitations 161.10 Major constraints 171.10.1 Agronomic aspects 171.10.2 The commercial perspective 181.10.3 Public anxiety over BCAs 191.10.4 Technical issues 201.10.5 Virulence and efficacy 201.11 Conclusion and future prospects 23References 242 Postharvest Damages of Mandarin (Citrus reticulata Blanco) and Its Management 27N. Chakraborty, N. S. Gupta, S. K. Basu, and K. Acharya2.1 Introduction 272.2 Diseases and disorders in mandarins 282.2.1 Postharvest diseases of mandarins 282.2.2 Physiological disorders in mandarins 292.2.3 Postharvest loss of mandarins 302.3 Strategies for postharvest management 312.3.1 Physical methods 312.3.2 Chemical methods 322.3.3 Biological methods 322.4 Naturally occurring antifungal compounds for biocontrol 342.5 Induced resistance 342.6 Conclusion and future prospects 35References 363 Yeasts: Bio-Bullets for Postharvest Diseases of Horticultural Perishables 41Neeta Sharma and Richa Tiwari3.1 Introduction 413.2 Presence of an antagonist 443.3 Introduction of the yeast antagonist in the postharvest system of horticultural perishables 443.3.1 Yeast as a natural antagonist 443.3.2 Yeast as an artificially introduced antagonist 453.3.3 Application methods of yeast antagonist for biosuppression of the pathogen 453.4 Commercial production 493.4.1 Properties of an ideal antagonist suitable for commercialization 493.4.2 Characteristics required for commercial production 503.4.3 Biocontrol yeast products 513.5 Problems in product development and registration 523.6 Enhancement of the bioactivity of the yeast antagonist 553.6.1 Mixed cultures with antagonistic yeast 553.6.2 Low levels of fungicides with a yeast antagonist 563.6.3 Exogenous substances with a yeast antagonist 573.6.4 Physical treatment with a yeast antagonist 583.7 Conclusion and future prospects 59References 604 Dissecting the Mechanisms of Action of Biocontrol Agents to Control Postharvest Diseases of Fruit 69Davide Spadaro4.1 Introduction 694.2 Studying the mechanism of action 704.3 Competition 714.4 The role of biofilm formation 724.5 Production of diffusible and volatile antimicrobial compounds 734.6 Parasitism and release of hydrolases 754.7 Induction of resistance 774.8 The role of oxidative stress 794.9 Conclusion and future prospects 80Acknowledgements 81References 815 Potential of PGPR Bacteria in Plant Disease Management 87Madhu Prakash Srivastava and Swati Sharma5.1 Introduction 875.2 Beneficial bacteria in soil 885.3 Rhizobacteria 895.3.1 Gram-positive bacteria as antagonists 895.3.2 Gram-negative bacteria 935.4 Bacterial parasites of nematodes 935.4.1 Pasteuria 935.5 Mechanisms involved in biocontrol 955.5.1 Structural mechanisms 955.5.2 Biochemical mechanisms 965.5.3 Competition for niche and nutrients 1035.5.4 Molecular mechanisms 1065.6 Conclusion and future prospects 106References 1086 Entophytic Microbes and Biocontrol of Plant Diseases 117Shradha Srivastava, Arpita Tripathi, and Rakesh Pandey6.1 Introduction 1176.2 How entophytes affect plants 1196.3 Entophytes in plant protection 1206.4 Entophytes’ interactions with fungi 1206.5 Interactions with viruses and bacteria 1226.6 Entophytes’ interactions with nematodes 1226.7 Entomopathogenic entophytes 1236.8 Entophytes in postharvest management of diseases 1246.9 Endophytic microorganisms with the potential to improve phytoremediation 1246.10 Mechanisms of entophytic protection 1256.10.1 Direct mechanisms 1256.10.2 Indirect mechanisms 1286.10.3 Ecological mechanisms 1296.11 Bioprospecting entophytes 1296.12 Conclusion and future prospects 130References 1317 AM Fungi: A Natural Bio-Protectant against Soil Pathogens 139Avantina S. Bhandari7.1 Introduction 1397.2 The rhizosphere 1407.3 Mycorrhiza 1417.3.1 Types of mycorrhizal associations 1427.4 Soil microbes and AMF dynamics 1437.5 The bio-communications of microbes and mycorrhizae 1437.5.1 Beneficial bio-communications 1447.5.2 The role of AMF in plant growth promotion (PGP) 1447.5.3 The antagonistic bio-communication 1457.6 The role of AMF in plant protection 1467.7 AMF as a potential natural bio-protectant 1467.8 AMF biocontrol efficacy and mechanisms 1487.8.1 Direct mechanisms 1487.8.2 Indirect mechanisms 1517.9 The genetic interpretation of induction 1547.9.1 The signalling pathways involved 1557.10 Conclusion and future prospects 155References 1578 Potential of Entomopathogenic Fungi in Bio-Management of Insect Pests 163Musarrat Haseeb and Ritu Srivastava8.1 Introduction 1638.2 Storage pests 1648.3 Insecticide resistance in storage pests 1648.4 The urgent need 1658.5 Entomopathogenic fungi 1668.5.1 Advantages 1678.5.2 Disadvantages 1688.6 Efficacy of entomopathogenic fungi 1688.7 Mode of infection 1708.8 Mode of action 1728.8.1 Oviposition deterrence activity 1728.8.2 Chitin inhibitor 1728.8.3 Bacterial septicaemia 1728.9 Virulence and viability 1738.10 Effect of temperature and relative humidity 1738.11 Compatibility of entomopathogens with botanicals 1748.12 Compatibility of entomopathogens with chemicals 1748.13 Production of entomopathogens 1758.14 Constraints on the production and commercialization of entomopathogens 1768.15 Conclusion and future prospects 177References 1779 The Multifaceted Role of the Trichoderma System in Biocontrol 183Richa Tiwari and Abhishek Tripathi9.1 Introduction 1839.2 Why Trichoderma? 1849.3 Mechanisms used by Trichoderma spp. 1849.3.1 Direct action 1859.3.2 Antibiotic activity and production of secondary metabolites 1869.3.3 Competition with soil microsphere 1899.3.4 Indirect action of the biocontrol agents 1899.4 Compatibility of the Trichoderma system with other microorganisms 1939.4.1 With mycorrhiza 1939.5 Other applications 1949.5.1 As a nematicide 1949.5.2 Against insects 1949.5.3 As a weedicide 1949.5.4 Diseases of fruits and vegetables 1959.6 Pesticide susceptibility 1959.7 Mass multiplication of Trichoderma 1959.8 Methods of mass multiplication 1969.8.1 Micropropagules 1969.9 Commercial use of Trichoderma 1979.10 Basic components of biocontrol systems 1999.10.1 Biocontrol strain 1999.10.2 Compatibility testing of Trichoderma 2009.10.3 Commercial potential 2009.10.4 Constraints on the commercialization of Trichoderma spp. BCAs 2039.11 Conclusion and future prospects 203References 20410 Ladybirds: Potential Bioagents against Plant Pests and Vectors 211Omkar and Geetanjali Mishra10.1 Insects and humans 21110.2 The rise of crop pests and their management 21110.3 Biocontrol rediscovered 21210.3.1 Types of biocontrol 21310.3.2 Shift from classical biocontrol 21410.4 Ladybirds: potential bioagents 21410.5 Pre-release studies 21610.5.1 Food: identification of target prey and optimization for mass production 21610.5.2 Predator interactions 21910.5.3 Temperature 22210.5.4 Light 22310.5.5 Age 22510.5.6 Mating and reproduction 22610.6 Mass production and release techniques 22710.7 Success stories 22710.8 The urgent need 229References 22911 Biomanagement of Phytonematodes 241Nupur Srivastava and Akhtar Haseeb11.1 Introduction 24111.2 Ecologically safe methods/products 24211.2.1 Mixed cropping/intercropping 24311.2.2 Crop rotation 24411.2.3 Soil amendment using natural products 24411.2.4 Chitin 25011.3 Antagonists of plant-parasitic nematodes 25011.3.1 Antagonistic bacteria 25211.3.2 Opportunistic parasitic bacteria 25311.3.3 Rhizobacteria 25511.3.4 Cry protein-forming bacteria 25611.4 Endophytic bacteria 25711.5 Nematophagous fungi 25711.6 Predacious nematodes 25811.7 Invertebrates 25811.8 Proposed mechanisms behind the antagonism 25911.8.1 Common by-products of decomposition 26011.8.2 Plant-specific toxins 26111.8.3 Stimulation of natural enemies of nematodes 26211.8.4 The Linford hypothesis 26211.8.5 The chitin hypothesis 26311.8.6 Plant tolerance 26311.8.7 Habitat modification 26411.9 Conclusion and future prospects 264References 26612 The Effect of Essential Oils on the Development of Phytopathogenic Fungi 273Jasenka ´ Cosi´c, Karolina Vrandeˇci´c, and Drazenka Jurkovic12.1 Introduction 27312.2 Essential oils and their effects 27412.3 Bioactivities of essential oils 27912.4 Antifungal effects 28112.5 Results 28212.6 Application of essential oils 28612.7 Conclusion and future prospects 28713 Chitosan: A Potential Antifungal Compound to Control Anthracnose Disease in Papaya 293Ilmi Hewajulge, Shanthi Wilson Wijeratnam, and Takeo Shiina13.1 Introduction 29313.2 Papaya (Carica papaya L.) 29513.2.1 Status of the papaya industry in the world 29613.2.2 Harvest maturity and postharvest handling 29713.2.3 Chemical constituents of papaya 29813.3 Major postharvest diseases of papaya 29913.3.1 Anthracnose disease in papaya 30013.3.2 Methods of control of postharvest pathogens 30213.3.3 Chitosan (poly (1–4) β, D-glucosamine) 30413.3.4 Chitosan as an elicitor response mechanism in plants 30713.3.5 Effect of chitosan on postharvest disease control and quality retention of horticultural commodities 30713.3.6 Effect of γ-irradiation on the antifungal properties of chitosan 30813.3.7 Effect of chitosan on anthracnose disease control of papaya 308References 31114 Induction of Defence Responses for Biological Control of Plant Diseases 321Shalini Srivastava and Vivek Prasad14.1 Introduction 32114.2 Plant protein-induced systemic resistance 32214.3 Ribosome-inactivating proteins 32514.4 Plant growth-promoting rhizobacteria 32614.5 Systemic acquired resistance 32914.6 Induction of SAR and role of PR-proteins and salicylic acid 33114.7 Conclusion and future prospects 332References 33315 Molecular Markers and Phytopathology 341Ayman M.H. Esh15.1 Introduction 34115.2 Types of molecular markers 34315.3 Hybridization-based markers 34515.3.1 Restriction fragment length polymorphism (RFLP) 34515.3.2 Microarrays 34615.4 PCR-based markers 34815.4.1 Random amplified polymorphic DNA (RAPD-PCR) 34815.4.2 Short simple repeats (SSRs) 35015.4.3 Inter-sequence simple repeats (ISSRs) 35115.4.4 PCR-RFLP 35215.4.5 Amplified fragment length polymorphism (AFLP) 35315.4.6 cDNA amplified fragment length polymorphism (cDNA-AFLP) 35715.5 Sequencing-based markers 35815.5.1 Internal transcribed sequence (ITS) and the intergenic spacer region (IGS) 35915.5.2 Single nucleotide polymorphism (SNP) 36015.6 Applications of molecular markers in plant pathogen genomic analysis 36215.6.1 Mapping and tagging of genes 36215.6.2 Plant pathogen species or strain detection, identification and polymorphism and genetic diversity 363References 36616 Deciphering the Pathogenic Behaviour of Phyto-Pathogens Using Molecular Tools 377H.B. Singh, Akansha Jain, Amrita Saxena, Akanksha Singh,Chetan Keswani, Birinchi Kumar Sarma, and Sandhya Mishra16.1 Introduction 37716.2 Bacteria 37916.2.1 Detection methods: past vs present 37916.2.2 Pulsed field gel electrophoresis (PFGE) 38016.2.3 Nucleic acid-based techniques 38116.2.4 Polymerase chain reaction 38116.2.5 Real-time PCR (RT-PCR) 38216.2.6 The loop-mediated isothermal amplification technique (LAMP) 38216.2.7 DNA array technology 38316.2.8 Biosensors 38416.3 Fungi 38516.3.1 Nucleic acid-based approaches 38616.3.2 PCR 38716.3.3 Fingerprinting approaches 38916.3.4 DNA hybridization technologies 38916.3.5 Immunological techniques 39016.4 Nematodes 39116.4.1 Non-polymerase chain reaction methods 39216.4.2 Restriction fragment length polymorphism (RFLP) analysis 39216.4.3 Polymerase chain reaction-based approaches 39216.5 Viruses 39516.5.1 Serological techniques 39516.5.2 Molecular-based detection techniques 39616.5.3 Polymerase chain reaction (PCR) 39616.5.4 Microarray 39716.6 Conclusion and future prospects 398References 39817 Is PCR-DGGE an Innovative Molecular Tool for the Detection of Microbial Plant Pathogens? 409Aly Farag El Sheikha and Ramesh Chandra Ray17.1 Detection methods of plant pathogens from the past to the present 40917.2 Molecular detection techniques of plant pathogens 41117.2.1 Detection of plant-pathogenic bacteria and viruses 41217.2.2 Molecular diagnostics of fungal plant pathogens 41617.3 Microbial plant pathogens: what we know and how can we benefit? 41817.4 PCR-DGGE: novel microbial pathogens detection tool…but how? 41917.4.1 What does PCR-DGGE do? 41917.4.2 Identifying microbial communities isolated from plant samples by PCR-DGGE 42017.4.3 PCR-DGGE: benefits and biases 42117.5 Conclusion and future prospects 424References 425Index 435

Dr Neeta Sharma is a senior faculty member in the Department of Botany at the University of Lucknow, India.

• Preface xviiList of Contributors xixAcknowledgments xxiii1 Biologicals: Green Alternatives for Plant Disease Management 1Neeta Sharma1.1 Introduction 11.2 Food supply on a collision course 21.3 The enormity of the problem 31.3.1 Overpopulation 31.3.2 Effective land usage 31.3.3 Water use 41.3.4 Energy use 41.4 Preventing food losses 41.5 Hazards from synthetic pesticides 51.6 A way out of this crisis 61.7 Types of biopesticides 61.7.1 Microbial pesticides 61.7.2 Plant-derived products 91.7.3 Semiochemicals 101.8 Strategies of biological control 101.9 Biopesticides: advantages and limitations 161.10 Major constraints 171.10.1 Agronomic aspects 171.10.2 The commercial perspective 181.10.3 Public anxiety over BCAs 191.10.4 Technical issues 201.10.5 Virulence and efficacy 201.11 Conclusion and future prospects 23References 242 Postharvest Damages of Mandarin (Citrus reticulata Blanco) and Its Management 27N. Chakraborty, N. S. Gupta, S. K. Basu, and K. Acharya2.1 Introduction 272.2 Diseases and disorders in mandarins 282.2.1 Postharvest diseases of mandarins 282.2.2 Physiological disorders in mandarins 292.2.3 Postharvest loss of mandarins 302.3 Strategies for postharvest management 312.3.1 Physical methods 312.3.2 Chemical methods 322.3.3 Biological methods 322.4 Naturally occurring antifungal compounds for biocontrol 342.5 Induced resistance 342.6 Conclusion and future prospects 35References 363 Yeasts: Bio-Bullets for Postharvest Diseases of Horticultural Perishables 41Neeta Sharma and Richa Tiwari3.1 Introduction 413.2 Presence of an antagonist 443.3 Introduction of the yeast antagonist in the postharvest system of horticultural perishables 443.3.1 Yeast as a natural antagonist 443.3.2 Yeast as an artificially introduced antagonist 453.3.3 Application methods of yeast antagonist for biosuppression of the pathogen 453.4 Commercial production 493.4.1 Properties of an ideal antagonist suitable for commercialization 493.4.2 Characteristics required for commercial production 503.4.3 Biocontrol yeast products 513.5 Problems in product development and registration 523.6 Enhancement of the bioactivity of the yeast antagonist 553.6.1 Mixed cultures with antagonistic yeast 553.6.2 Low levels of fungicides with a yeast antagonist 563.6.3 Exogenous substances with a yeast antagonist 573.6.4 Physical treatment with a yeast antagonist 583.7 Conclusion and future prospects 59References 604 Dissecting the Mechanisms of Action of Biocontrol Agents to Control Postharvest Diseases of Fruit 69Davide Spadaro4.1 Introduction 694.2 Studying the mechanism of action 704.3 Competition 714.4 The role of biofilm formation 724.5 Production of diffusible and volatile antimicrobial compounds 734.6 Parasitism and release of hydrolases 754.7 Induction of resistance 774.8 The role of oxidative stress 794.9 Conclusion and future prospects 80Acknowledgements 81References 815 Potential of PGPR Bacteria in Plant Disease Management 87Madhu Prakash Srivastava and Swati Sharma5.1 Introduction 875.2 Beneficial bacteria in soil 885.3 Rhizobacteria 895.3.1 Gram-positive bacteria as antagonists 895.3.2 Gram-negative bacteria 935.4 Bacterial parasites of nematodes 935.4.1 Pasteuria 935.5 Mechanisms involved in biocontrol 955.5.1 Structural mechanisms 955.5.2 Biochemical mechanisms 965.5.3 Competition for niche and nutrients 1035.5.4 Molecular mechanisms 1065.6 Conclusion and future prospects 106References 1086 Entophytic Microbes and Biocontrol of Plant Diseases 117Shradha Srivastava, Arpita Tripathi, and Rakesh Pandey6.1 Introduction 1176.2 How entophytes affect plants 1196.3 Entophytes in plant protection 1206.4 Entophytes’ interactions with fungi 1206.5 Interactions with viruses and bacteria 1226.6 Entophytes’ interactions with nematodes 1226.7 Entomopathogenic entophytes 1236.8 Entophytes in postharvest management of diseases 1246.9 Endophytic microorganisms with the potential to improve phytoremediation 1246.10 Mechanisms of entophytic protection 1256.10.1 Direct mechanisms 1256.10.2 Indirect mechanisms 1286.10.3 Ecological mechanisms 1296.11 Bioprospecting entophytes 1296.12 Conclusion and future prospects 130References 1317 AM Fungi: A Natural Bio-Protectant against Soil Pathogens 139Avantina S. Bhandari7.1 Introduction 1397.2 The rhizosphere 1407.3 Mycorrhiza 1417.3.1 Types of mycorrhizal associations 1427.4 Soil microbes and AMF dynamics 1437.5 The bio-communications of microbes and mycorrhizae 1437.5.1 Beneficial bio-communications 1447.5.2 The role of AMF in plant growth promotion (PGP) 1447.5.3 The antagonistic bio-communication 1457.6 The role of AMF in plant protection 1467.7 AMF as a potential natural bio-protectant 1467.8 AMF biocontrol efficacy and mechanisms 1487.8.1 Direct mechanisms 1487.8.2 Indirect mechanisms 1517.9 The genetic interpretation of induction 1547.9.1 The signalling pathways involved 1557.10 Conclusion and future prospects 155References 1578 Potential of Entomopathogenic Fungi in Bio-Management of Insect Pests 163Musarrat Haseeb and Ritu Srivastava8.1 Introduction 1638.2 Storage pests 1648.3 Insecticide resistance in storage pests 1648.4 The urgent need 1658.5 Entomopathogenic fungi 1668.5.1 Advantages 1678.5.2 Disadvantages 1688.6 Efficacy of entomopathogenic fungi 1688.7 Mode of infection 1708.8 Mode of action 1728.8.1 Oviposition deterrence activity 1728.8.2 Chitin inhibitor 1728.8.3 Bacterial septicaemia 1728.9 Virulence and viability 1738.10 Effect of temperature and relative humidity 1738.11 Compatibility of entomopathogens with botanicals 1748.12 Compatibility of entomopathogens with chemicals 1748.13 Production of entomopathogens 1758.14 Constraints on the production and commercialization of entomopathogens 1768.15 Conclusion and future prospects 177References 1779 The Multifaceted Role of the Trichoderma System in Biocontrol 183Richa Tiwari and Abhishek Tripathi9.1 Introduction 1839.2 Why Trichoderma? 1849.3 Mechanisms used by Trichoderma spp. 1849.3.1 Direct action 1859.3.2 Antibiotic activity and production of secondary metabolites 1869.3.3 Competition with soil microsphere 1899.3.4 Indirect action of the biocontrol agents 1899.4 Compatibility of the Trichoderma system with other microorganisms 1939.4.1 With mycorrhiza 1939.5 Other applications 1949.5.1 As a nematicide 1949.5.2 Against insects 1949.5.3 As a weedicide 1949.5.4 Diseases of fruits and vegetables 1959.6 Pesticide susceptibility 1959.7 Mass multiplication of Trichoderma 1959.8 Methods of mass multiplication 1969.8.1 Micropropagules 1969.9 Commercial use of Trichoderma 1979.10 Basic components of biocontrol systems 1999.10.1 Biocontrol strain 1999.10.2 Compatibility testing of Trichoderma 2009.10.3 Commercial potential 2009.10.4 Constraints on the commercialization of Trichoderma spp. BCAs 2039.11 Conclusion and future prospects 203References 20410 Ladybirds: Potential Bioagents against Plant Pests and Vectors 211Omkar and Geetanjali Mishra10.1 Insects and humans 21110.2 The rise of crop pests and their management 21110.3 Biocontrol rediscovered 21210.3.1 Types of biocontrol 21310.3.2 Shift from classical biocontrol 21410.4 Ladybirds: potential bioagents 21410.5 Pre-release studies 21610.5.1 Food: identification of target prey and optimization for mass production 21610.5.2 Predator interactions 21910.5.3 Temperature 22210.5.4 Light 22310.5.5 Age 22510.5.6 Mating and reproduction 22610.6 Mass production and release techniques 22710.7 Success stories 22710.8 The urgent need 229References 22911 Biomanagement of Phytonematodes 241Nupur Srivastava and Akhtar Haseeb11.1 Introduction 24111.2 Ecologically safe methods/products 24211.2.1 Mixed cropping/intercropping 24311.2.2 Crop rotation 24411.2.3 Soil amendment using natural products 24411.2.4 Chitin 25011.3 Antagonists of plant-parasitic nematodes 25011.3.1 Antagonistic bacteria 25211.3.2 Opportunistic parasitic bacteria 25311.3.3 Rhizobacteria 25511.3.4 Cry protein-forming bacteria 25611.4 Endophytic bacteria 25711.5 Nematophagous fungi 25711.6 Predacious nematodes 25811.7 Invertebrates 25811.8 Proposed mechanisms behind the antagonism 25911.8.1 Common by-products of decomposition 26011.8.2 Plant-specific toxins 26111.8.3 Stimulation of natural enemies of nematodes 26211.8.4 The Linford hypothesis 26211.8.5 The chitin hypothesis 26311.8.6 Plant tolerance 26311.8.7 Habitat modification 26411.9 Conclusion and future prospects 264References 26612 The Effect of Essential Oils on the Development of Phytopathogenic Fungi 273Jasenka ´ Cosi´c, Karolina Vrandeˇci´c, and Drazenka Jurkovic12.1 Introduction 27312.2 Essential oils and their effects 27412.3 Bioactivities of essential oils 27912.4 Antifungal effects 28112.5 Results 28212.6 Application of essential oils 28612.7 Conclusion and future prospects 28713 Chitosan: A Potential Antifungal Compound to Control Anthracnose Disease in Papaya 293Ilmi Hewajulge, Shanthi Wilson Wijeratnam, and Takeo Shiina13.1 Introduction 29313.2 Papaya (Carica papaya L.) 29513.2.1 Status of the papaya industry in the world 29613.2.2 Harvest maturity and postharvest handling 29713.2.3 Chemical constituents of papaya 29813.3 Major postharvest diseases of papaya 29913.3.1 Anthracnose disease in papaya 30013.3.2 Methods of control of postharvest pathogens 30213.3.3 Chitosan (poly (1–4) β, D-glucosamine) 30413.3.4 Chitosan as an elicitor response mechanism in plants 30713.3.5 Effect of chitosan on postharvest disease control and quality retention of horticultural commodities 30713.3.6 Effect of γ-irradiation on the antifungal properties of chitosan 30813.3.7 Effect of chitosan on anthracnose disease control of papaya 308References 31114 Induction of Defence Responses for Biological Control of Plant Diseases 321Shalini Srivastava and Vivek Prasad14.1 Introduction 32114.2 Plant protein-induced systemic resistance 32214.3 Ribosome-inactivating proteins 32514.4 Plant growth-promoting rhizobacteria 32614.5 Systemic acquired resistance 32914.6 Induction of SAR and role of PR-proteins and salicylic acid 33114.7 Conclusion and future prospects 332References 33315 Molecular Markers and Phytopathology 341Ayman M.H. Esh15.1 Introduction 34115.2 Types of molecular markers 34315.3 Hybridization-based markers 34515.3.1 Restriction fragment length polymorphism (RFLP) 34515.3.2 Microarrays 34615.4 PCR-based markers 34815.4.1 Random amplified polymorphic DNA (RAPD-PCR) 34815.4.2 Short simple repeats (SSRs) 35015.4.3 Inter-sequence simple repeats (ISSRs) 35115.4.4 PCR-RFLP 35215.4.5 Amplified fragment length polymorphism (AFLP) 35315.4.6 cDNA amplified fragment length polymorphism (cDNA-AFLP) 35715.5 Sequencing-based markers 35815.5.1 Internal transcribed sequence (ITS) and the intergenic spacer region (IGS) 35915.5.2 Single nucleotide polymorphism (SNP) 36015.6 Applications of molecular markers in plant pathogen genomic analysis 36215.6.1 Mapping and tagging of genes 36215.6.2 Plant pathogen species or strain detection, identification and polymorphism and genetic diversity 363References 36616 Deciphering the Pathogenic Behaviour of Phyto-Pathogens Using Molecular Tools 377H.B. Singh, Akansha Jain, Amrita Saxena, Akanksha Singh,Chetan Keswani, Birinchi Kumar Sarma, and Sandhya Mishra16.1 Introduction 37716.2 Bacteria 37916.2.1 Detection methods: past vs present 37916.2.2 Pulsed field gel electrophoresis (PFGE) 38016.2.3 Nucleic acid-based techniques 38116.2.4 Polymerase chain reaction 38116.2.5 Real-time PCR (RT-PCR) 38216.2.6 The loop-mediated isothermal amplification technique (LAMP) 38216.2.7 DNA array technology 38316.2.8 Biosensors 38416.3 Fungi 38516.3.1 Nucleic acid-based approaches 38616.3.2 PCR 38716.3.3 Fingerprinting approaches 38916.3.4 DNA hybridization technologies 38916.3.5 Immunological techniques 39016.4 Nematodes 39116.4.1 Non-polymerase chain reaction methods 39216.4.2 Restriction fragment length polymorphism (RFLP) analysis 39216.4.3 Polymerase chain reaction-based approaches 39216.5 Viruses 39516.5.1 Serological techniques 39516.5.2 Molecular-based detection techniques 39616.5.3 Polymerase chain reaction (PCR) 39616.5.4 Microarray 39716.6 Conclusion and future prospects 398References 39817 Is PCR-DGGE an Innovative Molecular Tool for the Detection of Microbial Plant Pathogens? 409Aly Farag El Sheikha and Ramesh Chandra Ray17.1 Detection methods of plant pathogens from the past to the present 40917.2 Molecular detection techniques of plant pathogens 41117.2.1 Detection of plant-pathogenic bacteria and viruses 41217.2.2 Molecular diagnostics of fungal plant pathogens 41617.3 Microbial plant pathogens: what we know and how can we benefit? 41817.4 PCR-DGGE: novel microbial pathogens detection tool…but how? 41917.4.1 What does PCR-DGGE do? 41917.4.2 Identifying microbial communities isolated from plant samples by PCR-DGGE 42017.4.3 PCR-DGGE: benefits and biases 42117.5 Conclusion and future prospects 424References 425Index 435