integrated management of diseases caused by fungi, …978-1-4020-85… · ·...

Integrated Management of Diseases Caused by Fungi, Phytoplasmaand Bacteria

Integrated Management of Plant Pests and Diseases

Published:

Volume 1General Concepts in Integrated Pest and Disease Management

edited by A. Ciancio and K.G. MukerjiISBN 978-1-4020-6060-1

Volume 2Integrated Management and Biocontrol of Vegetable and Grain

Crops Nematodesedited by A. Ciancio and K.G. Mukerji

ISBN 978-1-4020-6062-5

Forthcoming:

Volume 4Integrated Management of Fruit Crops and Forest Nematodes

edited by A. Ciancio and K.G. Mukerji

Volume 5Integrated Management of Arthropod Pests

and Insect Borne Diseasesedited by A. Ciancio and K.G. Mukerji

Integrated Managementof Diseases Caused by Fungi,

Phytoplasma and Bacteria

Edited by

A. CiancioC.N.R., Bari, Italy

and

K.G. MukerjiUniversity of Delhi, India

EditorsAurelio CiancioConsiglio Nazionale delleRicerche, Dipartimento

K.G. MukerjiUniversity of DelhiDept. BotanyNew Delhi-110007India

ISBN: 978-1-4020-8570-3 e-ISBN: 978-1-4020-8571-0

Library of Congress Control Number: 2008927634

c© 2008 Springer Science+Business Media B.V.No part of this work may be reproduced, stored in a retrieval system, or transmittedin any form or by any means, electronic, mechanical, photocopying, microfilming, recordingor otherwise, without written permission from the Publisher, with the exceptionof any material supplied specifically for the purpose of being enteredand executed on a computer system, for exclusive use by the purchaser of the work.

Printed on acid-free paper

9 8 7 6 5 4 3 2 1

springer.com

Istituto per la Protezione dellePianteVia G. Amendola, 122/D70126 BariItaly

Agroalimentare,

[email protected]

Cover Illustration: Bacterial Spot Fruit lesions. (Courtesy Jeffrey B. Jones)

CONTENTS

v

Contributors ............................................................................................................ xv Preface .................................................................................................................... xix

SECTION 1 - Diseases of Perennial Crops

1 Integrated Management of Stone Fruit Diseases ........................................... 3

A. Peter Sholberg and Frank Kappel

1. Introduction .................................................................................................... 3 2. Brown Rot ...................................................................................................... 5

2.1. Pathogen Identification and Disease Biology.......................................... 5 2.2. Integrated Management of Brown Rot .................................................... 8

3. Bacterial Canker........................................................................................... 12 3.1. Pathogen Identification and Disease Cycle ........................................... 12 3.2. Integrated Management of Bacterial Canker ......................................... 13

4. Leucostoma Canker...................................................................................... 15 4.1. Pathogen Identification and Disease Cycle ........................................... 15 4.2. Integrated Management of Leucostoma Canker .................................... 15

5. Powdery Mildew .......................................................................................... 16 5.1. Pathogen Identification and Disease Cycle ........................................... 16 5.2. Integrated Management of Powdery Mildew ......................................... 17

6. Postharvest Fruit Rots .................................................................................. 18 6.1. Pathogen Identification and Disease Cycle ........................................... 18 6.2. Integrated Control of Postharvest Fruit Rots ......................................... 19

References......................................................................................................... 21 2 Towards a Sustainable, Integrated Management of Apple Diseases .......... 27

Ralph L. Nicholson and Janna Beckerman

1. Introduction .................................................................................................. 27 2. The Spring Diseases ..................................................................................... 28

2.1. Apple Scab ............................................................................................ 28 2.1.2. Symptoms.................................................................................... 28 2.1.3. The Causal Pathogen ................................................................... 28 2.1.4. Disease Cycle .............................................................................. 28 2.1.5. Management ................................................................................ 29

2.2. Powdery Mildew .................................................................................. 33 2.2.1. Disease Cycle .............................................................................. 33 2.2.2. Management ................................................................................ 33

2.3. Fire Blight ............................................................................................. 34 2.3.1. Symptoms.................................................................................... 34 2.3.2. Management ................................................................................ 34 2.3.3. Root Stocks ................................................................................. 34

CONTENTS vi

2.3.4. Cultivars ...................................................................................... 35 2.3.5. Cultural Management .................................................................. 35 2.3.6. Chemical Management and Predictive Models ........................... 36 2.3.7. Removing Sources of Infection ................................................... 36

2.4. Rust Diseases......................................................................................... 37 2.4.1. Disease Cycle .............................................................................. 37 2.4.2. Management ................................................................................ 38

3. Summer Diseases ......................................................................................... 38 3.1. Bitter Rot ............................................................................................... 38

3.1.1. Symptoms.................................................................................... 38 3.1.2. Disease Cycle .............................................................................. 39 3.1.3. Management ................................................................................ 39

3.2. Flyspeck and Sooty Blotch .................................................................... 39 3.3. Disease Cycle ........................................................................................ 39 3.4. Management ......................................................................................... 40

4. Conclusions .................................................................................................. 40 References......................................................................................................... 41

3 Management and Ecology of Phytoplasma Diseases of Grapevine

and Fruit Crops............................................................................................... 43

Rita Musetti

1. Introduction .................................................................................................. 43 2. Phytoplasmas Diagnosis in Crops ................................................................ 46 3. Natural Transmission and Epidemiology ..................................................... 47 4. Plant Recovery ............................................................................................. 48 5. Phytoplasma Diseases and Management...................................................... 48

5.1. Grapevine Phytoplasmas ....................................................................... 49 5.1.1. Flavescence Dorée....................................................................... 50 5.1.2. Bois Noir ..................................................................................... 51

5.2. Fruit Trees Phytoplasmas ...................................................................... 52 5.2.1. Apple Proliferation .................................................................... 53 5.2.2. European Stone Fruit Yellows..................................................... 54 5.2.3. Pear Decline ................................................................................ 55

6. New Approaches and Perspectives............................................................... 56 References......................................................................................................... 56

4 Management of Citrus Diseases Caused by Phytophthora spp.................... 61

Santa Olga Cacciola and Gaetano Magnano Di San Lio

1. Introduction .................................................................................................. 61 2. Damages Caused by Phytophtora Root Rot ................................................. 62

2.1. Causal Agents........................................................................................ 64 2.2. Biology and Ecology ............................................................................. 65

2.2.1. Dissemination and Reproduction ............................................... 65 2.3. Epidemiology ........................................................................................ 65

CONTENTS vii

2.4. Symptomatic Diagnosis......................................................................... 67 2.4.1. Foot Rot or Gummosis ................................................................ 67 2.4.2. Fibrous Root Rot ........................................................................ 67 2.4.3. Brown Fruit Rot and Dieback of Twigs and Leaves ................... 68

2.5. Biological and Instrumental Diagnosis.................................................. 68 2.5.1. Baits............................................................................................. 68 2.5.2. Laboratory Analysis .................................................................... 68 2.5.3. Monitoring of Inoculum .............................................................. 69

2.5.3.1. Definition....................................................................... 69 2.5.3.2. Critical Values of Inoculum Density.............................. 69 2.5.3.3. Sampling ....................................................................... 70 2.5.3.4. Population Dynamics ...................................................... 71 2.5.3.5. Molecular Methods ......................................................... 71

3. Disease Management.................................................................................... 71 3.1. Interventions on the Host-Plant ............................................................. 71

3.1.1. Rootstock..................................................................................... 71 3.1.2. Grafting ....................................................................................... 72 3.1.3. Sanitary Practices in Nurseries .................................................... 72 3.1.4. Pruning ........................................................................................ 74 3.1.5. Surgery ........................................................................................ 74

3.2. Cultural Practices................................................................................... 74 3.2.1. Soil Preparation ........................................................................... 74 3.2.2. Irrigation Management ................................................................ 74 3.2.3. Fertilising .................................................................................... 75 3.2.4. Soil Management and Weeds Control ........................................ 76

3.3. Chemical Control................................................................................... 77 3.3.1. Systemic Fungicides.................................................................... 77

3.3.1.1. Trunk Gummosis ........................................................... 78 3.3.1.2. Root Rot......................................................................... 79 3.3.1.3. Brown Rot of Fruit......................................................... 80

4. Conclusions .................................................................................................. 80 References......................................................................................................... 81

5 Biological Control and Management of Chestnut Diseases......................... 85

Tullio Turchetti and Giorgio Maresi

1. Introduction .................................................................................................. 85 2. Diseases Appearence, Epidemic and Actual Situation ................................ 87

2.1. Chestnut Blight...................................................................................... 87 2.2. Ink Disease ............................................................................................ 89

3. Symptomatology .......................................................................................... 90 3.1. Chestnut Blight and Types of Cankers .................................................. 90 3.2. Ink Disease ............................................................................................. 93

4. Evolution of the Diseases ............................................................................. 96 4.1. Spread and Effectiveness of Hypovirulence.......................................... 96 4.2. Morphology, Physiology and ds-RNA Presence and Transmission......... 99

CONTENTS viii

4.3. Mixed Inoculum .................................................................................. 101 4.4. Chestnut Resistance............................................................................. 102 4.5. Environmental Factors......................................................................... 103 4.6. Ecological Factors in Ink Disease........................................................ 104 4.7. Soil Microflora Action......................................................................... 106

6. Diseases Management ............................................................................... 107 6.1. Blight, Silviculture and Biological Control ......................................... 107 6.2. Ink Disease Control ............................................................................. 110

7. Perspectives and Conclusions .................................................................... 111 References....................................................................................................... 112

6 The Esca Disease Complex........................................................................... 119

Giuseppe Surico, Laura Mugnai and Guido Marchi

1. Introduction ................................................................................................ 119 2. The Pathogens of the Esca Disease Complex............................................. 120

2.1. Tracheomycotic Fungi......................................................................... 120 2.2. Basidiomycetes Causing White Rot .................................................... 122

3. Symptoms................................................................................................... 123 3.1. Brown Wood Streaking of Rooted Cuttings ........................................ 123 3.2. Petri Disease (or ‘Black Goo’) ............................................................ 123 3.3. Esca (Young Esca) .............................................................................. 124 3.4. White Rot ............................................................................................ 125 3.5. Esca Proper.......................................................................................... 126 3.6. Apoplexy ............................................................................................. 127

4. Source of Inoculum and Spread ................................................................. 127 4.1. Infection Routes and Disease Distribution in the Vineyard................. 128

5. Control ....................................................................................................... 130 5.1. Control in the Nursery ......................................................................... 130 5.2. Control in the Field.............................................................................. 131

6. Conclusions ................................................................................................ 133 References....................................................................................................... 133

7 Integrated Management of Rosellinia necatrix Root Rot on Fruit

Tree Crops .................................................................................................... 137

Leonardo Schena, Franco Nigro and Antonio Ippolito

1. Introduction ................................................................................................ 137 2. Taxonomy .................................................................................................. 138 3. Host Range and Geographic Distribution................................................... 138 4. Symptoms................................................................................................... 140 5. Disease Cycle and Epidemiology............................................................... 143

5.1. Survival ............................................................................................... 143 5.2. Dispersal.............................................................................................. 144 5.3. Infection Process ................................................................................. 146

CONTENTS ix

6. Control ....................................................................................................... 146 6.1. Healthy Propagative Materials ........................................................... 147

6.1.1. Current Legislation in Europe .................................................. 147 6.1.2. Diagnostic Tools ....................................................................... 148

6.2. Cultural Control Methods.................................................................... 149 6.3. Fumigation........................................................................................... 150 6.4. Chemical Control................................................................................. 151 6.5. Physical Control .................................................................................. 151 6.6. Biological Control ............................................................................... 153

References....................................................................................................... 154

SECTION 2 - Diseases of Annual Crops

8 Simulation Models for Potato Late Blight Management and Ecology ..... 161

G. A. Forbes, W. E. Fry, J. L. Andrade-Piedra and D. Shtienberg

1. Introduction ................................................................................................ 161 2. Plant Disease Simulation............................................................................ 162

2.1. Simulation vs. Forecasting .................................................................. 162 2.2. The Cornell Experience ...................................................................... 163 2.3. Globalizing LB1990 .......................................................................... 164

3. Other Simulation Models ........................................................................... 168 4. Innovation and Future Directions for Late Blight Simulation.................... 169

4.1. Comparative Epidemiology................................................................. 169 4.2. Biological Control ............................................................................... 172 4.3. Geographic Zonation and Impact Assessment..................................... 173 4.4. Plant Breeding - Predicting Resistance Performance .......................... 173 4.5. Training ............................................................................................... 174

References....................................................................................................... 174

9 An example of Integrated Forecasting System for Phytophthora on Potato ........................................................................................ 179

Jan Hadders

1. Introduction ................................................................................................ 179 2. Disease Forecasting Models & Principles .................................................. 181

2.1. Sub Model 1a - Unprotected Crop by Growth of New Leaves............ 181 2.2. Sub Model 1b - Unprotected Crop by Degradation

and Wear-Off of Chemicals................................................................. 182 2.3. Sub Model 1- Unprotected Part of the Crop ........................................ 182 2.4. Sub Model 2 - Infection Events of the Disease ................................... 182 2.5. Sub Model 2a - Formation of Spores on Each Infected Leaf .............. 183 2.6. Sub Model 2b - Ejection and Dispersal of Spores into the Air............ 183 2.7. Sub Model 2c - Spores Germination and Penetration into

Unprotected Leaves ............................................................................ 183

infestans

CONTENTS x

2.8. Sub Model 3: Combination of Unprotected Leaf Area and Infection Events into Advice ........................................................ 185

3. Quality of Weather Forecasts ..................................................................... 186 4. Future Developments and Constraints........................................................ 187 References....................................................................................................... 188

10 Integrated Pest Management of Bacterial Fruit Blotch of Cucurbits ...... 191

Ron R. Walcott

1. Introduction ................................................................................................ 191 2. Background ................................................................................................ 192

2.1. Brief History........................................................................................ 192 2.2. BFB Etiology and Symptomatology.................................................... 193 2.3. Host Range and Geographic Distribution............................................ 195 2.4. Epidemiology ...................................................................................... 195

2.4.1. Seed Production......................................................................... 195 2.4.2. Transplant Production ............................................................. 196 2.4.3. Fruit Production Fields .............................................................. 197

2.5. Trends in Commercial Cucurbit Production........................................ 197 2.5.1. Hybrid Watermelon Cultivars .................................................. 197 2.5.2. Seedling Production .................................................................. 199

3. Integrated Management.............................................................................. 199 3.1. Avoidance............................................................................................ 199 3.2. Exclusion ............................................................................................. 200

3.2.1. Seed Health Testing................................................................... 200 3.2.2. Seed Treatments ........................................................................ 202

3.3. Protection............................................................................................. 204 3.3.1. Biocontrol Blossom Protection to Limit Seed Infection............ 204

3.4. Eradication........................................................................................... 204 3.5. Resistance............................................................................................ 205


11 Integrated Management of Tomato Bacterial Spot ................................... 211

A. Obradovic, J. B. Jones, B. Balogh and M. T. Momol

1. Introduction .............................................................................................. 211 2. Tomato Production .................................................................................... 212

2.1. Tomato Production Value.................................................................... 212 2.2. Cultivation Technologies..................................................................... 213 2.3. Tomato Bacterial Diseases .................................................................. 213

3. Bacterial Spot of Tomato ........................................................................... 214 3.1. Historical Perspective.......................................................................... 214 3.2. Host-Pathogen Interactions.................................................................. 215

3.2.1. Host Range ............................................................................... 215 3.2.2. Resistance and Avirulence Genes ............................................. 215

CONTENTS xi

3.3. Distribution of Pathogen Groups ........................................................ 216 3.4. Ecology and Epidemiology ................................................................ 216

4. Integrated Approach to Bacterial Spot Management.................................. 217 4.1. Bacterial Spot Control Practices and Recent Trials ............................ 217 4.2. Integrated Strategies ........................................................................... 219

References....................................................................................................... 221

12 Integrated Management of Verticillium Wilt of Tomato .......................... 225

Giovanni Bubici and Matteo Cirulli

1. Introduction ................................................................................................ 225 2. Integrated Control ...................................................................................... 228

2.1. Selecting Soil for Cultivation .............................................................. 228 2.2. Heat ..................................................................................................... 229 2.3. Solarization.......................................................................................... 229 2.4. Sanitation............................................................................................. 230 2.5. Tillage.................................................................................................. 230 2.6. Plant Residues ..................................................................................... 231 2.7. Weed Control....................................................................................... 231 2.8. Resistant Rootstocks............................................................................ 231 2.9. Cultivars .............................................................................................. 232 2.10. Fertilization ....................................................................................... 232 2.11. Irrigation............................................................................................ 233 2.12. Chemicals .......................................................................................... 234 2.13. Microbial Antagonists ....................................................................... 235

References....................................................................................................... 237

13 New Progress in the Integrated Management of Sclerotinia Rot of Carrot ....................................................................................................... 243

Cezarina Kora, Mary Ruth McDonald and Greg J. Boland

1. Introduction .............................................................................................. 243 2. The Disease ................................................................................................ 244

2.1. Damage and Symptoms ....................................................................... 244 2.2. Causal Organism ................................................................................. 245 2.3. Etiology and Epidemiology ................................................................. 246

2.3.1. Preharvest Epidemics ................................................................ 247 2.3.2. Postharvest Epidemics............................................................... 249

3. Disease Management.................................................................................. 249 3.1. Field Practices ..................................................................................... 250

3.1.1. Cultural Control ........................................................................ 250 3.1.2. Host Resistance ........................................................................ 252 3.1.3. Biological Control ..................................................................... 253 3.1.4. Chemical Control ...................................................................... 255 3.1.5. Disease Forecasting................................................................... 255

CONTENTS xii

3.2. Storage Practices ................................................................................. 258 3.2.1. Cultural Control......................................................................... 258 3.2.2. Biological Control ..................................................................... 259 3.2.3. Alternative Methods ................................................................. 259 3.2.4. Chemical Control ...................................................................... 260

4. Recommendations on Integrated Management .......................................... 261 4.1. Reduction of Inoculum ...................................................................... 261 4.2. Reduction of Infection Rate ................................................................ 262 4.3. Reduction of Epidemic Duration ......................................................... 262 4.4. Proposed Integrated Disease Management Programs ......................... 262

5. Conclusions and Future Prospects.............................................................. 263 References....................................................................................................... 264

14 Integrated Management of Key Diseases of Cotton and Rice ................... 271

O. P. Sharma and O. M. Bambawale

1. Introduction ................................................................................................ 271 2. Identification of Diseases ........................................................................... 272 3. The Concept of Integrated Disease Management....................................... 273 4. Integrated Disease Management in Cotton................................................. 274

4.1. Seedling Diseases ................................................................................ 275 4.2. Bacterial Blight ................................................................................... 276 4.3. Alternaria Leaf Spot ............................................................................ 277 4.4. Grey Mildew........................................................................................ 277 4.5. Myrothecium Leaf Spot....................................................................... 278 4.6. Cercospora Leaf Spot ......................................................................... 279 4.7. Helminthosporium Leaf Spot ............................................................. 279 4.8. Macrophomina Leaf Spot and Stem Canker........................................ 280 4.9. Late Season Phoma Blight................................................................... 280 4.10. Rust ................................................................................................... 280 4.11. Leaf Crumple..................................................................................... 281 4.12. Cotton Leaf Curl Virus (CLCV)........................................................ 281 4.13. Tobacco Streak Virus ........................................................................ 281 4.14. Root Rot ........................................................................................... 282 4.15. Verticillium Wilt ............................................................................... 283 4.16. Fusarium Wilt ................................................................................... 283 4.17. New Wilt or Parawilt ........................................................................ 284 4.18. Boll Rots and Lint Diseases .............................................................. 285

5. Integrated Disease Management in Rice .................................................... 286 5.1. Blast..................................................................................................... 287 5.2. Brown Spot ......................................................................................... 289 5.3. Bacterial Leaf Blight .......................................................................... 290 5.4. Bacterial Leaf Streak .......................................................................... 291 5.5. Sheath Blight ...................................................................................... 292 5.6. Sheath Rot ......................................................................................... 294 5.7. Fusarium Wilt or “Bakanae” .............................................................. 294

CONTENTS xiii

5.8. Stem Rot ............................................................................................. 295 5.9. Tungro Virus ...................................................................................... 295 5.10. False Smut ........................................................................................ 296 5.11. Post-Harvest Diseases ....................................................................... 297


15 Biological and Integrated Means to Control Rust Diseases ...................... 303

Salvatore Moricca and Alessandro Ragazzi

1. Introduction ................................................................................................ 303 2. Biological Control ...................................................................................... 305

2.1. Suppression of Rust Agents................................................................. 306 2.1.1. Tuberculina spp. ........................................................................ 306 2.1.2. Verticillium spp. ........................................................................ 307 2.1.3. Cladosporium spp...................................................................... 308 2.1.4. Sphaerellopsis philum ............................................................... 310 2.1.5. Scytalidium uredinicola............................................................. 310 2.1.6. Aphanocladium album............................................................... 311

3. Diseases Suppression Mechanisms ............................................................ 311 3.1. Competition for Nutrients and Space ................................................. 311 3.2. Direct Parasitism ................................................................................. 312 3.3. Antibiosis............................................................................................. 312 3.4. Induction of Plant Resistance .............................................................. 312 3.5. Improvement of Host Fitness .............................................................. 312

4. Main Problems with Biological Control..................................................... 313 5. Eradication ................................................................................................. 317 6. Defining Hazard Areas............................................................................... 318

6.1. Quarantine ........................................................................................... 319 6.2. Cultural Practices................................................................................. 319 6.3. Chemical Control................................................................................. 320 6.4. Plant Breeding for Resistance.............................................................. 321


SECTION 3 - Advances in Management Tools

16 DNA Fingerprinting Methods for Microbial Pathogens:

Application to Diagnostics, Taxonomy and Plant Disease Management.................................................................................................. 333

Keith R. Mitchelson and Salvatore Moricca

1. Introduction ................................................................................................ 333 2. Polymorphism Detection Methodologies ................................................... 335

2.1. Genetic Fingerprinting by Fragment Sizing ........................................ 337

CONTENTS xiv

2.1.1. Ribotyping................................................................................. 337 2.2. Ribosomal RNA Detection.................................................................. 338 2.3. Random Genetic Loci.......................................................................... 339

2.3.1. RAPD Fingerprinting ................................................................ 339 2.3.2. AFLPs........................................................................................ 340

2.4. STR Fragment Fingerprinting ............................................................. 341 2.4.1. DNA Shape Analyses ................................................................ 341

3. Combined Analyses.................................................................................... 342 3.1. Genetic Mapping ................................................................................ 343 3.2. PFGE Karyotyping of Fungi for Pathovar Identification .................... 344

4. Gene and Genomic Analysis ...................................................................... 345 4.1. Quantitative Real-Time PCR............................................................... 345 4.2. Microarrays for SNP Genotyping........................................................ 346

4.2.1. Microarray Chip-Based Automated Analysers.......................... 347 4.2.2. Microarray Analysis of Gene Expression.................................. 347

5. DNA Sequence Analysis ............................................................................ 349 5.1. Whole Genome Sequencing ................................................................ 349 5.2. Massively Parallel Sequence Analysis ................................................ 350 5.3. Metagenomic Sequencing.................................................................... 350 5.4. Analysis by Capillary Electrophoresis (CE)........................................ 352

5.4.1. CE Analysis by Size Separation ................................................ 352 5.4.2. CE Analysis by Fragment Shape ............................................... 353 5.4.3. Advanced Analytical Devices ................................................... 353

5.4.3.1. Miniaturized CE-Based Devices.................................. 353 5.4.3.2. Portable Microelectromechanical Systems (MEMS)

for On-Site Analysis ................................................... 354 6. Conclusions ................................................................................................ 355 References....................................................................................................... 355

17 Endophytic Fungi for Pest and Disease Management ............................... 365

Susheel Kumar, Nutan Kaushik, Ruangelie Edrada-Ebel, Rainer Ebel and Peter Proksch 1. Introduction ................................................................................................ 365 2. Endophytic Fungi ....................................................................................... 366 3. Bioactivity of Endophytic Fungi ................................................................ 367 4. Endophytic Metabolites as Source of New Pesticides................................ 368 5. Conclusions ................................................................................................ 382 References....................................................................................................... 383

Index...................................................................................................................... 389

CONTRIBUTORS

xv

Jorge L. Andrade-Piedra Papa Andina Initiative, International Potato Center (CIP), Apartado 17 21 1977, Quito, Ecuador B. Balogh Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL 32611, USA O. M. Bambawale National Centre for Integrated Pest Management, IARI Campus, New Delhi-110 012, India Janna L. Beckerman Department of Botany and Plant Pathology, Purdue University 915 West State Street West Lafayette, IN 47907-2054 USA Greg J. Boland Department of Environmental Biology, University of Guelph, Canada Giovanni Bubici Dipartimento di Biologia e Patologia Vegetale, Università degli Studi di Bari, Via Amendola 165/A, 70126 Bari, Italy

Santa Olga Cacciola Dipartimento di Chimica Biologica, Chimica Medica e Biologia Molecolare, University of Catania, Viale Andrea Doria 6, 95126 Catania, Italy Matteo Cirulli Dipartimento di Biologia e Patologia Vegetale, Università degli Studi di Bari, Via Amendola 165/A, 70126 Bari, Italy Ruangelie Edrada-Ebel, Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Germany Rainer Ebel Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Germany G. A. Forbes International Potato Center, Apartado 1558, Lima 12, Peru W. E. Fry College of Agriculture and Life Sciences, Cornell University, Ithaca NY, 14853 USA

xvi CONTRIBUTORS

Jan Hadders Dacom PLANT-Service BV, P.O. Box 2243 7801 CE Emmen, The Netherlands Antonio Ippolito Dipartimento di Protezione delle Piante e Microbiologia Applicata University of Bari, Via Amendola 165/A 70126, Bari, Italy Jeffrey B. Jones Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL 32611, USA Frank Kappel Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia, Box 5000, 4200 Highway 97 Canada V0H 1Z0 Nutan Kaushik Plant Biotechnology, Environmental and Industrial Biotechnology Division, The Energy and Resources Institute (TERI), Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi 110 003, India Cezarina Kora Pest Management Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Bldg 57 Ottawa, ON, K1A 0C6, Canada

Susheel Kumar Plant Biotechnology, Environmental and Industrial Biotechnology Division, The Energy and Resources Institute (TERI), Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi 110 003, India Gaetano Magnano di San Lio Dipartimento di Gestione dei Sistemi Agrari e Forestali, Faculty of Agriculture, Mediterranean University of Reggio Calabria, 89122 Reggio Calabria, Italy Guido Marchi Dipartimento di Biotecnologie Agrarie, Sezione Patologia Vegetale, Piazzale delle Cascine 28, 50144 Firenze, Italy Giorgio Maresi

IASMA Research Center, Natural Resources Department, Via E. Mach 1, 38010 San Michele all’Adige (TN), Italy Mary Ruth McDonald Department of Plant Agriculture University of Guelph, Canada Keith R. Mitchelson The Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, China

CONTRIBUTORS xvii

M. T. Momol Plant Pathology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville FL 32611, USA Salvatore Moricca Dipartimento di Biotecnologie Agrarie, Sezione di Patologia Vegetale, Università di Firenze Piazzale delle Cascine, 28 50144 - Firenze

Laura Mugnai Dipartimento di Biotecnologie Agrarie, Sezione Patologia Vegetale, Piazzale delle Cascine 28, 50144 Firenze, Italy Rita Musetti Dipartimento di Biologia e

Università di Udine, Via delle Scienze, 208, 33100 Udine, Italy

Ralph L. Nicholson† Department of Botany and Plant Pathology, Purdue University 915 West State Street West Lafayette, IN 47907-2054 USA

Franco Nigro Dipartimento di Protezione delle Piante e Microbiologia Applicata, University of Bari, Via Amendola 165/A 70126, Bari, Italy

Aleksa Obradovic Plant Pathology Department, Faculty of Agriculture, University of Belgrade, 11080 Belgrade - Zemun, Serbia Peter Proksch Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Germany Alessandro Ragazzi Dipartimento di Biotecnologie Agrarie, Sezione di Patologia Vegetale, Università di Firenze Piazzale delle Cascine, 28 50144 - Firenze

Leonardo Schena Dipartimento di Gestione dei Sistemi Agrari e Forestali,

Mediterranean University of Reggio Calabria, 89122, Reggio Calabria, Italy O. P. Sharma National Centre for Integrated Pest Management, IARI Campus, New Delhi-110 012, India Peter Sholberg Agriculture and Agri-Food Canada, Pacific Agri-Food Research Centre, Summerland, British Columbia, Box 5000, 4200 Highway 97 Canada V0H 1Z0

Faculty of Agriculture,

Protezione delle Piante,

xviii CONTRIBUTORS

D. Shtienberg Department of Plant Pathology, ARO, The Volcani Center, Bet Dagan 50250, Israel Giuseppe Surico Dipartimento di Biotecnologie Agrarie, Sezione Patologia Vegetale, Piazzale delle Cascine 28, 50144 Firenze, Italy

Tullio Turchetti Consiglio Nazionale delle Ricerche, Istituto per la Protezione delle Piante, Via Madonna del Piano, 50019 Sesto Fiorentino, (FI) Italy Ron R. Walcott Department of Plant Pathology,

Athens, GA 30607 USA

The University of Georgia,

PREFACE

This volume focuses on integrated pest and disease management (IPM/IDM) and biocontrol of some key diseases of perennial and annual crops. It continues a series originated during a visit of prof. K. G. Mukerji to the CNR Plant Protection Institute in Bari (Italy), in November 2005. Both editors aim at a series of five volumes embracing, in a multi-disciplinary approach, advances and achievements in the practice of crop protection, for a wide range of plant parasites and pathogens. Two volumes of the series were already produced, dedicated to general concepts in IPM and to management and biocontrol of nematodes of grain crops and vegetables.

This Volume deals, in particular, with diseases due to bacteria, phytoplasma and fungi. Every day, in any agroecosystem, farmers face problems related to plant diseases. Since the beginning of agriculture, indeed, and probably for a long time in the future, farmers will continue to do so. Every year, plant diseases cause severe losses in the global production of food and other agricultural commodities, worldwide. Plant diseases are not limited to episodic events occurring in single farms or crops, and should not be regarded as single independent cases, affecting only farms on a local scale. The impact of plant disease epidemics on food shortage ignited, in the last two centuries, deep cultural, social and demographic changes, affecting million human beings, through i.e. migration, death and hunger. The effects of severe epidemics, like those due to Phytophthora infestans, are well documented in plant pathology and even in history treatises and literature, and their legacy is still valid today. For this reason a disease causal agent should not only be regarded as a noxious factor limiting crop production or lowering farmers’ incomes, but also as a potential threat for the whole food production chain, worldwide. Global epidemics of basic food crops are still a potential issue and a risk that should be considered when planning the welfare of any community, at any scale.

This statement explains the attention devoted to plant diseases, and the efforts deployed for their management and control. As for other disciplines concerning plant protection, we reached today a mature stage in which the optimism initially underlining the widespread use of chemicals and fumigants lent space to a more pragmatic, comprehensive and integrated vision of control. There is, indeed, a general concern about the negative consequences related to the widespread use of chemicals, including not only environmental issues like pollution or contamination, but also the insurgence of resistance in the target organism populations, as well as the farmers’ health hazards represented by the use and manipulation of chemicals.

A wide literature already covers several aspects of chemical or biological control, but there is a widespread interest for a more holistic vision of IPM. In this series we tried to fill this gap, aiming at producing an informative coverage for a wide range of cropping systems. Chapters are organized in a first Section dealing with diseases of perennial crops, followed by a second one for annual crops, and a third final Section dealing with advances in DNA application for management, detection and diagnosis, and potentials of endophytes for disease control.

In the first chapter, disease management of stone fruit crops (apricot, cherry,

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peach, nectarine and plum) is reviewed. These include important diseases like brown

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rot blossom blight and fruit rot. Research showed the importance of latent infections in brown rot cycle, allowing options for a better disease management. Brown rot is controlled by fungicides, but resistance to benzimidazoles is widespread and appears to be developing further. Cultivars resistant to brown rot, although not yet commercially available, could be helpful for selection of new resistant clones. Other important stone fruit diseases like bacterial canker, Leucostoma canker, powdery

cankers cannot be controlled with chemicals, but they are managed using an integrated approach relying on resistance, good horticultural practices and exclusion. Resistance to fungicides in powdery mildew is developing, so the use of spray oils with fungicides is examined. New fungicides are available for the postharvest problems like fruit rots caused by Monilinia spp., Botrytis cinerea and Rhizopus spp., but they need careful management to avoid resistance. The development of new molecular techniques for pathogens identification and their use in disease forecasting and risk management is improving control of stone fruit diseases.

In the second chapter, the major diseases of apples, their management strategies and the problems related to sustainable productions are discussed. Guidelines for sustainable, integrated management of main apple diseases are reviewed, including effective and sustainable tactics. Resistance plays a crucial role in the management of apple diseases, and management problems include the development of fungicide resistance as wel as breakdown of host resistance. Symptoms, causal pathogens, disease cycles and management practices are reviewed for main spring diseases like apple scab, powdery mildew, fire blight and rust diseases. Problems like fungicide resistance and availability of plant resistance are discussed, together with applications of cultural and chemical management with predictive models. Symptoms, disease cycles and management issues are also reviewed for summer diseases, like bitter rot, flyspeck and sooty blotch.

Third chapter follows dealing with the management and ecology of phytoplasma diseases of grapevine and fruit crops. Management of phytoplasma-infected plants focussed on controlling the insect vectors and on roguing infected crops and weeds. Actual management concepts rely on environment compatible measures and on cultural practices. The introduction of disease-resistance genes into cultivated crops togheter with the use of resistance-inducing microorganisms represent potential tools to control phytoplasma diseases.

The fourth chapter deals with citrus diseases caused by Phytophthora spp., with reference to root rot, gummosis and brown rot of fruits. Some aspects of the biology and ecology of P. citrophthora and P. nicotianae are revised, like dissemination, reproduction and epidemiology. The symptomatic diagnosis of main diseases are reviewed, including foot rot or gummosis, fibrous root rot, brown fruit rot and dieback of twigs and leaves. Biological and instrumental diagnosis and laboratory tests for monitoring, sampling and population dynamics studies are revised. Management methods based on interventions on the host-plant, rootstock resistance, grafting as well as sanitary practices in nurseries are shown, with pruning, surgery and cultural practices, i.e. fertilization, irrigation, soil management and weeds control. Chemical control methods are also reviewed, with reference to the use of systemic fungicides for control of trunk gummosis, root rot and brown rot of fruits.

mildew and postharvest fruit rots are also reviewed. Both bacterial and Leucostoma

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In the following review of biological control and management of chestnut diseases, the main strategies for efficient biological control and management of chestnut blight and ink diseases caused by Cryphonectria parasitica, Phytophthora cambivora and P. cinnamomi are discussed. The cankers of chestnut blight are described, as well as the characters of the different infections caused by C. parasitica. The diseases evolution, the spread and effectiveness of hypovirulence are also revised, considering morphology, physiology, presence and transmission of dsRNAs. Chestnut resistance, the role of environmental and other ecological factors in ink disease, including soil microflora, are then discussed. The role of silviculture and biological control strategies for blight and ink disease management are also revised. Improvements in the management of chestnut disease need a better understanding of the ecological dynamic of chestnut ecosystems. An holistic approach including all the factors involved in chestnut trees ecology is proposed in planning the management of such ecosystems, and in undertaking best conservation and improvement measures.

Esca is a grapevine wood disease that seriously affects grapevine yield and longevity, comprising a number of distinct diseases in which the main fungal agents (primarily vascular pathogens) invade the vines, not only through field wounds but also as a result of nursery practices. When vines become infected in the nursery, the developing diseases may vary from Petri decline to full-blown esca, with or without white decay. No chemical control is available and sanitary practices in the nursery are suggested as the best way to eliminate or at least reduce pre-planting infections by the tracheomycotic fungi. In absence of chemical prevention, preventive and curative actions in the field can lower infections or hamper symptom appearance in esca-infected vines.

In the following chapter, the integrated management of root rot caused by the fungus Rosellinia necatrix on fruit tree crops is revised. This is a soil borne pathogen causing a disease known as “white root rot”. The pathogen, widespread in temperate and tropical climates, shows an increasing trend of attacks on several host species. Economic losses are serious in the nurseries and on orchard trees, and many field crops and weeds can also be severely damaged. The pathogen, mainly disseminated by propagating material, can survive in soil for many years. Control strategies, including cultural practices, soil disinfestations, chemical treatments, soil solarization and biological control are expensive and not always resolutive. White root rot control largely depends on pathogen exclusion through the use of R. necatrix-free propagating material and planting in healthy soils. A fundamental role is played by rules promoting trade of healthy propagating materials, and by the availability of new molecular detection tools.

The second Section, on annual crops, begins with a review of simulation models for potato late blight management. Potato late blight is widely studied and particular attention was given to the mathematical description of its development. Several simulation models are avilable and this chapter focuses primarily on versions developed at Cornell University and other research centres. The most recent version of the model was validated in the highland tropics and several other countries and cropping systems. Late blight simulators, used to evaluate disease management scenarios, were also used for other purposes, including sensitivity

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analysis of resistance components, comparative epidemiology, development of forecasting models and education. The potential of disease simulation will continue to improve, thanks to supporting technologies, both in computing power and weather data acquisition.

A review about the potentials of the decision support systems approach then follows, with an example of integrated forecasting system for management of Phytophthora infestans on potato. The PLANT-Plus® system initially developed in the Netherlands by Dacom, allowed management of P. infestans on-farm since 1994. The system is based on the life cycle of P. infestans, combining infection events with the unprotected part of the crop, and was extended with models for Alternaria solani and several other fungi or insect pests, in different crops. Another modules include the irrigation management system based on meteo data and soil moisture sensors, and models for potato tuber infection and fertilizers management. The platform enables data communication between farmer, consultants, processors and other users, allowing the most appropriate interface to be chosen. Different output types include SMS text messaging, fax and e-mail warnings. An integrated weather forecast provides a predictive risk assessment for the coming days. The disease models require the availability of automatic, on-farm weather data and were developed in cooperation with experts from different areas and countries. The model will recommend when to apply a new spray and what type of chemical to use, i.e. contact, translaminar or systemic. The benefits were demonstrated in field trials and evaluations all over the world, and provide safe spraying programmes with lowest possible use of chemicals.

A subsequent chapter deals with the integrated management of bacterial fruit blotch (BFB) of cucurbits, the most economically important bacterial disease of cucurbits worldwide. The causal agent is Acidovorax avenae subsp. citrulli. This chapter explores the current understanding of the biology and epidemiology of BFB and the integrated management strategies currently available. BFB is a seed transmitted disease, affecting all stages of cucurbit crops and causing destructive fruit rots. Like many phytobacterial diseases, the chemical options for management are limited and primarily include copper-based compounds. The unavailability of resistant cucurbits cultivars makes management difficult. An integrated approach to exclude primary inoculum through production of clean seeds is suggested, through isolation of seed fields, inspection and certification, seed health testing, seedling inspection and copper-based disease control. Despite the efforts to exclude the pathogen from cucurbit production, BFB outbreaks occur sporadically, worldwide. For a more effective integrated management, a better understanding of the disease epidemiology and pathogenesis is needed in fruit and seed production. Additionally, understanding the role of blossoms in seed infection revealed potential avenues for integrated disease management.

In the following chapter, a review of the progress in the integrated management of Sclerotinia rot of carrot is given. Bacterial diseases play an important role in the world agriculture by reducing yields and marketability of crops or by limiting their production in areas with environmental conditions conducive for disease development. Plant pathogenic bacteria show several obstacles for efficient plant protection practices. In spite of technological advances, there is no bactericide that

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can be efficiently used to control plant bacterial diseases. Due to lack of chemicals, plant pathologists search for alternatives i.e. the integration with preventive measures to develop sustainable control strategies. Management of tomato bacterial spot currently relies on use of pathogen-free seed and transplants, elimination of volunteer tomato plants, resistant cultivars and application of a copper-based bactericides. These practices are ineffective in hot and humid weathers that favor the pathogen spread and the disease development. New technologies, i.e. systemic acquired resistance inducers and biocontrol agents, integrated with conventional practices, represent new options in plant protection and increased disease management efficiency.

A review follows about the integrated management of Verticillium wilt of tomato. The disease is caused by Verticillium dahliae and V. albo-atrum, and its incidence and epidemiology are revised. Verticillium wilts are generally controlled by a combination of measures aiming at reducing severity and delaying the disease progress, including resistant cultivars or rootstocks, management of soil inoculum, reduction of propagules spread and manipulation of epidemiological factors. Further methods, including crop rotation, solarization, sanitation, tillage and weed control, fertilization, irrigation, chemical treatments and use of microbial antagonists, are also revised.

Sclerotinia rot, caused by the fungus Sclerotinia sclerotiorum, is an important disease of carrot in the field and during storage. Chapter 13 describes control methods, emphasizing emerging strategies supported by new information on its etiology and epidemiology. Prospects and recommendations are given to integrate current and emerging control methods for sustainable management. The primary strategy to manage Sclerotinia rot is the integration of methods reducing within-field sources of inoculum, suppressing the development of the fungus, and reducing the infection rate in the field and/or storage. The integrated strategy recommended in this review aims at achieving disease suppression through sanitation of soil and equipment, monitoring the crop development and microclimate, modifying the microclimate through canopy manipulation, predicting the disease and timing the application of control practices, as required. Breeding carrot cultivars for an upright and compact top growth may offer important contributions to the sustainable management of Sclerotinia rot.

Chapter 14 describes the integrated management of key diseases of cotton and rice. Issues related to disease identification and based on symptoms and presence of pathogens are discussed, as they are very important for a successful management. The main integrated management concepts are discussed, together with technologies combining a variety of control measures, including the conservation of existing natural enemies, crop rotation, intercropping and cultivation of pest-resistant varieties. Cotton diseases considered include seedling diseases, bacterial blight, Alternaria leaf spot, grey mildew and leaf spots caused by Myrothecium, Cercospora, Helminthosporium, Macrophomina, stem canker, late season Phoma blight, rust (Phakopsora gossypii), leaf crumple, Cotton Leaf Curl Virus, Tobacco Streak Virus, root rot, Verticillium and Fusarium wilts, new wilt or parawilt, boll rots and lint diseases. Rice diseases include rice blast, brown spot, bacterial leaf blight and leaf

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streak, sheath blight, sheath rot, Fusarium wilt or “Bakanae”, stem rot, Tungro Virus, false smut and post-harvest diseases.

A further review describes biological and integrated means to control rust diseases. In Chapter 15 the strategies avilable in rust control, with a special emphasis on biological control, are discussed in the light of evidence showing that disease control is most effective when an integrated approach is followed. A survey of the fungal antagonists (hyperparasites) most effective against rust pathogens is given. Their mode of action is described, and the main problems concerning biological control are discussed. The value and limitations of other control measures (eradication, use of hazard areas, quarantine, cultural practices, chemical treatments, and plant breeding for disease resistance) are also outlined. A consideration of all control measures suggests that crop protection requires an holistic approach, integrating a broad range of control techniques.

In the third and final section, two innovating research fields are revised: i) the use of DNA fingerprinting methods for microbial pathogens diagnostics, with potentials in taxonomy and plant disease and ii) the management of pests and diseases through the exploitation of endophytic fungi and their metabolites.

In the final chapter a new field of investigation with exciting perspectives in IPM/IDM is revised. Endophytes are non-pathogenic microorganisms inhabiting the interior of healthy plants, with potentials for crop protection. Many cultivated and wild type plants investigated showed presence of endophytic fungal metabolites including guanidine and pyrrolizidine alkaloids, indole derivatives, sesquiterpenes or isocoumarin derivatives. These metabolites show beneficial effects on crop plants and many of them have pesticidal and antimicrobial activity against plant as well as human pests and pathogens. Full potentials and efforts needed for their full exploitation are discussed.

In conclusion, our attempts to provide new options in management solutions available worldwide, in a broad range of agricultural systems, yielded a comprehensive compilation. We acknowledge the Author’s contributions for their outstanding work. Thanks to their experience, efforts and determination in seeking and applying advanced solutions in their research and field work, we hope we were

Advanced DNA-based techniques improved the identification and charac-terization of microbial pathogens, resulting in an accurate testing for pathogen identi-fication, sub-species-level DNA fingerprinting, pathogen-load testing and disease spread monitoring. These applications are instrumental to the study of plant disease epidemiology, so that adequate control measures can be accordingly implemented. In Chapter 16, a survey of the most popular DNA profiling techniques is given, together with some new molecular methods. Combinations of different analytical techniques are also proposed as a useful approach for low throughput bioassays. Advantages and disadvantages of each single test are considered and key issues (i.e. sampling, validation, large-scale testing) are discussed. An outline of emerging high-throughput molecular technologies, improving diagnostic approaches and disease management, is also provided.

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exaustive, will result helpful for any interested reader, inspiring and supporting the research efforts today necessary in the field and laboratory work as well.

A. C.

K. G. M.

able to provide a further tool, useful in the comprehension and sustainable management of plant pests and diseases. Our hope is that this volume, even if not

integrated management of diseases caused by fungi, …978-1-4020-85… · ·...

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