Plant Pathogens: Detection and Management for Sustainable Agriculture [1 ed.] 1771887885, 9781771887885

Table of contents :
Cover
Half Title
Title Page
Copyright Page
About the Editors
Contents
Contributors
Abbreviations
Preface
PART I: Viral and Fungal Disease and Management
1. Viral Diseases of Okra in Ghana and Their Management
2. Current and Prospective Approaches for Plant Virus Diseases Detection
3. Virus Afflictions of Anticancerous Medicinal Plant Catharanthus roseus (L.) G.Don
4. Important Diseases of Papaya and Their Integrated Disease Management
5. Fungal Diversity under Different Agri-Systems and Their Beneficial Utilization in Plant Health Management
6. Mycoflora Associated with Paddy Varieties
7. Plant Disease Detection and Management: An Overview
PART II: Nematode Diseases and Management
8. Role of Biological Agents for the Management of Plant Parasitic Nematodes
9. Principles and Concepts of Integrated Nematode Management in Major Crops
PART III: Biocontrol
10. Lichens: A Novel Group of Natural Biopesticidal Sources
11. Antimicrobial Peptides from Biocontrol Agents: Future Wave in Plant Disease Management
PART IV: Biotechnological Approaches and the Impact of Climate Change
12. Plant Disease Management Using Biotechnology: RNA Interference
13. Engineering Plastid Pathways: An Environment-Friendly Alternative for in Planta Transformation
14. Impact of Meteorological Variables and Climate Change on Plant Diseases
Color insert of illustrations
Index

Citation preview

PLANT PATHOGENS

Detection and Management for Sustainable Agriculture

PLANT PATHOGENS

Detection and Management for Sustainable Agriculture

Edited by

Pradeep Kumar

Ajay K. Tiwari

Madhu Kamle

Zafar Abbas

Priyanka Singh

Apple Academic Press Inc. 4164 Lakeshore Road Burlington ON L7L 1A4, Canada

Apple Academic Press Inc. 1265 Goldenrod Circle NE Palm Bay, Florida 32905, USA

© 2020 by Apple Academic Press, Inc. Exclusive worldwide distribution by CRC Press, a member of Taylor & Francis Group No claim to original U.S. Government works International Standard Book Number-13: 978-1-77188-788-5 (Hardcover)

International Standard Book Number-13: 978-0-42905-721-2 (eBook)

All rights reserved. No part of this work may be reprinted or reproduced or utilized in any form or by any electric, mechanical or other means,

now known or hereafter invented, including photocopying and recording, or in any information storage or retrieval system, without permis­ sion in writing from the publisher or its distributor, except in the case of brief excerpts or quotations for use in reviews or critical articles.

This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission and

sources are indicated. Copyright for individual articles remains with the authors as indicated. A wide variety of references are listed. Reason­ able efforts have been made to publish reliable data and information, but the authors, editors, and the publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors, editors, and the publisher have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged, please write and let us know so we may rectify in any future reprint. Trademark Notice: Registered trademark of products or corporate names are used only for explanation and identification without intent to infringe.

Library and Archives Canada Cataloguing in Publication Title: Plant pathogens : detection and management for sustainable agriculture / edited by Pradeep Kumar [and four others].

Other titles: Plant pathogens (Oakville, Ont.)

Names: Kumar, Pradeep (Professor of biotechnology), editor.

Series: Innovations in plant science for better health.

Description: Includes bibliographical references and index.

Identifiers: Canadiana (print) 20190137231 | Canadiana (ebook) 20190137274 | ISBN 9781771887885 (hardcover) | ISBN 9780429057212 (ebook) Subjects: LCSH: Phytopathogenic microorganisms. | LCSH: Phytopathogenic microorganisms—Detection. | LCSH: Phytopathogenic microorganisms—Control. | LCSH: Sustainable agriculture. Classification: LCC SB731 .P63 2019 | DDC 632/.3—dc23

Library of Congress Cataloging-in-Publication Data Names: Kumar, Pradeep (Professor of biotechnology), editor. | Tiwari, A. K. (Ajay K.), editor. | Kamle, Madhu, editor. | Abbas, Zafar (Professor of botany), editor. | Singh, Priyanka, 1975- editor. Title: Plant pathogens : detection and management for sustainable agriculture / edited by Pradeep Kumar, Ajay K. Tiwari, Madhu Kamle, Zafar Abbas, Priyanka Singh. Description: 1st edition. | Palm Bay, Florida : Apple Academic Press, 2019. | Includes bibliographical references and index. | Summary: “Plant Pathogens: Detection and Management for Sustainable Agriculture addresses the most critical issues in the management of emerging diseases throughout the world. Experts in plant pathology from internationally renowned institutes share their research and examine key literature on vital issues in pathogen disease diagnosis and management. They look at both traditional pathology as well as new and advanced biotechnological and molecular diagnosis approaches. This book is divided into four parts, covering viral and fungal disease detection and management, nematode diseases and management, bio-control, and biotechnological approaches and impact of climate change. The authors look at the challenges of crop protection against diseases caused by plant pathogens for the most economically important crops, including fruits, vegetables, and cereals. The establishment and management of plant diseases using conventional and eco­ friendly methods are discussed with an emphasis on the use of beneficial microbes and modern biotechnological approaches. Plant Pathogens: Detection and Management for Sustainable Agriculture focuses on expert disease diagnosis and integrated management practices with molecular diagnostic techniques to achieve disease free-plants from a wide array of pathogens. The volume will be a valuable source of information for those involved with and studying plant pathology and crop disease management”-- Provided by publisher. Identifiers: LCCN 2019026294 (print) | LCCN 2019026295 (ebook) | ISBN 9781771887885 (hardcover) | ISBN 9780429057212 (ebook) Subjects: LCSH: Phytopathogenic microorganisms--Research. Classification: LCC SB732.5 .P53 2019 (print) | LCC SB732.5 (ebook) | DDC 632/.3072--dc23 LC record available at https://lccn.loc.gov/2019026294 LC ebook record available at https://lccn.loc.gov/2019026295 Apple Academic Press also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic format. For information about Apple Academic Press products, visit our website at www.appleacademicpress.com and the CRC Press website at www.crcpress.com

About the Editors

Pradeep Kumar, PhD Pradeep Kumar, PhD, is currently working as an Assistant Professor in the Department of Forestry, North Eastern Regional Institute of Science and Technology (NERIST) Deemed to be University-MHRD, Government of India, Nirjuli, Arunachal Pradesh, India. Before he joined NERIST, he worked as an international research professor/assistant professor in the Department of Biotechnology, Yeungnam University, South Korea. He was Postdoctorate Researcher in the Department of Biotechnology Engi­ neering, Ben-Gurion University of the Negev, Israel, and was awarded a PBC-outstanding Post-Doc Fellowship for more than three years. His areas of research and expertise are wide, including microbial biotech­ nology, plant pathology, bacterial genetics, insect-pest biocontrol, gene expression, cry genes, and molecular biology. He has been honored with an international travel grant from Ben-Gurion University of Negev, Israel, to attend an international conference. He was awarded with prestigious Early Career Research Award from Department of Science & Technology, Government of India. He is the recipient of a best paper presentation and the Narasimhan Award by the Indian Phytopathological Society, India. He has presented several oral and poster presentations at various national and international conferences. He has published three book and 50 research and review articles in peer-reviewed journals and several book chapters with international publishers, including Springer, CABI, Bentham, and Apple Academic Press. He is serving as an associate editor for PLOS ONE, BMC-Complementary and Alternative Medicine, a guest editor for Evidence Based Complementary and Alternative Medicine, and he also provides his services to over 30 journals as editor, editorial board member, technical editor, and peer reviewer. Ajay Kumar Tiwari, PhD Ajay K. Tiwari, PhD, is a Scientific Officer at the UP Council of Sugar­ cane Research, Shahjahnapur, UP, India. He has published 70 research articles, nine review articles in national and international journals, several book chapters in edited books, and has also authored several edited books

vi

About the Editors

published by Springer, Taylor & Francis, and others. He has submitted more than 150 nucleotide sequences of plant pathogens to GenBank. He is a regular reviewer of many international journals as well as an editorial board member. He is Managing Editor of the journal Sugar Tech and Chief Editor of the journal Agrica. He has received several young researcher awards and was nominated for the Narshiman Award by the Indian Phytopathological Society, India. Dr. Tiwari is also the recipient of many international travel awards given by governmental agencies in India and other countries. He has visited Belgium, Brazil, China, Italy, Germany, and Thailand for conferences and workshops and has delivered several invited talks at Oman University for PhD students on phytoplasma disease diagnosis and management. Dr. Tiwari has been involved in the research on molecular characterization and management of agricultural plant pathogens for the last nine years. Currently, he is working on molecular characterization of sugarcane phytoplasmas and their secondary spread in nature. He is a regular member of several professional organizations, including the British Society of Plant Pathology, Indian Phytopathological Society, Sugarcane Technologists Association of India, International Society of Sugarcane Technologists, Society of Sugarcane Research and Promotion, and others. Dr. Tiwari earned his PhD from CCS University, Meerut, Uttar Pradesh, India. Madhu Kamle Madhu Kamle is currently working as an Assistant Professor in Depart­ ment of Forestry, North Eastern Regional Institute of Science & Tech­ nology, Nirjuli, Arunachal Pradesh, India. Her area of research is plant biotechnology, plant–microbe interaction, microbial genomics, and plant disease diagnosis. She did her PhD in plant biotechnology at ICAR­ CISH, Lucknow, and Bundelkhand University, Jhansi, India. She had been awarded a prestigious PBC Outstanding Post-doctoral Fellowship (2014–2016) from the Council of Higher Education, Israel, and is a recipient of a post-doc fellowship from the Jacob Blaustein Institute of Desert Research, Ben Gurion University, Israel (2013–2014). She has also worked as an International Research Professor in the School of Biotech­ nology, Yeungnam University, Gyeongsan, Republic of Korea. She has 10 years of research experience and has published 25 research papers in peer-reviewed journals, 10 book chapters, and one edited book from Springer Nature, Switzerland. She is working as an editor for Science

About the Editors

vii

Alert journals and Taylor & Francis journals, and as a reviewer for various Springer, Taylor & Francis, Frontiers, and PLOS journals. She is a life member of the Nano-Molecular Society and member of the American Society of Microbiology. Zafar Abbas, PhD Zafar Abbas, PhD, is a Senior Associate Professor and Chairman in the P. G. Department of Botany at G. F. College, M. J. P. Rohilkhand University in Shahjahanpur, Uttar Pradesh, India. He has 40 years of research experi­ ence in plant and crop physiology, with a specialization in plant nutrition. He has attended several national and international seminars and confer­ ences. At present, eight PhD students have completed their doctorate degrees under his supervision. Dr. Abbas is a life member and member of editorial boards of several Indian and foreign journals and societies, and he has authored a book and has published over 30 articles. Priyanka Singh, PhD Priyanka Singh, PhD, is a Scientific Officer of the Uttar Pradesh Council of Sugarcane Research, (UPCSR) Shahjahanpur, India. She has worked at the Indian Institute of Sugarcane Research, Lucknow, India, for nine years. She has 19 years of research experience with a specialization in organophosphorus chemistry and in the area of cane quality/posthar­ vest management of sugar losses with the help of chemicals as well as ecofriendly compounds. She has extensive experience using electrolyzed water to preserve cane quality and is responsible for the first time that it was reported that electrolyzed water has immense potential to be used in the sugar industry to preserve postharvest sucrose losses. She has synthesized and characterized 37 new organophosphorus compounds belonging to the chalcone series, of which two important chemicals (chalcone thiosemicarbazone and chalcone dithiocarbazate) were found to be highly fungitoxic to the sugarcane parasitic fungi Colletotrichum falcatum, Fusarium oxysporum, and Curvularia pallescens. She has worked on the extraction of volatile constituents from higher plants and their biological activity against agricultural pests. She has also worked on the management of postharvest formation of nonsugar and polysaccharide compounds in sugarcane and the effect of bioproducts on growth, yield, and quality of sugarcane and soil health. She has also worked on indicators of postharvest losses in sugarcane and reported that mannitol is one of the most important indicators.

viii

About the Editors

Presently she is working on varietal spectrum of sugarcane for the selection of elite sugarcane varieties so as to recommend the proper vari­ etal balance of sugarcane varieties in Uttar Pradesh, as well as working on modulating the activities of sucrose metabolizing enzymes through bio­ active silicon (orthosilicic acid) for increased cane and sugar productivity, which will benefit farmers as well as the sugar industry in remarkable way. She is also managing and working on a project on “Assessment of postharvest quality deterioration in promising sugarcane varieties under sub-tropical condition” which is expected to reduce postharvest losses and will increase sugar recovery. She is carrying a project on “Varietal screening for jaggery” production at UPCSR, Shahjahanpur, for the recommendation of elite sugarcane varieties for commercial production of jaggery. Dr. Singh is a research advisor for a dissertation on genetic diversity in sugarcane and a training advisor for MSc students. She has organized several short-term training programs on techniques in microbiology, biotechnology, and molecular biology. She received an “Award of Excel­ lence” from Sinai University, Al Arish, Egypt, in 2008. She is also serving as Managing Editor for the journal Sugar Tech and as Executive Editor for journal Agarica. In addition, she is a reviewer for several international journals. She is one of the editors of the Proceeding of International Conference IS-2011. A prolific author, Dr. Singh has authored a book on innovative healthy recipes with jaggery, edited three books on postharvest management of sugarcane, written several annual reports, written on 100 years of sugarcane research, and published three book chapters and more than 50 research papers in various national and international journals and proceedings. She has attended several national and international confer­ ences and workshops in China, Egypt, Thailand, and India, and has coor­ dinated technical as well as plenary sessions in India, China, and Egypt. Dr. Singh completed her PhD on “Efficacy of organophophorus deriva­ tives against fungal pathogens of sugarcane” in 2000 from DDU, Gora­ khpur University (Uttar Pradesh, India). She was awarded a postdoctoral fellowship from DST, New Delhi in the years 2006 and 2010.

Contents

Contributors............................................................................................. xi

Abbreviations ...........................................................................................xv

Preface ...................................................................................................xvii

PART I: Viral and Fungal Disease and Management ......................... 1

1.

Viral Diseases of Okra in Ghana and Their Management ...................... 3

Elvis Asare-Bediako

2.

Current and Prospective Approaches for Plant Virus

Diseases Detection ..................................................................................... 15

Touseef Hussain, and Quazi Mohd. Imranul Haq

3.

Virus Afflictions of Anticancerous Medicinal Plant Catharanthus roseus (L.) G.Don .............................................................. 35

Deepa Srivastava and K. Shukla

4.

Important Diseases of Papaya and Their Integrated

Disease Management ................................................................................ 67

Diganggana Talukdar, Utpal Dey, and G. P. Jagtap

5.

Fungal Diversity under Different Agri-Systems and Their Beneficial Utilization in Plant Health Management .............................. 89

Vibha

6.

Mycoflora Associated with Paddy Varieties.......................................... 123

Shveta Malhotra

7.

Plant Disease Detection and Management: An Overview ................... 157

S. M. Yahaya

PART II: Nematode Diseases and Management.............................. 179

8.

Role of Biological Agents for the Management of

Plant Parasitic Nematodes ..................................................................... 181

Aamir Raina, Mohammad Danish, Samiullah Khan, and Hisamuddin

Contents

x

9.

Principles and Concepts of Integrated Nematode Management

in Major Crops ........................................................................................ 201

B. S. Sunanda and Ravulapenta Sathish

PART III: Biocontrol.......................................................................... 229

10. Lichens: A Novel Group of Natural Biopesticidal Sources ................. 231

Vinayaka S. Kanivebagilu and Archana R. Mesta

11. Antimicrobial Peptides from Biocontrol Agents:

Future Wave in Plant Disease Management......................................... 241

Vivek Sharma and Richa Salwan

PART IV: Biotechnological Approaches and the Impact of

Climate Change............................................................................ 269

12. Plant Disease Management Using Biotechnology: RNA Interference .................................................................................... 271

Naresh Pratap Singh and Vaishali

13. Engineering Plastid Pathways: An Environment-Friendly

Alternative for in Planta Transformation ............................................. 287

Bhavin S. Bhatt and Achuit K. Singh

14. Impact of Meteorological Variables and Climate Change on

Plant Diseases .......................................................................................... 313

A. K. Misra, S. B. Yadav, S. K. Mishra, and M. K. Tripathi

Color insert of illustrations ........................................................................ A – H

Index ................................................................................................................. 329

Contributors

Elvis Asare-Bediako

Department of Crop Science, University of Cape Coast, Cape Coast, Ghana. E-mail: [email protected]

Bhavin S. Bhatt

Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat. E-mail: [email protected]

Mohammad Danish

Department of Botany, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India. E-mail: [email protected]

Utpal Dey

Division of Crop Production, ICAR Research Complex for NEH Region, Umiam 793103, Meghalaya, India. E-mail: [email protected]

Quazi Mohd. Imranul Haq

Deparment of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Sultanate of Oman

Hisamuddin

Department of Botany, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India

Touseef Hussain

Division of Plant Pathology, ICAR—Indian Agricultural Research Institute, Pusa, New Delhi 110012, India. E-mail: [email protected]

G. P. Jagtap

Department of Plant Pathology, College of Horticulture, VNMKV, Parbhani, Maharashtra, India

Vinayaka S. Kanivebagilu

Department of Botany, Kumadvathi First Grade College, Shimoga Road, Shikaripura 577427, Shimoga, Karnataka, India. E-mail: [email protected]

Samiullah Khan

Department of Botany, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India

Shveta Malhotra

Arya Mahila PG College, Shahjahanpur 242001, Uttar Pradesh, India. E-mail: [email protected]

Archana R. Mesta

Department of Botany, Kumadvathi First Grade College, Shimoga Road, Shikaripura 577427, Shimoga, Karnataka, India

xii

Contributors

S. K. Mishra

Punjab Agricultural University, Regional Station, Faridkot 151203, Punjab, India

A. K. Misra

Department of Agricultural Meteorology, B.A. College of Agriculture, Anand Agricultural University, Anand 388110, Gujarat, India. E-mail: [email protected]

Aamir Raina

Department of Botany, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India

Richa Salwan

Department of Veterinary Microbiology, CSK-Himachal Pradesh Agricultural University, Palampur 176062, India

Ravulapenta Sathish

Senior Research Fellow (Entomology), National Institute of Plant Health Management (NIPHM), Hyderabad 500030, India

Vivek Sharma

Department of Plant Pathology, CSK-Himachal Pradesh Agricultural University, Palampur 176062, India. E-mail: [email protected]

K. Shukla

Department of Botany, D.D.U. Gorakhpur University, Gorakhpur, Uttar Pradesh, India

Achuit K. Singh

Crop Improvement Division, ICAR Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India. E-mail: [email protected]

Naresh Pratap Singh

Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India. E-mail: [email protected]

Deepa Srivastava

Department of Botany, D.D.U. Gorakhpur University, Gorakhpur, Uttar Pradesh, India

B. S. Sunanda

Assistant Scientific Officer (Nematology) and Centre In-charge, AICRP (Nematode). E-mail: [email protected]

Diganggana Talukdar

Department of Plant Pathology and Microbiology, College of Horticulture, Central Agricultural University, Sikkim, India

M. K. Tripathi

College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, Madhya Pradesh, India

Vaishali

Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India

Vibha

Department of Plant Physiology, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India. E-mail: [email protected]

Contributors

xiii

S. B. Yadav

Department of Agricultural Meteorology, B.A. College of Agriculture, Anand Agricultural University, Anand 388110, Gujarat, India

S. M. Yahaya

Department of Biology, Kano University of Science and Technology, Wudil P.M.B. 3244, Nigeria. E-mail: [email protected]

Abbreviations

AMP ANN BA BADH BCA CBD CCN CMV CYMV DP dsRNA ELISA EPSPS FOL FYM GUS HAD IR LSC NDH NDR NRPS OLCD OMD PCR PEG PGPR pHBA PPN PSB PSF PSMs PYVV

antimicrobial peptide artificial neural network betaine aldehyde betaine aldehyde dehydrogenase biocontrol agent cannabidol cereal cyst nematode cucumber mosaic virus Catharanthus yellow mosaic virus Dhan Pant double-stranded ribonucleic acid enzyme-linked immunosorbent assay 5-enol-pyruvyl shikimate-3-phosphate synthase Fusarium oxysporum f. sp. lycopersici farm yard manure β-glucuronidase helicase-dependent amplification inverted repeat large single copy NADH-dehydrogenase Narendra nonribosomal peptide synthetase okra leaf curl disease okra mosaic disease polymerase chain reaction polyethylene glycol plant growth promoting rhizobacteria p-hydroxybenzoic acid plant parasitic nematodes phosphorus solubilizing bacteria phosphorus solublizing fungi phosphate solubilizing microorganisms potato yellow vein virus

Abbreviations

xvi

RBS RFLP RKN RNAi RPA SCP siRNA SSC TCP TIBA tsp TSWV UTR VOC

ribosomal-binding site restriction fragment length polymorphism root-knot nematodes RNA interference recombinase polymerase amplification soluble crude protein small interfering RNA small single copy tri-calcium phosphate tissue blot immunoassay total soluble protein tomato spotted wilt virus untranslated region volatile organic compound

Preface

Plant Pathogens: Detection and Management for Sustainable Agricul­ ture addresses one of the most critical issues for the management of emerging diseases throughout the world. Plant diseases caused by fungi, bacteria, viruses, etc., collectively represent a significant burden to crop production and a threat to global food security and agriculture sustainability. The agricultural productivity must increase with the global population increase and the climate change scenario. The diagnosis of plant diseases can be difficult at the early stages of disease on individual crops as well as at the early stages of an epidemic. However, for many diseases, symptoms do appear during early stages, and thus based on diagnosis, the applicable management approaches, including cultural, chemical, biological, have been considered worldwide for sustainable productivity. Accurate estimates of disease incidence, disease severity, and the negative effects of diseases on the quality and quantity of agricultural produce are important for field crops, horticulture, plant breeding, and for improving the fungicide efficacy as well as for the basic and applied research. Therefore, it is significant to have expert disease diagnosis and integrated management practices advanced with molecular diagnostic techniques to obtain disease-free plants from a wide array of pathogens. This book volume consists of 14 chapters and basically provides expert knowledge on new approaches, updated techniques, and useful informa­ tion on crop diseases caused by various pathogenic agents and also on their management. This book is divided into four parts: Part I includes viral and fungal disease management and contains seven chapters; Part II consists of nematode diseases and management and contains two chap­ ters; Part III consists of biocontrol and contains two chapters; and Part IV consists of biotechnological approaches and the impact of climate change and contains three chapters. In this book, expert researchers share their research knowledge and key literature on vital issues covering the pathogen disease diagnosis and management addressing with traditional pathology as well as biotechno­ logical approaches with advanced molecular diagnosis approaches. We

xviii

Preface

are extremely delighted and grateful to all the authors for their expert contributions in the form of chapters, making this volume edition possible. We are extremely grateful to the staff of Apple Academic Press and others concerned with CRC Press and Taylor & Francis Group for their untiring effort and immense support throughout. This book presents intense information on crop disease diagnosis and management for sustainable agriculture and would be extremely helpful for wide array of researchers, scientists, and academicians. We also hope that it will be useful to all concerned. —Pradeep Kumar Ajay K. Tiwari Madhu Kamle Zafar Abbas Priyanka Singh

PART I

Viral and Fungal Disease and Management

CHAPTER 1

Viral Diseases of Okra in Ghana and Their Management ELVIS ASARE-BEDIAKO*

Department of Crop Science, University of Cape Coast, Cape Coast, Ghana *

Corresponding author. E-mail: [email protected]

ABSTRACT Viral diseases are major biotic factors that affect productivity of okra (Abel­ moschus esculentus L. Moench) worldwide. Okra mosaic disease (OMD) caused by Okra mosaic virus (OkMV; genus Tymovirus; family Tymoviridae) and Okra leaf curl disease (OLCD) caused by a complex of begomoviruses: Cotton leaf curl Gezira virus (CLCuGV]), Okra yellow crinkle virus (OYCrV), Hollyhock leaf crumple virus (HoLCrV), and Okra leaf curl virus (OLCV) are the major viral diseases of okra in West Africa including Ghana. OLCD and OMD are commonly observed among okra crops in Ghana, with disease incidence of up to 100% depending on the okra cultivar and stage of growth. Management of OLCD and OMD involves the use of both synthetic and phytopesticides against the Bemisia tabaci and Podagrica spp. vectors, respectively, as well as the use of compost and fertilizers to ensure healthy growth of plant and to improve the tolerance of plants against viral infection. Resistance and tolerant okra genotypes have so been identified and their integration with phytopesticides and judicious use of chemical pesticides is recommended for effective management of these viral diseases. 1.1 BACKGROUND Okra (Abelmoschus esculentus L. Moench) is a member of the family Malvaceae and a native to West and Central Africa but is now widely

4

Plant Pathogens: Detection and Management for Sustainable Agriculture

grown throughout the tropics (Kochhar, 1986; Schippers, 2000). The world production of common okra as fresh vegetable is estimated at 1.7 million tons year−1 (Schippers, 2000; Asare-Bediako et al., 2014). Ghana is the eighth largest producer of okra in the world (FAOSTAT, 2014). Okra crop is the third most important vegetable in Ghana after pepper and tomato, with production of 80,000 tons estimated at $51, 189,000 USD (FAOSTAT, 2011; 2013). It can be grown anywhere in Ghana but the major producing centers are Brong Ahafo, Ashanti, Northern, Volta, Greater Accra, and Central regions (NARP, 1993). Okra production provides livelihood, employment, and income to rural smallholder farmers and retailers in urban centers. Okra is an important fruit vegetable crop in Ghana, and a source of energy for human consumption (Babatunde, 2007). The crop is a rich source of protein, fat, carbohydrate, fiber, thiamine, riboflavin, nicotinamide, and ascorbic acid (Hamon, 1988; Schippers, 2000; Babatunde, 2007). It also contains significant amount of potassium, magnesium, calcium, and iron (Hamon and Charrier, 1997). Okra is a multipurpose fruit vegetable due to its diverse uses of the fruits (pods), fresh leaves, buds, flowers, stems, and seeds (Mihretu et al., 2014). Immature okra fruits and fresh leaves are usually consumed as vegetables while the dried fruits are ground into powder and used in stews and soups (Siemonsma, 1982a). Okra seeds can be used as substitutes or additives in feed preparation (Purseglove, 1974), in the preparation of okra seed meal (Martin and Roberts, 1990), in the confectionery industry (Adetuyi et al., 2011), and in blood plasma replace­ ment or blood volume expander. In spite of the significant contribution (75%) of the West and Central African region including Ghana to okra production in Africa, average productivity in the region (2.5 t ha−1) is far below that of East (6.2 t ha−1) and North Africa (8.2 t ha−1) (FAOSTAT, 2008). In Ghana, yield potential of up to 3.0 t ha−1 has been reported for Okra (MoFA, 2007), depending on the cultivar, harvesting frequency, and period for harvesting (Cudjoe et al., 2005) but current average yield is 2.1 t ha−1 (FAOSTAT, 2014). The wide yield gap of okra in Ghana could be attributed to several production constraints including biotic and abiotic factors. Insect pests and plant viruses are important biotic factors causing severe constraints on the productivity of okra in Ghana (Obeng-Ofori and Sackey, 2003; Asare-Bediako et al., 2014a). Viral diseases are major constraints to okra production world­ wide (Ndunguru and Rajabu, 2004; Asare-Bediako et al., 2014a, b). The

Viral Diseases of Okra in Ghana and Their Management

5

productivity of okra is affected by at least 19 plant viruses. Of these, Okra mosaic virus (OkMV; genus Tymovirus; family Tymoviridae), Bhendi yellow vein mosaic virus (BYVMV, genus Begomovirus), Cotton leaf curl Gezira virus (CLCuGV, genus Begomovirus), and Okra leaf curl virus (OLCuV; genus Begomovirus) are the most common and well-studied (Brunt et al., 1990; Swanson and Harrison, 1993; Tiendrebego et al., 2010; Sayed et al., 2014). Okra mosaic disease (OMD) and okra leaf curl disease (OLCD) are the common viral diseases affecting okra production in Ghana (Siemonsma, 1991; Norman, 1992; Asare-Bediako et al., 2014a). Okra yellow vein mosaic virus (OYVMV) is a major limiting factor to okra production in India (Sayed et al., 2014). 1.2 OKRA MOSAIC DISEASE OMD caused by OkMV is the most common viral disease of okra in West Africa including Ghana. The virus contains a single-stranded positivesense RNA (approximately 6.2 kb) with isometric particles of 28 nm in diameter with icosahedral symmetry and 32 morphological units (Koenig and Givord, 1974; Givord and Hirth, 1973). OkMV is transmitted in a nonpersistent manner by flea beetles (Podagrica species) (Brunt et al., 1990, 1996). The virus can also be mechanically transmitted (Koenig and Givord, 1974). It has a wide host range, and infects 105 plant species and varieties in 23 dicotyledonous families (Givord and Hirth, 1973) including both crop and weed species. Symptoms of OkMV infection are prevalent in okra fields in Ghana. Field surveys conducted by Asare-Bediako et al. (2014c) at the Komenda– Edina–Eguafo–Abirem (KEEA) municipality of the Central region showed mean disease incidences ranging from 78% to 83%. A recent field survey carried out by Agyarko (2016) revealed mean OMD incidences of 67.6%, 76.2%, and 75% at the coastal savannah, forest, and transition agroecological zones, respectively, of the Central region of Ghana. The corresponding mean symptom severity scores at these three zones were 1.60, 2.04, and 1.9, respectively, indicating mild infection (Agyarko, 2016). Field trial involving 20 okra genotypes showed disease incidence of up to 100% depending on the cultivars and the growth stage (AsareBediako et al., 2017). Double antibody sandwich ELISA (DAS-ELISA) detected OkMV in all the 20 okra genotypes. Prevalence of OMD in okra fields has also been reported in Ivory Coast (Givord et al., 1972; Fauquet

6

Plant Pathogens: Detection and Management for Sustainable Agriculture

and Thouvenel, 1987) and Nigeria (Koenig and Givord, 1974; Alegbejo, 2001; Fajinmi and Fajinmi, 2010). Common symptoms associated with OkMV infection of okra include mosaic, vein chlorosis, and vein-banding and stunted growth (Koenig and Givord, 1974; Brunt et al., 1990; Swanson and Harrison, 1993). OMD has been reported to cause yield losses of up to 100% in okra crops (Atiri, 1984; Alegbejo, 2001). 1.3 OKRA LEAF CURL DISEASE Okra leaf curl disease (OLCD) is a major constraint on okra production in West Africa. In Africa, the disease is associated with a number of bego­ moviruses of the family Geminiviridae, which are transmitted by Bemisia tabaci Genn. (Brown and Bird, 1992; Brown and Czosnek, 2002; Brown, 2007, 2010). These begomoviruses include: Cotton leaf curl Gezira virus (CLCuGV; [Tiendrebego et al., 2010]), Okra yellow crinkle virus (OYCrV; [Shih et al., 2007]), and Hollyhock leaf crumple virus (HoLCrV; [Bigarré et al., 2001; Idris et al., 2002]), and Okra leaf curl virus (OLCuV; [Brunt et al., 1990; Swanson and Harrison, 1993]). The disease causes leaf wrinkle, curl, vein distortion, leaf yellowing, stunted growth, and reduced yields (Askira, 2012). OLCD has been reported to cause yield losses of up to 100% depending on the date of planting, cultivar, and locality (Fauquet and Thouvenel, 1987; Brown and Bird, 1992; Basu, 1995). The average economic losses due to OLCD have been estimated between 11,100 USD and 1950 USD for 1 ha of crop, depending on the okra variety (Tiendre­ bego et al., 2010a). Report by Asare-Bediako et al. (2014a) revealed high incidences and severities of both OLCD in all the communities surveyed in the KEEA municipality of the Central region of Ghana. Furthermore, survey conducted by Agyarko (2016) revealed the highest mean incidence and symptom severity of OLCD at the coastal savannah zone, followed by the forest zone and then the transition zone of the Central region. Field experiment involving 20 okra accessions conducted by Agyarko (2016) at the coastal savannah zone of the Central region showed disease incidence of up to 100% depending on the cultivar. Field trial conducted by OppongSekyere in the forest zone of the Ashanti region of Ghana involving 25 okra accessions showed high incidence of OLCD. OLCD has also been reported in other African countries including Burkina Faso (Tiendrebego et al., 2010), Cameroon (Leke, 2010), Ivory Coast (N’Guessan et al., 1992), Mali (Konet al., 2009), Nigeria (Atiri and Ibidapo, 1989; Alegbejo, 1997;

Viral Diseases of Okra in Ghana and Their Management

7

Askira, 2012), Niger (Shih et al., 2009), Nigeria (Askira, 2012), and Sudan (Idris and Brown. 2002). 1.4 MANAGEMENT OF VIRAL DISEASES Effective management of viral diseases is quite pertinent in order to improve yields of okra. Various strategies are employed in the manage­ ment of plant virus diseases and these are mainly directed at preventing virus infection by eradicating the source of infection to prevent the virus from reaching the crop, reducing the spread of the disease by managing its vector, using virus-free planting material, and planting resistant vari­ eties (Naiduand Hughes, 2003). Karim (2016) stated that although most farmers practice strict monitoring or calendar spraying with chemical insecticides to control insects that vector these viruses, they still observe severe yellowing on plants and probably because viruses responsible for the yellowing are not mainly insect-transmitted. 1.4.1 THE USE OF RESISTANT VARIETIES Study conducted by Asare-Bediako et al. (2014c) revealed that the majority of farmers acquire their planting materials (okra seeds) from their own farm (uncertified source) and this practice contributes to the spread of diseases. The planting of resistant cultivars has therefore been universally considered the most effective method to control diseases caused by viruses in okra. In screening 21 okra genotypes against OkMV infection, Asare-Bediako et al. (2017) showed that nine genotypes GH2052, GH2063, GH2026, GH3760, GH5302, GH5332, GH5793, GH6105, and UCCC6 exhibited mild symp­ toms of OMD, and were less susceptible to flea beetle infestation and associated leaf damage during both major and minor cropping seasons in Ghana. Asare-Bediako et al. (2016) also identified okra genotypes GH3760, GH2052, GH5332, UCC6, GH5302, GH5793, and GH2063 showed mild symptoms of OLCD, when they screened 21 okra genotypes against OLCV infection under natural conditions. In assessing the performance of 25 okra accessions against viral infection, Oppong-Sekyere (2011) identified accessions Atuogya-tenten, GH3736 Fetri, Atuogya-tiatia, Atuogya-Asante, and GH4376 Atuogya to show high tolerance to OLCD/OMD and pests. He also reported that

8

Plant Pathogens: Detection and Management for Sustainable Agriculture

accessions KNUST/SL1/07Nkrumahene, DA/08/02Dikaba, DA/08/03Sheo mana, DA/08/004Agbodro, DA/08/02Asontem, DA/08/02Sheo mana, DA/08/001Wun mana, and GH 5787Asontem did not show any signs of viral infestation, and hence can be said to exhibit field resistance against viral infection. In screening A. esculentus and A. callei cultivars against OLCD and OMD, under field conditions in Nigeria, Udengwu, and Dibua (2014) identified A. callei cultivars EbiOgwu, Ojoogwu, Tongolo, VLO, Oruufie, and Ogolo to be resistant to these two viral diseases. They discussed the potential of incorporating these resistant genes from A. callei cultivars into the susceptible A. esculentus cultivars. 1.5 MANAGEMENT OF THE VECTOR WITH INSECTICIDES AND PHYTOPESTICIDES According to Naidu and Hughes (2003) and Bhagati and Goswami (1992), management of viral disease can be directed at controlling the vector that transmits the virus. Positive correlations between incidences of viral diseases and the vectors that transmit them have been reported in several host plant–vector–viruspathosystems (Bhagati and Goswami, 1992). In Ghana, positive association between the populations of B. tabaci and the severity of OLCD has been reported by Asare-Bediako et al. (2014b). They demonstrated that phytopesticides can significantly reduce the B. tabaci vector population and reduce incidence and severity of OLCD, leading to improved fruit yield. Aqueous neem leaf and garlic extracts were found to be more effective than that of mahogany, bougainvillea, chili pepper, and pawpaw leaves in reducing the populations of whitefly and decreasing incidence and severity of OLCD (Asare-Bediako et al., 2014b). These botanicals have been shown to possess virus inhibition, and insectrepellent/ anti-feedant properties (Schmutterer, 1990; Revkin, 2000; Nevala, 2000; Asare-Bediako et al., 2014b). In assessing the effectiveness of different plant extracts against Podagrica spp. infestation and OMD, Asare-Bediako et al. (2014a) indicated that the phytopesticides exhibited moderate to high level of efficacy in decreasing the insect populations and the incidence and severity of OMD. Botanicals or plant leaf extracts have been used in the control of OMV in which karamja extract treated plants had minimal virus incidence, maximum plant height, flower production, fruit forma­ tion, and highest yield as reported by Bhyan et al. (2007). Obeng-Ofori

Viral Diseases of Okra in Ghana and Their Management

9

and Sackey (2003) also reported Actellic (synthetic pesticides), neem seed extract (botanical), and Bacillus thurigiensis (Bt bacteria) are very effective in reducing the population and damage caused by the major insect pests of okra including flea beetles and whiteflies, thereby improving yield and quality of okra fruits. 1.5.1 ALTERING THE PLANTING DATE It has been reported that the ecology of the flea beetle and whitefly vectors should be ascertained so as to alter the planting date of okra such that the period of vector abundance coincides with the growth stage when plants are old enough to tolerate effects of viral infection on the field (Fajinmi and Fajinmi, 2010a). Agyarko (2016) observed significantly higher infes­ tations of whitefly and higher final severity of OLCD in the dry season than in the wet season. This suggests that dry season plantings of okra can result in higher vector (whitefly) infestations and severe viral infections than wet season plantings. Similarly, Asare-Bediako et al. (2017) observed that the overall mean severity of OMD recorded at 10 weeks after planting in the minor cropping season was significantly higher than that of the major cropping season. 1.5.2 THE USE OF PHYSICAL BARRIER TO CONTROL THE FLEA BEETLE VECTORS Fajinmi and Fajinmi (2010b) reported that when a netting barrier is erected around okra plants till 21 days after emergence, it excludes the plants from infestations by flea beetles which vector OkMV and hence decreases incidence of OMD. 1.5.3 THE USE OF SOIL AMENDMENT Application of compost also reduced incidence and severity of OMD, and improved the yield and quality of okra fruits though it did not significantly influence the population of flea beetles that infested the okra plants (Agyei et al., 2017). According to Badejo and Togun (1998), compost application ensures release of nutrients in balanced proportions

10

Plant Pathogens: Detection and Management for Sustainable Agriculture

that prevent excessive gaseous and leaching losses to ensure synchrony between nutrient supply and crop uptake. This in turn ensures healthy growth of okra plants which improves the resistance and/or tolerance of the plants to viruses and pests attacks, thereby improving yield and quality of produce (Agyei et al., 2017). 1.5.4 INTEGRATED PEST AND DISEASE MANAGEMENT APPROACH Classical integrated pest management (IPM) employs a systematic combi­ nation of practices (hygienic, cultural, agronomic), the use of natural control mechanisms employing natural enemies and plant extract, in addition to the judicious use of chemical pesticides to achieve economic management of pest levels above an economic threshold. This has been adopted as the national crop protection policy for Ghana (Kyofa-Boamah et al., 2005). IPM against viral diseases and pests of okra involves planting of resistant varieties, rogueing out of diseased plants, rotation with non-hosts crops, avoiding smoking when handling or working in okra fields, controlling insect vectors with recommended insecticides and/or use of insecticidal soaps before disease spread (MoFA, 2013). In Ghana, crude neem seed extracts and Bacillus thurigiensis (Bt) can be used effectively by farmers as a component of IPM in okra (Obeng-Ofori and Sackey, 2003). 1.6 CONCLUSIONS OMD and OLCD have been demonstrated as the major viral diseases affecting okra production in Ghana. These diseases are prevalent in Ghana with disease incidences of up to 100% reported depending on the cultivar. Incidence and severity of OLCD are highest at the coastal savannah zone, followed by forest while the transition agroecological zone had the lowest. Field screening of okra genotypes against viral infection showed genotypes with tolerance and resistance to both OMD and OLCD. Other management strategies adopted so far include the use of physical barrier (wire netting), both synthetic pesticides and phytopesticides against insect vectors and the use of soil amendment (compost/fertilizers). Integration of various methods to ensure effective management of these diseases is therefore recommended.

Viral Diseases of Okra in Ghana and Their Management

11

KEYWORDS

• • • • • •

okra viruses okra mosaic disease viruses management strategies pesticides

REFERENCES Adetuyi, F. O.; Osagie, A. U.; Adekunle, A. T. Nutrient, Antinutrient, Mineral and Zinc Bioavailability of Okra Abelmoschus esculentus (L) Moench Variety. Am. J. Food Nutr. 2011, 1 (2), 49–54. Agyei K. F.; Asare-Bediako, E.; Amissah, R.; Daniel Okae-Anti, D. Influence of Compost on Incidence and Severity of Okra Mosaic Disease and Fruit Yield and Quality of Two Okra (Abelmoschus esculentus L. Moench) Cultivars. Int. J. Plant Soil Sci. 2017, 16 (1), 1–14. Alegbejo, M. D. In Evaluation of Okra Genotype for Resistance to Okra Mosaicvirus, 15th Annual Conference of the Horticultural Society of Nigeria, National Horticultural Research Institute: Ibadan, 1997; p 60. Agyarko, F. Studies of Okra Mosaic and Okra Leaf Curl Disease in the Central Region of Ghana. M.Phil. Thesis, Department of Crop Science, School of Agriculture, University of Cape Coast, Ghana, 2016, p 150. Asare-Bediako, E.; Agyarko, F.; Verbeek, M.; Taah, K. J.; Asare, A. T.; Frimpong, K.; Agyei, K. F.; Sarfo; Eghan, M. J.; Combey, R. Variation in the Susceptibility of Okra (Abelmoschus esculentus L. Moench) Genotypes to Okra Mosaic Virus and Podagrica Species under Field Conditions. J. Plant Breed. Crop Sci. 2017, 9 (6), 79–89. Asare-Bediako, E.; Agyarko, F.; Kingsley, J.; Taah, K. J.; Aaron Asare, T. A.; Agyei Frimpong, K.; Sarfo, J. Phenotypic and Serological Screening of Okra Genotypes for Resistance Against Okra Mosaic Disease. RUFORUM Working Document Series (ISSN 1607-9345) No. 14, 2016, pp 571–580. Asare-Bediako, E.; Addo-Quaye, A. A.; Bi-Kusi, A. Comparative Efficacy of Phytopesti­ cides in the Management of Podagrica spp and Mosaic Disease on Okra (Abelmoschus­ esculentus L). Am. J. Exp. Agric. 2014a, 4 (8), 879–889. Asare-Bediako, E.; Addo-Quaye, A. A.; Bi-Kusi, A. Comparative Efficacy of Plant Extracts in Managing Whitefly (Bemisia Tabaci Gen) and Leaf Curl Disease in Okra (Abelmoschus esculentus L). Am. J. Agric. Sci. Technol. 2014b, 2 (1), 31–41.

12

Plant Pathogens: Detection and Management for Sustainable Agriculture

Asare-Bediako, E.; Van der Puije, G. C.; Taah, K. J.; Abole, E. A.; Baidoo, A. Prevalence of Okra Mosaic and Leaf Curl Diseases and Podagrica spp. Damage of okra (Albelmoschus esculentus) Plants. Int. J. Curr. Res. Acad. Rev. 2014c, 2 (6), 260–271. Askira, A. B. A Survey on the Incidence of Okra leaf curl virus on Okra in Lake Alau Area of Borno State, Nigeria. Int. J. Agric. 2012, 4 (1), 1–6. Atiri, G. I.; Ibidapo, B. Effect of Combined and Single Infections of Mosaic and Leaf Curl Virus on Okra Growth and Yield. J. Agric. Sci. 1989, 112, 413–418. Badejo, M. A.; Togun, A. O. Strategies and Tactics of Sustainable Agriculture in the Tropics. College Press Ltd., 1998. Basu, A. N. Bemisia Tabaci (Gen.) Crop Pest and Principal Whitefly Vector of Plant Viruses. West View Press: Boulder, San Francisco, Oxford, 1995, p 183. Bhagathi, V. K.; Goswani, B. K. Incidence of Yellow Vein Mosaic Disease on Okra in Relation to Whitefly Population and Different Sowing Time. Ind. J. Virol. 1992, 8, 37–39. Bhyan, B. S.; Alam, M. M.; Ali, M. S. Effect of Plant Extracts on Okra Mosaic Virus Incidence and Yield Related Parameters of Okra. Asian J. Agric. Res. 2007, 1 (3), 112–118. Brown, J. K.; Bird, J. Whitefly Transmitted Geminiviruses and Associated Disorders in the Americas and the Caribbean Basin. Plant Dis. 1992, 76, 220–226. Brunt, A.; Crabtree, K.; Gibbs, A. J. Viruses of Tropical Plants. CAB International: Wallingford: UK, 1990. Cudjoe, A. R.; Kyofa-Boamah, M.; Nkansah, G. O.; Braun, M.; Owusu, S.; Adams, E.; Monney, E.; Attasi, R.; Owusu, P.; Sarpong, S. Commercial Okra Production in Ghana— Good Agricultural Practices/Code of Practice and IPM Strategies. In Handbook of Crop Protection Recommendations in Ghana, Ministry of Food and Agriculture, Accra; Kyofa-Boamah, M., Blay, E., Braun, M., Kuehn, A., Eds; 2005; pp 75–92. Fajinmi, A. A.; Fajinmi, O. B. Epidemiology of Okra mosaic virus on Okra under Tropical Conditions. Int. J. Vegetable Sci. 2010a, 16 (3), 287–296. Fajinmi, A. A.; Fajinmi, O. B. Incidence of Okra Mosaic Virus at Different Growth Stages of Okra Plants (Abelmoschus esculentus L. Moench) under Tropical Condition. J. Gen. Mol. Virol. 2010b, 2 (1), 028–031. FAOSTAT. Food and Agricultural Organization of the United Nations. Online and Multilingual Database, FAO, Rome, Italy. http://faostat.fao.org/foastat/ Givord, L; Hirth, L. Identification, Purification and Some Properties of a Mosaic Virus of Okra (Hibiscus esculentus). Ann. Appl. Biol. 1973, 74, 359–370. Hamon, S.; Charrier, A. Les Gombos. In: L’amelioration des plantestropicales; Charrier, A., Jacquot, M., Hamon, S., Nicholas, D., Eds; CIRAD/ORSTOM: Montpellier, France, 1997; pp 313–333. Hamon, S. Evolutionary Organization of Its Kind Abelmoschus (okra). Co-adaptation and Evolution of Two Species Grown in West Africa, A. esculentus and A. caillei. Paris, ORSTOM, DTP Works and Documents, 1988, p 191. Idris, A. M.; Brown, J. K. Molecular Analysis of Cotton Leaf Curl Virus-Sudan Reveals an Evolutionary History of Recombination. Virus Genes 2002, 24, 249–256. Kochhar, S. L. Tropical Crops. A Text Book of Economic Botany. Macmillan Publishers Ltd.: London and Basingstoke; Macmillan Indian Ltd, 1986, pp 467. Kon, T.; Rojas, M. R.; Abdourhame, I. K.; Gibertson, R. L. Roles and Interactions of Begomoviruses and Satellite DNAs Associated with Okra Leaf Curl Disease in Mali, West Africa. J. Gen Virol. 2009, 90 (4), 1001–1013.

Viral Diseases of Okra in Ghana and Their Management

13

Konate, G.; Barrow, N.; Fargette, D.; Swanson, M. M.; Harrison, B. D. Occurrence of Whitefly-transmitted Geminiviruses in Crops in Burkina-Faso, and their Serological Detection and Differentiation. Ann. Appl. Biol. 1995, 126, 121–129. Kyofa-Boamah, M.; Blay, E.; Braun, M.; Kuehn, A. Commercial Okra Production in Ghana-Good Agricultural Practices/Code of Practice and IPM Strategies: A. Handbook of Crop Protection; Recommendations in Ghana, Ministry of Food and Agriculture: Accra, 1995; pp 75–92. Leke, W. N. Molecular Epidemiology of Begomoviruses that Infect Vegetable Crops in Southwestern Cameroon. Swedish University of Agricultural Sciences, Uppsala, 2010. Available at: http://pub.epsilon.slu.se/id/eprint/2338 (accessed April 22, 2016). Mihretu, Y.; Wayessa, G.; Adugna, D. Multivariate Analysis among Okra (Abelmoschus esculentus (L.) Moench) Collection in South Western Ethiopia. J. Plant Sci. 2014, 9 (2), 43–50. Ministry of Food and Agriculture (MoFA) Okra Production. Horticultural Development Unit, MoFA, Accra, 2013. Naidu, R. A.; Hughes, J. D. A. Methods for the Detection of Plant Virus Diseases. Plant Virol. Sub Saharan Africa, 2003, 233–253. National Agricultural Research Project (NARP) Horticultural Crops. Vol. 3, Accra: NARP, CSIR, 1993. Ndunguru, J.; Rajabu, A. C. Effect of Okra Mosaic Virus Disease on the Above-ground Morphological Yield Components of Okra in Tanzania. Scientia Horticulturae 2004, 99 (3), 225–235. Nevala, A. E. In the Southwest, a New Plant Reserve Protects the Mother of All Chilies. National Wildlife, 2000, pp 14. N’Guessan, K. P.; Fargette, D.; Fauquet, C.; Thouvenel, J. C. Aspects of the Epidemiology of Okra Leaf Curl Virus in Cote d’Ivoire. Trop Pest Manage. 1992, 38, 122–126. Norman, J. C. Tropical Vegetable Crops. Arthur H. Stockwell Ltd.: Devon, UK, 1992; p 252. Obeng-Ofori, D.; Sackey, J. Field Evaluation of Non-synthetic Insecticides for the Management of Insect Pests of Okra Abelmoschus esculentus (L.) Moench in Ghana. Ethiopian J. Sci. 2003, 26, 145–150. Oppong-Sekyere, D. Assessment of Genetic Diversity in a Collection of Ghanaian Okra Germplasm (Abelmoschus Spp. L) Using Morphological Markers. M.Sc. Thesis, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, 2011; p 96. Purseglove, J. W Tropical Crops: Dicotyledons. Longman Group, EUA: London, 1974; pp 17–30. Revkin, A. C. Need Elephant Repellent? Try This Hot Pepper Brew. The New York Times, 2000. Sayed, S. S.; Rana, D.; Krishna, G.; Reddy, P. S.; Bhattacharya, P. S. Association of Bego­ movirus with Okra (Abelmoschus esculentus L.) Leaf Curl Virus Disease in Southern India. SAJ Biotechnol. 2014, 1 (1), 102. Schippers R. R. African Indigenous Vegetables: An Overview of the Cultivated Species, 2000. Schmutterer, H. Properties and Potential of Natural Pesticides from the Neem Tree, Azadirachta indica. Ann. Rev. Entomol. 1990, 35, 271–297. Siemonsma, J. S. Abelmoschus: A Taxonomical and Cytogenetical Overview. Int. Crop Network Ser. 5. Int. Board Plant Genet. Resources, Rome, Italy, 1991, 52–68.

14

Plant Pathogens: Detection and Management for Sustainable Agriculture

Siemonsma, Y. La culture du gombo (Abelmoschus spp.) Itgume fruit tropical avec Reference Spéciale de la Cote d'Ivoire. Thesis, University of Wageningen, The Netherlands, 1982. Sinnadurai, S. Vegetable Production in Ghana. Acta Horticulturae. (ISHS) 1973, 33, 25–28. Swanson, M. M.; Harrison, B. D. Serological Relationships and Epitope Profiles of Isolates of Okra Leaf Curl Gemini Virus from Africa and the Middle East. Biochimie. 1993, 75 (8), 707–711. Tiendrebego, F.; Lefeuvre, P.; Hoareau, M.; Villemot, J.; Konate, G.; Traore, A. S.; Baro, N.; Traore, V. S.; Reynaud, B.; Traore, O.; Lett, J. -M. Molecular Diversity of Cotton Leaf Curl Gezira Virus Isolates and Their Satellite DNAs Associated with Okra Leaf Curl Disease in Burkina Faso. Virol. J. 2010, 7 (1), 48–49. Tindall, H. Vegetables in the Tropics. London: Macmillan Press Ltd, 1986. Udengwu, O. S.; Dibua, U. E. Screening of Abelmoschus esculentus and Abelmoschu scallei Cultivars for Resistance Against Okra Leaf Curl and Okra Mosaic Viral Diseases, Under Field Conditions in South Eastern Nigeria. African J. Biotechnol. 2014, 13 (48), 4419–4429.

CHAPTER 2

Current and Prospective Approaches for Plant Virus Diseases Detection TOUSEEF HUSSAIN1,* and QUAZI MOHD. IMRANUL HAQ2 Department of Botany, Plant Pathology Section, Aligarh Muslim University, Aligarh-202002, India 1

Deparment of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Sultanate of Oman

2

*

Corresponding author. E-mail: [email protected]

ABSTRACT Due to the globalization of trade through the Free Trade Agreement and rapid climate change patterns, promotes the transfer of virus from one country to another and its hosts and vectors, therefore, the diagnosis of viral diseases is getting more important now a days. The lack of general reliability of the methods of visual identification and the variability in the characteristic expression within the host plant, it is very difficult to detect virus infections in the plants. For effective management practices, it is necessary to reduce the spread of diseases, to monitor the health of the plants and detect pathogens in the initial stage. Because the symptoms of viral diseases are not different with great diversity and are confused with abiotic stresses, symptomatic diagnosis may not be appropriate. DNA-based (PCR, RCA) and serological methods (ELISA) now provide essential tools for accurate plant disease diagnosis, in addition to the tradi­ tional visual scouting for symptoms. From the last three decades, different forms of (ELISAs), has been developed based on serological principle, that have been widely used. Although serological and PCR-based methods are the most available and effective to confirm the diagnosis of the disease, volatile, provide immediate results and can be used to detect infections in

16

Plant Pathogens: Detection and Management for Sustainable Agriculture

asymptomatic stages. We explain how these tools will help plant disease management and complement serological and DNA-based methods. 2.1 INTRODUCTION Plant viruses diseases are one of the major threats all around the world, which cause loss of billion dollars per year by destroying various economi­ cally important crops.43 Plant virus symptoms occur on stems, leaves, flowers, or fruits and vary from mild to severe damage, slow growth, and rarely death of the plant.1 Important aspects like agronomic, economic, and social impact are frequently influenced by a wide range of viruses infecting plants. Early stage detection of viruses which causes infection is crucial to reduce economic losses. For diagnostic purpose, biological indexing and sero­ logical enzyme-linked immunosorbent assay (ELISA) are most exten­ sively and most widely used methods. Furthermore, modern molecular techniques have revolutionized plant virus detection and identification. During early research, detection and identification of plant on symp­ tomatology of infected plants was not reliable because the symptoms differed depending on the cultivar, growth stage, and virus strain, etc. Biological assays are still most commonly and frequently used diagnostic methods for many plant viruses until now because the methods are simple and easy.21,39 Previously, virus diagnosis was mainly done by virology specialist having many years of experience. Rolling circle amplification (RCA) is reliable, convenient, and cheaper than polymerase chain reaction (PCR) for the diagnosis of plant viruses with small single-stranded circular DNA including geminiviruses. In future, this shortcut will extensively speed up the genomics of gemini, circo, and nanoviruses.58 2.2 HISTORY Globally, horticultural and agricultural crops are infected by plant viruses and are a major threat to them. Methods for detection and identifica­ tion of viruses play a crucial role in virus disease control. Diagnostic techniques for plant viruses are mainly divided in two major categories: biological properties and intrinsic properties of the virus itself. Detection methods depend on ELISA, immunoblotting, and coat protein includes

Current and Prospective Approaches for Plant Virus

17

agglutination tests. Viral nucleic acid-based techniques like prospective, dot-blot hybridization are more accurate than other diagnostic methods. This diagnostic method for plant viruses provides increased sensitivity, more flexibility, and specificity for quick diagnosis of plant virus diseases. Early molecular hybridization technologies were rapidly supplanted by more powerful nucleic acids amplification methods based on the PCR. Although molecular methods are highly discriminatory, allowing strain typing, routine testing has been hampered by problems in reproducibility. Continuous efforts have been made to overcome these barriers. Improved systems to prepare plant or insect samples have been developed. Efforts have also been directed at increasing the sensitivity and specificity of detection, which can be limited by the high content of enzyme inhibitors in plant materials. Nested and multiplex PCR offer high sensitivity and the possibility to detect several targets in one assay, respectively. There are many other technologies, which allow the amplification of nucleic acids in an isothermal reaction (nucleic acid sequence-based amplification [NASBA] or reverse transcription loop-mediated isothermal amplification [RT-LAMP] procedures). High-throughput testing has been achieved by real-time polymerase chain reaction (RT-PCR), in which the automation of PCR combined with fluorimetry. RT-PCR simultaneously permits detec­ tion and quantification of targets gene. In the near future, nucleic acid arrays and biosensors assisted by nanotechnology could revolutionize the methodology for diagnosis of plant viruses. New technologies are slow, which requires more knowledge of what makes a better routine diagnostic methods to begin, which also requires rate of uptake of understanding. This can be achieved by keeping in mind the two most successfully used plant geminivirus detection methods: RT-PCR and ELISA. The publication based on ELISA method for the diagnosis of plum pox virus (PPV; genus Potyvirus, family Potyviridae) and Arabis mosaic virus (ArMV; genus Nepovirus, family Secoviridae) by Clark and Adams55 was a major hike in virus diagnostics. 2.3 PRINCIPLES OF SEROLOGY Serological tests are important for the final confirmation of an unknown plant virus and also to study the virus species and strains relationship. The most important advantage of this serology method is based on the specificity between viral antigen (Ag) and antibody (Ab).

18

Plant Pathogens: Detection and Management for Sustainable Agriculture

Study of serums, especially their reactions and properties, is called serology. Detection of plant viruses with direct immunoblotting is done in this technique. The antiserum is used to detect plant viruses. Antise­ rums are produced by injecting an Ag into rabbit or goat. Any protein or substance that the animal’s immune system recognizes as foreign is known as antigen. The polyclonal Ab’s are also used which is produced by purifying a particular Ag and injecting the purified virus (the Ag, the virus particle) into rabbit. All the plant virus detection techniques that use antisera are known as serological techniques. Virus particles and associated proteins have many epitopes with different amino acid sequences and have the ability of inducing the specific Ab’s production (Fig. 2.1). The virus particles, their protein capsid, and the different types of virus induced proteins can function as Ag’s.39,56,57,59,60

FIGURE 2.1 Diagrammatic representation of (A) structure of an immunoglobulin G (IgG) molecule. Fab, F(ab)2, and Fc represent fragments obtained by enzyme cleavage of IgG, (B) antigen binding site. Source: biologydiscussion.com

The significance of the serological methods for the study of plant viruses and plant viral diseases was demonstrated for the first time by the pioneer work of Purdy-Beale.42

Current and Prospective Approaches for Plant Virus

19

2.4 DIAGNOSIS Viruses cannot be isolated and grown on cell-free media as fungi or bacteria, as they are obligate parasites, but they have to be maintained on susceptible host plants by artificial inoculation at regular intervals, under controlled conditions.40 Many different types of viruses may exhibit same symptoms and the disease phenotype can give only less information for disease diagnosis purpose. Many specific and reliable techniques used for virus identification mainly depend on the different aspects of the viruses such as pathogenicity, transmissibility, architecture of virus particles, presence of virus-specific skeleton in infected cells, properties of the protein coat. Most extensively, Ab-based technique used for diagnostic of viruses is known as ELISA. In this method, the plant tissue extract being tested for virus detection incubated in the well of ELISA plate. Then, Ab is added which binds to the specific Ag (the virus particle). Secondary Ab linked to an enzyme is supplemented which gets attached to the previous Ab already existed in the well. After washing, a colorless substrate is supplemented which produces colored product (yellow) after reaction that indicates the existence of virus and the intensity of the color is used to calculate the virus concentration. After the development of ELISA, new methods have been focused. Nucleic acid spot hybridizations (NASH) have been generally used for some plant viruses and viroids. PCR technique published in the early 1990s is most extensively used method for plant virus diagnostics.61 2.5 CLASSIFICATION OF VIRUSES According to Baltimore Classification System, based on the way in which a virus produces messenger RNA (mRNA) during infection, the viruses have been classified into seven major groups: i) ii) iii) iv) v) vi) vii)

Group I: double-stranded DNA viruses Group II: single-stranded DNA viruses Group III: double-stranded RNA viruses Group IV: positive-sense single-stranded RNA viruses Group V: negative-sense single-stranded RNA viruses Group VI: reverse transcribing Diploid single-stranded RNA viruses Group VII: reverse transcribing circular double-stranded DNA viruses

20

Plant Pathogens: Detection and Management for Sustainable Agriculture

Within each of these groups, many different characteristics are used to classify the viruses into families, genera, and species. Typically, combina­ tions of characters are used and some of the most important are: particle morphology, genome properties, biological properties, and serological properties. 2.5.1 PARTICLE MORPHOLOGY Amongst plant viruses, the most frequently encountered shapes are: 2.5.1.1 ISOMETRIC Apparently spherical and (depending on the species) from about 18nm in diameter upwards. The example here shows Tobacco necrosis virus, genus Necrovirus with particles 26 nm in diameter.

2.5.1.2 ROD-SHAPED About 20–25 nm in diameter and from about 100 to 300 nm long. These appear rigid and often have a clear central canal (depending on the staining method used). Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Tobacco mosaic virus, genus Tobamovirus with particles 300 nm long.

Current and Prospective Approaches for Plant Virus

21

2.5.1.3 FILAMENTOUS Usually about 12 nm in diameter and more flexuous than the rod-shaped particles. They can be up to 1000 nm long, or even longer in some instances. Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Potato virus Y, genus Potyvirus with particles 740 nm long.

22

Plant Pathogens: Detection and Management for Sustainable Agriculture

2.5.1.4 GEMINATE Twinned isometric particles about 30 × 18 nm. These particles are diag­ nostic for viruses in the family Geminiviridae which are widespread in many crops especially in tropical regions. The example here shows Maize streak virus, genus Mastrevirus.

2.5.1.5 BACILLIFORM Short round-ended rods. These come in various forms up to about 30 nm wide and 300 nm long. The example here shows Cocoa swollen shoot virus, genus Badnavirus with particles 28 × 130 nm.

Current and Prospective Approaches for Plant Virus

23

2.6 DETECTION OF PLANT VIRUSES BASED ON BIOLOGICAL PROPERTIES 2.6.1 SYMPTOMATOLOGY The plant virus symptoms are mainly used to describe a disease and also for the removal of infected plants from the field to control the diseases. Visual observation of the symptoms is comparatively simple, whereas several factors such as time of infection, host plant variety, virus strain, and environment can affect the symptoms.31 However, some viruses cause asymptomatic infection. It is mandatory that visual observation for symptoms is done in addition with other confirmatory tests to make sure of the meticulous diagnosis.3 2.7 PLANT VIRUS TRANSMISSION TESTS This test is very important for virus investigation, identity, vector transmission, and mechanical transmission to susceptible host plants.21 Mechanical transmission is possible with minimum facilities and the symptoms produced allow both the detection and identification of large number of plant viruses.18 For other plant, mechanically transmissions are not possible as well as the viruses of small fruit can be identified through graft/vector transmission.16,37,38 2.8 PHYSICAL PROPERTIES OF PLANT VIRUSES Physical properties of the plant viruses (such as dilution end point, longevity in vitro, and thermal inactivation point) used to measure infec­ tivity of the virus, even though these physical properties are not consistent and not recommended for plant virus diagnostic purpose.15 2.9 BIOCHEMICAL TECHNIQUES Virus infection causes many changes in biochemical and physiological activity of the host plants. Infection caused by the viruses could be detected by variability pattern in isozyme of infected and healthy leaves, determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis technique.

24

Plant Pathogens: Detection and Management for Sustainable Agriculture

2.10 DETECTION PLATFORMS Few methods for virus detection are extensively used to find out the prod­ ucts of various amplicons. Common gel electrophoresis techniques are widely applicable method to check the application; however, this is time consuming. 2.11 ISOTHERMAL METHODS A simple method to get isothermal DNA amplification is to separate the double-stranded DNA strands of the template in a non-thermal way, such as, PCR, helicase-dependent amplification (HDA),63 and recombinase poly­ merase amplification (RPA)62 are two examples of this approach. At a single temperature, the HDA can be performed, but a brief incubation at 95–96°C before adding HDA enzymes increasing the sensitivity has been shown. The main benefit of RPA is short time for reaction to take place usually $120 billion p.a.11,12 As per the reports of the Karssen and Moens,13 Moens et al.,14 more than 100 RKN species are infecting thousands of plant species and remains a serious threat to the sustainable food production across the globe. Up to now, there are about 3400 species of nematodes that are plant parasitic. The recent reports advocate 250 species from 43 genera reflect phytosanitary risk yet there are may be many species of phytosanitary importance.15 The most important genera in terms of juvenile diffusion include Globodera, Heterodera, and Meloidogyne of the family Heteroderidae. 8.1.3 CYST CEREAL NEMATODES The wheat and barley production has incurred huge losses due to cyst cereal nematodes such as Heterodera avenae and is posing a major threat to these crops in many regions of the world. It has been observed that cereal cyst nematode cause significant yield losses especially under rainfed conditions and less irrigated regions of Australia, China, Pakistan, and the United States. Yield loss due to cereal cyst nematode (CCN) are 15%–20% on wheat in Pakistan,16 17%–77% on barley and 40%–92% on wheat in Saudi Arabia,17 20% on barley and 23%–50% on wheat in Australia,18 42% on rainfed wheat in Turkey.19 There has been a reduction of about 50% on barley yield due to H. latipons in Cyprus20 in China about

186

Plant Pathogens: Detection and Management for Sustainable Agriculture

33% yield loss in cucumber have been reported by.21 The nematodes have also caused a huge reduction in yield of about 87%.22 There are several obstacles in estimating the perfect crop loss caused due to nematodes. The current statistics reflect massive economic loss on the yield of about US $9 million in India, £3 million in Europe, and about AUS $72 million in Australia has incurred due to the CCN infestation.19 8.2 MANAGEMENT OF NEMATODES With regard to population explosion and food security, management of parasitic nematode should be given utmost importance with novel strategies. Because it is too difficult to eliminate the nematodes from the soil, the overall goal of proper management is to reduce the nematode populace to least possible level. As per the reports of Food and Agriculture Organization,23 it has estimated that more than 800 million people face starvation. Plant diseases play a critical role in decreasing the agricultural productivity and is considered as the biggest threat to sustainable food production across the globe.24 As per the reports of Nicol et al.,19 about 12% of world total food production is lost due to PPN. This is a huge quantity to be ignored and hence the need of the hour is to keep it as low as possible. The best viable approach to attain the objective is through the management of nematodes. In past management of nematodes have been principally carried out through the use of chemicals; however, this method is having a wide spectrum of limitation and, therefore, it is mandatory to substitute this with some suitable approach. Chemical nematicides are costly, unavailable, and pose a harmful effect on the environment.25 8.2.1 BIOLOGICAL CONTROL OF NEMATODES The apprehension over the deleterious effects of chemical nematicides on the environment and human health has facilitated the need for safer, ecofriendly control measures. The biological control of nematode growth and populace offers a promising substitute for the vigorous use of chemical nematicides. Biological control relying on soil microorganisms may offer feasible and sustainable perspectives in many agrosystems for management of nematodes. This is considered as an appropriate to chemical nematicides as it is cheap, readily available, and eco-friendly; in addition

Role of Biological Agents

187

to this, it plays a crucial role in facilitating the sustainability in agricultural production.26 The reduction in root galling expressed in terms of RootKnot Index form the basis for the assessment of efficiency of biocontrol agents in the management of PPN.27 Biocontrol agents also have the ability to improve the plant health and the hence overall productivity. Several organisms have been shown possess antagonistic activity against PPN28,29 among these fungi have proved to best in terms of efficiency and efficacy. 8.2.2 NEMATOPHAGOUS FUNGI Nematophagous fungi are a class of microfungi that have the ability to capture, kill, and digest nematodes. Numerous fungal strains have been assessed for their antagonistic action against nematodes and it has been proven that fungi possess some striking features to act as best biocontrol agent of nematodes, for example, enzymes like collagenase, chitinases, and serine protease have the ability to rupture the cuticle of adult nematode or eggshells, thereby causing significant mortality at very early stage.30 The cuticle of adult nematode is mainly composed of proteins, keratin, collagen, and fibers while as the chitin forms the major portion of nematode egg. Therefore, the degradation of collagen through the fungal collagenase is believed to be essential for the control of nematode population.30 The fungi employ the association of mechanical activity along with the hydrolytic enzymes to penetrate the nematode cuticle. The enzymes degrade the main constituent (protein and chitin) of nematode cuticle and egg shells. 8.2.3 MECHANISM OF INFECTION The nematophagous fungi involve a wide array of hydrolytic enzymes in infecting the nematodes and nematode eggs, these are discussed in next section. 8.2.3.1 SUBTILASES Spatafora et al.31 have reported that Pezizomycotina contains the filamentous, sporocarp-producing nematophagous fungi is the largest subphylum of Ascomycota. As per the reports of Yang et al,32 fungal extracellular

188

Plant Pathogens: Detection and Management for Sustainable Agriculture

enzymes have been recognized as a strong tool to penetrate and infect the nematodes. Li et al,33 are of the opinion that subtilisin-like serine proteases, amongst the extracellular enzymes, have been exalted as the essential enzyme with central roles in penetrating and colonizing their nematode host. In 1990, the first serine protease from V. suchlasporium was isolated, purified, characterized, and tested positive for the activity of degrading certain cyst nematode proteins.30 Importantly, intriguing evidence emerged suggesting that subtilisin-like serine proteases isolated from nematode-trapping fungi regulate important processes of penetration, degradation, and digestion of nematode cuticles.34-39 Several kinds of serine protease including PII and Aoz1 from Arthrobotrys oligospora,40 pSP-3 from Paecilomyces lilacinus41 and VCP1 from Paecilomyces chlamydosporia42 have been isolated, purified and cloned. These enzymes disrupt the interrupt the physiological integrity of the nematode cuticle that facilitates penetration and colonization. 8.2.3.2 CHITINASES The potential of fungi as biocontrol agent has proved a great promise to sustain the agriculture and reduce the crop loss incurred by the wide spectrum of nematodes. The degradation of chitin of nematode egg shell through the action of fungal extracellular enzymes has been supported by several workers.43 Chitinases, a prerequisite for hyphal growth participate in infection of mycoparasites and nematopathogenic fungi are a class of inducible enzyme that catalyzes chitin, the main constituent of nematode cuticles.44 Tikhonov et al.45 identified and purified CHI43, the first chitinase with nematicidal activity. As per the reports of Huang et al.,30 the activity of chitinase CHI43 obtained from nematophagous fungi of V. chlamydosporium and V. suchlasporium increased with time when cultured in medium with containing colloidal chitin as the main source of C and N. Chitinase of CHI43 or/ and serine protease of P32 treated eggs of G. pallida revealed the prominent effect of CHI43 on degradation of nematode eggshell.30 Scars and slight peelings were recorded on the egg surfaces when CHI43 or P32 were applied individually, however, a combination of CHI43 and P32 caused more serious damage. Thus, overall experimentation concluded the involvement of chitinase in the disruption of the cuticle of nematode eggshells. Furthermore, it was also revealed that a combination of

Role of Biological Agents

189

different hydrolytic enzymes, including chitinase and serine protease, proved to be more efficient in keeping the nematode population density low. Recently, RKN (Meloidogyne javanica) was kept under control by the exogenous application of Trichoderma harzianum BI46 and concluded that different concentrations (102–108 spores/mL) of T. harzianum BI reduced nematode infection proportionally with the increase in chitinase activity in comparison to control. Trichoderma spp. has been studied by different workers as a biological control agent against nematode diseases of crops.47,48 Several scientists are of the opinion that T. harzianum have the potential to act as an effective bioagent for the management of the citrus nematode.49,50 Windham et al.51 treated the soil with T. harzianum and T. koningii preparation and reported a huge reduction in egg production in the RKN Meloidogyne arenaria. Seifullah and Thomas52 studied and confirmed by the low-temperature scanning electron microscopy, the parasitism of Globodera rostochiensis by the exogenous application of T. harzianum. Rao et al.,49 and Sharon et al.,50, advocated that T. harzianum isolates can decrease the M. javanica infection to a greater extent. They further studied the antagonistic effect in detail and have proposed the mechanism of action in the following two ways: 1. Boost in the activity and/ or pool of chitinase and protease enzymes result in direct parasitism of nematode eggs and larva through the breakdown of chitin and proteins.50,53 2. Indirect parasitism involves the development of systemic resistance. Chitinase and protease which reflect antifungal activities appear to participate in the Meloidogyne javanica Trichoderma spp. interaction.50 Sahebani and Hadavi46 have shown that T. harzianum BI can be used as an efficient biocontrol agent against M. javanica. In addition to this, their experimentation also demonstrated that inoculation of tomato seedlings with T. harzianum can notably mitigate the population of this nematode and hence disease severity. 8.2.3.3 COLLAGENASE Collagenases are the group of calcium and zinc-dependent enzymes that have the ability to hydrolyze collagen in their native triple helix

190

Plant Pathogens: Detection and Management for Sustainable Agriculture

and denatured form. Collagenases are becoming increasingly important commercially. Collagenases have the ability to damage the nematode cuticle as the collagen forms the main constituent of nematode cuticle. Bedoya et al.54 observed the collagenolytic activity of proteolytic enzymes in 10 different isolates of Paracoccidioides brasiliensis. Their results indicated that about 70% and 80% of the isolates secrete collagenolytic enzymes. These results further support the view that P. brasiliensis has the capability to secrete collagenolytic enzymes and can be used in the control wide of nematode attack. Tosi et al.55 have demonstrated the antagonistic activity of collagenolytic enzymes secreted by a nematophagous Antarctic fungus Arthrobotrys tortor and a wide range of species of the genus Arthrobotrys against Caenorhabditis elegans. The results showed a threefold increase in the collagenase secreted by the A. tortor in comparison to other species and hence it was concluded that this fungus offers a promising strategy for the nematode management. Several workers have advocated that the production of collagenolytic proteases from nematode-trapping fungi can be exploited for commercial purposes.40 Nematode-trapping fungi, potent biological control agents are unique in capturing the plant parasitic nematodes by employing several trapping devices. These fungi harbor a wide array of trapping devices including adhesive networks, adhesive columns, constricting rings, adhesive knobs, and nonconstricting rings to capture, kill, and digest nematodes. A striking example nematode-trapping fungi is A. oligospora, which employs special hype of 3D networks along with the secretion of extracellular enzymes to capture, penetrate, and immobilize nematodes.30 Schenck et al.56 have demonstrated the production of collagenase production in Nematode-trapping fungi such as Arthrobotrys amerospora. 8.2.4 VOLATILE ORGANIC COMPOUNDS WITH NEMATICIDAL ACTIVITIES FROM FUNGAL ISOLATES Some of workers have also demonstrated that the volatile organic compounds (VOCs) produced by fungi such as Aspergillus candidus, Penicillium brevicompactum, Penicillium clavigerum, Penicillium cyclopium, Emericella nidulans, Penicillium crustosum, Penicillium expansum, Tritirachium oryzae, and Penicillium glabrum have been shown to harbor great antagonistic activity against plant pathogens in general and

Role of Biological Agents

191

nematodes in particular.57,58 Freire et al.,59 while working with Fusarium oxysporum, identified VOCs substances with very strong immobility and mortality to M. incognita and reduced infectivity. They further showed that Fusarium oxysporum and F. solani isolates also led to 88%–96% mortality to Meloidogyne incognita second-stage juveniles. Riga et al.60 evaluated the VOCs produced by the fungus Muscodor albus and recorded that in vitro second stage juveniles (J2) ranging from 82% to 95% in Paratrichodorus allius, Pratylenchus penetrans, and Meloidogyne chitwoodi. 8.2.5 NEMATOPHAGOUS BACTERIA Numerous bacterial isolates and most prominent among them are Pseudomonas spp. and Pasteuria spp.as they possess strong nematicidal activities against RKN.61-63 A very high number of Bacillus isolates have also been identified and found to have nematicidal properties against M. javanica in vitro64 and in vivo65-67. Very little is known about the mechanism involved, however, as per the reports of Adam et al.,68 Bacillus subtilis isolates play a crucial role in alleviating gall formation and also induced systemic resistance in tomato plants, thereby reducing nematode infectivity. Padgham and Sikora,69 also report similar results and advocate that an isolate of Bacillus megaterium to inhibit or reduce root penetration and migration of M. graminicola to the root zone of rice plants. In the last few decades, there has been a mounting interest in the exploration of bacterial antagonists of nematodes.70 Oosterdorp and Sikora,71 have demonstrated that nematode invasion of roots can be reduced by Rhizobacteria treatment to seeds before sowing. During the putrefaction of organic matter in the soil, several bacteria release metabolic byproducts, enzymes, and toxins which may make these organisms as essential natural antagonists of nematodes. 8.3 PASTEURIA PENETRANS Hewlett et al.72 have recently, reported another group of nematode antagonists, Pasteuria penetrans, cosmopolitan in distribution in agricultural soils feed as obligate parasites of nematodes.73 Several workers70,74,75 have advocated that Pasteuria species, potential economical and ecofriendly biological control agents can considerably control plant-parasitic

192

Plant Pathogens: Detection and Management for Sustainable Agriculture

nematodes affecting wide range of plants such as egg-plant, wheat, tobacco, tomato, soybean, bean, pepper, peanut, rye, cucumber, chickpea, grape, mung, and okra. 8.3.1 MECHANISM OF INFECTION Pasteuria penetrans is a potent biocontrol agent for the RKN Meloidogyne spp. A four-step proposed mechanism is as follows: 1. Attachment of Pasteuria spores to the nematode cuticles. 2. Spore germination inside the roots. 3. Formation and proliferation of microcolonies inside the female nematode 4. Finally, the release of endospores after the disruption of the genital system of the female nematode.76,77

8.3.2 RHIZOBACTERIA Some free-living soil bacteria produce a good amount of nematicidal compounds and can be commercialized. Several researchers have at randomly screened rhizosphere bacteria for nematicidal property about 8% were shown to possess activity. Isolates of Agrobacterium spp, Bacillus spp, and Pseudomonas spp, are known for their antagonistic activity against soil-borne bacterial and fungal pathogens also have the potential to eradicate a wide range of nematodes. Li et al.78 studied Rhizobacteria for inhibition of the RKN and soil-borne fungal pathogens, they further report that isolates such as Brevibacillus brevis or Bacillus subtilis have proven to have strong nematicidal activity by causing the severe mortality of J2 larvae of Meloidogyne spp. to a greater extent. Similarly, Insunza et al.79 have shown that 16 bacteria isolates out of 44 reduced 50%–100% nematode population densities such as Paratrichodorus pachydermous and Trichodorus primitives. Ali et al.80 have reported that soil drenching with B. subtilis and P. aeruginosa significantly declined the root-rot, root-knot infection, and nematode population in Vigna mungo.

Role of Biological Agents

193

8.4 PREDACIOUS NEMATODES Cobb81 was the first who gave the idea of using predatory nematode for management of plant-parasitic nematode. Later, Steiner and Heinly82 reported the use of Clarkus papillatus for controlling Meloidogyne spp. and other plant-parasitic nematodes in sugar beet fields. Over the past few years, interest in using potent predators such as mononchids, dorylaimids, aphelenchids, and diplogasterids for nematode control has risen. Among them dorylaimida predators have greater efficiency and are highly effective bioagents because of their short life cycles, chemotaxis sense and resistance to adverse conditions.83 The most beneficial and promising aspect of the dorylaimid, nygolaimid, and diplogasterid predators is that maintenance of their populations is very easy and their resistance to unfavorable environmental conditions as they will remain sufficient in soil even in the absence of prey nematodes.84 They have the ability to reduce population density of plant parasitic nematodes in virtually all soils and also produce nutrients in the available form to plant, which improves plant health to withstand nematode infectivity. Lal et al.85 found that an increase in the population of predatory nematode incidentally reduces the population of RKN. Significant decrease in the population densities of M. incognita and potato cyst nematode Globodera rostochiensis was due to the presence of a predatory nematode, P. punctatus.86 The opinion of Khan and kim83 stated that dorylaimids are highly effective biocontrol predators because their population densities can be easily enhanced by the addition of organic nutrient. 8.5 SUMMARY Over the past two decades, a vast study has been undertaken to identify, screen, and evaluate the biocontrol potential of a variety of microorganisms for the management of nematode. But only a few commercial biocontrol products from the beneficial microorganism, such as bacteria, fungi, and other organisms with nematicidal activity, have been commercialised in the agriculture sector. The development and subsequent implementation of bioagents are quite hectic on a large scale.87 The most important about the development of a commercial biocontrol agent is that it must be capable of targeting host in a laboratory test. In order to develop effective biocontrol strategies, a comprehensive understanding of the mechanisms and vast exploration of the interactions among nematodes, such as soil

194

Plant Pathogens: Detection and Management for Sustainable Agriculture

microbiota, plant microenvironment, and ecological implication must be understood. In the past few years, it has been very well emphasized and reviewed on the interactions between the microorganism and nematode; plant and environment88–91, including integrated pest management (IPM), are very effective and eco-friendly methods to decline the pest infectivity. The IPM aims at the synergistic impact of biocontrol and other methods, such as biofertilizers, soil nutrient amendments, cultivation of resistant plant varieties, and crop rotation at appropriate times, so that they improve plant health and by increasing rhizospheric colonization and enhance antagonistic activity against nematode.89,92,93 To achieve the overall motive, we need to have accurate knowledge about biology, ecology, and mechanisms of infection of antagonistic organisms. Detailed insight about the underlying mechanism understanding on the molecular level of the various biocontrol agents not only will lead to a proper and effective nematode management decision, but also could pave a way to the development of novel biocontrol strategies for the management of plantparasitic nematodes. Advances in molecular biology have widened the horizon of our knowledge and now we are able to explore the underlying molecular mechanisms of infection and signaling pathway that enable the defense system. This may give knowledge about mass production of biocontrol agents that can be used commercially. KEYWORDS • • • • •

biocontrol biological agents nematode root-knot nematodes yield loss

REFERENCES 1. Powell, N. T. Interactions Between Nematodes and Fungi in Disease Complexes. Ann. Rev. Phytopathol. 1971, 9 (1), 253–274.

Role of Biological Agents

195

2. Ngangbam, A. K.; Devi, N. B. An Approach to the Parasitism Genes of the Root-Knot Nematode. Int. J. Phytopathol. 2012, 1 (1), 81–87. 3. Gaur, H. S.; Perry, R. N. The Biology and Control of the Plant-Parasitic Nematode Rotylenchulus reniformis. Agric. Zool. Rev. 1991, 4, 177–212. 4. Renčo, M.; Kováčik, P. Response of Plant Parasitic and Free-Living Soil Nematodes to Composted Animal Manure Soil Amendments. J. Nematol. 2012, 44 (4), 329–336. 5. Gaur, H. S.; Perry, R. N. The Use of Soil Solarization for Control of Plant-Parasitic Nematodes. Nematological Abstracts, 1991, 60 (4), 153–167. 6. Kaşkavalci, G. Effects of Soil Solarization and Organic Amendment Treatments for Controlling Meloidogyne incognita in Tomato Cultivars in Western Anatolia. Turk. J. Agric. For. 2007, 31 (3), 159–167. 7. Sikora, R. A.; J. Bridge, J. L. Starr. “Management Practices: An Overview of Integrated Nematode Management Technologies.” Plant Parasitic Nematodes in Subtropical and Tropical Agriculture, 2nd ed. CAB International: Wallingford, 2005; pp 793–825. 8. Roberts, P. A. Current Status of the Availability, Development, and Use of Host Plant Resistance to Nematodes. J. Nematol. 1992, 24 (2), 213–227. 9. Hockland, S.; Niere, B.; Grenier, E.; Blok, V.; Phillips, M.; Den Nijs, L.; Anthoine, G.; Pickup, J.; Viaene, N. An Evaluation of the Implications of Virulence in Non-European Populations of Globodera pallida and G. rostochiensis for Potato Cultivation in Europe. Nematology 2012, 14 (1), 1–13. 10. McSorley, R. Host Suitability of Potential Cover Crops for Root-Knot Nematodes. J. Nematol. 1999, 31 (4S), 619–623. 11. Karuri, H. W.; Olago, D.; Neilson, R.; Njeri, E.; Opere, A.; Ndegwa, P. PlantParasitic Nematode Assemblages Associated with Sweet Potato in Kenya and Their Relationship with Environmental Variables. Trop. Plant Pathol. 2017, 42 (1), 1–12. 12. Wachira, P. M.; Kimenju, J. W.; Okoth, S. A.; Mibey, R. K. Stimulation of NematodeDestroying Fungi by Organic Amendments Applied in Management of Plant Parasitic Nematode. Asian J. Plant Sci. 2009, 8 (2), 153–159. 13. Karssen, G.; Moens, M; Root-Knot Nematodes. In Plant Nematology, Perry, R. N.; Moens, M., Eds.; CABI Publishing: Wallingford, UK, 2006; pp 59–90. 14. Moens, M.; Perry, R. N.; Starr, J. L. Meloidogyne Species: a Diverse Group of Novel and Important Plant Parasites. In Root-knot Nematodes; Roland N. Perry, Maurice Moens, James L. Starr, Eds.; CABI International Publisher: Oxfordshire, UK, 2009; Vol. 1, pp 1–13. 15. Singh, S. K.; Hodda, M.; Ash, G. J. Plant‐Parasitic Nematodes of Potential Phytosanitary Importance, Their Main Hosts and Reported Yield Losses. Eppo Bull. 2013, 43 (2), 334–374. 16. Nicol, J. M.; Rivoal, R.; Trethowan, R. M.; Van Ginkel, M.; Mergoum, M.; Singh, R. P. CIMMYT’s Approach to Identify and Use Resistance to Nematodes and SoilBorne Fungi, in Developing Superior Wheat Germplasm. In Wheat in a Global Environment; Springer: Netherlands, 2001; pp 381–389. 17. Ibrahim, A. A.; Al-Hazmi, A. S.; Al-Yahya, F. A.; Alderfasi, A. A. Damage Potential and Reproduction of Heterodera avenae on Wheat and Barley under Saudi Field Conditions. Nematology 1999, 1 (6), 625–630. 18. Abidou, H.; El-Ahmed, A.; Nicol, J. M.; Bolat, N.; Rivoal, R.; Yahyaoui, A. Occurrence and Distribution of Species of the Heterodera avenae Group in Syria and Turkey. Nematologia Mediterranea 2005, 33 (2), 195–201.

196

Plant Pathogens: Detection and Management for Sustainable Agriculture

19. Nicol, J. M.; Turner, S. J.; Coyne, D. L.; Den Nijs, L.; Hockland, S.; Maafi, Z. T. Current Nematode Threats to World Agriculture. In Genomics and Molecular Genetics of Plant-Nematode Interactions; Springer: Netherlands, 2011; pp 21–43 20. Nicol, J. M.; Rivoal, R. Global Knowledge and Its Application for the Integrated Control and Management of Nematodes on Wheat. In Integrated Management and Biocontrol of Vegetable and Grain Crops Nematodes; Springer: Netherlands, 2008; pp 251–294. 21. Kayani, M. Z.; Mukhtar, T.; Hussain, M. A. Effects of Southern Root Knot Nematode Population Densities and Plant Age on Growth and Yield Parameters of Cucumber. Crop Protect. 2017, 92, 207–212. 22. Jones, J. T.; Haegeman, A.; Danchin, E. G.; Gaur, H. S.; Helder, J.; Jones, M. G.; Kikuchi, T.; Manzanilla‐López, R.; Palomares‐Rius, J. E.; Wesemael, W. M.; Perry, R. N. Top 10 Plant‐Parasitic Nematodes in Molecular Plant Pathology. Mol. Plant Pathol. 2013, 14 (9), 946–961. 23. FAO. World Food and Agriculture. Food and Agriculture Organization of the United Nations: Rome, 2013. 24. Strange, R. N.; Scott, P. R. Plant Disease: A Threat to Global Food Security. Ann. Rev. Phytopathol. 2005, 43, 83–116 25. Quesada-Moraga, E.; Herrero, N.; Zabalgogeazcoa, Í. Entomopathogenic and Nematophagous Fungal Endophytes. In Advances in Endophytic Research. Springer: India, 2014; pp 85–99 26. Atandi, J. G.; Haukeland, S.; Kariuki, G. M.; Coyne, D. L.; Karanja, E. N.; Musyoka, M. W.; Fiaboe, K. K.; Bautze, D.; Adamtey, N. Organic Farming Provides Improved Management of Plant Parasitic Nematodes in Maize and Bean Cropping Systems. Agric., Ecosys. Environ. 2017, 247, 265–272. 27. Khan, T.; Shadab, S.; Afroz, R.; Aziz, M. A.; Farooqui, M. Study of Suppressive Effect of Biological Agent Fungus, Natural Organic Compound and Carbofuran on Root Knot Nematode of Tomato (Lycopersicon esculentum). J. Microbiol. Biotechnol. Res. 2017, 1 (1), 7–11. 28. Costa, S. R.; van der Putten, W. H.; Kerry, B. R. Microbial Ecology and Nematode Control in Natural Ecosystems. In Biological Control of Plant-Parasitic Nematodes; Springer: Netherlands, 2011; pp 39–64. 29. Stirling, G. R. Biological Control of Plant-Parasitic Nematodes: An Ecological Perspective, a Review of Progress and Opportunities for Further Research. In Biological Control of Plant-Parasitic Nematodes; Springer: Netherlands, 2011; pp 1–38. 30. Huang, X.; Zhao, N.; Zhang, K. Extracellular Enzymes Serving as Virulence Factors in Nematophagous Fungi Involved in Infection of the Host. Res. Microbiol. 2004, 155 (10), 811–816. 31. Spatafora, J. W.; Sung, G. H.; Johnson, D.; Hesse, C.; O’Rourke, B.; Serdani, M.; Spotts, R.; Lutzoni, F.; Hofstetter, V.; Miadlikowska, J. Reeb, V. A Five-Gene Phylogeny of Pezizomycotina. Mycologia 2006, 98 (6), 1018–1028. 32. Yang, J.; Tian, B.; Liang, L. and Zhang, K. Q.; 2007. Extracellular Enzymes and the Pathogenesis of Nematophagous Fungi. Appl. Microbiol. Biotechnol. 2007, 75 (1), 21–31. 33. Li, J.; Yu, L.; Yang, J.; Dong, L.; Tian, B.; Yu, Z.; Liang, L.; Zhang, Y.; Wang, X.; Zhang, K. New Insights into the Evolution of Subtilisin-Like Serine

Role of Biological Agents

34. 35. 36. 37. 38.

39. 40. 41. 42. 43. 44. 45. 46. 47. 48.

197

Protease Genes in Pezizomycotina. BMC Evolut. Biol. 2010, 10 (1), https://doi. org/10.1186/1471-2148-10-68. Wang, B.; Liu, X.; Wu, W.; Liu, X.; Li, S. Purification, Characterization, and Gene Cloning of an Alkaline Serine Protease from a Highly Virulent Strain of the NematodeEndoparasitic Fungus Hirsutella rhossiliensis. Microbiol. Res. 2009, 164 (6), 665–673. Wang, R. B.; Yang, J. K.; Lin, C.; Zhang, Y.; Zhang, K. Q. Purification and Characterization of an Extracellular Serine Protease from the Nematode‐Trapping Fungus Dactylella shizishanna. Lett. Appl. Microbiol. 2006, 42 (6), 589–594. Yang, J.; Huang, X.; Tian, B.; Wang, M.; Niu, Q.; Zhang, K. Isolation and Characterization of a Serine Protease from the Nematophagous Fungus, Lecanicillium psalliotae, Displaying Nematicidal Activity. Biotechnol. Lett. 2005, 27 (15), 1123–1128. Yang, J.; Li, J.; Liang, L.; Tian, B.; Zhang, Y.; Cheng, C.; Zhang, K. Q. Cloning and Characterization of an Extracellular Serine Protease From the Nematode-Trapping Fungus Arthrobotrys conoides. Arch. Microbiol. 2007a, 188 (2), 167–174. Yang, J.; Liang, L.; Zhang, Y.; Li, J.; Zhang, L.; Ye, F.; Gan, Z.; Zhang, K.Q. Purification and Cloning of a Novel Serine Protease from the Nematode-Trapping Fungus Dactylellina varietas and Its Potential Roles in Infection Against Nematodes. Appl. Microbiol. Biotechnol. 2007b, 75 (3), 557–565. Zhang, Y.; Liu, X.; Wang, M. Cloning, Expression, and Characterization of Two Novel Cuticle-Degrading Serine Proteases from the Entomopathogenic Fungus Cordyceps sinensis. Res. Microbiol. 2008, 159 (6), 462–469. Minglian, Z.; Minghe, M.; Keqin, Z. Characterization of a Neutral Serine Protease and its Full-Length cDNA from the Nematode-Trapping Fungus Arthrobotrys oligospora. Mycologia 2004, 96 (1), 16–22. Bonants, P. J.; Fitters, P. F.; Thijs, H.; den Belder, E.; Waalwijk, C.; Henfling, J. W. D. A Basic Serine Protease from Paecilomyces lilacinus with Biological Activity Against Meloidogyne hapla Eggs. Microbiology 1995, 141 (4), 775–784. Morton, C. O.; Hirsch, P. R.; Peberdy, J. P.; Kerry, B. R. Cloning of and Genetic Variation in Protease VCP1 from the Nematophagous Fungus Pochonia chlamydosporia. Mycol. Res. 2003, 107 (1), 38–46. Seidl, V. Chitinases of Filamentous Fungi: A Large Group of Diverse Proteins with Multiple Physiological Functions. Fungal Biol. Rev. 2008, 22 (1), 36–42. Takaya, N.; Yamazaki, D.; Horiuchi, H.; Ohta, A.; Takagi, M. Intracellular Chitinase Gene from Rhizopus oligosporus: Molecular Cloning and Characterization. Microbiology 1998, 144 (9), 2647–2654. Tikhonov, V. E.; Lopez-Llorca, L. V.; Salinas, J.; Jansson, H. B. Purification and Characterization of Chitinases from the Nematophagous Fungi Verticillium chlamydosporium and V. suchlasporium. Fungal Genet. Biol. 2002, 35 (1), 67–78. Sahebani, N.; Hadavi, N. Biological Control of the Root-Knot Nematode Meloidogyne javanica by Trichoderma harzianum. Soil Biol. Biochem. 2008, 40 (8), 2016–2020. Chérif, M.; Benhamou, N. Cytochemical Aspects of Chitin Breakdown during the Parasitic Action of a Trichoderma sp. on Fusarium oxysporum f. sp. radicislycopersici. Phytopathology 1990, 80 (12), 1406–1414. Chet, I. Trichoderma-Application, Mode of Action and Potential as Biocontrol Agent of Soilborn Plant Pathogenic Fungi. In Innovative Approaches to Plant Disease Control; Chet, I., Ed.; John Wiley & Sons: New York, 1987; pp 137–160.

198

Plant Pathogens: Detection and Management for Sustainable Agriculture

49. Rao, M. S.; Reddy, P. P.; Nagesh, M. Evaluation of Plant Based Formulations of Trichoderma harzianum for the Management of Meloidogyne incognita on Egg Plant. Nematologia Mediterranea 1998, 26 (1), 59–62. 50. Sharon, E.; Bar-Eyal, M.; Chet, I.; Herrera-Estrella, A.; Kleifeld, O.; Spiegel, Y. Biological Control of the Root-Knot Nematode Meloidogyne javanica by Trichoderma harzianum. Phytopathology 2001, 91 (7), 687–693. 51. Windham, G. L.; Windham, M. T.; Williams, W. P. Effects of Trichoderma spp. on Maize Growth and Meloidogyne arenaria Reproduction. Plant Dis. 1989, 73 (6), 493–495. 52. Seifullah, P.; Thomas, B. J. Studies on the Parasitism of Globodera rostochiensis by Trichoderma horzianum Using Low Temperature Scanning Electron Microscopy. Afro-Asian J. Nematol. 1996, 6, 117–122 53. Suarez, B.; Rey, M.; Castillo, P.; Monte, E.; Llobell, A. Isolation and Characterization of PRA1, a Trypsin-Like Protease from the Biocontrol Agent Trichoderma harzianum CECT 2413 Displaying Nematicidal Activity. Appl. Microbiol. Biotechnol. 2004, 65 (1), 46–55. 54. Bedoya-Escobar, V. I.; Naranjo-Mesa, M. S.; Restrepo-Moreno, A. Detection of Proteolytic Enzymes Released by the Dimorphic Fungus Paracoccidioides brasiliensis. J. Med. Vet. Mycol. 1993, 31 (4), 299–304. 55. Tosi, S.; Annovazzi, L.; Tosi, I.; Iadarola, P.; Caretta, G. Collagenase Production in an Antarctic Strain of Arthrobotrys Tortor Jarowaja. Mycopathologia 2002, 153 (3), 157–162. 56. Schenck, S.; Chase, T.; Rosenzweig, W. D.; Pramer, D. Collagenase Production by Nematode-Trapping Fungi. Appl. Environ. Microbiol. 1980, 40 (3), 567–570. 57. Schalchli, H.; Tortella, G.R.; Rubilar, O.; Parra, L.; Hormazabal, E.; Quiroz, A. Fungal Volatiles: An Environmentally Friendly Tool to Control Pathogenic Microorganisms in Plants. Crit. Rev. Biotechnol. 2016, 36 (1), 144–152. 58. Fischer, G.; Schwalbe, R.; Möller, M.; Ostrowski, R.; Dott, W. Species-Specific Production of Microbial Volatile Organic Compounds (MVOC) by Airborne Fungi from a Compost Facility. Chemosphere 1999, 39 (5), 795–810. 59. Freire, E. S.; Campos, V. P.; Pinho, R. S. C.; Oliveira, D. F.; Faria, M. R.; Pohlit, A. M.; Noberto, N. P.; Rezende, E. L.; Pfenning, L. H.; Silva, J. R. C. Volatile Substances Produced by Fusarium oxysporum from Coffee Rhizosphere and Other Microbes Affect Meloidogyne incognita and Arthrobotrys conoides. J. Nematol. 2012, 44 (4), 321–328. 60. Riga, E.; Lacey, L. A.; Guerra, N. Muscodor Albus, a Potential Biocontrol Agent Against Plant-Parasitic Nematodes of Economically Important Vegetable Crops in Washington State, USA. Biol. Control 2008, 45 (3), 380–385. 61. Cho, M. R.; Na, S. Y.; Yiem, M. S. Biological Control of Meloidogyne arenaria by Pasteuria penetrans. J. Asia-Pacific Entomol. 2000, 3 (2), 71–76. 62. Timper, P.; Kone, D.; Yin, J.; Ji, P.; Gardener, B. B. M. Evaluation of an AntibioticProducing Strain of Pseudomonas fluorescens for Suppression of Plant-Parasitic Nematodes. J. Nematol. 2009, 41 (3), 234 p. 63. Bagheri, N.; Ahmadzadeh, M.; Heydari, R. Effects of Pseudomonas fluorescens Strain UTPF5 on the Mobility, Mortality and Hatching of Root-Knot Nematode Meloidogyne javanica. Arch. Phytopathol. Plant Protect. 2014, 47 (6), 744–752.

Role of Biological Agents

199

64. Ashoub, A. H.; Amara, M. T. Biocontrol Activity of Some Bacterial Genera Against Root-Knot Nematode, Meloidogyne incognita. J. Am. Sci. 2010, 6 (10), 321–328. 65. Oliveira, D. F.; Campos, V. P.; Amaral, D. R.; Nunes, A. S.; Pantaleão, J. A.; Costa, D. A. Selection of Rhizobacteria Able to Produce Metabolites Active Against Meloidogyne exigua. Eur. J. Plant Pathol. 2007, 119 (4), 477–479. 66. Wei, L.; Shao, Y.; Wan, J.; Feng, H.; Zhu, H.; Huang, H.; Zhou, Y. Isolation and Characterization of a Rhizobacterial Antagonist of Root-Knot Nematodes. PloS One 2014, 9 (1), e85988. 67. Xiong, J.; Zhou, Q.; Luo, H.; Xia, L.; Li, L.; Sun, M.; Yu, Z. Systemic Nematicidal Activity and Biocontrol Efficacy of Bacillus firmus Against the Root-Knot Nematode Meloidogyne incognita. World J. Microbiol. Biotechnol. 2015, 31 (4), 661–667. 68. Adam, M.; Heuer, H.; Hallmann, J. Bacterial Antagonists of Fungal Pathogens Also Control Root-Knot Nematodes by Induced Systemic Resistance of Tomato Plants. PloS One. 2014, 9 (2), e90402. 69. Padgham, J. L.; Sikora, R. A. Biological Control Potential and Modes of Action of Bacillus megaterium Against Meloidogyne graminicola on Rice. Crop Protect. 2007, 26 (7), 971–977. 70. Dickson, D. W.; Oostendorp, M.; Giblin-Davis, R. M.; Mitchell, D. J. Control of Plant-Parasitic Nematodes by Biological Antagonists. Pest Manag. Subtrop., Biol. Control - FL Perspect. 1994, 575–601 71. Oostendorp, M.; Sikora, R. A.; Seed Treatment with Antagonistic Rhizobacteria for the Suppression of Heterodera schachtii Early Root Infection of Sugar Beet. Rev. Nematol. 1989, 12 (1), 77–83. 72. Sayre, R. M.; Starr, M. P. Bacterial Diseases as Antagonists of Nematodes. In Diseases of Nematodes, Poinar, G. O, Jansson, H. B., Eds.; CRC Press: Boca Raton, FL, 1988; Vol. 1, pp 70–101. 73. Chen, Z. X.; Dickson, D. W.; McSorley, R.; Mitchell, D. J.; Hewlett, T. E. Suppression of Meloidogyne Arenaria Race 1 by Soil Application of Endospores of Pasteuria penetrans. J. Nematol. 1996, 28 (2), 159–168. 74. Hewlett, T. E.; Cox, R.; Dickson, D. W.; Dunn, R. A. Occurrence of Pasteuria spp. in Florida. J. Nematol. 1994, 26 (4S), 616–619. 75. Weibelzahl-Fulton, E.; Dickson, D. W.; Whitty, E. B. Suppression of Meloidogyne incognita and M. javanica by Pasteuria penetrans in Field Soil. J. Nematol. 1996, 28 (1), 43–49. 76. Mankau, R.; Imbriani, J. L.; Bell, A. H. SEM Observations on Nematode Cuticle Penetration by Bacillus penetrans. J. Nematol.1976, 8 (2), 179–181. 77. Sayre, R. M.; Wergin, W. P. Bacterial Parasite of a Plant Nematode: Morphology and Ultrastructure. J. Bacteriol. 1977, 129 (2), 1091–1101. 78. Li, B.; Xie, G. L.; Soad, A.; Coosemans, J. Suppression of Meloidogyne javanica by Antagonistic and Plant Growth-Promoting Rhizobacteria. J. Zhejiang Univ. Sci. B 2005, 6 (6), 496–501. 79. Insunza, V.; Alström, S.; Eriksson, K. B. Root Bacteria from Nematicidal Plants and Their Biocontrol Potential Against Trichodorid Nematodes in Potato. Plant Soil 2002, 241 (2), 271–278.

200

Plant Pathogens: Detection and Management for Sustainable Agriculture

80. Ali Siddiqui, I.; Ehetshamul‐Haque, S.; Shahid Shaukat, S. Use of Rhizobacteria in the Control of Root Rot–Root Knot Disease Complex of Mungbean. J. Phytopathol. 2001, 149 (6), 337–346. 81. Cobb, N.A. A genus of Free-Living Predatory Nematodes: Contributions to a Science of Nematology VI: (With 75 Illustration in the Text). Soil Sci. 1917, 3 (5), 431–486. 82. Steiner, G.; Heinly, H. The Possibility of Control of Heterodera radicicola and Other Plant-Injurious Nemas by Means of Predatory Nemas, Especially by Mononchus papillatus Bastian. J. Washington Acad. Sci. 1922, 12 (16), 367–386. 83. Khan, Z.; Kim, Y. H. A Review on the Role of Predatory Soil Nematodes in the Biological Control of Plant Parasitic Nematodes. Appl. Soil Ecol. 2007, 35 (2), 370–379. 84. Webster, J. M. Nematode and Biological Control. In Economic Nematology; Webster, J. M. Ed.; Academic Press: New York, 1972; p 563. 85. Lal, A.; Sanwal, K.C.; Mathur, V. K. Changes in the Nematode Population of Undisturbed Land with the Introduction of Land Development Practices and Cropping Sequences. Indian J. Nematol. 1983, 13 (2), 133–140. 86. Small, R. W. The Effects of Predatory Nematodes on Populations of Plant Parasitic Nematodes in Pots. Nematologica 1979, 25 (1), 94–103. 87. Meyer, S. L. United States Department of Agriculture–Agricultural Research Service Research Programs on Microbes for Management of Plant‐Parasitic Nematodes. Pest Manag. Sci. 2003, 59 (6–7), 665–670. 88. Kerry, B. R. Rhizosphere Interactions and the Exploitation of Microbial Agents for the Biological Control of Plant-Parasitic Nematodes. Ann. Rev. Phytopathol. 2000, 38 (1), 423–441. 89. Barker, K.R. Perspectives on Plant and Soil Nematology. Ann. Rev. Phytopathol. 2003, 41 (1), 1–25. 90. Davies, K. G. Interactions between Nematodes and Microorganisms: Bridging Ecological and Molecular Approaches. Adv. Appl. Microbiol. 2005, 57, 53–78. 91. Dong, L. Q. Zhang, K. Q. Microbial Control of Plant-Parasitic Nematodes: A FiveParty Interaction. Plant Soil 2006, 288 (1–2), 31–45. 92. Barker, K. R.; Koenning, S. R. Developing Sustainable Systems for Nematode Management. Ann. Rev. Phytopathol.1998, 36 (1), 165–205. 93. Meyer, S. L.; Roberts, D. P. Combinations of Biocontrol Agents for Management of Plant-Parasitic Nematodes and Soilborne Plant-Pathogenic Fungi. J. Nematol. 2002, 34 (1), 1–8.

CHAPTER 9

Principles and Concepts of Integrated Nematode Management in Major Crops B. S. SUNANDA1,* and RAVULAPENTA SATHISH2

Assistant Scientific Officer (Nematology) and Centre In-charge, AICRP (Nematode) 1

Senior Research Fellow (Entomology), National Institute of Plant Health Management (NIPHM), Hyderabad 500030, India

2

*

Corresponding author. E-mail: [email protected]

ABSTRACT Plant parasitic nematodes are hidden enemies of crops. The symptoms of the damage they cause are not easily recognizable. Their microscopic size further reduces the chances of being recognized as the causal organisms of any damage. Some nematodes predispose plants to other pathogens, while other nematodes act as various vectors. On a worldwide basis, these worms are estimated to cause crop yield losses of over US$ 78 billion. These losses are estimated to be over 14% in the developing countries and about 9% in the developed countries. For the management the use of disease or pathogen free planting materials is most recommended method of nematode exclusion. However, in case where there is no availability of such material, treatment of infected plant material is essential before planting. In current chapter we are summarizing the loss caused by nematode, historical development of nematode study, and their management strategies. 9.1 INTRODUCTION Erstwhile, the Andhra Pradesh state (which includes the present states of Andhra Pradesh and Telangana) is considered as seed hub of South

202

Plant Pathogens: Detection and Management for Sustainable Agriculture

India with more than 400 seed companies and seedling nurseries around Hyderabad. The state produces major cereals, millets, pulses, vegetables, fruits, and commercial crops like cotton, tobacco, and sugarcane. In addition, protected cultivation in polyhouses is catching up by mostly growing vegetables and cut flowers. Nematodes which are often least considered for management have become serious threats for majority of horticultural and field crops both under open field and protected cultivation. Though efforts on identification of plant-parasitic nematodes of Andhra Pradesh are very less but have started more than five decades ago. Progress on management of nematode diseases in Andhra Pradesh is limited to a few crops. In 2014, the state was bifurcated into Andhra Pradesh and Telangana. In the erstwhile Andhra Pradesh, universities such as Osmania University, Hyderabad and Acharya NG Ranga Agricultural University (now PJTSAU, Rajendranagar, Bapatla, and Tirupathi campuses), Hyderabad, national institutes like Directorate of Rice Research (now IIRR), Directorate of Oilseeds Research (IIOR), National Institute of Plant Health Management (NIPHM), and National Bureau of Plant Genetic Resources, (NBPGR) Regional Station and international institute, International Crops Research Institute for Semi-Arid Tropics conducted nematological activities. 9.1.1 AGRO CLIMATIC ZONES AND MAJOR CROPS OF ANDHRA PRADESH The agrarian state has a geographical area of 1,62,760 sq km spread over in 13 districts. The state is a part of the peninsular shield and has three physiographic divisions. There are five different types of soils to cultivate a wide range of crops. Red soils occupy about 65% of the state, while black soils account for about 25%. The alluvial soils of riverine and marine deposits occupy about 5% of the area. The others are coastal sands, laterite soils, and so on. Out of 162.76 lakh ha, 62.35 lakh ha (38.3 %) area is put to net cultivation including fisheries during 2014–15. The state has 36.63 lakh ha forest (22.5%) and 22.59 lakh ha (13.9%) fallow lands. Based on the amount and distribution of rainfall, the state has been divided into six Agro-climatic zones (Table 9.1) The rainfall of the state ranges between 500 mm in the scarce zone and 1400 and above, in high altitude tribal areas. Among the food crop grown, rice dominates in the state followed by sugarcane, groundnut, cotton, and mesta. Other principal crops grown are soghum, bajra, maize, ragi, horse gram, black gram, green

Principles and Concepts of Integrated Nematode Management

203

gram, red gram, cowpea, sesame, sunflower, and tobacco are popular. Horticulture sector also contributes to the state GDP. The major fruits cultivated are mango, banana, acid lime, orange, amla, plantations, guava, papaya, sapota, pomegranate, custard apple, musk melon, watermelon, and cashew nut. With regard to vegetables, tomato, brinjal, chili, onion, tapioca, cucurbits, beans, cabbage, cauliflower, and drumstick are the prominent ones. Commercial crops such as sugarcane, tobacco, turmeric, ginger, curry leaf, coconut, betel leaf, arecanut, tamarind, and coffee are also under cultivation. Flowers such as jasmine, rose, crossandra, marigold, and chrysanthemum provide income as well as employment. TABLE 9.1

Agro-climatic Zones of Andhra Pradesh.

Sl. No.

Agro climatic Zone

Districts

1

North coastal

Srikakulam, Vizayanagaram, and Visakhapatnam

2

Godavari zone

East Godavari and West Godavari

3

Krishna

Krishna, Guntur, and Prakasam

4

Southern

Chittoor, YSR Kadapa, and S.P.S.Nellore

5

Scarce rainfall

Kurnool and Ananthapur

6

High altitude and tribal

Srikakulam, Visakhapatnam and East Godavari

Source: Department of Agriculture, Andhra Pradesh (2014–2015).

The state has a total population of 49.83 million (Census, 2011), with density of 308 per sq km and literacy level of 67.41%. With these potentials, the state has gained first rank in terms of fish production, fish exports, and egg production. 9.1.2 AGRO CLIMATIC ZONES AND MAJOR CROPS OF TELANGANA The state is bestowed with diverse tropical and sub-tropical climatic conditions. The region has an area of 114.84 lakh ha and population of 352.87 lakhs as per 2011 census. The Krishna and Godavari rivers flow through the state from West to East. Based on climatic parameters that is, rainfall, soils, and cropping pattern and so on, the state (10 districts) is divided into four agro-climatic zones (Table 9.2). The agricultural planning for each zone is supported with the research and recommendations of Regional Agricultural Research Stations of Professor Jaya Shankar, Telangana State

Plant Pathogens: Detection and Management for Sustainable Agriculture

204

Agriculture University (PJTSAU) set up within each zone. More than 51% of the total geographical area is under cultivation and 23.89% under forest. Agriculture is dominated by rain-fed cultivation. TABLE 9.2

Agro Climatic Zones of Telangana.

Sl. no. Name of the zone

Districts

1

Northern Telangana zone

Karimnagar, Nizamabad, and Adilabad

2

Central Telangana zone

Warangal, Khammam, and Medak

3

Southern Telangana zone

Mahbubnagar, Nalgonda, and Rangareddy (+ Hyderabad)

4

High altitude and tribal areas zone

High altitude and tribal areas of Khammam and Adilabad districts

Source: Department of Agriculture Telangana (2014–2015).

In Telangana state crops grown in both Kharif and Rabi seasons put together cover an area of 53.15 lakh ha. The important crops grown are rice 14.15 lakh ha, maize 6.91 lakh ha, pulses 3.11 lakh ha, groundnut 0.12 lakh ha, cotton 16.93 lakh ha, chilies 0.73 lakh ha, and sugarcane 0.72 lakh ha. 75% of area was sown in kharif and the remaining area of 25% was cultivated in Rabi season during 2014–15. Horticulture sector in Telangana has emerged as a potential player in the economy. Enterprising and progressing farming community is willing to adopt new technologies that is, green houses, mulching, drip automation and so on. Horticulture sector contributes approximately 5.16% GSDP (Rs. 18,703 crores) of the state. Telangana stands 1st in turmeric production. In vegetables, it stands 11th in area and 13th in production. In case of fruits, the state stands 3rd in area and 8th in production. Vegetables constitute 71% of the total horticulture cropped area followed by spices and flowers. Export potential is very high for mango, banana and vegetables, and flowers. International Airport has Potential to become major export hub. 9.2 HISTORICAL DEVELOPMENTS OF NEMATOLOGY IN ANDHRA PRADESH AND TELANGANA STATES Research on nematodes in united Andhra Pradesh dates back to 1960s when V. M. Das first published his work on soil nematodes of Andhra Pradesh (Das, 1960). Root-knot nematode problem on tobacco led to creation of the post of nematologist by ICAR in Central Tobacco Research

Principles and Concepts of Integrated Nematode Management

205

Institute and early work on tobacco nematode management is classical from Andhra Pradesh. Several entomologists were trained in Nematology from the Agricultural University completing their Ph.Ds from the Division of Nematology, Indian Agricultural Research Institute, New Delhi in late 60s and early 70s. However, nematology work worth mentioning happened after the report of Kalahasti Malady from South zone of Andhra Pradesh and the classical work was done including development of resistant varieties of groundnut is a landmark in the history of Nematology. Nematology could not be established as a separate Division in the University of Agriculture till now. A nematologist position filled in Central Plant Protection and Training Institute, Hyderabad (now known as National Institute of Plant Health Management) started training in Nematology and also reported the widespread occurrence of white tip nematode on paddy in the region. A new regional station was started in 1985 by the National Bureau of Plant Genetic Resources of ICAR. Nematologist from NBPGR Regional Station, Hyderabad started operating for quarantine processing of global germplasm exchange and evaluation of germplasm for nematode resistance. In 1986, a nematologist post was filled in International Crops Research Institute for Semi-Arid Tropics and the work on survey to detect nematode problems, screening germplasm of groundnut, pigeon pea, and chickpea started systematically including the research on nematode management. Later, a nematologist post was filled in Directorate of Rice Research (now known as Indian Institute of Rice Research), Hyderabad. Rice nematode problems detection, germplasm screening, and their management received greater attention from the region. Indian Institute of Oilseeds Research filled its Nematologist position recently and the nematode problems of oilseeds started receiving attention. Some of the significant events in the history of nematology research in the erstwhile Andhra Pradesh are given below: • • •

1960—First Nematology Thesis on Soil Nematodes in India from Erstwhile Andhra Pradesh. 1971—Pigeon pea cyst nematode (Heterodera cajani) reported on pigeon pea in Andhra Pradesh. 1971—Distribution of (Heterodera avenae, H. zeae, H. cajani, and Anguinatritici) in India. Indian J. Nematol. 1, 106–111.

206

Plant Pathogens: Detection and Management for Sustainable Agriculture

•

1975–76—Kalahasti Malady, A Serious Disease Caused by Nematode, Tylenchorhynchus brevilineatus in Groundnut was Recorded from Nellore and Chittoor districts. 1984—A Nematode Disease of Peanut Caused by Tylenchorhynchus brevilineatus. Plant Dis., 68 (6), pp 526–529. 1979—Widespread Damage to Paddy due to White-tip Nematode, A. besseyi in Ranga Reddy District Around Hyderabad. 1979—A Serious Outbreak of White Tip Nematode Disease Aphelenchoides besseyi in Rice Crops at Hyderabad. Indian J. Plant Prot. 7, 218–219. 1986—Meloidogyne javanica Recognised as Pest on Acid Lime/ Citrus Orchards 1986—Occurrence of Meloidogyne javanica on Citurs in Andhra Pradesh (India). Int. Nematol. Network Newsl. 3, 9–10. 1978—Reported Banana Burrowing Nematode (Radopholus similis) in Major Banana Growing Areas of Andhra Pradesh. 1978—Occurrence and Distribution of Radopholus similis (Cobb, 1983) Thorne, 1949 in South India. Indian J. Nematol. 8, 49–58. 1991—Systematic Survey Conducted Root Knot Nematode (Meloidogyne incognita) Occurrence and Damage in Vegetables. 2008—Diversity and Community Structure of Major Plant Parasitic Nematodes in Selected Districts of Andhra Pradesh, India, Indian J. Nematol. 38, 68–74. 1994—Citrus Nematode Tylenchulus semipenetrans predominantly, Followed by Reniform Nematode Rotylenchulus reniformis, Spiral and Lesion Nematodes Recorded on Citrus. 1994—Occurrence and Distribution of Tylenchulus semipenetrans in Andhra Pradesh. Indian J. Nematol. 24, 106–111. 1995—First Report of Rice Root-knot Nematode, Meloidogyne graminicola. 1991—Reported Root-knot Nematode, (Meloidogyne javanica) Race-3 is an Important Nematode Parasite of Groundnut. 1991—Occurrence of Meloidogyne jauanica on Groundnut in Andhra Pradesh, India. Indian J. Nematol., 21, 166. 1995—Host Races of Meloidogyne jauanica, with Preliminary Evidence that the “Groundnut race” is Widely Distributed in India. Int. Arachis Newsl., 15: 43–44. 2001—Ufra Nematode Reported from Andhra

• • • • • • • • • • • • • • • •

Principles and Concepts of Integrated Nematode Management

• • • • • • • • •

207

2001—Ufra Nematode, (Ditylenchus angustus) is Seed Borne Crop Protection 21(1), 75–76. 2005—Record of Ufra Nematode, Ditylenchus angustus on Rice in Andhra Pradesh, India. Oryza 42 (3), 242–243. 2001—25% of Maize Growing Area Infested with Maize Cyst Nematode, Heterodera zeae 2006—Incidence of Meloidogyne incognita on Pomegranate was Reported from Anathapur District of Andhra Pradesh. 2007—A New Report of Root-knot Nematode, Meloidogyne incognita on Pomegranate, (punica granatum) from Andhra Pradesh. Indian J. Nematol. 2007, 37 (2), 201. 2006—M. incognita, Pratylenchus coffeae and Radopholus similis on Banana from Andhra Pradesh. 2006—Community Structure of Plant Parasitic Nematodes in Banana Plantations of Andhra Pradesh, India. Indian J. Nematol. 36, 209–212. 2014—Establishment of Separate Full fledge Nematology Laboratory at National Institute of Plant Health Management (NIPHM) Rajendranagar, Hyderabad. 2016—First Center of All India Coordinated Research Project on Nematodes and cropping systems, sanctioned by division of Nematology, ICAR – IARI, New Delhi NIPHM Hyderabad as voluntary Center of AICRP (Nematodes) vide F.No. CS 4-4/2014PP, September 7, 2016.

9.3 DIVERSITY OF PHYTO-NEMATODES IN ANDHRA PRADESH In view of diverse ecosystems and a large number of crops cultivated, huge nematode diversity is reported in the erstwhile Andhra Pradesh. An account of diversity of plant-parasitic nematode species and known races is given below: 9.3.1 SEDENTARY ENDO PARASITES Root knot nematodes, M. incognita, M. javanica, M. arenaria, and M. graminicola are reported. M incognita is a pest on pulses, oilseeds, cotton, vegetables, tuber crops, betel vine, and among the fruits, banana,

208

Plant Pathogens: Detection and Management for Sustainable Agriculture

pomegranate, muskmelon, and grapes. M. incognita is reported on several other hosts including corkwood tree. Prevalence of M. incognita race-2 was confirmed in tomato, chili, and brinjal ecosystems. M. javanica is reported to be pest on groundnut, vegetables including gherkin and banana. Race-3 of M. javanica on groundnut is prevalent in the south and scarce rainfall zones of Andhra Pradesh. M. arenaria on groundnut and M. graminicola mostly on upland rice are known to occur. Root-knot nematodes are a major problem in protected cultivation on vegetables and horticultural nurseries known from Telangana. Recently, M. enterolobii has become a menace for guava nurseries and cultivation in Telangana. Cyst nematodes, Heterodera cajani on pigeon pea and other pulses and H. zeae on maize are major pests while other cyst nematodes reported are H. sorghi on sorghum, H. raskii, and Bilobodera spon grasses are reported. H. cajani is also reported on castor from Telangana. 9.3.2 SEMI-ENDOPARASITES Reniform nematode is pest on maize, pulses particularly pigeon pea, oilseeds particularly castor, sunflower and groundnut, cotton, turmeric, vegetables, banana, grapes, acid lime, and sweet orange. Renifrom nematode is highly prevalent on grapes and castor in Telangana, while it occurs in the south zone of Andhra Pradesh on citrus species while on cotton it occurs in both AP and Telangana. Tylenchulus semipenetrans on acid lime and sweet orange was predominant among the plant parasitic nematode community having the highest absolute frequency, absolute density, and prominence value that were recorded maximum level in clay soils followed by clay loam, sandy loam, and laterite soils. Ufra nematode, Ditylenchus angustus has been found infecting irrigated rice in Godavari delta of Andhra Pradesh. 9.3.3 MIGRATORY ENDOPARASITES The Burrowing nematode, Radopholus similis is reported as pest on banana from coastal ecosystem and also known to infest several vegetables. Lesion nematodes reported on rice, maize, pulses, groundnut, cotton, vegetables, acid lime, sweet orange, and banana. Pratylenchus penetrans, P. pratensis, P. zeae, P. coffeae, P. thornei, and P. delattrei are predominant lesion nematode species. Lesion nematodes are important on rice, maize, cotton,

Principles and Concepts of Integrated Nematode Management

209

and vegetables both in Andhra Pradesh and Telangana. In Andhra Pradesh, lesion nematodes are pests mainly on banana, groundnut, and citrus. P. zeae on maize, P. coffeae on banana, and P. thornei on pulses deserve attention for further studies. Hirschmannella oryzae is a pest commonly encountered in irrigated rice ecosystems. 9.3.4 ECTOPARASITES Stunt, spiral, lance, dagger, and stubby root nematodes and several other ectoparasites are reported both from Telangana and Andhra Pradesh. Most important disease that attracted attention is Kalahasti malady of groundnut attributed to Tylenchorhynchus brevilineatus from the south zone of AP. Later in one of the surveys in ground affected with Kalahasti malady in south zone of AP, M. arenaria was also detected. T. capitatus, T. digitatus, and several other unknown species are reported to be associated with several crops. Among the spiral nematodes, Helicotylenchus multicinctus is the most important on banana, although it is reported on several other crops such as maize, pulses, oilseeds, and vegetables. Other species reported are H. dihystera, H. imperialis, H. incises, and so on. Several other ectoparasites are recorded in the rhizosphere of different crops that include Macroposthonia ornata, some species of Ditylenchus, Basirolaimus, Xiphinema, and Trichodorus. A large number of nonplant parasites (predators, parasites, entomopathogens, and other soil nematodes) are reported from Andhra Pradesh and Telangana which are not covered as it is beyond scope of this article. 9.4 MAJOR NEMATODE PROBLEMS OF THE STATE 9.4.1 NEMATODE DISEASE OF RICE Rice being a staple food crop is being infected by about 300 nematode species belonging to 35 genera. Among them, nematode species from ten genera are economically important in rice production of different agroecological conditions. Three are reported from Andhra Pradesh they are Ditylenchus angustus responsible for Ufra disease, Meloidogyne graminicola responsible for root knot-disease and Pratylenchus spp. causing lesion disease (Prasad et al., 2012).

Tomato, chilli, brinjal, okra, French Naidu et al. (2007) bean, gherkin, onion, bitter gourd, pulses, banana Tomato, chilli, gherkin, groundnut, pulses, paddy, sorghum, mango, marigold, crossandra, chrysanthemum Tomato, chilli, bitter gourd, and banana Tomato, chilli, brinjal, onion, groundnut, and pulses Groundnut, pulses, and paddy

Meloidogyne incognita race-2

Helicotylenchus sp.

Radopholus similis

Rotylenchulus reniformis

Tylenchorhynchus brevilineatus

Nellore

Tylenchorhychus brevilineatus

Groundnut

Cotton Rotylenchulus reniformis, Meloidogyne incognita, Pratylenchus pratensis, Haplolaimus spp., Tylenchorhychus spp., Xiphenema spp., Pratylenchus spp.

Khammam

Reddy et al. (1984)

Murali and Vanita Das (2014).

Tomato, brinjal, okra, chilli, onion, Prasad Rao et al. cabbage, ridge gourd, bitter gourd, (2007) snake gourd, cucurbits, beans, and cluster bean

Rotylenchulus reniformis, Helicotylenchus dihystera, Meloidogyne incognita, Pratylenchus delattrei, Hoplolaimus sp., Xiphinema sp., Tylenchorhynchus sp., Helicotylenchus incises, Tylenchus sp., Hirschmanniella oryzae, Aphelenchus sp., Tylenchorhynchus capitatus, Criconema sp., Meloidogyne javanica, Mononchus sp.

Kurnool, Kadapa, Prakasam, Mahaboobnagar, and Ananthapur

Source Sudheer et al. (2007)

Chittoor

Crop Pomegranate

Nematode

Meloidogyne incognita

District

Ananthapur

TABLE 9.3 Plant-parasitic Nematodes Reported from Different Districts of Erstwhile Andhra Pradesh State (Includes Present Telangana and Andhra Pradesh States) 210

Plant Pathogens: Detection and Management for Sustainable Agriculture

Crop

Tylenchorhynchus spp.,

Helicotylenchus spp.,

Neorylenchus spp.,

Pratylenchus spp.,

Basirolaimus spp.,

Xiphinema spp.,

Meloidogyne spp

Chittoor

Cuddapha

Godawari East

Godawari West

Guntur

Karimnagar

Khammam

Karnool

Aphelenchoides besseyi

Heterodera raskii n. sp.

Meloidogyne incognita race 2

Hyderabad

Hyderabad

Rangareddy

Warangal

Prakasam

Nellore

Tylenchulus semipenetrans,

Rotylenchulus reniformis,

Anantapur

Tomato, chilli, and brinjal

Bulb grass (Cyperusbulbosus)

Rice

Citrus

Nematode

Groundnut Bitylenchus brevilineatus, Pratylenchus spp, Basirolaimus spp., Tylenchorhynchus spp. Basiria spp., Ecphyadophora spp., Nothotylenchus spp., Sakia spp., and Tenunemelus sp. Heterodera spp. Meloidogyne spp. Rotylenchulus Reniformis

District

Chittore and Nellore

TABLE 9.3  (Continued) Source

Kiranbabu et al. (2011)

Basnet and Jayaprakash (1984).

Savitri et al. (1998)

Mani (1994)

Mani and Ratnakumar (1990).

Principles and Concepts of Integrated Nematode Management 211

Radopholus similis

Hoplolaimus seinhorsti

Tylenchorhynchus sp.

West Godavari, East Godavari, Guntur, Nellore

Rotylenchu ssp.

Rotylenchulus reniformis

West Godavari, East Godavari, Guntur, Nellore

Hyderabad

Hoplolaimu ssp.

West Godavari, East Godavari, Guntur, Nellore

East Godavari

Banana

Helicotylenchus multicinctus

West Godavari, East Godavari, Guntur, Nellore

M. javanica

Radopholus similis

West Godavari

Nellore

Banana

Pratylenchus coffeae

West Godavari, East Godavari, Guntur, Nellore

Cauliflower

Banana

Banana

Banana

Banana

Banana

Banana

Banana

Banana

Meloidogyne incognita

West Godavari, East Godavari, Guntur, Nellore

Crop

Nematode

District

TABLE 9.3  (Continued)

Luc (1957)

Sundararaju (2006)

Source

212 Plant Pathogens: Detection and Management for Sustainable Agriculture

Meloidogne incognita, Helicotylenchus sp., Helicotylenchus sp., Tylenchorhychus sp., Pratylenchus sp.

Rotylenchus reniformis

Meloidogne incognita, Pratylenchus sp., Hoplolaimus sp.

Warangal

Warangal

Warangal

Meloidogne incognita, Xiphinema sp., Helicotylenchus Okra sp., Tylenchorhychus sp., Pratylenchu ssp.

Warangal

Brinjal

Chilli

Tomato

Maize

Cotton

Maize

Rotylenchus reniformis

Heterodera zeae

AP

Sorghum

Heterodera sp., Helicotylenchus sp.

Heterodera sorghi

AP

Maize

Warangal

Pratylenchus thornei

Hyderabad

Crop

Warangal

Nematode

District

TABLE 9.3  (Continued)

Vindhyarani and Raghuramulu (2011)

Kaushal et al. (2007)

Sharma and Sharma (1988)

Singh and Khan (1981)

Source

Principles and Concepts of Integrated Nematode Management 213

214

Plant Pathogens: Detection and Management for Sustainable Agriculture

9.4.1.1 CROP LOSSES Estimation of crop losses due to these nematodes in Andhra Pradesh is not exactly assessed. However, 5% to 100% losses are reported from other epidemic states in case of Ufra disease, 16% to 32 % in root-knot disease and 13% to 33 % in lesion nematode incidence.

MAP 9.1

(See color insert.)

Principles and Concepts of Integrated Nematode Management

215

9.4.1.2 SYMPTOMS Infection of D. angustus causes mosaic or chlorotic discoloration in emerging leaves. Yellowish or pale green splash-patterns on affected leaves and leaf sheaths are noticed. The appearance of brown to dark brown spots on leaves and leaf sheaths is common. At the reproductive stage of crop, nematodes reach the space between the inner sides of imbricate whorl of leaf sheaths to feed on the ear primordia and developing ear heads. As a result, ear heads emerge in a twisted and crinkled manner with empty spikelet or do not emerge at all. The combined symptoms are called as Ufra. TABLE 9.4 Crop Wise Distribution of Plant Parasitic Nematodes in Andhra Pradesh and Telangana States. Sl. no.

Crop

Nematode reported

1

Maize

Helicotylenchus Pratylenchus zeae Heterodera zeae

2

Pulses

Pratylenchus coffeae Pratylenchus Meloidogynes spp Rotylenchulus reniformis Heterodera cajani Pratylenchus thornei Helicotylenchus spp.

3

Oilseed crops

Meloidogyne spp. Rotylenchulus reniformis Tylenchorhynchus spp. Helicotylenchus spp.

4

Vegetable crops

Meloidogyne spp. Rotylenchulus reniformis Tylenchorhynchus spp Helicotylenchus spp.

5

Fiber crops

Meloidogyne incognita Rotylenchulus reniformis Helicotylenchus spp. Pratylenchus spp.

216

Plant Pathogens: Detection and Management for Sustainable Agriculture

TABLE 9.4  (Continued) Sl. no.

Crop

Nematode reported

6

Banana

Helicotylenchus multicinctus Pratylenchus spp. Meloidogyne incognita Rotylenchulus reniformis Radopholus similis Pratylenchus spp.

7

Citrus

Tylenchulus semipenetrans

8

Grape

Meloidogyne incognita

9

Betelvine

Meloidogyne incognita

10

Tuber crops

Meloidogyne incognita

Rotylenchulus reniformis

Source: Economically Important Plant Parasitic Nematodes Distribution ATLAS–2010, ICAR, New Delhi.

Root-knot nematode affected plants show depletion in vigor, stunted growth, chlorotic, and curled leaves in nurseries and main field. The nematode infection is characterized by the formation of small galls near the tips of the roots. Excessive branching of affected roots occurs. In case of lesion nematode infestation, plant show chlorosis of leaves, stunted, and smothered growth in patches, swollen with water-soaked lesions which develop into black necrotic lesions on the root surface are noticed. Often infected roots decay, when such plants are pulled infected root portions and associated population remain in the soil. 9.4.1.3 MANAGEMENT Ufra disease 9.4.1.3.1 Cultural Management Burning of infested stubbles, preventing flood water from the river, completely drying fields when they are fallowed, plowing to destroy loci

Principles and Concepts of Integrated Nematode Management

217

of infection in stubbles and rotation with non-host crops are the best practices. Growing a non-host crop under crop rotation is also recommended. 9.4.1.3.2 Host Plant Resistance Cultivars such as IR63142-J8-B-2-1, Rayada 16-06, CN 540, NC 493, TCA 55, Brazil-65, Rayada 16-05, Rayada 16-06, Rayada 16-07, Rayada 16-08, Rayada 16- 011, Rayada 16-013, Ba Tuc, AR 9, IR 13437-20-P1, and IR 17643-4 are found tolerant to resistant to Ufra. 9.4.1.3.3 Chemical management It is managed by application of carbofuran @ 0.75 kg a.i. /ha at transplanting and 1.5 kg a.i. /ha in main field. Two foliar sprays with carbosulfan 40 EC at 0.2% followed by two sprays of triazophos 40 EC at 0.2% is also effective. 9.4.2 ROOT-KNOT NEMATODE 9.4.2.1 CULTURAL MANAGEMENT Soil application of FYM, Crop rotation with non-host crops which is, sweet potato, cowpea, sesamum, castor, sunflower, soybean, turnip, and cauliflower inhibit nematode development. In situ green manuring with marigold and burning of 15 cm deep rice hulls are also useful in reducing nematode population. 9.4.2.2 BIOLOGICAL MANAGEMENT Application of Pseudomonas flourescens @ 20 g/m2 was found to be effective in reducing the nematode numbers. Isolates of Trichoderma are also the potential biological control agents of M. graminicolain rice. 9.4.2.3 CHEMICAL MANAGEMENT Carbofuran, phorate, isazophos, cartap, carbosulfan, or quinalphos when given as soil application @ 1 kg a.i. /ha significantly reduce the root galling.

218

Plant Pathogens: Detection and Management for Sustainable Agriculture

9.4.3 PIGEON PEA CYST NEMATODE Heterodera cajani was found to cause 16%–34% of yield losses and in maize Rotylenchulus reniformis was reported to cause 8% losses. Three chickpea cultivars (N 31, N 59, and ICCC 42) and a promising chickpea breeding line (ICCV 90043) have been identified as tolerant to the rootknot nematode, and two promising short-duration pigeon pea breeding lines (ICPL 83024 and ICPL 85045) and selections from medium-duration lines (ICPLs 8357, 85068, 85073, 89050, 89051, and 90097) have been identified as tolerant to the reniform nematode (Sharma, 1997). 9.4.4 KALAHASTI MALADY OF GROUNDNUT During 1975–76, a severe disease of peanut characterized by reduction in pod size and brownish discoloration of pod surface was noticed near Kalahasti village of Andhra Pradesh and since then it is popularly known as Kalahasti malady. This disease was reportedly caused by the nematode Tylenchorhynchus breveliniatus (Reddy et al., 1984) 9.4.4.1 CROP LOSSES Estimation of crop losses due to Kalahasti malady was limited to visual estimation and was accounted to cause 40%–60% yield loss. 9.4.4.2 SYMPTOMS Affected plants have small, brownish yellow lesions on pegs, pod stalks, and developing young pods. The margins of the lesions will be slightly elevated because of the proliferation of host cells around the lesion. Pod stalks were reduced in length, kernel becomes discolored. Affected plants will be stunted and dark green in color. 9.4.4.3 MANAGEMENT Field application of aldicarb 10G or carbofuron 3G @ 6 kg a.i. /ha reduced the nematode population considerably (Reddy et al., 1984).

Principles and Concepts of Integrated Nematode Management

219

9.4.5 ROOT-KNOT NEMATODE IN POMEGRANATE Pomegranate, a commercial fruit crop of the state was found infested by Meloidogyne incognita in Ananthapur district during the survey conducted in kharif (2006). 9.4.5.1 CROP LOSSES Infested plants were stunted resulting in economic yield losses and more than 5-year-old plants were worst affected with small and shriveled fruits unfit for marketing. 9.4.5.2 DAMAGE SYMPTOMS Infested plants exhibited yellowing of foliage resulting in stunted plant growth with less number of fruits or undersize fruits or no fruits which might be due to the nematode-induced nutritional deficiency. In severe cases, galls were predominantly found on entire root system. The young galls were white in color turned to light brown and hardy when they became old. The intensity of root-knot nematode damage increased with increase in age of the plant. Five-year old plants were severely affected by root-knot nematode (Sudheer et al., 2007). 9.4.5.3 MANAGEMENT There are technologies officially communicated or recommended for management of this nematode in pomegranate. However, farmers are tackling the problem on their own by adopting crop rotation and application of neem cake. 9.4.6 LESION NEMATODE 9.4.6.1 CULTURAL MANAGEMENT Crop rotation with Phaseolus radiates decreases the root-lesion nematode, application of neem or mahua, mustard, karanj, pongamia, groundnut, or

220

Plant Pathogens: Detection and Management for Sustainable Agriculture

cotton cakes will reduce the nematode population. Growing greengram or blackgram as inter crop or in rotation with rice also helps in reducing the populations of lesion nematodes 9.4.6.2 CHEMICAL MANAGEMENT Application of carbofuran or phorate @ 1 kg a.i./ha soil in the affected crops reduces the nematode injury and avert losses in grain yield up to 48.5%. 9.5 TECHNOLOGIES DEVELOPED Over the past four years, National Institute of Plant Health Management has been advocating ad-hoc recommendations for management of root-knot nematode which is most commonly noticed. Use of FYM and neem cake fortified with Paecilomyces lilacinus, Trichoderma viride, and Pseudomonas fluorescens is tested, found promising and recommended for poly houses especially for hybrid vegetables where pesticide residue is a major concern. Crop rotation with non-hosts has also been found in field conditions for vegetables such as tomato, chili, and brinjal to reduce root-knot nematode population. In case of guava, Meloidogyne enterolobii is of immediate concern of everyone stakeholder. Strict quarantine measures are advised to nursery units engaged in importing of seedlings. Field management of this nematode by integrated approach using chemicals and biocontrol agents is at final stage and after validation, it will be transferred to other farmers during next season. Besides this, Indian Institute of Rice Research (IIRR) is developing technologies for integrated nematode management in rice and also working on identification of resistant cultivars in collaboration with AICRP (Nematodes). In case of pigeon pea and chickpea ICRISAT has developed resistant lines but very limited literature is available about their practical exploitation. 9.6 EMERGING NEMATODE PROBLEMS 9.6.1 GUAVA DECLINE Guava decline, a deadly disease due to root-knot nematodes (Meloidogyne sp.) and Fusarium wilt disease complex is spreading at an alarming rate in

Principles and Concepts of Integrated Nematode Management

221

Andhra Pradesh and Telangana states. The disease was first time recorded from Rangareddy, Sangareddy, Medak, and Nalgonda districts of Telangana, and East and West Godavari districts of Andhra Pradesh by National Institute of Plant Health Management (NIPHM) in 2015. 9.6.1.1 CROP LOSSES In infected fields, incidence of this disease varied from 40% to 80% and in some nurseries, 90%–100% incidence was noticed. Nurseries growers had no other option but to destroy an entire lot of saplings in order to prevent its further spread and produce new healthy saplings. On an average 30%–60% yield loss is caused due to this disease and in severe cases, up to 100% loss is observed in guava orchards (Figs 9.1 and 9.2).

FIGURE 9.1 entrolobii.

(See color insert.) Guava orchard showing infestation of Meloidogyne

FIGURE 9.2 (See color insert.) Guava seedlings and roots showing galls and drying symptoms.

222

Plant Pathogens: Detection and Management for Sustainable Agriculture

9.6.1.2 SYMPTOMS It causes chlorosis, stunted growth, wilting, extensive root galling, partial to complete rotting of roots which ultimately cause death of plants both in nurseries and orchards. The symptoms start with yellowing of plants followed by withering, giving the tree barren look and roots revealing a dirty root appearance with beaded knots. Plants become flaccid, broken reveal a hollow twig. Wilted leaves, leaf dropping, drying of branches, and decline in productivity are also witnessed. Underground symptoms included root galls and partially rotted roots. Roots are completely galled of varying size with a dirty appearance and many of them were compound galls. In association with the wilt causing fungi, there is extensive rotting of roots and death of plants within months. 9.6.1.3 MANAGEMENT 9.6.1.3.1 Cultural Practices • • • •

Movement of nematode infected root stocks across the states should be strictly restricted. Use of nematode-free saplings for planting. Removal and destruction of nematode infected saplings or trees. Maintaining the orchard free from weeds and alternate hosts.

9.6.1.3.2 Nematode Management in Nurseries Treatment of soil mixture used for raising guava rootstocks: •

•

A ton of soil mixture has to be mixed with 50–100 kg of neem cake or pongamia cake enriched with the bio-pesticides such as 1 kg Paecilomyces lilacinus, 1 kg Pseudomonas fluorescens, and 1 kg Trichoderma harzianum. 5 kg of Carbofuran/phorate can also be added to one ton of soil mixture.

Principles and Concepts of Integrated Nematode Management

223

9.6.1.3.3 Integrated Management Practices • •

•

•

• • •

Apply 3–4 kg of bio-pesticide enriched vermicompost/farm yard manure (FYM)/compost per plant at an interval of 3–4 months. Mix 20 kg of bio-pesticide enriched neem cake/pongamia cake in 200 L water, leave it for two days. This can be used for drenching @ 2–3 L/plant or filter it thoroughly and use it for sending along with the drip, once at an interval of 15–20 days. Farmers have been advised to apply carbofuron 3G @ 100 g/plant mixed with 1 kg sand to facilitate uniform application around the trunk of each plant. After 15 days, apply neem cake @ 500 g/plant fortified with Trichoderma viridi, Pseudomonas fluroscens, and Paecilomyces lilicinous bio-control agents (100:2:2:1). Neem cake will act as bio nematicide and bio-control agent will restrict the growth of the parasitic nematodes by way of parasitism, competition, and suppression. For edible and fleshy fruit crops application of neem cake fortified with bio-control agents and the use of neem oil for drenching are safe. Use FYM 15 kg/plant as source of nutrition fortified with Trichoderma and Pseudomonas (100:1:1) to enhance the impact of biocontrol agents and encourage early recovery. It is advised to apply neem cake 200 g/pit fortified with bioagents at the time of planting as a precautionary measure. As a precautionary measure, farmers should avoid infested seedlings for planting. For nursery operators, proper soil solarisation is recommended to cure their potting soil for nematodes and other microorganisms. The chemical soil fumigants available in the market shall be used under the supervision of plant protection officials.

Both in Telangana and Andhra Pradesh, new nematode problems are emerging every year. Due to poor knowledge of plant-parasitic nematode diseases and their symptoms among the growers, often nematode diseases go unnoticed. Adoption of modern cultivation technologies such as polyhouse cultivation, greenhouse, and shade house cultivation has attracted the attention toward nematode diseases. Because nematodes have become number one enemies of all these protected cultivation practices. In both the states, flower and vegetable crops under protected cultivation are suffering from severe nematode diseases. In open field also, vegetables

224

Plant Pathogens: Detection and Management for Sustainable Agriculture

such as tomato, brinjal, chili, okra, capsicum, and so on are suffering from various kind of nematode infestations. Field crops such as pigeon pea, rice, and groundnut are no longer free from nematodes. The synergistic effect of nematode and wilt causing Fusarium spp. in pigeon pea has become a complex challenge for breeders and pathologists. Horticulture is the major revenue generating sector in both the states and is very lucrative. Many are engaged in nursery entrepreneurship importing and marketing of various fruits, flowers, and hybrid seedlings. However, nematodes are hindering this market, especially quarantine nematodes. Recently NIPHM has identified Root-knot nematode Meloidogyne enterolobaii based on perennial pattern in guava fields causing severe wilt and death of affected trees. The source was traced to the guava seedlings imported from Taiwan and Bangladesh. This quarantine nematode has caused complete loss of affected guava orchards. Recently the Project Coordinator, All India Coordinated Research Project (AICRP), Nematodes and his team have visited the affected orchards and prepared an action plan to mitigate this problem in coordination with NIPHM. 9.7 MAJOR EXTENSION ACTIVITIES Management of nematode disease was a major challenge among the farmers of both Telangana and Andhra Pradesh. In order to educate farmers and disseminate the technologies for effective management, various extension activities were implemented regularly by nematology section of NIPHM across both the states. • • • •

About 12 on campus and 7 off-campus trainings were organized to farmers for creating awareness about nematode diseases, their symptoms, economic importance, and management. Over the past four years, more than 300 farmers’ fields were visited for diagnosis of nematode diseases and recommended management practices. Demonstrations were organized for nematode management in vegetables using organic amendments mixed with biopesticides. 19 exclusive training programs on nematodes were organized to the ICAR/SAU/KVK scientists, agriculture, horticulture, and extension officials from state Department of Agriculture on detection and diagnosis of nematode disease in fields and poly houses.

Principles and Concepts of Integrated Nematode Management

• • •

•

• •

225

Participated in exhibitions, kisan melas, and workshops to showcase the technologies of eco-friendly management of plant-parasitic nematodes. Information on nematodes was published in pamphlets, bulletins, and folders in local language and distributed among the farmers. A one-day workshop was organized to horticultural officers and nursery growers at Kadiyam, Rajmandary in Andhra Pradesh in collaboration with Nursery Growers Association to sensitize about the importance of quarantine nematodes in guava and its management. Stake holders’ meetings are also organized especially of protected cultivation growers and progressive horticultural farmers to get the feedback of technologies transferred and revalidation of adopted technologies. Analysis of soil for nematode infestation and issuing test report for the establishment of new polyhouses growers. Providing consultancy service for the farmers about nematode management in horticulture crops.

9.8 SUCCESS STORIES OF TECHNOLOGY ADOPTION AND NEMATODE MANAGEMENT Response to technology adoption in nematode management is very good in case of guava cultivation. However, the result is very quick and encouraging in protected cultivation. Numbers of poly houses around Hyderabad and guava growers have been adopted nematode control measures suggested by NIPHM and are successfully operating. KEYWORDS • • • • •

nematode horticultural crops economic loss symptomology management stratgies

226

Plant Pathogens: Detection and Management for Sustainable Agriculture

REFERENCES Basnet, C. P.; Jayaprakash, A. Heterodera raskiin. sp. (Heteroderidae: Tylenchina), a Cyst Nematode on Grass from Hyderabad. J. Nematol. 1984, 16 (3), 213–216. Das, V. M. Studies on Nematode Parasites of Plants in Hyderabad. Zeitschriftt fur Prasitenkunde 1960, 19, 553–605. Joshi, P. K.; Singh, N. P.; Singh, N. N.; Gerpacio, R. V.; Pingali, P. L. Maize in India: Production Systems, Constraints and Research Priorities; D.F., CIMMYT: Mexico, 2005. Kaushal, K. K.; Srivastava, A. N.; Pankaj, Chawla, G.; Singh, K. Cyst forming nematodes in India: A Review. Indian J. Nematol. 2007, 37, 1–7. Kiranbabu, T.; Raghuprakash, K. R.; Varaprasad, K. S.; Sivaramakrishnan, S.; Anuradha, G. Identification of Prevalent Race of Root Knot Nematode in Ranga Reddy District of Andhra Pradesh. Pest Manag. Horticult. Ecosyst. 2011, 17 (2), 156–158. Koshy, P. K.; Swarup, G. Distribution of Heterodera avenae, H. zeae, H. cajani and Anguina tritici in India. Indian J. Nematol. 1971, 1, 106–111. Mani, A. Occurrence of Meloidogyne javanica on citurs (India) Int. Nematol. Netwk. News 1986, 3, 9–10. Mani, A.; Ratna Kumar. Plant Parasitic Nematodes Associated with Groundnut in Andhra Pradesh. Indian J. Nematol. 1990, 20 (1), 44–48. Mani, A. Occurrence and Distribution of Tylenchulus semipenetrans in Andhra Pradesh. 1994, 24 (2), 106–111. Murali, A.; Vanita Das, V. Biodiversity of Plant Parasitic Nematodes Associated with Cotton in Khammam District of Andhra Pradesh, India. Inter. J. Pharm. 2014, 5 (10), 795–797. Naidu H.; Harinath, P.; Haritha, V.; John Sudheer, M. Community Analysis of Plant Parasitic Nematodes in Chittoor district of Andhra Pradesh. Ind. J. Nematol. 2007, 37 (2), 207–211. Prasad, J. S.; Somasekhar, N.; Varaprasad, K. S. Status of Rice Nematode Research in India, 2012; pp 1–7, http://www.rkmp.co.in. Prasada Rao, G.M.V.; John Sudheer, M.; Priya, P. Community Analysis of Plant Parasitic Nematodes Associated with Vegetable Crops in Selected Districts of Andhra Pradesh. Ind. J. Nematol. 2007, 37 (2), 221–213. Reddy, D. D. R.; Subrahmanyam, P.; Sankara Reddy, G. H.; Raja Reddy, C.; Siva Rao, D. V. A Nematode Disease of Peanut Caused by Tylenchorhynchus brevilineatus. Plant Dis. 1984, 68, 526–529. Savitri, H.; Wahab, T.; Sattar, M. A.; Reddy, B. M.; Wahab, T. Prevalence of White Tip Nematode (Aphelenchoides besseyi Christie) in Rice Samples of Andhra Pradesh. J. Res. 1998, 26, 74–76. Sharma, R.; Prasad, J. S. First Record of Meloidogynegraminicola on Rice in Andhra Pradesh. Oryza 1995, 32, 59. Sharma, S. B. In Diagnosis of Key Nematode Pests of Chickpea and Pigeonpea and Their Management. Proceedings of a Regional Training Course, 25-30 Nov 1996, ICRISAT, Patancheru, India. Patancheru 502 324, Andhra Pradesh, India: International Crops Research Institute for the Semi-Arid Tropics, 1997, p 112. Sharma, S. B.; Sharma, R. Occurrence of the Sorghum Cyst Nematode, f-Ieteroderasorghi in Andhra Pradesh. Ind. J. Nematol. 1988, 18, 329.

Principles and Concepts of Integrated Nematode Management

227

Singh, D. B; Khan, E. Morphological Variations in Populations of Pratylenchus thornei Sher and Allen, 1953. Ind. J. Nematol. 1981, 11, 53–60. Sudheer; Mohan, J.; Kalaiarasan, P.; Senthamarai, M. Report of Root-Knot Nematode, Meloidogyne incognita on Pomegranate, Punicagranatum L. from Andhra Pradesh. Ind. J. Nematol. 2007, 3 (2), 201–202. Sundararaju, P. Community Structure of Plant Parasitic Nematodes in Banana Plantations of Andhra Pradesh, India. Indian J. Nematol. 2006, 36 (2), 209–212. Vindhya Rani, P.; Raghu Ramulu, G. Distribution of Plant–Parasitic Nematodes in Selected Agro-ecosystems. Asian J. Animal Sci. 2011, 6 (2), 203–205.

PART III Biocontrol

CHAPTER 10

Lichens: A Novel Group of Natural Biopesticidal Sources VINAYAKA S. KANIVEBAGILU* and ARCHANA R. MESTA

Department of Botany, Kumadvathi First Grade College, Shimoga Road, Shikaripura 577427, Shimoga, Karnataka, India *

Corresponding author. E-mail: [email protected]

ABSTRACT Lichens are commonly used as spices and they have been used in traditional medicine from age-old days in various parts of India and world. The lichens have unique secondary metabolites when compared with higher plants and have found their uses in many fields such as medicine, dyes, cosmetics, deodorants, preservatives, and also in biopesticides. Large quantities of agricultural products are wasted every year due to insects, pests, and weeds. Various chemicals have been used to overcome this problem. The synthetic pesticides have an adverse effect on the health of human beings and other creatures and also lead to different types of environmental pollution. There are about 800 known metabolites from lichens such as salazinic acid, usnic acid, gyrophoric acid, stictic acid, and so on. Among these secondary metabolites, most are found to have pesticidal effect. Barbatic acid and barbatolic acids show antimicrobial activity. Diffractaic acid and evernic acids are known for their fungicidal effects. Hence, the present study aims at the biological control of pests and insects by utilizing the lichen substances as a potential source. 10.1 INTRODUCTION Lichens are one of the important floral communities and they play a key role in ecological succession. Lichens are the simplest form of plants

232

Plant Pathogens: Detection and Management for Sustainable Agriculture

consisting of a symbiotic phenotype of nutritionally specialized fungi in association with green algae or cyanobacterium. The phycobiont help in food synthesis through photosynthesis mechanism; mycobiont gives protection to the algae. Lichens were well known as the first colonizer of xeric succession on the earth1 and are distributed in all forms of environments from cold desert to evergreen forests of the tropical regions. There are a wide range of habitats throughout the world which dominate about 8% of terrestrial ecosystem. About 20,000 lichens are reported from all over the world. Higher level of defense chemicals are produced in the organisms which grow slowly in the low resource habitats.2 Lichens are very slow growing organisms; they are well known for their active metabolites, and mostly these compounds are synthesized by mycobiont of lichen.3 The metabolites produced by lichens are unique in nature. The lichen metabolites are weak acids as they help in the breakdown of sedimentary rocks and provide a loose substrate for other nonvascular and vascular plants. These secondary metabolites play an ecological role like antiallergens, antiherbivory in lichens.4 Lichen substances such as usnic acid, barbatic acid, fumaric acid, and protocetraric acids act as allergens and diffractic acid, barbatic acid, and isousnic acid affect the growth of higher plants.5,6 10.2 IMPORTANCE OF LICHENS These lichen substances have a wide range of uses. These are used in human and animal food, medicines, preparation of dyes, perfume industries, and also in the pollution monitoring problems. Lichens are capable of curing disease like blood and heart problems, brochiolities, antiobisity, piles, dyspepsia, scabies, digestive problems, and so on.7,8,9 Medicinal uses of lichens have been practiced since centuries in countries like America, Europe, China, and India.10 In recent years, researchers have focused on the application aspects of lichens. The pesticidal effect of lichen makes them aone important biological insecticide.11,12 10.3 HISTORY AND DEVELOPMENT OF BIOPESTICIDES Food is the basic necessity of all living organism including human beings. According to Food and Agricultural Organization (FAO), in 2001 the

Lichens: A Novel Group of Natural Biopesticidal Sources

233

population of the world was estimated to be 6.134 billion. The population of the world in 2016 was 7.4 billion and this population is found to be increasing year by year especially in developing countries. This increasing population requires additional agricultural production every year. To fulfill the requirement of additional agricultural products, the biodiverse agricultural land should not be converted into monoculture agricultural land. Instead, the scope toward the improvement in crop productivity should be encouraged. About 40–42% of the produced crops are destroyed by the pests, insects, diseases, and weeds.13,14 To overcome this problem many chemical fertilizers, pesticides, and insecticides have been used. The use of these synthetic pesticides and insecticides causes the environmental pollution such as water, air, and soil pollution; they also affect the health of humans and other organisms. This has made the researchers to think about the natural products from plants and other organisms as a potential source of pesticides and insecticides, which supports an eco-chemical method in the pest control.15 The uses of higher plants as antifungal, antimicrobial, insecticidal, and pesticidal material have been well documented in different parts of the world.16,17 In traditional methods plant parts like leaves and roots were used for protective storage of crops.18,19 Hence these are best source for the development of biochemical-based pesticides. Till today, about 6000 species of angiosperm belonging to 235 families have been recorded for anti-insect property.20 10.4 POTENTIAL UTILIZATION OF LICHEN METABOLITES The utilization of lichen as traditional medicine has been known since the time of very first civilization.21 Because of the presence of different secondary metabolites, lichens have been used for medicines, perfumes, cosmetics, dyes, food, and as pesticides. Many of the lichen substances exhibit antimicrobial, antioxidant, cytotoxic properties, and reported as potential source of pharmaceutically useful chemical.22 These lichen secondary metabolites have importance in ecological key roles for protecting against biotic (herbivore, competition) and abiotic (UV light) activities.23 The lichen having unusual chemical substances have potential bioactive sources used for development of novel biopesticides23 (Table 10.1). More than 50–60% of lichens showed with antibacterial or antibacterial or antiviral properties.24 Many researchers have been carried out to prove the antifungal and antimicrobial activity of the lichens.

Plant Pathogens: Detection and Management for Sustainable Agriculture

234 TABLE 10.1

Activity of Lichen Metabolites.

Sl. no. Compound name

Chemical class

Use or potential use

1.

(–)-16〈-hydroxykaurane

Diterpene

Cytotoxic

2.

(+) and (–) isousnic acid

Usnic acid

Antimicrobial fungicidal

3.

(+) and (–) usnic acid

Usnic acid

Antimicrobial fungicidal herbicidal

4.

16-O-acetylleucotylic acid

Triterpene

Antimicrobial

5.

7-acetoxy-22-hydro-hopane

Triterpene

Antimicrobial

6.

Alectosarmentin

Dibenzofuran

Antimicrobial

7.

Atranorin

para-depside

Fungitoxic

8.

Barbatic acid

Para-depside

PSII inhibitor

9.

Didymic acid

Dibenzofuran

Antimicrobial

10.

Diffractaic acid

Para- depside

Fungitoxic

11.

Durvilldiol

Triterpene

Antimicrobial

12.

Durvillonol

Triterpene

Antimicrobial

13.

Entothein

Dibenzopyranone

Bactericidal

14.

Epanorin

Pulvinic acid

Antifeedant

15.

Eulecanorol

Triterpene

Antimicrobial

16.

Fallacinal

Anthraquinone

Antimicrobial

17.

Friedelin

Triterpene

Antimicrobial

18.

Gyrophoric acid

Para-depside

PSII inhibitor

19.

Haemathamnolic acid

meta- depside

PSII inhibitor

20.

Hiascic acid

para- depside

Fungitoxic

21.

Lecanoric acid

para- depside

Fungitoxic PSII inhibitor

22.

Leprapinic acid

Pulvinic acids

Antibacterial

23.

Leucotylic acid

Triterpene

Antimicrobial

24.

Leucotylin

Triterpene

Antimicrobial

25.

Phlebic acid

Triterpene

Antimicrobial

26.

Pinastric acid

Pulvinic acids

Atiherbivory

27.

Polyporic acid

Terphenylquinone

Antibacterial

28.

Pulvinic dilactone

Pulvinic acids

Antifeedant

29.

Pyxinic acid

Triterpene

Antimicrobial

30.

Retigeranic acid

Triterpene

Antimicrobial

31.

Retigerdiol

Triterpene

Antimicrobial

32.

Rhizocarpic acid

Pulvinic acids

Antifeedant

33.

Rugulosin

Anthraquinone

Antimicrobial

Lichens: A Novel Group of Natural Biopesticidal Sources

235

TABLE 10.1  (Continued) Sl. no. Compound name

Chemical class

Use or potential use

34.

Stictaurin

Pulvinic acids

Antifeedant

35.

Taraxene

Triterpene

Antimicrobial

36.

Thiophanic acid

Xanthones

Fungicidal

37.

Thiophaninic acid

Xanthones

Fungicidal

38.

Triterpene C

Triterpene

Antimicrobial

39.

Triterpene D

Triterpene

Antimicrobial

40.

Ursolic acid

Triterpene

Cytotoxic

41.

Vulpinic acid

Pulvinic acids

Anti-herbivory

42.

Zeorin

Triterpene

antimycobacterial

10.4.1 ANTIFUNGAL ACTIVITY Antifungal and antimicrobial activity of extracts from Usnea species is experimentally proved.25 Different concentrations of lichen extracts have variable degree of lichen activity.26 Everniastrum cirrhatum, Nephroma arcticum, Parmelia tinctorum, Ramalina farinacea, Telochistes flavicans, and Usnea undulata show effective antifungal activity.27,28,29 Heterodermia leuocomela, E. cirrhatum, Leptogium sp., Lobaria sp., Cladonia species were effective against humans, plant, and mammalian pathogenic fungi.30,31 Letharia vulpine and Peltigera rufescens shows toxicity against Sitophilus granaries.32 10.4.2 ANTIMICROBIAL ACTIVITY Secondary metabolites like depsides and depsidones group of compounds such as pulvinic acid, usnic acid, aliphatic acids, and orcinol type are well known for their effective antimicrobial activity.33 Leishmanicidal and antiprotozoal activity of secondary metabolites from lichens were first reported by Fournet.34 Evernia prunastri, Everniastrum cirrhratum, Platismatia glauca, Parmelia flaventior, Parmotrema pseodotinctorum, Parmelia saxatilis, P. kamstachandalis, Ramalina hossei, R. pollinaria, R. polymorpha, Umbilicaria nylanderiana, and Usnea pictoides were well known for their antimicrobial activity35–42 (Table 10.1). Cladonia delicate, C. glauca,

236

Plant Pathogens: Detection and Management for Sustainable Agriculture

C. borbonica, Parmelia conspersa, P. physodes, P. rudecta, Thamnolia vermicularis, Umbilicaria papulosa, Xanthoria parietiana show antibacterial activity.43 The extracts from Rocella montagnei, Heterodermia burnetiae, R. hossei, and H. burnetiae are known to have an inhibitory effect against diseases like dental caries, burn, and urinary tract infections and other infections which are caused by the microorganisms such as Streptococcus aureus, Enterococcus faecalis, E. coli, and Klebsiella pneumonia.44 Usnic acid is reported for inhibitory effect against tuberculosis-causing bacteria45 and Staphylococcus cureus.46 10.4.3 INSECTICIDAL ACTIVITY Many lichen secondary metabolites are known for their insecticidal activity. Lichen substances such as usnic acid, selazinic acid, sekikaic acid, tannins, terpenoides, and steroids are well known for its insecticidal effect.47 The extracts of Heterodermia leucomela, P. tinctorum, P. pseudotictorum, Pyxine consocians, Ramalina nervulosa, R. pacifica, R. hossei, R. conduplicans, Rocella montagnei, Usnea galbinifera, and U. longissima are well known for their insecticidal, larvicidal, and antihelminthic activity.40,47–51 Some special compounds like 4-O-methylcryptochlorophaeic acid, lichexanthone, 3,6-dimethyl-2-hydroxy-4-methoxybenzoic acid, and cabraleadiol monoacetate showed significant larvicidal activity.51 10.4.4 ANTIHERBIVORY The growth of the plant is inhibited by many of the lichen substances.51–53 These lichen substances act as antifeedants for insects and animals.54–58 The secondary metabolites from lichens have the capacity to inhibit the seed germination in vascular plants and spore germination in mosses.55 10.5 CONCLUSION The use of synthetic pesticide causes dangerous environmental pollution and lead to the death of nontargeted organism. Hence, the use of biopesticide has been encouraged as there is no harm to the environment and also

Lichens: A Novel Group of Natural Biopesticidal Sources

237

to other organisms. The secondary metabolites produced by lichens were unique in nature and they have produced a diverse group of secondary metabolites like depsides, despidones, and pulvinic acid. The antimicrobial, antiinsecticidal, and antiherbivore properties of the lichen compounds have made the lichen as a potential source of biopesticide. KEYWORDS • • • • • • •

antiherbivorous antimicrobial biopesticides leishmanicidal lichen Ramalina secondary metabolite

REFERENCES 1. Taylor, T. N.; Hass, H.; Remy, W.; Kerp, H. The Oldest Fossil Lichen. Nature 1995, 378, 244–244. 2. Coley, P. D. Effect of Plant Growth Rate and Leaf Lifetime on the Amount and Type of Anti-herbivore Defense. Oecologia 1988, 74, 531–536. 3. Ahmadjian, V. The Lichen Symbiosis; Wiley: New York, 1993; p 250. 4. Lawrey, J. D. Lichen Secondary Compounds: Evidence for a Correspondence Between Antiherbivore and Antimicrobial Function. Bryologist 1989, 92, 326–328. 5. Follmann, G.; Nakagava, M. Keimhemmung von Angiospermensamen durch Flechtenstoffe. Naturwissenschaften 1963, 50, 696–697. 6. Huneck, S.; Scheiber, K.; Wachstumsregulatorische Eigenschaften von Flechten- und Moos- Inhaltsstoffen. Phytochemistry 1972, 11, 2429–2434. 7. Saklani, A.; Upreti, D. K. Folk Uses of Some Lichens in Sikkim. J. Ethnopharmacol. 1992, 27, 229–233. 8. Lal, B.; Upreti D. K. Ethnobotanical Notes on Three Indian Lichens. Lichenologist 1995, 27, 77–79. 9. Negi, H. R.; Kareem, A. Lichens: The Unsung Heroes. Amrut 1996, 1, 3–6. 10. Romagni, J. G., Dayan, F. E. Structural Diversity of Lichen Metabolites and Their Potential Use. In Advances in Microbial Toxin Research and its Biotechnological Exploitation; Upadhyay, R. K. Ed.; Kluwer Academic and Plenum Publishers: New York, 2002; pp 151–170.

238

Plant Pathogens: Detection and Management for Sustainable Agriculture

11. Dayan, F. E.; Romagni, J. G. Structural Diversity of Lichen Metabolites and Their Potential for Use. In Advances in Microbial Toxin Research and Its Biotechnological Exploitation; R. Upadhyaya, Ed.; Kluwer Academic/Plenum Publishers, 2002. 12. Emsen, B.; Yildirim, E.; Aslan, A.; Anar, M.; Ercisli, S. Insecticidal Effect of the Extracts of Cladonia foliacea (Huds.) Willd. and Flavoparmelia caperata (L.) Hale Against Adults of the Grain Weevil, Sitophilus granarius (L.) (Coleoptera: Curculionidae). Egypt. J. Biol. Pest Contr. 2012, 22, 145–149. 13. Yildirim, E.; Emsen, B.; Aslan, A.; Bulak, Y.; Ercisli, S. Insecticidal Activity of Lichens Against the Maize Weevil, Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae). Egypt. J. Biol. Pest Contr. 2012, 22, 151–156. 14. Agrios, N. G. Plant Pathology; Academic: San Diego, 1997. 15. Oerke, E. C.; Dehne, H. W.; Shoenbeck, F.; Weber, A. Estimated Losses in Major Food and Cash Crops; Elsevier: London, 1994. 16. Dubey, N. K., Shukla, R., Kumar, A., Singh, P., Prakash, B. Prospects of Botanical Pesticides in Sustainable Agriculture. Curr. Sci. 2010, 98 (4), 479–480. 17. Dalziel, J. M. The Useful Plants of West Tropical Africa; Crown Agents for Overseas Governments: London, 1937. 18. Ayensu, S. Medicinal Plants of West Africa; Reference Publications: Algonae, 1978. 19. Tripathi, P.; Dubey, N. K. Exploration of Natural Products as an Alternative Strategy to Control Post Harvest Fungal Rotting of Fruits and Vegetable. Postharvest Biol. Technol. 2004, 32, 235–245. 20. Rajendran, S.; Sriranjini, V. Plant Products as Fumigants for Stored Product Insect Control. J. Stored Prod. Res. 2008, 44, 126–135. 21. Saxena, R. C. Botanical Pest Control. In Critical Issues in Insect Pest Management; G. S. Dhaliwal, Heinrichs, Eds.; Commonwealth Publisher: New Delhi, India, 1998; pp 155–179. 22. Nayaka, S.; Upreti, D. K.; Khare, R. Medicinal Lichens of India. In Drugs from Plants, 2010. 23. Molnár, K.; Farkas, E. Current Results on Biological Activities of Lichen Secondary Metabolites: A Review. Z. Naturforsch. 2010, 65, 157–173. 24. Franck, E.; Dayan.; Joanne, G.; Romagni. Lichens as a Potential Source of Pesticides; Pest. Outlook 2001, 229–232. 25. Dayan, F. E.; Romagni, J. G. Lichens as a Potential Source of Pesticides; Pest. Outlook. 2001, 6, 229–232. 26. Crittenden, D.; Porter, N. Lichen Forming Fungi: Potential Sources of Novel Metabolites. Trends Biotechnol. 1991, 9, 409–414. 27. Prasad, C.; Manoharachary; Kunwar, I. K. Effect of Lichen Extracts on the Growth of Fungi. Ind. Bot. Soc. 1994, 73, 353–354. 28. Cansaran, D.; Kahya, D.; Yurdakulol, E.; Atakol, A. Identification and Quantification of Usnic Acid from the Lichen Usnea Species of Anatolia and Antimicrobial Activity. Zeitschrift für Naturforschung 2006, 61 (11–12), 773–776. 29. Land, C. J.; Lundstrom, H. Inhibition of Fungal Growth by Water Extracts From the Lichen Nephroma arcticum. Lichenologist 1998, 30, 259–262. 30. Kekuda, P. T. R.; Vinayaka, K. S.; Swathi, D.; Suchitha, Y.; Venugopal, T. M.; Mallikarjun, N. Mineral Composition, Total Phenol Content and Antioxidant Activity

Lichens: A Novel Group of Natural Biopesticidal Sources

31. 32. 33. 34. 35.

36. 37.

38.

39.

40. 41.

42.

43. 44.

239

of a Macrolichen Everniastrum cirrhatum (Fr.) Hale (Parmeliaceae). E-J. Chem. 2011, 8 (4), 1886–1894. Saklani, A.; Jain, S. K. Cross Cultural Ethnobotany of North India; Deep: New Delhi, 1994; pp 31–32. Shahi, S. K.; Shukla, A. C.; Dikshit, A.; Upreti, D. K. Use of Lichen as Antifungal Drug Against Superficial Fungal Infections. Arom. Plant Sci. 2000, 22 (4A) and 23 (1A), 169–172. Esimone, C. O.; Eck, G.; Duong, T. N. Potential Antirespiratory Syncytial Virus Lead Compounds from Aglaia Species. Pharmazie 63, 1–6. Azenha, G.; Iturriaga, T.; Michelangeli F. I.; Rodriguez, E. Ethnolichenology, Biochemical Activity, and Biochemistry of Amazonian Lichen Species. Cornell Univ. Undergrand Res. Prog. Biodivers. 1998, 1, 8–14. Fournet, A.; Ferreira, M. E.; Rojas de Arias, A.; Torres de Ortiz, S.; Inchausti, A.; Yaluff, G.; Quilhot, W.; Fernandez, E.; Hidalgo, M. E. Activity of Compounds Isolated from Chilean Lichens Against Experimental Cutaneous Leishmaniasis. Comp. Biochem. Physiol. C. 1997, 116, 51–54. Honda, N. K.; Pavan, F. R.; Coelho, R. H. Antimycobacterial Activity of Lichen Substances. Phytomedicine 2010, 17, 328–332. Kumar, P. S. V.; Kekuda, P. T. R.; Vinayaka, K. S.; Sudharshan, S. J.; Mallikarjun, N.; Swathi, D. Studies on Antibacterial, Anthelmintic and Antioxidant Activities of a Macrolichen Parmotrema pseudotinctorum (des. Abb.) Hale (Parmeliaceae) from Bhadra Wildlife Sanctuary, Karnataka. Int. J. PharmTech Res. 2010a, 2 (2), 1207–1214. Pavithra, G. M.; Vinayaka, K. S.; Rakesh, K. N.; Junaid, S.; Dileep, N.; Kekuda, P. T. R.; Siddiqua, S.; Naik, A. S. Antimicrobial and Antioxidant Activities of a Macrolichen Usnea pictoides G. Awasthi (Parmeliaceae). J. Appl. Pharm. Sci. 2013, 3 (08), 154–160. Swathi, D.; Suchitha, Y.; Kekuda, P. T. R.; Venugopal, T. M.; Vinayaka, K. S.; Mallikarjun, N.; Raghavendra, H. L. Antimicrobial, Anthelmintic and Insecticidal Activity of a Macrolichen Everniastrum cirrhatum (Fr.) Hale. Int. J. Drug Dev. Res. 2010, 2 (4), 780–789. Kekuda, T. R. P.; Vinayaka, K. S.; Kumar, S. V. P.; Sudharshan, S. J. Antioxidant and Antibacterial Activity of Lichen Extracts, Honey and Their Combination. J. Pharm. Res. 2009, 2 (12), 1875–1879. Vinayaka, K. S.; Krishnamurthy, Y. L.; Kekuda, P. T. R.; Kumar, P. S. V.; Sudharshan, S. J.; Chinmaya, A. Larvicidal and Wormicidal Efficacy of Methanolic Extracts of Five Macrolichens Collected from Bhadra Wildlife Sanctuary. Biomedicine 2009, 29 (4), 327–331. Gulluce, M.; Aslan, A.; Sokmen, M.; Sahin, F.; Adiguzel, A.; Agar, G.; Sokmen, A. Screening the Antioxidant and Antimicrobial Properties of the Lichens Parmelia saxatilis, Platismatia glauca, Ramalina pollinaria, Ramalina polymorpha and Umbilicaria nylanderiana. Phytomedicine 2006, 13, 515–521. Mazid, M. A.; Hasan, C. M.; Rashid, M. A. Antibacterial Activity of Parmelia kamstchandalis. Fitoterapia 1999, 70, 615–617. Florencio, B. Antibacterial Substances from Lichens. Econ. Bot. 1952, 6 (4), 402–406.

240

Plant Pathogens: Detection and Management for Sustainable Agriculture

45. Kekuda, P. T. R.; Vivek, M. N. et al. Biocontrol Potential of Parmotrema Species Against Colletotrichum capsici Isolated from Anthracnose of Chilli. J. Biol. Sci. Opin. 2014, 2 (2), 166–169. 46. Vartia, K. O. Antibiotics in Lichens. In The Lichens; V. Ahmadjian, M. E. Hale, Jr., Eds.; Academic Press: New York, 1973; pp 547– 561. 47. Asahina, Y.; Shibata, S. Chemistry of Lichen Substances. Jpn. Soc. Prom. Sci. Ueno, 1954. 48. Praveen Kumar, S. V.; Prashith Kekuda, T. R.; Vinayaka, K. S.; Swathi, D.; Chinmaya A. Insecticidal Efficacy of Ramalina hossei H. Magn and G. Awasthi and Ramalina conduplicans vain. Macrolichens from Bhadra Wildlife Sanctuary, Karnataka. Biomedicine 2010, 30 (1), 100–102. 49. Kumar, P. S. V.; Kekuda, P. T. R.; Vinayaka, K. S.; Swathi, D.; Mallikarjun, N.; Nishanth, B. C. Studies on Proximate Composition, Antifungal and Anthelmintic Activity of a Macrolichen Ramalina hossei H. Magn & G. Awasthi. Int. J. Biotechnol. Biochem. 2010b, 6 (2), 191–201. 50. Vinayaka, K. S.; Kumar, P. S. V.; Mallikarjun, N.; Kekuda, P. T. R. Studies on Insecticidal Activity and Nutritive Composition of a Macrolichen Parmotrema pseudotinctorum (des. Abb.) Hale (Parmeliaceae). Drug Inv. Today 2010, 2 (2), 102–105. 51. Kumar, P. S. V.; Kekuda, P. T. R.; Vinayaka, K. S.; Sudharshan, S. J. Anthelmintic and Antioxidant Efficacy of two Macrolichens of Ramalinaceae. Pharm. J. 2009, 1 (4), 238–242. 52. Boustie, Joel.; Grube, Martin. Lichen-A Promising Source of Bioactive Secondary Metabolites. Plant Gen. Res. 2005, 3 (2), 273–287. 53. Ramaut, J. L.; Thonar, J. Inhibition de la Germination de Differentes Grains d’ Angiosperms par Evernia prunastri (L.) Ach. I. An. R. Soc. Esp. Fis. Quim. 1972, 68, 575–595. 54. Ramaut, J. L., Thonar, J. Inhibition de la Germination de Differentes Grains d’ Angiosperms par Evernia prunastri (L.) Ach. II. An. R. Soc. Esp. Fis. Quim. 1972b, 68, 597–607. 55. Lawrey, J. D. Vulppiinic Acid Pinastric Acids as Lichen Antiherbivore Compounds: Contrary Evidence. Bryologist 1983, 86, 365–369. 56. Lawrey, J. D. Biological Role of Lichen Substances. Bryologist 1986, 89, 111–122. 57. Ahad, A. M.; Goto, Y.; Kiuchi, F.; Tsuda, Y.; Kondo, K.; Sato, T. Nematocidal Principles in “Oakmoss Absolute” and Nematocidal Activity of 2,4-dihydroxybenzoates. Chem. Pharm. Bull. 1991, 39, 1043–1046. 58. Emmerich, R.; Giez, I.; Lange, O. L.; Proksch, P. Toxicity and Antifeedant Activity of Lichen Compounds Against the Polyphagous Herbivorous Insect Spodoptera Littoralis. Phytochemistry 1993, 33, 1389–1394. 59. Giez, I.; Lange, O. L.; Proksch, P. Growth-retarding Activity of Lichen Substances Against the Polyphagous Herbivorous Insect Spodoptera littoralis. Biochem. Ecol. 1994, 22, 113–120.

CHAPTER 11

Antimicrobial Peptides from Biocontrol Agents: Future Wave in Plant Disease Management VIVEK SHARMA1* and RICHA SALWAN2

University Centre for Research and Development, Chandigarh University, Gharuan 140413, Punjab, India 1

Richa Salwan, College of Horticulture and Forestry, Neri, Hamirpur (HP) 177 001, India

2

*

Corresponding author. E-mail: [email protected]

ABSTRACT Microbes play an important role in affecting plant health. The nonpathogenic microbes such as Bacillus spp., Actinobacteria, Pseudomonads, Rhizobium and Trichoderma offer a sustainable, ecofriendly and economical solution for the management of various crop diseases compared with chemical-based management practices. Several mechanisms including production of cell wall hydrolases and bioactive secondary metabolites targeting the plant pathogens are considered to play important roles in the biocontrol activity of these microbes. In particular, the production of low-molecular weight peptides having ability to target the pathogen cell wall or membrane offer attractive choice for future plant disease management. These peptides are broadly categorized into ribosomal and nonribosomal peptides. The genomes of beneficial microbes harbor wide gene clusters of ribosomal-synthesized peptides in canonical fashion, whereas peptides of nonribosomal are modular in their organization. The posttranslational modified peptides of ribosomal origin include lanthipeptides, tail-cyclized peptides, sactipeptides, unmodified bacteriocins, and

242

Plant Pathogens: Detection and Management for Sustainable Agriculture

other large antimicrobial proteins. On the other side, the antimicrobial peptides (AMPs) synthesized by nonribosomal peptide synthetase enzyme complexes represent a diverse class of peptaibols. This chapter highlights the nature, mechanism, and the potential of these AMPs from beneficial microbes for the biological management of plant diseases. 11.1 INTRODUCTION The global food security is a major concern worldwide and significant loss in crops by pathogenic microbes such as bacteria and fungi account for ~10% of the total loss at global level (Strange and Scott, 2005). The management of plant diseases is largely based on use of synthetic chemicals which causes considerable side effects to ecosystem in the form of pollutants (Makovitzki et al., 2007). The emergence of drug-resistant “ESKAPE” pathogens presents a challenging task and requires alternate measures for combating the pathogen (Gill et al., 2015). Furthermore, the genetic variation and continuous coevolution of plant pathogens often leads to the origin of highly virulent strains of pathogens which are often difficult to manage. Therefore, the development of highly effective and ecofriendly measures is the focus of current agriculture research. The, noncytotoxic membrane-targeting peptides having lipopolysaccharide (LPS)-binding affinities have emerged as promising candidates for plant disease management in agricultural applications (Datta et al., 2015). Antimicrobial peptides (AMPs) of 5–100 amino acids have a broad spectrum of activity against various organism (Bahar and Ren, 2013). These AMPs are valuable resource for students, researchers, and have emerged as novel antibiotics for a long time. The history of AMPs started in 1939, when Dubos (1939a) showed the efficacy of Bacillus extract which was proved to protect mice from pneumococci infection (Dubos, 1939b). In subsequent studies, Hotchkiss and Dubos (1940) identified an AMP and named it as gramicidin. After that, the efforts on AMPs have gained extensive speed. The rapid-action and broad-spectrum antimicrobial activities of these low-molecular peptides have emerged as potential therapeutics for microbial infections caused by antibiotic-resistant strains of bacteria (Hancock, 1997; Brogden, 2005; Sahl, 2006; Datta et al., 2016). Despite a higher variability in their sequence, mass, charge, and structure, the AMPs are generally small peptides and constitute a class

Antimicrobial Peptides from Biocontrol Agents

243

of molecules with wide distribution in nature. The next-generation AMPs have gained attention due to the antimicrobial activity against different microbes including bacteria, fungi, and viruses. Also, a number of organisms including plants, animals, and humans are known to produce AMPs in response to their defense against pathogens. The effectiveness of these molecules against pathogens which are resistant to conventional drugs offers several advantages (Aoki et al., 2012). The development of agriculturally relevant transgenic plants expressing AMPs can prove a sustainable approach in combating plant diseases and also decreases concurrent pathogens ability to develop resistance (Wang et al., 2011). Besides targeting the membrane, some of AMPs can directly interact and inhibit important pathways related to DNA replication and protein synthesis (Brogden, 2005) even at low concentration. These AMPs contain an active site for intracellular target (Otvos et al., 2000; Kragol et al., 2001) or inhibition of cell wall synthesis such as nisin (Brumfitt et al., 2001). For majority of antifungal AMPs, their ability to target cell does not have clear relation with their structures, for example, antifungal peptides with α-helical (Jiang et al., 2008) or extended (Lee et al., 2003), and β-sheet structure (Barbault et al., 2003). The antifungal AMPs have been reported for causing death of fungi either by targeting cell wall (De Lucca et al., 1998, 1999) or by targeting intracellular processes (Lee et al., 1999). The ability of AMPs to efficiently bind fungal cells and then causing either the disruption of fungal membranes (Terras et al., 1992) or altering, membrane permeabilization (Van der 2010), or formation of pores in the membrane directly (Moerman et al., 2002). The studies also revealed that AMPs-mediated activity is less vulnerable to develop resistance than other methods (Datta et al., 2015). Furthermore, the promising AMPs are capable of killing bacteria under in vitro conditions at very low dose in the range from 0.25 to 4 µgmL–1. The additional benefits of these peptides include their ability to destroy the target cells rapidly, broad spectrum activity, and effectiveness against already antibiotic-resistant pathogens. The continuous and massive use of fungicides and pesticides in agriculture sectors have led to the development of resistance among pathogens and created several environmental and health risks. These peptides can be explored as an alternative to their chemical counterpart for the protection of plants/animals against diseases. Therefore, these low-molecular peptides offer exciting possibilities over conventional

244

Plant Pathogens: Detection and Management for Sustainable Agriculture

antibiotics. A number of Bacillus species have been explored for the production of AMPS such as fusaricidins, iturins, fengycins, polymixins, and agrastatins (Stein, 2005), and reported for their synergistic antifungal activity against a variety of phytopathogens. Under in vitro conditions, a strong inhibitory effect of lipopeptide against F. oxysporum, Pythium ultimum, Rhizoctonia solani, Rhizopus sp., and B. cinerea has been described (Ongena et al., 2005; Table 11.1). Similarly, the pretreatment of bean seedlings with B. subtilis M4 supernatant prior resulted in a decrease in disease symptoms (Breen et al., 2015). The antimicrobial potential of these AMPs has also been described in planta. The modes-of-action of certain AMPs such as fengycins and peptaibols resulted not only in the inhibition of the plant pathogen but also led to increase disease resistance through systemic resistance and the production of phenolic compounds (Ongena et al., 2005; Montesinos, 2007). The results of the biotechnological research as well as genetic engineering related to AMPs have proven their potential over the period of time in reducing economic losses to various agricultural crops caused by pathogens. Therefore, this study provides a unifying view of both peptides of ribosomal and nonribosomal origin which is so far studied differently. In this book chapter, focus is given on understanding the functional and structural characteristics of both ribosomal and nonribosomal derived AMPs from biocontrol and plant growth-promoting bacteria (PGPB). A historical preview of their development, functional mechanisms, and recent developments in bioinformatics research in relation to AMPs are also discussed. 11.2 TYPES OF AMPs The AMPs of microbial origin can be broadly classified into: (1) ribosomal represented by majority of bacteria and (2) nonribosomal of fungal origin depending upon their synthesis. Ribosomal peptides results from the cleavage of a precursor protein. The nonribosomal peptides synthesized through nonribosomal peptide synthetases (NRPS) are represented by modular complexes which are found in an operon in bacteria or clusters of gene in eukaryotes and synthesize one peptide per operon or cluster (Breen et al., 2015). A common general centric model of both theses peptides is their ability to interact with membrane.

Yuan et al., 2011; 2012

Zhang et al., 2013

Bacillomycin D, fengycins A, and B

Bacillomycin D and of Ralstonia solanacearum themacrolactin family, macrolactin A, 7-O-malonylmacrolactin A, and 7-O-succinyl macrolactin A

Fengycins and unknown lipopeptides

B. amyloliquefaciens strain Q-426

B. amyloliquefaciens strain NJN-6

Bacillus atrophaeus strain CAB-1

Bacillus subtilis strains Fengycin-type cyclopeptides S499 and M4 was

Arrebola et al., Alternaria citri, Botryosphaeria sp., 2010 Colletotrichum gloeosporioides, Fusicoccum aromaticum, Lasiodiplodia theobromae, Penicillium crustosum, and Phomopsis perse

Lipopeptides, fengycins, iturins, and surfactins, along with bacillomycin

Bacillus amyloliquefaciens strain PPCB004

Control of grey mould rot in apple fruits caused by Botrytis cinerea (Ongena et al., 2005)

B. cinerea and Sphaerotheca fuliginea

F. oxysporum f. sp. spinaciae

Antagonistic to E. carotovora and the root pathogenic fungus F. solani and Fusarium acuminatum

Polymixin B

Paenibacillus B2

Ongena et al., 2005

Zhao et al., 2014

Selim et al., 2005

Ongena et al., 2005

F. oxysporum, Pythium ultimum, Rhizoctonia solani, Rhizopus sp., and B. cinerea.

Fengycin homologs

B. subtilis strain M4

Gueldner et al., 1988

control of peach brown rot caused by Monilinia fructicola

Iturin

Ribosomal

Reference

Bacillus subtilis B-3 was

Antifungal

Antimicrobial Peptides Used Against Pathogens in Agricultural Crops.

Microbial origin AMP types

TABLE 11.1 Antimicrobial Peptides from Biocontrol Agents 245

Shi et al., 2012 Ascochyta citrullina, B. cinerea, F. oxysporum, Phytophthora parasitica, and V. dahlia Oh et al., 2002; Neuhof et al., 2007 Neuhof et al., 2007 Ritieni et al., 1995; Neuhof et al., 2007 Neuhof et al., 2007

Atroviridins A–C Neoatroviridins Gram-positive bacteria and phytopathogenic fungi – – – programmed cell death in Fusarium oxysporum plant fungal pathogens

Induce resistance against GramLi et al., 2014 negative Pectobacterium carotovorum subsp. carotovorum in Chinese cabbage

Trichoderma pseudokoningii strain SMF2

Trichokindins I–X Trichorzin HA I Harzianins

Paracelsin E, Saturnisporins SA II and IV

Trichovirins II, Trichodecenin I Suzukacillin A Alamethicin F50

Trichokonin VI

Trichokonins

Trichoderma pseudokoningii strain SMF2

T. atroviride

T. harzianum

T. saturnisporum

T. viride

T. pseudokoningii

T. pseudokoningii

Shi et al., 2012

Deravel et al., 2014

Bremia lactucae

B. subtilis strains BBG131 and BBG125,

Nonribosomal

Reference

Antifungal

Microbial origin AMP types

TABLE 11.1  (Continued) 246 Plant Pathogens: Detection and Management for Sustainable Agriculture

Antimicrobial Peptides from Biocontrol Agents

247

FIGURE 11.1 (See color insert.) Antimicrobial peptides of ribosomal origin are synthesized using canonical pathway, whereas nonribosomal origin in general includes peptaibols which are synthesized through modular pathway. Still irrespective of their origin, both AMPs either target cell membrane or intracellular pathways.

The main structural characteristics of AMPs include their high affinity and selectivity for membranes (Melo et al., 2009) which is determined by the amino acid composition, charge, hydrophobicity, amphipathicity, H-bonding, and flexibility (Findlay and Zhanel, 2010). The net positive charge on peptide is considered essential for initial binding to the negative charged membrane of bacteria, and thus allows selective discrimination between bacterial and host cell membrane, whereas its hydrophobic nature helps in insertion into membrane followed by perturbation (Lohner and Blondelle, 2005; Henderson and Lee, 2013; Malanovic and Lohner, 2016). The AMPs of animal and plant origin are endogenous and are composed of 10–50 amino acids (Malanovic and Lohner, 2016). These are cationic in nature due to excess of lysine and arginine amino acids and can behave as constitutive or inducible after pathogen infection. The structural composition of these peptides can be α-helical or β-sheet elements which is further stabilized by intramolecular disulphide (Malanovic and Lohner, 2016).

248

Plant Pathogens: Detection and Management for Sustainable Agriculture

11.2.1 BIOGENESIS OF PEPTIDES The NRPS produce a wide variety of peptides in bacteria and fungi. Although structurally diverse, most of these nonribosomal peptides share a common biosynthetic pathway, that is, presence of multienzyme thio template mechanism. The constituents of the peptides are connected sequentially by the corresponding peptide synthetase system, which is first activated as acyl adenylates through the utilization of ATP as energy source. The activation share its similarity to aminoacyl-tRNA synthetases involved in translation during protein synthesis. However, presence of peptide synthetases instead of tRNA intermediates is involved in covalent linking of the activated amino acid as carboxy thioester (Pavela-Vrancic et al., 1994). This module of peptide synthetase works in semiautonomous fashion. The module activates and modifies a single residue of the final peptide. Each module can be partitioned into three repeating sites: adenylation, thiolation, and condensation (Daniel and Filho, 2007a). 11.2.2 RIBOSOMAL PEPTIDES AND THEIR STRUCTURE The AMPs of ribosomal origin are produced both by prokaryotes and eukaryotes, and are important component of defense against microbes (Aoki et al., 2012). In general, majority of these peptides are cationic and usually amphiphilic in nature, therefore target the cells by altering cell membrane permeability. Based on the structural organization, the ribosomal peptides are classified into different groups either having a high content of one or two amino acid, usually proline. Structurally, these are predominantly β-sheet structure containing intramolecular disulfide bonds, or α-helical structure with amphiphilic regions (Sarika et al., 2012; Holaskova et al., 2014; Carneiro et al., 2015) or extended, and loop. The α-helix and β-sheet structural groups are more common and among them α-helical peptides are explored in majority (Powers and Hancock, 2003). The best known examples of such AMPs are protegrin, magainin, cyclic indolicin, and coiled indolicin (Huang et al., 2010). β-sheet peptides are composed of minimum of two β-strands and share disulfide bonds between them (Bulet et al., 2004). Ribosomal peptides are difficult to predict in silico from transcriptomic and genomic sequencing projects due to their small size and high diversity and lack of generic

Antimicrobial Peptides from Biocontrol Agents

249

cleavage sites that could indicate a potential peptide. The advancement in bioinformatics tools has led to in silico annotation and identification of microbial genome for these peptides (Aleti et al., 2015). The most comprehensive AMPs database to date, named ADAM, is publically available and currently contains 7007 unique peptide sequences and 759 structures (http://bioinformatics.cs. ntou.edu.tw/ADAM/links.html) (Lee et al., 2015; Breen et al., 2015).

FIGURE 11.2a (See color insert.) Ribosomal-derived antimicrobial peptides from bacterial source.

Many of biocontrol agents (BCAs) including gram-negative Pseudomonas fluorescens and gram-positive Bacillus subtilis/amyloliquefaciens are known to produce AMPs like cyclodipopeptides (cLPs) which includes surfactins, iturins, and fengycins, or pseudopeptides (Table 11.2).

250

Plant Pathogens: Detection and Management for Sustainable Agriculture

Majority of AMPs are encoded by genes, while others are products of secondary metabolism or synthesized by NRPS (Giessen and Marahiel, 2012). Certain AMPs are generated after posttranslational modifications and have cyclic structure or contain unusual amino acids (Laverty et al., 2011; Tables 11.2 and 11.3). Furthermore, independent of their origin, these AMPs can provide resistance against fungal or bacterial pathogens in plant species (Rahnamaeian et al., 2009). Hence, they present innovative approaches for plant protection in agriculture (Fig. 11.2b) (Holaskova et al., 2015). 11.2.3 NON-RIBOSOMAL PEPTIDES AND THEIR STRUCTURE The nonribosomal-derived peptides are represented by peptaibols which are either linear or rarely cyclic in structure (Fig. 11.2b). These nonribosomal peptides are synthesized by modular peptide synthetases (NRPSs) (Fig. 11.1), and contained 5–20 amino acid residues which are often rich in the nonproteinogenic α-aminoisobutyric acid (Aib) (Szekeres et al., 2005; Lee and Kim, 2015; Patel et al., 2015). Similar to ribosomal-derived AMPs, the peptaibols are amphipathic with hydrophilic and hydrophobic domains. Additionally, a high proportion of nonproteinogenic amino acids such as α-aminoisobutyrate (A, Aib), α,α-dialkylated amino acid residues, and isovaline and 2-amino-6-hydroxy-4-methyl-8- oxodecanoic acid is hallmark of these peptides. The C-terminal is usually amino alcohol phenylalaninol or leucinol or 2-(2-aminopropyl) methylaminoethanol and the N-acyl group is usually acetyl (Daniel and Filho, 2007b). Peptaibols are categorized into three groups depending upon the length of the amino acid sequences. The group I contains 18–20 amino acid residues long and group II are represented by 11–16 amino acid residues. The group III contains 6 or 10 residues (Daniel and Filho, 2007) out of ~1250–1300 peptaibiotics known (Ayers et al. 2012; Carroux et al. 2013; Kimonyo and Brückner 2013; Röhrich et al. 2012; Röhrich et al. 2013a, b; Chen et al. 2013; Panizel et al. 2013; Ren et al. 2013; Stoppacher et al. 2013). So far, over 950 nonribosomal synthesized peptides have been identified from Trichoderma/Hypocrea which accounts over 80% from this BCA alone (Brückner et al. 1991; Degenkolb and Brückner et al., 2009). The unique membrane-altering bioactivity due to amphipathic and helical nature is possibly considered to play role in assisting root colonization and defense (Röhrich, et al., 2015).

Structure

dehydroalanine/dehydrobutyrine, lanthionine/methyl-lanthionine residues

Example

Heterocyclic ring of oxazoles and thiazoles derived from serine/ threonine and cysteine by enzymatic cyclodehydration and dehydrogenation

Nitrogenous macrocycle being central of piperidine/pyridine/dehydropi- peridine and including additional thiazoles and dehydrated amino acid residues

Glycosylated residues.

N-terminal macrolactam ring that is threaded by the C-terminal tail resulting in a unique lasso structure–the so-called lariat knot

Linear azole-containing peptides (LAPs)

Thiopeptides

Glycocins

Lasso peptides

Sublancin 168

Thiocillins

Microcin B17 streptolysin S plantazolicin A&B

unusual sulfur to α-carbon crossSubtilosin A inks, which are catalyzed by radical S-adenosylmethionine (SAM) enzymes in a leader peptide-dependent manner

Amylocyclicin

Subtilin

Sactipeptides

Head to tail direct linkage of their N- and C-terminal cyclized peptides amino acids

Subclass

Lanthipeptides

Class

RiPPs

TABLE 11.2  Classification of Ribosomal-derived Antimicrobial Peptides. Microbes

References

(Kawulka et al., 2003; Noll et al., 2011; Flühe et al., 2012; Yang and Donk 2013

Gonzalez et al., 200; Maqueda et al., 2008; Van Belkum et al., 2011; Scholz et al., 2014

Kleerebezem 2004; Kleerebezem et al. 2004

B. subtilis

B. cereus ATCC 14579

Maksimov et al., 2012; Hegemann et al., 2015

Stepper et al., 2011

Bowers et al., 2010; Just-Baringo et al., 2014

Nizet et al., 2000; E. coli, LAB B. amyloliquefaciens, Heddle et al., 2001; B. methylotrophicus Melby et al., 2011; Scholz et al., 2011; Banala et al., 2013

B. subtilis

B. amyloliquefaciens FZB42

B. subtilis

Antimicrobial Peptides from Biocontrol Agents 251

252

Plant Pathogens: Detection and Management for Sustainable Agriculture

TABLE 11.3 Selected Database of Antimicrobial Peptides of Bacterial and Fungal Origin. Sr. No. 1. 2. 3.

Database

Antimicrobial peptides

Reference

BAGEL2 Peptaibol APD

Ribosomal Peptaibol-Nonribsomal Ribosomal and non ribosomal

4.

DAMPD

5.

DBAASP

Updated natural AMPs and contained 1232 AMPs presently Ribosomal and nonribosomal

de Jong et al., 2010 Whitmore and Wallace, 2004 Wang et al., 2009; Wang et al., 2016 Seshadri et al., 2012

6.

CyBase

7.

Gogoladze et al., 2014; Pirtskhalava et al., 2016 Wang et al., 2008

Cyclic backbone, in which N- and C-terminals are linked by a peptide bond, including cyclotides and bacteriocins BACTIBASE Bacteriocins, bacterial AMPs that Hammami et al., 2010 display growth-inhibition activity against other closely related bacteria

FIGURE 11.2b (See color insert.) Peptaibol of Trichoderma representing nonribosomal-derived antimicrobial peptides from Trichoderma reesei Aib as light blue and other sky blue.

Antimicrobial Peptides from Biocontrol Agents

253

The α,-dialkyl α-amino acids, or 1-aminocyclopropane-1-carboxylic acid (Acc) family having molecular mass between 0.5 and 2.1 kDa contained 4–21 amino acids with unusual nonproteinogenic amino acids and/or lipoamino acids. The N-terminus is acylated N-terminus, and in linear peptide the C-terminus contains amide bond. The second subfamily of peptaibiotics contained β-amino alcohol and the C-terminus of these peptides contain polyamine, free amino acid, amide, 2,5-diketopiperazine, or a sugar alcohol (Fig. 11.3) (Degenkolb and Brückner, 2008; Stoppacher et al., 2013). The peptides produced by biocontrol fungus such as Trichoderma spp. are known to possess broad-spectrum antimicrobial activity (Fig. 11.2b) (Song et al., 2006; Shi et al., 2012). In addition, the biological roles of these peptide includes the elicitation of systemic resistance in tobacco and Chinese cabbage (Luo et al., 2010; Li et al., 2014) root colonization, and programmed cell death induction in tumor cells (Shi et al., 2010; Shi et al., 2016).

FIGURE 11.3 (See color insert.) Multiple alignment of nonribosomal-derived antimicrobial peptides (AMPs) such as peptaibols of Trichoderma origin.

11.2.4 MODE OF ACTION AMPs have varied structural and biological properties. In general, majority of these AMPs share cationic backbone and the amphipathic arrangement target the negatively charged bacterial membrane through electrostatic interaction. Further the segregation of the charged side from a hydrophobic one permits these molecules to enter into the hydrophobic microbial membrane and ultimately leading to membrane disruption and cell death

254

Plant Pathogens: Detection and Management for Sustainable Agriculture

(Brogden, 2005; Izadpanah and Gallo, 2005). Based on the centric general peptide–membrane interaction, four models: barrel-stave, carpet-like, toroidal-pore, and disordered toroidal pore have been proposed for their function (Melo et al., 2009). So far, it is well accepted that the different physicochemical properties of the phospholipid bilayer membranes allow AMPs to discriminate between bacterial and host cell membranes (Lohner 2001; Lohner and Staudegger, 2001). Cholesterol being a main biomolecule of eukaryotic membrane and its absence in bacterial cell membranes is proposed to play an important role in imparting selectivity (Malanovic and Lohner, 2016). Furthermore, the neutral lipids in model membranes have been demonstrated to inhibit damage to lipid vesicles by different AMPs (Matsuzaki et al., 1995; Lee et al., 2015).

FIGURE 11.4 (See color insert.) Organization of ribosomal-derived antimicrobial peptides (AMPs) in the genome of Bacillus species mostly used as biocontrol agents; green color indicates AOI type of antimicrobial peptides.

Antimicrobial Peptides from Biocontrol Agents

255

In the classical membrane disruption model, the APMs incorporate themselves across the membrane and then cause disruption of the outer membrane eventually leading to the death of the target cell. In barrel-stave model, the peptides tend to assemble and form channels in transmembrane in the form of a barrel where hydrophobic parts of peptide aligned with the lipid bilayer and the hydrophilic regions of AMPs constitute the inner part of the pore (Zhang, et al., 2001; Melo et al., 2009). In carpet-like model, AMPs act as detergent and forms micelles or cluster at the membrane surface and leads to cooperative permeabilization of the cytoplasmic membrane. Initially, the AMPs cover the lipid bilayer membrane in a carpet-like fashion and under appropriate conditions, the peptides align themself into the cell membrane due to their detergent-like properties. In toroidal-pore/wormhole model, the hydrophilic part of AMPs remains bounded throughout the polar region of the phospholipid membrane and develop a stable curvature or the membrane phospholipids bend backward upon themselves after magainin monomers which ultimately leads to toroidal pore formation. The disordered toroidal pore represents a modification of toroidal pore model. Here, slightly flexible peptide conformations are formed and the inner side of the pore is also surrounded by hydrophilic region of phospholipid (Li, et al., 2012; Rocha et al., 2012; Bahar and Ren, 2013; Carneiro et al., 2015). The adsorption of these AMPs such as Nguyen to the membrane can be increased by coupling them with anions across the bilayer using oxidized phospholipids or other substance (Mattila et al., 2008; Nguyen et al., 2011) or alternatively using molecular electroporation techniques which can increase the membrane permeability transiently (Gifford et al., 2005). The specificity of AMPs for microbial cells compared with host cells results from the high amount of anionic lipids in the bacterial cell membrane and electrical-potential gradient. During interaction with bacterial membranes, AMPs usually undergo structural changes in the form of aggregates and hence responsible for antimicrobial activity (Kaiserer et al., 2003). Amphipathicity resulting from segregation of apolar and polar residues upon secondary structure formation favors the internalization of the peptide and in turn membrane perturbation. In gram-positive bacteria, before interaction with the cytoplasmic membrane, the peptidoglycan layer and teichoic acids of bacteria may help in penetration, interaction with AMPs and acts as a ladder in targeting membrane interaction and then affect domain organization by lipid segregation which affects membrane

256

Plant Pathogens: Detection and Management for Sustainable Agriculture

permeability. Unlike antibiotics which inhibits the peptidoglycan biosynthesis, the AMPs directly target the cell wall precursors containing highly conserved lipid II which can induce membrane pore formation and hence its disruption (Malanovic and Lohner, 2016). In Gram-negative bacteria, LPS acts as a barrier for AMPs interaction by inhibiting the entry of antimicrobial proteins and other antibiotics (Datta et al., 2015).

FIGURE 11.5 (See color insert.) Schematic representation of mode of action of antimicrobial peptides A-Torroidal, B-Carpet-like model high concentrations of peptide molecules disrupt the membrane in a detergent-like manner breaking the lipid bilayer into set of separate micelles. C- Barrel stave in which hydrophobic regions of AMPs align with the tails of the lipids and the hydrophilic residues form the inner surface of the forming pore and D- Toroidal pore model in which peptides aggregates and hydrophilic heads of the lipids are electrostatically dragged by charged residues of AMPs.

Similar to AMPs of ribosomal origin, the amphipathic nature of peptaibols of nonribosomal origin is the likely basis of their biological activities in the formation of voltage-dependent ion channels in lipid membranes (Béven et al., 1999; Chugh and Wallace, 2001), which is responsible for their antimicrobial, antitumor activity, and the ability to elicit plant defense (Szekeres et al., 2005). For example, alamethicin, the most extensively studied long- sequence peptaibol, is well known for its antimicrobial

Antimicrobial Peptides from Biocontrol Agents

257

activity and the ability to induce plant resistance (Leitgeb et al., 2007; Kredics et al., 2013). 11.2.5 INTRACELLULAR TARGETS Membrane interactions remain important even for intracellular-targeting peptides because they must have means of translocation. As referred in Figure 11.2, AMPs can also act on multiple intracellular targets, modulating gene expression or inhibiting enzymatic processes important for cell viability maintenance. Some AMPs have the ability to interfere with the metabolism of nucleic acids, as is the case Microcidin B17 targets the DNA gyrase-inhibiting DNA replication (Collin et al., 2013). The peptide MccJ25 of bacterial origin may compromise RNA polymerase activity by preventing the transcription process (Mathavan and Beis, 2012). Other peptides may directly act on proteins synthesis as in the case of apidecins and oncocins, causing a blockage in the formation of new protein products through binding of ribosomal proteins (Krizsan et al., 2014). Changes in cell wall synthesis process can be triggered by peptides with antimicrobial intracellular targets. Mediated receptor binding was observed for Lactococcin G and Enterocin 1071 which binds to UPPP, an enzyme involved in cell wall synthesis. The antibiotic class of antimicrobial peptides produced by bacteria may serve as important precursors for the synthesis of peptidoglycan or by activation of autolysins (Oppegård et al., 2007). 11.3 MINING FOR AMPS IN GENOMIC DATA The small ORFs hence small size, classical activity, screening, and characterization are often excluded. Thus, there is need for in silico genomic annotations of data (Hancock and Lehrer, 1998; de Jong et al., 2010). Further mining microbial genomes for ribosomal and nonribosomal peptide is a challenging task due to the lack of substantial homology, sequencing, and structural information of these antimicrobial peptides. Still continuous research on AMPs and evolution of molecular tools varying from genomic to metagenomic data have led to the development and improvement of genome mining software for automated screening of AMPs gene clusters.

258

Plant Pathogens: Detection and Management for Sustainable Agriculture

BAGEL3 (http://bagel.molgenrug.nl/), a follow-up of previous BAGEL and BAGEL2 web-based databases, identifies putative bacteriocins on the basis of three subclasses: Class I contains RiPPs of less than 10 kDa, which is divided into more than 12 supported subclasses; class II contains unmodified peptides not fitting the criteria of the first database; class III contains antimicrobial proteins larger than 10 kDa. BAGEL3 database is a versatile fast tool valid for modified and nonmodified AMPs produced from cultural and nonculturalable bacteria (Table 11.3). BAGEL3 either uses DNA nucleotide sequences in FASTA format as input file or alternatively from drop-down menu bacteria of choice can be selected. The input DNA sequences are analyzed in parallel either for bacteriocin or RiPP or precursor-based mining directly (Zhao and Kuipers, 2016). The peptaibols database (http://peptaibol.cryst.bbk.ac.uk/) store all structural and sequence information of nonribosomal AMPs known as peptaibols, whereas synthetic analogues of peptaibol are excluded from this database. From database, the sequence section allows searches of the peptaibol name, group, motif, and mold, whereas structural section provided information of their structural features. 11.4 ANALYSIS AND PLANT ACTIVITY ASSAY OF AMPS The AMPs due to their small size are difficult to resolve using Laemmli– SDS-PAGE which is also known as Glycine–SDS-PAGE. Therefore, Tricine–SDS-PAGE is the preferred electrophoretic system for resolving proteins less than 30 kDa (Schägger, 2006). For antimicrobial activity, young plants/seedlings are preferred choice and can be inoculated using clip inoculation-based method. For optimum results, a log phase bacterial culture can be washed with distilled water and then resuspended in phosphate buffer 10 mM, pH 7.4 to a cell density of 108 cells/mL. For infection, either sterile scissors dipped into cell suspension or an insulin needle can be used by pricking the veins of the leaves and then bacterial cell suspension can be applied using a cotton swab. Control sets of plants were inoculated with phosphate buffer (pH 7.4) alone and bacterial cell suspension pre incubated for 5 h with AMPs can be used to inoculate the plants. The plants are then observed daily for symptoms after post-infection (dpi). The plants can be uprooted and compared for morphological changes for further analysis (Datta et al., 2015).

Antimicrobial Peptides from Biocontrol Agents

259

11.5 FUTURE AND CONCLUSION The traditional methods of using hazardous chemicals for agricultural pathogen management has led to development of resistance among pathogens as well as created several environmental and health risks. These AMPs have gained the attention of many researchers due to their efficacy against a broad range of pathogens. The use of AMPs for crop protection can play important role in the management of plant pathogens (Datta et al., 2015) and currently, these AMPs have emerged as alternative for conventional methods of plant disease management. Despite the promise of AMPs against a vast range of pathogens, several successful stories on the use of antimicrobial peptides in food and agriculture sectors indicate the promising future of these peptides. In agricultural sector, AMPs with antimicrobial potential and their advantage to induce plant immune responses are proving useful due to their minimal side effects to the environment. Many of current AMPs have been used for developing transgenic plants with increased resistance to pathogens under laboratory conditions. The transgenic cotton plants expressing the tobacco peptide NaD1 which can target PIP2 of fungal membrane have been found to enhance the resistance to fungal pathogens in field conditions (Gaspar et al., 2014) and against several other filamentous fungi under in vitro conditions (Lay et al., 2003; Gaspar et al., 2014). So far, a large numbers of peptaibols amino acid sequences have been discovered due to the advances in spectroscopic and MS techniques (Breen et al., 2015). MS techniques have played vital role in the complete sequencing of peptaibols isolated from BCAs Trichoderma species. To the best of our knowledge, transgenic plants have only been attempted and developed with ribosomal or artificially designed AMPs. Developing transgenic plants using nonribosomal AMPs is a challenging task as they do not undergo translational synthesis. Additionally, research investment into the biosynthetic mechanism used by the NRPS system and cloning of their peptide synthetase genes and their modulation could be optimized for the production of these peptides for various biotechnological and pharmacological applications. The successful stories on the use of antimicrobial peptides in agriculture and food industry indicate a promising future for extensive application of these peptides. Although the genetic manipulation with antimicrobial peptide-encoding genes has been done for plants and animals, still such strategies and products may still have a long way to go before being confirmed by regulatory bodies to surmount technical problems before being accepted as applicable ones.

260

Plant Pathogens: Detection and Management for Sustainable Agriculture

KEYWORDS • • • • •

biocontrol antimicrobial peptides ribosomal nonribosomal management

REFERENCES Aleti, G.; Sessitsch, A.; Brader, G. Genome Mining: Prediction of Lipopeptides and Polyketides from Bacillus and Related Firmicutes. Comput. Struct. Biotechnol. J. 2015, 13, 192–203, doi: 10.1016/j.csbj.2015.03.003. Aoki, W.; Kuroda, K.; Ueda, M. Next Generation of Antimicrobial Peptides as Molecular Targeted Medicines. J. Biosci. Bioeng. 2012, 114 (4), 365–370. http://doi.org/10.1016/j. jbiosc.2012.05.001. Ayers, S.; Ehrmann, B. M.; Adcock, A. F; Kroll, D. J; Carcache de, Blanco. E. J.; Shen, Q; Swanson, S. M.; Falkinham, J. O. III.; Wani, M. C.; Mitchell, S. M.; Pearce, C. J.; Oberlies, N. H. Peptaibols from Two Unidentified Fungi of the Order Hypocreales with Cytotoxic, Antibiotic, and Anthelmintic Activities. J. Pept. Sci. 2012, 18, 500–510. Bahar, A. A.; Ren, D. Antimicrobial Peptides. Pharmaceuticals 2013, 6 (12), 1543–1575. http://doi.org/10.3390/ph6121543. Banala, S.; Ensle, P.; Sussmuth, R. D. Total Synthesis of the Ribosomally Synthesized Linear Azole-containing Peptide Plantazolicin A From Bacillus Amyloliquefaciens. Angew. Chem. Int. Ed. 2013, 52 (36), 9518–9523. Barbault, F.; Landon, C.; Guenneugues, M.; Meyer, J. P.; Schott, V.; Dimarcq, J. L.; Vovelle, F. Solution Structure of alo-3: A New Knottin-type Antifungal Peptide from the Insect Acrocinus longimanus. Biochemistry 2003, 42, 14434–14442. Bower, A. A.; Walsh, C. T.; Acker, M. G. Genetic Interception and Structural Characterization of Thiopeptide Cyclization Precursors from Bacillus cereus. J. Am. Chem. Soc. 2010, 132 (35), 12182–12184. Breen, S.; Solomon, P. S.; Bedon, F.; Vincent, D. Surveying the Potential of Secreted Antimicrobial Peptides to Enhance Plant Disease Resistance. Front. Plant Sci. 2015, 900. http://doi.org/10.3389/fpls.2015.00900. Brogden, K. A. Antimicrobial Peptides: Pore Formers or Metabolic Inhibitors in Bacteria? Nat. Rev. Microbiol. 2005, 3, 238–250. Brückner, H.; Graf, H. Paracelsin, a Peptide Antibiotic Containing α-aminoisobutyric Acid, Isolated from Trichoderma reesei Simmons. Part A Experientia. 1983, 39, 528–530. Brückner, H.; Becker, D.; Gams, W.; Degenkolb, T. Aib and Iva in the Biosphere: Neither Rare Nor Necessarily Extraterrestrial. Chem. Biodivers. 2009, 6, 38–56.

Antimicrobial Peptides from Biocontrol Agents

261

Brumfitt, W.; Salton, M. R.; Hamilton-Miller, J. M. Nisin, Alone and Combined With Peptidoglycan-Modulating Antibiotics: Activity Against Methicillin-Resistant Staphylococcus Aureus And Vancomycin-Resistant Enterococci. J. Antimicrob. Chemother. 2002, 50, 731–734. Bulet, P.; Stocklin, R.; Menin, L. Anti-microbial Peptides: From Invertebrates to Vertebrates. Immunol. Rev. 2004, 198, 169–184. Carneiro, V. A.; Duarte, H. S.; Prado, M. G. V.; Silva, M. L.; Teixeira, M. S.; Santos, Y. M. V. Antimicrobial Peptides: From Synthesis To Clinical Perspectives. In The Battle Against Microbial Pathogens: Basic Science, Technological Advances and Educational Program; A. Méndez-Vilas, Ed., 2015, pp 81–90. Carroux, A; van Bohemen, A-I.; Roullier, C.; Robiou du Pont, T.; Vansteelandt, M.; Bondon, A.; Zalouk-Vergnoux, A.; Pouchus, Y. F.; Ruiz N. Unprecedented 17-residue Peptaibiotics Produced by Marine-derived Trichoderma atroviride. Chem Biodivers. 2013, 10, 772–786. Daniel, J. F.; Filho, E. R. Peptaibols of Trichoderma. Nat. Prod. Reps. 2007, 24, 1128–1141. http://doi.org/10.1039/b618086h. Datta, A.; Ghosh, A.; Airoldi, C.; Sperandeo, P.; Mroue, K. H.; Jiménez-Barbero, J.; Bhunia, A. Antimicrobial Peptides: Insights Into Membrane Permeabilization, Lipopolysaccharide Fragmentation and Application in Plant Disease Control. Scientific Reports 2015, 5, 11951. http://doi.org/10.1038/srep11951. de Jong, A.; van Heel, A. J.; Kok, J.; Kuipers, O. P. BAGEL2: Mining for Bacteriocins in Genomic Data. Nucleic Acids Res. 2010, 38 (2), 647–651. http://doi.org/10.1093/nar/ gkq365. De Lucca, A. J.; Walsh, T. J. Antifungal peptides: Novel Therapeutic Compounds Against Emerging Pathogens. Antimicrob. Agents Chemother. 1999, 43, 1–11. De Lucca, A. J.; Bland, J. M.; Jacks, T. J.; Grimm, C.; Walsh, T. J. Fungicidal and Binding Properties of the Natural Peptides Cecropin B and Dermaseptin. Med. Mycol. 1998, 36, 291–298. Degenkolb, T.; Brückner, H. Peptaibiomics: Towards a Myriad of Bioactive Peptide Containing Cα-dialkylamino Acids. Chem. Biodivers. 2008, 5, 1817–1843. Dubos, R. J. Studies on a Bactericidal Agent Extracted From A Soil Bacillus: I. Preparation of the Agent. Its Activity In Vitro. J. Exp. Med. 1939a, 70, 1–10. Dubos, R. J. Studies on a Bactericidal Agent Extracted from a Soil Bacillus: II Protective Effect of the Bactericidal Agent Against Experimental Pneumococcus Infections in Mice. J. Exp. Med. 1939b, 70, 11–17. Findlay, B.; Zhanel, G. G.; Schweizer, F. Cationic Amphiphiles, A New Generation of Antimicrobials Inspired by the Natural Antimicrobial Peptide Scaffold. Antimicrob. Agents Chemother. 2010, 54, 4049–4058. Flühe, L.; Knappe, T. A.; Gattner, M. J.; Schäfer, A.; Burghaus, O.; Linne, U.; et al. The Radical SAM Enzyme Alba Catalyzes Thioether Bond Formation in Subtilosin A. Nat. Chem. Biol. 2012, 8 (4), 350–357. Gaspar, Y. M.; McKenna, J. A.; McGinness, B. S.; Hinch, J.; Poon, S.; Connelly, A. A.; et al. Field Resistance to Fusarium oxysporum and Verticillium dahliae in Transgenic Cotton Expressing the Plant Defensin NaD1. J. Exp. Bot. 2014, 65, 1541–1550. doi: 10.1093/jxb/eru021.

262

Plant Pathogens: Detection and Management for Sustainable Agriculture

Giessen, T. W.; Marahiel, M. A. Ribosome-independent Biosynthesis of Biologically Active Peptides: Application of Synthetic Biology to Generate Structural Diversity. FEBS Lett. 2012, 586, 2065–2075. Gifford, J. L.; Hunter, H. N.; Vogel, H. J. Lactoferricin: A Lactoferrin-derived Peptide with Antimicrobial, Antiviral, Antitumor and Immunological Properties. Cell Mol. Life Sci. 2005, 62, 2588–2598. Gill, E. E.; Franco, O. L.; Hancock, R. E. W. Antibiotic Adjuvants: Diverse Strategies for Controlling Drug-resistant Pathogens. Chem. Biol. Drug Des. 2015, 85 (1), 56–78. http://doi.org/10.1111/cbdd.12478. Gonzalez, C., Langdon, G. M., Bruix, M., Galvez, A., Valdivia, E., Maqueda, M., et al. Bacteriocin AS-48, A Microbial Cyclic Polypeptide Structurally and Functionally Related to Mammalian Nk-Lysin. Proc. Natl. Acad. Sci. USA. 2000, 97 (21), 11221–11216. Hancock, R. E. Peptide Antibiotics. Lancet 1997, 349, 418–422. Hancock, R. E. W.; Lehrer, R. Cationic Peptides: A New Source of Antibiotics. Trends Biotechnol. 1998, 6, 10747–10751. Heddle, J. G.; Blance, S. J.; Zamble, D. B.; Hollfelder, F.; Miller, D. A.; Wentzell, L. M.; et al. The Antibiotic Microcin B17 is a DNA Gyrase Poison: Characterisation of the Mode of Inhibition. J. Mol. Biol. 2001, 307 (5), 1223–1234. Hegemann, J. D.; Zimmermann, M.; Xie, X.; Marahiel, M. A. Lasso Peptides: An Intriguing Class of Bacterial Natural Products. Acc. Chem. Res. 2015, 48 (7), 1909–1919. Henderson, J. M.; Lee, K. Y. C. Promising Antimicrobial Agents Designed from Natural Peptide Templates. Curr. Opin. Solid State Mater. Sci. 2013, 17, 175–192. Holaskova, E.; Galuszka, P.; Frebort, I.; Oz, M. T. Antimicrobial Peptide Production and Plant-based Expression Systems for Medical and Agricultural Biotechnology. Biotechnol. Advances 2014, 33 (6), 1005–1023. http://doi.org/10.1016/j.biotechadv.2015.03.007. Hotchkiss, R. D.; Dubos, R. J. Fractionation of the Bactericidal Agent from Cultures of a Soil Bacillus. J. Biol. Chem. 1940, 132, 791–792. Huang, Y. B.; Huang, J. F.; Chen, Y. X. Alpha-helical Cationic Antimicrobial Peptides: Relationships of Structure and Function. Protein Cell 2010, 1, 143–152. Izadpanah, A.; Gallo, R. L. Antimicrobial Peptides. J. Am. Acad. Dermatol. 2005, 52, 381–390. Jenssen, H.; Hamill, P.; Hancock, R. E. W. Peptide Antimicrobial Agents. Clin. Microbiol. Rev. 2006, 19, 491–511. Jiang, Z.; Vasil, A. I.; Hale, J. D.; Hancock, R. E.; Vasil, M. L.; Hodges, R. S. Effects of Net Charge and the Number of Positively Charged Residues on the Biological Activity of Amphipathic Alpha-helical Antimicrobial Peptides. Biopolymers 2008, 90, 369–383. Just-Baringo, X.; Albericio, F.; Alvarez, M. Thiopeptide Antibiotics: Retrospective and Recent Advances. Mar Drugs. 2014, 12 (1), 317–351. Kaiserer, L.; Oberparleiter, C.; Weiler-Görz, R.; Burgstaller, W.; Leiter, E.; Marx, F. Characterization of the Penicillium chrysogenum Antifungal Protein PAF. Arch. Microbiol. 2003, 180 (3), 204–210. Kawulka, K.; Sprules, T.; McKay, R. T.; Mercier, P.; Diaper, C. M.; Zuber, P.; et al. Structure of Subtilosin A, an Antimicrobial Peptide from Bacillus Subtilis with Unusual Posttranslational Modifications Linking Cysteine Sulfurs to Alpha-carbons of Phenylalanine and Threonine. J. Am. Chem. Soc. 2003, 125 (16), 4726–4727. Kimonyo, A.; Brückner, H. Sequences of Metanicins, 20-residue Peptaibols from the Ascomycetous Fungus CBS 597.80. Chem. Biodivers. 2013, 10, 813–826.

Antimicrobial Peptides from Biocontrol Agents

263

Kleerebezem, M. Quorum Sensing Control of Lantibiotic Production; Nisin and Subtilin Autoregulate Their Own Biosynthesis. Peptides 2004, 25 (9), 1405–1414. Kleerebezem, M.; Bongers, R.; Rutten, G.; de Vos, W. M.; Kuipers, O. P. Autoregulation of Subtilin Biosynthesis in Bacillus subtilis: The Role of the Spa-box in Subtilin-responsive Promoters. Peptides 2004, 25 (9), 1415–1424. Kragol, G.; Lovas, S.; Varadi, G.; Condie, B. A.; Hoffmann, R.; Otvos, L. The Antibacterial Peptide Pyrrhocoricin Inhibits the Atpase Actions if DNAk and Prevents Chaperoneassisted Protein Folding. Biochemistry 2001, 40, 3016–3026. Krizsan, A.; Volke, D.; Weinert, S.; Sträter, N.; Knappe, D.; Hoffmann, R. Insect-derived Proline-rich Antimicrobial Peptides Kill Bacteria by Inhibiting Bacterial Protein Translation at the 70S Ribosome. Angew. Chem. Int. Ed. Engl. 2014, 53 (45), 12236–9. doi: 10.1002/anie.201407145. Epub 2014 Sep 12. Laverty, G.; Gorman, S. P.; Gilmore, B. F. The Potential of Antimicrobial Peptides as Biocides. Int. J. Mol. Sci. 2011, 12, 6566–6596. Lay, F. T.; Brugliera, F.; Anderson, M. A. Isolation and Properties of Floral Defensins from Ornamental Tobacco and Petunia. Plant Physiol. 2003, 131, 1283–1293. doi: 10.1104/ pp.102.016626. Lee, D. G.; Kim, H. K.; Kim, S. A.; Park, Y.; Park, S. C.; Jang, S. H.; Hahm, K. S. Fungicidal Effect of Indolicidin and Its Interaction with Phospholipid Membranes. Biochem. Bioph. Res. Co. 2003, 305, 305–310. Lee, D. W.; Kim, B. S. Antimicrobial Cyclic Peptides for Plant Disease Control. Plant Pathol. J. 2015, 31, 1–11. doi: 10.5423/PPJ.RW.08.2014.0074. Lee, Y. T.; Kim, D. H.; Suh, J. Y.; Chung, J. H.; Lee, B. L.; Lee, Y.; Choi, S. Structural Characteristics of Tenecin 3, An Insect Antifungal Protein. Biochem. Mol. Biol. Int. 1999, 47, 369–376. Lee, D. K.; Bhunia, A.; Kotler, S. A.; Ramamoorthy, A. Detergent-type Membrane Fragmentation by MSI-78, MSI-367, MSI-594, and MSI-843 Antimicrobial Peptides and Inhibition by Cholesterol: A Solid-state Nuclear Magnetic Resonance Study. Biochemistry 2015, 54, 1897–1907. Lee, H. T.; Lee, C. C.; Yang, J. R.; Lai, J. Z.; Chang, K. Y. A Large-scale Structural Classification of Antimicrobial Peptides. Biomed. Res. Int. 2015, 475062. doi: 10.1155/2015/475062. Li, H. Y.; Luo, Y.; Zhang, X. S.; Shi, W. L.; Gong, Z. T.; Shi, M.; Chen, L. L.; Chen, X. L.; Zhang, Y. Z.; Song, X. Y. Trichokonins from Trichoderma pseudokoningii SMF2 Induce Resistance Against Gram-negative Pectobacterium carotovorum subsp. carotovorum in Chinese Cabbage. FEMS Microbiol. Lett. 2014, 354, 75–82. Lohner, K. Development of Novel Antimicrobial Agents: Emerging Strategies. Horizon Scientific Press: Wymondham, UK, 2001; p 270. Lohner, K.; Staudegger, E. Are we on the Threshold of the Post-antibiotic Era? In Development of Novel Antimicrobial Agents: Emerging Strategies; Lohner, K., Ed.; Horizon Scientific Press: Wymondham, UK, 2001, pp 1–15. Lohner, K.; Blondelle, S. E. Molecular Mechanisms of Membrane Perturbation by Antimicrobial Peptides and the Use of Biophysical Studies in the Design of Novel Peptide Antibiotics. Comb. Chem. High Throughput Screen 2005, 8, 241–256. Malanovic, N.; Lohner, K. Antimicrobial Peptides Targeting Gram-positive Bacteria; Wang G, Ed.; Pharmaceuticals 2016, p 59. doi:10.3390/ph9030059.

264

Plant Pathogens: Detection and Management for Sustainable Agriculture

Makovitzki, A.; Viterbo, A.; Brotman, Y.; Chet, I.; Shai, Y. Inhibition of Fungal and Bacterial Plant Pathogens In Vitro and in Planta with Ultrashort Cationic Lipopeptides. Appl. Environ. Microbiol. 2007, 73, 6629–6636. Maksimov, M. O.; Pan, S. J.; James, L. A. Lasso Peptides: Structure, Function, Biosynthesis, and Engineering. Nat. Prod. Rep. 2012, 29 (9), 996–1006. Maqueda, M.; Sanchez-Hidalgo, M.; Fernandez, M.; Montalban-Lopez, M.; Valdivia, E.; Martinez-Bueno, M. Genetic Features of Circular Bacteriocins Produced by Grampositive Bacteria. FEMS Microbiol. Rev. 2008, 32 (1), 2–22. Mathavan I., Beis K. The Role of Bacterial Membrane Proteins in the Internalization of Microcin MccJ25 and MccB17. Biochem. Soc. Trans. 2012, 40, 1539–154310.1042/ BST20120176 [PubMed]. Matsuzaki, K.; Sugishita, K.; Fujii, N.; Miyajima, K. Molecular Basis for Membrane Selectivity of an Antimicrobial Peptide, Magainin 2. Biochemistry 1995, 34, 3423–3429. Mattila, J. P.; et al. Oxidized Phospholipids as Potential Molecular Targets for Antimicrobial Peptides. Biochim. Biophys. Acta 2008, 1778, 2041–2050. Melby, J. O.; Nard, N. J.; Mitchell, D. A. Thiazole/Oxazole-modified Microcins: Complex Natural Products from Ribosomal Templates. Curr. Opin. Chem. Biol. 2011, 15 (3), 369–378. Melo, M. N.; Ferre, R.; Castanho, M. A. Antimicrobial Peptides: Linking Partition, Activity and High Membrane-nound Concentrations. Nat. Rev. Microbiol. 2009, 7, 245–250. Moerman, L.; Bosteels, S.; Noppe, W.; Willems, J.; Clynen, E.; Schoofs, L.; Thevissen, K.; Tytgat, J.; Van Eldere, J.; van der Walt, J.; et al. Antibacterial and Antifungal Properties of α-helical, Cationic Peptides in the Venom of Scorpions from Southern Africa. Eur. J. Biochem. 2002, 269, 4799–4810. Montesinos, E. Antimicrobial Peptides and Plant Disease Control. FEMS Microbiol. Lett. 2007, 270 (1), 1–11. Neuhof, T.; Dieckmann, R.; Druzhinina, I. S.; Kubicek, C. P.; von Döhren, H. Intactcell MALDI-TOF Mass Spectrometry Analysis of Peptaibol Formation by the Genus Trichoderma/Hypocrea: Can Molecular Phylogeny of Species Predict Peptaibol Structures? Microbiology 2007, 153 (10), 3417–3437. Nguyen, L. T.; Haney, E. F.; Vogel, H. J. The Expanding Scope of Antimicrobial Peptide Structures and Their Modes of Action. Trends Biotechnol. 2011, 29 (9) 464–472. Nizet, V.; Beall, B.; Bast, D. J.; Datta, V.; Kilburn, L.; Low, D. E.; et al. Genetic Locus for Streptolysin S Production by Group A Streptococcus. Infect Immun. 2000, 68 (7), 4245–4254. Noll, K. S.; Sinko, P. J.; Chikindas, M. L. Elucidation of the Molecular Mechanisms of Action of the Natural Antimicrobial Peptide Subtilosin Against the Bacterial Vaginosisassociated Pathogen Gardnerella vaginalis. Probiotics Antimicrob. 2011, 3 (1), 41–47. Oh, S. U.; Yun, B. S.; Lee, S. J.; Kim, J. H.; Yoo, I. D. Atroviridins A-C and Neoatroviridins A-D, Novel Peptaibol Antibiotics Produced by Trichoderma Atroviride F80317. I. Taxonomy, Fermentation, Isolation and Biological Activities. J. Antibiot. 2002, 55 (6), 557–564. Ongena, M.; Jacques, P.; Toure, Y.; Destain, J.; Jabrane, A.; Thonart, P. Involvement of Fengycin-type Lipopeptides in the Multifaceted Biocontrol Potential of Bacillus subtilis. Appl. Microbiol. Biotechnol. 2005, 69, 29–38.

Antimicrobial Peptides from Biocontrol Agents

265

Oppegård, C.; Fimland, G.; Thorbæk, L.; Nissen-Meyer, J. Analysis of the Two-peptide Bacteriocins Lactococcin G and Enterocin 1071 by Site-directed Mutagenesis. Appl. Environ. Microbiol. 2007, 73 (9), 2931–2938. doi:10.1128/AEM.02718-06. Otvos, L.; Rogers, M. E.; Consolvo, P. J.; Condie, B. A.; Lovas, S.; Bulet, P.; BlaszczykThurin, M. Interaction Between Heat Shock Proteins and Antimicrobial Peptides. Biochemistry 2000, 39, 14150–14159. Panizel, I.; Yarden, O.; Ilan, M.; Carmeli, S. Eight New Peptaibols from Sponge-associated Trichoderma Atroviride. Mar. Drugs 2013, 11, 4937–4960. Patel, S.; Ahmed, S.; Eswari, J. S. Therapeutic Cyclic Lipopeptides Mining from Microbes: Latest Strides and Hurdles. World J. Microbiol. Biotechnol. 2015, 31, 1177–1193. doi: 10.1007/s11274-015-1880-8. Pavela-Vrancic, M.; Van Liempt, H.; Pfeifer, E.; Freist, W.; Von Dohre, H. Nucleotide Binding by Multi Enzyme Peptide Synthetases. Eur. J. Biochem. 1994, 220, 535–542. Pirtskhalava, M.; Gabrielian, A.; Cruz, P.; Griggs, H. L.; Squires, R. B.; Hurt, D. E.; Grigolava, M.; Chubinidze, M.; Gogoladze, G.; Vishnepolsky, B.; Alekseev, V.; Rosenthal, A.; Tartakovsky M. DBAASP v.2: An Enhanced Database of Structure and Antimicrobial/ Cytotoxic Activity of Natural and Synthetic Peptides. Nucl. Acids Res. 2016, 44 (D1), D1104–D1112. Powers, J. P.; Hancock, R. E. The Relationship Between Peptide Structure and Antibacterial Activity. Peptides 2003, 24, 1681–1691. Rahnamaeian, M.; Langen, G.; Imani, J.; Khalifa, W.; Altincicek, B.; vonWettstein, D.; et al. Insect Peptide Metchni Kowin Confers on Barley a Selective Capacity for Resistance to Fungal Ascomycetes Pathogens. J. Exp. Bot. 2009, 60, 4105–4114. Ren, J.; Xue, C.; Tian, L.; Xu, M.; Chen, J.; Deng, Z.; Proksch, P.; Lin, W. Asperelines A-F, Peptaibols from the Marine-derived Fungus Trichoderma asperellum. J. Nat. Prod. 2009, 72, 1036–1044. Ritieni, A.; Fogliano, V.; Nanno, D.; Randazzo, G.; Altomare, C.; Perrone, G.; Bottalico, A.; Maddau, L.; Marras, F. Paracelsin E, A New Peptaibol from Trichoderma saturnisporum. J. Nat. Prod. 1995, 58, 1745–1748. Röhrich, C. R.; Iversen, A.; Jaklitsch, W. M.; Voglmayr, H.; Berg, A.; Dörfelt, H.; Thrane, U.; Vilcinskas, A.; Nielsen, K. F.; von Döhren, H.; Brückner, H.; Degenkolb, T. Hypopulvins, Novel Peptaibiotics from the Polyporicolous Fungus Hypocrea pulvinata, are Produced During Infection of its Natural Hosts. Fungal Biol. 2012, 116, 1219–1231. Röhrich, C. R.; Iversen, A.; Jaklitsch, W. M.; Voglmayr, H.; Vilcinskas, A.; Nielsen, K. F.; Thrane, U.; von Döhren, H.; Brückner, H.; Degenkolb, T. Screening the Biosphere: The Fungicolous Fungus Trichoderma phellinicola, a Prolific Source of Hypophellins, New 17-, 18-, 19-, and 20-residue Peptaibiotics. Chem. Biodivers. 2013a, 10, 787–812. Röhrich, C. R.; Vilcinskas, A.; Brückner, H.; Degenkolb, T. The Sequences of the Elevenresidue Peptaibiotics: Suzukacillins-B. Chem. Biodivers. 2013b, 10, 827–837. Röhrich, C. R.; Voglmayr, H.; Iversen, A.; Vilcinskas, A. Europe PMC Funders Group Front Line Defenders of the Ecological Niche! Screening the Structural Diversity of Peptaibiotics from Saprotrophic and Fungicolous Trichoderma/Hypocrea Species. Fungal Diversity 2015, 69 (1), 117–146. Sahl, H. G. Optimizing Antimicrobial Host Defense Peptides. Chem. Biol. 2006, 13, 1015–1017.

266

Plant Pathogens: Detection and Management for Sustainable Agriculture

Sarika; Iquebal, M. A.; Rai, A. Biotic Stress Resistance in Agriculture Through Antimicrobial Peptides. Peptides 2012, 36 (2), 322–330. Schägger, H. Tricine–SDS-PAGE. Nat. Protocol 2006, 1 (1), 16–23. http://doi.org/10.1038/ nprot.2006.4. Scholz, R.; Molohon, K. J.; Nachtigall, J.; Vater, J.; Markley, A. L.; Sussmuth, R. D.; et al. Plantazolicin, A Novel Microcin B17/Streptolysin S-like Natural Product from Bacillus Amyloliquefaciens FZB42. J. Bacteriol. 2011, 193 (1), 215–224. Scholz, R.; Vater, J.; Budiharjo, A.; Wang, Z.; He, Y.; Dietel, K.; et al. Amylocyclicin, A Novel Circular Bacteriocin Produced by Bacillus amyloliquefaciens FZB42. J. Bacteriol. 2014, 196 (10), 1842–1852. Shi, M.; Wang, H. N.; Xie, S. T.; Luo, Y.; Sun, C. Y.; Chen, X. L.; Zhang, Y Z. Antimicrobial Peptaibols, Novel Suppressors of Tumor Cells, Targeted Calcium-mediated Apoptosis and Autophagy in Human Hepatocellular Carcinoma Cells. Mol. Cancer 2010, 9, 26–41. Shi, M.; Chen, L.; Wang, X. W.; Zhang, T.; Zhao, P. B.; Song, X. Y.; Sun, C. Y.; Chen, X. L.; Zhou, B. C.; Zhang, Y. Z. Antimicrobial Peptaibols from Trichoderma Pseudokoningii Induce Programmed Cell Death in Plant Fungal Pathogens. Microbiology 2012, 158, 166–175. Shi, W. L., Chen, X. L., Wang, L. X., Gong, Z. T., Li, S., Li, C. L., et al., Song, X. Y. Cellular and Molecular Insight into the Inhibition of Primary Root Growth of Arabidopsis Induced by Peptaibols, A Class of Linear Peptide Antibiotics Mainly Produced by Trichoderma spp. J. Exp Bot. 2016, 67 (8), 2191–205. http://doi.org/10.1093/jxb/erw023. Song, X. Y.; Shen, Q. T.; Xie, S. T.; Chen, X. L.; Sun, C. Y.; Zhang, Y. Z. Broad- spectrum Antimicrobial Activity and High Stability of Trichokonins from Trichoderma koningii SMF2 Against Plant Pathogens. FEMS Microbiol. Lett. 2006, 260, 119–125. Stein, T. Bacillus subtilis Antibiotics: Structures, Syntheses and Specific Functions. Mol. Microbiol. 2005, 56, 845–857. Stepper, J.; Shastri, S.; Loo, T. S.; Preston, J. C.; Novak, P.; Man, P.; et al. Cysteine S-glycosylation, a New Post-translational Modification Found in Glycopeptide Bacteriocins. FEBS Lett. 2011, 585 (4), 645–650. Stoppacher, N.; Neumann, N. K.; Burgstaller, L.; Zeilinger, S.; Degenkolb, T.; Brückner, H.; Schuhmacher, R. The Comprehensive Peptaibiotics Database. Chem. Biodivers. 2013, 10, 734–743. Strange, R. N.; Scott, P. R. Plant Disease: A Threat to Global Food Security. Annu. Rev. Phytopathol. 2005, 43, 83–116. Sutyak, K. E.; Wirawan, R. E.; Aroutcheva, A. A; Chikindas, M. L. Isolation of the Bacillus Subtilis Antimicrobial Peptide Subtilosin from the Dairy Product-derived Bacillus Amyloliquefaciens. J. Appl. Microbiol. 2008, 104 (4), 1067–1074. Szekeres, A.; Leitgeb, B.; Kredics, L.; Antal, Z.; Hatvani, L.; Manczinger, L.; Vágvölgyi, C. Peptaibols and Related Peptaibiotics of Trichoderma. Acta Microbiologica et Immunologica Hungarica 2005, 52, 137–168. Terras, F. R.; Schoofs, H. M.; De Bolle, M. F.; Van Leuven, F.; Rees, S. B.; Vanderleyden, J.; Cammue, B. P.; Broekaert, W. F. Analysis of Two Novel Classes of Plant Antifungal Proteins from Radish (Raphanus sativus L.) Seeds. J. Biol. Chem. 1992, 267, 15301–15309. Van Belkum, M. J.; Martin-Visscher, L. A.; Vederas, J. C. Structure and Genetics of Circular Bacteriocins. Trends Microbiol. 2011, 19 (8), 411–418.

Antimicrobial Peptides from Biocontrol Agents

267

Van der Weerden, N. L.; Hancock, R. E.; Anderson, M. A. Permeabilization of Fungal Hyphae by the Plant Defensin Nad1 Occurs Through a Cell Wall-dependent Process. J. Biol. Chem. 2010, 285, 37513–37520. Wang, G.; Li, X.; Wang, Z. APD2: The Updated Antimicrobial Peptide Database and Its Application in Peptide Design. Nucleic Acids Res. 2009, 37, D933–D937. Wang J.; Wong E. S.; Whitley J. C.; Li J.; Stringer J. M.; Short K. R.; et al. Ancient Antimicrobial Peptides Kill Antibiotic-resistant Pathogens: Australian Mammals Provide New Options. PLoS One 2011, 6:e24030. 10.1371/journal.pone.0024030. Wang, G.; Li, X.; Wang, Z. APD3: The Antimicrobial Peptide Database as a Tool for Research and Education. Nucleic Acids Res. 2016, 44, D1087–D1093. Whitmore, L.; Wallace, B. A. The Peptaibol Database: a Database for Sequences and Structures of Naturally Occurring Peptaibols. Nucleic Acids Res. 2004, 32, D593–D594. doi:10.1093/nar/gkh077. Yang, X., van der Donk, W. A. Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products: New Insights into the Role of Leader and Core Peptides During Biosynthesis. Chemistry 2013, 19 (24), 7662–7677. Yokoyama, S.; Iida, Y.; Kawasaki, Y.; Minami, Y.; Watanabe, K.; Yagi, F. The ChitinBinding Capability of Cy-Amp1 From Cycad Is Essential To Antifungal Activity. J. Pept. Sci. 2009, 15, 492–497. Zhang, L.; Rozek, A.; Hancock, R. E. Interaction of Cationic Antimicrobial Peptides with Model Membranes. J. Biol. Chem. 2001, 276, 35714–35722.

PART IV Biotechnological Approaches and the Impact of Climate Change

CHAPTER 12

Plant Disease Management Using Biotechnology: RNA Interference NARESH PRATAP SINGH1,* and VAISHALI SHAMI1

Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut (U.P), 250110, India.

1

*

Corresponding author. E-mail: [email protected]

ABSTRACT World food supply is still threatened by various biotic stresses despite of substantial advances in plant disease management strategies. The situation demands judicious blending of conventional, unconventional and frontier technologies. Biotechnological novel techniques such as tissue culture and genetic engineering help us to achieve this goal by producing new organisms and or products that can be used in variety of ways. In this regard, RNA interference (RNAi) has emerged as a powerful technology for controlling various challenging diseases caused by viruses, fungi and bacteria. RNAi is a mechanism for RNA-guided regulation of gene expression in which double-stranded ribonucleic acid (dsRNA) inhibits the expression of genes with complementary nucleotide sequences. The application of tissue-specific or inducible gene silencing together help in silencing several genes simultaneously will result in protection of crops against destructive pathogens. RNAi application has resulted in successful control of many economically important diseases in plants. 12.1 INTRODUCTION Currently, science has developed alot in reference to agriculture but still no significant tool developed to control over plant diseases caused by

272

Plant Pathogens: Detection and Management for Sustainable Agriculture

various pathogens such as fungi, viruses etc. Currently, more than 70% major crops yield is lost due to pathogen attack (Wani et al., 2010). With the advent of new technologies in plant genomics, including structural and functional genomics using biotechnological tools for developing improved crops and vegetables such as in rice (Hackauf 2009, Jeon 2008), wheat (Gill 2007), brassica (Wang 2008), maize (Diwedi 2008), soybean (Canon 2008), cotton (Chaudhary 2008) and vegetable crops (Lehtonen 2008). Most of the crops mainly vegetables are susceptible to plethora of biotic stresses like viruses, bacteria, fungal pathogens, insect pests and nematode parasites. Among the different types of biotic stresses, fungal and viral pathogens causes major loss in crop yields and pose huge economic losses globally (Wani et al 2010). The conventional methods to combat plant fungal pathogens includes breeding strategy, limits by the availability of resistant cultivars and evolution of fungal pathogenic races which makes the crop plants susceptible (Gilbert et al 2006) which is major drawback of this method. Plant diseases are usually controlled by the use of chemicals. The overdose use of chemicals may effects the human health, safety and cause environmental risks as well (Gilbert et al., 2006). Today, pathogens like fungi, viruses have evolved the resistant mechanisms through genetic adjustment, by which pathogen becomes less sensitive towards agrochemicals (Yang 2012). This has fuelled a continual search for novel and alternate strategies for management of fungal pathogens. The silencing of such genes which are required for the invasion, growth of phytopathogenic fungi may be used as an ideal strategy for fungal disease management. 12.2 ABOUT RNAi RNA interference (RNAi) has turned out to be an effective way to control infection caused by fungal pathogens, through silencing of vital genes associated with pathogens. In other words, crop plants expressing dsRNA targeting essential genes in fungal pathogens i.e., plant-mediated pathogen gene silencing has evolved as an emerging strategy to combat fungal pathogens in crop plants. In 1998, Fire and Mello discovered RNAi in Caenorhabditis elegans (Fire 1998). Now-a-days it is considered to be a powerful functional genomics tool to silence any gene of interest with tightly controlled sequence specificity by introducing dsRNA or small interfering RNA (siRNA) containing the target gene sequences into cells or organisms (Agarwal 2003). The loss of functions and altered phenotypes

Plant Disease Management Using Biotechnology

273

represented by result analysis prove to be the most readily interpretable method for experimentally validating the cellular function of genes (Bhadauria 2009). RNAi pathway can be induced by presence of dsRNA, which can be formed by various ways such as RNA viruses, inverted repeats, in vitro transcribed dsRNA, expressed dsRNA or transgenes in genetically modified organisms. 12.3 WORKING OF RNAi RNA interference refers collectively to diverse RNA based processes that all result in sequence-specific inhibition of gene expression at the transcription, mRNA stability or translational level. The unifying features of this phenomena are the production of small RNAs (21-26 nucleotides (nt) that act as specific determinants for down-regulating gene expression (Issac,1992) and the requirement for one or more members of Argonaute family of protein (Maloy, 2005). RNAi operates by triggering the action of dsRNA intermediates, which are processed into RNA duplexes of 21-24 mucleotides by a ribonuclease III like enzyme called Dicer (Mehrotra and Aggarwal, 2003). Once produced, these small RNA molecules or short interfering RNAs (siRNAs) are incorporated in a multi-subunit complex called RNA induced silencing complex (RISC) (Mehrotra and Aggarwal, 2013): RISC is formed by a siRNA and an endonuclease among other component. The siRNAs within RISC acts as a guide to target the degradation of complementary messenger RNAs (mRNAs). When dsRNA molecules produced during viral replication trigger gene silencing, the process is called virus-induced gene silencing (VGS) (Maloy, 2005). One interesting feature of RNA silencing in plants is that once it is triggered in a certain cell, a mobile signal is produced and spread through the whole plant causing the entire plant to be silenced. This silencing process is also enhanced by the enzymatic activity of the RISC complex, mediating multiple turnover reaction (Broglie et al., 1991). Furthermore, production of the secondary siRNAs leads to enrichment of silencing via its spread from the first activated cell to neighboring cells, and systematically through system (Maloy, 2005). The cell to cell spread can be mediated as passive spread of the small RNAs via plasmodesmata, since it does not spread into meristematic cells. The discovery of RNA binding protein (PSRPI) in the phloem and its stability to build 25 ntssRNA species add

274

Plant Pathogens: Detection and Management for Sustainable Agriculture

further to the argument that siRNAs (24- 26nt) are the key components for systemic silencing signal (Brain and Beathle, 2003). The first successful demonstration of RNAi like pathway in fungi came in 1992 with the pioneer research of Romano and Machino (Machino 1992). 12.4 INDUCTION METHODS OF RNAi IN PLANTS The first biggest difficulty is the transfer of the such active molecules that will switch on the RNAi pathway in plants. The various methods for the delivery of dsRNA or siRNA into different cells and tissue which include not only the transformation with dsRNA forming vectors for respective gene(s) by an Agrobacterium mediated transformations (Wterhouse et al., 2001, Chuang et al., 2000) but also the delivery of (a) dsRNA of uidA GUS (β-glucuronidase) and TaGLP2a: GFP (green fluorescent protein) reporter genes into epidermal cells of maize, barley and wheat by particle bombardment (Schweizer et al., 2000), (b) introducing a Tobacco rattle virus (TRV)-based vector in tomato plants by infiltration (Liu et al., 2002a), (c) delivery of dsRNA into tobacco suspension cells by cationic oligopeptide polyarginine-siRNA complex, (d) delivery of siRNA into cultured cells of rice, cotton and slash pine for gene silencing by nanosense pulsed laser-induced stress wave (LISW) (Tang et al., 2006). The most reliable and significant approachesd from above said to transfer dsRNA into plants cells are agroinfiltration, micro-bombardment and VIGS which are discussed below. 12.4.1 AGROINFILTRATION METHOD The transfer of Agrobacterium carrying similar DNA constructs into the intracellular spaces of leaves for inducing RNA silencing is known as agroinoculation or agroinfiltration (Hilly J.M and Liu Z, 2007). Agroinfiltration in mostly cases is used to induce systemic silencing or to know the effect of suppressor genes. Cytoplasmic RNAi can be induced efficiently in plant cells by agroinfiltration, which is similar to the expression of T-DNA vectors after delivery by Agrobacterium tumefaciens. The transiently expressed DNA encodes either an ss- or dsRNA, which is typically a hairpin (hp) RNA (Johansen L.K and Carrington J.C, 2001, Voinnet O, 2001).

Plant Disease Management Using Biotechnology

275

12.4.2 MICROBOMBARDMENT METHOD In this method, particles coated with dsRNA, siRNA or DNA that encode hairpin constructs as well as sense or antisense RNA, activate the RNAi pathway are bombarded with cells. Synthetic siRNAs are delivered into plants by biolistic pressure to cause silencing of GFP expression. The silencing effect of RNAi is detected after a day of bombardment, and it continues upto 3 to 4 days of post bombardment. Silencing occurred after 1 or 2 weeks and spread later in the vascular tissues of the non-bombarded leaves that were closest to the bombarded ones. Approximately after one month or above, the loss of GFP expression was seen cells. RNA blot hybridization with systemic leaves indicated delivery of siRNAs which cause systemic silencing by accumulation (Klahre et al., 2002). 12.4.3 VIRUS-INDUCED GENE SILENCING (VIGS) METHOD Viruses, such as Tobacco mosaic virus (TMV), Potato virus X (PVX) and TRV, can be used for both protein expression and gene silencing(Kumagai et al., 1995, Mallory et al., 2002). RNA virus-derived expression vectors may have potent anti-silencing proteins so they will not be used as silencing vectors always(Kumagai et al., 1995, Palmer K.E and Rybicki E.P, 2001). Similarly, DNA viruses also have not been used extensively as expression vectors due to their size constraints for movement (Kjemtrup et al., 1998). Firstly, Dallwitz M.J and Zurcher E.J, 1996, demonstrated RNA viruses by inserting sequences into TMV and then for DNA viruses by replacing the coat protein gene with a homologous sequence(Kjemtrup et al., 1998). These reports used for gene silencing phytoene desaturase (PDS) and chalcone synthase (CHS), which provide a measure of the tissue specificity of silencing. The PDS gene protects the chlorophyll from photo oxidation. By silencing this gene, a significant decrease in leaf carotene content that resulted into the appearance of photo bleaching symptom (Liu et al., 2002c, Turnage et al., 2002). In the same way, over expression of CHS gene causes an albino phenotype in place of deep orange color(Cogoni et al., 1994). As a result, their action as a phenotypic marker helps in easy understanding of the mechanism of gene silencing. Most viruses are plus-strand RNA viruses or satellites, whereas Tomato golden mosaic virus (TGMV) and Cabbage leaf curl virus (CaLCuV) are DNA viruses. Both types of viruses induces silencing of endogenous genes but the extent of silencing spread and the

276

Plant Pathogens: Detection and Management for Sustainable Agriculture

severity of viral symptoms vary in different host plants(Teycheney P.Y and Tepfer M, 2001). The continuous development of virus-based silencing vectors can extend VIGS to economically important plants and protection from diseases. 12.5 RNAi DISEASES MANAGEMENT Our global food supply is still threatened by various types of pathogens and pests .The edvent of new researches/technologies are to develop to respond more efficiently and effectively to this problem. Today, RNAi technology has emerged as one of the most potential and promising strategies for building up the resistance in plants to overcome the loss caused by various fungal, bacteria, viral and nematode diseases (Singh, 2005). Many of the examples listed below illustrate the possibilities for commercial exploitation of this inherent biological mechanism to generate disease resistant plants in the future by taking advantage of this approach e.g. including; Cladosporium fulvum (Singh, 2001) Magnaporthae oryzae, Venturia inaequalis and Neurospora crassa (Singh, 2005). 12.5.1 MANAGEMENT OF PLANT FUNGAL INFECTIONS USING RNAi A potential approach of RNAi-based “host plant mediated pathogen gene silencing” for efficient control of fungal pathogens infecting various agronomical important crop plants found to be the efficient new biotechnological tool. Small non-coding RNAs which play a vital role in the process called RNA silencing. RNAi operates in both plants and animals, and use double stranded RNAi (dsRNA) for degradation or inhibiting transcription and translation in fungi, viruses, bacteria (Maloy, 2005, Mehrotra and Aggarwal, 2003). The concept behind this method is the down-regulation of vital fungal genes required for fungal invasion, normal growth and pathogenesis by the uptake of dsRNA/siRNAs produced by transgenic plants (Rajam et al 1998; Khatri 2007). RNA-mediated gene silencing (RNA silencing) is used as a reverse tool for gene targeting in fungi. The hypermorphic mechanism of RNA interference implies that this technique can also be applicable to all those plant pathogenic fungi, which are polyploid and polykaryotic in nature. Simultaneous silencing of several unrelated genes by introducing a single chimeric construct has

Plant Disease Management Using Biotechnology

277

been demonstrated in the case of Venturia inaequalis (Fitzgerald et al., 2004). HCf-1, a gene that codes for a hydrophobin of the tomato pathogen C. fulvum (Spanu, 1997), was cosuppressed by ectopic integration of homologous transgenes. Transformation of Cladosporium fulvum with DNA containing a truncated copy of the hydrophobin gene HCf-1 caused co-suppression of hydrophobin synthesis in 30% of the transformants. The co-suppressed isolates had a hydrophilic phenotype, lower levels of HCf-1 mRNA than wild type and contain multiple copies of the plasmid integrated as tandem repeats at ectopic sites in the genome (Hamada and Spanu, 1998). The transcription rate of HCf-1 in the co-suppressed isolates was higher than in the untransformed strains, suggesting that silencing acted at the post-transcriptional level (Hamada and Spanu, 1998). Similarly, the silencing of cgl1 and cgl2 genes using the cgl2 hairpin construct in Cladosporium fulvum has also been reported (Segers et al. 1999), which can be helpful for protecting the consumable products of vegetables and fruit crops from the post harvest diseases caused by different plant pathogens in the future. Fitzgerald et al. (2004), using the hairpin vector technology, have been able to trigger simultaneous high frequency silencing of a green fluorescent protein (GFP) transgene and an endogenous trihydroxynaphthalene reductase gene (THN) in V.inaequalis. High frequency gene silencing was achieved using hairpin constructs for the GFP or the THN genes transferred by Agrobacterium (71 and 61%, respectively). Similarly, multiple gene silencing has been achieved in Cryptococcus neoformans using chimeric hairpin constructs (Liu et al., 2002) and in plants using partial sense constructs (Abbott et al., 2002). ). Tinoco et al. (2010), reported that the GUS specific siRNAs expressed in the transgenic tobacco could lead to the GUS gene silencing in the GUS transformed Fusarium verticillioides’ transformants. They concluded that this could be a result of movement of silencing signal through the germinating spores into the fungal cells. The transgenic lettuce plants expressing a GUS dsRNA could induce specific gene silencing in the parasitizing plant Triphysaria versicolor expressing GUS gene (Tomilov et al., 2008). 12.5.2 MANAGEMENT OF PLANT PATHOGENIC VIRUSES USING RNAi RNAi technology may be used for viral disease control in human cell lines (Bitko and Barik, 2001; Novina et al., 2002; Jacque et al., 2002) and also

278

Plant Pathogens: Detection and Management for Sustainable Agriculture

helpful in protecting viral infections in plants (Waterhouse et al., 2001; Ullu et al., 2002). Generating virus-resistant plants was first done in potato (Waterhouse et al., 1998; Chapman et al., 2004). DNA viruses like Gemini viruses Mungbean yellow mosaic India virus (MYMIV) was expressed as hairpin construct and used as biolistically to inoculate MYMIV-infected black gram plants which showed a complete recovery from infection, which lasted until senescence (Pooggin et al., 2003). RNAi-mediated silencing of Gemini viruses using transient protoplast assay where protoplasts were cotransferred with an siRNA designed to replicase (Rep)-coding sequence of African cassava mosaic virus (ACMV) and the genomic DNA of ACMV resulted in 99% reduction in Rep transcripts and 66% reduction in viral DNA (Vanitharani et al., 2003; Ruiz-Ferrer and Voinnet, 2007). Multiple suppressors have been reported in Citrus tristeza virus (Lu et al., 2003). A 273-bp (base pair) sequence of the Arabidopsis miR159 a pre-miRNA transcript expressing amiRNAs can be used against the viral suppressor genes to provide resistance against Turnip yellow mosaic virus and Turnip mosaic virus infection (Niu et al., 2006). Different amiRNA vector was used to target the 2 b viral suppressor of the Cucumber mosaic virus (CMV), which blocked the slicer activity of AGO1and confer resistance to CMV infection in transgenic tobacco (Qu et al., 2007). A strong correlation between virus resistance and the expression level of the 2 b-specific amiRNA was shown for individual plant lines. It is significantly proved from abovementioned reports that the RNA components, such as ssRNA, dsRNA, and/or siRNA of the silencing pathways are appropriate targets of most viral suppressors and help in protection of plants from viral infections using RNAi technology. 12.6 CONCLUSION WITH FUTURE PROSPECTS To feed the expanding human population leads the high stress on agroecosystems to control plants from various biotic stresses. RNAi and miRNA technologies of gene silencing is gaining the novel importance not only in functional genomics but also having great tendency of higher silencing efficiency of vital gene of pathogen to control disease. The RNA silencing is highly sequence specific and it is technologically efficient and economical as well. Therefore, this technique has great potential in agriculture specifically for nutritional improvement of plants and the management of pathogenic plant diseases. Researches on sRNAs have provided lots

Plant Disease Management Using Biotechnology

279

of studies regarding their types, functions, etc. But still the information is not enough. Various report of researches helped to classified sRNAs into mainly three categories, miRNAs, siRNAs, and piRNAs, while many new types of sRNAs are under exploration. In plants, both miRNAs and siRNAs are present. They act collectively as well as individually to help the plants with their maintenance, homeostasis, and survival under adverse conditions. Various researches marked RNAi technology as powerful tool to combat plant pathogens in the near future. Development of vectors that can suppress the RNAi pathway but overexpress transgenes in a tissuespecific manner will revolutionize this field in future. Presently, substantial researches are being conducted to find the role of miRNAs and siRNAs in biotic stresses. Regulation by sRNAs may be used as a promising tool to improve yields, quality, or resistance to various pathogenic diseases and environmental stresses. Discovery of more sRNAs in plant system will help researchers to manipulate these sRNAs in favor of plant growth and development. Hence, it will be very appropriate to call sRNA “an efficient molecule of the millennium.” KEYWORDS • • • • • •

RNA interference disease management crop improvement biotic and abiotic stress transformation genetic engineering

REFERENCES Abbott, J. C.; Barakate, A.; Pincon, G.; Legrand, M.; Lapierre, C.; Mila, I.; Schuch, W.; Halpin, C. Simultaneous Suppression of Multiple Genes by Single Transgenes. Downregulation of Three Unrelated Lignin Biosynthetic Genes in Tobacco. Plant Physiol. 2002, 128, 844–853. Adenot, X.; Elmayan, T.; Lauressergues, D.; Boutet, S.; Bouche, N.; Gasciolli, V.; Ucheret, H. Uncoupled Production of ta-siRNAs in Hypomorphic rdr6 and sgs3 Mutants Uncovers

280

Plant Pathogens: Detection and Management for Sustainable Agriculture

a Role for TAS3 in AGO7-DCL4-DRB4-mediated Control of Leaf Morphology. Curr. Biol. 2006, 16 (9), 927–932. Agrawal, N.; Dasaradhi, P. V.; Mohmmed, A.; Malhotra, P.; Bhatnagar, R. K.; et al. RNA Interference: Biology, Mechanism, and Applications. Microbiol. Mol. Biol. Rev. 2003, 67, 657–685. Allen, E.; Xie, Z.; Gustafson, A. M.; Carrington, J. C. MicroRNA-directed Phasing During Trans-acting siRNA Biogenesis in Plants. Cell 2005, 121, 207–221. Ambros, V. The Functions of Animal MicroRNAs. Nature 2004, 431, 350–355. Bartel, D. P. MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 2004, 116, 281–297. Baulcombe, D. C. RNA Silencing in Plants. Nature 2004, 431, 356–363. Baumberger, N.; Baulcombe, D. C. Arabidopsis ARGONAUTE1 is an RNA Slicer that Selectively Recruits Micrornas and Short Interfering RNAs. Proc. Natl. Acad. Sci. 2005, 102, 11928–11933. Bhadauria, V.; Banniza, S.; Wei, Y.; Peng, Y. L. Reverse genetics for functional genomics of phytopathogenic fungi and oomycetes. Comp. Funct. Genomics 2009, 11. doi: 10.1155/2009/380719. Bitko, V.; Barik, S. Phenotypic Silencing of Cytoplasmic Genes with Sequence Specific Double Stranded Short Interfering RNA and Its Applications in the Reverse Genetics of Wild Type Negative Strand RNA Virus. BMC Microbiol. 2001, 1, 34–44. Bohmert, K.; Camus, I.; Bellini, C.; Bouchez, D.; Caboche, M.; Benning, C. AGO1 Defines a Novel Locus of Arabidopsis Controlling Leaf Development. EMBO J. 1998, 17, 170–180. Borsani, O.; Zhu, J.; Verslues, P. E.; Sunkar, R.; Zhu, J. K. Endogenous siRNAs Derived From a Pair of Natural Cis-antisense Transcripts Regulate Salt Tolerance in Arabidopsis. Cell 2005, 123, 1279–1291. Brain, C. F.; Beathle, G. A. An Overview of Plant Defences Against Pathogen and Herbivores. Plant Health Instructor 2003, 1. doi:10.1094/PHI-I-2008-0226-01. Brennecke, J.; Hipfner, D. R.; Stark, A.; Russell, R. B.; Cohen, S. M. Bantam Encodes a Developmentally Regulated MicroRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene Hid in Drosophila. Cell 2003, 113, 25–36. Broglie, K. I.; Chet, M.; Holliday, M. N. Transgenic Plants with Enhanced Resistance. Cell 1991, 123, 1279–1291. Cakir, C.; Tör, M. Factors Influencing Barley Stripe Mosaic Virus-mediated Gene Silencing in Wheat. Physiol. Mol. Plant Pathol. 2010, 74, 246–253. Cannon, S. Legume Comparative Genomics. Genet. Genomics Soybean 2008, 35–54. Cao, X.; Zhou, P.; Zhang, X.; Zhu, S.; Zhong, X.; Xiao, Q.; Ding, B.; Li, Y. Identification of an RNA Silencing Suppressors from a Plant Double Stranded RNA Virus. J. Virol. 2005, 79, 13018–13027. Chapman, E. J.; Prokhnevsky, A. I.; Gopinath, K.; Dolja, V. V.; Carrington, J. C. Viral RNA Silencing Suppressors Inhibit the micro-RNA Pathway at an Interphase Step. Genes Dev. 2004, 18, 1179–1186. Chaudhary, B.; Hovav, R.; Rapp, R.; Verma, N.; Udall, J. A.; Wendel, J. F. Global Analysis of Gene Expression in Cotton Fibers from Wild and Domesticated Gossypium barbadense. Evol. Dev. 2008, 10, 567–582.

Plant Disease Management Using Biotechnology

281

Chen, J.; Li, W. X.; Xie, D.; Peng, J. R.; Ding, S. W. Viral Virulence Protein Suppresses RNA Silencing-mediated Defense but Upregulates the Role of MicroRNA in Host Gene Regulation. Plant Cell 2004, 16 (5), 1302–1313. Chen, X. A microRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development. Science 2004, 303, 2022–2025. Chen, X.; Liu, J.; Cheng, Y.; Jia, D. HEN1 Functions Pleiotropically in Arabidopsis Development and Acts in C Function in the Flower. Development 2002, 129, 1085–1094. Chuang, C. F.; Meyerowtiz, E. M. Specific and Heritable Genetic Interference by Double-stranded RNA in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 2000, 97, 985–4990. Cogoni, C.; Romano, N.; Macino, G. Suppression of Gene Expression by Homologous Transgenes. Antonie Leeuwenhoek Int. J. Gen. Mol. Microbiol. 1994, 65, 205–209. Dallwitz, M. J.; Zurcher, E. J. Plant Viruses Online. In Descriptions and Lists from the VIDE Database, Brunt, A. A.; Crabtree, K.; Dallwitz, M. J.; Gibbs, A. J.; Watson, L.; Zurcher, E. J., Eds.; CAB International: UK, 1996; p 1484. Ding, X. S.; Schneider, W. L.; Chaluvadi, S. R.; Rouf Mian, R. M.; Nelson, R. S. Characterization of a Brome Mosaic Virus Strain and Its Use as a Vector for Gene Silencing in Monocotyledonous Hosts. Mol. Plant Microbe Interact. 2006, 19, 1229–1239. Du, T.; Zamore, P. D. MicroPrimer: The Biogenesis and Function of MicroRNA. Development 2005, 132, 4645–4652. Dwivedi, S.; Perotti, E.; Ortiz, R. Towards Molecular Breeding of Reproductive Traits in Cereal Crops. Plant Biotech. J. 2008, 6, 529–559. Emery, J. F.; Floyd, S. K.; Alvarez, J.; Eshed, Y.; Hawker, N. P.; Izhaki, A.; Baum, S. F.; Bowman, J. L. Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes. Curr. Biol. 2003, 13, 1768–1774. Erdmann, V. A., et al. Regulatory RNAs. Cell Mol. Life Sci. 2001, 58, 1–18. Fagwalawa, L. D.; Kutama, A. S.; Yakasai, M. T. Current Issues in Plant Disease Control: Biotechnology and Plant Disease. Bayero J. Pure Appl. Sci. 2013, 6 (2), 121–126. Finnegan, E. J.; Matzke, M. A. The Small RNA World. J. Cell Sci. 2003, 116, 4689–4693. Fire, A.; Xu, S.; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; et al. Potent and Specific Genetic Interference by Double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391, 806–811. Fitxgerald, A.; Van Kha, J. A.; Plummer, K. M. Simultaneous Silencing of Multiple Genes in the Apple Scab Fungus Venturia Inaequalis, by Expression of RNA With Chimeric Inverted Repeats. Fungal Genet. Biol. 2004, 41, 963–971. Fofana, I. B.; Sangare, A.; Collier, R.; Taylor, C.; Fauquet, C. M. A Geminivirus-induced Gene Silencing System for Gene Function Validation in Cassava. Plant Mol. Biol. 2004, 56, 613–624. Fujii, H.; Chiou, T. J.; Lin, S. I.; Aung, K.; Zhu, J. K. A miRNA Involved in Phosphatestarvation Response in Arabidopsis. Curr. Biol. 2005, 15, 2038–2043. Gasciolli, V.; Mallory, A. C.; Bartel, D. P.; Vaucheret, H. Partially Redundant Functions of Arabidopsis DICER like Enzymes and a Role for DCL4 in Producing Trans-acting siRNAs. Curr. Biol. 2005, 15, 1494–1500. Gil, S. J.; Candela, H.; Ponce, M. R. Plant microRNAs and Development. Int. J. Dev. Biol. 2005, 49, 733–744.

282

Plant Pathogens: Detection and Management for Sustainable Agriculture

Gilbert, J.; Jordan, M.; Somers, D. J.; Xing, T.; Punja, Z. K. Engineering Plants for Durable Disease Resistance. In Multigenic and Induced Systemic Resistance in Plants; Springer: New York, 2006. Gill, B. S.; Li, W.; Sood, S.; Kuraparthy, V.; Friebe, B. R.; Simons, K. J.; Zhang, Z.; Faris, J. D. Genetics and Genomics of Wheat Domestication-driven Evolution. Israel J. Plant Sci. 2007, 55, 223–229. Goldoni, M.; Azzalin, G.; Macino, G.; Cogoni, C. Efficient Gene Silencing By Expression of Double Stranded RNA in Neurospora crassa. Fungal Genet. Biol. 2004, 41, 1016–1024. Guleria, P.; Mahajan, M.; Bhardwaj, J.; Yadav, S. K. Plant Small RNAs: Biogenesis, Mode of Action and Their Roles in Abiotic Stresses. Genom. Proteom. Bioinform. 2011, 9 (9), 183–199. Gustafson, A. M.; Allen, E.; Givan, S.; Smith, D.; Carrington, J. C.; Kasschau, K. D. ASRP: The Arabidopsis Small RNA Project Database. Nucleic Acids Res. 2005, 33, D637–D640. Hackauf, B.; Rudd, S.; van der Voort, J. R.; Miedaner, T.; Wehling, P. Comparative Mapping of DNA Sequences in Rye (Secale cereale L.) in Relation to the Rice Genome. Theor. Appl. Genet. 2009, 118, 371–384. Hamada, W.; Spanu, P. D. Co-suppression of the Hydrophobin gene Hcf-1 Is Correlated with Antisense RNA Biosynthesis in Cladosporium fulvum. Mol. Gen. Genet. 1998, 259, 630–638. Hammond, T. M.; Keller, N. P. RNA Silencing in Aspergillus nidulans is Independent of RNA-dependent RNA Polymerase. Genetics 2005, 169, 607–617. Hilly, L. K.; Liu, Z. An Overview of Small RNAs. In Regulation of Gene Expression in Plants; Bassett, C. L., Ed.; Springer-Verlag: Berlin, 2007; pp 123–147. Hiraguri, A.; Itoh, R.; Kondo, N.; Nomura, Y.; Aizawa, D.; Murai, Y.; Koiwa, H.; Seki, M.; Shinozaki, K.; Fukuhara, T. Specific Interactions Between Dicer-like Proteins and HYL1/DRB-family dsRNA-binding Proteins in Arabidopsis thaliana. Plant Mol. Biol. 2005, 57, 173–188. Holzberg, S.; Brosio, P.; Gross, C.; Pogue, G. P. Barley Stripe Mosaic Virus-induced Gene Silencing in a Monocot Plant. Plant J. 2002, 30, 315–327. Issac, S. Biotechnology in the Study of Fungalplant Interaction; Chapman and Mall: London, 1992, pp 327–382. Jacque, J. M.; Triques, K.; Stevenson, M. Modulation of HIV-1 Replication by RNA Interference. Nature 2002, 418, 435–438. Jeon, J.; Choi, J.; Park, J.; Lee, Y. H. Functional Genomics in the Rice Blast Fungus to Unravel the Fungal Pathogenicity. J. Zhejiang Univ. Sci. B. 2008, 9, 747–752. Johansen, L. K.; Carrington, J. C. Silencing on the Spot. Induction and Suppression of RNA Silencing in the Agrobacterium-mediated Transient Expression System. Plant Physiol. 2001, 126, 930–938. Jones-Rhoades, M. W.; Bartel, D. P.; Bartel, B. Micro- RNAs and Their Regulatory Roles in Plants. Annu. Rev. Plant Biol 2006, 57, 19–53. Kadotani, N.; Nakayashiki, H.; Tosa, Y.; Mayama, S. RNA Silencing in the Pathogenic Fungus Magnaporthe oryzae. Mol. Plant-Microb. Interact. 2003, 16, 769–776. Khatri, M.; Rajam, M. V. Targeting Polyamines of Aspergillus Nidulans by Sirna Specific to Fungal Ornithine Decorboxylase Gene. Med. Mycol. 2007, 45, 211–220. Khraiwesha, B.; Zhua, J. K.; Zhuc, J. Role of miRNAs and siRNAs in Biotic and Abiotic Stress Responses of Plants. Biochim. Biophys. Acta. 2012, 1819 (2), 137–148.

Plant Disease Management Using Biotechnology

283

Kim, V. N. Small RNAs: Classification, Biogenesis, and Function. Mol. Cells 2005, 19, 1–15. Kim, V. N., et al. Biogenesis of Small RNAs in Animals. Nat. Rev. Mol. Cell Biol. 2009, 10, 126–139. Kjemtrup, S.; Sampson, K. S.; Peele, C. G.; Nguyen, L. V.; Conkling, M. A. Gene Silencing from Plant DNA Carried by a Geminivirus. Plant J. 1998, 14, 91–100. Klahre, U.; Crete, P.; Leuenberger, S. A.; Iglesias, V. A.; Meins, F. High Molecular Weight RNAs and Small Interfering RNAs Induce Systemic Post Transcriptional Gene Silencing in Plants. Proc. Natl Acad. Sci. USA 2002, 99, 11981–11986. Kumagai, M. H.; Donson, J.; della-Cioppa, G.; Harvey, D.; Hanley, K. Grill, L. K. Cytoplasmic Inhibition of Carotenoid Biosynthesis with Virus-derived RNA. Proc. Natl Acad. Sci. USA 1995, 92, 1679–1683. Lee, R. C.; Feinbaum, R. L.; Ambros, V. The C. elegans Heterochronic Gene lin-4 Encodes Small RNAs with Antisense Complementarity to lin-14. Cell 1993, 75, 843–854. Lehtonen, M. J.; Somervuo, P.; Valkonen, J. P. T. Infection with Rhizoctonia solani Induces Defense Genes and Systemic Resistance in Potato Sprouts Grown Without Light. Phytopathology 2008, 98, 1190–1198. Li, H. W.; Ding, S. W. Antiviral Silencing in Animals. FEBS Lett. 2005, 579, 5965–5973. Li, J.; Yang, Z.; Yu, B.; Liu, J.; Chen, X. Methylation Protects miRNAs and siRNAs from a 3-end Uridylation Activity in Arabidopsis. Curr. Biol. 2005, 15, 1501–1507. Liu, Y. L.; Schiff, M.; Kumar, D. S. P. Virus Induced Gene Silencing in Tomato. Plant J. 2002, 31, 777–786. Liu, Q.; Singh, S. P.; Green, A. G. High-stearic and High-oleic Cottonseed Oils Produced by Hairpin RNA Mediated Post-transcriptional Gene Silencing. Plant Physiol. 2002c, 129, 1732–1743. Lu, C.; Fedoroff, N. A mutation in the Arabidopsis HYL1 Gene Encoding A dsRNA Binding Protein Affects Responses to Abscisic Acid, Auxin, and Cytokinin. Plant Cell 2000, 12, 2351–2366. Lu, C.; Tej, S. S.; Luo, S.; Haudenschild, C. D.; Meyers, B. C.; Green, P. J. Elucidation of the Small RNA Component of the Transcriptome. Science 2005, 309, 1567–1569. Lu, R.; Martin-Hernandez, A. M.; Peart, J. R.; Malcuit, I.; Baulcombe, D. C. Virus Induced Gene Silencing in Plants. Methods 2003, 30, 296–303. Mallory, A. C.; Parks, G.; Endres, M. W.; Baulcombe, D.; Bowman, L. H. The Ampliconplus System for High-level Expression of Transgenes in Plants. Nat. Biotechno. 2002, 20, 622–625. Mallory, A. C.; Reinhart, B. J.; Jones-Rhoades, M. W.; Tang, G.; Zamore, P. D.; Barton, M. K.; Bartel, D. P. MicroRNA Control of PHABULOSA in Leaf Development: Importance of Pairing to the MicroRNA 5_ Region. EMBO J. 2004, 23, 3356–3364. Maloy, O. C. Plant Disease Management. Plant Instructor 2005, 0202–0201. Matsukura, C.; Aoki, K.; Fukuda, N.; Mizoguchi, T.; Asamizu, E.; Saito, T.; Shibata, D.; Ezura, H. Comprehensive Resources for Tomato Functional Genomics Based on the Miniature Model Tomato Micro-Tom. Curr. Genomics 2008, 9, 436–443. Mehrotra, R. S.; Aggarwal, A. Plant Pathology, 2nd ed.; Tata McGraw Hill Publishing Company Limited, 2003, pp. 411–423. ISBN-10: 9383286490. Nakayashiki, H. RNA Silencing in Fungi: Mechanisms and Applications. Fed. Eur. Biochem. Soc. Lett. 2005, 579, 5950–5970.

284

Plant Pathogens: Detection and Management for Sustainable Agriculture

Niu, Q. W.; Lin, S. S.; Reyes, J. L.; Chen, K. C.; Wu, H. W.; Yeh, S. D.; Chua, N. H. Expression of Artificial MicroRNAs in Transgenic Arabidopsis thaliana Confers Virus Resistance. Nat. Biotechnol. 2006, 24, 1420–1428. Novina, C. D.; Murray, M. F.; Dykxhoorn, D. M.; Beresford, P. J.; Riess, J.; Lee, S. K.; Collman, R. G.; Lieberman, J.; Shanker, P.; Sharp, P. A. siRNA-directed Inhibition of HIV-1 Infection. Nat. Mediterr. 2002, 8, 681–686. Palatnik, J. F.; Allen, E.; Wu, X.; Schommer, C.; Schwab, R.; Carrington, J. C.; Weigel, D. Control of Leaf Morphogenesis by MicroRNAs. Nature 2003, 425, 257–263. Palmer, K. E.; Rybicki, E. P. Investigation of the Potential of Maize Streak Virus to Act as an Infectious Gene Vector in Maize Plants. Arch. Virol. 2001, 14, 1089–1104. Panthee, D. R.; Chen, F. Genomics of Fungal Disease Resistance in Tomato. Curr. Genomics 2010, 11, 30–39. Parizotto, E. A.; Dunoyer, P.; Rahm, N.; Himber, C.; Voinnet, O. In Vivo Investigation of the Transcription, Processing, Endonucleolytic Activity, and Functional Relevance of the Spatial Distribution of a Plant miRNA. Genes Dev. 2004, 18, 2237–2242. Peragine, A.; Yoshikawa, M.; Wu, G.; Albrecht, H. L.; Poethig, R. S. SGS3 and SGS2/ SDE1/RDR6 Are Required for Juvenile Development and the Production of Transacting siRNAs in Arabidopsis. Genes Dev. 2004, 18, 2368–2379. Pooggin, M.; Shivaprasad, P. V.; Veluthambi, K.; Hohn, T. RNAi Targetting of DNA Viruses. Nat. Biotechnol. 2003, 21, 131–132. Publishing Co. PVT. LTD. New Delhi; pp 178–189 Qi, Y.; Denli, A. M.; Hannon, G. J. Biochemical Specialization Within Arabidopsis RNA Silencing Pathways. Mol. Cell 2005, 19, 421–428. Qu, J.; Ye, J.; Fang, R. X. Artificial microRNA-mediated Virus Resistance in Plants. J. Virol. 2007, 81, 6690–6699. Rajam, M. V. Polyamine Biosynthetic Pathway: A Potential Target for Plant Chemotherapy. Curr. Sci. 1998, 74, 729–731. Reinhart, B. J.; Slack, F. J.; Basson, M.; Pasquinelli, A. E.; Bettinger, J. C.; Rougvie, A. E.; Horvitz, H. R.; Ruvkun, G. The 21-nucleotide let-7 RNA Regulates Developmental Timing in Caenorhabditis elegans. Nature 2000, 403, 901–906. Reinhart, B. J.; Weinstein, E. G.; Rhoades, M. W.; Bartel, B.; Bartel, D. P. MicroRNAs in Plants. Genes Dev. 2002, 16, 1616–1626. Rhoades, M.; Reinhart, B.; Lim, L.; Burge, C.; Bartel, B.; Bartel, D. Prediction of Plant MicroRNA Targets. Cell 2002, 110, 513–520. Romano, N.; Macino, G. Quelling: Transient Inactivation of Gene Expression in Neurospora Crassa by Transformation with Homologous Sequences. Mol. Microbiol. 1992, 6, 3343–3353. Rubio-Somoza, I., et al. Regulation and Functional Specialization of Small RNA–target Nodes During Plant Development. Curr. Opin. Plant Biol. 2009, 12, 622–627. Ruiz-Ferrer, V.; Voinnet, O. Viral Suppression of RNA Silencing: 2b Wins the Golden Fleece by Defeating Argonaute. Bioassays 2007, 29, 319–323. Rymarquis, L. A., et al. Diamonds in the Rough: mRNA-like Non-coding RNAs. Trends Plant Sci. 2008, 13, 329–334. Schauer, S. E.; Jacobsen, S. E.; Meinke, D. W.; Ray, A. DICER-LIKE1: Blind Men and Elephants in Arabidopsis development. Trends Plant Sci. 2002, 7, 487–491.

Plant Disease Management Using Biotechnology

285

Schweizer, P.; Pokorny, J.; Schulze-Lefert, P.; Dudler, R. Double Stranded RNA Interference with Gene Functions at the Single Cell in Cereals. Plant J. 2000, 24, 895–903. Scofield, S. R.; Huang, L.; Brandt, A. S.; Gill, B. S. Development of a Virus-induced Gene Silencing System for Hexaploid Wheat and Its Use in Functional Analysis of the Lr21 Mediated Leaf Rust Resistance Pathway. Plant Physiol. 2005, 138, 2165–2173. Segers, G. C.; Hamada, W.; Oliver, R. P.; Spanu, P. D. Isolation and Characteristaion of Five Different Hydrophobin-encoding cDNA from the Fungal Tomato Pathogen Cladosporium fulvum. Mol. Gen. Genet. 1999, 261, 644–652. Singh, R. S. Plant Disease Management; Oxford and IBN New Delhi, 2001; pp 234–245. ISBN-10: 1578081602. Singh, R. S. Introduction to Principles of Plant Pathology, 4th edn.; Oxford and IBH, 2005. ISBN-9788120415515. Stricklin, S. L., et al. C. elegans Noncoding RNA Genes. In WormBook, The C. elegans Research Community, Ed.; WormBook, 2005. doi/10.1895/wormbook.1.1.1. Szymanski, M., et al. Noncoding RNA Transcripts. J. Appl. Genet. 2003, 44, 1–19. Talbot, N. J.; Kershaw, M. J.; Wakley, G. E.; de Vries, O. M. H.; Wessels, J. G. H.; Hamer, J. E. MPG1 Encodes a Fungal Hydrophobin Involved in Surface Interactions During Infection-related Development of Magnaporthe grisea. Plant Cell 1996, 8, 985–999. Tang, W.; Weidner, D. A.; Hu, B. Y.; Newton, R. J.; Hu, X. Efficient Delivery of Small Interfering RNA to Plant Cells by a Nanosecond Pulsed Laser-induced Wave for Post Transcriptional Gene Silencing. Plant Sci. 2006, 171, 375–381. Telfer, A.; Poethig, R. S. Hasty: A Gene That Regulates the Timing of Shoot Maturation in Arabidopsis Thaliana. Development 1998, 125, 1889–1898. Teycheney, P. Y.; Tepfer, M. Virus Specific Spatial Differences in the Interference with Silencing of the chs-A Gene in Non-transgenic Petunia. J. Gen. Virol. 2001, 82, 1239–1243. Tinoco, M. L.; Dias, B. B.; Dall’Astta, R. C.; Pamphile, J. A.; Aragão, F. J. In vivo Transspecific Gene Silencing in Fungal Cells by in Planta Expression of a Double-stranded RNA. BMC Biol. 2010, 8, 27. Tomilov, A. A.; Tomilova, N. B.; Wroblewski, T.; Michelmore, R.; Yoder, J. I. Transspecific Gene Silencing Between Host and Parasitic Plants. Plant J. 2008, 56, 389–397. Turnage, M. A.; Muangsan, N.; Peele, C. G.; Robertson, D. Geminivirus-based Vectors for Gene Silencing in Arabidopsis. Plant J. 2002, 30, 107–117. Ullu, E.; Djikeng, A.; Shi, H.; Tschudi, C. RNA Interference: Advances and Questions. Phil. Trans. Royal Soc. London British Biol. Sci. 2002, 29, 65–70. Vanitharani, R.; Chellappan, P.; Fauquet, C. M. Short Interfering RNA-mediated Interference of Gene Expression and Viral DNA Accumulation in Cultured Plant Cells. Proc. Natl Acad. Sci. USA 2003, 100, 9632–9636. Vaucheret, H. Post-transcriptional Small RNA Pathways in Plants: Mechanisms and Regulations. Genes Dev. 2006, 20, 759–771. Vaucheret, H.; Vazquez, F.; Crété, P.; Bartel, D. P. The Action of ARGONAUTE1 in the miRNA Pathway and Its Regulation by the miRNA Pathway are Crucial for Plant Development. Genes Dev. 2004, 18, 1187–1197. Vazquez, F.; Gasciolli, V.; Crété, P.; Vaucheret, H. The Nuclear dsRNA Binding Protein Hyl1 is Required for Microrna Accumulation and Plant Development, but Not Posttranscriptional Transgene Silencing. Curr. Biol. 2004a, 14, 346–351.

286

Plant Pathogens: Detection and Management for Sustainable Agriculture

Vazquez, F.; Vaucheret, H.; Rajagopalan, R.; Lepers, C.; Gasciolli, V.; Mallory, A. C.; Hilbert, J. L.; Bartel, D. P.; Crete, P. Endogenous Trans-acting siRNAs Regulate the Accumulation of Arabidopsis mRNAs. Mol. Cell 2004b, 16, 69–79. Voinnet, O. RNA Silencing as a Plant Immune System against Viruses. Trends Genet. 2001, 17, 449–459. Wang, X. J.; Gaasterland, T.; Chua, N. H. Genomewide Prediction and Identification of Cis-natural Antisense Transcripts in Arabidopsis thaliana. Genome Biol. 2005, 6, R30. Wang, N.; Wang, Y. J.; Tian, F.; King, G. J.; Zhang, C. Y.; Long, Y.; Shi, L.; Meng, J. L. A Functional Genomics Resource for Brassica Napus, Development of an EMS Mutagenized Population and Discovery of FAE1 Point Mutations by Tilling. New Phytologist 2008, 180, 751–765. Wani, S. H.; Sanghera, G. S. Genetic Engineering for Viral Disease Management in Plants. Notulae Scientia Biologicae 2010a, 2, 20–28. Wani, S. H.; Sanghera, G. S.; Singh, N. B. Biotechnology and Plant Disease Control-role of RNA Interference. Am. J. Plant Sci. 2010b, 1, 55–68. Waterhouse, P. M.; Graham, M. W.; Wang, M. B. Virus Resistance and Gene Silencing in Plants can be Induced by Simultaneous Expression of Sense and Antisense RNA. Proc. Natl. Acad. Sci. USA 1998, 95, 13959–13964. Waterhouse, P. M.; Wang, M. B.; Lough, T. Gene Silencing as an Adaptive Defense against Viruses. Nature 2001, 411, 834–842. Xie, Z.; Kasschau, K. D.; Carrington, J. C. Negative Feedback Regulation of Dicer-Like1 in Arabidopsis by MicroRNA-guided mRNA. Curr. Biol. 2003, 13, 784–789. Xie, Z.; Johansen, L. K.; Gustafson, A. M.; Kasschau, K. D.; Lellis, A. D.; Zilberman, D.; Jacobsen, S. E.; Carrington, J. C. Genetic and Functional Diversification of Small RNA Pathways in Plants. PLoS Biol. 2004, 2, 642–652. Xie, Z.; Allen, E.; Fahlgren, N.; Calamar, A.; Givan, S. A.; Carrington, J. C. Expression of Arabidopsis MIRNA genes. Plant Physiol. 2005a, 138, 2145–2154. Xie, Z.; Allen, E.; Wilken, A.; Carrington, J. C. DICER-Like 4 Functions in Trans-acting Small Interfering RNA Biogenesis and Vegetative Phase Change in Arabidopsis thaliana. Proc. Natl. Acad. Sci. 2005b, 102, 12984–12989. Yang, J.; Lu, Z.; Luo, Y.; Bi, W.; Zhu, M.; Zhang, K. Q. Involvement of the Putative G-Protein a Subunit Gene PNGPA1 in the Regulation of Growth, Sensitivity to Fungicides, and Osmotic Stress in Phytophthora nicotianae. Afr. J. Microbiol. Res. 2012, 6, 680–689. Yoshikawa, M.; Peragine, A.; Park, M. Y.; Poethig, R. S. A Pathway for the Biogenesis of Trans-acting siRNAs in Arabidopsis. Genes Dev. 2005, 19, 2164–2175.

CHAPTER 13

Engineering Plastid Pathways: An Environment-Friendly Alternative for in Planta Transformation BHAVIN S. BHATT1 and ACHUIT K. SINGH2,*

Shree Ramkrishna I nstitute of Computer Education and Applied Sciences, Surat, Gujarat, India 1

Crop Improvement Division, ICAR Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India

2

*

Corresponding author. E-mail: [email protected]

ABSTRACT The chloroplast, site of photosynthesis in higher plants and algae, fixes atmospheric CO2 to sugar and thus occupies a central position as the primary source of food. Every living organisms are directly or indirectly associated for their food requirements and thus survival to these green “plants.” Plastids of higher plants are semiautonomous and they represent cellular fraction of the cell, transmitted maternally during reproduction. Chloroplast genome is circular, self-replicating, multicopy number, highly polyploid, and has its own transcription–translation machinery. Chloroplast genome, plastome, represents 10–20% of total cellular genome despite of small size and codes for as many 130 genes. Due to their circular genome nature, plastome offers a homely environment to “incoming” transgene embedded in a circular vehicle, provides more chances of site-specific integration through homologous recombination. Transgene restraint due to lack of pollen transmission and maternal inheritance offers a great advantage over facile methods of plant genetic transformation through nuclear genome. Furthermore, high level of

288

Plant Pathogens: Detection and Management for Sustainable Agriculture

transgene expression and lack of gene silencing are an added advantage of plastid transformation. The study of chloroplast genome transformation leads to understanding of biochemistry and physiology of plastid metabolism. This article summarizes plastome organization and regeneration, the transformation process, and highlights selected applications of transplastomic technologies in basic and applied research. 13.1 INTRODUCTION The current global population of the world is 6.4 billion and is experiencing steady increase by each year and expected to reach 10 billion by the year 2050.1 On the other hand, the rate of agricultural yield remains stagnant due to either crop loss by various stresses or poor quality yield.2 Such agricultural food product digression results in widening the existing gap between demand and supply and ultimately leads to malnutrition or starvation, mainly to underdevelop or developing country people.3 Traditional methods of crop improvement programs often includes selective breeding for desired traits, which is now no more applicable for increasing productivity or quality, where such colossal gap exists between demand and supply. Furthermore, urbanization and marginal or salty acreage are stretching the gap to an extent to be filled by such traditional options. The only hope to this situation seems to be “Green Revolution.” As our understanding about system biology and genetic traits contributing to quality and yield has been increased to several fold, it can be combined with traditional breeding programs to produce good amount of “grain” crops. The term Green Revolution has been used by the popular press to describe the spectacular increase in cereal–grain production during the past several years. Father of green revolution and 1970 Nobel Peace Prize winner, Norman Borlaug also sees hopes in biotechnology to ameliorate environmental concerns, while meeting the rising demand for agricultural production.4 The main concerns lies in plant transgenic is to combat with various stresses that plant experience in the natural environments. The stresses that plant exhibit can be broadly classified into biotic (fungal, bacterial, viral, etc., infection) and abiotic stress (drought, salinity, etc.). Also, transgenic variety for better or improved yield through the incorporation of novel DNA into the genome possess stress on performance of plant.5,6 Such transgenics, although often offers better products, are severely criticized and compounded by negative public sentiment through the fear of

Engineering Plastid Pathways

289

transgene escape via pollen or seeds. Without the universal public acceptance and clearance from regulatory agencies, such recent advancements are of limited use, up to the bench only. The bench-proven technologies can only be translated to the field once it assures concomitant threat to the environment. Since much threat to sow transgenic crops centered on its spread and disturbance of native habitat and diversity, solving this problem through restricted or no spreading of such crop or crop parts allows use of transgenic by wider range of people. Crop plants possess two genomes in addition to that of the nucleus, the organelle genomes of mitochondria and chloroplasts. These cytoplasmic organelles are transferred to progeny, upon division, by mother cells. Such maternal inheritance checks any spread of novel genes in the native environment. Chloroplasts genetic engineering of higher plants may offer the potential to mitigate certain limitations of agricultural productivity. Technological advances, most notably the invention of the particle accelerator7 and the ability to express foreign genes in plastids,8,9 have provided the opportunity to explore the chloroplast genome as a new platform to address current and future demands for improved food production. Such novel idea has already been explored for number of traits conferring to plants like insect resistance, herbicide resistance, salt tolerance, drought tolerance, phytoremediation, etc. Results of such experiments are very promising and will cast plastid transformation as most widely accepted technology in future for in planta transformation/s. Green plants are autotrophic in nature and hence they directly or indirectly are important for all forms of present day living organisms for their food requirement. The central mechanisms, exclusively found in green plants is photosynthesis and is maintained in chloroplasts which are present in all plants, with the exception of the few parasitic plants which have lost autotrophy. To maintain a high photosynthetic capacity, the number of chloroplasts per cell has tremendously increased during evolution. Endosymbiotic theory suggests that chloroplasts have originated from cyanobacteria. Mereschkowsky in 1905 first suggested this hypothesis after an observation by Schimper in 1883.10 Such first-generation endosymbionts gave birth to second- and third-generation endosymbionts by engulfing the previous organism. Such series of endosymbionts shows degree of changes in structure and appearance of chloroplast. For example, Protists, Euglenozoa, etc. are second-generation endosymbionts containing

290

Plant Pathogens: Detection and Management for Sustainable Agriculture

chloroplasts, forming chloroplasts with three or four membrane layers. In the alga Chlorella, there is only one chloroplast, which is bell shaped. In higher plants, chloroplasts are derived from proplastids, from pre-existing chloroplasts or from other forms of plastids. Many a times, chloroplasts are referred as different names depending upon their tissue existence. There are several types of plastid including: (1) chlorophyll containing chloroplasts; (2) yellow, orange, or red carotenoid-containing chromoplasts; (3) starch-storing amyloplasts; (4) oil-containing elaioplasts; (5) proplastids (plastid precursors found in most plant cells); and (6) etioplasts (partially developed chloroplasts that form in dark-grown seedlings). The conversion of photosynthetic chloroplasts into yellow carotenoid-rich chromoplasts is seen in the ripening of bananas; the conversion of chloroplasts to lycopene-containing red chromoplasts is seen in the ripening of tomatoes. Each compartment of the eukaryotic cell is unique. A particular biochemistry can be favored in one compartment (e.g., chloroplasts or chromoplasts), while the environment in another compartment (e.g., the cytoplasm) is unfavorable. Protoplastids are originated from meristematic cells and developed according to tissue type to which they are located. Seed germination in soil is light independent process. Etioplasts, present in cotyledon cells, are marked with pseudocrystalline structure, the prolamellar body, and many ribosomes to support active “compartmental” translation and setting up the photosynthetic apparatus.11 In the presence of light, thylakoids are formed, emerging from the crystalline body. The determination of the components of the chloroplast genetic system and the analysis of their regulation is essential in at least two ways: (1) Determining pathways for early chloroplast division and differentiation and (2) to understand spatial and temporal expression of chloroplast genome. The chloroplast is surrounded by a double-layered composite membrane, which is analogous to the outer and inner membranes of the ancestral cyanobacteria, with an intermembrane space; further, it has reticulations, or many infoldings, filling the inner spaces. The chloroplast has its own DNA, which codes for redox proteins involved in electron transport in photosynthesis; this is termed as the plastome. Plastome is a kind of ancestral genome, mostly similar in organization and structure to prokaryotic genome. Presence of such exclusive genome, chloroplasts are emerging as new sight for novel gene transformation.

Engineering Plastid Pathways

291

13.2 CHLOROPLAST GENOME ORGANIZATION The chloroplast genomes of vascular plants and most algae are quite similar. The structure and organization of chloroplast genomes deduce greatest diversity and differences with respect to nuclear genome counterparts. With one possible exception of Acetabularia, all known chloroplast genomes are circular DNA molecules. Size variation is greatest among green algae in which most chloroplast genomes range between about 85 and 300 kb, while that of angiosperm is 120–180 kb in range, with majority is 135–160 kb. Pioneering works of Kowallik and Herrmann (1970) identified a series of discrete areas spread throughout the plastid, which supports the hypothesis of nucleoid organization of plastid genome.12 These nucleoids are readily observed in chloroplasts stained by DAPI (4', 6- diamidino2-phenylindole) using fluorescent microscopy.13 The plastid DNA, also named plastid chromosome or plastome, is a circular double-stranded, negatively supercoiled molecule with 85% single copy sequences and multicopy number per plastid, organized into several nucleoids. Nucleoids appear interconnected in young and mature chloroplasts. A small number of nucleoids are present in proplastids but this number is readily increased as plastid matures. During active plastid development and division, nucleoids are attached with inner membrane of plastid through protein named PEND (plastid envelope DNA binding) and might be involved in DNA replication. Such PEND association is diminished upon maturation and sets nucleotides free to attach with formed thylekoid membrane. The plastid chromosome exists as a negatively supercoiled molecule.14 The analysis of DNA conformation by pulse-field electrophoresis showed that molecules are present as monomers, dimers, trimers, and tetramers in a relative amount of 1, 1/3, 1/9, and 1/27, respectively. A number of genes have been located on the circle and one of the important features is the presence of two copies of the ribosomal DNA sequences. These sequences are often but not always present on a large inverted repeat. Other genes mapped include those for the large subunit of RuBP-Case (ribulose-1, 5-bisphosphate oxygenase/carboxylase), tRNAs, subunits of ATP synthase, and cytochrome oxidase.15 Plastid genome organization and structural features are conserved during the path of evolution. The circular molecule can be divided into three distinct domains: large single copy (LSC), small single copy (SSC), and the inverted repeat (IR) which is present in exact duplicate separated by the two single copy

292

Plant Pathogens: Detection and Management for Sustainable Agriculture

regions. Restriction fragment length polymorphism (RFLP) analysis indicates that the molecule exists in two orientations present in equimolar proportions within a single plant.16 The circular molecule undergoes interconversion to a dumbbell-shaped conformation that is believed to be facilitated by the presence of the IR. Concerted evolution within the IR suggests intramolecular recombination between the repeats is a possible mechanism. The plastid RecA homolog is thought to be responsible for the site-specific integration of foreign DNA sequences in the plastid genome by homologous recombination. The A (adenine)–T (thymine) content is not evenly distributed in the plastome. It is higher in noncoding regions and is lower in regions coding for tRNA and for the rRNAs. The plastome of higher plants contains four ribosomal RNA genes, 30 tRNA genes, more than 72 genes encoding polypeptides, and several conserved reading frames (ycf) coding for proteins of yet unknown function (Fig. 13.1).17,18 Transcriptome of chloroplast represents total pool of RNA required for polypeptide synthesis required for chloroplast functioning, and no RNA is transported from outside chloroplast. The plastid genes coding for polypeptides can be classified into several categories: genes coding for prokaryotic RNA polymerase core enzyme; genes coding for proteins of the translational apparatus; for the photosynthetic apparatus and genes coding for subunits of the NADH-dehydrogenase (NDH). 13.3 CHLOROPLAST TRANSFORMATION 13.3.1 HISTORY AND DEVELOPMENT In plant cell, there are three gene factories, which are working independently and are available for in planta transformations are nucleus, chloroplast, and mitochondria. For very obvious reason, expression of foreign genes by nuclear transformation is most adapted route since long. When concept was emerged, chloroplast genetic engineering is limited to transform foreign gene/s to propoplasts followed by in vitro propagation. Such procedure is very tedious and requires up to date and accurate methodology for transformation and plant regeneration.9,19 Later, invention of newer advanced methods for transformation have eroded out such protracted procedures and allowed direct introduction of foreign genes into chloroplast embedded in plant cell. Furthermore, availability of newer marker genes for selection of true transformants has made plastid transformation as one of the good

Engineering Plastid Pathways

293

alternative for sustainable agriculture. Boynton et al. (1988) first reported stable transgene integration in intact chloroplast in Chlamydomonas.7 After the first in situ chloroplast transformation in Chlamydomonas reinhardtii, notion had been extended to higher plant, Nicotiana tabacum.9,20 Up to date, plastid transformation has extended to many other higher plants, such as Arabidopsis,21 grape,22 potato,23 lettuce,24 soybean,25 cotton,26 carrot,27 and tomato.28 However, plastid transformation is routine only in tobacco and with no known reason, the efficiency of transformation is much higher in tobacco than any other plants.29 With technical developments of transformation system, plastid gene expression and plastome gene availability, “transplastomic” studies is widely getting attention of plant biologists.

FIGURE 13.1 General structure of chloroplast genome. IR, inverted repeat region; LSC, large single copy subunit; SSC, small single copy subunit.

294

Plant Pathogens: Detection and Management for Sustainable Agriculture

13.3.2 TRANSFORMATION METHOD DEVELOPMENT There are apparent differences between transgenomic and transplastomic procedures (Table 13.1). Unlike nuclear transformation, genetic transformation in plastids follows integration of transgene through homologous recombination. Transgene should be flanked by plastid DNA sequences for site-specific insertion (Fig. 13.2).30 Foreign gene transplantation to plastid, in general, involves four distinct steps. 1. Construction and delivery of foreign gene cassette into chloroplast. 2. Integration of foreign gene with chloroplast geneome through homologus recombination. 3. Selection of transformants. 4. Regeneration of true and stable transformants expressing desired trait/s of foreign gene/s transplanted. TABLE 13.1

Apparent Differences of Nuclear and Chloroplast Genome of Angiosperms. Nuclear genome

Chloroplast genome

Chromosomes Present in duplicate copies, one of Multiple copies. ~60–100 copies per which serves as a dominant allele plastid and ~50–60 plastids per cell. of gene while other is recessive. Circular form Linear form Genetic organization

Genes are varied in a range of thousand per chromosome

~120–150 genes per plastome

Gene arrangements

Monocistronic. One gene is under Polycistronic. In an operon cluster, the control of single promoter as in prokaryotic genome. Many genes are under the control of single promoter c and be transcribed together

FIGURE 13.2 (See color insert.) Foreign gene integration in chloroplast genome through homologous recombination.

Engineering Plastid Pathways

295

Biolistic or particle bombardment method is generally employed for chloroplast transformation, in which the plasmid containing a marker gene and the gene of interest were introduced into chloroplasts or plastids. The foreign genes were inserted into plasmid DNA by homologous recombination via the flanking sequences at the insertion site. Also, Agrobacterium31 and polyethylene glycol (PEG)32-mediated transformation procedures were adopted in earlier days; they were quickly diminished due to lower transformation/regeneration capacity. The first successful chloroplast transformation in Chlamydomonas reinhardtii was employed by particle bombardment. The availability of standardized protocols for efficient transformation and regeneration, make biolistic is a choice of procedure (Table 13.2). TABLE 13.2 Chloroplast Transformation Methods and Expressed Foreign Gene for Selected Plant Species. Species

Selection of transformants Photosynthetic Chlamydomonas Particle bombardment proficiency reinhardtii PEG Spectinomycin Nicotiana tabaccum Particle Kanamycin Nicotiana bombardment tabaccum Particle Spectinomycin Arabidopsis bombardment thaliana Particle Spectinomycin Daucus carota bombardment (carrot) Rice

Methods

Particle bombardment

Expressed genes

Reference

atpB (ATP Synthase β Subunit) Rrn16 (16S rRNA)

[7]

Npt II (Neomycin Phosphotransferase) aadA (Aminoglycoside adenyl transferase) BADH (betaine aldehyde dehydrogenase) Spectinomycin aadA and GFP

[20] [33] [21] [27]

[34]

13.3.3 SELECTABLE/SCREENABLE MARKER GENE/S Plastid DNA is present in multiple copies, hence choice of selectable marker genes are critically important to achieve uniform transformation of all genome copies during an enrichment process that involves gradual sorting out of nontransformed plastids on a selective medium.29 The first selection marker gene used in chloroplast transformation was plastid 16S rRNA (rrn16) gene.20 Transgenic lines were selected by spectinomycin resistance and the efficiency was low. The alternate is aadA gene encoding

296

Plant Pathogens: Detection and Management for Sustainable Agriculture

aminoglycoside 3′-adenylyltransferase was used as a selection marker gene35,36 which increases recovery of plastid transformants. Kanamycinresistant gene npt II was used as a selectable marker for plastid transformation in tobacco, but the transformation efficiency was low. A dramatic improvement in plastid transformation efficiency was obtained by a highly expressed neo gene, confers resistance to kanamycin. The bacterial bar gene, encoding phosphinothricin acetyltransferase, has also been tested as a marker gene, but it was not good enough.37 Another marker gene is the betaine aldehyde dehydrogenase (BADH) gene which confers resistance to betaine aldehyde. Chloroplast transformation efficiency was 25-fold higher with betaine aldehyde (BA) selection than with spectinomycin in tobacco.19 Transgenic carrot plants expressing BADH could be grown in the presence of high concentrations of NaCl (up to 400 mM).27 But there is no additional report about the use of BA selection. 13.3.4 INSERTION SITES As discussed earlier, plastid transformation is always accomplished by homologous recombination and hence insertion cassette should possess left and right flanking sequences each with 1–2 kb in size from the host plastid genome.38 The site of insertion in the plastid genome is determined by the choice of ptDNA (plastid DNA) segment flanking the marker gene and the gene of interest. Insertion of foreign DNA in intergenic regions of the plastid genome had been accomplished at 16 sites, of which three are most commonly used. Two of three insertion sites are located in IR, insertion in which results into rapid doubling of transgene, while the rest one is in the LSC region of the ptDNA, and the gene inserted should have only one copy per ptDNA.39 13.3.5 REGULATORY SEQUENCES The gene expression level in plastids is predominately determined by promoter sequence and 5′-untranslated region (UTR) elements.40 Therefore, plastid expression vectors should have apposite 5′-UTRd including a ribosomal-binding site. The foremost aim of plastid transformation is expression of transgene at a higher level for protein production. Such high level protein production and accumulation from expression of the transgene is achieved

Engineering Plastid Pathways

297

by strong promoter upstream of transgene, which supports multicopy transcription of gene. Protein accumulation from the transgene depends on the 5′-UTR inserted upstream of the open reading frame encoding the genes of interest. Plastid rRNA operon (rrn) promoter (Prrn) promoter provides such higher level of inducible gene expression and may provide amplification up to 10,000-fold. Stability of the transgenic mRNA is ensured by the 5′-UTR and 3′-UTR sequences flanking the transgenes. 13.3.6 CONTROLLED EXPRESSION OF PLASTID TRANSGENE IN PLANTS Although plastid gene expression provides numbers of advantages over nuclear transformation, it mainly lacks tightly controllable systems for transgene expression and tissue-specific developmentally regulated control mechanisms. Deleterious phenotypic effect and significant metabolic burden due to higher level of transgene expression calls for tissue or organ or stage definite transgene expression. Deleterious effects are often results of constitutive transgene expression which could be accomplished by making transgene expression dependent on an inducer. Such inducible systems can be constructed by expression of marker gene under the pressure of external stimuli. Examples are β-glucuronidase (GUS) reporter gene under the control of phage T7 promoter was introduced into the plastid genome of plants. GUS expression was dependent on nuclear-encoded plastid targeted T7 RNA polymerase (T7 RNAP) activity.41 More recently, a Lac repressor-based IPTG-inducible expression system for plastids has been reported for external control of plastid gene expression which is based entirely on plastid components and can therefore be established in a single transformation step.42 13.3.7 CHLOROPLAST TRANSFORMATION: ENVIRONMENT FRIENDLY AND ADVANTAGEOUS IN PLANTA TRANSFORMATION ALTERNATIVE Chloroplasts are main source of photosynthesis in plants and green algae. They are the sites which fix atmospheric CO2 to organic carbon and thus harboring autotrophy to plants and are the primary source of the world’s food productivity and they sustain life on this planet. Apart from working as “food factories,” plastids are also nature’s cleaning agents which are actively involved in evolution of oxygen, sequestration of carbon,

298

Plant Pathogens: Detection and Management for Sustainable Agriculture

production of starch, synthesis of amino acids, fatty acids, and pigments, and key aspects of sulfur and nitrogen metabolism. The main advantage with plastid transformation is lower environmental risks through biological containment.19,43 In most angiosperm plant species, plastid genes are maternally inherited44,45 and therefore transgenes in these plastids are not disseminated by pollen, thus abolishing any chances of transgenes spread through breeding. This makes plastid transformation a valuable tool for the creation and cultivation of genetically modified plants without unnecessary escape of transgene to nearby habitats and allows coexistence of conventional and genetically modified crop.19,46 Cytoplasmic male sterility presents a further genetic engineering approach for transgene containment.47 Stable integration of transgene through site-specific homologous recombination results into accumulation of large amounts of foreign protein (up to 46% of total leaf protein) due to the polyploidy of the plastid genetic system with up to 10,000 copies of the chloroplast genome in each plant cell. Such site-specific integration into the chloroplast genome by homologous recombination of flanking chloroplast DNA sequences present in the chloroplast vector eliminates the concerns of position effect which is frequently observed in nuclear transformations.19 Other advantages seen in chloroplast transgenic plants include the lack of transgene silencing and transgene stacking, that is, simultaneous expression of multiple transgenes, creating an opportunity to produce multivalent vaccines in a single transformation step. Moreover, foreign proteins synthesized in chloroplasts are properly folded with appropriate posttranscriptional modifications, including disulfide bonds48,49 and lipid modifications50 Furthermore, plant-derived therapeutic proteins are free of human pathogens and mammalian viral vectors. Therefore, plastids provide a viable alternative to conventional production systems such as microbial fermentation or mammalian cell culture. Comparison between transgenomic and transplastomic technologies is summarized in Table 13.3. 13.4 APPLICATIONS OF PLASTID TRANSFORMATION 13.4.1 ENGINEERING THE CHLOROPLAST GENOME FOR HERBICIDE RESISTANCE A herbicide, commonly known as a weed killer, is a type of pesticide used to kill unwanted plants. Glyphosate is a potent, broad-spectrum herbicide that is highly effective against grasses and broad-leaf weeds. Glyphosate works

Engineering Plastid Pathways

299

by competitive inhibition of an enzyme in the aromatic amino acid biosynthetic pathway, 5-enol-pyruvyl shikimate-3-phosphate synthase (EPSPS).51 Unfortunately, like most commonly used herbicides, glyphosate does not distinguish crops from weeds, thereby restricting its use. The apparent solution to this problem is engineering of desired crop for herbicide resistance. However, this approach raises the concern that if the engineered resistance gene escapes via pollen dispersal, it might result in resistant weeds or might cause genetic pollution among other crops.52 Since chloroplasts are maternally inherited, they offer a solution to this problem. The chloroplast of pollen is metabolically active but the plastid DNA is lost during pollen maturation and hence is not transmitted to the next generation.53,54 In addition, the target proteins for many herbicides are compartmentalized within the chloroplast. Petunia EPSPS nuclear gene is expressed in chloroplast and resultant transgenic plants are resistant to 10-fold higher levels of glyphosate than the lethal dosage, and the transgene is maternally inherited. Recently, the Agrobacterium EPSPS gene (C4) was expressed in tobacco plastids and resulted in 250-fold higher levels of the glyphosate-resistant C4 protein than were achieved via nuclear transformation. Even though C4 expression in plastids was enhanced more than nuclear expression levels, field tolerance to glyphosate remained the same, showing that higher levels of expression do not always proportionately increase herbicide tolerance.55 Similarly, expression of bar gene in the plastid genome provides herbicide resistance in an environmentally proscribed manner.37 TABLE 13.3

Comparison Between Transgenomic and Transplastomic Technologies.

Property Biological containment

Transgenomic technologies Nuclear genes are inherited equally from both parents. There will be high risk of transgene transfer into nearby nontransgenic plants. Level of gene expression is limited as there is only one gene copy number per cell.

Transplastomic technologies Chloroplasts are maternally inherited in most of angiosperms. There is no risk of transgene transmission through pollen to undesired non transgenic plants. Level of Level of gene expression is high as expression number of chloroplasts per cell is high. It has been estimated that chloroplast transformation will result in 40% of rise in transgenic protein production. Gene silencing There will be chance of no The transgene expression in chloroplast expression of transgene through is more stable. Transgene expression is posttranscriptional gene silencing or independent of effect of nuclear gene through RNA interference. silencing.

300

Plant Pathogens: Detection and Management for Sustainable Agriculture

TABLE 13.3  (Continued) Property

Transgenomic technologies

Transplastomic technologies

Elimination of Nuclear genes are universally toxic effects of expressed in all parts of the plant. transgenes

Chloroplast gene is downregulated in non-green parts of the plants (viz. flowers, fruits etc.). The effect of transgene products in these parts is minimum. Multiple gene Expression of polycistronic mRNA, Chloroplast can able to express transfer under single promoter, is not polycistronic mRNA, under single successful in nuclear transformation. promoter. Thus, a bacterial operon or complete biosynthetic pathway genes can be transformed to chloroplast genome. Protein Nuclear genes are translated through Chloroplast possess 70S ribosome, which synthesis eukaryotic 80S ribosomes, which is more suitable for expression of bacterial is not suitable for microbial gene genes. translation. Frequency Frequency of nuclear transformation Frequency of chloroplast transformation is higher. is lower. Section Mendelian inheritance of transgenes. Maternal inheritance of transgenes. To procedures Selection can be done in F1 hybrids. obtain pure line of hybrids, it require 2-4 generations and selection pressure. Method of The transgene transfer into chloroplast is Many biological (Agrobacterium transformation mediated) and non-biological very peculiar process and require stringent (Biolistic) methods are standardized regeneration protocol from chloroplast. and available in literature Site of Transgenomic transgenes will show Transplastomic transgenes show product accumulation their expression uniformly in any accumulation in green parts of the plants parts of the plants. only.

13.4.2 ENGINEERING BACTERIAL OPERONS VIA CHLOROPLAST GENOMES IN POLYCISTRONIC MANNER Typical eukaryotic and hence plant nuclear mRNAs are monocistronic. This poses a serious drawback when engineering multiple genes or metabolic engineering, end product of either of which is resultant of cascade of pathway.56,57 For such nuclear transformations, single genes were first introduced into individual plants, which were then backcrossed to reconstitute the entire pathway or the complete protein.58 The striking example is “Golden” rice expressing a biosynthetic pathway for β-carotene expression.59 By contrast, most chloroplast genes are arranged in an operon structure under the action of single promoter and cotranscribed as polycistronic RNAs, which are subsequently processed

Engineering Plastid Pathways

301

to form translatable transcripts. Therefore, introduction of multiple chloroplast transgenes arranged in an operon should allow expression of entire pathways in a single transformation event. Recently, the Bt cry2Aa2 three gene operon was used as a model system to test the feasibility of multigene operon expression in engineered chloroplasts.60 Operon-derived Cry2Aa2 protein accumulates in transgenic chloroplasts as cuboidal crystals, to a level of 45.3% of the total soluble protein (tsp) and remains stable even in senescing leaves (46.1%). This is the highest level of foreign gene expression ever reported in transgenic plants, killing insects that are exceedingly difficult to control.61 Importantly, pollens are free of such insecticidal proteins, thus eliminating potential harm to nontarget insects. This first demonstration of bacterial operon expression in transgenic plants opens the door to engineer novel pathways in a single transformation event. 13.4.3 ENGINEERING THE CHLOROPLAST GENOME FOR PATHOGEN RESISTANCE Plant pathogens possess serious threat to crop yields and quality, sometimes up to 100% depending upon infection severity. Hence, continuous efforts are made to engineer plants that are resistant to pathogenic bacteria and fungi. Amphipathic peptides are possible hope for fighting a battle against such pathogens. Such amphipathic peptides like MSI- 99 forms α-helical molecule with affinity for the negatively charged phospholipids found in the outer membrane of bacteria and fungi. Upon contact with these membranes, aggregation of individual peptides forms barrel-like structure embedding the plasma membrane of bacteria or fungi, resulting in lysis. Because of the concentration-dependent action of antimicrobial peptides, MSI- 99 was expressed via the chloroplast genome to accomplish high-dose release at the point of infection. In vitro and in planta assays confirmed that the peptide was expressed at high levels (up to 21.5% tsp) and retained biological activity against Pseudomonas syringae, a major plant pathogen.61 Importantly, growth and development of the transgenic plants were unaffected by hyper expression of MSI-99 within chloroplasts. Because the outer membrane is an essential and highly conserved part of all microbial cells, microorganisms are unlikely to develop resistance against these peptides. Therefore, these results give a new option in the combat against phytopathogens.

302

Plant Pathogens: Detection and Management for Sustainable Agriculture

13.4.4 ENGINEERING THE CHLOROPLAST GENOME FOR DROUGHT TOLERANCE Apart from phytopathogens, abiotic stress like water stress caused by drought, salinity, or freezing also possesses great risk to the plant growth and development.62 Trehalose is a non-reducing disaccharide of glucose which is synthesized by the trehalose-6-phosphate (T6P) synthase and trehalose-6-phosphate phosphatase complex in Saccharomyces cerevisiae. Trehalose protects against damage imposed by these stresses.63,64 Therefore, engineering high levels of trehalose in plants might confer drought tolerance.65 Again, gene containment in transgenic plants is a serious concern when plants are genetically engineered for drought tolerance because of the possibility of creating drought-tolerant weeds and passing on undesired pleiotropic traits to related crops. On the other hand, it is always desirable to have high level of expression of transgene in plant. Both of these two opposite consequences can be solved via the chloroplast genome instead of the nuclear genome. Recently, the yeast trehalose phosphate synthase (TPS1) gene was introduced into the tobacco chloroplast and nuclear genomes to study the resultant phenotypes and chloroplast transgenic plants showed up to 25-fold higher accumulation of trehalose than nuclear transgenic plants. Also, nuclear transgenic plants with significant amounts of trehalose accumulation exhibited a stunted phenotype, sterility, and other pleiotropic effects, whereas chloroplast transgenic plants grew normally and had no visible pleiotropic effects. Investigations have confirmed that trehalose functions by protecting the integrity of biological membranes rather than regulating water potential.66 Therefore, this study shows that compartmentalization of trehalose within chloroplasts confers drought tolerance without undesirable phenotypes. 13.4.5 ENGINEERING THE CHLOROPLAST GENOME TO OBTAIN TRANSGENIC PLANT LACKING ANTIBIOTIC RESISTANCE GENE Every genetic transformation procedures require stringent selection procedures for true transformation. Traditional vectors include one or more antibiotic resistance gene/s, which confer resistance to respective antibiotics.67 Such antibiotic resistance passes to human or other microflora by horizontal gene transfer, when consumed. There is concern that their overuse might lead to the development of resistant bacteria.68 Therefore, several studies have

Engineering Plastid Pathways

303

explored strategies for engineering chloroplasts that are free of antibioticresistance markers. One strategy includes use of native chloroplast marker system from distinct species for selection. Such strategy, in addition to gene containment, should ease public concerns over genetically modified crops. The spinach BADH gene has been developed as a plant-derived selectable marker to transform chloroplast genomes.69 The selection process involves conversion of toxic betaine aldehyde (BA) by the chloroplast-localized BADH enzyme to nontoxic glycine betaine, which also serves as an osmoprotectant.70,71 Because the BADH enzyme is present only in chloroplasts of a few plant species adapted to dry and saline environments, it is suitable as a selectable marker in many crop plants. The transformation study showed that BA selection was 25-fold more efficient than spectinomycin, exhibiting rapid regeneration of transgenic shoots within 2 weeks. Another approach to develop marker-free transgenic plants is to eliminate the antibiotic resistance gene after transformation using endogenous chloroplast recombinases that delete the marker genes via engineered direct repeats. Recently, another strategy to eliminate selectable marker genes has been developed, using the P1 bacteriophage CRE-lox site-specific recombination system. Altogether, these reports show that efficient removal of selectable marker(s) from chloroplast genomes is feasible.72,73 13.4.6 RESEARCH ON RNA EDITING Plastid transformation played an important role in understanding the RNA editing process by mainly three approaches, namely, minigenes, translational fusion with a reporter gene, and incorporation of an editing segment in the 3' UTR.74 The most complete information is available for the psbL editing site. psbL is a plastid photosynthetic gene, in which the translation initiation codon is created by conversion of an ACG codon to an AUG codon at the mRNA level. 13.4.7 “PHARMING” THROUGH “FARMING”: CHLOROPLAST AS A BIOREACTOR FOR PRODUCTION OF PHARMACEUTICAL PRODUCTS Expression and production of human proteins/therapeutics in chloroplast has an added advantage over the usage of prokaryotic cellular machineries that they stably express “eukaryotic” form of protein. Protein function, especially of enzymes and hormones’, is largely dependent upon their

304

Plant Pathogens: Detection and Management for Sustainable Agriculture

three-dimensional spatial structure, which are the results of cascade of several posttranslational mechanisms. Such mechanism is either absent or in trivial stage to correctly fold human originated proteins. Hence, the use of microbial cells as bioreactors limits at this stage. Being a part of eukaryotic cell, chloroplast offers such correct folding to be used directly as therapeutics over other added advantages.75,76 Stable expression of a pharmaceutical protein in chloroplasts was first reported for GVGVP, a protein-based polymer with medical uses such as wound coverings, artificial pericardia, and programmed drug delivery.77 Human ST (hST) is a multimeric soluble protein which was expressed inside chloroplasts in a soluble, biologically active and disulfide-bonded form.78 The type I IFNs (interferrons) are cytokines that are produced and evoke immune response against range of human pathogens, parasites, tumor cells, and allogeneic cells from graft. IFNa2b ranks third in world market use for a biopharmaceutical, behind only insulin and erythropoietin. IFNa2b was expressed in tobacco chloroplasts with levels of up to 20% of tsp or 3 mg/g of leaf (fresh weight) and facilitated the first field production of a plant-derived human blood protein.79,80 13.4.8 PLASTIDS AS VACCINE BIOREACTORS As opposed to injected subunit vaccines, oral delivery and low-cost purification make plastid-derived subunit production quite plausible.81 Such plastid-derived vaccines produced very hopeful results when tested in animal models. They are capable of inducing correct line of immune defense when given orally and also withstand a pathogen challenge. The only drawback of plant-derived vaccines is their bioavailability and controlled release at the site of action. However, bioencapsulation can protect the vaccine in the stomach and gradually releases the antigen in the gut. Vaccine antigens against cholera,82 tetanus,83 anthrax,84 and plague85 have been expressed in transgenic chloroplasts. Bioterrorism is an increased threat in the post 9/11 world. Anthrax is always fatal if not treated immediately. Weapon grade spores can be produced and stored for decades and can be spread by missiles, bombs, or even through the mail. Because of this, it is an ideal biological warfare agent.86 Plastid produced anthrax vaccine is an immediate workable option in such case. Recently, malaria vaccine has been produced by engineering chloroplast of Chlamydomonas.87

Engineering Plastid Pathways

305

13.4.9 PLASTIDS AS BIOMATERIAL BIOREACTORS Besides vaccine antigens, biomaterial and amino acids have also been expressed in chloroplasts. Normally, p-hydroxybenzoic acid (pHBA) is produced in small quantities in all plants by series of 10 consecutive reactions from pyruvate, while in E. coli, ubiC-encoded chorismate pyruvate lyase catalyzes the direct conversion of chorismate to pyruvate and pHBA. Stable integration of the ubiC gene into the tobacco chloroplast resulted in hyperexpression of the enzyme and accumulation of this polymer up to 25% of dry weight.88 In another study, the gene for thermostable xylanase was expressed in the chloroplasts of tobacco plants.89 Xylanase accumulated in the cells to approximately 6% of tsp. Zymography assay demonstrated that the estimated activity was 140,755 units per kg fresh leaf tissue. The use of chloroplast for molecular pharming suggests that chloroplast contain mechanism for correct folding and stable accumulation of foreign protein. Despite of such proceedings of chloroplast molecular biology, expression of many important sugar conjugated proteins, glycoproteins, are not expressed due to the fact that N- or O-glycosylation is required for stability and functionality of many proteins. 13.4.10 ENGINEERING THE CHLOROPLAST GENOME OF EDIBLE CROP PLANTS Apart from leaves, plastid are also present, in other forms, to other parts of plant, mainly in rudimentary or developing form, many of which are edible. Pharming in such “edible” compartment for the production of orally delivered pharmaceuticals is very propitious approach for delivery. Chromoplast in tomato and amyloplast in potato has recently been explored for the feasibility of an approach. Western blot analysis revealed more promising result in tomato that protein expression was almost doubled in fruits than that of the leaves while in potato, results are not very promising since accumulation is much lower in microtubers. This study predicts the feasibility of expressing high-levels of foreign proteins in the plastids of edible plant organs.28

306

Plant Pathogens: Detection and Management for Sustainable Agriculture

13.5 CONCLUSION Chloroplast genetic engineering is an exciting technology that has the tremendous competence for gaining “Green Revolution” in a true sense. The plastid transformation offers gene amplification along with gene stacking due to their multicopy number and operon organized genome. Also, maternal inheritance restricts spread of transgene is an added advantage. Plastid genetic engineering has become a powerful tool for basic research in plastid biogenesis and function. Recent advances in plastid engineering provide an efficient platform for the production of therapeutic proteins, vaccines, and biomaterials using an environmentally friendly approach. Although concept of environmentally sustained plant transformation through chloroplast compartmentalization is older now, there are many challenges for successive use of this technique for diverse range of plant materials. A main lacunae lie is the unavailability of chloroplast genome sequences and species specific transformation vectors, to which transformation efficiency depends greatly. Plastid transformation inexorably followed by plant regeneration in vitro. Hence, accurate in vitro regeneration protocol should be available in hand for successful regeneration of transformed plants. Overall, plastid transformation and related technologies are now on the horizon. In spite of being overlooked by the transgenomic technologies earlier days, noticeable environmental constrains put forward plastid transformation again in the light. Such initiatives, surely in future will give new way of understanding molecular processes and thus provide newer route of societal upliftment through better and healthier plants and plant products. KEYWORDS • • • • •

plastome chloroplast transformation transplastomic technologies transgene in planta

Engineering Plastid Pathways

307

REFERENCES 1. O’ Neill, B. C.; Balk, D.; Brickman, M.; Ezra, M. A Guide to Global Population Projection. Demogr. Res. 2011, 4 (8), 203–288. 2. Oerke, E. -C.; Dehen, H. -W. Safeguarding Production: Losses in Major Crops and the Role of Crop Protection. Crop Protect 2004, 23, 275–285. 3. Rice, A. L.; Sacco, L.; Hyder, A.; Black, R. E. Malnutrition as an Underlying Cause of Childhood Deaths Associated with Infectious Diseases in Developing Countries. Bull. World Health Organization 2000, 78 (10), 1207–1221. 4. Borlaug, N. The Green Revolution, Peace and Humanity. “Nobel Lecture”, Nobel Peace Prize, 1970. 5. Goto, F.; Yoshihara, T.; Shigemoto, N.; Toki, S.; Takaiwa, S. Iron Fortification of Rice Seed by the Soybean Feitin Gene. Nat. Biotechnol. 1999, 17, 282. 6. Chin, H. G.; Kim, G. D.; Martin, I.; Mersha, F.; Evans, T. C. Jr.; Chen, L.; Xu, Mq.; Pradhan, S. Protein Trans Splicing in Transgenic Plant Chloroplast: Reconstruction of Herbicide Resistance from Split Genes. Proc. Natl. Acad. Sci. USA 2003, 100 (8), 4510–4515. 7. Boynton, J. E., et al. Chloroplast Transformation in Chlamydomonas with High Velocity Micropojectiles. Science 1988, 240 (4858), 1534–1538. 8. Daniell, H.; McFadden, B. A. Uptake and Expression of Bacterial and Cyanobacterial Genes by Isolated Cucumber Etioplasts. Proc. Natl. Acad. Sci. USA 1987, 84 (18), 6349–6353. 9. Daniell, H., et al. Transient Foreign Gene Expression in Chloroplasts of Cultured Tobacco Cells After Bolistic Delivery of Chloroplast Vectors. Proc. Natl. Acad. Sci. USA 1990, 87 (1), 88–92. 10. Martin, W.; Kowallik, K. V. On the Nature and Origin of Chromatophores (Plastids) in the Plant Kingdom: Annotated English Translation of Mereschkowsky’s 1905 Paper. Eur. J. Phycol. 1999, 34, 287–295. 11. Mache, R.; Mache, S. L. Chloroplast Genetic System of Higher Plants: Chromosome Replication, Chloroplast Division and Elements of the Transcriptional Apparatus. Curr. Sci. 2001, 80 (2), 217–224. 12. Hermann, R. G.; Kowallik, K. V. Selective Presentation of DNA–Region and Membranes in Chloroplast and Mitochondria. J. Cell Biol. 1970, 45, 198–202. 13. Kubista, M.; Aakerman, B.; Norden, B. Characterization of Interaction Between DNA and 4’, 6-Diamidino-2-Phenylindole by Optical Spectroscopy. Biochemistry 1987, 26 (14), 4545–4553. 14. Sato, N. et al. Molecular Characterization of the PEND Protein, a Novel BZIP Protein Present in the Envelope Membrane That Is the Site of Nucleoid Replication in Developing Plastids. Plant Cell 1998, 10, 859–872. 15. Barbrook, A. C.; Howe, C. J.; Kurniawan, D. P.; Tarr, S. J. Organization and Expression of Organelle Genome. Phil. Trans. Royal Soc. B. 2010, 365, 785–797. 16. Palmer, J. D. Chloroplast DNA Exists in Two Orientations. Nature 1983, 92, 301. 17. Sugiura, M. The Chloroplast Genome. Plant Mol. Biol. 1992, 19, 149–168. 18. Regert, B. J.; Fairfieldt, S. A.; Epler, J. L.; Barnett, W. E. Identification and Origin of Some Chloroplast Aminoacyl-tRNA Synthetases and tRNAs. Proc. Natl. Acad. Sci. USA 1970, 67 (3), 1207–1213.

308

Plant Pathogens: Detection and Management for Sustainable Agriculture

19. Daniell, H. Molecular Strategies for Gene Containment in Transgenic Crops. Nat. Biotechnol. 2002, 20, 581–586. 20. Svab, Z.; Hajdukiewicz, P.; Maliga, P. Stable Transformation of Plastids in Higher Plants. Proc. Natl. Acad. Sci. USA 1990, 87, 8526–8530. 21. Sikdar, S. R.; Serino, G.; Chaudhuri, S.; Maliga, P. Plastid Transformation in Arabidopsis Thaliana. Plant Cell Reports 1998, 18, 20–24. 22. Hou, B. K.; Zhou, Y. H.; Wan, L. H.; Zhang, Z. L.; Shen, G. F.; Chen, Z. H.; Hu, Z. M. Chloroplast Transformation in Oilseed Rape. Transgenic Res. 2003, 12, 111–114. 23. Sidorov, V. A.; Kasten, D.; Pang, S. Z.; Hajdukiewicz, P. T. J.; Staub, J. M.; Nehra, N. S. Stable Chloroplast Transformation in Potato: Use of Green Fluorescent Protein as a Plastid Marker. Plant J. 1999, 19, 209–216. 24. Lelivelt, C.; McCabe, M.; Newell, C.; DeSnoo, C.; Dun, K.; Birch-Machin, I.; Gray, J.; Mills, K.; Nugent, J. Stable Plastid Transformation in Lettuce (Lactuca sativa L.). Plant Mol. Biol. 2005, 58, 763–774. 25. Dufourmantel, N.; Pelissier, B.; Garcon, F.; Peltier, G.; Ferullo, J. M.; Tissot, G. Generation of Fertile Transplastomic Soybean. Plant Mol. Biol. 2004, 55, 479–489. 26. Kumar, S.; Dhingra, A.; Daniell, H. Stable Transformation of the Cotton Plastid Genome and Maternal Inheritance of Transgenes. Plant Mol. Biol. 2004, 56, 203–216. 27. Kumar, S.; Dhingra, A.; Daniell, H. Plastid-expressed Betaine Aldehyde Dehydrogenase Gene in Carrot Cultured Cells, Roots, and Leaves Confer Enhanced Salt Tolerance. Plant Physiol. 2004, 136, 2843–2854. 28. Ruf, S.; Hermann, M.; Berger, I. J.; Carrer, H.; Bock, R. Stable Genetic Transformation of Tomato Plastids and Expression of a Foreign Protein in Fruit. Nat. Biotechnol. 2001, 19, 870–875. 29. Maliga, P. Plastid Transformation in Higher Plants. Annu. Rev. Plant Biol. 2004, 55, 289–313. 30. Maliga, P. Engineering the Plastid Genome of the Higher Plants. Curr. Opin. Plant Biol. 2002, 5, 164–172. 31. Block, M. D.; Schell, J.; Montagu, M. V. Chloroplast Transformation by Agrobacterium tumefaciens. EMBO J. 1985, 4, 1367–1372. 32. Golds, T.; Maliga, P.; Koop, H. U. Stable Plastid Transformation in Peg-treated Protoplasts of Nicotiana tabacum. Nat. Biotechnol. 1993, 11, 95–97. 33. Carrer, H.; Hockenberry, T. N.; Svab, Z;, Maliga, P. Kanamycin Resistance as a Selectable Marker for Plastid Transformation in Tobacco. Mol. Gen. Genet. 1993, 241, 49–56. 34. Lee, S. M., et al. Plastid Transformation in the Monocotyledonous Cereal Crop, Rice (Oryza sativa) and Transmission of Transgenes to Their Progeny. Mol. Cells 2006, 21, 401–410. 35. Goldschmidt-Clermont, M. Transgenic Expression of Aminoglycoside Adenine Transferase in the Chloroplast: A Selectable Marker for Site-directed Transformation of Chlamydomonas. Nucleic Acids Res. 1991, 19, 4083–4089. 36. Svab, Z.; Maliga, P. High-frequency Plastid Transformation in Tobacco by Selection for a Chimeric aadA Gene. Proc. Natl. Acad. Sci. USA 1993, 90, 913–917. 37. Lutz, K. A. Expression of Bar in Plastid Genome Confers Herbicide Resistance. Plant Physiol. 2001, 125, 1585–1590.

Engineering Plastid Pathways

309

38. Zoubenko, O. V.; Allison, L. A.; Svab, Z.; Maliga, P. Efficient Targeting of Foreign Genes into the Tobacco Plastid Genome. Nucleic Acids Res. 1994, 22, 3819–3824. 39. Staub, J. M.; Maliga, P. Long Regions of Homologous DNA Are Incorporated into the Tobacco Plastid Genome by Transformation. Plant Cell 1992, 4, 39–45. 40. Deng, X. –W.; Gruissem, W. Control of Plastid Gene Expression During Development: The Limited Role of Transcriptional Regulation. Cell 1987, 49 (3), 379–387. 41. McBride, K. E.; Schaaf, D. J.; Daley, M.; Stalker, D. M. Controlled Expression of Plastid Transgenes in Plants Based on a Nuclear DNA-encoded and Plastid-targeted T7 RNA Polymerase. Proc. Natl. Acad. Sci. USA 1994, 91, 7301–7305. 42. Muhlbauer, S. K.; Koop, H. U. External Control of Transgene Expression in Tobacco Plastids Using the Bacterial Lac Repressor. Plant J. 2005, 43, 941–946. 43. Khan, M. S.; Khalid, A. M.; Malik, K. Intein-mediated Protein Trans-splicing and Transgene Containment in Plastids. Trends Biotechnol. 2005, 23 (5), 217–221. 44. Reboud, X.; Zeyl, C. Organelle Inheritance in Plants. Heredity 1994, 72, 132–140. 45. Connett, M. B. Mechanisms of Maternal Inheritance of Plastids and Mitochondria: Developmental and Ultrastructural Evidence. Plant Mol. Biol. Reporter 1987, 4 (4), 193–205. 46. Daniell, H. Transgene Containment by Maternal Inheritance: Effective or Elusive? Proc. Natl. Acad. Sci. USA 2007, 104, 6879–6880. 47. Ruiz, O. N.; Daniell, H. Engineering Cytoplasmic Male Sterility Via the Chloroplast Genome by Expression of β-Ketothiolase. Plant Physiol. 2005, 138, 1232–1246. 48. Verma, D., Daniell, H. Chloroplast Vector Systems for Biotechnology Applications. Plant Physiol. 2007, 145, 1129–1143. 49. Ruhlman, T.; Ahangari, R.; Devine, A.; Samsam, M.; Daniell, H. Expression of Cholera Toxin B-Proinsulin Fusion Protein in Lettuce and Tobacco Chloroplasts-Oral Administration ProtectsAgainst Development of Insulitis on Non-obese Diabetic Mice. Plant Biotechnol. J. 2007, 5, 495–510. 50. Glenz, K.; Bouchon, B.; Stehle, T.; Wallich, R.; Simon, M. M.; Warzecha, H. Production of a Recombinant Bacterial Lipoprotein in Higher Plant Chloroplasts. Nat. Biotechnol. 2006, 24, 76–77. 51. Shah, D. M., et al. Engineering Herbicide Tolerance in Transgenic Plants. Science 1986, 233, 478–481. 52. Ruf, S.; Karcher, D.; Bock, R. Determining the Transgene Containment Level Provided by Chloroplast Transformation. Proc. Natl. Acad. Sci. USA 2007, 104 (17), 6998–7002. 53. Scott, S. E.; Wilkinson, M. J. Low Probability of Chloroplast Movement from Oilseed Rape (Brassica napus) Into Wild Brassica Rapa. Nat. Biotechnol.1999, 17, 390–392. 54. Daniell, H.; Muthukumar, B.; Lee, S. B. Marker Free Transgenic Plants: Engineering the Chloroplast Genome Without the Use of Antibiotic Selection. Curr. Genet. 2001, 39, 109–116. 55. Ye, G. -N.; Colburn, S. M.; Xu, C. W.; Hajdukiewicz, P. T. J.; Staub, J. M. Persistence of Unselected Transgenic DNA During a Plastid Transformation and Segregation Approach to Herbicide Resistance. Plant Physiol. 2003, 133, 402−410. 56. Quesada-Vargas, T.; Ruiz, O. N.; Daniell, H. Characterization of Heterologous Multigene Operons in Transgenic Chloroplasts: Transcription, Processing, and Translation. Plant Physiol. 2005, 138, 1746–1762.

310

Plant Pathogens: Detection and Management for Sustainable Agriculture

57. Zhang, J. - Y.; Zhang, Y.; Song, Y. -R. Chloroplast Genetic Engineering in Higher Plants. Acta Botanica Sinica 2003, 45 (5), 509–516. 58. Nawrath, C., et al. Targeting of the Polyhydroxybutyrate Biosynthetic Pathway to the Plastids of Arabidopsis Thaliana Results in High Levels of Polymer Accumulation. Proc. Natl. Acad. Sci. USA 1994, 91, 12760–12764. 59. Ye, X., et al. Engineering the Provitamin A (Β-Carotene) Biosynthetic Pathway into (Carotenoid) Free Rice Endosperm. Science 2000, 287, 303–305. 60. De Cosa, B. Overexpression of yhe Bt Cry2aa2 Operon in Chloroplast Leads to Formation of Insecticidal Crystals. Nat. Biotechnol. 2001, 19, 71–74. 61. DeGray, G.; Rajasekaran, K.; Smith, F.; Sanford, J.; Daniell, H. Expression of an Antimicrobial Peptide Via the Chloroplast Genome to Control Phytopathogenic Bacteria and Fungi. Plant Physiol. 2001, 127, 852–862. 62. Grover, A. et al. Understanding Molecular Alphabets of the Plant Abiotic Stress Responses. Curr. Sci. 2001, 80 (2), 206–216. 63. ByKylie, F.; Mackenzie, T. K.; Singh, K. K.; Brown, A. D. Water Stress Plating Hypersensitivity of Yeasts: Protective Role of Trehalose in Sacharomyces cerevisiae. J. Gen. Microbiol. 1998, 134, 1661–1666. 64. Oscar, J. M. G.; Kees, V. D. Trehalose Metabolism in Plants. Trends Plant Sci. 1999, 4 (8), 315–319. 65. Pilon-Smits, et al. Trehalose Producing Transgenic Tobacco Plants Show Improved Growth Performance Under Drought Stress. J. Plant Physiol. 1998, 152, 525–532. 66. Romero, C., et al. Expression of Yeast Trehalose-6 -Phosphate Synthase Gene in Transgenic Tobacco Plants: Pleiotropic Phenotypes Include Drought Tolerance. Planta 1997, 201, 293–297. 67. Iamtham, S.; Day, A. Removal of Antibiotic Resistance Genes from Transgenic Tobacco Plastids. Nat. Biotechnol. 2000, 18, 1172–1176. 68. Chambers, P. A.; Duggan, P. S.; Heritage, J.; Forbes, J. M. The Fate of Antibiotic Resistance Marker Genes in Transgenic Plant Feed Material Fed to Chicken. J. Antimicrob. Chemother. 2002, 49, 161–164. 69. Rathinasabapathy, B.; McCue, K. F.; Gage, D. A.; Hanson, A. D. Metabolic Engineering of Glycine Betaine Synthesis: Plant Betaine Aldehyde Dehydrogenases Lacking Typical Transit Peptides are Targeted to Tobacco Chloroplast Where They Confer Aldehyde Resistance. Planta 1994, 193, 155–162. 70. Rontein, D.; Basse, G.; Hanson, A. D. Metabolic Engineering of Osmoprotectant Accumulation in Plants. Metabolic Eng. 2002, 4 (1), 49–56. 71. Ashraf, M.; Foolad, M. R. Roles of Glycine Betaine and Proline in Improving Plant Abiotic Stress Resistance. Environ. Exp. Botany 2007, 59 (2), 206–216. 72. Corneille, S.; Lutz, K.; Svab, Z.; Maliga, P. Efficient Elimination of Selectable Marker Genes from the Plastid Genome by the CRE-lox Site-specific Recombination System. Plant J. 2001, 27 (2), 171–178. 73. Hajdukiewicz, P. T. J.; Gilbertson, L.; Staub, J. M. Multiple Pathways for Cre/ Lox-mediated Recombination in Plastids. Plant J. 2001, 27 (2), 161–170. 74. Shikanai, T. RNA Editing in Plant Organelles: Machinery, Physiological Function and Evolution. Cellular Mol. Life Sci. 2006, 63, 698–708. 75. Ma, J. K.; Drake, P. M.; Christou, P. The Production of Recombinant Pharmaceutical Proteins in Plants. Nat. Rev. Genet. 2003, 4, 794–805.

Engineering Plastid Pathways

311

76. Miao, Y.; Ding, Y.; Sun, Q. -Y.; Xu, Z. –F.; Jiang, L. Plant Bioreactors for Pharmaceuticals. Biotechnol. Genetic Eng. Rev. 2008, 25, 363–380. 77. Guda, C., et al. Stable Expression of Biodegradable Protein Based Polymer in Tobacco Chloroplasts. Plant Cell Reports 2000, 19, 257–262. 78. Staub, J. M., et al. High-yield Production of a Human Therapeutic Protein in Tobacco Chloroplasts. Nat. Biotechnol. 2000, 18, 333–338. 79. Arlen, P. A., et al. Field Production and Functional Evaluation of Chloroplast-derived Interferon-Α2b. Plant Biotechnol. J. 2007, 5 (4), 511–525. 80. Daniell, H. Production of Biopharmaceuticals and Vaccines in Plants via the Chloroplast Genome. Biotechnol. J. 2006, 1 (10), 1071–1079. 81. Sala, F., et al. Vaccine Antigen Production in Transgenic Plants: Strategies, Gene Constructs and Perspectives. Vaccine 2003, 21, 803–808. 82. Daniell, H. Expression of Cholera Toxin B Subunit Gene and Assembly as Functional Oligomers in Transgenic Tobacco Chloroplasts. J. Mol. Biol. 2001, 311, 1001–1009. 83. Tregoning, J. S., et al. Expression of Tetanus Toxin Fragment C in Tobacco Chloroplasts. Nucleic Acids Res. 2003, 31, 1174–1179. 84. Watson, J.; Koya, V.; Leppla, S. H.; Daniell, H. Expression of Bacillus Anthracis Protective Antigen in Transgenic Chloroplasts of Tobacco, a Nonfood/Feed Crop. Vaccine 2004, 22, 4374–4384. 85. Daniell, H.; Chebolu, S.; Kumar, S.; Singleton, M.; Falconer, R. Chloroplast-derived Vaccine Antigens and Other Therapeutic Proteins. Vaccine 2005, 23, 1779–1783. 86. Jernigan, J. A., et al. Bioterrorism-related inhalational anthrax: The First 10 Cases Reported in the United States. Emerging Infectious Dis. 2001, 7 (6), 933–944. 87. Dauvillee, D., et al. Engineering the Chloroplast Targeted Malarial Vaccine Antigens in Chlamydomonas Starch Granules. PLoS One 2010, 5 (12), e15424. 88. Viitanen, P. V.; Devine, A. L.; Khan, M. S.; Deuel, D. L.; Van Dyk, D. E.; Daniell, H. Metabolic Engineering of the Chloroplast Genome Using Escherichia Coli Ubic Gene Reveals That Chorismate is a Readily Abundant Plant Precursor for P-Hydroxybenzoic Acid Biosynthesis. Plant Physiol. 2004, 136, 4048–4060. 89. Daniell, H.; Khan, M. S.; Allison, L. Milestones in Chloroplast Genetic Engineering: An Environmentally Friendly Era in Biotechnology. Trends Plant Sci. 2004, 7 (2), 84–91.

CHAPTER 14

Impact of Meteorological Variables and Climate Change on Plant Diseases A. K. MISRA,1* S. B. YADAV2, S. K. MISHRA,3 and M. K. TRIPATHI4

Monsoon Mission Division, Indian Institute of Tropical Meteorology, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India

1

Punjab Agricultural University, Regional Research Station, Faridkot 151203, Punjab, India

2

Department of Agrometeorology, Punjab Agricultural University, Regional Research Station, Faridkot 151203, Punjab, India

3

Department of Natural Resource Management, College of Horticulture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Mandsaur 458001, Madhya Pradesh, India

4

*

Corresponding author. E-mail: [email protected]

ABSTRACT Plant disease is an output of abnormal changes in the physiological processes resulting from biotic and abiotic factors. The individual weather elements as well as their combination play an important role in the disease occurrence and their infestations. Therefore, agrometeorological information becomes pivotal for prediction of disease outbreaks for effective and judicious use of control measures, the prediction of crop yields and of the market potential for the crop. The major meteorological factors responsible for the plant disease outbreaks are temperature (both air and soil), precipitation (rainfall and dew), moisture (relative humidity, soil moisture), solar radiation (intensity and cloudiness), wind, etc. Among these variables, temperature and moisture are considered as the most important factors since all the pathogen have an optimum temperature requirement

314

Plant Pathogens: Detection and Management for Sustainable Agriculture

range for their growth and disease development becomes accelerated in this range. In the similar manner, pathogen replicates with a very high rate under favorable moisture conditions, which enhances the severity of disease incidence and intensity. Apart from this, soil moisture content plays its dominant role on the severity of soilborne diseases, while solar radiation affects the epidemiology and has a profound influence on the developmental cycle of the parasite. Wind speed influences dispersal of the pathogen, disease spread, and epidemic development. Apart from all these meteorological variables, climate change has emerged as another major threat in recent times which may bring new diseases and challenges ahead. It is expected that climate change may affect plant–pathogen interactions as well as disease epidemiology, hence an effective planning and management will be required to overcome this challenge to achieve the food security for all. 14.1 INTRODUCTION Globally, agricultural activities are highly sensitive to weather aberrations. Plant diseases are one of the most significant factors that affect the global food production and their severity varies with crops and regions. The Great Bengal Famine in India during 1943 is a classic example which was triggered by a simple fungus and resulted in the deaths of about 3 million peoples. Total estimated losses for major food and cash crops in various regions of the world have been brilliantly described by Oerke et al. (1994) and it has been found that due to disease alone, there are 16% yield losses in eight of the most important food and cash crops including rice, wheat, maize, barley, cotton, coffee, etc. Hardwick (2002) has summarized that combined damage due to pests and diseases reduces about 30% global food production, whereas Strange and Scott (2005) estimated minimum 10% food production losses only due to plant diseases. Similarly, Savary et al. (2012) summarized that direct yield losses between 20% and 40% of global agricultural productivity are caused by pathogens, animals, and weeds. Gautam et al. (2013) reported total loss of attainable yield of cotton may be as high as 82% after including losses occurred due to postharvest wastage and quality deterioration. Plant disease is mainly caused due to the alteration in their physiological process caused by biotic or abiotic factors. Biotic factors include living organisms, for example, fungi, bacteria, viruses, nematodes, insects, and

Impact of Meteorological Variables and Climate Change

315

animals while the abiotic factors include weather elements (e.g., heat, cold and drought, freezing and wind injury, excessive precipitation, etc.), pH, nutrition, chemical injury, nutrient deficiency, and inappropriate cultural practices. There are three crucial factors often referred as “the plant disease triangle” which are responsible for an infectious plant disease to occur: 1. A susceptible host plant in vulnerable state. 2. Presence of the pathogen/parasite to cause the disease. 3. Environmental conditions favorable for disease development. 14.2 EFFECT OF WEATHER ELEMENTS ON PLANT DISEASES Significant role of weather for the commencement and development of plant disease has been established by several researchers (Miller, 1953; Colhoun, 1973; Hardwick, 2002; Te Beest, et al., 2008; Das et al., 2011). Pathogens have their own environmental requirements for infection; therefore, agrometeorological information becomes crucial for protecting the crop through optimal use of available resources. If plant losses through diseases and pests can be reduced to zero and weather information can be efficiently exploited along with the introduction of high yielding varieties, the food production may be enhanced to significant level. Different diseases occur at different seasons based on their climatic requirement. For example, most of the powdery mildew diseases are observed in late summer. Weather affects growth and development of plants in several ways. Every plant disease requires specific temperature, humidity, wind, radiation, soil quality, and nutrition for their growth. If these conditions are unfavorable for them, there may be a high probability for the plants to be affected by diseases. The pathogens also require certain set of optimum conditions that must continue for a critical period for infection to occur. When environmental conditions (both in air and soils) are favorable, disease development accelerate causing rapid colonization of host tissues and disease spread. It has been observed that specific temperature ranges along with high humidity enhances the possibility for many fungal diseases (Hardwick, 2002). For instance, high humidity, rainfall, or dew with a combination of 10–15°C ambient air temperature have been found to be suitable for yellow rust disease of wheat in Punjab (Gill et al., 2012). The progress and development of powdery mildew disease in mustard was at peak when maximum temperature ranged between 27.2°C and 28.9°C and

316

Plant Pathogens: Detection and Management for Sustainable Agriculture

afternoon relative humidity ranged between 27 and 42% in the Saurashtra region of Gujarat, India (Kanzaria et al., 2013). Kumar and Chakravarty (2008) developed a weather based forewarning model for predicting the white rust incidence for Brassica using hourly weather observations for temperature, relative humidity, and sunshine duration which resulted in the development of a thumb rule for forewarning of white rust. The impact of individual weather events on plant epidemiology has been summarized below. 14.2.1 TEMPERATURE Temperature is considered as one of the most significant weather factor that affect host, pathogen, and disease development together. The heat stress in plants reduces photosynthetic and transpiration efficiencies and adversely affects root development with negative impact on crop yields. It also influences all the three sections of disease epidemiology, namely, the incubation period, the generation time, and the infectious period. All the disease pathogen has a specific optimum temperature range for their growth and activities and under favorable conditions, disease development continues till the healthy plant tissue is alive. As the air temperature gets closer to the optimum for the host development, the likelihood of getting infestation decreases and vice-versa. For example, majority of rice varieties are vulnerable for rice blast disease if the night temperature is less than 26°C. When the temperature goes beyond this limit, the symptoms of rice blast are rarely observed. In general, extreme temperatures are harmful for the pathogens but incremental temperature changes can lead to dissimilar effects. For a vector living in such environment where the mean temperature approaches to the extremes of physiological tolerance limit for the pathogen, a minor change in temperature may also have detrimental effect for the pathogen. On the other hand, a vector that lives in low temperature environment, a minute rise in temperature may enhance the development, incubation, and replication of the pathogens. The rate of the disease cycle has a direct relationship with temperatures; hence, it increases with increase in temperature often resulting in rapid epidemics development. In a study conducted by Jhorar et al. (1997) for Indian Punjab, a linear relationship between maximum temperature and ascochyta blight disease of chickpea was obtained. Coakley et al. (1999) reported that the host plants, namely, wheat and oats became extremely

Impact of Meteorological Variables and Climate Change

317

susceptible to rust diseases with increase in temperature while some other forage species became resistant to fungi. Similar to air temperature, soil temperature is another important factor that affects the physiology of a plant. Du and Tachibana (1994) observed that high root temperature may enhance root respiration in cucumber plants. When the roots temperature increases, its dry weight and pectin content along with leaf area reduces while root sugars, predominantly raffinose, increases to a significant instant. Leaf blight disease becomes severe in warm soils. However, moist soils with low temperature have been found as ideal for fungal root diseases. Reddick (1917) has concluded that changes in soil temperature have more profound effect on the host physiology as compared with air temperatures. Likewise, Fir et al. (1983) found soil temperature to be the critical limiting factor for the root rot disease which determines the timing and severity of this disease. Arora and Pareek (2013) suggested that high soil temperature coupled with low moisture content favors charcoal rot disease of Sorghum at Rajasthan in India. Pivonia et al. (2002) concluded that soil temperature has its profound effect on the incidence of melon collapse which was resulted due to Monosporascus cannonballus. High correlation between soil temperatures (above 20°C) and Monosporascus cannonballus in the first month after planting was observed. Artificial heating of plots till 35°C during the winter season boosted the disease effects up to 85%. 14.2.2 PRECIPITATION There are various forms of precipitation but rain and dew are most significant in plant disease epidemics. The intensity of rain which is a function of the velocity, size, and number of the water droplets are of critical importance for the determination of wetness of the plant surface and pathogen dispersal in plant communities. Rain removes spores and pollen from the surface of crop by washing them or by shaking impact. Raindrops act as a transport medium for spores which carry away spores with them from one place to another, thus helping in the spread and transfer of disease to new places (Van der Wal, 1978). Moreover, raindrops also help in inoculum dispersal into areas where the pathogen is not present through rainsplash (Huber et al., 1998; Geagea et al., 2000).

318

Plant Pathogens: Detection and Management for Sustainable Agriculture

Among the several attributes of rain, the time, frequency, and duration are crucial factors that determine the plant wetness as well as pathogen’s dispersal by trickling and splashing of rain water. The combined effect of these factors affects the plant disease epidemic outbreaks. High rainfall has been found to have a positive correlation with chickpea blind incidence during the winter season. On the other hand, summer rains have been reported to have a negative stimulus on the disease. When the spring chickpeas in the Mediterranean region get regular rains during the harvest season, the impact of ascochyta blight of chickpea becomes severe in North-West India and Pakistan (Malhotra et al., 1996). Schwartz et al. (2003) developed a multiple regression model to find the relationship of rainfall and temperature with bacterial leaf blight disease caused by Xanthomonas campestris and Pantoea ananatis for onion in Colorado, USA. They found that these parameters, that is, rainfall and temperature have significant influence on disease symptoms during late vegetative and early reproductive stages. Singh et al. (2010) reported that rainfall during the 3rd week of January was having favorable role in the formation and further multiplication of secondary spordia of karnal bunt disease in wheat in Karnal region of Haryana, India. A recent study conducted by Pal et al. (2017) reported that heavy rainfall was found to be conducive for initiation of the sheath blight disease of rice, while low and intermittent rainfall of 13–38 mm was found to have a favorable effect for progression of the disease. Dew is another important form of precipitation and a vital source of moisture in certain arid regions. Dew is the moisture which condenses from the atmosphere on surfaces near the ground including plants, soils, leaves, etc. (Leopold, 1951). The dew is a major source of leaf wetness or free moisture which is a prime requirement for disease infection in several plants such as leaf blight on sweet corn (Levy and Pataky, 1992) or foliar infection of tomato (Byrne et al., 1998). The presence of dew on plant leaf surface significantly reduces the transpiration from the plant. 14.2.3 MOISTURE Both air or soil moisture plays a pivotal role in the incidence of pest and diseases. All fungal pathogens affecting plants are strongly influenced by the moisture in different forms. In case, pathogen moisture requirements

Impact of Meteorological Variables and Climate Change

319

are fulfilled under favorable conditions, it replicates with the maximum possible rate which enhances the severity of disease incidence and intensity. Water movement in a crop canopy is generally associated with rain. Moisture content of air and soil at any place are highly dependent on precipitation. It is a well-known fact that precipitation enhances the moisture content of air, namely, relative humidity of any place due to evaporation. Evaporation results in the cooling and increases the absolute moisture content of the air at a small scale. Similarly, rainfall also increases the soil moisture content of a place and has a major role in soil water dynamics (Xu et al., 2012; Li et al., 2016). Furthermore, moisture is also known to be a major determining factor for growth and development of various microorganisms, for example, a fungi. Soil moisture content plays its dominant role on the severity of soil-borne diseases. Moderate temperature and moderate humidity are favorable for most of the pests and diseases. As the individual effect of soil moisture on plant disease epidemiology for field crops are difficult to predict, limited research findings are available for this. In general, soil moisture is known to have its impact on plant water potentials to which pathogens in leaves, stems, and fruits are subjected (Van der Wal, 1978). Soil water content influences the microbial activity through its influence on under surface water movement. It is the most critical factor for the determination of Macrophomina phaseolina infection to the host plant (Dhingra and Sinclair, 1975; Short et al., 1980). Soil moisture is also a major contributor for root rot disease in several important crops including chickpea (Bhatti and Kraft, 1992), wheat (Gill et al., 2001), and navy bean (Tu and Tan, 2003). Atmospheric moisture also termed as humidity (or relative humidity) is another form of free water which is a significant factor for plant disease development. Sometimes, high relative humidity in the absence of free water could be sufficient enough for spore germination. In normal scenario, humidity is an efficient indicator of wetness and dryness of the plant surface especially for leaves (Jhorar et al., 1998; Sentelhas et al., 2008). High relative humidity (80–90%) near the leaf and other plant surfaces is sufficient enough to bring infection with spores of several fungi. Ambient air humidity affects the host without directly influencing the pathogen. Humidity requirement for the germination of various fungus spores for a number of categories such as fungi, downy mildews, powdery mildews, and rusts have been summarized by Yarwood (1978). He found that among the various fungi, Aspergillus niger is having the lowest

320

Plant Pathogens: Detection and Management for Sustainable Agriculture

humidity requirement of 76%; however, for occurrence of Monilinia fructicola and Venturia inaequalis, more than 95% humidity is favorable. High air moisture level favors bacterial infection, while low humidity prevents it. For occurrence of all three types of rust diseases for wheat in India, higher than 70% relative humidity is a necessity (Mavi, 1994). The combined effect of air temperature and relative humidity on the pathogen intensity for gray leaf spot on maize leaves has been found to be significant. Similarly, the maximum rate of spore production has been reported in the temperature range of 25–30°C when RH was nearly 100% (Paul and Munkvold, 2005). 14.2.4 RADIATION Solar radiation affects the epidemiology of pathogens in two ways, that is, directly as well as indirectly. Direct effect of radiation includes its influence on the developmental cycle of the parasite due to diurnal and seasonal changes in radiation. Certain disease only develop when there is absence of solar exposure to the plants, for example, shade has been found to be beneficial for the coffee rust as compared with direct sunlight in standard fruit load conditions (López-Bravo et al., 2012). Indirect effect includes effect of radiation intensity at different wavelengths on the parasite and host plant (Friesland and Schroedter, 1988). It has been reported by Kirkham et al. (1974) that erratic and short reductions in sunlight intensity showed a marked lack of reproducibility in scab disease of apple plants. Recently David et al. (2016) found that the solar radiation and relative humidity were most effective predictors of ascospore release because these are most influential meteorological factors for the release of ascospores of Fusarium graminearum. 14.2.5 WIND Wind also influences the crop plants in several ways including plant growth, reproduction, distribution, death, as well plant evolution (Nobel, 1981; Ennos, 1997; de Langre, 2008). However, complete understanding of plant response to wind is a complex phenomenon which has not been fully understood (Onoda and Anten, 2011). Wind effects on plants may be categorized as physiological or mechanical. The physiological impact

Impact of Meteorological Variables and Climate Change

321

of wind may include effects on transpiration (Dixon and Grace, 1984), photosynthesis (Sinoquet et al., 2001; Smith and Ennos, 2003), and insect communication (Cocroft and Rodríguez, 2005; de Langre, 2008). Cold wind may result in chilling injury, while hot winds may result in plant sunburn. In a longer time series, wind influences the plant development and alters their morphology (Smith and Ennos, 2003). The mechanical impacts of wind include uprooting, lodging, flower and fruit shedding, as well as soil erosion (Cleugh et al., 1998; Onoda and Anten, 2011). Wind adversely affects the dew formation and helps raindrops and dew to dry quickly. Therefore, it reduces the likelihood of disease infection in this context. However, it also helps in dispersal of several organisms including pollen, plant propagules, and disease organisms at distant places. McCartney (1994) and Bock et al. (2011) found that wind speed and rainfall are the major contributors for dispersal of spores and pollen from crops. In this context Bock et al. (2010) observed a direct linear relationship between bacterial densities with wind speed. Wind speed reduction also reduces dispersal of the pathogen, resulting in the lesser disease spread and epidemic development. Hence, wind suppression techniques, for example, windbreaks help in minimizing the numbers of bacteria dispersed in the orchards. 14.2.6 CLIMATE CHANGE Climate change has become a reality now and the whole world is witnessing it as one of the biggest threat in near future. It is expected that there will be increase in temperature and changes in the rainfall or precipitation patterns in addition to increase in the severity and frequency of hazardous extreme weather events. During recent decades, climate changes have resulted in major impacts on natural and anthropogenic systems throughout the globe including oceans. Emission of greenhouse gases from anthropogenic sources is considered as the most significant driver of climate change. There are very high chances that till 2100, the global mean temperature may rise between 1.8°C and 4.0°C. However, this heating of earth may not be uniform across the globe and their impact will be higher on glaciers and land areas as compared with ocean. Agriculture is considered as one of the most climate vulnerable sector and a minor alteration in climate may affect the crop production to a significant level. Climate change affects all the four pillars of food

322

Plant Pathogens: Detection and Management for Sustainable Agriculture

security, namely, food availability, access to food, utilization, and stability (Wheeler and von Braun, 2013). As per an estimate, average temperature increase of 2°C may shrink the world GDP by 1% and also reduce the per capita income of Africa and South Asia in the range of 4–5% (World Bank, 2010). An increase in the temperature in the range of 2.5–4.9°C may reduce the rice yields by 32–40% and wheat yields by 41–52 % which may reduce the Indian GDP by 1.8–3.4% (Kalisch et al., 2011). 14.3 IMPACT OF CLIMATE CHANGE ON PLANT DISEASES It is expected that climate change will directly influence the occurrence of various plant diseases and their severity. Carbon dioxide (CO2) is the main greenhouse gas responsible for climate change. However, it has a beneficial impact over several plant growth and developmental processes. In numerous studies conducted worldwide, it has been reported that with the increased concentration of the CO2 in atmosphere, there will be significant improvement in the plant biomass and yield. Higher CO2 concentrations enhance the plant photosynthetic activities which can favor the better productivity and improved water and nutrient cycles. Manning and Tiedemann (1995) reported that increased CO2 concentrations is helpful for several plant diseases, for example, leaf spots, rusts, powdery mildew, and blights as it increases the size and density of the plant canopy combined with a higher microclimate relative humidity. Another important greenhouse gas, namely, ozone (O3) helps to enhance the senescence processes and necrosis and also promote attacks on plants by necrotrophic fungi. Furthermore, higher ozone concentrations modify the structure and properties of leaf surfaces in such a way that it affects the inoculation and infection process. Since climate change may result in higher temperature and increased carbon dioxide concentrations, which may result in to the spreading of pathogen and vector distributions to new geographical locations. It will provide newer opportunities for the pathogen to hybridize and spread of disease epidemic. Temperature is a major limiting factor for determining the period for reproduction of several pathogens. Longer seasons resulted from increased temperatures will provide additional time for the evolution of pathogens. In addition to this, the pathogen evolution may become faster due to the presence of large pathogen populations (Gautam et al.,

Impact of Meteorological Variables and Climate Change

323

2013). Susceptibility of cereal crops increases due to enhancement in temperature. High night temperatures, especially during winter seasons help in the pathogens survival. It also enhances the life cycles of vectors and fungi with increased sporulation and aerial fungal infection (YáñezLópez et al., 2012). Due to climate change led global warming, disease primarily caused by fungi are expected to experience elongated periods of temperatures which is considered to be optimum for pathogen growth and reproduction activities. However, the effects of higher temperature on plants will not be uniform during all the seasons. During winter season, warming may help to relieve the plant stress, while it may cause heat stress during summers (Garrett et al., 2006). 14.4 CONCLUSION Weather and its associated variables have a predominant role in the disease infestations. Weather elements influence several biological aspects of the host plants, namely, phenology, sugar and starch contents, root and shoot biomass, etc. Diseases severity also depends on weather changes. Therefore, it is advisable to understand the combination of weather elements that may result in to disease outbreak so that risk of plant diseases can be minimized or avoided. Climate change has become another major threat in recent times which may bring new diseases and challenges ahead. And proper planning and execution is a necessity to overcome with the challenges ahead. KEYWORDS • • • • • •

weather plant disease infection abiotic factors climate change environmental conditions

324

Plant Pathogens: Detection and Management for Sustainable Agriculture

REFERENCES Arora, M.; Pareek, S. Effect of Soil Moisture and Temperature on the Severity of Charcoal Rot of Sorghum Macrophomina Charcoal Rot of Sorghum. Ind. J. Scientific Res. 2013, 4 (1), 155–158. Bhatti, M. A.; Kraft, J. M. Influence of Soil Moisture on Root Rot and Wilt of Chickpea. Plant Dis. 1992, 76 (12), 1259–1262. Bock, C. H.; Graham, J. H.; Gottwald, T. R.; Cook, A. Z.; Parker, P. E. Wind Speed Effects on the Quantity of Xanthomonas Citri Subsp. Citri Dispersed Downwind ffrom Canopies of Grapefruit Trees Infected with Citrus Canker. Plant Dis. 2010, 94 (6), 725–736. https://doi.org/10.1094/PDIS-94-6-0725. Bock, C. H.; Gottwald, T. R.; Cook, A. Z.; Parker, P. E.; Graham, J. H. The Effect of Wind Speed on Dispersal of Splash-borne Xanthomonas Citri Subsp. Citri at Different Heights and Distances Downwind of Canker-infected Grapefruit Trees. J. Plant Pathol. 2011, 93 (3), 667–677. https://doi.org/10.4454/jpp.v93i3.1234 Byrne, J. M.; Hausbeck, M. K.; Meloche, C.; Jarosz, A. M. Influence of Dew Period and Temperature on Foliar Infection of Greenhouse-grown Tomato By Colletotrichum Coccodes. Plant Dis. 1998, 82 (6), 639–641. Cleugh, H. A.; Miller, J. M.; Böhm, M. Direct mechanical Effects of Wind on Crops. Agroforestry Sys. 1998, 41 (1), 85–112. https://doi.org/10.1023/A:1006067721039. Coakley, S. M.; Scherm, H.; Chakraborty, S. Climate Change and Plant Disease Management. Annu. Rev. Phytopathol. 1999, 37 (1), 399–426. https://doi.org/10.1146/annurev. phyto.37.1.399. Cocroft, R. B.; Rodríguez, R. L. The Behavioral Ecology of Insect Vibrational Communication. BioScience 2005, 55 (4), 323–334. Colhoun, J. Effects of Environmental Factors on Plant Disease. Annu. Rev. Phytopathol. 1973, 11 (1), 343–364. https://doi.org/10.1146/annurev.py.11.090173.002015. Das, S.; Pandey, V.; Patel, H. R.; Patel, K. I. Effect of Weather Parameters on Pest-disease of Okra During Summer Season in Middle Gujarat. J. Agrometeorol. 2011, 13 (1), 38–42. David, R. F.; BozorgMagham, A. E.; Schmale, D. G.; Ross, S. D.; Marr, L. C. Identification of Meteorological Predictors of Fusarium Graminearum Ascospore Release Using Correlation and Causality Analyses. Eur. J. Plant Pathol. 2016, 145 (2), 483–492. https:// doi.org/10.1007/s10658-015-0832-3. de Langre, E. Effects of Wind on Plants. Ann. Rev. Fluid Mechanics 2008, 40 (1), 141–168. https://doi.org/10.1146/annurev.fluid.40.111406.102135. Dhingra, O. D.; Sinclair, J. B. Survival of Macrophomina Phaseolina Sclerotia in Soil: Effects of Soil Moisture, Carbon, Nitrogen Ratios, Carbon Sources, and Nitrogen Concentrations. Phytopathology 1975, 65 (3), 236–240. https://doi.org/10.1094/Phyto-65-236. Dixon, M.; Grace, J. Effect of Wind on the Transpiration of Young Trees. Ann. Botany 1984, 53 (6), 811–819. Du, Y. C.; Tachibana, S. Effect of Supraoptimal Root Temperature on the Growth, Root Respiration and Sugar Content of Cucumber Plants. Scientia Horticulturae 1994, 58 (4), 289–301. https://doi.org/10.1016/0304-4238(94)90099-X. Ennos, A. R. Wind as an Ecological Factor. Trends Ecol. Evol. 1997, 12 (3), 108–111. https://doi.org/10.1016/S0169-5347(96)10066-5.

Impact of Meteorological Variables and Climate Change

325

Friesland, H.; Schroedter, H. The Analysis of Weather Factors in Epidemiology. In Experimental Techniques in Plant Disease Epidemiology; Kranz, J.; Rotem, H., Eds; Springer: Berlin, Heidelberg, 1988, pp 115–134. https://doi.org/10.1007/978-3-642-95534-1 Garrett, K. A.; Dendy, S. P.; Frank, E. E.; Rouse, M. N.; Travers, S. E. Climate Change Effects on Plant Disease: Genomes to Ecosystems. Annu. Rev. Phytopathol. 2006, 44 (1), 489–509. https://doi.org/10.1146/annurev.phyto.44.070505.143420. Gautam, H. R.; Bhardwaj, M. L.; Kumar, R. Climate Change and Its Impact on Plant Diseases. Curr. Sci. 2013, 105 (12), 1685–1691. https://doi.org/10.1016/j.eswa.2010.09.036. Geagea, L.; Huber, L.; Sache, I.; Flura, D.; McCartney, H. A.; Fitt, B. D. L. Influence of Simulated Rain on Dispersal of Rust Spores from Infected Wheat Seedlings. Agri. Forest Meteorol. 2000, 101 (1), 53–66. https://doi.org/10.1016/S0168-1923(99)00155-0. Gill, J. S.; Sivasithamparam, K.; Smettem, K. R. J. Effect of Soil Moisture at Different Temperatures on Rhizoctonia Root Rot of Wheat Seedlings. Plant Soil 2001, 231 (1), 91–96. https://doi.org/10.1023/A:1010394119522. Gill, K. K.; Sharma, I.; Jindal, M. M. Effect of Weather Parameters on the Incidence of Stripe Rust in Punjab. J. Agrometeorol 2012, 14(2), 167–169. Hardwick, N. V. Weather and Plant Diseases. Weather 2002, 57 (5), 184–190. https://doi. org/10.1002/wea.6080570507. Huber, L.; Madden, L. V.; Fitt, B. D. L. Rain-splash and Spore Dispersal: A physical Perspective. In The Epidemiology of Plant Diseases; Gareth Jones, D., Ed.; Springer: Dordrecht, Netherlands, 1998. https://doi.org/10.1007/978-94-017-3302-1_17. Jhorar, O. P.; Mathauda, S. S.; Singh, G.; Butler, D. R.; Mavi, H. S. Relationships Between Climatic Variables and Ascochyta Blight of chickpea in Punjab, India. Agri. Forest Meteorol. 1997, 87 (2–3), 171–177. https://doi.org/10.1016/S0168-1923(97)00014-2. Jhorar, O. P.; Butler, D. R.; Mathauda, S. S. Effects of Leaf Wetness Duration, Relative Humidity, Light and Dark on Infection and Sporulation by Didymella Rabiei on Chickpea. Plant Pathol. 1998, 47 (5), 586–594. https://doi.org/10.1046/j.1365-3059.1998.0280a.x. Kalisch, A.; Zemek, O.; Schellhardt, S. Adaptation in Agriculture. In Adaptation to Climate Change with a Focus on Rural Areas and India; Ilona Porsché; Anna Kalisch; Rosie Füglein Ed.: Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, New Delhi, India, 2011, 44–82. Kalisch, A.; Zemek, O.; Schellhardt, S. Adaptation in Agriculture. Adaptation to Climate Change with a Focus on Rural Areas and India 2011, 44–82. Kanzaria, K. K.; Dhruj, I. U.; Sahu, D. D. Influence of Weather Parameters on Powdery Mildew Disease of Mustard Under North Saurashtra Agroclimatic Zone. J. Agrometeorol. 2013, 15 (1), 86–88. Kirkham, D. S.; Hignett, R. C.; Ormerod, P. J. Effects of Interrupted Light on Plant Disease. Nature 1974, 247 (5437), 158–160. https://doi.org/10.1038/247158a0. Kumar, G.; Chakravarty, N. V. K. A Simple Weather Based Forewarning Model for White Rust in Brassica. J. Agrometeorol. 2008, 10 (1), 75–80. Leopold, L. B. Dew as a Source of Plant Moisture. Pacific Sci. 1951, 6, 259–261. Levy, Y.; Pataky, J. K. Epidemiology of Northern Leaf Blight on Sweet Corn. Phytoparasitica 1992, 20 (1), 53–66. https://doi.org/10.1007/BF02995636. Li, B.; Wang, L.; Kaseke, K. F.; Li, L.; Seely, M. K. The Impact of Rainfall on Soil Moisture Dynamics in a Foggy Desert. PLoS One 2016, 11 (10). https://doi.org/10.1371/journal. pone.0164982.

326

Plant Pathogens: Detection and Management for Sustainable Agriculture

López-Bravo, D. F.; Virginio-Filho, E. de M.; Avelino, J. Shade is Conducive to Coffee Rust as Compared to Full Sun Exposure Under Standardized Fruit Load Conditions. Crop Protection 2012, 38, 21–29. https://doi.org/10.1016/j.cropro.2012.03.011. Malhotra, R. S.; Singh, K. B.; Rheenen, H. A. van; Pala, M. Genetic Improvement and Agronomic Management of Chickpea with Emphasis on the Mediterranean Region. In Adaptation of Chickpea in the West Asia and North Africa Region; Saxena, N. P.; Saxena, M. C.; Johansen, C.; Virmani, S. M.; Harris, H., Eds; ICARDA: Aleppo, Syria, 1996, pp 217–232. Manning, W. J.; V. Tiedemann, A. Climate Change: Potential Effects of Increased Atmospheric Carbon Dioxide (CO2), Ozone (O3), and Ultraviolet-B (UV-B) Radiation on Plant Diseases. Environ. Pollution 1995. https://doi.org/10.1016/0269-7491(95)91446-R Mavi, H. S. Introduction to Agrometeorology, 2nd ed.; Oxford & IBH Publishing Co. Pvt. Ltd.: New Delhi, 1994. McCartney, H. A. Dispersal of Spores and Pollen from Crops. Grana 1994, 33 (2), 76–80. https://doi.org/10.1080/00173139409427835. Miller, P. R. The Effect of Weather on Diseases. Yearbook Agriculture 1953, 83–93. https:// doi.org/10.1002/j.1477-8696.1977.tb04568.x. Nobel, P. S. Wind as an Ecological Factor. In Physiological Plant Ecology I: Responses to the Physical Environment; O. L. Lange; P. S. Nobel; C. B. Osmond; H. Ziegler, Eds; Springer: Berlin, Heidelberg, 1981. https://doi.org/10.1007/978-3-642-68090-8_16. Oerke, E. C.; Dehne, H. W.; Schönbeck, F.;Weber, A. Crop Production and Crop Protection: Estimated Losses in Major Food and Cash Crops. Elsevier Science: Amsterdam, The Netherlands, 1994. Onoda, Y.; Anten, N. P. R. Challenges to Understand Plant Responses to Wind. Plant Signal. Behav. 2011, 6 (7), 1057–1059. https://doi.org/10.4161/psb.6.7.15635. Pal, R.; Mandal, D.; Kumar, M.; Panja, B. N. Effect of Weather Parameters on the Initiation and Progression of Sheath Blight of Rice. J. Agrometeorol. 2017, 19 (1), 39–43. Paul, P. A.; Munkvold, G. P. Influence of Temperature and Relative Humidity on Sporulation of Cercosporazeae-maydis and Expansion of Gray Leaf Spot Lesions on Maize Leaves. Plant Dis. 2005, 89 (6), 624–630. Pivonia, S.; Cohen, R.; Kigel, J.; Katan, J. Effect of Soil Temperature on Disease Development in Melon Plants Infected by Monosporascus Cannonballus. Plant Pathol. 2002, 51 (4), 472–479. https://doi.org/10.1046/j.1365-3059.2002.00731.x. Reddick, D. Effect of Soil Temperature on the Growth of Bean Plants and on Their Susceptibility to a Root Parasite. Am. J. Botany 1917, 4 (9), 513–519. Savary, S.; Ficke, A.; Aubertot, J. N.; Hollier, C. Crop Losses Due to Diseases and their Implications For Global Food Production Losses and Food Security. Food Security 2012, 4 (4), 519–537. https://doi.org/10.1007/s12571-012-0200-5. Schwartz, H. F.; Otto, K. L.; Gent, D. H. Relation of Temperature and Rainfall to Development of Xanthomonas and Pantoea Leaf Blights of Onion in Colorado. Plant Dis. 2003, 87 (1), 11–14. https://doi.org/10.1094/PDIS.2003.87.1.11. Sentelhas, P. C.; Dalla Marta, A.; Orlandini, S.; Santos, E. A.; Gillespie, T. J.; Gleason, M. L. Suitability of Relative Humidity as an Estimator of Leaf Wetness Duration. Agri. Forest Meteorol. 148 (3), 392–400. https://doi.org/10.1016/j.agrformet.2007.09.011. Shew, H. D.; Benson, D. M. Influence of Soil Temperature and Inoculum Density of Phytophthora Cinnamomi on Root Rot of Fraser Fir. Plant Dis. 1983, 67 (5), 522–524. https://doi.org/10.1094/PD-67-522.

Impact of Meteorological Variables and Climate Change

327

Short, G. E.; Wyllie, T. D.; Bristow, P. R. Survival of Macrophomina Phaseolina in Soal and in Residue of Soybean. Phytopathology 1980, 70 (1), 13–17. Singh, R.; Singh, R.; Singh, D.; Mani, J. K.; Karwasra, S. S.; Beniwal, M. S. Effect of Weather Parameters on Karnal Bunt Disease in Wheat in Karnal Region of Haryana. J. Agrometeorol. 2010, 12 (1), 99–101. Sinoquet, H.; Le Roux, X.; Adam, B.; Ameglio, T.; Daudet, F. A. RATP: A model for Simulating the Spatial Distribution of Radiation Absorption, Transpiration and Photosynthesis Within Canopies: Application to an Isolated Tree Crown. Plant Cell Environ. 2001, 24 (4), 395–406. https://doi.org/10.1046/j.1365-3040.2001.00694.x. Smith, V. C.; Ennos, A. R. The Effects of Air Flow and Stem Flexure on the Mechanical and Hydraulic Properties of the Stems of Sunflowers Helianthus Annuus l. J. Exp. Botany 2003, 54 (383), 845–849. https://doi.org/10.1093/jxb/erg068. Strange, R. N.; Scott, P. R. Plant Disease: A Threat to Global Food Security. Ann. Rev. Phytopathol. 2005, 43 (1), 83–116. https://doi.org/10.1146/annurev.phyto.43.113004.133839. Te Beest, D. E.; Paveley, N. D.; Shaw, M. W.; van den Bosch, F. Disease–weather Relationships for Powdery Mildew and Yellow Rust on Winter Wheat. Phytopathology 2008, 98 (5), 609–617. https://doi.org/10.1094/PHYTO-98-5-0609. Tu, J. C.; Tan, C. S. Effect of Soil Moisture on Seed Germination, Plant Growth and Root Rot Severity of Navy Bean in Fusarium Solani Infested Soil. Comm. Agri. Appl. Biol. Sci. 2003, 68 (4B), 609–612. Van der Wal, A. F. Moisture as a Factor in Epidemiology and Forecasting. In Water Deficits and Plant Growth; Kozlowski, T. T., Ed..; Academic Press, 1978, pp 253–295. https:// doi.org/https://doi.org/10.1016/B978-0-12-424155-8.50015-8 Wheeler, T.; von Braun, J. Climate Change Impacts on Global Food Security. Science 2013, 341 (508), 508–513. https://doi.org/10.1126/science.1239402. World Bank. World Development Report 2010. The World Bank: Washington DC, 2010. Xu, Q.; Liu, S.; Wan, X.; Jiang, C.; Song, X.; Wang, J. Effects of Rainfall on Soil Moisture and Water Movement in a Subalpine Dark Coniferous Forest in Southwestern China. Hydrol. Proc. 2012, 26 (25), 3800–3809. https://doi.org/10.1002/hyp.8400. Yáñez-López, R.; Torres-Pacheco, I.; Guevara-González, R. G.; Hernández-Zul, M. I.; Quijano-Carranza, J. A.; Rico-García, E. The Effect of Climate Change on Plant Diseases. Afr. J. Biotechnol. 2012, 11 (10), 2417–2428. https://doi.org/10.5897/AJB10.2442. Yarwood, C. E. Water and the Infection Process. In Water Deficits and Plant Growth; Kozlowski, T. T., Ed.; Academic Press Inc.; 1978, pp 141–173.

Index A Abelia latent tymovirus symptoms, 37 transmission, 44 Abelmoschus esculentus L. Moench. see Okra Alfalfa mosaic alfamovirus symptoms, 44 transmission, 44 Andhra Pradesh agro climatic zones and major crops commercial crops, 203 flowers, 203 horticulture sector, 203 rainfall, 202 diversity of phyto-nematodes ectoparasites, 209 migratory endoparasites, 208–209 sedentary endo parasites, 207–208 semi-endoparasites, 208 emerging nematode problems crop losses, 221 cultural practices, 222 guava decline, 220–221 integrated management practices, 223–224 major challenge, 224 management in nurseries, 222 success stories, 225 symptoms, 222 kalahasti malady of groundnut crop losses, 218 management, 218 symptoms, 218 lesion nematode chemical management, 220 cultural management, 219–220 pigeon pea cyst nematode, 218 plant-parasitic nematodes

crop wise distribution of, 215–216 reported, 210–213 pomegranate crop losses, 219 damage symptoms, 219 management, 219 root-knot nematode biological management, 217 chemical management, 217 cultural management, 217 technologies developed, 220 Urfa disease cultural management, 216–217 host plant resistance, 217 Antimicrobial peptides (AMPs) advancement in bioinformatics tools, 249 analysis and plant activity assay of, 258 bacterial and fungal origin database, 252 benefits, 243 biocontrol agents (BCAs), 249 biological roles, 253 biotechnological research, 244 cyclodipopeptides (cLPs), 249 ESKAPE, 242 fungicides and pesticides continuous and massive use of, 243 in genomic data, mining for BAGEL, 258 ORFs, 257 global food security, 242 lipopolysaccharide (LPS), 242 modes-of-action, 244 N-terminus, 253 peptaibol of Trichoderma, 252 ribosomal-derived antimicrobial peptides classification of, 251 structural characteristics, 247 transgenic plants, 243

Index

330 types, 244, 247 biogenesis of, 248 α-helix and β-sheet structural groups, 248 intracellular targets, 257 mode of action, 253–257 nonribosomal-derived peptides, 250, 253 ribosomal origin, 248–250 used against pathogens in agricultural crops, 245–246 Apple mosaic ilarvirus symptoms, 44 transmission, 44

B Bean poad mottle comovirus symptoms, 44 transmission, 44 Beat curly top hybrigemini virus symptoms, 45 transmission, 45 Belladonna mottle tymovirus symptoms, 45 transmission, 45

C CACAO yellow mosaic virus symptoms, 45 transmission, 45 Carnation mottle carmovirus symptoms, 45 transmission, 46 CASSAVA green mottle nepovirus symptoms, 46 transmission, 46 Catharanthus roseus (L.), 36 Abelia latent tymovirus, 37, 44 alfalfa mosaic alfamovirus, 44 apple mosaic ilarvirus, 44 bean poad mottle comovirus, 44 beat curly top hybrigemini virus, 45 Belladonna mottle tymovirus, 45 CACAO yellow mosaic virus, 45 carnation mottle carmovirus, 45–46 CASSAVA green mottle nepovirus, 46 cherry leaf roll nepovirus, 46

citrus leaf rugose ilarvirus, 46–47 citrus ringspot virus, 47 clover wound tumor phytoreovirus, 47 clover yellow mosaic potexvirus, 47 COWPEA severe mosaic comovirus, 47–48 cucumber mosaic cucumovirus, 48 cucumber mosaic virus subgroup IB, 48 dogwood mosaic nepovirus, 48 dulcamara mottle tymovirus, 49 ELM mottle ilarvirus, 49 Erysimum latent tymovirus, 49 foxtail mosaic potexvirus, 49–50 Humulus japonicas ilarvirus, 50 LILAC ring mottle ilarvirus, 50 literature on viruses, 37 Nandina mosaic potexvirus, 50 Narcissus mosaic potexvirus, 50 Okhra mosaic tymovirus, 51 particle size and shape of viruses, 41–43 pea seed-borne mosaic potyvirus, 51 peach enation nepovirus, 51 peanut stunt cucumovirus, 51–52 pepper ringspot tobravirus, 52 pepper venial mottle potyvirus, 52 plum american line pattern ilarvirus, 52–53 poplar mosaic calaravirus, 53 potato black ringspot nepovirus, 53 potato T trichovirus, 53 potato yellow vein disease, 53–54 prune dwarf ilarvirus, 54 prunus necrotic ringspot ilarvirus, 54 scrophularia mottle tymovirus, 54–55 spring beauty latent bromovirus, 54 tobacco mosaic satellite virus, 55 necrosic necrovirus, 56 rattle tobravirus, 55 ringspot nepovirus, 56 streak ilarvirus, 56 stunt varicosavirus, 56 tomato-spotted wilt ilarvirus, 57 tospovirus, 56–57 turnip crinkle carmovirus, 57 turtle apple mosaic ilarvirus, 57–58 watermelon mosaic-2 potyvirus, 58

Index

wild cucumber mosaic tymovirus, 58 worldwide distribution, 38–40 zantedeschia mild mosaic virus, 58 Catharanthus yellow mosaic virus (CYMV), 37 Cherry leaf roll nepovirus symptoms, 46 transmission, 46 Chloroplast genomes A (adenine)–T (thymine) content, 292 PEND, 291 plastid transformation biomaterial bioreactors, 305 drought tolerance, 302 edible crop plants, genome, 305 herbicide resistance, genome, 298–299 pathogen resistance, genome, 301 pharming through farming, 303–304 plastids as vaccine bioreactors, 304 polycistronic manner, bacterial operons via chloroplast genomes, 300–301 RNA editing, 303 transgenic plant lacking antibiotic resistance gene, 302–303 restriction fragment length polymorphism (RFLP) analysis, 292 transformation, 292 Agrobacterium, 295 angiosperms, nuclear and chloroplast genome, 294 Chlamydomonas Reinhardtian, 295 environment friendly and advantageous in planta, 297–298 foreign gene integration, 294 insertion sites, 296 method development, 294–295 methods and expressed foreign, 295 plastid transgene in plants, controlled expression, 297 polyethylene glycol (PEG), 295 regulatory sequences, 296–297 selectable/screenable marker gene/s, 295–296 structure of, 293 transgenomic and transplastomic technologies, 299–300

331 Citrus leaf rugose ilarvirus symptoms, 46 transmission, 46–47 Citrus ringspot virus symptoms, 47 transmission, 47 Clover wound tumor phytoreovirus symptoms, 47 transmission, 47 Clover yellow mosaic potexvirus symptoms, 47 transmission, 47 Combat plant conventional methods, 272 COWPEA severe mosaic comovirus, 47 symptoms, 48 transmission, 48 Cucumber mosaic cucumovirus symptoms, 48 transmission, 48 Cucumber mosaic virus subgroup IB symptoms, 48 transmission, 48

D Dogwood mosaic nepovirus symptoms, 48 transmission, 48 Double-stranded ribonucleic acid (dsRNA), 271 Dulcamara mottle tymovirus symptoms, 49 transmission, 49

E ELM mottle ilarvirus symptoms, 49 transmission, 49 Endosymbiotic theory, 289 Enzyme-linked immunosorbent assay (ELISA), 16 Erysimum latent tymovirus symptoms, 49 transmission, 49 Etioplasts, 290

Index

332

F Foxtail mosaic potexvirus symptoms, 49 transmission, 50

G Green plants, 289

H Humulus japonicas ilarvirus symptoms, 49 transmission, 50

I Insecticides and phytopesticides, management of vector botanicals or plant leaf extracts, 8 flea beetle vectors, 9 host plant–vector–viruspathosystems, 8 integrated pest management (IPM), 10 planting date, altering, 9 positive correlations, 8 soil amendment, use, 9–10

L Lichens, 231 activity, 234–235 biopesticides Food and Agricultural Organization (FAO), 232 higher plants, 233 defense chemicals, 232 importance medicinal uses, 232 metabolites, potential utilization antifungal activity, 235 antifungal and antimicrobial activity, 233 antiherbivory, 236 antimicrobial activity, 235–236 insecticidal activity, 236 LILAC ring mottle ilarvirus symptoms, 50 transmission, 50

N Nandina mosaic potexvirus symptoms, 50 transmission, 50 Narcissus mosaic potexvirus symptoms, 50 transmission, 50 Nematode problems of state disease of rice, 209 crop losses, 214 root-knot nematode, 216 symptoms, 215–216 Nematology Andhra Pradesh and Telangana states, 204–207

O Okhra mosaic tymovirus symptoms, 51 transmission, 51 Okra, 3 common symptoms, 5 crop, 4 DAS-ELISA, 5 field trial, 5 Komenda–Edina–Eguafo–Abirem (KEEA), 5 mosaic disease, 5 OkMV infection symptoms of, 5 production, 4 Okra leaf curl disease (OLCD) begomoviruses, 6 field trial, 6 KEEA municipality, 6

P Paddy varieties, mycoflora associated bakanae disease, 127 Bavistin on percent seed germination effect of, 143 blast, 126 brown spot disease, 127 cereals, 124 discoloration of grains, 129

Index

discoloration results, 125 false smut disease, 128 fungi, 125, 126 fungicides on seed germination and seed mycoflora effect of, 133–134 isolation of fungi, 131 internal seed mycoflora, 132 seed surface, 132 standard blotter method, 132 Karnal smut, 128 leaf scald caused, 127 maintenance of pure culture, 133 mechanical injuries, checking, 131 mycotoxins, 125 percent frequency of fungi, 133 percent seed germination, 131 fungi isolated from unsterilized and surface sterilized seeds, 134–138 paddy by using blotter method, 138–142 scab, 129 seed samples, collection paddy, 130–131 sheath blight disease, 127 sheath-rot disease, 128 spoilage of grains, 125 stack-burn disease, 127 storage fungi, 126 thiram on percent seed germination effect of, 143 Udbatta disease, 128 Papaya, 68 anthracnose, 70 control measures, 72 epidemiology, 71 etiology, 71 symptoms, 71 bacterial disease bacterial leaf spot, 76 internal yellowing, 77 purple stain rot, 77 black spot disease, 68 control measures, 70 epidemiology, 70 etiology, 69 symptoms, 69

333 damping–off seedlings control measures, 73 epidemiology, 72–73 symptoms, 73 fungal diseases anthracnose, 70–72 black spot, 68–70 damping–off seedlings, 72–73 Phytopthora blight, 73–75 powdery mildew, 75 Meleira disease, 80–81 phytoplasma disease bunchy top disease, 82–83 dieback, 81–82 powdery mildew control measures, 75 epidemiology, 75 etiology, 75 viral diseases papaya lethal yellowing virus, 79–80 papaya ringspot virus, 77–79 Pea seed-borne mosaic potyvirus symptoms, 51 transmission, 51 Peach enation nepovirus symptoms, 51 transmission, 51 Peanut stunt cucumovirus, 51–52 symptoms, 52 transmission, 52 Pepper ringspot tobravirus symptoms, 52 transmission, 52 Pepper venial mottle potyvirus symptoms, 52 transmission, 52 Phosphate solubilizing microorganisms (PSMs), 91 Plant disease, 314 climate change, impact carbon dioxide (CO2), 322 cereal crops, 323 temperature, 322 weather elements, effect air or soil moisture, 318–320 climate change, 321–322 diseases, 315

334 growth and development, 315 pathogens, 315 precipitation, 317–318 solar radiation, 320 temperature, 316–317 wind, 320–321 Plant disease detection bacteria, 164 caused by pathogens, 163–164 disease patterns and distribution, 174 identification of host specificity, 175–176 disorder changes in light, 161 environmental factors, 159–160 excessive or deficiency in nutrition, 161–163 insect pest, 158–159 moisture changes, 160–161 pesticide phytotoxicity, 163 temperature changes, 160 food crops and principal diseases, 165–166 losses of agricultural, 158 management correct plant identification, 170–171 disease identification, 169–170 healthy plant, 171–172 nematodes ectoparasitic nematodes, 167–168 endoparasitic nematodes, 167 pests on crop plants, 168–169 plant-parasitic nematodes, 168 pathogenic fungi, 164 quality and yield, 157 sign of symptoms identify biotic causal agents, 173–174 characteristic symptoms, 172 plant part affected, 174 symptom variability, 173 viruses, 169 Plant viruses diseases biochemical techniques, 23 detection platforms, 24 diagnosis, 19 diagnostic techniques, 16 ELISA technique, 25–26

Index

bioelectric recognition assay (BERA), 28 competitive fluorescence PCR (CF– PCR), 27–28 fluorescence RT–PCR using Taqman technology, 27 nitrocellulose membrane (NCM), 28 quartz crystal microbalance immunosensors, 27 tissue blot immunoassay, 27 horticultural and agricultural crops, 16 immunoelectron microscopy, 25 isothermal DNA amplification, 24 microscopic analysis, 24 molecular hybridization technologies, 17 physical properties, 23 real-time polymerase chain reaction (RT-PCR), 17 serological tests, 17–18 symptomatology, 23 transmission tests, 23 viral coat protein agglutination tests, 24–25 viral nucleic acid-based techniques, 17 Plant-parasitic nematodes (PPNs) agriculture economy impact, 185 cereal cyst nematode (CCN), 185–186 management, 182 biological control, 186–187 nematophagous fungi, 187 plant diseases, 186 mechanism of infection chitinases, 188–189 collagenases, 189–190 nematophagous bacteria, 191 subtilases, 187–188 Pasteuria penetrans, 191 mechanism of infection, 192 rhizobacteria, 192 predacious nematodes Clarkus papillatus, 193 solarization, 185 volatile organic compounds (VOCs), 190–191 yield loss, 183–184 Plum American line pattern ilarvirus symptoms, 52

Index

335

transmission, 52–53 Polymerase chain reaction (PCR), 16 Poplar mosaic calaravirus symptoms, 53 transmission, 53 Potato black ringspot nepovirus symptoms, 53 transmission, 53 Potato T trichovirus symptoms, 53 transmission, 53 Potato yellow vein disease symptoms, 53 transmission, 53–54 Protoplastids, 290 Prune dwarf ilarvirus symptoms, 53 transmission, 53–54 Prunus necrotic ringspot ilarvirus symptoms, 54 transmission, 54

R Restriction fragment length polymorphism (RFLP) analysis, 292 Rhizosphere harbors biocidal activity botanicals, 92 biological agents, 92 cropping system, fungal diversity pigeonpea cropping system, 96–97 soil mycoflora under rice-wheat cropping system, 94–96 decomposition mycoflora rice stubble, associated with, 97–99 soluble crude protein using cellulolytic fungi, production, 99 T. Harzianum, potential, 100 disease management Aspergillus niger, 104 Cladosporium cladosporioides, 104 fungal metabolites and amendments, effect, 109, 113–115 fungi on biometric parameters of moong crop, effect, 105 Fusarium oxysporum f. sp. lycopersici (FOL), 103

fusarium wilt of tomato, 103–104, 109 incubation period, effect, 104 mycoflora amended vermicompost, 108–109 P-solublizing fungi, effect, 105 Trichoderma harzianum, 104 weed extracts, effect, 106 weeds loaded with beneficial fungi, effect, 108 earthworms vermicomposting process and biometrical parameters, 110 experimental details phosphorus solublizing fungi (PSF), 94 pre-treated air-dried rice, 94 Species Richness (S), 93 standard formulae, 93 fungal loaded and nonloaded vermicompost extracts effect of, 111 microbes, 93 mineral availability bacteria, 102 documentation, 100 mycelial growth, 103 Penicilliun citrinum, 100–101 P-solublization, 100 P-solublizing fungi, 103 solublization of Zn, 102 tri-calcium phosphate (TCP), 100 plant heath and soil health problems, 91 tomato plant treatments on growth parameters of, 112 RNA interference (RNAi), 271 altered phenotypes, 272–273 diseases management plant fungal infections, 276–277 viral disease, 277–278 loss of functions, 272–273 plants, induction methods agroinfiltration method, 274 microbombardment method, 275 virus-induced gene silencing (VIGS) method, 275–276 working demonstration of, 274

Index

336 RNA induced silencing complex (RISC), 273 Rolling circle amplification (RCA), 16

S Scrophularia mottle tymovirus symptoms, 55 transmission, 55 Spring beauty latent bromovirus symptoms, 54 transmission, 54

T Telangana agro climatic zones and major crops, 203–204 Tobacco mosaic satellite virus symptoms, 55 transmission, 55 necrosic necrovirus symptoms, 55 transmission, 55 rattle tobravirus symptoms, 55 transmission, 55 ringspot nepovirus symptoms, 56 transmission, 56 streak ilar virus symptoms, 56 transmission, 56 stunt varicosavirus symptoms, 56 transmission, 56 Tomato-spotted wilt ilarvirus symptoms, 57

transmission, 57 tospovirus, 56 symptoms, 57 transmission, 57 Turnip crinkle carmovirus symptoms, 57 transmission, 57 Turtle apple mosaic ilarvirus symptoms, 57 transmission, 58

V Viral diseases, management resistant varieties, use, 7–8 strategies, 7 Viruses Baltimore classification system, 19 particle morphology bacilliform, 22 filamentous, 21 geminate, 22 isometric, 20 ROD-shaped, 20

W Watermelon mosaic-2 potyvirus symptoms, 57 transmission, 58 Wild cucumber mosaic tymovirus symptoms, 58 transmission, 58

Z Zantedeschia mild mosaic virus symptoms, 58 transmission, 58