Preface With shrinking area of cultivable lands and increasing human population to be fed, production of agricultural and horticultural commodities has become a stupendous task for the growers and administrators of all nations, especially the developing countries. To bridge the gap between the supply and demand of food grains and other produce, consistent and effective measures have to be taken to avoid losses due to various factors. Losses due to crop diseases caused by microbial plant pathogens are quite substantial. The plant pathologists have a noble responsibility for the supply of healthy and disease-free food and feed to the people and animals useful for mankind. Hence, there is an imperative need to develop effective systems for managing the diseases and to disseminate the information to the cultivators on the methods of protecting the crops and reducing the incidence of diseases which have the potential for destroying the crops at different stages of growth. This book has been designed to provide, in an easily understandable style, the necessary information on the microbial plant pathogens, the diseases caused by them, methods of detecting and identifying the pathogens, process of disease development, methods of assessing the losses due to the diseases, principles of disease management and the possible ways of integrating the practices to enhance the effectiveness of disease management. Basic plant pathological methods are described in Appendices. Glossary of frequently used terms in the study of microbial plant pathogens is also provided to help the students in enlarging their knowledge. It is hoped that the graduating students, researchers and teachers investigating different aspects of microbial plant pathogens and the diseases induced by them and desiring to update the information will find this book to be useful.

Human beings, considered to be the highly evolved living organisms, have been making consistent and constant efforts to lead comfortable life without much concern for the conservation of nature and adversities to other living and nonliving entities existing in the universe. To meet the requirements of food, feed, fibre, timber and other needs, the plants that could supply the above were selected and domesticated. When the useful plant species were cultivated over large areas repeatedly year after year, the problems afflicting plants that were not recognized earlier as constraints for crop cultivation, assumed monstrous proportions wiping out entire crops and ruining the livelihood of the people of that geographical location/country. World history is replete with numerous instances of huge crop losses caused by microbial plant pathogens resulting in malnutrition, hunger and death. Migration of millions of people to other countries for their survival, became unavoidable. Such historical evidences threatening the existence of humans necessitated to investigate the causes of destructive diseases like late blight and heliminthosporiose diseases affecting respectively potato and rice, the staple food of the largest populations of the world. In order to take appropriate measures for minimizing losses due to crop diseases and to mitigate the sufferings of man and the animals, application of various short- and long-term disease management strategies has become indispensable for the profitable cultivation of crops

Occurrence of various diseases affecting agricultural and horticultural crop is known for several centuries. However, critical examination of crop diseases to understand the nature of the causative agents and extent of losses induced by diseases and development of effective disease management systems were possible much later. Any deviation from normal form and function of plants is considered as ‘disease’. Both pathogenic (biotic) and physiogenic (abiotic) causes are involved in diseases of plants. Adverse environmental conditions such as extremes of temperature, light and oxygen, soil moisture, pH and polluted air may alter the physiological conditions of the plants. Nutritional deficiencies also affect various crops leading to considerable losses. Microbial plant pathogens–fungus-like oomycetes, fungi, bacteria, phytoplasmas, viruses and viroids–form the major group of biotic agents that induce different diseases of crop plants in the field as well as during transport and storage (Narayanasamy 2002,2006). Presentation of information in this book is confined to various aspects of the microbial plant pathogens and the diseases caused by them. Microbial pathogens may induce symptoms that may be visible externally and also in the deep-seated internal tissues which have to be examined using light or electron microscope. In the case of some diseases, the symptoms may be localized in different plant parts such as roots, leaves, stems, floral parts or seeds / fruits / vegetables. Such infections are known as local infection. On the other hand, the pathogen may spread from the point of entry into the host to other plant parts which exhibit characteristic symptoms. These diseases are termed as systemic diseases. In some cases, no recognizable visible symptom is produced although the pathogen is able to develop without inconveniencing the host plant species which are called as carriers and the infection is designated latent infection. Plant viruses are carried symptomlessly by many weed plant species which may serve as sources of infection for crop plants.

Detection and identification of the causes and diagnosis of the diseases rapidly and precisely are the basic requirements for developing effective crop disease management systems suitable for different ecosystems. Incorrect diagnosis leads to failure to contain the disease spread and consequent additional expenditure to the growers. Hence, it is essential that proper diagnostic procedures are followed to achieve the goal of reducing both quantitative and qualitative losses of agricultural and horticultural produce. Morphological, biological, biochemical, physiological, immunological and genomic characteristics of microbial plant pathogens have been carefully considered to develop rapid, sensitive and reliable methods of detection and identification of cause(s) of newly observed disease (s) in the locations concerned. Various methods of establishing the nature of microbial plant pathogens are discussed in detail in earlier publications

Plants are exposed to microbial pathogens at all growth stages from seeds to harvested produce. But they are resistant to numerous pathogens that are present in the environment and susceptible only to some of them. In other words, a plant species has built-in resistance mechanism to avoid or resist the invasion by many microbial pathogens. A pathogen may reach several plant species, but it can infect only a few plant species in the particular location or region. The process of pathogenesis or disease development is initiated when the pathogen reaches the plant surface that allows the initiation of infection. An organism is able to derive its nutrition from the susceptible host plant and becomes pathogenic. The physiological functions of such infected plants deviate from those of the healthy (normal) plants and suffer irreversibly to different magnitudes. The organism adversely affecting the plant growth and other functions to obtain nutrition is the pathogen. It develops rapidly or slowly in proportion to the levels of susceptibility / resistance of the host plant to the pathogen species concerned. Thus a plant species may be susceptible to some pathogens, while remains resistant / immune to other organisms that may be pathogenic to some other plant species. Depletion of compounds from the plants to meet the nutritional requirement of the pathogen leads to different kinds of external symptoms and internal changes due to derangement of normal metabolic functions of the host plant. The process of disease development in a susceptible host plant species is known as pathogenesis.

Although thousands of plant species exist on the earth, only those that were found to be useful for humans as food, feed, fiber, timber and other utility materials have been selected for domestication. When these plant species were affected by various biotic and abiotic causes, the necessity arose to determine the ways and means of protecting the valuable plants species and to understand the host plant defense mechanisms and pathogenic potential of the microbial pathogens causing enormous losses to the cultivators. All plant species have built-in resistance to most microbial plant pathogens existing in the environment. Susceptibility of plants to some of them is an exception, since they are endowed with genes which effectively nullify the possible adverse conditions created by the microorganism. Likewise, microbial pathogens possess genes for survival and pathogenicity to survive in the absence of susceptible plant species and to successfully establish infection in suitable plant species. The microbial pathogens have evolved highly specialized tactics to overcome the defense responses and to rapidly multiply in plants for their survival and perpetuation in a geographic location / ecosystem

Crops are grown with the primary aim of maximizing the profit for the cultivators. To achieve this goal, high yielding cultivars and suitable agricultural practices are selected. But due consideration is not given for the levels of susceptibility of the cultivars and some of the agricultural practices may enhance the chances of disease incidence and consequent losses. Hence, it becomes obligatory to determine the effects of crop cultivar and agricultural practices on the extent of disease incidence and to assess losses caused by microbial pathogens in different crops in an agroecosystem. Crop losses reflect the effects of various factors such as use of disease resistant cultivars, application of chemicals, biocontrol agents and preventive measures to reduce inoculum levels, introduction of new diseases and restriction of disease spread. Assessment of crop losses is essential to choose the most effective short- and long-term strategies of disease management. Disease assessment enables the plant pathologists is to gather quantitative information for evaluating disease management strategies, for undertaking surveys of losses and breeding for disease-resistant cultivars.

Various aspects of micorbial plant pathogens have been studied with the ultimate aim of gathering information that may be useful for development of effective disease management systems. Principles of management of crop diseases caused by microbial pathogens fall into three categories : exclusion, eradication and immunization. 7.1 Exclusion of Microbial Plant Pathogens Exclusion of microbial pathogens may be expected to reduce the amount or efficacy of the initial population of pathogens that may be introduced into a geographical location / field. Exclusion is an important component of management of diseases, if the initial population of pathogen is large. This approach is particularly effective in the case of monocyclic pathogens that complete their life cycle only once during one cropping season. The methods with the aim of excluding the introduction of pathogens or to prevent the build up of inoculum required for disease spread are generally applied elsewhere. Hence, they have lower level of visibility compared to other approaches. Introduction of new pathogens present in plant and plant materials into another country or locations within a country may be effectively prevented by establishing plant quarantines. Build up of inoculum of microbial pathogens can be reduced considerably by the use of disease-free plants or planting materials supplied through certification agencies. These regulatory programmes have to be manned by trained technical personnel and supported by adequate infrastructure in terms of equipments and mobility (Chapter 8).

Management of crop diseases by various methods of exclusion in order to reduce the pathogen population in a geographical location / country may be achieved by either preventing introduction of pathogens or by growing disease-free seeds and planting materials. In addition, the inoculum of a pathogen reaching newly planted crops may be significantly reduced by adopting appropriate cultural practices also. The contributions of these factors for successful cultivation of crops are discussed hereunder. 8.1 Prevention of Introduction of Microbial Pathogens Prevention of pathogen introduction is the primary responsibility of plant quarantines. Quarantines have been established by several countries by enacting appropriate laws that regulate the importation of plants, seeds and asexually propagated plant materials. These materials are placed in post-entry quarantines (PEQs) and examined by technical personnel for the presence of pathogens and pests. It is obligatory for the exporting countries to comply with the regulations of the importing countries. As the movement of plant products has increased enormously, following the adoption of the General Agreement on Tariffs and Trade (GATT), vigilant enforcement of sanitary and phytosanitary measures has become essential. The Food and Agriculture Organization (FAO) appointed an Expert Consultation on the Harmonization of Plant Quarantine Principles to formulate basic principles to determine standards for plant quarantine principles in relation to international trade (FAO 1991). According to the recommendations of the Expert Consultation, the sovereignty of the importing country is recognized and it has the right to implement the phytosanitary regulations deemed fit by that country. However, cooperation among countries was emphasized for the successful implementation of the recommendations by the member countries belonging to one of the eight regional plant protection organization set up after the International Plant Protection Convention (IPPC) held in 1951. A plant pathogen is recognized as of quarantine significance (QS), if its exclusion is considered to be essential to protect agriculture and natural vegetation of the importing country which has to be provide necessary infrastructure and trained personnel to prevent or delay its entry along possible routes. Lists of quarantine pathogens and the regulations to be followed are prepared by the importing country and made available to the exporting countries.

Physical and chemical techniques have been applied either alone or in combination with certain cultural practices to enhance the effectiveness of reducing pathogen inoculums and consequent reduction in disease incidence. Seeds and asexually propagated planting materials have been treated with physical and / or chemical methods in order to eliminate the pathogens from them and to build up disease-free stocks. Physical and chemical methods may be applied to reduce the inoculum present in plant debris as well as in the soil and water. Enough attention has not been bestowed to tackle the pathogens that may exist on fallen leaves or shoots from which infectible spores may be produced later.

Crop husbandry includes various cultural practices aimed at enhancing yields from a given unit of land. To achieve this aim, practices such as growing high yielding cultivars which are fertilizer responsive, high density planting and application of large quantities of different nutrients and frequent application of pesticides have been followed. Consequently these practices have been found to be responsible for some problems which were not associated with crops raised by adopting traditional agricultural practices. Thus the benefits of modern methods appeared to be lost, because of the unforeseen problems for which the effective solution have to be found out. Various methods that could be dovetailed with regular cultural practices have been shown to be useful in either reducing the existing pathogen inoculum or avoiding build up of inoculum in the field.

Chemicals have been in use to arrest the ill effects of plant diseases even in the prehistoric periods (1000 B.C.) (Ogawa et al. 1977), although the nature of the causative agent was not known at that time. A combination of chemicals was developed and demonstrated to be effective against the devasting downy mildew disease affecting grapevines by systematic investigations of Millardet (1882) in France. This mixture of copper sulphate and lime was named as Bordeaux mixture after the place where it was developed (Large 1940). Despite the development of hundreds of chemicals over the following decades, for the management of fungal diseases, Bordeaux mixture is still being used against certain diseases. Copper, sulphur - and mercury-based compounds were applied prior to the 1940s. After the end of World War II, several organic chemicals were released into the market to wage a losing war against the plant pathogens. The researchers and industry have now realized that microbial pathogens cannot be entirely suppressed or eliminated by chemicals or by any other means.

Methods of crop disease management are based on the principles of exclusion, eradication and immunization. Various methods of excluding the pathogens primarily through establishing plant quarantines and production of disease-free seeds and asexually propagated planting materials have been discussed earlier (Chapter 8). The pathogens that have been introduced and those that have established in a geographical location have to be eradicated by employing different methods for removal of infected plants, plant debris and alternate and alternative host plants for reducing pathogen inoculum and consequent reduction in disease incidence. Other methods may be broadly divided into two classes as chemical and nonchemical methods. The chemical methods involve the use of chemicals that may act indirectly by creating conditions unfavourable for the development of the disease (Chapter 9) or chemicals that have direct inhibitory activity on the pathogens (Chapter 11). Pathogen populations may be kept under check by adopting cultural practices either alone or in combination with chemical and nonchemical methods (Chapter 10). Biological agents have been employed for reducing pathogen inoculum or for inducing resistance in host plants resulting in different degrees of reduction in disease incidence. The methods involving the use of biological agents as a strategy of crop disease management are discussed in this chapter. Biological control methods aim to reduce the pathogen inoculum or disease producing activity of a pathogen by employing live microorganisms or using products of biological origin. Use of antagonistic microorganisms, avirulent strains of pathogens, cross-protection induced by mild strains of pathogens in susceptible host plants and induction of resistance in the susceptible crop cultivars are some of the approaches made to reduce the adverse effects of infection by microbial pathogens.

Plant diseases caused by microbial pathogens have been managed by using different methods which need to be applied every year or season, when the susceptible cultivars are grown. These methods are grouped as nongenetic methods, since no change in the host genome can be expected, when physical, chemical, cultural or biological control methods are employed. On the hand, if a change in the host genome is accomplished by either conventional breeding techniques or by biotechnological procedures, the progeny may show higher level of resistance to the target pathogen (s). The genotype or cultivar thus generated will show resistance during subsequent seasons till a new race of pathogen capable of overcoming the effects of resistance gene(s) is produced. Disease management through host resistance is considered as the most preferable option because of several advantages. Crop production is less expensive ; there is no need to apply any procedure for every crop season ; and chances of environmental pollution are absent, when a crop cultivar resistant to the disease (s) is grown. In addition, the build up of pathogen population is progressively reduced. Management of diseases by cultivating resistant varieties may be more effective and economical, if the benefits accumulating over a period of time and enlarging area with lapse of time are taken into consideration.

Resistance to diseases in plants may be enhanced by incorporating resistance genes in susceptible cultivars and this disease management strategy is considered to be the most desirable one. But unavailability of reliable sources of resistance and the requirement of long periods for development of cultivars with built-in resistance have limited the usefulness of this approach. Employing genetic engineering techniques for obtaining resistant cultivars appears to hold promise. However, in the light of expression of concern for the long term effects of genetically modified crops and plant products in several countries, the feasibility of exploiting the genetic engineering methods remains a question mark. In this context, the possibility of inducing natural disease resistance (NDR) mechanisms operating in existing cultivars with high yield potential to provide protection to crops and harvested produce against diseases, has attracted the attention of researchers in several countries. This approach does not involve the introduction of any foreign gene into the plant, but it regulates the expression of defense genes in the susceptible plants. Furthermore this approach is as safe as the use of genetically resistant cultivars for the preservation of environment, since the same mechanisms of resistance are activated in plants with either genetic resistance or induced resistance. Intensive research is being carried out to select effective agents that can be used as inducers of resistance in crop plants to contain various diseases, as alternatives to the development of resistant cultivars through conventional breeding and genetic engineering methods

Diseases are caused by different kinds of microorganisms which may primarily attack specific plant organs initially. They may be either confined to the organs in which infection is successfully initiated and may spread to other organs to cause secondary infection. The plant organs initially affected may not show characteristic symptoms in certain cases as in root rot and wilt diseases. The root infection is recognized much later, when yellowing (chlorosis) of the leaves is observed. It may become very difficult to save the infected plants at this stage, since the pathogen is well established in the deeper tissues of the infected plants. However, the spread of the disease to the adjacent plants may be prevented by protective treatments. Integration of various principles of management of crop diseases has to be followed for successful crop cultivation. The combination of practices that can be applied varies with different types of diseases and the crops affected. Hence, the integrated management of crop diseases is discussed for different groups of diseases affecting primarily different plant organs/ tissues. Fungal and bacterial pathogens remaining in the soil or plant debris left over after harvest of previous crops infect the root system initially and crown or the basal portions of the stem may also be affected later.

Plants have to transport water and nutrients absorbed by the roots from the soil and photosynthetic products from the leaves to other plant parts and storage tissues through the stem tissues. Infection by fungal and bacterial pathogens interferes with the movement of the essential materials leading to the derangement of several physiological functions to varying degrees and even collapse of the aerial plant parts. 16.1 Fungal Pathogens causing Diseases Affecting Stems of Plants Fungal pathogens cause blight, stem rot, rust, anthracnose, die-back and canker symptoms on the stem tissues of several crops. These pathogens may be soilborne or airborne generally, while some of them may spread through water also.

Several fungal and bacterial pathogens that are airborne settle on the foliar tissues of susceptible host plant species and initiate infection which spreads to other plant parts later. Fungal pathogens cause different types of leaf spots, downy mildews, powdery mildews and rust diseases commonly on various crops. The bacterial pathogens induce blights and rot diseases.

Fungal and bacterial pathogens infecting either directly or causing secondary infection of inflorescence may be responsible for greater losses than the pathogens infecting stems or foliage, if they do not cause the death of plants. The extent of earhead infection by the pathogen(s) is directly correlated to the quantum of yield losses.

Among the microbial pathogens, viral and phytoplasmal pathogens primarily depend on various vector species for their spread from infected plants to healthy plants in the same or distant locations. Hence, management of these diseases depends on the reduction of vector populations, in addition to the disease management strategies applicable to diseases caused by fungal and bacterial pathogens that are not transmitted by vectors. 19.1 Diseases caused by Viruses Plant viruses are transmitted through seeds, propagative plant materials and vectors such as mites, insects, nematodes and fungi. Hence, the strategies to manage these diseases vary depending on the nature of vectors involved in the transmission of viruses.

Postharvest diseases caused by fungal pathogens are more numerous than those due to bacterial pathogens. Infection by these pathogens may be initiated in the field before harvest, during transit or storage. These pathogens may remain dormant and become active, when the physiological conditions of the produce and environmental conditions become favourable. Symptoms characteristic of the diseases are observed as the produce age or ripen.

Appendix-1 1.1 Mounting Media and Stains for Fungal Pathogens A. Mounting media