The second edition includes a chapter on disease diagnosis and expanded coverage of fungicides as well as problems of controlling pathogens in crops and produce entering international trade. In the latter case molecular techniques are likely to play an increasing role in disease diagnosis. Nucleic acid and antibody technologies may also be deployed in future to justify the application of control measures such as fungicides. Indeed, fungicides continue to play a dominant role in maintaining the high standards of disease control evident within the intensive farming systems of the European Union (formerly the European Community or EC) despite efforts to reduce the production of commodities surplus to EU requirements. However, impending economic and legislative pressures, as well as concerns over the long term toxicological and environmental effects of pesticides, may lead to reductions in the quantity of fungicides applied to crops and greater reliance on other methods of disease control.

The text overall is still intended to be a broad introduction to the practices of disease control currently used by farmers and growers within the EU, and particularly in the UK.

Introduction

Confirmation that a plant problem is due to attack by a pathogen, and the identification of the causal agent, are important prerequisites to the selection of control measures. The extent to which disease has progressed also needs to be considered. Diagnosis of disease in the early stages of infection is important with pathogens which have a long latent period prior to symptom expression. Examples of such diseases include septoria on wheat and viruses in seed potatoes, whose early detection may enable control measures to be implemented before they reach damaging levels.

Diagnosis is based on one or more unique features of the causal agent or disease. These may include the appearance of the disease in the field, the morphology of an isolated microorganism, the unique immunological characteristics of the causal agent or the structure of its genetic material.

IDENTIFICATION BASED ON SYMPTOMS

Symptom assessment is the most common method of disease identification. In many cases, as seen in Chapter 2, characteristic symptoms are associated with particular diseases and these are often reflected in the common name of the disease. Accurate diagnosis of disease from symptoms often enables instant decisions to be made regarding the application of control measures – especially the selection and deployment of fungicides. Indeed, the importance of accurate diagnosis of disease is reflected by the fact that, in the UK, personnel undertaking the British Agrochemical Standards Inspection Scheme (BASIS) examinations must demonstrate a very high degree of proficiency in the identification of diseases on the major crops of the UK.

Within figures in this chapter that give details of fungicides, product examples are given along with the dose rate in grams per hectare and, in parentheses, the number of applications permitted at the time of publication of the text

Introduction

Crop protection in the intensive farming systems of the EU is mainly achieved with pesticides. The use of fungicides on crops has increased greatly in the UK since accession to the EU (then the EEC) in 1972. Surveys by staff of the Ministry of Agriculture, Fisheries and Food in the UK in the early 1970s showed that fewer than 20% of barley and 10% of wheat crops received applications of fungicides. In 2008 the Food and Environmental Research Agency (FERA) found that fungicides were the most extensively used pesticides on arable crops in the UK, with over 95% of crops being treated with one or more fungicidal compounds. Fungicides are routinely applied to field crops, with cereals such as wheat and barley receiving two or more applications during each growing season: potatoes may receive ten or more applications of fungicides in a single growing season to deter attacks by late blight. Where fungicides are used extensively on fruit and vegetable crops to prevent rots, scabs, grey mould and other diseases that may affect the appearance of crop produce, several applications may be made during the growing season, often close to harvest.

Introduction

The removal or destruction of inoculum of pathogens, especially prior to cropemergence and establishment, may prevent or at least delay the onset and spreadof disease. Complete elimination of pathogens is possible in enclosed growingareas such as glasshouses, but is difficult to achieve under field conditions.The sources of inoculum of pathogens of most field crops are so widespread thateradication is simply not a practical proposition.

Disposal of Crop Residues

The debris remaining after growth of protected crops should be taken out ofglasshouses and destroyed. This is particularly important with stems of spentcucumber and tomato plants, which may be covered in late season with conidia ofBotrytis cinerea. The roots of lettuce plants that havebeen attacked by B. cinerea should also be removed fromglasshouses. Crop remains and other debris should be removed from the nurseryand disposed of to green waste recycling sites or incinerated. Efficient windrowor in-vessel composting systems that utilise green waste will kill most plantpathogens.

Stubble and debris remaining after the harvest of cereal and oilseed rape cropsmay harbour several diseases, and burning was formerly the major (and forfarmers the easiest) method of disposal. Stubble burning, however, hasfrequently been carried out in an irresponsible manner and the practice wasbanned in the UK in 1992. Cereal and rape stubble is now primarily disposed ofby ploughing. Soil bacteria and fungi colonise and degrade ploughed-in cropdebris, and in doing so remove the intercrop habitat of some pathogens. Thehyphae and resting structures of pathogens may then perish. Consequently thesurvival of cereal pathogens as, for example, cleistothecia with powderymildews, pycnidia in the case of Mycosphaerella graminicola, hyphae and sporesof net blotch of barley may be reduced. However, some diseases such as eyespotof wheat can survive on straw buried in soil formore than 3 years, and theresting stages of some pathogens may survive even longer. The sclerotia ofSclerotinia sclerotiorumfor example, which form in the stem cavities of oilseedrape (Fig. 2.12), can remain viable in soil for at least 8 years.

Introduction

Plant breeding coupled with advances in crop protection technology has resulted in major increases in yield and improvements in the quality of many crops. Consistent improvements in crop yield and quality have taken place in the agricultural systems of member states of the European Union, where for many years financial incentives were provided to farmers to encourage self-sufficiency, particularly in cereals and oilseeds. Indeed some 70% of the total EU budget has been disbursed in the past to farmers and growers in the form of price support. Under such systems productivity greatly increased. For example, cereal production in the UK rose from 59% of total needs in 1971 to 103% in 1981, and by the early years of the twenty-first century the UK had developed a considerable export trade, with about 25% of the wheat crop being exported.

This intensification of production is reflected by substantial improvements in per hectare yields of all types of cereals (Fig. 8.1), and involved the growth of high-yielding cultivars, promoted by the use of substantial amounts of nitrogenous fertilisers, plant growth regulators to prevent lodging (2.2.2), and protection by applications of herbicides and fungicides. Such high-input growing systems led to the supply of some foodstuffs, notably grain, exceeding demand, resulting in accumulation and stockpiling of grain on occasions in some EU member states during the late twentieth century, even with efforts to export grain to non-EU countries. The provision of price support to farmers for the purpose of producing agricultural commodities surplus to the requirements in the EU is now recognised as anomalous, and efforts have been undertaken to redress this imbalance. The reform of the EU’s Common Agricultural Policy in 1992 included the introduction of compulsory set-aside land in most member states. As a consequence, the cereal hectarage of the UK fell by 13% in 1993, with the area of wheat in particular declining from almost 2.1 million ha in 1992 to less than 1.8 million ha in 1993. However, poor grain yields in some years (for example 2005–6), not only in the EU but also in the rest of the world, resulted in reductions of global grain stocks, and this led to a reversal of the policy of set-aside in the EU in 2007.

The economic impact of plant diseases probably first became apparent when plantswere grown together as crops. The majority of plant pathogens have a limitedhost range and many are species-specific. A mixed flora, where hosts of plantdiseases are intermingled with other species, acts as a buffering system withrespect to pathogens. The chances of pathogens finding fresh hosts in aspecies-rich habitat are much lower than in a crop consisting of a single plantspecies. Pathogens evolved over millions of years in species-rich habitats, andto succeed in finding new hosts they developed highly efficient mechanisms ofspread.

With the aggregation of plants together as crops, almost ideal conditions werecreated for the establishment and spread of pathogens. The continuous processesof selection and propagation of crop species have resulted in the situationtoday where the planting of large areas of land with crops of near-identicalgenotype is common. It is therefore not surprising that microorganisms that havean efficient dispersal mechanism, and that can infect crops, have on occasioncaused devastating losses in yield.

The historical importance of plant diseases and their economic and social effectshave been well documented. Currently, within the agricultural systems ofdeveloped countries, plant diseases are unlikely to cause crop losses to theextent of those associated with, for example, late blight of potato (Plate 1) inEire in the 1840s and in Germany in 1917–18. The development and use of cropprotection chemicals from the late nineteenth century onwards, and theestablishment of scientifically based plant breeding programmes in the earlytwentieth century, have led to reductions in losses due to disease. Despiteincreases in the yield and quality of crops over the past century, it isestimated that about 20–30% of potential crop yield is lost annually throughattack by plant pathogens and pests, and competition from weeds. Losses to thisextent or even greater may occur in less developed countries, but loss ofpotential yield due to attack by pathogens may be much less in crops ofcountries within the European Union. The EU is now self sufficient in manyfoodstuffs, and yields in excess of national and EU requirements occur with somecrops, notably cereals, for which a considerable export trade has developed insome countries such as the UK.

An extensive revision of the chapter on chemical control of disease and expanded coverage of both diagnosis of disease and deployment of resistant cultivars form part of this new edition. Diagnosis of disease is becoming ever more sophisticated, and if transgenic crops become as acceptable in the European Union as elsewhere in the world, major advances in durable disease control without recourse to the extensive use of fungicides may at last be realised.

The author of previous editions (W. R. Carlile) has worked almost solely with protected horticultural crops over the period 2006--2011, and has admired the careful use of cultural practice, sanitation and adoption of non-chemical methods for pest and disease control: a very different scenario from arable crops, with the principal link being the extraordinary progress in disease diagnosis based on molecular technologies, and perhaps to be surpassed by developments in nanotechnology.

In this respect Bill Carlile would like to pay tribute to colleagues at Bord na Mona in Newbridge, including James Spillane, Dearbhail Ni Chualain, Colman Hynes and Sarah Lombard, for their good company and encouragement. Equally, he would wish to acknowledge the continued interest and help from past graduates of Nottingham Trent University, particularly Chris Danks, now at Forsite Diagnostics; Mark Stevens, at Brooms Barn research station of the UK BBSRC; and staff of Eurofins (Agrisearch) at Melbourne, Derbyshire, especially Owen Scrimshaw.

The intensive nature of modern agriculture in the European Economic Community, with the demand for better standards of crop quality and yield has required a high degree of disease control. Increased attention to crop hygiene, the production of disease-resistance cultivars and particularly advances in fungicide technology and use have all contributed towards major improvements in crop yield and quality. However, yield increases have led to the accumulation of surpluses of certain agricultural commodities. The current revision of price support within the EEC for crops such as cereals may lead to an examination of input levels as part of an overall effort to reduce the costs of cultivation. This may be especially reflected in the selection and frequency of use of fungicides, and it is possible that with field crops such as cereals, greater reliance in the immediate future may be placed on innate host resistance to diseases. On the other hand, the demand for high quality fruit and vegetable produce is increasing. Strict hygiene, including the development of soilless growing systems for crops under glass, as well as the continued intensive use of fungicides to achieve consistent and thorough control of disease is likely to remain a feature of growing systems where quality is of prime importance. It is, however, in these systems that problems of fungicide resistance are most likely to occur, and the development of strategies to prevent fungicide resistance is recognised by many as a highly desirable objective.

Overall, the crop protection discipline is one of current development and change. This text provides a broad review of current practices adopted by farmers and growers to control diseases of major crops in the UK, describes some of the problems which have arisen following the deployment of these measures and indicates some of the future developments likely to occur in the sphere of crop disease control.

Introduction

Techniques of crop husbandry, including alterations in cropping systems and manipulation of cultivation practices, may provide control of weeds and pests, as well as diseases. Reducing the survival and spread of soil-borne diseases has been a particular objective of such cultural practices. Manipulation of microclimate in crops under glass can help to reduce levels of disease, and especially of pathogens favoured by high humidity.

Cropping systems

One of the advantages of crop rotation is that pathogens specific to a particular crop may be starved out in the absence of their hosts. Inoculum of pathogens surviving on crop residues can be reduced by incorporation of these residues into the soil (Section 4.2). Degradation of residues by saprophytic microorganisms in the soil will deprive the pathogen of a food source. Unless the pathogen has a resistant spore or sclerotial stage, it may perish. Rotational systems of growing have, however, declined considerably in the UK over the past 30 years. Many growers of protected crops tend to specialise, growing one or two vegetable or soft fruit crops such as tomatoes, cucumber, lettuce or strawberry. Planting of consecutive cereal crops is now common practice in some parts of the UK, and some farmers have raised cereals on the same land for 10 years or more.

Introduction

Within the huge number of microorganisms that exist, few are capable of causing disease in human beings, other animals and plants. External barriers to invasion include the skin and outer surfaces of animals, and the cuticle and bark in plants. Furthermore, in humans and many other higher vertebrates, internal mechanisms of defence such as antibodies may be produced as a response to microorganisms that breach structural defences. In plants, internal deterrents of microbial growth exist in the form of substances present in cell wall and intercellular spaces, and antimicrobial compounds may be released from vacuoles following cell damage. External stimuli may trigger the production and release of antimicrobial compounds from plants.

Evolution has led to the development of some intimate relationships between hosts and biotrophic pathogens. The latter are often host-specific, affecting only one species, and include many of the world's most important pathogens. The relationship between host and pathogen here occurs at gene level, and the interaction of gene products of host and pathogen determines whether the plant is resistant or susceptible. Currently most plant breeding programmes to produce cultivars resistant to plant diseases are associated with these specific host–pathogen systems.

Introduction

Surveys of disease incidence and severity have been carried out for important crops in many parts of the world. For example, the comprehensive surveys undertaken under the auspices of the Home Grown Cereals Authority (HGCA) record the incidence of diseases in the principal arable crops in the UK. However, it has often proved difficult to determine accurately in strict monetary terms losses due to attack by individual pathogens. Disease levels often vary greatly from season to season. Crop losses may result from attacks by more than one pathogen. Furthermore, crop growth is affected by other factors such as climate, soil type, and environmental and cultural conditions, and these factors frequently interact.

Consideration is given in this chapter to the aetiology and current importance of diseases of the principal arable crops and selected diseases of top fruit and protected crops grown in the UK. Features of the life cycle of pathogens that are particularly relevant to the development of control measures are emphasised.

This book is about life in dead trees. All over the world one can find a fascinating diversity of life forms in decaying wood – first and foremost a wide variety of fungi and insects. These organisms carry out the hidden but highly important work of wood decomposition.

A fundamental question frequently revisited in this book is: ‘Why is the species diversity of wood-inhabiting organisms so tremendously high?’ In most chapters we approach this question indirectly by highlighting the key properties of dead wood, along with the environmental factors and processes that bring about the diversity we can observe. We also discuss species richness explicitly in Chapter 11. There are at least two good reasons for addressing the biodiversity in dead wood. One is that the diversity of wood-inhabiting organisms is a multifaceted and interesting phenomenon that deserves attention for its own sake. Another reason is that this diversity is being seriously threatened due both to the loss and fragmentation of forests and because of the greatly reduced amount of dead wood in managed forests and other woodlands. Thus, we need to understand the role of dead wood for biodiversity in order to manage and maintain it while efficiently utilizing forest resources.

This chapter presents various forestry practices, from modest selective timberharvesting to plantation forestry. Particular attention is paid to differencesin the amount, quality and dynamics of dead wood between managed and naturalforests. The chapter also discusses management options and processes that mightimprove conditions for saproxylic species.

Many kinds of forestry practice exist, but it is beyond the scope of this chapterto give a full treatment of all aspects. Common to all types of forestry is thefact that trees are cut and removed from the forest. This clearly represents asituation of resource competition for the species dependent on dead wood. Inmany regions, clear-cutting and removing all the trees is the most commonharvesting method and has obvious negative effects on many saproxylic species(Figure 13.1). But other management regimes also show negative effects on thedead wood biota. Balancing the extraction of wood with the demands of saproxylicspecies is a difficult task – a topic that is discussed in the secondhalf of this chapter.

Amount, quality and dynamics of dead wood in managed forests

The most obvious ef ect of forestry is the extraction of trees for commercialpurposes. This will result in a loss of dead wood resources for saproxylicspecies, in terms of quantity, quality and dynamics.