General information on soilborne diseases

• Introduction
• Key features of soilborne plant pathogens
• Nature of diseases caused by soilborne plant pathogens

Introduction

The fungi have many important functions, largely unrecognised, in the biosphere. Although many species are beneficial, a considerable number are detrimental to our interests. There are approximately 100,000 species of fungi described in the literature and there are many, many more yet to be described. Many of these live saprophytically on dead organic matter on or in soil where they are regarded as the most important decomposers of plant residues and other organic matter. Many species produce the enzymes needed to degrade the lignin and cellulose in plant residues and so initiate the decomposition of these complex compounds.

More than 8,000 species of fungi are known to cause diseases of plants and most plants are susceptible to some fungal pathogens.

Some species of fungi, the mycorrhizae, live symbiotically on or in the roots of many plants. This relationship is basically parasitic but in many situations is probably beneficial to both the plant and the fungus. The growth of the plant is promoted by the improved uptake of some mineral nutrients while the fungus gains access to organic nutrients and shelter.

Fungi are common in soil, in air (mainly as spores) and on plant surfaces throughout the world in arid, tropical, temperate and alpine regions.

The diseases that are caused by fungal pathogens which persist (survive) in the soil matrix and in residues on the soil surface are defined as soilborne diseases. Thus the soil is a reservoir of inoculum of these pathogens, the majority of which are widely distributed in agricultural soils. However, some species show localised distribution patterns. Damage to root and crown tissues is hidden in the soil. Thus these diseases may not be noticed until the above-ground (foliar) parts of the plant are affected severely showing symptoms such as stunting, wilting, chlorosis and death.

These diseases are difficult to control because they are caused by pathogens which can survive for long periods in the absence of the normal crop host, often have a wide host range including weeds, chemical control often does not work well, is not practical or is too expensive and it is difficult to develop resistant varieties of plants. These diseases are often very difficult to diagnose accurately and the pathogens may be difficult to grow in culture and identify accurately.

Morphology
Fungi are thread-like, multicellular, non-motile micro-organisms which lack chlorophyll. The basic unit of a fungus is the microscopic thread-like hypha, which is essentially a tube with a rigid wall enclosing cytoplasm and nuclei. In the higher fungi the hypha is divided into cells by regular cross-walls or septa. A small pore in each septum allows interaction between the cytoplasm in adjacent cells. The so-called "lower fungi", which are now known as members of the Kingdom Chromista do not have septa and so the cytoplasm flows freely along the hyphae. Hyphae grow by elongation of the tip which is thin and plastic, unlike the rigid, relatively thick walls of the older part of the hypha. As the hypha elongates it branches laterally, a short distance from the tip. The branches also elongate and produce further branches, a process which results in a radial pattern of growth. The hyphal tips of some fungi are able to penetrate intact cell walls of both living and dead plant tissue. The ability of a fungus to elongate from the hyphal tip, to branch and to penetrate intact surfaces enables it to radiate in all directions over and through a substrate such as plant tissue, dead organic matter, or a laboratory growth medium. This process of growth over or through a substrate is called colonisation, and the hyphae collectively constitute a colony. A new colony develops from a spore, hyphal fragment or a multicellular vegetative structure called a sclerotium. The size of a colony is determined by the nature and extent of the substrate colonised by the fungus.

Physiology and ecology
Because the fungi lack chlorophyll they need an external source of organic compounds from which to synthesise the various materials needed for growth, that is, they are heterotrophic. The fungi secrete enzymes which break down solid materials into soluble compounds for absorption through their outer walls. They vary greatly in their ability to utilise different types of substrates. Some species are obligate parasites and are only able to utilise nutrients from living host tissue. The majority are saprophytic and obtain nutrients only from dead organic material such as plant residues. In addition there are species which are able to grow saprophytically or parasitically. Many species live saprophytically on residues on or in soil and have a major role in their decomposition.

Temperature, water potential and pH have a critical influence on the growth and survival of fungi. The optimum temperatures for growth of the majority of fungi are in the range 25 to 28°C with the minimum and maximum temperatures being 5 to 10°C and 33 to 35°C respectively. Thus most fungi cannot grow at the body temperature of man, 37°C. Optimum water potentials for growth range from -0.01 to -1.0 MPa depending on the species. Growth ceases between -5.0 and -15.0 MPa. Many fungi including important plant pathogens are able to grow at potentials which cause permanent wilting of crop plants. Slightly acidic conditions (pH 6 to 6.5) are optimum for the growth of most fungi. Although fungal growth ceases at low water potentials many species are adapted to survive quite well under such conditions, either as resistant spores, sclerotia, other specialised structures or as dormant hyphae in residues. In general, cold dry conditions favour fungal survival while hot wet conditions do not.

Reproduction
Most fungi are able to reproduce asexually and/or sexually, forming spores which serve as units for survival and/or dispersal. The spore can be defined as a small discrete propagative unit containing the genome of the fungus and sufficient nutrient reserves to enable the establishment of a new colony. Spores vary in size, shape, septation, colour and wall thickness. They are produced directly on the hyphae, on specialised hyphal branches, or on multicellular fruiting structures which range in size from approx. 0.2 mm to over 600 mm in diameter. Although the fungi are defined as non-motile, some species of the Oomycetes (lower fungi) produce motile spores called zoospores. These spores have small flagella which enable them to swim in water films over short distances.

Light and temperature commonly affect the formation of spores and fruiting structures. Temperature, and to a lesser extent light, also have a significant effect on hyphal colour and growth. Thus if colonies grow and reproduce under fluctuating conditions of temperature and light they may develop annular zonations with respect to colour, hyphal density and intensity of spore formation. The primary function of some spores is to ensure the long-term survival of the species in the absence of a suitable substrate, or during periods when other environmental conditions are unfavourable for growth. These spores are thick walled and remain where they form, germinating when contacted by a new substrate.

The primary function of the majority of the spores is, however, to enable geographic dispersal by rain splash or wind. Spores formed in a mucilaginous matrix are usually dispersed by rain splash, in small water droplets over a short distance. Wind dispersed spores are either ejected from a fruiting structure into the airstream or are formed in dry powdery masses which are swept up by air currents. Wind dispersal may carry spores over long distances but most are deposited within 100 metres of their origin. Deposition is a result of impaction, gravity or rain wash. Because a very high proportion of spores are deposited on surfaces unsuitable for fungal growth, vast numbers of spores are produced from each colony to ensure the continuity of the species when one substrate is exhausted.

Spores have an extremely important role in fungal diseases of plants. Airborne spores enable rapid spread of the fungus from plant to plant or crop to crop. Thick-walled spores such as chlamydospores are able to survive in soil for long periods and enable the pathogen to survive in the absence of a susceptible host. Some pathogens which affect crops grown over large areas, such as the stem-rust fungus of wheat, may produce vast quantities of spores which can be carried in the atmosphere as invisible spore clouds over hundreds of kilometres.

In addition to resistant spores the fungi have evolved various other modes of survival. Some species form resting-bodies called sclerotia, which consist of aggregations of hyphal cells into dense, rounded or irregular structures, generally ranging in size from 0.1 mm to 20 mm. In other species fruiting structures such as perithecia act as survival structures and release spores when conditions become favourable for spore germination and growth.

Key features of soilborne plant pathogens

Disease Symptoms
Many soilborne fungal plant pathogens cause disease of the roots or stem disrupting the uptake and translocation of water and nutrients from the soil. Therefore they commonly cause similar symptoms to drought and nutrient deficiencies; these include wilting, yellowing, stunting and plant death. Thus symptoms such as this do not necessarily indicate that a pathogen is causing disease.

Host Range
The majority of these pathogens have a wide host range and may cause different types of diseases on different hosts. A particular species may cause severe root rot on one host but only cause superficial and symptomless infection on the roots of another host. Crop rotation is not necessarily an appropriate control measure for some of these pathogens because of their wide host range which may include weeds. However some pathogens have a very narrow host range, e.g. forma speciales of the wilt pathogen Fusarium oxysporum. However, many of these formae speciales can persist by symptomless colonisation of the cortex of roots of non-host plants.

Epidemiology and Survival
In general these fungi can persist for long periods in soil in the absence of susceptible crops. Some species persist mainly as resistant hyphae in plant residues, in large pieces of stubble or small fragments. The inoculum of such pathogens declines gradually as the residues decompose. Decomposition is hastened by warm wet conditions and mechanical disruption caused by cultivation. Many species also persist as propagules which are adapted for long-term survival in soil. These include thick walled spores such as oospores and chlamydospores, together with sclerotia and microsclerotia.

Nature of diseases caused by soilborne plant pathogens

Root rot
These diseases are caused by a diverse group of fungi and related organisms. The most important genera include Pythium and Phytophthora, Rhizoctonia, Cylindrocladium and Armillaria. These diseases are characterised by a decay of the true root system; some pathogens are generally confined to the juvenile roots whilst others are capable of attacking older parts of the root system. Symptoms that are observable include wilting, leaf death and leaf fall, death of branches and limbs and in severe cases death of the whole plant. Some examples of these diseases are shown below.

Stem, collar and head rots
These diseases are also caused by a diverse group of pathogens including species of Phytophthora, Sclerotium, Rhizoctonia, Sclerotinia , Fusarium and occasionally Aspergillus niger. The most obvious symptom of these diseases is the decay of the stem at ground level. Quite often this decay can lead to symptoms of wilting, death of leaves and to death of the plant. Some examples of these diseases are shown below. In tropical agricultural ecosystems these fungi can cause stem, foliage and head rots during warm, wet conditions. Phytophthora spp. for example, can cause diseases such as heart rot of pineapple, blight of potato and tomato and some fruit rots in these conditions. Similarly Rhizoctonia spp. can cause leaf blight in maize and head rot of cabbage in warm wet weather.

Wilt diseases
The main species of fungi that cause these diseases are Fusarium oxysporum and Verticillium spp. The symptoms of these diseases include wilting of the foliage and internal necrosis of the vascular tissue in the stem of the plant. Some species of bacteria can also cause similar types of diseases. Some examples of these diseases are shown below.

Seedling blights and damping-off diseases
Various common names are used for diseases of seedlings such as seedling blight and damping-off. The fungi that commonly cause seedling death include Pythium, Phytophthora, Rhizoctonia, Sclerotium rolfsii and less commonly Fusarium spp.. These fungi can infect the seedling during the germination, pre-emergence or post-emergence phases of seedling establishment. Environmental factors which inhibit germination and emergence usually increase disease severity. Thus cold conditions, dry, or very wet soils or a hard soil surface commonly lead to increased seedling disease. In northern Vietnam Pythium, Rhizoctonia and Sclerotium rolfsii are commonly associated with seedling death of vegetables such as beans, cabbages and other cruciferous crops, cucurbits and tomato.