How to Control Soil Borne Pathogens? | Soil Management

Management of soil borne diseases depends on a thorough knowledge of the pathogen, the host plant, and the environmental conditions that favours the infection. In order for a disease to develop, all three factors must be present. The pathogen (a virulent, infectious agent) must have viable inoculum, such as zoospores, available to infect the host.

The host (a susceptible plant) must be exposed to the pathogen’s inoculum, and be physiologically susceptible to infection. Finally, the environmental conditions must be favourable for the infection of the plant and growth of the pathogen. For example, the soil must be saturated with water for a certain period of time in order for water moulds to develop and infect roots. An understanding of these pathogen-host-environment dynamics will help to devise a disease management strategy.

Integrated Disease Management (IDM) can be defined as a decision-based process involving coordinated use of multiple tactics for optimising the control of pathogen in an ecologically and economically fit manner. In most cases IDM consists of scouting with timely application of a combination of strategies and tactics.

These may include site selection and preparation, utilising resistant cultivars, altering planting practices, modifying the environment by drainage, irrigation, pruning, thinning, shading, etc., and applying pesticides, if necessary. But in addition to these traditional measures, monitoring of environmental factors (temperature, moisture, soil pH, nutrients, etc.), disease forecasting and establishing economic thresholds are important to the management scheme.

The timing of control measures is also critical. Management of a destructive disease such as Phytophthora root rot may require early implementation of appropriate management measures. Management of soil borne diseases is often difficult. Since there is no silver bullet to control these important diseases, it is always advisable to follow all available methods in an integrated manner to better manage soil borne diseases.

The major components of disease management summarised here are- host-plant resistance, cultural practices, biological control and chemical control. Even though these components will be dealt with individually, often the different components are complementary to each other with strong interaction among and between them and the environment and that it is essential to break away from relying on a single-technology and to adopt a more ecological approach built around a fundamental understanding of population biology at the local farm level and to rely on the integration of control components which are readily available to the resource-poor farmers.

Method # 1. Cultural Control:

I. Fertiliser Application

Excessive use of nitrogenous fertilisers should be avoided and instead balanced applications of fertilisers are to be followed. Application of fertilizers along with irrigation improves the overall plant health and plants stay away from diseases. Application of phosphatic and potasic fertilizers help to increase the immunity in host plants by enhancing the production of phytoalexins. For examples-

a) Management of Pythium and Phytophthora by application of phosphoric acid-

b) Application of gypsum reduces the incidence of Macrophomina in groundnut.

c) Application of ammonium bicarbonate reduces the viability of sclerotial bodies of S. rolfsii.

II. Flooding:

Flooding can leads to starvation, lack of oxygen and desiccation to plant pathogens which persist in the soil. For example-

a) Flooding fields for long periods or dry fallowing reduce the Fusarium, Sclerotinia sclerotiorum and nematodes.

b) Irrigation also helps to reduce the soil borne disease eg- charcoal rot caused by M. phaseolina.

III. Drainage:

Good drainage system can help in air circulation among plant roots for growth and also helpful in reducing the distribution of soilborne pathogen which can move by the help of excessive amount of water so management of irrigation water is necessary to minimize water dispersal of soil borne pathogens. For example; good soil drainage reduces the number and activity of certain oomycetes fungal pathogens (e.g. Pythium) and nematodes.

IV. Rouging:

Timely removal of infected and died plants from the field population, known as rouging. It can reduce the potential for inoculum build up.

V. Tillage Practices:

Summer deep ploughing of crop residues present in field which harbours the pathogen is more effective in reducing this important source of infection. Sub-soiling prior to planting was found to increase the green pea yields of root rot susceptible and tolerant cultivars planted in the soil infested with F. solani f. sp. pisi and Pythium ultimum.

VI. Plant Density:

Plant density influences the micro-climate and spread of the diseases. High density (closer spacing) raises atmospheric humidity and favours multiplication of many pathogenic fungi and bacteria. For example;

a) Wider spacing reduces the F. oxysporum f.sp. ciceri.

b) Severity of crown rot population in wheat increased due to high plant population.

c) High density planting in chillies leads to high incidence of damping off in nurseries.

VII. Weed Control:

Both host and non-host weeds favour disease development by influencing the factors resulting in more inoculum. This includes shading the soil and serving as organic substrate or food base for infection of the host crop. These also change the crop micro-climate and affect soil microflora.

VIII. Growing of Cover Crops:

Cover crops increases soil microbial diversity by enhancing the soil microflora.

a) Mustard and Brassica sp. (Broccoli) helps to reduce the load of soilborne pathogens.

b) The Brassica spp with high content of glucosinolates in their tissues and allylisothiocyanate in leaf extracts create unfavorable conditions for microbes.

c) The incorporation of leaves and/or roots of B. juncea is suggested against Rhizoctonia solani and Gaeumannomyces graminis var. tritici.

Method # 2. Crop Rotation

Generally soilborne pathogens survive in the soil and plant debris up to several years. Crop rotation will be helpful to control the soil borne inoculum because if the host is not present for particular number of years then the amount of inoculum will be reduced. Satisfactory control through crop rotation is possible with pathogens that are soil invaders in comparison to soil inhabitants. Crop rotation can still reduce populations of the pathogen e.g. Verticillium, Fusarium etc. in the soil and appreciable yields from the susceptible crop can be obtained every third or fourth year of rotation.

Method # 3. Soil Solarisation:

In this practice, the upper soil surface (5 cm soil) temperature increases up to 52°C by using the plastic mulch sheet over moist soil during sunny summer days. If sunny weather continues for several days, the increased soil temperature from solar heat, known as ‘soil solarisation’.

This increased temperature inactivates or kills many soilborne pathogens such as fungi, nematodes, and bacteria near the soil surface, thereby reducing the inoculum and the potential for disease. For example- Fusarium, Verticillium wilt and bacterial canker of tomato, Clavibacter michiganense, can be controlled by soil solarisation.

Method # 4. Soil Amendments:

Application of organic amendments like well decomposed FYM, saw dust, oil cakes, sulphur, lime etc. reduce the by producing several antagonistic chemicals toxic to disease producing soilborne pathogens. For examples-

a) Application of lime (2500 kg ha^-1) reduces the club root of cabbage by increasing soil pH to 8.5. Similarly application of sulphur (900 kg ha^-1) to soil brings the soil pH to 5.2 and reduces the incidence of common scab of potato caused by Streptomyces scabies.

b) Application of organic amendments like saw dust, straw, oil cake, etc., will effectively manage the diseases caused by Pythium, Phytophthora, Verticillium, Macrophomina, Phymatotrichum and Aphanomyces

c) Application of castor cake and neem leaves helps to reduce the foot rot of wheat.

Method # 5. Seed Treatment:

Seed treatment plays an important role in soilborne disease management. In this method very less quantity of pesticides are required as compared to foliar applications. Seed treatment with thiram and carbendazim @ 2-3 g kg ^-1 seed give satisfactory control against soilborne pathogens like Fusarium, Pythium, Rhizoctonia etc.

Nasreen and Ghaffar (2010) conducted an experiment on cucurbits to know the efficacy of fungicides as seed treatment against Fusarium solani and found that the maximum reduction in seedling mortality was obtained where seeds were treated with Topsin-M (4%) followed by Ridomil, Aliette, Benlate, Carbendazim, Mancozeb and Vitavax. Similarly root infection was significantly controlled by fungicidal treatments but with varied effect. Carbendazim and Topsin-M controlled maximum root infection by 6 and 8% respectively. Several antagonistic fungi (Trichoderma, Gliocladium) and bacteria (Pseudomonas, Penicillium, Bacillus, Enterobacter) are isolated for bio-control of disease causing pathogens present in soil.

These bio-agents are commercially available for seed treatment as well as soil application. Fusarium wilt can be effectively controlled by seed treatment with Trichoderma @ 4g kg^-1seed and soil application of 2.5 kg Trichoderma mixed in 25 kg FYM for one hectare.

Method # 6. Biological Control:

Biological control is the reduction of the amount of inoculums or disease producing activity of a pathogen accomplished by or through one or more organism other than inoculums.

It is the use of organism, gene or gene product to regulate a pathogen:

(i) By keeping below the economic threshold level

(ii) Retard or exclude infection

(iii) Maximising plant self defence.

There are, for example- several diseases in which the pathogen cannot develop in certain areas either because the soil, called suppressive soil, contains microorganisms antagonistic to the pathogen or because the plant that is attacked by a pathogen has also been inoculated naturally with antagonistic microorganisms before or after the pathogen attack.

Sometimes, the antagonistic microorganisms may consist of avirulent strains of the same pathogen that destroy or inhibit the development of the pathogen, as happens in hypo virulence and cross protection. Success in using microorganisms against plant pathogens started with the control of crown gall with Agrobacterium radiobacter K 84, and that of seedling blights caused by Pythium and Rhizoctonia with Trichoderma harizanum, Gliocaladium virens and Streptomyces griseus.

The strains of Trichoderma spp are opportunistic invaders, fast growing, prolific producers of spores and powerful antibiotic. These are some of ideal characters which make them a very successful bioagent. This process is often accelerated by adding composts or manures, which enrich the soil with antagonistic microflora.

a. Vesicular Arbuscular Mycorrhizal (VAM) and Disease Suppression: nitriding

Mycorrhizae are formed as a result of mutualist symbioses between fungi and plants and occur on most plant species. Because they are formed early in the development of the plants, they represent nearly ubiquitous root colonists that assist plants with the uptake of nutrients (especially phosphorus and micronutrients).

The mycorrhizal fungi protect plant roots from diseases in several ways:

i. By providing a physical barrier to the invading pathogen – Physical protection is more likely to exclude soil insects and nematodes than bacteria or fungi. VAM fungi have been found to reduce the incidence of root-knot nematode. However, some studies have shown that nematodes can penetrate the fungal mat.

ii. Various mechanisms also allow VAM fungi to increase a plant’s stress tolerance – This includes the intricate network of fungal hyphae around the roots which block pathogen infections. Inoculation of apple-tree seedlings with the VAM fungi Glomus fasciculatum and G. macrocarpum suppressed apple replant disease caused by phytotoxic myxomycetes.

iii. By providing antagonistic chemicals – Mycorrhizal fungi can produce a variety of antibiotics and other toxins that act against pathogenic organisms. VAM fungi indirectly suppress plant pathogens and enhances nutrition to plants; bring about morphological changes in the root by increased lignification and cause changes in the chemical composition of the plant tissues like antifungal chitinase, isoflavonoids, etc.

iv. By competing with the pathogen.

v. By increasing the nutrient-uptake ability of plant roots – For example, improved phosphorus uptake in the host plant has commonly been associated with mychorrhizal fungi when plants are not deprived of nutrients, they are better able to tolerate or resist disease-causing organisms.

vi. By changing the amount and type of plant root exudates – Pathogens on certain exudates will be at a disadvantage as the exudates change. Two pot experiments were carried out in the greenhouse at Agriculture Research Center, Giza, Egypt, to study the effect of VAM and T. viride as deterrents against R. solani and F. solani disease on growth and quality of sugar beet. Among all the treatments plants treated with mycorrhiza and T. viride recorded higher survival rates in sugar beet plants.

In field studies with eggplant, fruit numbers went from an average of 3.5 per plant to an average of 5.8 per plant when inoculated with Gigaspora margarita mycorrhizal fungi. Average fruit weight per plant went from 258 grams to 437 grams. A lower incidence of Verticillium wilt was also realized in the mycorrhizal plants.

Method # 7. Chemical Control:

Chemical pesticides are generally used to protect plant surfaces from infection or to eradicate a pathogen that has already infected a plant. From many decades fungicides played an important role in disease control. In the 1960s, systemic fungicides started gradually to replace the older non-systemic chemicals with more effectiveness and specificity in disease control.

However, the non-systemic fungicides such as mancozeb, chlorothalonil, copper and sulphur based products continued to have a good share of the market, especially in developing countries because of their lower cost. More recently, new classes of fungicides were developed with significant impact on disease control. These include anilinopyrimidines, phenoxyquinolines, oxazolidinediones, spiroketalamines, phenylpyrroles, strobilurins and activators of systemic acquired resistance.

The availability of a variety of new products with narrow and broad specificity, offer important disease control options, however, their practical application continues to face the risk of creation of resistant pathogen populations. Experience accumulated over the last few decades clearly showed that fungicidal application had a better impact when used within an IDM strategy.

In addition, public concern has increasingly influenced the fungicide industry in developing effective products with low mammalian toxicity and environmental impact and low residues in food, to meet international health standards and compatibility in integrated pest management programs. Chemical control includes soil treatment (such as fumigation), disinfestations of warehouses, sanitation of handling equipment and control of insect vectors of pathogens.

Soil Treatment by Chemicals:

Pre-planting and post-planting application of chemicals for soil treatment is effective preventive method for controlling the soilborne pathogens but pre-planting application more effective to escape the plants from pathogen infection. Fungicides used for soil treatments include metalaxyl, carbendazim (Bavstin), diazoben, pentachloronitrobenzene (PCNB) etc.

Chemicals in plant disease are used to create the toxic barrier between the host surface and pathogen. Drenching with copper oxychloride 0.2% or Bordeaux mixture 1% suitable for controlling the damping-off diseases while soil drenching with Trifloxystrobin + Tebuconazole @ 0.75g litre ^-1 water for control the Rhizoctonia spp.

Method # 8. Host-Plant Resistance:

Host plant resistance has been an apt choice in all the crop improvement programs and is essential to recommend the cultivars directly for cultivation in endemic areas, infested with soil borne fungus. Although the resistant variety is always one of the best way in reducing the loss due to soli borne plant pathogens. Disease resistant plants are obvious and effective control measure because resistance can be both competing and long lasting.

A plant can express the resistance through the action of a single gene that confers the immunity (resistance to certain races of Fusarium) or through multiple genes that results in a broad resistance to many pathogens. Single-gene resistance, called the vertical resistance, limits both the level of infection and the production of the inoculums. This sort of resistance can be overcome, however, by new strain of the target pathogen. Multi-gene resistance, called horizontal resistance, allows some disease to develop but limits it to a tolerable level.

Efficient field, greenhouse and laboratory procedures to evaluate chickpea and pigeonpea lines for resistance to Fusarium wilt have been developed and standardised at ICRISAT. In India, host plant resistance to Fusarium wilt of tomato was studied by evaluating a collection of 134 cultivars, breeding lines and alien species of tomato. Out of these genotypes, eight possessed high degree of resistance to race of F. oxysporum f. sp. Lycopersici. Similarly, Chauhan (1988) studied the reaction of several varieties lines of tomato to Fusarium wilt at Hissar. Out of 142 advance lines of chilli, 16 were resistant and 48 were moderately resistant.

Incorporation of resistance by conventional breeding techniques in susceptible cultivars has been achieved against many vascular wilt pathogens such as Fusarium and Verticillium spp. in a few crops. However, it is too much to expect in case of soil borne pathogens such as Fusarium to have stable resistance because of variability of the pathogen.