Chapter 3: Manage plant diseases

Plant diseases pose significant challenges to crop productivity and food security in Kenya, where agriculture remains a critical sector for livelihoods and economic growth. Managing plant diseases effectively requires a deep understanding of the nature of these diseases, accurate diagnosis through specimen collection and testing, and knowledge of their classification. This chapter equips applied biology professionals with the essential concepts and practical skills necessary to identify, classify, and manage plant diseases in diverse agricultural contexts, from smallholder farms to commercial horticulture enterprises.

3.1 Plant Diseases

A plant disease is a harmful, usually progressive change in the structure or function of a plant, caused by a living agent or by an unfavourable physical or chemical condition. An applied biologist who manages a teaching nursery, a research plot or a greenhouse at a field station must be able to name the problem correctly, because the control for a fungal leaf spot, a nutrient deficiency and a virus infection are completely different. Example: a technician who sprays a fungicide on tomato seedlings that are really short of calcium wastes chemicals and loses time while the real fault continues.

This topic first fixes the vocabulary of plant pathology, then shows how infected specimens are collected and tested, and finally classifies plant diseases by cause.

3.1.1 Meaning of Terms

Plant pathology uses a small set of precise terms. Using them correctly lets staff in a research plot, a teaching laboratory and a diagnostic laboratory describe the same problem in the same words. The terms fall into three groups: the disease and its cause, the host plant, and infection and spread.

Terms about the disease and its cause

• Disease: a continuous disturbance of the normal functions of a plant that shows as symptoms and reduces growth, quality or yield. A mechanical injury such as hail damage happens once and does not progress, so it is an injury and not a disease.
• Pathogen: a living organism that causes disease, for example a fungus, a bacterium, a nematode or a parasitic plant. Viruses and viroids are not cells, but they are also classed as pathogens.
• Pathogenicity: the ability of a pathogen to cause disease in a host.
• Virulence: the degree of damage a particular strain of a pathogen causes. Two strains of the same fungus can both be pathogenic yet differ widely in virulence.
• Causal agent: the specific organism or factor that produces a disease, such as the fungus Fusarium oxysporum f. sp. lycopersici for Fusarium wilt of tomato.
• Abiotic disorder: a disorder caused by a non-living factor such as nutrient imbalance, drought, frost or chemical injury. It does not spread from plant to plant.

Terms about the host

• Host: the plant that a pathogen infects and feeds on. A pathogen with a narrow host range, such as the maize streak virus, attacks only grasses, while Ralstonia solanacearum attacks many plant families.
• Susceptibility: the degree to which a host can be damaged by a pathogen. A susceptible variety develops severe disease under conditions where a resistant one stays healthy.
• Resistance: the ability of a plant to prevent or limit infection or the growth of the pathogen. A tolerant plant is infected but suffers little loss of yield.
• Symptom: the visible reaction of the plant to the disease, such as wilting, leaf spots, yellowing, galls or stunting.
• Sign: the visible presence of the pathogen itself, such as fungal spores, rust pustules, mycelium or bacterial ooze. A sign is direct evidence of the cause, whereas a symptom may be produced by several different causes.
• Syndrome: the full set of symptoms that occur together and characterise a disease.

Terms about infection and spread

• Inoculum: any part of the pathogen that can start an infection, for example spores, sclerotia, bacterial cells, virus particles or nematode eggs.
• Infection: the process by which a pathogen enters a host and establishes itself in it. Infection is not the same as disease: a plant may be infected before any symptom appears.
• Incubation period: the time between infection and the first symptom.
• Disease cycle: the chain of events from survival of the pathogen between seasons, through inoculum production, spread, infection and colonisation, to the return to a survival stage. Breaking any link of the cycle reduces the disease.
• Vector: an organism, usually an insect such as an aphid or a whitefly, that carries and transmits a pathogen from one plant to another.
• Disease triangle: the idea that disease occurs only when a susceptible host, a virulent pathogen and a favourable environment meet at the same time. Removing one side of the triangle prevents disease.
• Epidemic: a rapid increase of a disease in a plant population over a wide area or a short time.

3.1.2 Collection and Testing of Infected Plant Specimens

A correct diagnosis depends on the quality of the specimen. A dried, rotten or badly labelled sample can lead to a wrong diagnosis even in a well equipped laboratory. Collection therefore follows a fixed routine, and testing moves from simple observation to more specialised methods only when needed.

Tools and materials for collecting specimens

Procedure for collecting a specimen

1. Walk through the plot and note how the problem is spread: in patches, along rows, around the edge or across the whole plot. The pattern helps to tell an infectious disease from a soil or management problem.
2. Choose plants that show early or active symptoms. Plants that are already dead or rotten usually carry secondary organisms that hide the real cause.
3. Sample the whole range of symptoms, including a healthy plant of the same variety and age taken from nearby, so that the laboratory can compare the two.
4. Clean the secateurs or scalpel with ethanol before each plant. Cut leaves, stems or fruits so that each piece contains both diseased and healthy tissue. For wilting or root problems, lift the entire plant with its roots and some soil.
5. Place leaf and stem samples in paper bags. Place roots and soil in polythene bags. Do not add water, and do not pack fresh, wet leaves tightly in sealed plastic for long periods because they rot.
6. Label every bag at once with a unique number, crop and variety, plant part, date, collector and field location, and enter the same number in the notebook with a description of the symptoms and the field pattern.
7. Place the bags in the cool box, away from direct sun. Never leave specimens in a closed vehicle.
8. Wash hands and clean boots, tools and the collection area before moving to another plot, so that pathogens are not carried to healthy crops.

Transport and storage

Specimens should reach the laboratory as soon as possible, ideally within 24 hours. Until then they are kept cool but not frozen, because freezing damages the tissue and kills many pathogens. A specimen that is suspected to carry a quarantine pest is reported to the national plant health regulator, the Kenya Plant Health Inspectorate Service (KEPHIS), and is handled as the regulator directs.

Laboratory testing techniques

Testing proceeds in stages, from the simplest and cheapest method to the most specific.

• Macroscopic examination: the whole specimen is examined with the naked eye and a hand lens for lesions, rots, galls, discoloured vascular tissue and visible signs.
• Microscopic examination: a thin section or a scraping of the lesion is mounted in water or stain and examined under a compound microscope for spores, hyphae, bacterial streaming or nematodes.
• Moist chamber incubation: specimens are kept in a humid container for a few days so that fungi sporulate and can be identified from their spores.
• Culture isolation: small pieces of tissue are surface sterilised and placed on a nutrient medium. Potato dextrose agar is widely used for fungi and nutrient agar for bacteria. Pure cultures are then identified from colony and spore characteristics.
• Bacterial ooze test: a cut stem from a wilting plant is suspended in clear water, and a thin stream of milky bacterial cells flowing from the cut end points to a bacterial wilt.
• Serological tests: enzyme-linked immunosorbent assay (ELISA) and lateral flow strips use antibodies to detect a specific virus or bacterium in plant sap.
• Molecular tests: polymerase chain reaction (PCR) detects the genetic material of the pathogen and is used to confirm viruses, bacteria and fungi, including strains that look alike under the microscope.
• Nematode extraction: nematodes are separated from soil or root tissue with a sieve or a Baermann funnel and counted under a dissecting microscope.
• Pathogenicity test (Koch's postulates): the suspected pathogen is found in every diseased plant, isolated into pure culture, inoculated into healthy plants of the same species so that the same disease develops, and then isolated again from those plants and shown to be the same organism.

Every result is recorded against the specimen number, and diseased material left over after testing is autoclaved or burnt so that it does not infect the nursery or the greenhouse.

3.1.3 Classification of Plant Diseases

Plant diseases are classified first by the kind of agent that causes them. Biotic diseases are caused by living agents (bacteria, fungi, viruses and nematodes), and abiotic diseases are caused by non-living factors. The five groups below follow this classification.

Diseases can also be grouped in other useful ways:

• Infectious and non-infectious: infectious diseases spread from plant to plant through wind, water, soil, tools or vectors, and non-infectious diseases do not.
• Systemic and localised: a systemic disease moves through the vascular system and affects the whole plant, as in bacterial wilt or a virus infection, while a localised disease stays in one part, as in a leaf spot.
• Seed-borne, soil-borne and air-borne: the group names the main way the pathogen survives and reaches the host. Common bacterial blight of beans is carried on seed, Fusarium wilt persists in the soil, and rusts are carried by wind.

3.1.3.1 Bacterial Diseases

Bacteria are single-celled organisms without a nucleus. They enter plants through wounds and natural openings such as stomata and hydathodes, and multiply in the spaces between cells or in the vascular tissue. They spread by splashing rain and irrigation water, contaminated tools, insects, infected seed and planting material.

• Typical symptoms: water-soaked spots that turn brown, sudden wilting, soft and foul-smelling rots, cankers and galls, and sticky bacterial ooze.
• Bacterial wilt of tomato and potato: caused by Ralstonia solanacearum, which blocks the xylem, so that the plant wilts although the soil is moist. The ooze test is positive and the pathogen persists in the soil.
• Black rot of cabbage and kale: caused by Xanthomonas campestris pv. campestris, which produces yellow V-shaped lesions from the leaf edge and blackens the veins. The bacterium is seed-borne.
• Common bacterial blight of beans: caused by Xanthomonas axonopodis pv. phaseoli, which produces water-soaked spots with yellow halos on leaves and pods. It is carried on seed.
• Soft rot: caused by Pectobacterium and related bacteria that dissolve the middle lamella of storage organs such as potato tubers and cabbage heads.
• Crown gall: caused by Agrobacterium tumefaciens, which forms rough tumour-like galls at the base of woody and herbaceous plants.
• Control principles: use clean seed and planting material, rotate with non-host crops, clean tools between plants, remove and destroy infected plants, avoid overhead irrigation and wounding, and choose resistant varieties where they exist.

3.1.3.2 Fungal Diseases

Fungi are organisms with threads called hyphae and with spores. They cause a large share of plant diseases. Spores are spread by wind, water splash, soil, seed, tools and insects, and they germinate when leaf wetness and temperature are suitable.

• Typical symptoms: leaf spots and blights, powdery or downy growth on leaves, rust-coloured pustules, smuts, wilting, damping-off of seedlings, cankers and fruit rots.
• Common signs: spore masses, powdery or woolly mycelium, pustules and tiny black fruiting bodies on the lesion.

Late blight of potato and tomato, caused by Phytophthora infestans, is often grouped with fungal diseases, as is damping-off caused by Pythium. Both causal organisms are oomycetes, water moulds that are only distantly related to true fungi, and they are controlled with different fungicides. Control of fungal diseases combines resistant varieties, crop rotation, field sanitation, wide spacing for air movement, careful irrigation and, when needed, fungicides applied on label instructions.

3.1.3.3 Viral Diseases

Viruses are particles made of nucleic acid in a protein coat. They multiply only inside living cells, cannot be cured once a plant is infected, and spread within the plant through the vascular system. Most spread between plants by insect vectors, by infected cuttings and other vegetative planting material, by contaminated cutting tools and sap, and in some crops by seed.

• Typical symptoms: mosaic and mottled leaves, yellowing, leaf curling and distortion, ring spots, stunting and poor fruit set. Symptoms resemble nutrient deficiency, so laboratory testing is needed to confirm a virus.
• Maize lethal necrosis: a co-infection of maize chlorotic mottle virus with a potyvirus such as sugarcane mosaic virus, which causes yellowing from the leaf edge and early death of young plants.
• Maize streak: transmitted by leafhoppers and recognised by pale streaks along the veins.
• Cassava mosaic disease: transmitted by the whitefly Bemisia tabaci and by infected cuttings, with distorted and mottled leaves.
• Tomato yellow leaf curl: transmitted by whiteflies, with upward-curled, yellow, stunted leaves.
• Banana bunchy top: transmitted by the banana aphid Pentalonia nigronervosa and by suckers, with dwarfed plants and narrow upright leaves.
• Control principles: plant virus-free material, control vectors, rogue (remove) infected plants early, disinfect cutting tools, remove weeds that host the virus and use resistant or tolerant varieties.

3.1.3.4 Nematode Infections

Nematodes are microscopic, unsegmented roundworms. Plant-parasitic nematodes pierce root cells with a hollow stylet and feed on the contents. They spread through infested soil, irrigation water, planting material, tools and boots. Their damage also opens the root to fungi and bacteria, so wilt complexes are common.

• Root symptoms: galls or knots on the roots, dark lesions, stunted and bushy roots and root rot.
• Above-ground symptoms: stunting, yellowing and wilting in patches that do not respond to water or fertiliser.
• Root-knot nematodes (Meloidogyne species): produce swollen galls on roots of tomato, beans and many vegetables.
• Lesion nematodes (Pratylenchus species): cause brown to black lesions on roots of maize, banana and many other crops.
• Burrowing nematode (Radopholus similis): destroys banana roots, so the plant topples.
• Cyst nematodes: females swell into cysts on the roots that survive in soil for years.
• Diagnosis: roots are inspected for galls and lesions, and nematodes are extracted from soil and roots and counted under the microscope.
• Control principles: use clean planting material, rotate with non-host crops, fallow, solarise soil in nurseries, add organic matter, and plant resistant varieties.

3.1.3.5 Diseases Caused by Abiotic Factors

Abiotic factors are non-living conditions that harm plants. They produce symptoms that look like infectious diseases, but there is no pathogen, and the damage does not spread from plant to plant.

• Nutrient deficiency: nitrogen shortage turns older leaves uniformly pale yellow, magnesium shortage gives yellowing between the veins, and calcium shortage causes blossom-end rot of tomato fruit.
• Nutrient toxicity and salinity: excess salts or fertiliser burn leaf margins and stunt growth.
• Water stress: drought causes wilting and leaf scorch, and waterlogging starves roots of oxygen so that leaves yellow and roots rot.
• Temperature extremes: frost blackens young tissue, and heat causes sunscald on fruit and leaves.
• Soil pH: very acid or alkaline soil locks up nutrients and can release toxic levels of some elements.
• Chemical injury: herbicide drift or a wrongly mixed pesticide causes leaf cupping, twisting, spotting and scorch.
• Physical injury: hail, strong wind and mechanical damage tear leaves and bruise stems.

Several clues suggest an abiotic cause: damage that follows a sprayer track, a low spot or a soil boundary, the sudden appearance of symptoms on many plants at once, no signs of a pathogen under the hand lens or microscope, and no spread to neighbouring plants over time. Tests include soil pH and electrical conductivity, soil and leaf tissue analysis and a review of recent fertiliser, irrigation and chemical applications.

Chapter Summary

This chapter explored the concept of plant diseases, beginning with the explanation of key terms related to plant pathology. It detailed the procedures for collecting and testing infected plant specimens, emphasizing accurate diagnosis to inform effective management strategies. The classification of plant diseases was examined comprehensively, covering the major categories of bacterial, fungal, viral, and nematode infections. Each category was discussed in terms of its causes and characteristics, highlighting how these pathogens affect plant health. Additionally, the chapter addressed diseases caused by abiotic factors, recognizing that non-living environmental conditions can also lead to plant disorders. Understanding these diverse causes is essential for developing integrated approaches to disease control. Overall, the chapter provided a foundational framework for identifying, diagnosing, and classifying plant diseases to support effective plant health management.