Clinical plant pathology

Introduction
Control of plant diseases is crucial to the reliable production of food, and it provides significant
reductions in agricultural use of land, water, fuel and other inputs. Plants in both natural and
cultivated populations carry inherent disease resistance, but there are numerous examples of
devastating plant disease impacts (see Irish potato famine Bengal femine, Chestnut blight), as
well as recurrent severe plant diseases (see rice blast, soybean cyst nematode, citrus canker).
However, disease control is reasonably successful for most crops. Disease control is achieved by
use of plants that have been bred for good resistance to many diseases, and by plant cultivation
approaches such as crop rotation, use of pathogen-free seed, appropriate planting date and plant
density, control of field moisture, and pesticide use. Across large regions and many crop species,
it is estimated that diseases typically reduce plant yields by 10% every year in more developed
settings, but yield loss to diseases often exceeds 20% in less developed settings. Continuing
advances in the science of plant pathology are needed to improve disease control, and to keep up
with changes in disease pressure caused by the ongoing evolution and movement of plant
pathogens and by changes in agricultural practices. Plant diseases cause major economic losses
for farmers worldwide. The Food and Agriculture Organization estimates indeed that pests and
diseases are responsible for about 25% of crop loss. To solve this issue, new methods are needed
to detect diseases and pests early, such as novel sensors that detect plant odours and spectroscopy
and biophotonics that are able to diagnostic plant health and metabolism.

Plant pathology

Plant pathology is the scientific study of diseases in plants caused by pathogens (infectious
organisms) and environmental conditions (physiological factors). Organisms that cause
infectious disease include fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms,
phytoplasmas, protozoa, nematodes and parasitic plants. Not included are ectoparasites like
insects, mites, vertebrate, or other pests that affect plant health by consumption of plant tissues.
Plant pathology also involves the study of pathogen identification, disease etiology, disease
cycles, economic impact, plant disease epidemiology, plant disease resistance, how plant
diseases affect humans and animals, pathosystem genetics, and management of plant diseases.
Clinical pathology
Clinical pathology is a laboratory specialty that is concerned with the diagnosis of disease based
on the laboratory analysis of infected organs, using the tools of chemistry, microbiology, and
molecular pathology in close collaboration with laboratory technologists.
Clinical plant pathology
Rapid and accurate diagnosis of plant health problems is essential to maintaining healthy
landscapes, forests, farms, public spaces – everywhere plants are found.

Clinical plant pathology may be described as a plant diagnostic laboratory or a plant clinic which
provides information regarding identification of diseases as well as their remedies using
infected plant parts such as, root, shoot, stem, leaf, flower, fruit etc. as well as tissues and
environmental issues that threaten the plant.

Objectives of a plant pathology clinic:

• To diagnosis important plant diseases and identify the pathogen associated with a specific
disease.
• To diagnosis routine plant disease in plants, potting mix, soil and water
• To test specific diseases for seed crops to meet export requirements
• To select and use the most appropriate technique for the diagnosis.
• To write disease diagnosis reports within due time and to suggest the control measure.
• To diagnosis an unknown plant disease.
• To test plant pathogen to fulfil nursery accreditation and export requirements.
• Nematode analysis of roots and soils for horticulture and broadacre crops
• Plant virus identification

Identification of plant diseases in a plant pathology clinic

Early detection and accurate diagnosis is essential for the effective management of plant disease.
Thus the first step in studying any disease is its timely detection of the diseased plant. Quick
initial detection of plant diseases in a plant pathology clinic is largely based on the signs and
symptoms of disease.[3]

A. Signs: Signs are the visible physical presence of either the pathogen itself or the structures
formed by the pathogen.
B. Symptoms: Symptoms are the visible changes that occur in the host plant in response to
infection by pathogens. For any disease in a given plant, there is the characteristic expression of
symptoms, usually occurring in a sequential series during the course of the disease. This series of
symptoms depicting the disease picture is referred to as the disease syndrome.

Morphological symptoms may be exhibited by the entire plant or by any organ of the plant.
Primarily, morphological symptoms of plant diseases can be categorized into 6 different types.

• 1 Necroses
o 1.1 Necrosis in Storage organs
o 1.2 Necrosis in Green tissues
o 1.3 Necrosis in Woody tissues
• 2 Abnormalities in growth
o 2.1 Hypoplasia & Atrophy
o 2.2 Hyperplasia & Hypertrophy
▪ 2.2.1 Enlargement of leaves and fruits
▪ 2.2.2 Enlargement of stems and roots
• 3 Metaplastic symptoms
• 4 Proleptic symptoms
• 5 Color changes
• 6 Wilts
1. Necroses
Necroses are caused due to necrosis or death of plant cells. The affected plant tissue usually turns
brown to black in color. Necrotic symptoms could appear in any part of the plant such as in
storage organs, in green tissues, or in woody tissues.

1.1 Necrosis in Storage organs

Death of cells in storage organs terminates in decomposition or decay referred to as a rot. Two
types of rots are identified as Dry rot and Wet rot on storage tissues.

Soft rots are those where the pathogen breaks down the host cell walls, resulting in the
exudation of juices from the infected tissue. The organ becomes mushy or pulpy and a foul smell
often develops due to colonization by secondary invaders. Many fungi and bacteria cause soft
rots on several fruits and vegetables. Species of the fungus, Rhizopus and bacterium Erwinia are
two such commonly found pathogens causing soft rots.
In a dry rot, the storage organ becomes hard and dry, and in some diseases, there is rapid loss of
water and the infected organs become shriveled, wrinkled, and leathery. Dry rots showing such
symptoms are referred to as mummifications.

1.2 Necrosis in Green tissues: Necroses on green tissue are termed differently based on the
nature of symptoms and the type of green tissue. The term, damping off refers to the sudden
wilting and topping over of seedlings as a result of extensive necrosis of tender tissue of the roots
and stem near the soil line, due to the attack of soil-borne pathogens such as fungus, Pythium.
A spot refers to a well-defined area of gray or brown necrotic tissue. Spots are very common on
leaves and fruits and are probably the most familiar necrotic symptom
Minute or very small spots are sometimes referred to as flecks or specks.
When dark mycelia of a fungal pathogen appear on the surface of necrotic spot, blotting the
leaves, shoots, an stems as large and irregular spots, the symptom is referred to as a blotch.
Net necrosis is a symptom resulting from an irregular pattern of anastomoses between streaks or
stripes.
Blights are characterized by the rapid death of entire leaves including the veins or parts of the
leaves. Blights also could occur on flowers and stems.
Firing is sudden drying, collapse and death of entire leaves. Firing occurs in response to the
activity of root rot and vascular wilt pathogens.
Scald is the term used to describe the blanching of epidermal and adjacent tissues of fruits and
occasionally of leaves.
The sudden death of unopened buds or inflorescence is referred to as blast.
Extensive necrosis of fruits that resemble in premature dropping is called shelling.

1.3 Necrosis in Woody tissues: Necrosis of woody tissue often brings about various types of
die-back symptoms. Dieback is the extensive necrosis of a shoot from its tip downwards.
Restricted necrosis of the bark and cortical tissue of stems and roots is termed as a canker. In
cankers, necrotic tissue in the sunken lesions is sharply limited, usually by a callus from adjacent
healthy tissue.
When woody tissues are diseased, they may exude different kinds of substances. When the
exudate is gummy, the symptom is called gummosis, while it is resinosis when it is resinous. If
the exudate is neither gummy nor resinous, it is described as bleeding.

2. Abnormalities in growth
Many disease symptoms are associated with growth changes in diseased plants. These could be
caused by either reduced growth due to hypoplasia and atrophy or excessive growth due to
hyperplasia and hypertrophy.

2.1 Hypoplasia & Atrophy

Hypoplasia is the failure of plants or plant organs to develop fully due to a decreased production
of the number of cells. Hypoplasia results in plants or plant parts of sub-normal size.
Atrophy is the reduction in the size of plant cells produced. This also results in stunted plants or
plant parts.[8]
Dwarfing is the failure of a plant or a plant part to attain its full size.
Rosetting is a condition where the internode of a plant do not elongate, and hence, the leaves
appear close together in a cluster.

2.2 Hyperplasia & Hypertrophy

Hyperplasia is the enlargement of a plant tissue due to excessive increase in the number of plant
cells produced. Hyperplasia results in overdevelopment in size of plants or plant organs.
Hypertrophy is excessive growth due to the enlargement of individual cells. This condition also
results in the overdevelopment in size of plants or plant organs.

2.2.1 Enlargement of leaves and fruits

Several symptoms expressing enlargement of leaves and fruits are commonly observed among
diseased plants.
Curling which is the bending of the shoot or the rolling of the leaf, is a result of over-growth on
one side of an organ. Often viral diseases cause such leaf distortions due to irregular growth of
the lamina. Extreme reduction of the leaf lamina brings about the symptom known as the Shoe-
string effect.
Scab consists of raised, rough, and discrete lesions. These are often sunken and cracked, giving a
typical scabby appearance.
Localized swellings or enlargement of epidermal cells due to excessive accumulation of water is
termed intumescence and the diagnostic symptom is the appearance of a blister.

2.2.2 Enlargement of stems and roots

Symptoms causing enlargement of stems and roots are termed differently based on their nature.
Excessive accumulation of food material in stems, above a constricted area produces a swelling
termed sarcody.
Localized swellings that involve entire organs are termed tumefaction. Commonly exhibited
tumefactions are galls, clubs, and knots.
The outgrowth of tissue in response to wounding is known as a callus. Callus formation is found
to form around most cankers.

3. Metaplastic symptoms: Metaplastic symptoms are those which form when tissues change
from one form to another. Such symptoms include phyllody, the development of floral organs
into leaf-like structures, juvenillody, the development of juvenile seedlings on mature plants and
russeting, a superficial browning of surfaces of fruits and tubers due to suberization.

4. Proleptic symptoms: Proleptic symptoms result from the development of tissues earlier than
usual. Examples include prolepsis, the premature development of a shoot from a bud, proleptic
abscission, the premature formation of abscission layers and restoration, the unexpected
development of organs that are normally rudimentary.

5. Color changes: Changes in the color of plant tissue are a common symptom of plant disease.
Often these color changes are brought about by the yellowing of normal green tissue due to the
destruction of chlorophyll or a failure to form chlorophyll. Such repression of leaf color may be
complete or partial.

When color repression is complete, it is known as albication. However, the more common,
partial repression is referred to as chlorosis.
Patches of green tissue alternating with chlorotic areas are described as a mosaic. Mosaic is a
symptom caused by many viruses. Based on the intensity and the pattern of discoloration,
mosaics are termed differently. Irregular patches of distinct light and dark areas are known as
mottling. Streaking and ring spots are still other distinct types of discolorations. Ring spots are
circular masses of chlorosis with a green center. Vein clearing and vein banding are yet other
common color changes on leaves.

6. Wilts: Wilting is due to loss of turgor in plant tissue resulting in the dropping of plant parts.
They are common symptom in diseases where the pathogen or the toxic metabolites it produces
affects the vascular tissue of the host plant. Interference in water transport brought about by the
infection of these vascular pathogens leads to wilting. Unlike wilting due to low soil moisture,
wilting due to the activity of these pathogens cannot be overcome by watering the plants.
Infected plants eventually die.

Distinguishing Abiotic and Biotic Problems

The first step is to determine whether the problem is caused by an infectious agent, and this can
be difficult. Plant symptoms caused by biotic factors such as infectious diseases and arthropod
pests are often similar to damage caused by other factors. Leaf spots, chlorosis, blights,
deformities, defoliation, wilting, stunting and plant death can be common symptoms of both
biotic and abiotic problems; therefore, the presence of these symptoms does not necessarily mean
the problem is a disease. Some general guidelines for distinguishing abiotic and biotic problems
follow and are summarized in table 1.

Table 1 DISTINGUISHING ABIOTIC AND BIOTIC PROBLEMS

Characteristics Abiotic Biotic
often affects several species or often affects one species or cultivar of
Hosts
plants of various ages the same age
often related to environmental or
Pattern of plant physical factors or cultural often initially observed in random or
symptoms practices; may be regular or irregular locations
uniform
relatively uniform, extent of relatively uneven, time of appearance
Rate of symptom
damage appears similar among and damage severity varies among
development
plants affected plants
no evidence of the kinds of pests or presence of insects, mites,
Signs
pathogens known to cause the fungal mycelium and spore clusters,
 current symptoms bacterial ooze, mollusks; products
produced by pests such as
honeydew/sooty mold, cast skins,
frass, or
mollusk slime.
is not infectious, is not progressive, infectious, spreads on host over time
Spread commonly caused by one incident if environmental conditions are
and does not spread suitable
possibly caused by pests that
have affected this crop during
possibly previously associated with
previous growing seasons or are
Recurrence current or prior environmental
known to
conditions or cultural practices
commonly affect this crop species or
cultivar

Biotic problems.
Identifying biotic problems is sometimes facilitated if signs of a pathogen, primarily the growth
of a fungus, are present. The most obvious examples of such signs are the mycelium and spores
produced by rusts and powdery and downy mildews. However, in other cases nonpathogenic
fungi can grow on top of damaged plant tissues and appear to be signs of a pathogen, resulting in
possible misdiagnoses.
Biotic problems often affect one species or cultivar of the same age and typically are initially
observed in random or irregular locations; symptoms appear at varying times, and severity varies
among affected plants. Biotic problems are infectious, spreading when environmental conditions
are favorable, and may be associated with pests that have affected the crop. This infectious
aspect is important, as biotic diseases will many times be progressive and continue to affect
additional tissues and more plants.
Abiotic problems.
In contrast to biotic factors, abiotic problems often affect several species or plants of various
ages; typically, damage is relatively uniform, doesn't spread and is often not progressive. Abiotic
problems are not associated with pests. They are often caused by a single incident and are related
to environmental or physical factors or cultural practices. Once the responsible factor has
dissipated and is no longer affecting the plant, the plant may grow out of the problem and
develop new, normal appearing foliage.