Vegetable Diseases Caused by
Soilborne Pathogens
STEVEN T. KOIKE is Plant Pathology Advisor, University of California Cooperative Extension,
Monterey County; KRISHNA V. SUBBARAO is Plant Pathology Specialist, Department of Plant
Pathology, UC Davis; R. MICHAEL DAVIS is Plant Pathology Specialist, Department of Plant
Pathology, UC Davis; and THOMAS A. TURINI is Plant Pathology Advisor, University of
California Cooperative Extension, Imperial County.
Soilborne plant pathogens can significantly reduce yield and quality in vegetable
crops. These pathogens are particularly challenging because they often survive in soil
for many years and each vegetable crop may be susceptible to several species.
Simultaneous infections from multiple soilborne pathogens sometimes result in a dis-
ease complex that can further damage the crop. Many diseases caused by soilborne
pathogens are difficult to predict, detect, and diagnose. In addition to this, the soil
environment is extremely complex, making it a challenge to understand all aspects of
diseases caused by soilborne pathogens.
Special terms are used when discussing soilborne pathogens. Pathogens are the
biological agents that cause or incite the problem. Symptoms are the visible reactions
(e.g., root decay, tissue discoloration, crown rot, wilting of foliage, etc.) of the plant
when it is infected and colonized by the pathogen. The collective manifestation of
symptoms caused by the pathogens is the disease. In contrast to a symptom, a sign is
the visible evidence of the presence of the pathogen itself (e.g., mycelial growth, large
sclerotia, bacterial ooze, or nematode cysts). Inoculum is the biological object (e.g.,
spore, mycelium, sclerotium, cells) that is able to infect the host and cause the dis-
ease. The term soilborne pathogens, therefore, can be defined as pathogens that cause
plant diseases via inoculum that comes to the plant by way of the soil.
The most familiar diseases caused by soilborne pathogens are probably rots that
affect belowground tissues (including seed decay, damping-off of seedlings, and root
and crown rots) and vascular wilts initiated through root infections. A few soilborne
pathogens, however, cause foliar diseases with symptoms and damage appearing on
aboveground parts of plants. For example, the lettuce anthracnose pathogen survives
in the soil in the form of tiny resting structures (microsclerotia). When raindrops
splash pathogen-laden soil particles onto lettuce leaves, the fungus moves onto the
plants and causes a leaf spot disease. Similarly, the soilborne pathogen Sclerotinia scle-
rotiorum survives in soil as sclerotia. Under certain environmental conditions, the
sclerotia produce tiny mushroom-like structures (apothecia) that release aerial spores;
these spores then land on susceptible foliage and cause a foliar disease.
Because soil ecology is so complex, it is also important that we define the eco-
logical roles of soilborne pathogens. Soilborne pathogens can generally be divided
into soil inhabitants (those able to survive in soil for a relatively long time) and soil
invaders or soil transients (those only able to survive in soil for a relatively short
time). Many soilborne plant pathogens also can function and live as non-pathogenic
soil organisms under certain conditions. If these pathogens are in contact with dead
and decaying plant tissues, they can grow and survive on these substrates and thus be
seen as saprobes or saprophytes (organisms that live on decaying organic matter).
PUBLICATION 8099
UNIVERSITY OF
CALIFORNIA
Division of Agriculture
and Natural Resources
http://anrcatalog.ucdavis.edu
http://www.universityofcalifornia.edu
http://ucanr.org
http://anrcatalog.ucdavis.edu
MAJOR PATHOGEN GROUPS
The agents that cause soilborne diseases make up a diverse group. Fungi, which are
multicellular microorganisms, cause most soilborne vegetable diseases and so are con-
sidered the most important pathogen group. Plant-pathogenic fungi fall into five main
taxonomic classes based on morphological and biological characteristics:
Plasmodiophoromycetes, Zygomycetes, Oomycetes, Ascomycetes, and Basidiomycetes.
Some species of Ascomycetes and Basidiomycetes form a second type of spore that is
asexually produced. These asexual stages are placed in an additional, separate class,
the Fungi Imperfecti. Notable Oomycetes pathogens include Aphanomyces, Bremia,
Phytophthora, and Pythium. Important Ascomycetes are Monosporascus and Sclerotinia.
Examples of soilborne Fungi Imperfecti pathogens are Fusarium, Rhizoctonia, and
Verticillium. Plasmodiophora brassicae (causal agent of clubroot disease of brassicas)
and Spongospora subterranea (causal agent of powdery scab of potato) are the main
soilborne Plasmodiophoromycetes pathogens. Many soilborne fungi persist in soil for
long periods because these organisms produce resilient survival structures like
melanized mycelium, chlamydospores, oospores, and sclerotia. The thin-walled
mycelium typical of many fungi survives for only a short time in the soil.
Bacteria are single-celled organisms that have rigid cell walls but lack a mem-
brane-bound nucleus. Fewer diseases are caused by soilborne bacterial pathogens
than by fungal pathogens. Examples of such bacteria are Erwinia, Rhizomonas, and
Streptomyces. Pathogens in the Pseudomonas and Xanthomonas groups usually persist
in the soil for only a short time.
There are few soilborne viruses that affect vegetable crops. Viruses are subcellu-
lar entities composed of genetic material with a surrounding protein coat. Once the
genetic material of a plant virus is inserted into a host cell, it causes the cells to man-
ufacture more virus particles. Virus disease symptoms include stunting of the plant,
tissue distortions, and discolorations of foliage and fruit. Soilborne viruses generally
survive only in the living tissues of the host plant or in the nematode or fungal vec-
tors that transmit them to the plant hosts. Lettuce big vein disease, for instance, is
caused by the Mirafiori lettuce virus; the virus is present inside a primitive soil fungus
(Olpidium brassicae) that moves in soil water, attaches itself to lettuce roots, and
transmits the virus. Another example of a soilborne virus that affects vegetables is the
lettuce necrotic stunt virus (LNSV). This is an unusual case in that LNSV has no
known biological vector, but is found in river water and in soils contaminated by
such water.
Nematodes are tiny, nonsegmented roundworms. Soilborne plant-parasitic nema-
todes spend most of their lives in the soil, either as external feeders on plant roots or
as residents inside roots. Nematodes affect crops by reducing plant vigor and growth.
In an affected field, some plants will be heavily infested and others will not, with the
result that the overall crop will mature unevenly or the quality of the produce will be
lower. In soil, plant parasitic nematodes either live freely or are present as eggs or
durable cysts. Root knot nematodes (Meloidogyne species) cause a general reduction
in vigor for many plant species and can cause severe distortions and swellings of
roots, particularly affecting the marketability of root crops such as carrots. Cyst nema-
todes (Heterodera species) can survive in the soil for long periods because the mature
body of the female cyst nematode dries in the form of a leathery cyst, protecting the
eggs within. Needle nematodes (Longidorus africanus) feed on the growing points at
the tips of the roots, causing root tips to swell and causing roots to fork or branch
out. Stubby root nematodes (Paratrichodorus species) reduce the length of roots.
2ANR Publication 8099
BIOLOGY OF SOILBORNE PATHOGENS
Survival. A soilborne pathogen’s ability to survive in soil depends in part on the bio-
logical group to which it belongs. Few bacterial pathogens are true, long-term soil
inhabitants; most survive for limited periods as saprobes on plant debris or roots, or
directly in the soil. These species’ bacterial cells do not produce resilient endospores
and the vegetative cells are not particularly resilient in adverse environments. Some
species survive by secreting slimy material that dries to form protective layers around
the cells, enabling them to withstand unfavorable conditions.
Fungal pathogens survive in soil as saprobes on host plant debris or on other
types of organic matter present in soil, or as free-living organisms living directly in
the soil. Many of these fungi produce resilient survival structures on organic materi-
als; the structures are released into the soil by tillage operations and through decom-
position of the infected material. Survival structures can withstand low or high tem-
perature extremes, dry conditions, and periods when no suitable host is present.
Environmental factors, however, may affect how long the survival structures remain
viable. The sclerotia of some root-infecting pathogens can be sensitive to desiccation.
Low soil temperatures can be detrimental to pathogens that are adapted to warmer
conditions. Such conditions can limit the development of pathogens such as
Macrophomina phaseolina on beans and Sclerotium rolfsii on various crops.
Distribution of pathogens in soil. The horizontal and vertical distribution of soil-
borne pathogens depends on production practices, cropping history, and a variety of other
factors. Along a vertical axis, the inoculum of most root pathogens lies within the top 10
inches of the soil profile, the layers where host roots and tissues and other organic sub-
strates are found. On the horizontal plane, distribution of inoculum in a field is usually
aggregated in areas where a susceptible crop has been grown: survival structures produced
in diseased tissues are likely to remain in the area where the affected hosts have grown.
Because tillage operations involve fragmenting, moving, and burying plant
residues, tillage can result in the vertical and horizontal redistribution of pathogens.
Pathogen propagules can be moved both deeper and shallower in the soil profile.
Deeper-placed propagules can have adverse effects on the survival of these structures.
On the other hand, exposure to heat, cold, and drying may kill pathogens that have
been brought to the soil surface. On a horizontal scale, tillage redistributes inoculum
that was at first present in just a few infested areas and spreads it throughout the
field. Eventually, the inoculum produced after each susceptible crop could be spread
to previously uninfested areas, contributing to increased disease on succeeding crops.
The greatest concentration of nematodes usually occurs in the top 6 inches of soil,
though nematodes have been recovered from as deep as 4 to 5 feet. Nematode distrib-
ution in fields is irregular and usually dictated by the presence of host roots and root
exudates and the movement of soil.
Factors that influence infection. Many factors in the soil influence the activity
of soilborne pathogens and diseases: soil type, texture, pH, moisture, temperature,
and nutrient levels are among them. Soil is a porous mixture of inorganic particles,
organic matter, air, and water. Soil texture, which results from the size of mineral par-
ticles, and soil structure, which is the arrangement of soil particles into groups (aggre-
gates), significantly influence the development of root disease. Well-aerated, well-
drained soils create conditions that discourage root diseases. Soils that drain poorly,
however, tend to favor the survival and distribution of soilborne pathogens such as
Pythium, Phytophthora, and Aphanomyces. Fusarium and Verticillium wilts can also be
more severe in wet soils than in dry soils. Only a few root diseases are favored by
drier soils (for example, common scab of potato caused by Streptomyces scabies).
3ANR Publication 8099
Soil pH is another important factor influencing the development of certain soil-
borne diseases. A classic example is clubroot disease of crucifers caused by
Plasmodiophora brassicae. Clubroot is a major problem in acidic soils (5.7 pH or
lower). The disease is dramatically reduced when the pH rises from 5.7 to 6.2 and is
virtually eliminated at soil pH values greater than 7.3 to 7.4. This disease, which once
posed a major threat in the Salinas Valley, has been managed for decades by liming
the soil to raise the pH. Similarly, common scab of potatoes is favored by a pH of 5.2
to 8.0 but is reduced dramatically by soil pH values lower than 5.2.
Soil temperature is generally a less critical factor for soilborne problems on veg-
etable crops. Colder soil temperatures usually slow pathogen development and reduce
the severity of disease. Under warmer temperatures, pathogens grow and develop
more rapidly and can cause more disease. Melon vine decline (caused by
Monosporascus cannonballus) and sudden wilt (caused by Pythium aphanidermatum)
are two cucurbit diseases that are favored by high temperatures.
Another factor that has a major influence on soilborne disease is plant nutrition.
The effect of nitrogen has received the most extensive study. High levels of soil nitro-
gen increase the growth rates of crops, enhance the growth of tender, succulent plant
tissue, and prolong the plants’ vegetative phase. Plants in this condition may be more
vulnerable to attack by some soilborne pathogens. Low levels of soil nitrogen weaken
plants and also predispose them to attack by some pathogens.
The type of nitrogen fertilizer can also indirectly affect soil pH and thus have an
effect on soilborne diseases. The positive charge on an ammonium ion allows it to be
adsorbed by plant roots, resulting in the release of hydrogen ions into the surround-
ing soil. These additional hydrogen ions lower the soil’s pH; consequently, diseases
that are more common in acidic soils increase in severity when ammonium nitrogen
fertilizer is applied.
In contrast, nitrates can favor other diseases by altering the virulence and growth
of the pathogens and by increasing host susceptibility. These effects can be seen with
the vascular wilt pathogens. Research indicates that an increase in nitrate levels can
increase the severity of Verticillium wilt but reduce that of Fusarium wilt; however,
higher ammonium levels can cause Fusarium wilt to be more severe. Other soil nutri-
ents may also have an affect on soilborne diseases, but they have not been studied as
extensively as nitrogen.
Ecology. Soilborne pathogens share the soil environment with many other organ-
isms and compete with them for limited resources. In addition, many of the microor-
ganisms in soil are directly or indirectly antagonistic to soilborne pathogens. Direct
antagonism takes place when, because of the environmental niche it occupies in the
soil environment, an organism excludes a pathogen from the soil, or when an organ-
ism parasitizes soilborne pathogens. With indirect antagonism, the microflora may
release substances that are toxic to the pathogen. In some soils, called suppressive
soils, antagonistic microflora suppress the activity and development of soilborne
pathogens to such a great extent that they significantly reduce the instance of plant
disease. Researchers are attempting to create suppressive soil conditions deliberately
by introducing microorganisms into the soil or by incorporating certain crop residues
that enhance microbial growth and diversity. An example of this research is the recent
use of broccoli residue to enhance suppression of Verticillium dahliae and Sclerotinia
minor pathogens.
4ANR Publication 8099
DIAGNOSING SOILBORNE DISEASES
Diagnosing a soilborne disease, in general, is not much different from diagnosing a
disease that occurs on aboveground plant parts. Here are a few procedures that may
prove useful:
• Prepare a list of known suspected soilborne pathogens. A particular crop being
grown in a specific region generally is susceptible to a relatively short list of soilborne
pathogens. By compiling this list ahead of time, you can narrow the group of
pathogens to watch for (see Table).
• Carefully examine all parts of affected plants. Complete observation of roots,
crowns, and other belowground plant parts is essential. You have to consider the
symptoms that you observe aboveground together with the belowground symptoms in
order to get a complete picture of a plant’s condition.
• Watch for symptoms that occur in noticeable patterns, non-random distributions,
or in association with physical features at the sites. For example, if symptomatic
plants are associated with irrigation patterns or areas of excess water, that information
can influence your diagnosis.
• Collect a representative sample for laboratory analysis. Plants must be carefully dug
up so as to preserve roots and other belowground plant parts. The sample should con-
sist of a sufficient number of diseased plants showing typical symptoms as well as a
few healthy specimens for comparison. A qualified plant diagnostic laboratory can
then confirm the actual cause of the soilborne disease.
• Keep a record of the soilborne diseases that you confirm at each site. This type of
historic record can be especially useful later on because soilborne pathogens tend to
persist for long periods of time. If you know which pathogens have been observed in
a field, you can make better crop rotation decisions.
SOILBORNE DISEASE CONTROL STRATEGIES
Management of soilborne diseases depends on a thorough knowledge of the pathogen,
the host plant, and the environmental conditions that favor infection. In order for a
disease to develop, all three factors must be present. The pathogen (a virulent, infec-
tious 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 favorable 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
molds to develop and infect roots. An understanding of these pathogen-host-environ-
ment dynamics will help you devise a disease management strategy.
An effective disease management option must be economical: that is, the value
of the crop saved must exceed the cost of control. For this reason, assessments of dis-
ease incidence, disease severity, and potential crop loss are key factors when consider-
ing control strategies. The careful, regular monitoring of fields and the thorough
examination of symptomatic plants are essential steps. 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. Besides
being economically sound, a management strategy should also be simple, safe, inex-
pensive to apply, and sufficiently effective to reduce diseases to acceptable levels. Few
management options possess all of these desirable qualities, however, so it usually is
best to integrate multiple management options (e.g., planting resistant varieties, fol-
lowing beneficial cultural practices, and applying disease-control materials).
5ANR Publication 8099
Table. Important soilborne diseases and examples of management strategies*
Crop Disease Pathogen Symptoms and signs Examples of management†
Apiaceae
Carrot Bacterial Erwinia carotovora, Soft, sunken, dull orange lesions Plant in well-drained soil.
soft rot E. chrysanthemi on taproots or rot of lower portions Avoid overwatering, especially
of taproots. during warm weather.
Cavity spot Pythium violae Small, elliptical, superficial Apply fungicides.
lesions on taproots. Plant in well-drained soil.
Cottony rot Sclerotinia sclerotiorum Soft, watery rot of stems and foliage. Apply fungicides.
Profuse white mycelium and Provide ventilation down rows
black sclerot
