Phytopathology

Overview
Phytopathology (plant pathology) is the scientific study of plant diseases caused by pathogens (infectious diseases) 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 insects, mites, vertebrate or other pests that affect plant health by consumption of plant tissues. Plant Pathology also involves the study of the identification, etiology, disease cycle, economic impact, epidemiology, pathosystem genetics and management of plant diseases.

The "Disease triangle" is a central concept of plant pathology for infectious diseases. It is based on the principle that disease is the result of an interaction between a host, a pathogen, and environment condition.

Fungi


The majority of phytopathogenic fungi belong to the Ascomycetes and the Basidiomycetes.

The fungi reproduce both sexually and asexually via the production of spores. These spores may be spread long distances by air or water, or they may be soil bourne. Many soil bourne spores, normally zoospores and capable of living saprophytically, caring out the first part of their lifecycle in the soil.

Fungal diseases can be controlled through the use of fungicides in agriculture, however new races of fungi often evolve that are resistant to various fungicides.

Significant fungal plant pathogens
 * Ascomycetes
 * Fusarium spp.
 * Thielaviopsis spp. (Causal agents of: canker rot, black root rot, Thielaviopsis root rot)
 * Verticillium spp.
 * Magnaporthe grisea (T.T. Hebert) M.E. Barr; causes blast of rice and gray leaf spot in turfgrasses
 * Basidiomycetes
 * Rhizoctonia spp.
 * Phakospora pachyrhizi Sydow; causes Soybean rust
 * Puccinia spp.; causal agents of severe rusts of virtually all cereal grains and cultivated grasses

Oomycetes


The oomycetes are fungal-like organisms that until recently used to be mistaken for fungi. They include some of the most destructive plant pathogens including the genus Phytophthora which includes the casual agents of potato blight and sudden oak death.

Despite not being closely related to the fungi, the oomycetes have developed very similar infection strategies and so many plant pathologists group them with fungal pathogens.

Significant oomycete plant pathogens
 * Pythium spp.
 * Phytophthora spp.; including the causal agent of the Great Irish Famine (1845-1849)

Rice blast is hemibiotrofic

Bacteria


Most bacteria that are associated with plants are actually saprophytic, and do no harm to the plant itself. However, a small number, around 100 species, are able to cause disease. Bacterial diseases are much more prevalent in sub-tropical and tropical regions of the world.

Most plant pathogenic bacteria are rod shaped (bacilli). In order to be able to colonise the plant they have specific pathogenicity factors. There are 4 main bacterial pathogenicity factors:

1. Cell wall degrading enzymes - used to break down the plant cell wall in order to release the nutrients inside. Used by pathogens such as Erwinia to cause soft rot.

2. Toxins These can be non-host specific, and damage all plants, or host specific and only cause damage on a host plant.

3. Phytohormones - for example Agrobacterium changes the level of Auxin to cause tumours.

4. Exopolysaccharides - these are produced by bacteria and block xylem vessels, often leading to the death of the plant.

Bacteria control the production of pathogenicity factors via quorum sensing.

Significant bacterial plant pathogens
 * Proteobacteria
 * Xanthomonas spp.
 * Pseudomonas spp.

Phytoplasmas ('Mycoplasma-like organisms') and spiroplasmas


Phytoplasma and Spiroplasma are a genre of bacteria that lack cell walls, and are related to the mycoplasmas which are human pathogens. Together they are referred to as the mollicutes. They also tend to have smaller genomes than true bacteria. They are normally transmitted by sap-sucking insects, being transferred into the plants phloem where it reproduces.

Viruses, viroids and virus-like organisms


There are many types of plant virus, and some are even asymptomatic. Normally plant viruses only cause a loss of yield. Therefore it is not economically viable to try to control them, the exception being when they infect perennial species, such as fruit trees.

Most plant viruses have small, single stranded RNA genomes. These genomes may only encode 3 or 4 proteins: a replicase, a coat protein, a movement protein to allow cell to cell movement and sometimes a protein that allows transmission by a vector.

Plant viruses must be transmitted from plant to plant by a vector. This is normally an insect, but some fungi, nematodes and protozoa have been shown to be viral vectors.

Nematodes


Nematodes are small, multicelluar wormlike creatures. Many live freely in the soil, but there are some species which parasitize plant roots. They are mostly a problem in tropical and subtropical regions of the world, where they may infect crops. Root knot nematodes have quite a large host range, whereas cyst nematodes tend to only be able to infect a few species. Nematodes are able to cause radical changes in root cells in order to facilitate their lifestyle.

Protozoa
There are a few examples of plant diseases caused by protozoa. They are transmitted as zoospores which are very durable, and may be able to survive in a resting state in the soil for many years. They have also been shown to transmit plant viruses.

When the motile zoospores come into contact with a root hair they produce a plasmodium and invade the roots.

Parasitic plants
Parasitic plants such as mistletoe and dodder are included in the study of phytopathology.

Physiological plant disorders
Significant abiotic disorders can be caused by:
 * Natural
 * Drought
 * Frost damage, and breakage by snow and hail
 * Flooding and poor drainage
 * Nutrient deficiency
 * Salt deposition and other soluble mineral excesses (e.g. gypsum)
 * Wind (windburn, and breakage by hurricanes and tornadoes)
 * Lightning and wildfire (also often man-made)
 * Man-made (arguably not abiotic, but usually regarded as such)
 * Soil compaction
 * Pollution of air and/or soil
 * Salt from winter road salt application
 * Herbicide over-application
 * Poor education and training of people working with plants (e.g. lawnmower damage to trees)
 * Vandalism

Epidemiology
An epidemic is a disease increase in a population that is normally severe and widespread. Disease epidemics in plants can cause huge losses in yield of crops as well threatening to wipe out entire species of tree such as was the case with Dutch Elm Disease and could occur with Sudden Oak Death. An epidemic of late potato blight led to the Great Irish Famine (1845-1849) and the loss of many lives.

Factors Effecting Epidemics
There are three major factors in the development of plant disease epidemics: the presence of large numbers of susceptible host plants (often provided by agriculture), a virulent pathogen and favourable environmental conditions. Together these three factors are referred to as the plant disease trangle, as pictured right. But this is a somewhat basic representation of the factors effecting the progression of an epidemic.

Sometimes a fourth factor of time is added as the time at which a particular infection occurs, and the length of time conditions remain viable for that infection, can also play an important role in epidemics. The age of the plant species can also play a role, as cerytain species change in their levels of disease resistance as they mature a process known as ontogenic resistance.

When a pathogen requires a vector to be spread then for an epidemic to occur the vector must be plentiful and active.

Types of Epidemics
Monocyclic epidemics are caused by pathogens with a low birth rate and death rate meaning they only have one infection cycle per season. They are typical of soil born diseases such as Fusarium wilt of flax. Polycyclic epidemics are caused by pathogens capable of several infection cycles a season. These are most often caused by airborne diseases such as powdery mildew. Bimodal polycyclic epidemics can also occur. For example in brown rot of stone fruits the blossoms and the fruits are infected at different times.

For some diseases it is important to consider the disease occurrence over several growing seasons especially if growing the crops in monoculture year after year or growing perennial plants. Such conditions can mean that the innoculum produced in one season can be carried over to the next leading to a build of an innoculum over the years. In the tropics there are no clear cut breaks between growing seasons as there are in temperate regions and this can lead to accumulation of innoculum.

Epidemics that occur under these conditions are referred to as polyetic epidemics and can be caused by both monocylcic and polycyclic pathogens. Apple powdery mildew is an example of a polyetic epidemic caused by a polycyclic pathogen and Dutch Elm disease monocyclic pathogen that can give rise to a polyetic epidemic.

Management

 * Quarantine
 * Cultural
 * Plant resistance
 * Chemical
 * Biological
 * Integrated