Phytopathology

Plant pathology (also phytopathology) is the scientific study of plant diseases caused by pathogens (infectious diseases) and environmental conditions (physiological factors). Organisms that cause infectious disease include fungi, 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, how plant diseases affect humans and animals, pathosystem genetics and management of plant diseases.

Contents

» Plant pathogens
» Fungi
» Ascomycetes
» Basidiomycetes
» Oomycetes
» Bacteria
» Phytoplasmas ('Mycoplasma-like organisms') and spiroplasmas
» Viruses, viroids and virus-like organisms
» Nematodes
» Protozoa
» Parasitic plants
» Physiological plant disorders
» Epidemiology
» Management

Plant pathogens

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 borne. Many soil borne spores, normally zoospores and capable of living saprotrophically, carrying 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 causal agents of potato late 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 hemibiotrophic

Bacteria

Most bacteria that are associated with plants are actually saprotrophic, and do no harm to the plant itself. However, a small number, around 500 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
» Burkholderia
» Proteobacteria
» Xanthomonas spp.
» Pseudomonas spp.

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, multicellular 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. Dodder, for example, is used as a conduit for the transmission of viruses or virus-like agents from a host plant to either a plant that is not typically a host or for an agent that is not graft-transmissible.

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

Main article: Plant Disease Epidemiology

Management

» Quarantine
Wherein a diseased patch of vegetation or individual plants are isolated from other, healthy growth. Specimens may be destroyed or relocated into a greenhouse for treatment/study. Another option is to avoid introduction of harmful non-native organisms by controlling all human traffic and activity (for e.g., AQIS) although legislation and enforcement are key in order to ensure lasting effectiveness.

» Cultural
Farming in some societies is kept on a small scale, tended by peoples whose culture includes farming traditions going back to ancient times. (An example of such traditions would be lifelong training in techniques of plot terracing, weather anticipation and response, fertilization, grafting, seed care, and dedicated gardening.) Plants that are intently monitored often benefit not only from active external protection, but a greater overall vigor as well. While primitive in the sense of being the most labor-intensive solution by far, where practical or necessary it is more than adequate.

» Plant resistance
Sophisticated agricultural developments now allow growers to choose from among systematically cross-bred species to ensure the greatest hardiness in their crops, as suited for a particular region's pathological profile. Breeding practices have been perfected over centuries, but with the advent of genetic manipulation even finer control of a crop's immunity traits is possible. (The engineering of food plants may be less rewarding however, as higher output is frequently offset by popular suspicion and negative opinion about this "tampering" with nature.

» Chemical
Many natural and synthetic compounds exist that could be employed to combat the above threats. This method works by directly eliminating disease-causing organisms or curbing their spread; however it has been shown to have too broad an effect, typically, to be good for the local ecosystem. From an economic standpoint all but the simplest natural additives may disqualify a product from "organic" status, potentially reducing the value of the yield.

» Biological
Crop rotation may be an effective means to prevent a parasitic population from becoming well established, as an organism affecting leaves would be starved when the leafy crop is replaced by a tuberous type, etc. Other means to undermine parasites without attacking them directly may exist.

» Integrated
The use of two or more of these methods in combination offers a higher chance of effectiveness.