Plant pathology (also phytopathology) 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 eating 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.
Control of plant diseases is crucial to the reliable production of food, and it provides significant problems 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 such as Irish potato famine and chestnut blight, as well as recurrent severe plant diseases like rice blast, soybean cyst nematode, and 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 diagnose plant health and metabolism.
Most phytopathogenic fungi belong to the Ascomycetes and the Basidiomycetes. The fungi reproduce both sexually and asexually via the production of spores and other structures. Spores may be spread long distances by air or water, or they may be soilborne. Many soil inhabiting fungi are capable of living saprotrophically, carrying out the part of their life cycle in the soil. These are facultative saprotrophs. Fungal diseases may be controlled through the use of fungicides and other agriculture practices. However, new races of fungi often evolve that are resistant to various fungicides. Biotrophic fungal pathogens colonize living plant tissue and obtain nutrients from living host cells. Necrotrophic fungal pathogens infect and kill host tissue and extract nutrients from the dead host cells. Significant fungal plant pathogens include:
The oomycetes are fungus-like organisms. 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. Particular species of oomycetes are responsible for root rot.
Despite not being closely related to the fungi, the oomycetes have developed similar infection strategies. Oomycetes are capable of using effector proteins to turn off a plant's defenses in its infection process. Plant pathologists commonly group them with fungal pathogens.
Significant oomycete plant pathogens include:
Some slime molds in Phytomyxea cause important diseases, including club root in cabbage and its relatives and powdery scab in potatoes. These are caused by species of Plasmodiophora and Spongospora, respectively.
Most bacteria that are associated with plants are actually saprotrophic and do no harm to the plant itself. However, a small number, around 100 known species, are able to cause disease. Bacterial diseases are much more prevalent in subtropical and tropical regions of the world.
Most plant pathogenic bacteria are rod-shaped (bacilli). In order to be able to colonize the plant they have specific pathogenicity factors. Five main types of bacterial pathogenicity factors are known: uses of cell wall-degrading enzymes, toxins, effector proteins, phytohormones and exopolysaccharides.
Pathogens such as Erwinia species use cell wall-degrading enzymes to cause soft rot. Agrobacterium species change the level of auxins to cause tumours with phytohormones. Exopolysaccharides are produced by bacteria and block xylem vessels, often leading to the death of the plant.
Significant bacterial plant pathogens:
Phytoplasma and Spiroplasma are genera 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 most other bacteria. They are normally transmitted by sap-sucking insects, being transferred into the plant's phloem where it reproduces.
There are many types of plant virus, and some are even asymptomatic. Under normal circumstances, plant viruses cause only a loss of crop 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. However some plant viruses also have double stranded RNA or single or double stranded DNA genomes. These genomes may encode only three or four proteins: a replicase, a coat protein, a movement protein, in order to allow cell to cell movement through plasmodesmata, and sometimes a protein that allows transmission by a vector. Plant viruses can have several more proteins and employ many different molecular translation methods.
Plant viruses are generally transmitted from plant to plant by a vector, but mechanical and seed transmission also occur. Vector transmission is often by an insect (for example, aphids), but some fungi, nematodes, and protozoa have been shown to be viral vectors. In many cases, the insect and virus are specific for virus transmission such as the beet leafhopper that transmits the curly top virus causing disease in several crop plants.
Nematodes are small, multicellular wormlike animals. Many live freely in the soil, but there are some species that parasitize plant roots. They are a problem in tropical and subtropical regions of the world, where they may infect crops. Potato cyst nematodes (Globodera pallida and G. rostochiensis) are widely distributed in Europe and North and South America and cause worth of damage in Europe every year. Root knot nematodes have quite a large host range, they parasitize plant root systems and thus directly affect the uptake of water and nutrients needed for normal plant growth and reproduction, whereas cyst nematodes tend to be able to infect only a few species. Nematodes are able to cause radical changes in root cells in order to facilitate their lifestyle.
There are a few examples of plant diseases caused by protozoa (e.g., Phytomonas, a kinetoplastid). They are transmitted as durable zoospores that may be able to survive in a resting state in the soil for many years. Further, they can transmit plant viruses. When the motile zoospores come into contact with a root hair they produce a plasmodium which invades the roots.
Parasitic plants such as mistletoe and dodder are included in the study of phytopathology. Dodder, for example, is used as a conduit either for the transmission of viruses or virus-like agents from a host plant to a plant that is not typically a host or for an agent that is not graft-transmissible.
Spores: Spores of phytopathogenic fungi can be a source of infection on host plants. Spores first adhere to the cuticular layer on leaves and stems of host plant. In order for this to happen the infectious spore must be transported from the pathogen source, this occurs via wind, water, and vectors such as insects and humans. When favourable conditions are present, the spore will produce a modified hyphae called a germ tube. This germ tube later forms a bulge called an appressorium, which forms melanized cell walls to build up tugour pressure. Once enough turgor pressure is accumulated the appressorium asserts pressure against the cuticular layer in the form of a hardened penetration peg. This process is also aided by the secretion of cell wall degrading enzymes from the appressorium. Once the penetration peg enters the host tissue it develops a specialized hyphae called a haustorium. Based on the pathogens life cycle, this haustorium can invade and feed neighbouring cells intracellularly or exist intercellulary within a host.
Abiotic disorders can be caused by natural processes such as drought, frost, snow and hail; flooding and poor drainage; nutrient deficiency; deposition of mineral salts such as sodium chloride and gypsum; windburn and breakage by storms; and wildfires. Similar disorders (usually classed as abiotic) can be caused by human intervention, resulting in soil compaction, pollution of air and soil, salinisation caused by irrigation and road salting, over-application of herbicides, clumsy handling (e.g. lawnmower damage to trees), and vandalism.
Epidemiology: The study of factors affecting the outbreak and spread of infectious diseases.
A disease tetrahedron (disease pyramid) best captures the elements involved with plant diseases. This pyramid uses the disease triangle as a foundation, consisting of elements such as: host, pathogen and environment. In addition to these three elements, humans and time add the remaining elements to create a disease tetrahedron.
History: Plant disease epidemics that are historically known based on tremendous losses:
- Irish potato late blight
- Dutch elm disease 
- Chestnut blight in North America
Factors affecting epidemics:
Host: Resistance or susceptibility level, age and genetics.
Pathogen: Amount of inoculum, genetics, and type of reproduction
Plant disease resistance is the ability of a plant to prevent and terminate infections from plant pathogens.
Structures that help plants prevent disease are: cuticular layer, cell walls and stomata guard cells. These act as a barrier to prevent pathogens from entering the plant host.
Once diseases have over come these barriers, plant receptors initiate signalling pathways to create molecules to compete against the foreign molecules. These pathways are influenced and triggered by genes within the host plant and are susceptible to being manipulated by genetic breeding to create varieties of plants that are resistant to destructive pathogens.
Plant pathology has developed from antiquity, starting with Theophrastus, but scientific study began in the Early Modern period with the invention of the microscope, and developed in the 19th century.
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