Plant pathology

Most phytopathogenic fungi belong to the phyla Ascomycota and Basidiomycota. 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 soil borne. 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:

Rice blast, caused by a necrotrophic fungus

• Fusarium spp. (Fusarium wilt disease)
• Thielaviopsis spp. (canker rot, black root rot, Thielaviopsis root rot)
• Verticillium spp.
• Magnaporthe grisea (rice blast)
• Sclerotinia sclerotiorum (cottony rot)

• Ustilago spp. (smuts) smut of barley
• Rhizoctonia spp.
• Phakospora pachyrhizi (soybean rust)
• Puccinia spp. (severe rusts of cereals and grasses)
• Armillaria spp. (honey fungus species, virulent pathogens of trees)

The oomycetes are fungus-like organisms.[5] They include some of the most destructive plant pathogens including the genus Phytophthora, which includes the causal agents of potato late blight[5] and sudden oak death.[6][7] 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.[8] Plant pathologists commonly group them with fungal pathogens.

Significant oomycete plant pathogens include:

• Pythium spp.
• Phytophthora spp., including the potato blight of the Great Irish Famine (1845–1849)

Some slime molds in Phytomyxea cause important diseases, including clubroot in cabbage and its relatives and powdery scab in potatoes. These are caused by species of Plasmodiophora and Spongospora, respectively.

Crown gall disease caused by Agrobacterium

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.[9] 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.

Bacteria control the production of pathogenicity factors via quorum sensing.

Vitis vinifera with "Ca. Phytoplasma vitis" infection

Significant bacterial plant pathogens:

• Burkholderia[10]
• Pseudomonadota
  • Xanthomonas spp.
  • Pseudomonas spp.
• Pseudomonas syringae pv. tomato causes tomato plants to produce less fruit, and it "continues to adapt to the tomato by minimizing its recognition by the tomato immune system."[11]

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.

Tobacco mosaic virus

There are many types of plant viruses, and some are asymptomatic or latent. 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.[12] One example is mosaic disease of tobacco where leaves are dwarfed and the chlorophyll of the leaves is destroyed. Another example is Bunchy top of banana, where the plant is dwarfed, and the upper leaves form a tight rosette.

Root-knot nematode galls

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 $300 million 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,[13] 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 also beneficial nematodes that can be used as a biological control for crop-destroying pests. A promising example is the effectiveness of the nematode Steinernema rarium PAM25 against the Drosophila suzuki, a type of fruit fly.[14]

There are a few examples of plant diseases caused by protozoa (e.g., Phytomonas, a kinetoplastid).[15] 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.

Some colourless parasitic algae (e.g., Cephaleuros) also cause plant diseases.

Parasitic plants such as broomrape, mistletoe and dodder are included in the study of phytopathology. Dodder, for example, can be a conduit 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.

A diseased patch of vegetation or individual plants can be isolated from other, healthy growth. Specimens may be destroyed or relocated into a greenhouse for treatment or study.

Another option is to avoid the introduction of harmful nonnative organisms by controlling all human traffic and activity (e.g., the Australian Quarantine and Inspection Service), although legislation and enforcement are crucial in order to ensure lasting effectiveness. Today's volume of global trade is providing—and will continue to provide—unprecedented opportunities for the introduction of plant pests.[McC 1] In the United States, even to get a better estimate of the number of such introductions, and thus the need to impose port and border quarantine and inspection, would require a substantial increase in inspections.[McC 2] In Australia a similar shortcoming of understanding has a different origin: Port inspections are not very useful because inspectors know too little about taxonomy. There are often pests that the Australian Government has prioritised as harmful to be kept out of the country, but which have near taxonomic relatives that confuse the issue. And inspectors also run into the opposite - harmless natives, or undiscovered natives, or just-discovered natives they need not bother with but which are easy to confuse with their outlawed foreign family members.[BH 1]

X-ray and electron-beam/E-beam irradiation of food has been trialed as a quarantine treatment for fruit commodities originating from Hawaii. The US FDA (Food and Drug Administration), USDA APHIS (Animal and Plant Health Inspection Service), producers, and consumers were all accepting of the results - more thorough pest eradication and lesser taste degradation than heat treatment.[24]

The International Plant Protection Convention (IPPC) anticipates that molecular diagnostics for inspections will continue to improve.[25] Between 2020 and 2030, IPPC expects continued technological improvement to lower costs and improve performance, albeit not for less developed countries unless funding changes.[25]

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 from not only active external protection but also a greater overall vigor. While primitive in the sense of being the most labor-intensive solution by far, where practical or necessary it is more than adequate.

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.

Many natural and synthetic compounds can 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.

Crop rotation may be an effective means to prevent a parasitic population from becoming well-established. For example, protection against infection by Agrobacterium tumefaciens, which causes gall diseases in many plants, by dipping cuttings in suspensions of Agrobacterium radiobacter before inserting them in the ground to take root. Other means to undermine parasites without attacking them directly may exist.

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