Plant pathology

Life cycle of the black rot pathogen, Xanthomonas campestris pathovar campes

Plant pathology (also phytopathology) is the scientific study of diseases in plants caused by pathogens (infectious organisms) and environmental conditions (physiological factors).^[1] 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 consumption 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.

Overview

Control of plant diseases is crucial to the reliable production of food, and it provides significant reductions 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 (see Irish potato famine, chestnut blight), as well as recurrent severe plant diseases (see rice blast, soybean cyst nematode, 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 diagnostic plant health and metabolism.^[2]

Plant pathogens

Powdery mildew, a biotrophic fungus

Fungi

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 known as 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. See the powdery mildew and rice blast images, below.

Rice blast, caused by a necrotrophic fungus

Significant fungal plant pathogens include:

Ascomycetes

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

Basidiomycetes

• Ustilago spp. (causal agents of smut)
• Rhizoctonia spp.
• Phakospora pachyrhizi (causal agent of soybean rust)
• Puccinia spp. (causal agents of severe rusts of virtually all cereal grains and cultivated grasses)
• Armillaria spp. (the so-called honey fungus species, which are virulent pathogens of trees and produce edible mushrooms)

Fungus-like organisms

Oomycetes

The oomycetes are not true fungi but are fungus-like organisms.^[3] They include some of the most destructive plant pathogens including the genus Phytophthora, which includes the causal agents of potato late blight^[3] and sudden oak death.^[4][5] Particular species of oomycetes are responsible for root rot.

Despite not being closely related to the fungi, the oomycetes have developed very similar infection strategies. Oomycetes are capable of using effector proteins to turn off a plant's defenses in its infection process.^[6] Plant pathologists commonly group them with fungal pathogens.

Significant oomycete plant pathogens

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

Phytomyxea

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.

Bacteria

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.^[7] 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^[8]
• Proteobacteria
  • 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."^[9]

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 most other bacteria. They are normally transmitted by sap-sucking insects, being transferred into the plants phloem where it reproduces.

Tobacco mosaic virus

Viruses, viroids and virus-like organisms

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.^[10]

Nematodes

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, 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.

Protozoa and algae

There are a few examples of plant diseases caused by protozoa (e.g., Phytomonas, a kinetoplastid).^[11] They are transmitted as zoospores that 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.

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

Parasitic plants

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.

Common pathogenic infection methods

• Cell wall-degrading enzymes: These are used to break down the plant cell wall in order to release the nutrients inside.
• Toxins: These can be non-host-specific, which damage all plants, or host-specific, which cause damage only on a host plant.
• Effector proteins: These can be secreted into the extracellular environment or directly into the host cell, often via the Type three secretion system. Some effectors are known to suppress host defense processes. This can include: reducing the plants internal signaling mechanisms or reduction of phytochemicals production.^[12] Bacteria, fungus and oomycetes are known for this function.^[3][13]

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, soil, or both

Salt from winter road salt application or irrigation

Herbicide over-application

Poor education and training of people working with plants (e.g. lawnmower damage to trees)

Vandalism

Orchid leaves with viral infections

Epidemiology

Disease resistance

Management

Quarantine

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., AQIS), although legislation and enforcement are crucial 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 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.

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

(See: pesticide application) 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.

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.

Timeline of plant pathology

300–286 BC Theophrastus, father of botany, wrote and studied diseases of trees, cereals and legumes^[14]

1665 Robert Hooke illustrates a plant-pathogenic fungal disease, rose rust

1675 Anton van Leeuwenhouek invents the compound microscope, in 1683 describes bacteria seen with the microscope^[14]

1729 Pier Antonio Micheli, father of mycology, observes spores for the first time, conducts germination experiments^[14]

1755 Tillet reports on treatment of seeds^[14]

1802 Lime sulfur first used to control plant disease

1845–1849 Potato late blight epidemic in Ireland

1853 Heinrich Anton de Bary father of modern mycology, establishes that fungi are the cause, not the result, of plant diseases,^[14] publishes "Untersuchungen uber die Brandpilze"

1858 Julius Kühn publishes "Die Krankheiten der Kultergewachse"

1865 M. Planchon discovers a new species of Phylloxera, which was named Phylloxera vastatrix.^[15]

1868–1882 Coffee rust epidemic in Sri Lanka

1875 Mikhail Woronin identified the cause of clubroot as a "plasmodiophorous organism" and gave it the name Plasmodiophora brassicae

1876 Fusarium oxysporum f.sp. cubense, responsible for Panama disease, discovered in bananas in Australia^[16]

1878–1885 Downy mildew of grape epidemic in France

1879 Robert Koch establishes germ theory: diseases are caused by microorganisms^[14]

1882 Lehrbuch der Baumkrankheiten (Textbook of Diseases of Trees), by Robert Hartig, is published in Berlin, the first textbook of forest pathology.

1885 Bordeaux mixture introduced by Pierre-Marie-Alexis Millardet to control downy mildew on grape

1885 Experimental proof that bacteria can cause plant diseases: "Erwinia amylovora" and fire blight of apple

1886–1898 Recognition of plant viral diseases: Tobacco mosaic virus

1889 Introduction of hot water treatment of seed for disease control by Jensen

1902 First chair of plant pathology established, in Copenhagen

1904 Mendelian inheritance of cereal rust resistance demonstrated

1907 First academic department of plant pathology established, at Cornell University

1908 American Phytopathological Society founded

1910 Panama disease reaches Western Hemisphere ^[16]

1911 Scientific journal Phytopathology founded

1925 Panama disease reaches every banana-growing country in the Western Hemisphere^[16]

1951 European and Mediterranean Plant Protection Organization (EPPO) founded

1967 Recognition of plant pathogenic mycoplasma-like organisms

1971 T. O. Diener discovers viroids, organisms smaller than viruses^[17]

The historical landmarks in plant pathology are taken from^[18] unless otherwise noted.

See also

References

External links

• International Society for Plant Pathology
• Australasian Plant Pathology Society
• American Phytopathological Society
• British Society for Plant Pathology
• Food Security Journal
• Contributions toward a bibliography of peach yellows, 1887–1888 Digital copy of scientist Erwin Frink Smith's manuscript on peach yellows disease.
• Erwin Frink Smith Papers Index to papers of Smith (1854–1927) who was considered the "father of bacterial plant pathology" and worked for the United States Department of Agriculture for over 40 years.
• Plant Health Progress, Online journal of applied plant pathology
• Pacific Northwest Fungi, online mycology journal with papers on fungal plant pathogens
• Rothamsted Plant Pathology and Microbiology Department
• New Mexico State University Department of Entomology Plant Pathology and Weed Science
• Pathogen Host Interactions Database (PHI-base)
• Grape Virology
• Opportunity in Plant Pathology
• Facebook page for Asian Association of Societies for Plant Pathology