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 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 the Great Famine of Ireland 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. It 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 application of pesticides. Continuing advances in the science of plant pathology are needed to improve disease control, to keep up with the ongoing evolution and movement of plant pathogens, and to keep pace with changes in agricultural practices.
Plant diseases cause major economic losses for farmers worldwide - see §Economic impact. 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. The Food and Agriculture Organization estimates that pests and diseases are responsible for about 25% of crop loss. To solve this, 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.
In most pathosystems, virulence is dependent on hydrolases - and the wider class of cell wall degrading proteins - that degrade the cell wall. The vast majority of CWDPs are pathogen-produced and pectin-targeted (for example, pectinesterase, pectate lyase, and pectinases). For microbes the cell wall polysaccharides are themselves a food source, but mostly just a barrier to be overcome.
Many pathogens also grow opportunistically when the host breaks down its own cell walls, most often during fruit ripening.
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 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:[ citation needed ]
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.
Bacteria control the production of pathogenicity factors via quorum sensing.
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 es, 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.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.
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, 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.
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.
Some colourless parasitic algae (e.g., Cephaleuros ) also cause plant diseases.[ citation needed ]
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.
Some abiotic disorders can be confused with pathogen-induced disorders. Abiotic causes include 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, salinization caused by irrigation and road salting, over-application of herbicides, clumsy handling (e.g. lawnmower damage to trees), and vandalism.[ citation needed ]
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 overcome these barriers, plant receptors initiate signaling 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.
Among defense mechanisms, chemical deterrence of pest settling and feeding, like the induction of defensive compounds, may be a key strategy for reducing herbivore damage.
Before control measures can be taken, the pathogen must be detected. Ancient methods of leaf examination and breaking open plant material by hand are now augmented by newer technologies. These include molecular pathology assays such as polymerase chain reaction (PCR), RT-PCR and loop-mediated isothermal amplification (LAMP).Although PCR can detect multiple molecular targets in a single solution there are limits. Bertolini et al 2001, Ito et al 2002 and Ragozzino et al 2004 developed PCR methods for multiplexing six or seven plant pathogen molecular products and Persson et al 2005 for multiplexing four with RT-PCR. More extensive molecular diagnosis requires PCR arrays.
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.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. 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.
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.
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.[ citation needed ]
The use of two or more of these methods in combination offers a higher chance of effectiveness.
As of 2018 [update] the most costly diseases of the most produced crops worldwide are:
|Crop||Disease Latin name||Disease common name|
|Banana and plaintain||banana bunchy top virus (BBTV)||banana bunchy top|
|Mycosphaerella fijiensis||black sigatoka|
|Fusarium oxysporum f.sp. cubense||Panama disease|
|Barley||Fusarium graminearum||Fusarium head blight|
|Blumeria graminis f. sp. hordei||powdery mildew|
|Puccinia graminis f. sp. hordei||barley stem rust|
|Cassava||African cassava mosaic virus (ACMVD)||African cassava mosaic disease|
|Xanthomonas axonopodis pv. manihotis||bacterial blight|
|cassava brown streak virus (CBSV)||cassava brown streak disease|
|Cotton||Xanthomonas citri pv. malvacearum||bacterial blight|
|Fusarium oxysporum f. sp. vasinfectum||Fusarium wilt|
|Verticillium dahliae||Verticillium wilt|
|Maize/corn||Aspergillus flavus||Aspergillus ear rot|
|Fusarium graminearum||Giberella stalk and ear rot|
|Cercospora zeae-maydis||grey leaf spot|
|Palm fruit||Ganoderma orbiforme/Ganoderma boninense||Basal stem rot|
|Phytophthora palmivora||bud rot|
|Peanut||groundnut rosette virus (GNV)||Groundnut rosette disease|
|GNV satellite RNA|
|groundnut rosette assistor virus (GRAV)|
|Potato||Ralstonia solanacearum||Potato brown rot|
|Phytophthora infestans||late blight|
|Rapeseed and mustard||Leptosphaeria maculans||Phoma stem canker|
|Sclerotinia sclerotiorum||Sclerotinia stem rot|
|Rice||Magnaporthe oryzae||rice blast|
|Xanthomonas oryzae pv. oryzae||rice bacterial blight|
|Rhizoctonia solani||sheath blight|
|Sorghum and millet||Colletotrichum sublineolum||Anthracnose|
|Exserohilum turcicum||Turcicum leaf blight|
|Soybean||Heterodera glycines||soybean cyst nematode disease|
|Phakopsora pachyrhizi||Asian soybean rust|
|Sugar beet||Cercospora beticola||Cercospora leaf spot|
|beet necrotic yellow vein virus (BNYVV)||rhizomania|
|Sugarcane||Leifsonia xyli subsp. xyli||Ratoon stunting|
|Colletotrichum falcatum||red rot|
|Sweet potato||sweet potato feathery mottle virus (SPFMV)||sweet potato virus disease (SPVD)|
|sweet potato chlorotic stunt virus (SPCSV)|
|Tomato||Phytophthora infestans||late blight|
|tomato yellow leaf curl virus (TYLCV)||tomato yellow leaf curl|
|Wheat||Fusarium graminearum||Fusarium head blight|
|Puccinia graminis||wheat stem rust|
|Puccinia striiformis||wheat yellow rust|
|yam mosaic virus (YMV)||yam mosaic disease|
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.
This section needs expansion. You can help by adding to it. (July 2017)
Oomycota forms a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, called oomycetes. They are filamentous and heterotrophic, and can reproduce both sexually and asexually. Sexual reproduction of an oospore is the result of contact between hyphae of male antheridia and female oogonia; these spores can overwinter and are known as resting spores. Asexual reproduction involves the formation of chlamydospores and sporangia, producing motile zoospores. Oomycetes occupy both saprophytic and pathogenic lifestyles, and include some of the most notorious pathogens of plants, causing devastating diseases such as late blight of potato and sudden oak death. One oomycete, the mycoparasite Pythium oligandrum, is used for biocontrol, attacking plant pathogenic fungi. The oomycetes are also often referred to as water molds, although the water-preferring nature which led to that name is not true of most species, which are terrestrial pathogens.
Fungicides are biocidal chemical compounds or biological organisms used to kill parasitic fungi or their spores. A fungistatic inhibits their growth. Fungi can cause serious damage in agriculture, resulting in critical losses of yield, quality, and profit. Fungicides are used both in agriculture and to fight fungal infections in animals. Chemicals used to control oomycetes, which are not fungi, are also referred to as fungicides, as oomycetes use the same mechanisms as fungi to infect plants. Fungicides can either be contact, translaminar or systemic. Contact fungicides are not taken up into the plant tissue and protect only the plant where the spray is deposited. Translaminar fungicides redistribute the fungicide from the upper, sprayed leaf surface to the lower, unsprayed surface. Systemic fungicides are taken up and redistributed through the xylem vessels. Few fungicides move to all parts of a plant. Some are locally systemic, and some move upwardly.
A leaf spot is a limited, discoloured, diseased area of a leaf that is caused by fungal, bacterial or viral plant diseases, or by injuries from nematodes, insects, environmental factors, toxicity or herbicides. These discoloured spots or lesions often have a centre of necrosis or cell death. Symptoms can overlap across causal agents, however differing signs and symptoms of certain pathogens can lead to the diagnosis of the type of leaf spot disease. Prolonged wet and humid conditions promote leaf spot disease and most pathogens are spread by wind, splashing rain or irrigation that carry the disease to other leaves.
Biopesticides, a contraction of 'biological pesticides', include several types of pest management intervention: through predatory, parasitic, or chemical relationships. The term has been associated historically with biological pest control – and by implication, the manipulation of living organisms. Regulatory positions can be influenced by public perceptions, thus:
This is a glossary of some of the terms used in phytopathology.
Damping off is a horticultural disease or condition, caused by several different pathogens that kill or weaken seeds or seedlings before or after they germinate. It is most prevalent in wet and cool conditions.
Thielaviopsis basicola is the plant-pathogen fungus responsible for black root rot disease. This particular disease has a large host range, affecting woody ornamentals, herbaceous ornamentals, agronomic crops, and even vegetable crops. Examples of susceptible hosts include petunia, pansy, poinsettia, tobacco, cotton, carrot, lettuce, tomato, and others. Symptoms of this disease resemble nutrient deficiency but are truly a result of the decaying root systems of plants. Common symptoms include chlorotic lower foliage, yellowing of plant, stunting or wilting, and black lesions along the roots. The lesions along the roots may appear red at first, getting darker and turning black as the disease progresses. Black root lesions that begin in the middle of a root can also spread further along the roots in either direction. Due to the nature of the pathogen, the disease can easily be identified by the black lesions along the roots, especially when compared to healthy roots. The black lesions that appear along the roots are a result of the formation of chlamydospores, resting spores of the fungus that contribute to its pathogenicity. The chlamydospores are a dark brown-black color and cause the "discoloration" of the roots when they are produced in large amounts.
Pythium irregulare is a soil borne oomycete plant pathogen. Oomycetes, also known as "water molds", are fungal-like protists. They are fungal-like because of their similar life cycles, but differ in that the resting stage is diploid, they have coenocytic hyphae, a larger genome, cellulose in their cell walls instead of chitin, and contain zoospores and oospores.
Pythium ultimum is a plant pathogen. It causes the damping off and root rot diseases of hundreds of diverse plant hosts including corn, soybean, potato, wheat, fir, and many ornamental species. P. ultimum belongs to the peronosporalean lineage of oomycetes, along with other important plant pathogens such as Phytophthora spp. and many genera of downy mildews. P. ultimum is a frequent inhabitant of fields, freshwater ponds, and decomposing vegetation in most areas of the world. Contributing to the widespread distribution and persistence of P. ultimum is its ability to grow saprotrophically in soil and plant residue. This trait is also exhibited by most Pythium spp. but not by the related Phytophthora spp., which can only colonize living plant hosts.
Alternaria solani is a fungal pathogen that produces a disease in tomato and potato plants called early blight. The pathogen produces distinctive "bullseye" patterned leaf spots and can also cause stem lesions and fruit rot on tomato and tuber blight on potato. Despite the name "early," foliar symptoms usually occur on older leaves. If uncontrolled, early blight can cause significant yield reductions. Primary methods of controlling this disease include preventing long periods of wetness on leaf surfaces and applying fungicides. Early blight can also be caused by Alternaria tomatophila, which is more virulent on stems and leaves of tomato plants than Alternaria solani.
Melampsora lini is a species of fungus and plant pathogen found in Ireland and commonly known as flax rust.
Meloidogyne javanica is a species of plant-pathogenic nematodes. It is one of the tropical root-knot nematodes and a major agricultural pest in many countries. It has many hosts. Meloidogyne javanica reproduces by obligatory mitotic parthenogenesis (apomixis).
Plant disease epidemiology is the study of disease in plant populations. Much like diseases of humans and other animals, plant diseases occur due to pathogens such as bacteria, viruses, fungi, oomycetes, nematodes, phytoplasmas, protozoa, and parasitic plants. Plant disease epidemiologists strive for an understanding of the cause and effects of disease and develop strategies to intervene in situations where crop losses may occur. Destructive and non-destructive methods are used to detect diseases in plants. Additionally, understanding the responses of the immune system in plants will further benefit and limit the loss of crops. Typically successful intervention will lead to a low enough level of disease to be acceptable, depending upon the value of the crop.
A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from the other eukaryotic kingdoms, which by one traditional classification include Plantae, Animalia, Protozoa, and Chromista.
Biotic stress is stress that occurs as a result of damage done to an organism by other living organisms, such as bacteria, viruses, fungi, parasites, beneficial and harmful insects, weeds, and cultivated or native plants. It is different from abiotic stress, which is the negative impact of non-living factors on the organisms such as temperature, sunlight, wind, salinity, flooding and drought. The types of biotic stresses imposed on an organism depend the climate where it lives as well as the species' ability to resist particular stresses. Biotic stress remains a broadly defined term and those who study it face many challenges, such as the greater difficulty in controlling biotic stresses in an experimental context compared to abiotic stress.
Plant disease resistance protects plants from pathogens in two ways: by pre-formed structures and chemicals, and by infection-induced responses of the immune system. Relative to a susceptible plant, disease resistance is the reduction of pathogen growth on or in the plant, while the term disease tolerance describes plants that exhibit little disease damage despite substantial pathogen levels. Disease outcome is determined by the three-way interaction of the pathogen, the plant and the environmental conditions.
Forest pathology is the research of both biotic and abiotic maladies affecting the health of a forest ecosystem, primarily fungal pathogens and their insect vectors. It is a subfield of forestry and plant pathology.
In biology, a pathogen in the oldest and broadest sense, is any organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.
Alternaria brassicicola is a fungal necrotrophic plant pathogen that causes black spot disease on a wide range of hosts, particularly in the genus of Brassica, including a number of economically important crops such as cabbage, Chinese cabbage, cauliflower, oilseeds, broccoli and canola. Although mainly known as a significant plant pathogen, it also contributes to various respiratory allergic conditions such as asthma and rhinoconjunctivitis. Despite the presence of mating genes, no sexual reproductive stage has been reported for this fungus. In terms of geography, it is most likely to be found in tropical and sub-tropical regions, but also in places with high rain and humidity such as Poland. It has also been found in Taiwan and Israel. Its main mode of propagation is vegetative. The resulting conidia reside in the soil, air and water. These spores are extremely resilient and can overwinter on crop debris and overwintering herbaceous plants.
Hemibiotrophs are the spectrum of plant pathogens, including bacteria, oomycete and a group of plant pathogenic fungi that keep its host alive while establishing itself within the host tissue, taking up the nutrients with brief biotrophic-like phase. It then, in later stages of infection switches to a necrotrophic life-style, where it rampantly kills the host cells, deriving its nutrients from the dead tissues.