Plant pathology or phytopathology is the scientific study of plant diseases caused by pathogens (infectious organisms) and environmental conditions (physiological factors). [1] Plant pathology 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.
Plant pathogens, organisms that cause infectious plant diseases, include fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms, phytoplasmas, protozoa, nematodes and parasitic plants. [2] In most plant pathosystems, virulence depends on hydrolases and enzymes that degrade the cell wall. The vast majority of these act on pectins (for example, pectinesterase, pectate lyase, and pectinases). For microbes, the cell wall polysaccharides are both a food source and a barrier to be overcome. Many pathogens grow opportunistically when the host breaks down its own cell walls, most often during fruit ripening. [3] Unlike human and animal pathology, plant pathology usually focuses on a single causal organism; however, some plant diseases have been shown to be interactions between multiple pathogens. [4]
To colonize a plant, pathogens have specific pathogenicity factors, of five main types: uses of cell wall–degrading enzymes, toxins, effector proteins, phytohormones, and exopolysaccharides.
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. [9]
Epidemiology is the study of factors affecting the outbreak and spread of infectious diseases. [10]
A disease triangle describes the basic factors required for plant diseases. These are the host plant, the pathogen, and the environment. Any one of these can be modified to control a disease. [11]
Plant disease resistance is the ability of a plant to prevent and terminate infections from plant pathogens. Structures that help plants prevent pathogens from entering are the cuticular layer, cell walls and stomata guard cells. Once pathogens 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 can manipulated by genetic breeding to create resistant varieties. [12]
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). [13] Although PCR can detect multiple molecular targets in a single solution there are limits. [13] 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. [13] More extensive molecular diagnosis requires PCR arrays. [13] The primary detection method used worldwide is enzyme linked immunosorbent assay. [14]
Crop rotation is a traditional and sometimes effective means of preventing 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. [15]
Plant pathology has developed from antiquity, starting with Theophrastus in the ancient era, but scientific study began in the Early Modern period with the invention of the microscope, and developed in the 19th century. [16]
Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are caused by the insertion of a small segment of DNA, from a plasmid into the plant cell, which is incorporated at a semi-random location into the plant genome. Plant genomes can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors.
The transfer DNA is the transferred DNA of the tumor-inducing (Ti) plasmid of some species of bacteria such as Agrobacterium tumefaciens and Agrobacterium rhizogenes . The T-DNA is transferred from bacterium into the host plant's nuclear DNA genome. The capability of this specialized tumor-inducing (Ti) plasmid is attributed to two essential regions required for DNA transfer to the host cell. The T-DNA is bordered by 25-base-pair repeats on each end. Transfer is initiated at the right border and terminated at the left border and requires the vir genes of the Ti plasmid.
Plant diseases are diseases in plants caused by pathogens and environmental conditions. 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, vertebrates, or other pests that affect plant health by eating plant tissues and causing injury that may admit plant pathogens. The study of plant disease is called plant pathology.
Phytoplasmas are obligate intracellular parasites of plant phloem tissue and of the insect vectors that are involved in their plant-to-plant transmission. Phytoplasmas were discovered in 1967 by Japanese scientists who termed them mycoplasma-like organisms. Since their discovery, phytoplasmas have resisted all attempts at in vitro culture in any cell-free medium; routine cultivation in an artificial medium thus remains a major challenge. Phytoplasmas are characterized by the lack of a cell wall, a pleiomorphic or filamentous shape, a diameter normally less than 1 μm, and a very small genome.
Magnaporthe grisea, also known as rice blast fungus, rice rotten neck, rice seedling blight, blast of rice, oval leaf spot of graminea, pitting disease, ryegrass blast, Johnson spot, neck blast, wheat blast and Imochi (稲熱), is a plant-pathogenic fungus and model organism that causes a serious disease affecting rice. It is now known that M. grisea consists of a cryptic species complex containing at least two biological species that have clear genetic differences and do not interbreed. Complex members isolated from Digitaria have been more narrowly defined as M. grisea. The remaining members of the complex isolated from rice and a variety of other hosts have been renamed Magnaporthe oryzae, within the same M. grisea complex. Confusion on which of these two names to use for the rice blast pathogen remains, as both are now used by different authors.
Dickeya dadantii is a gram-negative bacillus that belongs to the family Pectobacteriaceae. It was formerly known as Erwinia chrysanthemi but was reassigned as Dickeya dadantii in 2005. Members of this family are facultative anaerobes, able to ferment sugars to lactic acid, have nitrate reductase, but lack oxidases. Even though many clinical pathogens are part of the order Enterobacterales, most members of this family are plant pathogens. D. dadantii is a motile, nonsporing, straight rod-shaped cell with rounded ends, much like the other members of the genus, Dickeya. Cells range in size from 0.8 to 3.2 μm by 0.5 to 0.8 μm and are surrounded by numerous flagella (peritrichous).
In phytopathology, antagonism refers to the action of any organism that suppresses or interferes with the normal growth and activity of a plant pathogen, such as the main parts of bacteria or fungi.
Medical microbiology, the large subset of microbiology that is applied to medicine, is a branch of medical science concerned with the prevention, diagnosis and treatment of infectious diseases. In addition, this field of science studies various clinical applications of microbes for the improvement of health. There are four kinds of microorganisms that cause infectious disease: bacteria, fungi, parasites and viruses, and one type of infectious protein called prion.
Pantoea agglomerans is a Gram-negative bacterium that belongs to the family Erwiniaceae.
Curtobacterium flaccumfaciens is a Gram-positive bacterium that causes disease on a variety of plants. Gram-positive bacteria characteristics include small irregular rods, lateral flagella, the ability to persist in aerobic environments, and cells containing catalase. In the interest of studying pathogenicity in plants, this species is broken down further into pathovars, which help to better describe the pathogen.
Pythium myriotylum is a soil-borne oomycete necrotroph that has a broad host range, this means that it can infect a wide range of plants.
Pectobacterium carotovorum is a bacterium of the family Pectobacteriaceae; it used to be a member of the genus Erwinia.
Alternaria citri is a fungal plant pathogen that causes black rot in citrus plants.
Pythium sulcatum is a chromalveolate plant pathogen infecting carrots. Because this organism was once thought to be a type of fungus, it is still often treated as such.
Extracellular polymeric substances (EPSs) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPSs establish the functional and structural integrity of biofilms, and are considered the fundamental component that determines the physicochemical properties of a biofilm. EPS in the matrix of biofilms provides compositional support and protection of microbial communities from the harsh environments. Components of EPS can be of different classes of polysaccharides, lipids, nucleic acids, proteins, lipopolysaccharides, and minerals.
Resistance genes (R-Genes) are genes in plant genomes that convey plant disease resistance against pathogens by producing R proteins. The main class of R-genes consist of a nucleotide binding domain (NB) and a leucine rich repeat (LRR) domain(s) and are often referred to as (NB-LRR) R-genes or NLRs. Generally, the NB domain binds either ATP/ADP or GTP/GDP. The LRR domain is often involved in protein-protein interactions as well as ligand binding. NB-LRR R-genes can be further subdivided into toll interleukin 1 receptor (TIR-NB-LRR) and coiled-coil (CC-NB-LRR).
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.
In biology, a pathogen, in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.
Tsune Kosuge was an American plant pathologist and plant biochemist who researched plant–microbe interactions. He was particularly known for his work on bacterial-synthesized plant hormones in plant tumors. He was a professor in the department of plant pathology at the University of California, Davis, from 1971 until his death, serving as departmental chair (1974–80).
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