Plant disease epidemiology is the study of disease in plant populations. Much like

disease A disease is a particular abnormal condition that negatively affects the structure or function of all or part of an organism, and that is not immediately due to any external injury. Diseases are often known to be medical conditions that a ...

s of humans and other animals,

plant diseases 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, oomy ...

occur due to pathogens such as

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

viruses A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

fungi A fungus ( : fungi or funguses) 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 ...

oomycetes 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 ...

nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant-Parasitism, parasitic nematodes also known as eelworms. They are a diverse animal phylum inhab ...

phytoplasmas 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-lik ...

protozoa Protozoa (singular: protozoan or protozoon; alternative plural: protozoans) are a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris. Histo ...

, and

parasitic plant A parasitic plant is a plant that derives some or all of its nutritional requirements from another living plant. They make up about 1% of angiosperms and are found in almost every biome. All parasitic plants develop a specialized organ called the ...

s. 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. Plant disease epidemiology is often looked at from a multi-disciplinary approach, requiring

biological Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary in ...

statistical Statistics (from German: ''Statistik'', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industria ...

agronomic Agricultural economics is an applied field of economics concerned with the application of economic theory in optimizing the production and distribution of food and fiber products. Agricultural economics began as a branch of economics that spe ...

and

ecological Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps wi ...

perspectives. Biology is necessary for understanding the pathogen and its life cycle. It is also necessary for understanding the physiology of the crop and how the pathogen is adversely affecting it. Agronomic practices often influence disease incidence for better or for worse. Ecological influences are numerous. Native species of plants may serve as reservoirs for pathogens that cause disease in crops.

Statistical model A statistical model is a mathematical model that embodies a set of statistical assumptions concerning the generation of Sample (statistics), sample data (and similar data from a larger Statistical population, population). A statistical model repres ...

s are often applied in order to summarize and describe the complexity of plant disease epidemiology, so that disease processes can be more readily understood. For example, comparisons between patterns of disease progress for different diseases, cultivars, management strategies, or environmental settings can help in determining how plant diseases may best be managed.

Policy Policy is a deliberate system of guidelines to guide decisions and achieve rational outcomes. A policy is a statement of intent and is implemented as a procedure or protocol. Policies are generally adopted by a governance body within an organ ...

can be influential in the occurrence of diseases, through actions such as restrictions on imports from sources where a disease occurs. In 1963 J. E. van der Plank published "Plant Diseases: Epidemics and Control", a seminal work that created a theoretical framework for the study of the epidemiology of plant diseases. This book provides a theoretical framework based on experiments in many different host pathogen systems and moved the study of plant disease epidemiology forward rapidly, especially for fungal foliar pathogens. Using this framework we can now model and determine thresholds for epidemics that take place in a homogeneous environment such as a mono-cultural crop field.

Elements of an epidemic

Disease epidemics in plants can cause huge losses in yield of crops as well threatening to wipe out an entire

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

such as was the case with

Dutch Elm Disease Dutch elm disease (DED) is caused by a member of the sac fungi (Ascomycota) affecting elm trees, and is spread by elm bark beetles. Although believed to be originally native to Asia, the disease was accidentally introduced into Americas, America ...

and could occur with

Sudden Oak Death James Green aka "Sudden" is a fictional character created by an English author Oliver Strange in the early 1930s as the hero of a series, originally published by George Newnes Books Ltd, set in the American Wild West era. Oliver Strange died i ...

. An epidemic of potato late blight, caused by ''

Phytophthora infestans ''Phytophthora infestans'' is an oomycete or water mold, a fungus-like microorganism that causes the serious potato and tomato disease known as late blight or potato blight. Early blight, caused by ''Alternaria solani'', is also often called "pot ...

'', led to the

Great Irish Famine The Great Famine ( ga, an Gorta Mór ), also known within Ireland as the Great Hunger or simply the Famine and outside Ireland as the Irish Potato Famine, was a period of starvation and disease in Ireland from 1845 to 1852 that constituted a ...

and the loss of many lives. Commonly the elements of an epidemic are referred to as the “disease triangle”: a susceptible host, pathogen, and conducive environment. For a disease to occur all three of these must be present. Below is an illustration of this point. Where all three items meet, there is a disease. The fourth element missing from this illustration for an epidemic to occur is time. As long as all three of these elements are present disease can initiate, an epidemic will only ensue if all three continue to be present. Anyone of the three might be removed from the equation though. The host might out-grow susceptibility as with high-temperature adult-plant resistance, the environment changes and is not conducive for the pathogen to cause disease, or the pathogen is controlled through a fungicide application for instance. Sometimes a fourth factor of

time Time is the continued sequence of existence and events that occurs in an apparently irreversible succession from the past, through the present, into the future. It is a component quantity of various measurements used to sequence events, to ...

is added as the time at which a particular infection occurs, and the length of time conditions remain viable for that infection, can also play an important role in epidemics. The age of the plant species can also play a role, as certain species change in their levels of disease resistance as they mature; in a process known as ontogenic resistance. If all of the criteria are not met, such as a susceptible host and pathogen are present, but the environment is not conducive to the pathogen infecting and causing disease, a disease cannot occur. For example, corn is planted into a field with corn residue that has the fungus ''Cercospora zea-maydis'', the causal agent of

Grey leaf spot Grey leaf spot (GLS) is a foliar fungal disease that affects maize, also known as corn. GLS is considered one of the most significant yield-limiting diseases of corn worldwide. There are two fungal pathogens that cause GLS: ''Cercospora zeae-may ...

of corn, but if the weather is too dry, and there is no leaf wetness the

spore In biology, a spore is a unit of sexual or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plants, algae, f ...

s of the fungus in the residue cannot germinate and initiate infection. Likewise, it stands to reason if the host is susceptible and the environment favours the development of disease but the pathogen is not present there is no disease. Taking the example above, the corn is planted into a ploughed field where there is no corn residue with the fungus ''Cercospora zea-maydis'', the causal agent of

of corn, present but the weather means extended periods of leaf wetness, there is no infection initiated. When a pathogen requires a vector to be spread then for an epidemic to occur the vector must be plentiful and active. Image:Plant_Disease_Triangle.png, Plant disease triangle illustration

Types of epidemics

Pathogens cause monocyclic epidemics with a low

birth rate The birth rate for a given period is the total number of live human births per 1,000 population divided by the length of the period in years. The number of live births is normally taken from a universal registration system for births; populati ...

and

death rate Mortality rate, or death rate, is a measure of the number of deaths (in general, or due to a specific cause) in a particular population, scaled to the size of that population, per unit of time. Mortality rate is typically expressed in units of de ...

, meaning they only have one infection cycle per season. They are typical of soil-borne diseases such as

Fusarium wilt Fusarium wilt is a common vascular wilt fungal disease, exhibiting symptoms similar to Verticillium wilt. This disease has been investigated extensively since the early years of this century. The pathogen that causes Fusarium wilt is ''Fusarium o ...

flax Flax, also known as common flax or linseed, is a flowering plant, ''Linum usitatissimum'', in the family Linaceae. It is cultivated as a food and fiber crop in regions of the world with temperate climates. Textiles made from flax are known in ...

. Polycyclic epidemics are caused by pathogens capable of several infection cycles a season. They are most often caused by airborne diseases such as

powdery mildew Powdery mildew is a fungal disease that affects a wide range of plants. Powdery mildew diseases are caused by many different species of ascomycete fungi in the order Erysiphales. Powdery mildew is one of the easier plant diseases to identify, as ...

Bimodal In statistics, a multimodal distribution is a probability distribution with more than one mode (statistics), mode. These appear as distinct peaks (local maxima) in the probability density function, as shown in Figures 1 and 2. Categorical, ...

polycyclic epidemics can also occur. For example, in brown rot of

stone fruit In botany, a drupe (or stone fruit) is an indehiscent fruit in which an outer fleshy part (exocarp, or skin, and mesocarp, or flesh) surrounds a single shell (the ''pit'', ''stone'', or ''pyrena'') of hardened endocarp with a seed (''kernel'') ...

s the

blossom In botany, blossoms are the flowers of stone fruit trees (genus ''Prunus'') and of some other plants with a similar appearance that flower profusely for a period of time in spring. Colloquially, flowers of orange are referred to as such as wel ...

s and the

fruit In botany, a fruit is the seed-bearing structure in flowering plants that is formed from the ovary after flowering. Fruits are the means by which flowering plants (also known as angiosperms) disseminate their seeds. Edible fruits in particu ...

s are infected at different times. For some diseases it is important to consider the disease occurrence over several growing seasons, especially if growing the crops in

monoculture In agriculture, monoculture is the practice of growing one crop species in a field at a time. Monoculture is widely used in intensive farming and in organic farming: both a 1,000-hectare/acre cornfield and a 10-ha/acre field of organic kale are ...

year after year or growing

perennial plant A perennial plant or simply perennial is a plant that lives more than two years. The term ('' per-'' + '' -ennial'', "through the years") is often used to differentiate a plant from shorter-lived annuals and biennials. The term is also wide ...

s. Such conditions can mean that the

inoculum In biology, inoculum refers to the source material used for inoculation. ''Inoculum'' may refer to: * In medicine, material that is the source of the inoculation in a vaccine * In microbiology, propagules: cells, tissue, or viruses that are used t ...

produced in one season can be carried over to the next leading to a build of inoculum over the years. In the

tropics The tropics are the regions of Earth surrounding the Equator. They are defined in latitude by the Tropic of Cancer in the Northern Hemisphere at N and the Tropic of Capricorn in the Southern Hemisphere at S. The tropics are also referred to ...

there are no clear-cut breaks between growing seasons as there are in

temperate In geography, the temperate climates of Earth occur in the middle latitudes (23.5° to 66.5° N/S of Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout t ...

regions and this can lead to accumulation of inoculum. Epidemics that occur under these conditions are referred to as ''polyetic'' epidemics and can be caused by both monocyclic and polycyclic pathogens. Apple powdery mildew is an example of a polyetic epidemic caused by a polycyclic pathogen and Dutch Elm disease a polyetic epidemic caused by a monocyclic pathogen.

Detecting diseases

There are many different ways to spot a disease both destructively and non-destructively. In order to understand the cause, affects, and cure for a disease, the non-destructive method is more favorable. They are techniques where sample preparation and/or repetitive processes are not necessary for measuring and observing the conditions of the plants’ health. Non-destructive approaches may include image processing, imaging-based, spectroscopy based, and remote sensing. Photography, digital imaging, and image analysis technology are useful tools to set up for image processing. Valuable data are extracted from these images and then are analyzed for diseases. But before any analysis happens, image acquisition is the first step. And within this step contains three stages. First, is energy which is the light source of illuminating from the object of interest. Second, is the optical system such as a camera to focus on the energy. Third, is the energy measured by the sensor. To continue with the image processing, there is a pre-process where one can make certain that there are no factors such as background, size, shape of leave, light, and camera effects the analysis. After the pre-process, image segmentation is used to split the image between regions of disease and non-disease. In these images, there features of color, texture, and shape that can be extracted and used for the analysis. Altogether, these information can help classify the diseases. Imaging-based approaches for the detection has two main methods, fluorescence imaging and hyper-spectral imaging. Fluorescence imaging helps identify the metabolic conditions of the plant. In order to do so, a tool is used to present light onto the chlorophyll complex of the plant. Hyper-spectral imaging is used to obtain reflected images. Such methods consist of the spectral information divergence (SID) where it can assess the spectral reflectance by looking at wavelength bands. Another non-destructive approach is spectroscopy. This is where the electromagnetic spectrum and matter becomes involved. There are visible and infrared spectroscopy, fluorescence spectroscopy, and electric impedance spectroscopy. Each spectroscopy gives information including the types of radiation energy, the types of material, the nature of interaction, and more. Finally, the last non-destructive approach is the application of remote sensing in plant diseases. This is where data is obtained without having to be with the plant while observing. There is hyper-spectral and multispectral in remote sensing. Hyper-spectral helps provide high spectral and spatial resolution. Multispectral remote sensing provides the severity of the disease. there is a need for further development of

antibody An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

- and

molecular marker A molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. For another example, some proteins can be ...

-tests for new pathogens and occurrence of known pathogens in new hosts, and also a need for further global integration of

quarantine A quarantine is a restriction on the movement of people, animals and goods which is intended to prevent the spread of disease or pests. It is often used in connection to disease and illness, preventing the movement of those who may have been ...

and

surveillance Surveillance is the monitoring of behavior, many activities, or information for the purpose of information gathering, influencing, managing or directing. This can include observation from a distance by means of electronic equipment, such as c ...

Immune System

Plants can show many signs or physical evidence of fungal, viral or bacterial infections. This can range from rusts or molds to not showing anything at all when a pathogen invades the plant (occurs in some viral diseases in plants). Symptoms which are visible effects of diseases on the plant consist of changes in color, shape or function. These changes in the plant coordinates with their response to pathogens or foreign organisms that is negatively effecting their system. Even though plants do not have cells that can move and fight foreign organisms and they do not have a somatic adaptive immune system, they do have and depend on innate immunity of each cell and on systemic signals. In responses to infections, plants have a two-branched innate immune system. The first branch has to recognize and respond to molecules that are similar to classes of microbes, this includes non-pathogens. On the other hand, the second branch responds to pathogen virulence factors, either directly or indirectly to the host.

Pattern recognition receptor Pattern recognition receptors (PRRs) play a crucial role in the proper function of the innate immune system. PRRs are germline-encoded host sensors, which detect molecules typical for the pathogens. They are proteins expressed, mainly, by cells of ...

s (PRRs) are activated by recognition of pathogen or microbial-associated molecular patterns known as

PAMPs Pathogen-associated molecular patterns (PAMPs) are small molecular motifs conserved within a class of microbes. They are recognized by toll-like receptors (TLRs) and other pattern recognition receptors (PRRs) in both plants and animals. A vast arra ...

or MAMPs. These leads to PAMP-Triggered Immunity or Pattern-Triggered Immunity (PTI) where PRRs causes intracellular signaling, transcriptional reprogramming, and biosynthesis of a complex output response that decreases colonization. In addition, R genes also known as Effector-Triggered Immunity is activated by specific pathogen “effectors” that can trigger a strong antimicrobial response. Both PTI and ETI assist in plant defense through activation of DAMP which is Damage-associated Compounds. Cellular changes or changes in gene expression are activated through ion channel gating, oxidative burst, cellular redox changes, or protein kinase cascades through PTI and ETI receptors.

Impact

Through 2013 invasive

tree disease 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, oomyc ...

s had killed about 100 million

elm Elms are deciduous and semi-deciduous trees comprising the flowering plant genus ''Ulmus'' in the plant family Ulmaceae. They are distributed over most of the Northern Hemisphere, inhabiting the temperate and tropical-montane regions of North ...

trees combined in the

United Kingdom The United Kingdom of Great Britain and Northern Ireland, commonly known as the United Kingdom (UK) or Britain, is a country in Europe, off the north-western coast of the continental mainland. It comprises England, Scotland, Wales and North ...

and

United States The United States of America (U.S.A. or USA), commonly known as the United States (U.S. or US) or America, is a country primarily located in North America. It consists of 50 states, a federal district, five major unincorporated territorie ...

and 3.5 billion

American chestnut The American chestnut (''Castanea dentata'') is a large, fast-growing deciduous tree of the beech family native to eastern North America. As is true of all species in genus Castanea, the American chestnut produces burred fruit with edible nuts. ...

trees.

References

External links

Ecology and epidemiology in the R programming environment
- Open access modules published in The Plant Health Instructor Phytopathology Agronomy Epidemiology Plant diseases