Decomposition is the process by which organic substances are broken down into simpler matter. The process is a part of nutrient cycle and is essential for recycling the finite matter that occupies physical space in the biosphere. Bodies of living organisms begin to decompose shortly after death. Animals, such as worms, also help decompose the organic materials. Organisms that do this are known as decomposers. Although no two organisms decompose in the same way, they all undergo the same sequential stages of decomposition. The science which studies decomposition is generally referred to as "taphonomy" from the Greek word "taphos", meaning tomb.

One can differentiate abiotic from biotic decomposition (biodegradation). The former means "degradation of a substance by chemical or physical processes, e.g., hydrolysis. The latter means "the metabolic breakdown of materials into simpler components by living organisms", typically by microorganisms.

Biodegradation is the disintegration of materials by bacteria, fungi, or other biological means.

The term is often used in relation to: biomedicine, waste management, ecology, and the bioremediation of the natural environment. It is now commonly associated with environmentally-friendly products, capable of decomposing back into natural elements.

Although often conflated, "biodegradable" is distinct in meaning from: "compostable". While biodegradable simply means "can be consumed by microorganisms", "compostable" makes the further specific demand that the object break down under composting conditions.

Organic material can be degraded aerobically (with oxygen) or anaerobically (without oxygen). Decomposition of biodegradable substances may include both biological and abiotic steps.

Biodegradable matter is generally organic material that provides a nutrient for microorganisms. These are so numerous and diverse that a huge range of compounds can be biodegraded, including hydrocarbons (oils), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and pharmaceutical substances.

Microorganisms secrete biosurfactant, an extracellular surfactant, to enhance this process.

Citrus Black Spot is a fungal disease caused by Guignardia citricarpa. This Ascomycete fungus affects citrus plants throughout subtropical climates, causing a reduction in both fruit quantity and quality. Symptoms include both fruit and leaf lesions, the latter being critical to inter-tree dispersal. Strict regulation and management is necessary to control this disease since there are currently no citrus varieties that are resistant.

False melanose lesions are characterized by many small, tan, slightly raised lesions. The lesions are much smaller than the hard spot variety with an average diameter of less than 1 mm (.04 in).

They are found on unripe fruit and are difficult to observe later in the season. Unlike hard spot lesions, no pycnidia are present.

A person experiencing caries may not be aware of the disease. The earliest sign of a new carious lesion is the appearance of a chalky white spot on the surface of the tooth, indicating an area of demineralization of enamel. This is referred to as a white spot lesion, an incipient carious lesion or a "microcavity". As the lesion continues to demineralize, it can turn brown but will eventually turn into a cavitation ("cavity"). Before the cavity forms, the process is reversible, but once a cavity forms, the lost tooth structure cannot be regenerated.

A lesion that appears dark brown and shiny suggests dental caries were once present but the demineralization process has stopped, leaving a stain. Active decay is lighter in color and dull in appearance.

As the enamel and dentin are destroyed, the cavity becomes more noticeable. The affected areas of the tooth change color and become soft to the touch. Once the decay passes through enamel, the dentinal tubules, which have passages to the nerve of the tooth, become exposed, resulting in pain that can be transient, temporarily worsening with exposure to heat, cold, or sweet foods and drinks. A tooth weakened by extensive internal decay can sometimes suddenly fracture under normal chewing forces. When the decay has progressed enough to allow the bacteria to overwhelm the pulp tissue in the center of the tooth, a toothache can result and the pain will become more constant. Death of the pulp tissue and infection are common consequences. The tooth will no longer be sensitive to hot or cold, but can be very tender to pressure.

Dental caries can also cause bad breath and foul tastes. In highly progressed cases, an infection can spread from the tooth to the surrounding soft tissues. Complications such as cavernous sinus thrombosis and Ludwig angina can be life-threatening.

Putrefaction is the fifth stage of death, following pallor mortis, algor mortis, rigor mortis, and livor mortis. This process references the breaking down of a body of a human or animal post mortem (meaning after death). In broad terms, it can be viewed as the decomposition of proteins, and the eventual breakdown of the cohesiveness between tissues, and the liquefaction of most organs. This is caused by the decomposition of organic matter by bacterial or fungal digestion, which causes the release of gases that infiltrate the body's tissues, and leads to the deterioration of the tissues and organs.

The approximate time it takes putrefaction to occur is dependent on various factors. Internal factors that affect the rate of putrefaction include the age at which death has occurred, the overall structure and condition of the body, the cause of death, and external injuries arising before or after death. External factors include environmental temperature, moisture and air exposure, clothing, burial factors, and light exposure.

The first signs of putrefaction are signified by a greenish discoloration on the outside the skin on the abdominal wall corresponding to where the large intestine begins, as well as under the surface of the liver.

Certain substances, such as carbolic acid, arsenic, strychnine, and zinc chloride, can be used to delay the process of putrefaction in various ways based on their chemical make up. At body farms, facilities which study the process of decomposition as well as how these substances affect the rate of putrefaction, cadavers are put in different environmental conditions to study how the process of decomposition can be affected. There are six University Body Farm Research Facilities in the world, all located within the United States, which include the University of Tennessee at Knoxville, Western Carolina University, Texas State University, Sam Houston State University, Southern Illinois University, and Colorado Mesa University. Two prospective body farms will open outside the United States, in Australia and India.

Tooth decay, also known as dental caries or cavities, is a breakdown of teeth due to acids made by bacteria. The cavities may be a number of different colors from yellow to black. Symptoms may include pain and difficulty with eating. Complications may include inflammation of the tissue around the tooth, tooth loss, and infection or abscess formation.

The cause of caries is acid from bacteria dissolving the hard tissues of the teeth (enamel, dentin and cementum). The acid is produced from food debris or sugar on the tooth surface. Simple sugars in food are these bacteria's primary energy source and thus a diet high in simple sugar is a risk factor. If mineral breakdown is greater than build up from sources such as saliva, caries results. Risk factors include conditions that result in less saliva such as: diabetes mellitus, Sjogren's syndrome and some medications. Medications that decrease saliva production include antihistamines and antidepressants. Caries is also associated with poverty, poor cleaning of the mouth, and receding gums resulting in exposure of the roots of the teeth.

Prevention of dental caries includes regular cleaning of the teeth, a diet low in sugar, and small amounts of fluoride. Brushing the teeth twice per day and flossing between the teeth once a day is recommended by many. Fluoride may be from water, salt or toothpaste among other sources. Treating a mother's dental caries may decrease the risk in her children by decreasing the numbers of certain bacteria. Screening can result in earlier detection. Depending on the extent of destruction, various treatments can be used to restore the tooth to proper function or the tooth may be removed. There is no known method to grow back large amounts of tooth. The availability of treatment is often poor in the developing world. Paracetamol (acetaminophen) or ibuprofen may be taken for pain.

Worldwide, approximately 2.3 billion people (32% of the population) have dental caries in their permanent teeth. The World Health Organization estimates that nearly all adults have dental caries at some point in time. In baby teeth it affects about 620 million people or 9% of the population. They have become more common in both children and adults in recent years. The disease is most common in the developed world due to greater simple sugar consumption and less common in the developing world. Caries is Latin for "rottenness".

Age of Death: Stillborn fetuses and infants putrefy slowly due to their sterility. Generally, younger people putrefy more quickly than older people.

Condition of the Body: A body with a greater fat percentage and less lean body mass will have a faster rate of putrefaction, as fat retains more heat and it carries a larger amount of fluid in the tissues.

Cause of Death: The cause of death has a direct relationship to putrefaction speed, with bodies that died from acute violence or accident generally putrefying slower than those that died from infectious diseases. Certain poisons, such as potassium cyanide or strychnine may also delay putrefaction, while chronic alcoholism will speed it.

External Injuries: Antemortem or postmortem injuries can speed putrefaction as injured areas can be more susceptible to invasion by bacteria.

Among those animals that have a heart, the "fresh" stage begins immediately after the heart stops beating. From the moment of death, the body begins cooling or warming to match the temperature of the ambient environment, during a stage called algor mortis. Shortly after death, within three to six hours, the muscular tissues become rigid and incapable of relaxing, during a stage called rigor mortis. Since blood is no longer being pumped through the body, gravity causes it to drain to the dependent portions of the body, creating an overall bluish-purple discolouration termed livor mortis or, more commonly, lividity.

Once the heart stops, the blood can no longer supply oxygen or remove carbon dioxide from the tissues. The resulting decrease in pH and other chemical changes cause cells to lose their structural integrity, bringing about the release of cellular enzymes capable of initiating the breakdown of surrounding cells and tissues. This process is known as autolysis.

Visible changes caused by decomposition are limited during the fresh stage, although autolysis may cause blisters to appear at the surface of the skin.

The small amount of oxygen remaining in the body is quickly depleted by cellular metabolism and aerobic microbes naturally present in respiratory and gastrointestinal tracts, creating an ideal environment for the proliferation of anaerobic organisms. These multiply, consuming the body's carbohydrates, lipids, and proteins, to produce a variety of substances including propionic acid, lactic acid, methane, hydrogen sulfide, and ammonia. The process of microbial proliferation within a body is referred to as putrefaction and leads to the second stage of decomposition, known as bloat.

Blowflies and flesh flies are the first carrion insects to arrive, and they seek a suitable oviposition site.

In practice, almost all chemical compounds and materials are subject to biodegradation processes. The significance, however, is in the relative rates of such processes, such as days, weeks, years or centuries. A number of factors determine the rate at which this degradation of organic compounds occurs. Salient factors include light, water and oxygen. Temperature is also important because chemical reactions proceed more quickly at higher temperatures. The degradation rate of many organic compounds is limited by their bioavailability. Compounds must be released into solution before organisms can degrade them.

Biodegradability can be measured in a number of ways. Respirometry tests can be used for aerobic microbes. First one places a solid waste sample in a container with microorganisms and soil, and then aerates the mixture. Over the course of several days, microorganisms digest the sample bit by bit and produce carbon dioxide – the resulting amount of CO serves as an indicator of degradation. Biodegradability can also be measured by anaerobic microbes and the amount of methane or alloy that they are able to produce. In formal scientific literature, the process is termed bioremediation.

Iron (Fe) deficiency is a plant disorder also known as "lime-induced chlorosis". It can be confused with manganese deficiency. A deficiency in the soil is rare but iron can be unavailable for absorption if soil pH is not between about 5 and 6.5. A common problem is excessive alkalinity of the soil (the pH is above 6.5). Also, iron deficiency can develop if the soil is too waterlogged or has been overfertilised. Elements like calcium, zinc, manganese, phosphorus, or copper can tie up iron if they are present in high amounts.

Iron is needed to produce chlorophyll, hence its deficiency causes chlorosis. For example, iron is used in the active site of glutamyl-tRNA reductase, an enzyme needed for the formation of 5-Aminolevulinic acid which is a precursor of heme and chlorophyll.

Symptoms include leaves turning yellow or brown in the margins between the veins which may remain green, while young leaves may appear to be bleached. Fruit would be of poor quality and quantity. Any plant may be affected, but raspberries and pears are particularly susceptible, as well as most acid-loving plants such as azaleas and camellias.

At the time of death, a condition called "primary flaccidity" occurs. Following this, the muscles stiffen in rigor mortis. All muscles in the body are affected. Starting between two and six hours following death, rigor mortis begins with the eyelids, neck, and jaw. The sequence may be due to different lactic acid levels among different muscles, which is directly related to the difference in glycogen levels and different types of muscle fibers.

Rigor mortis then spreads to the other muscles, including the internal organs, within the next four to six hours. The onset of rigor mortis is affected by the individual's age, sex, physical condition, and muscular build. Rigor mortis may not be perceivable in many infant and child corpses due to their smaller muscle mass.

Rigor mortis (Latin: "rigor" "stiffness", "mortis" "of death"), the third stage of death, is one of the recognizable signs of death, caused by chemical changes in the muscles post mortem, which cause the limbs of the corpse to stiffen. In humans, rigor mortis can occur as soon as 4 hours post mortem.

In addition to symptoms related to the provoking cause, sepsis is frequently associated with either fever, low body temperature, rapid breathing, elevated heart rate, confusion, and edema. Early signs are a rapid heart rate, decreased urination, and high blood sugar. Signs of established sepsis include confusion, metabolic acidosis (which may be accompanied by faster breathing and lead to a respiratory alkalosis), low blood pressure due to decreased systemic vascular resistance, higher cardiac output, and dysfunctions of blood coagulation (where clotting may lead to organ failure).

The drop in blood pressure seen in sepsis may lead to shock. This may result in light-headedness. Bruising or intense bleeding may occur.

Foodborne illness (also foodborne disease and colloquially referred to as food poisoning) is any illness resulting from the food spoilage of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food, as well as toxins such as poisonous mushrooms and various species of beans that have not been boiled for at least 10 minutes.

Symptoms vary depending on the cause, and are described below in this article. A few broad generalizations can be made, e.g.: The incubation period ranges from hours to days, depending on the cause and on how much was consumed. The incubation period tends to cause sufferers to not associate the symptoms with the item consumed, and so to cause sufferers to attribute the symptoms to gastroenteritis for example.

Symptoms often include vomiting, fever, and aches, and may include diarrhea. Bouts of vomiting can be repeated with an extended delay in between, because even if infected food was eliminated from the stomach in the first bout, microbes (if applicable) can pass through the stomach into the intestine and begin to multiply. Some types of microbes stay in the intestine, some produce a toxin that is absorbed into the bloodstream, and some can directly invade deeper body tissues.

Sepsis is a life-threatening condition that arises when the body's response to infection causes injury to its own tissues and organs. Common signs and symptoms include fever, increased heart rate, increased breathing rate, and confusion. There also may be symptoms related to a specific infection, such as a cough with pneumonia, or painful urination with a kidney infection. In the very young, old, and people with a weakened immune system, there may be no symptoms of a specific infection and the body temperature may be low or normal, rather than high. Severe sepsis is sepsis causing poor organ function or insufficient blood flow. Insufficient blood flow may be evident by low blood pressure, high blood lactate, or low urine output. Septic shock is low blood pressure due to sepsis that does not improve after reasonable amounts of intravenous fluids are given.

Sepsis is caused by an immune response triggered by an infection. Most commonly, the infection is bacterial, but it may also be from fungi, viruses, or parasites. Common locations for the primary infection include lungs, brain, urinary tract, skin, and abdominal organs. Risk factors include young or old age, a weakened immune system from conditions such as cancer or diabetes, major trauma, or burns. An older method of diagnosis was based on meeting at least two systemic inflammatory response syndrome (SIRS) criteria due to a presumed infection. In 2016, SIRS was replaced with qSOFA which is two of the following three: increased breathing rate, change in level of consciousness, and low blood pressure. Blood cultures are recommended preferably before antibiotics are started, however, infection of the blood is not required for the diagnosis. Medical imaging should be used to look for the possible location of infection. Other potential causes of similar signs and symptoms include anaphylaxis, adrenal insufficiency, low blood volume, heart failure, and pulmonary embolism, among others.

Sepsis usually is treated with intravenous fluids and antibiotics. Typically, antibiotics are given as soon as possible. Often, ongoing care is performed in an intensive care unit. If fluid replacement is not enough to maintain blood pressure, medications that raise blood pressure may be used. Mechanical ventilation and dialysis may be needed to support the function of the lungs and kidneys, respectively. To guide treatment, a central venous catheter and an arterial catheter may be placed for access to the bloodstream. Other measurements such as cardiac output and superior vena cava oxygen saturation may be used. People with sepsis need preventive measures for deep vein thrombosis, stress ulcers and pressure ulcers, unless other conditions prevent such interventions. Some might benefit from tight control of blood sugar levels with insulin. The use of corticosteroids is controversial. Activated drotrecogin alfa, originally marketed for severe sepsis, has not been found to be helpful, and was withdrawn from sale in 2011.

Disease severity partly determines the outcome. The risk of death from sepsis is as high as 30%, from severe sepsis as high as 50%, and from septic shock as high as 80%. The number of cases worldwide is unknown as there is little data from the developing world. Estimates suggest sepsis affects millions of people a year. In the developed world approximately 0.2 to 3 people per 1000 are affected by sepsis yearly, resulting in about a million cases per year in the United States. Rates of disease have been increasing. Sepsis is more common among males than females. The medical condition has been described since the time of Hippocrates. Septicemia and blood poisoning are terms that referred to the microorganisms or their toxins in the blood and are no longer commonly used.

Foodborne illness usually arises from improper handling, preparation, or food storage. Good hygiene practices before, during, and after food preparation can reduce the chances of contracting an illness. There is a consensus in the public health community that regular hand-washing is one of the most effective defenses against the spread of foodborne illness. The action of monitoring food to ensure that it will not cause foodborne illness is known as food safety. Foodborne disease can also be caused by a large variety of toxins that affect the environment.

Furthermore, foodborne illness can be caused by pesticides or medicines in food and natural toxic substances such as poisonous mushrooms or reef fish.

Most cases of CWD occur in adult animals; the youngest animal diagnosed with natural CWD was 17 months. The disease is progressive and always fatal. The first signs are difficulties in movement. The most obvious and consistent clinical sign of CWD is weight loss over time. Behavioral changes also occur in the majority of cases, including decreased interactions with other animals, listlessness, lowering of the head, tremors, repetitive walking in set patterns, and nervousness. Excessive salivation and grinding of the teeth also are observed. Most deer show increased drinking and urination; the increased drinking and salivation may contribute to the spread of the disease.

Ketoacidosis is a metabolic state associated with high concentrations of ketone bodies, formed by the breakdown of fatty acids and the deamination of amino acids. The two common ketones produced in humans are acetoacetic acid and β-hydroxybutyrate.

Ketoacidosis is a pathological metabolic state marked by extreme and uncontrolled ketosis. In ketoacidosis, the body fails to adequately regulate ketone production causing such a severe accumulation of keto acids that the pH of the blood is substantially decreased. In extreme cases ketoacidosis can be fatal.

Ketoacidosis is most common in untreated type 1 diabetes mellitus, when the liver breaks down fat and proteins in response to a perceived need for respiratory substrate. Prolonged alcoholism may lead to alcoholic ketoacidosis.

Ketoacidosis can be smelled on a person's breath. This is due to acetone, a direct by-product of the spontaneous decomposition of acetoacetic acid. It is often described as smelling like fruit or nail polish remover. Ketosis may also give off an odor, but the odor is usually more subtle due to lower concentrations of acetone.

Treatment consists most simply of correcting blood sugar and insulin levels, which will halt ketone production. If the severity of the case warrants more aggressive measures, intravenous sodium bicarbonate infusion can be given to raise blood pH back to an acceptable range. However, serious caution must be exercised with IV sodium bicarbonate to avoid the risk of equally life-threatening hypernatremia.

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) of mule deer, white-tailed deer, elk (or "wapiti"), moose, and reindeer. As of 2016, CWD had only been found in members of the deer family. First recognized as a clinical "wasting" syndrome in 1967 in mule deer in a wildlife research facility in northern Colorado, USA, it was identified as a TSE in 1978 and has spread to free-ranging and captive populations in 23 US states and two Canadian provinces. CWD is typified by chronic weight loss leading to death. No relationship is known between CWD and any other TSE of animals or people.

Although reports in the popular press have been made of humans being affected by CWD, a study by the Centers for Disease Control and Prevention suggests, "[m]ore epidemiologic and laboratory studies are needed to monitor the possibility of such transmissions".

The epidemiological study further concluded, "[a]s a precaution, hunters should avoid eating deer and elk tissues known to harbor the CWD agent (e.g., brain, spinal cord, eyes, spleen, tonsils, lymph nodes) from areas where CWD has been identified".

Gestaltzerfall (German for "shape decomposition") refers to a type of visual agnosia and is a psychological phenomenon where delays in recognition are observed when a complex shape is stared at for a while as the shape seems to decompose into its constituting parts. With regards to kanji, a study has shown that delays are most significant when the characters are of the same size. When characters to recognize are of different sizes, delays are observed only when they are of different patterns.

The phenomenon was first described and named by C. Faust in 1947 as a symptom of the bilateral region of the parieto-occipital sulcus after a through and through bullet wound of this region. Afterwards, when the subject stared at a truck for a while the truck seemed to decompose into its motor, chassis, driver cab and the person could only focus on one of these parts until he briefly closed his eyes or looked away which reset the shape to the complete truck again.

The characteristic of orthographic satiation as opposed to semantic satiation is that meaning remains intact. It was suggested that this is different from semantic satiation and from the stimulus familiarization effect because orthographic satiation occurs after the perceivers have access to lexical meaning.

There are several terms which were in general use, but are no longer recommended.

The best-known symptom of bubonic plague is one or more infected, enlarged, and painful lymph nodes, known as buboes. After being transmitted via the bite of an infected flea, the "Y. pestis" bacteria become localized in an inflamed lymph node where they begin to colonize and reproduce. Buboes associated with the bubonic plague are commonly found in the armpits, upper femoral, groin and neck region. Acral gangrene (i.e., of the fingers, toes, lips and nose) is another common symptom.

Because of its bite-based mode of transmission, the bubonic plague is often the first of a progressive series of illnesses. Bubonic plague symptoms appear suddenly a few days after exposure to the bacterium. Symptoms include:

- Chills

- General ill feeling (malaise)

- High fever (39 °C; 102 °F)

- Muscle cramps

- Seizures

- Smooth, painful lymph gland swelling called a bubo, commonly found in the groin, but may occur in the armpits or neck, most often near the site of the initial infection (bite or scratch)

- Pain may occur in the area before the swelling appears

- Gangrene of the extremities such as toes, fingers, lips and tip of the nose.

Other symptoms include heavy breathing, continuous vomiting of blood (hematemesis), aching limbs, coughing, and extreme pain caused by the decay or decomposition of the skin while the person is still alive. Additional symptoms include extreme fatigue, gastrointestinal problems, lenticulae (black dots scattered throughout the body), delirium, and coma.

Drowning is defined as respiratory impairment from being in or under a liquid. It is further classified by outcome into: death, ongoing health problems, and no ongoing health problems. Drowning itself is quick and silent, although it may be preceded by distress which is more visible.

Generally, in the early stages of drowning, very little water enters the lungs: a small amount of water entering the trachea causes a muscular spasm that seals the airway and prevents the passage of both air and water until unconsciousness occurs. This means a person drowning is unable to shout or call for help, or seek attention, as they cannot obtain enough air. The instinctive drowning response is the final set of autonomic reactions in the 20–60 seconds before sinking underwater, and to the untrained eye can look similar to calm safe behavior. Lifeguards and other persons trained in rescue learn to recognize drowning people by watching for these movements. If the process is not interrupted, loss of consciousness due to hypoxia is followed rapidly by cardiac arrest. At this stage, the process is still usually reversible by prompt and effective rescue and first aid. Survival rates depend strongly on the duration of immersion.

In 2013, there were about 1.7 million cases of drowning. Unintentional drowning is the third leading cause of unintentional injury resulting in death worldwide. In 2013, it was estimated to have resulted in 368,000 deaths, down from 545,000 deaths in 1990. Of these deaths, 82,000 occurred in children less than five years old. It accounts for 7% of all injury related deaths (excluding those due to natural disasters), with 91% of these deaths occurring in low-income and middle-income countries. Drowning occurs more frequently in males and the young. The rate of drowning in populations around the world varies widely according to their access to water, the climate and the national swimming culture.