Pathogen in the context of Actinomycetota

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

Prokaryotes play important roles in ecosystems as decomposers recycling nutrients. Some prokaryotes are pathogenic, causing disease and even death in plants and animals. Marine prokaryotes are responsible for significant levels of the photosynthesis that occurs in the ocean, as well as significant cycling of carbon and other nutrients.

Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate inside the living cells of a host organism, because they need the replication machinery of the host to do so. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

When not inside a cell or in the process of infecting a cell, viruses exist in the form of independent particles called virions. A virion contains a genome (a long molecule that carries genetic information in the form of either DNA or RNA) surrounded by a capsid (a protein coat protecting the genetic material). The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the linear size of the average bacterium.

In medicine, public health, and biology, transmission is the passing of a pathogen causing communicable disease from an infected host individual or group to a particular individual or group, regardless of whether the other individual was previously infected. The term strictly refers to the transmission of microorganisms directly from one individual to another by one or more of the following means:

• airborne transmission – very small dry and wet particles that stay in the air for long periods of time allowing airborne contamination even after the departure of the host. Particle size < 5 μm.
• droplet transmission – small and usually wet particles that stay in the air for a short period of time. Contamination usually occurs in the presence of the host. Particle size > 5 μm.
• direct physical contact – touching an infected individual, including sexual contact
• indirect physical contact – usually by touching a contaminated surface, including soil (fomite)
• fecal–oral transmission – usually from unwashed hands, contaminated food or water sources due to lack of sanitation and hygiene, an important transmission route in pediatrics, veterinary medicine and developing countries.
• via contaminated hypodermic needles or blood products

Transmission can also be indirect, via another organism, either a vector (e.g. a mosquito or fly) or an intermediate host (e.g. tapeworm in pigs can be transmitted to humans who ingest improperly cooked pork). Indirect transmission could involve zoonoses or, more typically, larger pathogens like macroparasites with more complex life cycles. Transmissions can be autochthonous (i.e. between two individuals in the same place) or may involve travel of the microorganism or the affected hosts.

Water pollution (or aquatic pollution) is the contamination of water bodies, with a negative impact on their uses. It is usually a result of human activities. Water bodies include lakes, rivers, oceans, aquifers, reservoirs and groundwater. Water pollution results when contaminants mix with these water bodies. Contaminants can come from one of four main sources. These are sewage discharges, industrial activities, agricultural activities, and urban runoff including stormwater. Water pollution may affect either surface water or groundwater. This form of pollution can lead to many problems. One is the degradation of aquatic ecosystems. Another is spreading water-borne diseases when people use polluted water for drinking or irrigation. Water pollution also reduces the ecosystem services such as drinking water provided by the water resource.

Sources of water pollution are either point sources or non-point sources. Point sources have one identifiable cause, such as a storm drain, a wastewater treatment plant, or an oil spill. Non-point sources are more diffuse. An example is agricultural runoff. Pollution is the result of the cumulative effect over time. Pollution may take many forms. One would is toxic substances such as oil, metals, plastics, pesticides, persistent organic pollutants, and industrial waste products. Another is stressful conditions such as changes of pH, hypoxia or anoxia, increased temperatures, excessive turbidity, or changes of salinity). The introduction of pathogenic organisms is another. Contaminants may include organic and inorganic substances. A common cause of thermal pollution is the use of water as a coolant by power plants and industrial manufacturers.

The (oceanic) water column is a concept used in oceanography to describe the physical (temperature, salinity, light penetration) and chemical (pH, dissolved oxygen, nutrient salts) characteristics of seawater at different depths for a defined geographical point. Generally, vertical profiles are made of temperature, salinity, chemical parameters at a defined point along the water column. The water column is the largest, yet one of the most under-explored, habitats on the planet; it is explored to better understand the ocean as a whole, including the huge biomass that lives there and its importance to the global carbon and other biogeochemical cycles. Studying the water column also provides understanding on the links between living organisms and environmental parameters, large-scale water circulation and the transfer of matter between water masses.

Water columns are used chiefly for environmental studies evaluating the stratification or mixing of thermal or chemically stratified layers in a lake, stream or ocean. Some of the common parameters analyzed in the water column are pH, turbidity, temperature, hydrostatic pressure, salinity, total dissolved solids, various pesticides, pathogens and a wide variety of chemicals and biota.

Injury is physiological damage to the living tissue of any organism, whether in humans, in other animals, or in plants.

Injuries can be caused in many ways, including mechanically with penetration by sharp objects such as teeth or with blunt objects, by heat or cold, or by venoms and biotoxins. Injury prompts an inflammatory response in many taxa of animals; this prompts wound healing. In both plants and animals, substances are often released to help to occlude the wound, limiting loss of fluids and the entry of pathogens such as bacteria. Many organisms secrete antimicrobial chemicals which limit wound infection; in addition, animals have a variety of immune responses for the same purpose. Both plants and animals have regrowth mechanisms which may result in complete or partial healing over the injury. Cells too can repair damage to a certain degree.

A disease is a particular abnormal condition that adversely affects the structure or function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical conditions that are associated with specific signs and symptoms. A disease may be caused by external factors such as pathogens or by internal dysfunctions. For example, internal dysfunctions of the immune system can produce a variety of different diseases, including various forms of immunodeficiency, hypersensitivity, allergies, and autoimmune disorders.

In humans, disease is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, or death to the person affected, or similar problems for those in contact with the person. In this broader sense, it sometimes includes injuries, disabilities, disorders, syndromes, infections, isolated symptoms, deviant behaviors, and atypical variations of structure and function, while in other contexts and for other purposes these may be considered distinguishable categories. Diseases can affect people not only physically but also mentally, as contracting and living with a disease can alter the affected person's perspective on life.

In epidemiology, a disease vector is any living agent that carries and transmits an infectious pathogen such as a parasite or microbe, to another living organism. Agents regarded as vectors are mostly blood-sucking (hematophagous) arthropods such as mosquitoes. The first major discovery of a disease vector came from Ronald Ross in 1897, who discovered the malaria pathogen when he dissected the stomach tissue of a mosquito.The process of proving that a vector is responsible for transmitting pathogens is called vector incrimination.

The wolf (Canis lupus; pl.: wolves), also known as the grey wolf or gray wolf, is a canine native to Eurasia and North America. More than thirty subspecies of Canis lupus have been recognized, including the dog and dingo, though grey wolves, as popularly understood, include only naturally-occurring wild subspecies. The wolf is the largest wild extant member of the family Canidae, and is further distinguished from other Canis species by its less pointed ears and muzzle, as well as a shorter torso and a longer tail. The wolf is nonetheless related closely enough to smaller Canis species, such as the coyote and the golden jackal, to produce fertile hybrids with them. The wolf's fur is usually mottled white, brown, grey, and black, although subspecies in the arctic region may be nearly all white.

Of all members of the genus Canis, the wolf is most specialized for cooperative game hunting, as demonstrated by its physical adaptations to tackling large prey, its more social nature, and its highly advanced expressive behaviour, including individual or group howling. It travels in nuclear families, consisting of a mated pair accompanied by their offspring. Offspring may leave to form their own packs on the onset of sexual maturity and in response to competition for food within the pack. Wolves are also territorial, and fights over territory are among the principal causes of mortality. The wolf is mainly a carnivore and feeds on large wild hooved mammals as well as smaller animals, livestock, carrion, and garbage. Single wolves or mated pairs typically have higher success rates in hunting than do large packs. Pathogens and parasites, notably the rabies virus, may infect wolves.

The germ theory of disease is the currently accepted scientific theory for many diseases. It states that microorganisms known as pathogens or "germs" can cause disease. These small organisms, which are too small to be seen without magnification, invade animals, plants, and even bacteria. Their growth and reproduction within their hosts can cause disease. "Germ" refers not just to bacteria but to any type of microorganism, such as protists or fungi, or other pathogens, including parasites, viruses, prions, or viroids. Diseases caused by pathogens are called infectious diseases. Even when a pathogen is the principal cause of a disease, environmental and hereditary factors often influence the severity of the disease, and whether a potential host individual becomes infected when exposed to the pathogen. Pathogens are disease-causing agents that can pass from one individual to another, across multiple domains of life.

Basic forms of germ theory were proposed by Girolamo Fracastoro in 1546, and expanded upon by Marcus von Plenciz in 1762. However, such views were held in disdain in Europe, where Galen's miasma theory remained dominant among scientists and doctors.

In ecology, a niche is the match of a species to a specific environmental condition. It describes how an organism or population responds to the distribution of resources and competitors (for example, by growing when resources are abundant, and when predators, parasites and pathogens are scarce) and how it, in turn, alters those same factors (for example, limiting access to resources by other organisms, acting as a food source for predators and a consumer of prey). "The type and number of variables comprising the dimensions of an environmental niche vary from one species to another [and] the relative importance of particular environmental variables for a species may vary according to the geographic and biotic contexts".

A Grinnellian niche is determined by the habitat in which a species lives and its accompanying behavioral adaptations. An Eltonian niche emphasizes that a species not only grows in and responds to an environment, it may also change the environment and its behavior as it grows. The Hutchinsonian niche uses mathematics and statistics to try to explain how species coexist within a given community.

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. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology.

When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or virions, consisting of (i) genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope and are one-hundredth the size of most bacteria.

Virology is the scientific study of biological viruses. It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy.

The identification of the causative agent of tobacco mosaic disease (TMV) as a novel pathogen by Martinus Beijerinck (1898) is now acknowledged as being the official beginning of the field of virology as a discipline distinct from bacteriology. He realized the source was neither a bacterial nor a fungal infection, but something completely different. Beijerinck used the word "virus" to describe the mysterious agent in his 'contagium vivum fluidum' ('contagious living fluid'). Rosalind Franklin proposed the full structure of the tobacco mosaic virus in 1955.

A pyrena (/paɪˈriːnə/) or pyrene, commonly called a pit or stone, is the fruitstone within a drupe or drupelet produced by the ossification of the endocarp or lining of the fruit. It consists of a hard endocarp tissue surrounding one or more seeds (also called the "kernel"). The hardened endocarp which constitutes the pyrene provides a protective physical barrier around the seed, shielding it from pathogens and herbivory.

While many drupes are monopyrenous, containing only one pyrene, pome-type fruit with a hard, stony (rather than leathery) endocarp are typically polypyrenous drupes, containing multiple pyrenes.

Pesticides are substances that are used to control pests. They include herbicides, insecticides, nematicides, fungicides, and many others (see table). The most common of these are herbicides, which account for approximately 50% of all pesticide use globally. Most pesticides are used as plant protection products (also known as crop protection products), which in general protect plants from weeds, fungi, or insects.

In general, a pesticide is a chemical or biological agent (such as a virus, bacterium, or fungus) that deters, incapacitates, kills, or otherwise discourages pests. Target pests can include insects, plant pathogens, weeds, molluscs, birds, mammals, fish, nematodes (roundworms), and microbes that destroy property, cause nuisance, spread disease, or are disease vectors. Pesticides thus increase agricultural yields. Along with these benefits, pesticides also have drawbacks, such as potential toxicity to humans and other species.

Protection is any measure taken to guard something against damage caused by outside forces. Protection can be provided to physical objects, including organisms, to systems, and to intangible things like civil and political rights. Although the mechanisms for providing protection vary widely, the basic meaning of the term remains the same. This is illustrated by an explanation found in a manual on electrical wiring:

Some kind of protection is a characteristic of all life, as living things have evolved at least some protective mechanisms to counter damaging environmental phenomena, such as ultraviolet light. Biological membranes such as bark on trees and skin on animals offer protection from various threats, with skin playing a key role in protecting organisms against pathogens and excessive water loss. Additional structures like scales and hair offer further protection from the elements and from predators, with some animals having features such as spines or camouflage serving exclusively as anti-predator adaptations. Many animals supplement the protection afforded by their physiology by burrowing or otherwise adopting habitats or behaviors that insulate them from potential sources of harm. Humans originally began wearing clothing and building shelters in prehistoric times for protection from the elements. Both humans and animals are also often concerned with the protection of others, with adult animals being particularly inclined to seek to protect their young from elements of nature and from predators.

In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasitic, a mutualistic, or a commensalist guest (symbiont). The guest is typically provided with nourishment and shelter. Examples include animals playing host to parasitic worms (e.g. nematodes), cells harbouring pathogenic (disease-causing) viruses, or a bean plant hosting mutualistic (helpful) nitrogen-fixing bacteria. More specifically in botany, a host plant supplies food resources to micropredators, which have an evolutionarily stable relationship with their hosts similar to ectoparasitism. The host range is the collection of hosts that an organism can use as a partner.

An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable disease, is an illness resulting from an infection.

Infections can be caused by a wide range of pathogens, most prominently bacteria and viruses. Hosts can fight infections using their immune systems. Mammalian hosts react to infections with an innate response, often involving inflammation, followed by an adaptive response.