Microorganism in the context of Pharmacodynamics

The natural environment or natural world encompasses all biotic and abiotic things occurring naturally, meaning in this case not artificial. The term is most often applied to Earth or some parts of Earth. This environment encompasses the interaction of all living species, climate, weather and natural resources that affect human survival and economic activity.The concept of the natural environment can be distinguished as components:

• Complete ecological units that function as natural systems without massive civilized human intervention, including all vegetation, microorganisms, soil, rocks, plateaus, mountains, the atmosphere and natural phenomena that occur within their boundaries and their nature.
• Universal natural resources and physical phenomena that lack clear-cut boundaries, such as air, water and climate, as well as energy, radiation, electric charge and magnetism, not originating from civilized human actions.

In contrast to the natural environment is the built environment. Built environments are where humans have fundamentally transformed landscapes such as urban settings and agricultural land conversion, the natural environment is greatly changed into a simplified human environment. Even acts which seem less extreme, such as building a mud hut or a photovoltaic system in the desert, the modified environment becomes an artificial one. Though many animals build things to provide a better environment for themselves, they are not human, hence beaver dams and the works of mound-building termites are thought of as natural.

The history of life on Earth traces the processes by which living and extinct organisms evolved, from the earliest emergence of life to the present day. Earth formed about 4.54 ± 0.05 billion years ago (abbreviated as Ga, for gigaannum) and evidence suggests that life emerged prior to 3.7 Ga. The similarities among all known present-day species indicate that they have diverged through the process of evolution from a common ancestor.

The earliest clear evidence of life comes from biogenic carbon signatures and stromatolite fossils discovered in 3.7 billion-year-old metasedimentary rocks from western Greenland. In 2015, possible "remains of biotic life" were found in 4.1 billion-year-old rocks in Western Australia. There is further evidence of possibly the oldest forms of life in the form of fossilized microorganisms in hydrothermal vent precipitates from the Nuvvuagittuq Belt, that may have lived as early as 4.28 billion years ago, not long after the oceans formed 4.4 billion years ago, and after the Earth formed 4.54 ± 0.05 billion years ago. These earliest fossils, however, may have originated from non-biological processes.

Marine microorganisms are defined by their habitat as microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism (or microbe) is any microscopic living organism or virus, which is invisibly small to the unaided human eye without magnification. Microorganisms are very diverse. They can be single-celled or multicellular and include bacteria, archaea, viruses, and most protozoa, as well as some fungi, algae, and animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify viruses as microorganisms, but others consider these as non-living.

Marine microorganisms have been variously estimated to make up between 70 and 90 percent of the biomass in the ocean. Taken together they form the marine microbiome. Over billions of years this microbiome has evolved many life styles and adaptations and come to participate in the global cycling of almost all chemical elements. Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. They are also responsible for nearly all photosynthesis that occurs in the ocean, as well as the cycling of carbon, nitrogen, phosphorus and other nutrients and trace elements. Marine microorganisms sequester large amounts of carbon and produce much of the world's oxygen.

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.

Biological oceanography is the study of how organisms affect and are affected by the physics, chemistry, and geology of the oceanographic system. Biological oceanography may also be referred to as ocean ecology, in which the root word of ecology is Oikos (oικoσ), meaning ‘house’ or ‘habitat’ in Greek. With that in mind, it is of no surprise then that the main focus of biological oceanography is on the microorganisms within the ocean; looking at how they are affected by their environment and how that affects larger marine creatures and their ecosystem. Biological oceanography is similar to marine biology, but is different because of the perspective used to study the ocean. Biological oceanography takes a bottom-up approach (in terms of the food web), while marine biology studies the ocean from a top-down perspective. Biological oceanography mainly focuses on the ecosystem of the ocean with an emphasis on plankton: their diversity (morphology, nutritional sources, motility, and metabolism); their productivity and how that plays a role in the global carbon cycle; and their distribution (predation and life cycle).

The earliest known life forms on Earth may be as old as 4.1 billion years (or Ga) according to biologically fractionated graphite inside a single zircon grain in the Jack Hills range of Australia. The earliest evidence of life found in a stratigraphic unit, not just a single mineral grain, is the 3.7 Ga metasedimentary rocks containing graphite from the Isua Supracrustal Belt in Greenland. The earliest direct known life on Earth are stromatolite fossils which have been found in 3.480-billion-year-old geyserite uncovered in the Dresser Formation of the Pilbara Craton of Western Australia. Various microfossils of microorganisms have been found in 3.4 Ga rocks, including 3.465-billion-year-old Apex chert rocks from the same Australian craton region, and in 3.42 Ga hydrothermal vent precipitates from Barberton, South Africa. Much later in the geologic record, likely starting in 1.73 Ga, preserved molecular compounds of biologic origin are indicative of aerobic life. Therefore, the earliest time for the origin of life on Earth is at least 3.5 billion years ago and possibly as early as 4.1 billion years ago — not long after the oceans formed 4.5 billion years ago and after the formation of the Earth 4.54 billion years ago.

A prokaryote (/proʊˈkærioʊt, -ət/; less commonly spelled procaryote) is a microorganism whose usually single cell lacks a nucleus or other membrane-bound organelles. The word prokaryote comes from the Ancient Greek πρό (pró), meaning 'before', and κάρυον (káruon), meaning 'nut' or 'kernel'. In the earlier two-empire system, prokaryotes formed the empire Prokaryota. In the three-domain system, based upon molecular phylogenetics, prokaryotes are divided into two domains: Bacteria and Archaea. A third domain, Eukaryota, consists of organisms with nuclei.

Prokaryotes evolved before eukaryotes, and lack nuclei, mitochondria, and most of the other distinct organelles that characterize the eukaryotic cell. Some unicellular prokaryotes, such as cyanobacteria, form colonies held together by biofilms, and large colonies can create multilayered microbial mats. Prokaryotes are asexual, reproducing via binary fission. Horizontal gene transfer is common as well.

Bacteria 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 the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Like all animals, humans carry vast numbers (approximately 10 to 10) of bacteria. Most are in the gut, though there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. Bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector (biomining, bioleaching), as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. The ability to exhibit aerobic respiration may yield benefits to the aerobic organism, as aerobic respiration yields more energy than anaerobic respiration. Energy production of the cell involves the synthesis of ATP by an enzyme called ATP synthase. In aerobic respiration, ATP synthase is coupled with an electron transport chain in which oxygen acts as a terminal electron acceptor. In July 2020, marine biologists reported that aerobic microorganisms (mainly), in "quasi-suspended animation", were found in organically poor sediments, up to 101.5 million years old, 250 feet below the seafloor in the South Pacific Gyre (SPG) ("the deadest spot in the ocean"), and could be the longest-living life forms ever found.

Hand washing (or handwashing), also called hand hygiene, is the process of cleaning the hands with soap or handwash and water to eliminate bacteria, viruses, dirt, microorganisms, and other potentially harmful substances. Drying of the washed hands is part of the process as wet and moist hands are more easily recontaminated. If soap and water are unavailable, hand sanitizer that is at least 60% (v/v) alcohol in water can be used as long as hands are not visibly excessively dirty or greasy. Hand hygiene is central to preventing the spread of infectious diseases in home and everyday life settings. Meta-analyses have shown that regular hand washing in community settings can significantly reduce respiratory and gastrointestinal infection

The World Health Organization (WHO) recommends washing hands for at least 20 seconds before and after certain activities. These include the five critical times during the day where washing hands with soap is important to reduce fecal-oral transmission of disease: after using the toilet (for urination, defecation, menstrual hygiene), after cleaning a child's bottom (changing diapers), before feeding a child, before eating and before/after preparing food or handling raw meat, fish, or poultry.

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.

The nematodes (/ˈnɛmətoʊdz/ NEM-ə-tohdz or NEEM-; Ancient Greek: Νηματώδη; Latin: Nematoda), roundworms or eelworms constitute the phylum Nematoda. Species in the phylum inhabit a broad range of environments. Most species are free-living, feeding on microorganisms, but many are parasitic. Parasitic worms (helminths) are the cause of soil-transmitted helminthiases.

They are classified along with arthropods, tardigrades and other moulting animals in the clade Ecdysozoa. Unlike the flatworms, nematodes have a tubular digestive system, with openings at both ends. Like tardigrades, they have a reduced number of Hox genes, but their sister phylum Nematomorpha has kept the ancestral protostome Hox genotype, which shows that the reduction has occurred within the nematode phylum.

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.

The Oomycetes (/ˌoʊ.əˈmaɪsiːts/), or Oomycota, form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms within the Stramenopiles. 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 (or water moulds), although the water-preferring nature which led to that name is not true of most species, which are terrestrial pathogens.

Oomycetes were originally grouped with fungi due to similarities in morphology and lifestyle. However, molecular and phylogenetic studies revealed significant differences between fungi and oomycetes which means the latter are now grouped with the stramenopiles (which include some types of algae). The Oomycota have a very sparse fossil record; a possible oomycete has been described from Cretaceous amber.

Mating types are the microorganism equivalent to sexes in multicellular lifeforms and are thought to be the ancestor to distinct sexes. They also occur in multicellular organisms such as fungi.