Microorganism

# Overview
A microorganism (also spelled as microrganism) or microbe is an organism that is microscopic (too small to be seen by the human eye). The study of microorganisms is called microbiology. Microorganisms include bacteria, fungi, archaea or protists, but not viruses and prions, which are generally classified as non-living. Most microorganisms are single-celled, or unicellular, but some are microscopic, and some unicellular protists are visible to the average human.
Microorganisms live almost everywhere on Earth where there is liquid water, including hot springs, on the ocean floor, and deep inside rocks within Earth's crust. Microorganisms are critical to nutrient recycling in ecosystems as they act as decomposers. As some microorganisms can also fix nitrogen, they are an important part of the nitrogen cycle. However, pathogenic microbes can invade other organisms and cause diseases that kill millions of people every year.

# History

## Evolution
Single-celled microorganisms were the first forms of life to develop on earth, approximately 34 billion years ago. Further evolution was slow, and for about 3 billion years in the Precambrian eon, all organisms were microscopic. So, for most of the history of life on Earth the only form of life were microorganisms. Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms have changed little since the triassic period.
Most microorganisms can reproduce rapidly and microbes such as bacteria can also freely exchange genes by conjugation, transformation and transduction between widely-divergent species. This horizontal gene transfer, coupled with a high mutation rate and many other means of genetic variation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution has led to the recent development of 'super-bugs'  pathogenic bacteria that are resistant to modern antibiotics.

## Discovery
The existence of microorganisms was hypothesized during the late Middle Ages but they were not observed or proven until the invention of the microscope in the 17th century. In The Canon of Medicine (1020), Abu Ali ibn Sina (Avicenna) stated that bodily secretion is contaminated by foul foreign earthly bodies before being infected, but he did not view them as primary causes of disease. When the Black Death bubonic plague reached al-Andalus in the 14th century, Ibn Khatima and Ibn al-Khatib hypothesized that infectious diseases are caused by microorganisms which enter the human body. Such ideas became more popular in Europe during the Renaissance, particularly through the writing of the Italian monk Girolamo Fracastoro.
Prior to Anton van Leeuwenhoek's discovery of microorganisms in 1675, it had been a mystery as to why grapes could be turned into wine, milk into cheese, or why food would spoil. Leeuwenhoek did not make the connection between these processes and microorganisms, but using the microscope, he did establish that there were forms of life that were not visible to the naked eye. Leeuwenhoek's discovery, along with subsequent observations by Lazzaro Spallanzani and Louis Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.
Lazzarro Spallanzani found that microorganisms could only settle in a broth if the broth was exposed to the air. He also found that boiling the broth would sterilise it and kill the microorganisms. Louis Pasteur expanded upon Spallanzani's findings by exposing boiled broths to the air, in vessels that contained a filter to prevent all particles from passing through to the growth medium, and also in vessels with no filter at all, with air being admitted via a curved tube that would not allow dust particles to come in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported germ theory.
In 1876, Robert Koch established that microbes can cause disease. He did this by finding that the blood of cattle who were infected with anthrax always had large numbers of Bacillus anthracis. Koch also found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, causing the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, inject it into a healthy animal, and cause illness. Based upon these experiments, he devised criteria for establishing a causal link between a microbe and a disease in what are now known as Koch's postulates. Though these postulates cannot be applied in all cases, they do retain historical importance in the development of scientific thought and can still be used today.

# Classification
Microorganisms can be found almost anywhere in the taxonomic organization of life on the planet. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists and a number of fungi. Viruses are generally regarded as not living and therefore are not microbes, although the field of microbiology also encompasses the study of viruses.

## Prokaryotes
Prokaryotes are organisms that lack a cell nucleus and the other organelles found in eukaryotes. Prokaryotes are almost always unicellular, although some such as myxobacteria can aggregate into complex structures as part of their life cycle. These organisms are divided into two groups, the archaea and the bacteria.

### Bacteria
Bacteria are the most diverse and abundant group of organisms on Earth. Bacteria inhabit practically all environments where some liquid water is available and the temperature is below +140 C. They are found in sea water, soil, animals' gastrointestinal tracts, hot springs and even deep beneath the Earth's crust in rocks. Practically all surfaces which have not been specially sterilized are covered in bacteria. The number of bacteria in the world is estimated to be around five million trillion trillion, or 5  1030.
Bacteria are practically all invisible to the naked eye, with few extremely rare exceptions, such as Thiomargarita namibiensis. They are unicellular organisms and lack organelles. Their genome is usually a single loop of DNA, although they can also harbor small pieces of DNA called plasmids. Bacteria are surrounded by a cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission or sometimes by budding. Some species form extremely resilient spores, but for bacteria this is a mechanism for survival, not reproduction. Under optimal conditions bacteria can grow extremely rapidly and can double as quickly as every 10 minutes.

### Archaea
Archaea are also single-celled organisms that lack nuclei. In the past, the differences between bacteria and archaea were not recognised and archaea were classified with bacteria as part of the kingdom Monera. Archaea differ from bacteria in their genetics and biochemistry. For example, while bacterial cell membranes are made from phosphoglycerides with ester bonds, archaean membranes are made of ether lipids.
Archaea were originally described in extreme environments, such as hot springs, but have since been found in all types of habitats. Only now are scientists beginning to appreciate how common archaea are in the environment, with crenarchaeota being the most common form of life in the ocean, dominating ecosystems below 150 m in depth. These organisms are also common in soil and play a vital role in ammonia oxidation.

## Eukaryotes
All living things which are individually visible to the naked eye are eukaryotes (with few exceptions, such as Thiomargarita namibiensis), including humans. However, a large number of eukaryotes are also microorganisms. Unlike bacteria and archaea, eukaryotes contain organelles such as the cell nucleus, the Golgi apparatus and mitochondria in their cells. The nucleus is an organelle which houses the DNA that makes up a cell's genome. DNA itself is arranged in complex chromosomes.
Mitochondria are organelles vital in metabolism as they are the site of the citric acid cycle and oxidative phosphorylation. They evolved from symbiotic bacteria and retain a remnant genome. Like bacteria, plant cells have cell walls, and contain organelles such as chloroplasts in addition to the organelles in other eukaryotes. Chloroplasts produce energy from light by photosynthesis, and were also originally symbiotic bacteria.
Unicellular eukaryotes are those eukaryotic organisms that consist of a single cell throughout their life cycle.  This qualification is significant since most multicellular eukaryotes consist of a single cell called a zygote at the beginning of their life cycles. Microbial eukaryotes can be either haploid or diploid, and some organisms have multiple cell nuclei (see coenocyte). However, not all microorganisms are unicellular as some microscopic eukaryotes are made from multiple cells.

### Protists
Of eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a diverse group of organisms which are not easy to classify. Several algae species are multicellular protists, and slime molds have unique life cycles with unicellular, colonial, and multicellular stages.

### Animals
All animals are multicellular, but some are too small to be seen by the naked eye. Microscopic arthropods include dust mites and spider mites. Microscopic crustaceans include copepods and the cladocera. Another common group of microscopic animals are the rotifers, which are filter feeders that are usually found in fresh water.

### Fungi
The fungi have several unicellular species, such as baker's yeast (Saccharomyces cerevisiae).

### Plants
The green algae are a large group of photosynthetic eukaryotes that include many microscopic organisms. Although some green algae are classified as protists, others such as charophyta are classified with embryophyte plants, which are the most familiar group of land plants.

# Habitats and ecology
Microorganisms are found in almost every habitat present in nature. Even in hostile environments such as the poles, deserts, geysers, rocks, and the deep sea, some types of microorganisms have adapted to the extreme conditions and sustained colonies; these organisms are known as extremophiles. Extremophiles have been isolated from rocks as much as 7 kilometres below the earth's surface, and it has been suggested that the amount of living organisms below the earth's surface may be comparable with the amount of life on or above the surface. Extremophiles have been known to survive for a prolonged time in a vacuum, and can be highly resistant to radiation, which may even allow them to survive in space. Many types of microorganisms have intimate symbiotic relationships with other larger organisms; some of which are mutually beneficial (mutualism), while others can be damaging to the host organism (parasitism). If microorganisms can cause disease in a host they are known as pathogens.

## Extremophiles
Certain microbes have adapted so that they can survive and even thrive in conditions that are normally fatal to most lifeforms. Microorganisms have been found around underwater black smokers and in geothermal hot springs, as well as in extremely salty bodies of water.

## Soil microbes
The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. One way this can occur is in the nodules in the roots of legumes that contain symbiotic bacteria of the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium.

## Symbiotic microbes
Symbiotic microbes

# Importance
Microorganisms are vital to humans and the environment, as they participate in the Earth's element cycles such as the carbon cycle and nitrogen cycle, as well as fulfilling other vital roles in virtually all ecosystems, such as recycling other organisms' dead remains and waste products through decomposition. Microbes also have an important place in most higher-order multicellular organisms as symbionts. Many blame the failure of Biosphere 2 on an improper balance of microbes.

## Use in food
Microorganisms are used in brewing, baking and other food-making processes.
The lactobacillus / lactobacilli and yeasts in sourdough bread are especially useful. To make bread, one uses a small amount (20-25%) of "starter" dough which has the yeast culture, and mixes it with flour and water.  Some of this resulting dough is then saved to be used as the starter for subsequent batches.  The culture can be kept at room temperature and continue yielding bread for years as long as it remains supplied with new flour and water.  This technique was often used when "on the trail" in the American Old West.
Microorganisms are also used to control the fermentation process in the production of cultured dairy products such as yogurt and cheese. The cultures also provide flavour and aroma, and to inhibit undesirable organisms.

## Use in water treatment
Microbes are used in the biological treatment of sewage and industrial waste effluents.

## Use in energy
Microbes are used in fermentation to produce ethanol.

## Use in science
Microbes are also essential tools in biotechnology, biochemistry, genetics, and molecular biology. Microbes can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microbes for living fuel cells, and as a solution for pollution.

## Use in warfare
In the Middle Ages, dead corpses were thrown over walls during sieges, this meant that any bacteria carrying the disease that killed the person/creature would multiply in the vicinity of the opposing side.

# Importance in human health

## Human digestion
Microorganisms can form an endosymbiotic relationship with other, larger, organisms. For example, the bacteria that live within the human digestive system contribute to gut immunity, synthesise vitamins such as folic acid and biotin, and ferment complex undigestible carbohydrates.

## Diseases and immunology
Microorganisms are the cause of many infectious diseases. The organisms involved include bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoa, causing diseases such as malaria, sleeping sickness and toxoplasmosis; and also fungi causing diseases such as ringworm, candidiasis or histoplasmosis. However, other diseases such as influenza, yellow fever or AIDS are caused by viruses, which are not living organisms and are not therefore microorganisms. As of 2007, no clear examples of archaean pathogens are known, although a relationship has been proposed between the presence of some methanogens and human periodontal disease.

# Hygiene
Hygiene is the avoidance of infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms, particularly bacteria, are found practically everywhere, this means in most cases the reduction of harmful microorganisms to acceptable levels. However, in some cases it is required that an object or substance is completely sterile, i.e. devoid of all living entities and viruses. A good example of this is a hypodermic needle.
In food preparation microorganisms are reduced by preservation methods (such as the addition of vinegar), clean utensils used in preparation, short storage periods or by cool temperatures. If complete sterility is needed, the two most common methods are irradiation and the use of an autoclave, which resembles a pressure cooker.
There are several methods for investigating the level of hygiene in a sample of food, drinking water, equipment etc. Water samples can be filtrated through an extremely fine filter. This filter is then placed in a nutrient medium. Microorganisms on the filter then grow to form a visible colony. Harmful microorganisms can be detected in food by placing a sample in a nutrient broth designed to enrich the organisms in question. Various methods, such as selective media or PCR, can then be used for detection. The hygiene of hard surfaces, such as cooking pots, can be tested by touching them with a solid piece of nutrient medium and then allowing the microorganisms to grow on it.
There are no conditions where all microorganisms would grow, and therefore often several different methods are needed. For example, a food sample might be analyzed on three different nutrient mediums designed to indicate the presence of "total" bacteria (conditions where many, but not all, bacteria grow), molds (conditions where the growth of bacteria is prevented by e.g. antibiotics) and coliform bacteria (these indicate a sewage contamination).