Microorganism

A cluster of Escherichia coli bacteria magnified 10,000 times

A microorganism or microbe is a microscopic organism, which may be single-celled[1] or multicellular. The study of microorganisms is called microbiology, a subject that began with the discovery of microorganisms in the 1670s by Antonie van Leeuwenhoek.[2] Robert Hooke coined the term "cell" after viewing plant cells under his microscope. Later, in the 19th century, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In 1876 Robert Koch discovered that microorganisms cause diseases.

Microorganisms are very diverse and include all bacteria, archaea and most protozoa. This group also contains some fungi, algae, and some micro-animals such as rotifers. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists classify viruses and viroids as microorganisms, but others consider these as nonliving.[3][4] In July 2016, scientists identified a set of 355 genes from the last universal common ancestor of all life, including microorganisms, living on Earth.[5]

Microorganisms live in every part of the biosphere, including soil, hot springs, inside rocks at least 19 km (12 mi) deep underground, the deepest parts of the ocean, and at least 64 km (40 mi) high in the atmosphere.[6][7][8] Microorganisms, under certain test conditions, have been observed to thrive in the vacuum of outer space.[9][10] Microorganisms likely far outweigh all other living things combined. The mass of prokaryote microorganisms including the bacteria and archaea may be as much as 0.8 trillion tons of carbon, out of the total biomass of between 1 and 4 trillion tons.[11] Microorganisms appear to thrive in the Mariana Trench, the deepest spot in the Earth's oceans.[12][13] Other researchers reported related studies that microorganisms thrive inside rocks up to 580 m (1,900 ft; 0.36 mi) below the sea floor under 2,590 m (8,500 ft; 1.61 mi) of ocean off the coast of the northwestern United States,[12][14] as well as 2,400 m (7,900 ft; 1.5 mi) beneath the seabed off Japan.[15] In August 2014, scientists confirmed the existence of microorganisms living 800 m (2,600 ft; 0.50 mi) below the ice of Antarctica.[16][17] According to one researcher, "You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are."[12]

Microorganisms are crucial to nutrient recycling in ecosystems as they act as decomposers. As some microorganisms can fix nitrogen, they are a vital part of the nitrogen cycle, and recent studies indicate that airborne microorganisms may play a role in precipitation and weather.[18] Microorganisms are also exploited in biotechnology, both in traditional food and beverage preparation, and in modern technologies based on genetic engineering. A small proportion of microorganisms are pathogenic, causing disease and even death in plants and animals.[19]

Evolution

Single-celled microorganisms were the first forms of life to develop on Earth, approximately 3–4 billion years ago.[20][21][22] Further evolution was slow,[23] and for about 3 billion years in the Precambrian eon, all organisms were microscopic.[24] So, for most of the history of life on Earth, the only forms of life were microorganisms.[25] Bacteria, algae and fungi have been identified in amber that is 220 million years old, which shows that the morphology of microorganisms has changed little since the Triassic period.[26] The newly discovered biological role played by nickel, however — especially that brought about by volcanic eruptions from the Siberian Traps — may have accelerated the evolution of methanogens towards the end of the Permian–Triassic extinction event.[27]

Microorganisms tend to have a relatively fast rate of evolution. Most microorganisms can reproduce rapidly, and bacteria are also able to freely exchange genes through conjugation, transformation and transduction, even between widely divergent species.[28] This horizontal gene transfer, coupled with a high mutation rate and other means of transformation, allows microorganisms to swiftly evolve (via natural selection) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the development of multidrug resistant pathogenic bacteria, superbugs, that are resistant to antibiotics.[29]

Pre-microbiology

The possible existence of microorganisms was discussed for many centuries before their discovery in the 17th century. The existence of unseen microbial life was postulated by Jainism. In the 6th century BC, Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air and fire.[30] The Jain scriptures also describe nigodas, which are sub-microscopic creatures living in large clusters and having a very short life, which are said to pervade every part of the universe, even the tissues of plants and animals.[31] The earliest known idea to indicate the possibility of diseases spreading by yet unseen organisms was that of the Roman scholar Marcus Terentius Varro in a first century BC book titled On Agriculture in which he warns against locating a homestead near swamps:

… and because there are bred certain minute creatures that cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and they cause serious diseases.[32]

In The Canon of Medicine (1020), Abū Alī ibn Sīnā (Avicenna) suggested that tuberculosis and other diseases might be contagious.[33][34]

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or even without contact over long distances.[35]

These early claims about the existence of microorganisms were speculative, and while grounded on indirect observations, they had no systematized empirical basis. Microorganisms were neither proven, observed, nor accurately described until the 17th century with the invention of the microscope.

History of discovery

Antonie van Leeuwenhoek is acknowledged as the first to study microorganisms, using simple microscopes of his own design.
Lazzaro Spallanzani showed that boiling a broth stopped it from decaying.
Louis Pasteur showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.
Robert Koch showed that microorganisms caused disease.

Antonie Van Leeuwenhoek (1632–1723) is considered to be the father of microbiology as he was the first to undisputedly discover, observe, describe, study and conduct scientific experiments with microoorganisms, using simple single-lensed microscopes of his own design.[2][36] Robert Hooke, a contemporary of Leeuwenhoek, also used microscopes to observe microbial life; his 1665 book Micrographia describes these observations and coined the term cell.

Before Leeuwenhoek's discovery of microorganisms in 1675, it had been a mystery 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 a microscope, he did establish that there were signs of life that were not visible to the naked eye.[37][38] Leeuwenhoek's discovery, along with subsequent observations by Spallanzani and Pasteur, ended the long-held belief that life spontaneously appeared from non-living substances during the process of spoilage.

Lazzaro Spallanzani (1729–1799) found that boiling broth would sterilise it, killing any microorganisms in it. He also found that new microorganisms could only settle in a broth if the broth was exposed to air.

Louis Pasteur (1822–1895) 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 (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle which were infected with anthrax always had large numbers of Bacillus anthracis. Koch 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, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. Based on these experiments, he devised criteria for establishing a causal link between a microorganism and a disease and these are now known as Koch's postulates.[39] Although these postulates cannot be applied in all cases, they do retain historical importance to the development of scientific thought and are still being used today.[40]

On 8 November 2013, scientists reported the discovery of what may be the earliest signs of life on Earth—the oldest complete fossils of a microbial mat (associated with sandstone in Western Australia) estimated to be 3.48 billion years old.[41][42]

Classification and structure

Evolutionary tree showing the common ancestry of all three domains of life.[43] Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of some phyla are shown around the tree.

Microorganisms can be found almost anywhere on Earth. Bacteria and archaea are almost always microscopic, while a number of eukaryotes are also microscopic, including most protists, some fungi, as well as some micro-animals and plants. Viruses are generally regarded as not living and therefore not considered as microorganisms, although the field of microbiology includes virology, the study of viruses.[44][45]

Prokaryotes

Prokaryotes are organisms that lack a cell nucleus and other membrane-bound organelles. They are almost always unicellular, although some species such as myxobacteria can aggregate into complex structures as part of their life cycle.

Consisting of two domains, bacteria and archaea, the prokaryotes are the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 °C. They are found in water, soil, air, as the microbiome of an organism, hot springs and even deep beneath the Earth's crust in rocks.[46] Practically all surfaces that have not been specially sterilized are covered by prokaryotes. The number of prokaryotes is estimated to be around five million trillion trillion, or 5 × 1030, accounting for at least half the biomass on Earth.[47]

The biodiversity of the prokaryotes is unknown, but may be very large. A May 2016 estimate, based on laws of scaling from known numbers of species against the size of organism, gives an estimate of perhaps 1 trillion species on the planet, of which most would be microorganisms. Currently, only one-thousandth of one percent of that total have been described.[48]

Bacteria

Staphylococcus aureus bacteria magnified about 10,000x

Almost all bacteria are invisible to the naked eye, with a few extremely rare exceptions, such as Thiomargarita namibiensis.[49] They lack a nucleus and other membrane-bound organelles, and can function and reproduce as individual cells, but often aggregate in multicellular colonies.[50] Their genome is usually a single loop of DNA, although they can also harbor small pieces of DNA called plasmids. These plasmids can be transferred between cells through bacterial conjugation. Bacteria are surrounded by a cell wall, which provides strength and rigidity to their cells. They reproduce by binary fission or sometimes by budding, but do not undergo meiotic sexual reproduction. However, many bacterial species can transfer DNA between individual cells by a process referred to as natural transformation.[51][52] Some species form extraordinarily 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 20 minutes.[53]

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. However, in 1990 the microbiologist Carl Woese proposed the three-domain system that divided living things into bacteria, archaea and eukaryotes.[54] Archaea differ from bacteria in both their genetics and biochemistry. For example, while bacterial cell membranes are made from phosphoglycerides with ester bonds, archaean membranes are made of ether lipids.[55]

Archaea were originally described in extreme environments, such as hot springs, but have since been found in all types of habitats.[56] Only now are scientists beginning to realize 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.[57][58] These organisms are also common in soil and play a vital role in ammonia oxidation.[59]

Eukaryotes

Most living things that are visible to the naked eye in their adult form are eukaryotes, 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 that houses the DNA that makes up a cell's genome. DNA (Deoxyribonuclaic acid) itself is arranged in complex chromosomes.[60] 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.[61] 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.[61]

Unicellular eukaryotes 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 only at the beginning of their life cycles. Microbial eukaryotes can be either haploid or diploid, and some organisms have multiple cell nuclei.[62]

Unicellular eukaryotes usually reproduce asexually by mitosis under favorable conditions. However, under stressful conditions such as nutrient limitations and other conditions associated with DNA damage, they tend to reproduce sexually by meiosis and syngamy.[63]

Protists

Of eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a highly diverse group of organisms that are not easy to classify.[64][65] Several algae species are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.[66] The number of species of protists is unknown since only a small proportion has been identified. Studies from 2001-2004 have shown that a high degree of protist diversity exists in oceans, deep sea-vents, river sediment and an acidic river which suggests that a large number of eukaryotic microbial communities have yet to be discovered.[67][68]

A microscopic mite Lorryia formosa

Animals

Some micro-animals are multicellular but at least one animal group, Myxozoa, is unicellular in its adult form. Microscopic arthropods include dust mites and spider mites. Microscopic crustaceans include copepods, some cladocera and water bears. Many nematodes are also too small to be seen with the naked eye. A common group of microscopic animals are the rotifers, which are filter feeders that are usually found in fresh water. Some micro-animals reproduce both sexually and asexually and may reach new habitats by producing eggs which can survive harsh environments that would kill the adult animal. However, some simple animals, such as rotifers, tardigrades and nematodes, can dry out completely and remain dormant for long periods of time.[69]

Fungi

The fungi have several unicellular species, such as baker's yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe). Some fungi, such as the pathogenic yeast Candida albicans, can undergo phenotypic switching and grow as single cells in some environments, and filamentous hyphae in others.[70] Fungi reproduce both asexually, by budding or binary fission, as well by producing spores, which are called conidia when produced asexually, or basidiospores when produced sexually.

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. Algae can grow as single cells, or in long chains of cells. The green algae include unicellular and colonial flagellates, usually but not always with two flagella per cell, as well as various colonial, coccoid, and filamentous forms. In the Charales, which are the algae most closely related to higher plants, cells differentiate into several distinct tissues within the organism. There are about 6000 species of green algae.[71]

Ecology

Microorganisms are found in almost every habitat present in nature, including 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,[72] and it has been suggested that the amount of living organisms below the Earth's surface is comparable with the amount of life on or above the surface.[46] 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.[73] 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 and then they are sometimes referred to as microbes. Microorganisms play critical roles in Earth's biogeochemical cycles as they are responsible for decomposition and nitrogen fixation.

Extremophiles

Extremophiles are microorganisms that have adapted so that they can survive and even thrive in conditions that are normally fatal to most life-forms. For example, some species have been found in the following extreme environments:

Extremophiles are significant in different ways. They extend terrestrial life into much of the Earth's hydrosphere, crust and atmosphere, their specific evolutionary adaptation mechanisms to their extreme environment can be exploited in bio-technology, and their very existence under such extreme conditions increases the potential for extraterrestrial life.[81]

In soil

The nitrogen cycle in soils depends on the fixation of atmospheric nitrogen. This is achieved by a number of diazotrophs. 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.[82]

Symbiosis

A lichen is a symbiosis of a fungus with microbial algae. The algal partner is photosynthetic, enabling the fungus to live in habitats such as bare rocks where other sources of nutrition are not available.

Other fungi, including some edible mushrooms such as the cep, form mycorrhizal symbioses with trees. The fungi increase the supply of nutrients to the tree in return for a supply of energy.

Applications

Microorganisms are vital to humans and the environment, as they participate in the carbon and nitrogen cycles, as well as fulfilling other vital roles in virtually all ecosystems, such as recycling other organisms' dead remains and waste products through decomposition. Microorganisms 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 microorganisms.[83]

Food production

Microorganisms are used to make yoghurt, cheese, curd, kefir, ayran, xynogala, and other types of food. They are used to leaven bread, and to convert sugars to alcohol in wine and beer. Microorganisms are used in brewing, wine making, baking, pickling and other food-making processes.

They are also used to control the fermentation process in the production of cultured dairy products such as yogurt and cheese. The cultures also provide flavor and aroma, and inhibit undesirable organisms.[84]

Water treatment

The majority of all oxidative sewage treatment processes rely on a large range of microorganisms to oxidise organic constituents which are not amenable to sedimentation or flotation. Anaerobic microorganisms are also used to reduce sludge solids producing methane gas (amongst other gases) and a sterile mineralised residue. In potable water treatment, one method, the slow sand filter, employs a complex gelatinous layer composed of a wide range of microorganisms to remove both dissolved and particulate material from raw water.[85]

Energy

Microorganisms are used in fermentation to produce ethanol,[86] and in biogas reactors to produce methane.[87] Scientists are researching the use of algae to produce liquid fuels,[88] and bacteria to convert various forms of agricultural and urban waste into usable fuels.[89]

Chemicals, enzymes

Microorganisms are used for many commercial and industrial production of chemicals, enzymes and other bioactive molecules.

Organic acids produced by microbial fermentation include

Microorganisms are used for preparation of bioactive molecules and enzymes, including:

Science

Microorganisms are essential tools in biotechnology, biochemistry, genetics, and molecular biology. The yeasts (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are important model organisms in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated.[91] They are particularly valuable in genetics, genomics and proteomics.[92][93] Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living fuel cells,[94] and as a solution for pollution.[95]

Warfare

In the Middle Ages, as an early example of biological warfare, diseased corpses were thrown into castles during sieges using catapults or other siege engines. Individuals near the corpses were exposed to the pathogen and were likely to spread that pathogen to others.[96]

Soil

Microbes can make nutrients and minerals in the soil available to plants, produce hormones that spur growth, stimulate the plant immune system and trigger or dampen stress responses. In general a more diverse soil microbiome results in fewer plant diseases and higher yield.[97]

Human health

Human bacterial flora

Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The bacteria that live within the human digestive system contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates.[98]

Disease

Microorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoa, causing diseases such as malaria, sleeping sickness, dysentery 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 pathogenic viruses, which are not usually classified as living organisms and are not, therefore, microorganisms by the strict definition. No clear examples of archaean pathogens are known,[99] although a relationship has been proposed between the presence of some archaean methanogens and human periodontal disease.[100]

Hygiene

Hygiene is a set of practices to avoid infection or food spoiling by eliminating microorganisms from the surroundings. As microorganisms, in particular bacteria, are found virtually everywhere, harmful microorganisms may be reduced to acceptable levels rather than actually eliminated. In food preparation, microorganisms are reduced by preservation methods such as cooking, cleanliness of utensils, short storage periods, or by low temperatures. If complete sterility is needed, as with surgical equipment, an autoclave is used to kill microorganisms with heat and pressure.[101][102]

Etymology and pronunciation

The word microorganism (/ˌmaɪkroʊˈɔːrɡənɪzəm/) uses combining forms of micro- (from the Greek: μικρός, mikros, "small") and organism from the Greek: ὀργανισμός, organismós, "organism"). It is usually styled solid but is sometimes hyphenated (micro-organism), especially in older texts. The word microbe (/ˈmaɪkroʊb/) comes from μικρός, mikrós, "small" and βίος, bíos, "life".

See also

References

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