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Microorganism

History

Evolution

Further information: Timeline of 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 forms 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 has 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 is important in medicine, as it has led to the recent development of 'super-bugs' pathogenic bacteria that are resistant to modern antibiotics.

Pre-Microbiology

The possibility that microorganisms exist was discussed for many centuries before their actual discovery in the 17th century. 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 1st century BC book titled On Agriculture in which he warns against locating a homestead near swamps:

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

In The Canon of Medicine (1020), Ab Al ibn Sn (Avicenna) stated that bodily secretion is contaminated by foul foreign earthly bodies before being infected. He also hypothesized that tuberculosis and other diseases might be contagious, i.e. that they were infectious diseases, and used quarantine to limit their spread.

When the Black Death bubonic plague reached Andalusia in Spain, in the 14th century, Ibn Khatima wrote that infectious diseases were caused by contagious "minute bodies" that enter the human body. Later, 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.

All these early claims about the existence of microorganisms were speculative and were not based on any data or science. Microorganisms were neither proven, observed, nor correctly and accurately described until the 17th century. The reason for this was that all these early studies lacked the microscope.

History of microorganisms' discovery

See also: History of biology

Antonie van Leeuwenhoek, the first microbiologist and the first to observe microorganisms using a microscope.

Anton van Leeuwenhoek was the one of the first people to observe microorganisms, using a microscope of his own design, and made one of the most important contributions to biology. Robert Hooke was the first to use a microscope to observe living things; his 1665 book Micrographia contained descriptions of plant cells.

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 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.

Lazzaro Spallanzani found that boiling broth would sterilise it and kill any microorganisms in it. He also found that new microorganisms could only settle in a broth if the broth was exposed to the air. 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 1767, Dr. J. Z. Holwell reported that Indian physicians at the time knew that microbes caused diseases: "They lay it down as a principle, that the immediate cause of the smallpox exists in the mortal part of every human and animal form; that the mediate (or second) acting cause, which stirs up the first, and throws it into a state of fermentation, is multitudes of imperceptible animalculae floating in the atmosphere; that these are the cause of all epidemical diseases, but more particularly of the small pox."

In 1876, Robert Koch established that microbes can cause disease. He found that the blood of cattle who 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 microbe and a disease and these are now known as Koch's postulates. 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.

Classification and structure

Evolutionary tree showing the common ancestry of all three domains of life. 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 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, some fungi, as well as some animals and plants. Viruses are generally regarded as not living and therefore are not microbes, although the field of microbiology also encompasses the study of viruses.

Prokaryotes

Main article: Prokaryote

Prokaryotes are organisms that lack a cell nucleus and the 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 some liquid water is available and the temperature is below +140 C. They are found in sea water, soil, air, 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 by prokaryotes. The number of prokaryotes on Earth is estimated to be around five million trillion trillion, or 5 1030, accounting for at least half the biomass on Earth.

Bacteria

Main article: Bacteria

Staphylococcus aureus bacteria magnified about 10,000x

Bacteria are practically all invisible to the naked eye, with a few extremely rare exceptions, such as Thiomargarita namibiensis. They lack membrane-bound organelles, and can function and reproduce as individual cells, but often aggregate in multicellular colonies. 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 sexual reproduction. 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 10 minutes.

Archaea

Main article: 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. 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.

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 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. These organisms are also common in soil and play a vital role in ammonia oxidation.

Eukaryotes

Ostreococcus is the smallest known free living eukaryote with an average size of 0.8 m

Main article: Eukaryote

Most living things which 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 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

Main article: Protista

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. Several algae species are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms. The number of species of protozoa is uncertain, since we may have identified only a small proportion of the diversity in this group of organisms.

A microscopic mite Lorryia formosa.

Animals

Main article: Micro-animals

Mostly 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, while many nematodes are too small to be seen with the naked eye. Another particularly common group of microscopic animals are the rotifers, which are filter feeders that are usually found in fresh water. Micro-animals reproduce both sexually and asexually and may reach new habitats as eggs that survive harsh environments that would kill the adult animal. However, some simple animals, such as rotifers and nematodes, can dry out completely and remain dormant for long periods of time.

Fungi

Main article: Fungus

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. 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

Main article: Plant

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.

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

Main article: Extremophile

Extremophiles are microorganisms which 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:

Temperature: as high as 130 C (266 F), as low as 17 C (1.4 F)

Acidity/alkalinity: less than pH 0, up to pH 11.5

Salinity: up to saturation

Pressure: up to 1,000-2,000 atm, down to 0 atm (e.g. vacuum of space)

Radiation: up to 5kGy

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.

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 such as fungi and algae form an association in lichen. Certain fungi form mycorhizzal symbioses with trees that increase the supply of nutrients to the tree.

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

Main article: Fermentation (food)

Microorganisms are used in brewing, winemaking, 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 flavour and aroma, and inhibit undesirable organisms.

Use in water treatment

Main article: Sewage treatment

Specially-cultured microbes are used in the biological treatment of sewage and industrial waste effluent, a process known as bioaugmentation.

Use in energy

Main articles: Algae fuel, Cellulosic ethanol, and Ethanol fermentation

Microbes are used in fermentation to produce ethanol, and in biogas reactors to produce methane. Scientists are researching the use of algae to produce liquid fuels, and bacteria to convert various forms of agricultural and urban waste into usable fuels.

Use in science

Microbes are also 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. They are particularly valuable in genetics, genomics and proteomics. 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

Main article: Biological warfare

In the Middle Ages, diseased corpses were thrown into castles during sieges using catapults or other siege engines. Individuals near the corpses were exposed to the deadly pathogen and were likely to spread that pathogen to others.

Importance in human health

Human digestion

Further information: Human flora#Human bacterial flora and human health

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 indigestible carbohydrates.

Diseases and immunology

Main article: Pathogenic microbes

Microorganisms are the cause of 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 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. 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.

Importance in ecology

Further information: Decomposition

Microbes are critical to the processes of decomposition required to cycle nitrogen and other elements back to the natural world.

Hygiene

Main article: 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 be 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).

See also

Biological warfare

Biology

Culture collection

Microbial intelligence

Nanobacterium

Petri dish

Prokaryote

Soil contamination

Staining

Virus

Bacterium

Protozoa

Fungi

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^ Some Psychrophilic bacteria can grow at 17 C (1.4 F), and can survive near absolute zero.

^ Picrophilus can grow at pH -0.06.

^ The alkaliphilic bacteria Bacillus alcalophilus can grow at up to pH 11.5.

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^ See Deinococcus radiodurans

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^ Pimental, David (2007). Food, Energy, and Society. CRC Press. p. 289. ISBN 1-420-04667-5. 

^ Tickell, Joshua et al. (2000). From the Fryer to the Fuel Tank: The Complete Guide to Using Vegetable Oil as an Alternative Fuel. Biodiesel America. p. 53. ISBN 0-970-72270-2. 

^ Inslee, Jay et al. (2008). Apollo's Fire: Igniting America's Clean Energy Economy. Island Press. p. 157. ISBN 1-597-26175-0. 

^ Castrillo JI, Oliver SG (2004). "Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics". J. Biochem. Mol. Biol. 37 (1): 93106. PMID 14761307. http://www.jbmb.or.kr/fulltext/jbmb/view.php?vol=37&page=93. 

^ Suter B, Auerbach D, Stagljar I (2006). "Yeast-based functional genomics and proteomics technologies: the first 15 years and beyond". BioTechniques 40 (5): 62544. doi:10.2144/000112151. PMID 16708762. 

^ Sunnerhagen P (2002). "Prospects for functional genomics in Schizosaccharomyces pombe". Curr. Genet. 42 (2): 7384. doi:10.1007/s00294-002-0335-6. PMID 12478386. 

^ Soni, S.K. (2007). Microbes: A Source of Energy for 21st Century. New India Publishing. ISBN 8-189-42214-6. 

^ Moses, Vivian et al. (1999). Biotechnology: The Science and the Business. CRC Press. p. 563. ISBN 9-057-02407-1. 

^ Langford, Roland E. (2004). Introduction to Weapons of Mass Destruction: Radiological, Chemical, and Biological. Wiley-IEEE. p. 140. ISBN 0-471-46560-7. 

^ O'Hara A, Shanahan F (2006). "The gut flora as a forgotten organ". EMBO Rep 7 (7): 68893. doi:10.1038/sj.embor.7400731. PMID 16819463. 

^ Eckburg P, Lepp P, Relman D (2003). "Archaea and their potential role in human disease". Infect Immun 71 (2): 5916. doi:10.1128/IAI.71.2.591-596.2003. PMID 12540534. 

^ Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D (2004). "Methanogenic Archaea and human periodontal disease". Proc Natl Acad Sci USA 101 (16): 617681. doi:10.1073/pnas.0308766101. PMID 15067114. 

External links

Our Microbial Planet A free poster from the National Academy of Sciences about the positive roles of microbes.

"Uncharted Microbial World: Microbes and Their Activities in the Environment" Report from the American Academy of Microbiology

Understanding Our Microbial Planet: The New Science of Metagenomics A 20-page educational booklet providing a basic overview of metagenomics and our microbial planet.

Tree of Life Eukaryotes

Microbe News from Genome News Network

Microbes Patent List Microbes Related Patents

Medical Microbiology On-line textbook

Through the microscope: A look at all things small On-line microbiology textbook by Timothy Paustian and Gary Roberts, University of Wisconsin-Madison

MicrobeID.com Online Bacteria Identification Key and Probabilistic Identification Databases

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