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{{Redirect|Microbe}}{{short description|Microscopic living organism}}{{good article}}{{Use dmy dates|date=July 2012}}File:E coli at 10000x, original.jpg|thumb|upright=1.15|right|A cluster of Escherichia coli bacteriabacteriaA microorganism, or microbe,{{efn|The word microorganism ({{IPAc-en|ˌ|m|aɪ|k|r|oʊ-|ˈ|ɔːr|g|ə|n|ɪ|z|əm}}) uses combining forms of (wikt:micro-#Prefix|micro-) (from the , mikros, "small") and organism from the , organismós, "organism"). It is usually styled solid but is sometimes hyphenated (micro-organism), especially in older texts. The informal synonym microbe ({{IPAc-en|ˈ|m|aɪ|k|r|oʊ|b}}) comes from μικρός, mikrós, "small" and βίος, bíos, "life".}} is a microscopic organism, which may exist in its single-celled form or in a colony of cells.The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.WEB, Tyrell, Kelly April, Oldest fossils ever found show life on Earth began before 3.5 billion years ago,weblink 18 December 2017, University of Wisconsin–Madison, 18 December 2017, JOURNAL, Schopf, J. William, Kitajima, Kouki, Spicuzza, Michael J., Kudryavtsev, Anatolly B., Valley, John W., SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions, 2017, Proceedings of the National Academy of Sciences of the United States of America, PNAS, 115, 1, 53–58, 10.1073/pnas.1718063115, 29255053, 5776830, 2018PNAS..115...53S, Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

History and discovery

{{See also|History of biology|Microbiology#History}} File:Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg|thumb|upright|Antonie van Leeuwenhoek was the first to study microorganisms, using simple microscopemicroscopeFile:Spallanzani.jpg|thumb|upright|Lazzaro SpallanzaniLazzaro Spallanzani

Ancient precursors

File:Mahaveer swami.jpg|thumb|upright|150px|Vardhmana Mahavira postulated the existence of microscopic creatures in the 6th century BC.]]The possible existence of microorganisms was discussed for many centuries before their discovery in the 17th century. By the fifth century BC, the Jains of present-day India postulated the existence of tiny organisms called nigodas.BOOK, Jeffery D Long, Jainism: An Introduction,weblink 2013, I.B.Tauris, 978-0-85771-392-6, 100, These nigodas are said to be born in clusters; they live everywhere, including the bodies of plants, animals, and people; and their life lasts only for fraction of a second.BOOK, Upinder Singh, A History of Ancient and Early Medieval India: From the Stone Age to the 12th Century,weblink 2008, Pearson Education India, 978-81-317-1677-9, 315, According to the Jain leader Mahavira, the humans destroy these nigodas on a massive scale, when they eat, breathe, sit and move. Many modern Jains assert that Mahavira's teachings presage the existence of microorganisms as discovered by modern science.BOOK, Paul Dundas, The Jains,weblink 2003, Routledge, 978-1-134-50165-6, 106, 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 called the unseen creatures animalcules, and warns against locating a homestead near a swamp:Varro On Agriculture 1, xii LoebIn The Canon of Medicine (1020), Avicenna suggested that tuberculosis and other diseases might be contagious.JOURNAL, Tschanz, David W., Arab Roots of European Medicine, Heart Views, 4, 2,weblink yes,weblink" title="web.archive.org/web/20110503050312weblink">weblink 3 May 2011, BOOK, Advice to the Young Physician: On the Art of Medicine, {{google books, y, DoMVs4HuDAoC, 33, |last=Colgan|first=Richard |page=33 |publisher=Springer |year=2009 |isbn=978-1-4419-1033-2}}

Early modern

Akshamsaddin (Turkish scientist) mentioned the microbe in his work Maddat ul-Hayat (The Material of Life) about two centuries prior to Antonie Van Leeuwenhoek's discovery through experimentation: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.JOURNAL, Nutton, Vivian, The Reception of Fracastoro's Theory of Contagion: The Seed That Fell among Thorns?, Osiris (journal), Osiris, 1990, 2nd Series, Vol. 6, Renaissance Medical Learning: Evolution of a Tradition, 196–234, 301787, 10.1086/368701, Antonie Van Leeuwenhoek is considered to be the father of microbiology. He was the first in 1673 to discover, observe, describe, study and conduct scientific experiments with microoorganisms, using simple single-lensed microscopes of his own design.JOURNAL, Leeuwenhoek, A., Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs, Philosophical Transactions, 22, 509–18, 1753, 10.1098/rstl.1700.0013, 260–276, JOURNAL, Leeuwenhoek, A., Antony van Leeuwenhoek, Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them, Philosophical Transactions, 23, 1304–11, 1753, 10.1098/rstl.1702.0042, 277–288, JOURNAL, Nick Lane, Lane, Nick, The Unseen World: Reflections on Leeuwenhoek (1677) 'Concerning Little Animal', Philos Trans R Soc Lond B Biol Sci, 370, 1666, 20140344, 2015, 10.1098/rstb.2014.0344, 25750239, 4360124, Payne, A.S. The Cleere Observer: A Biography of Antoni Van Leeuwenhoek, p. 13, Macmillan, 1970 Robert Hooke, a contemporary of Leeuwenhoek, also used microscopy to observe microbial life in the form of the fruiting bodies of moulds. In his 1665 book Micrographia, he made drawings of studies, and he coined the term cell.JOURNAL, Gest, H., The remarkable vision of Robert Hooke (1635–1703): first observer of the microbial world, Perspect. Biol. Med., 48, 2, 266–72, 2005, 15834198, 10.1353/pbm.2005.0053,

19th century

File:Albert Edelfelt - Louis Pasteur - 1885.jpg|thumb|upright|left|Louis PasteurLouis PasteurLouis Pasteur (1822–1895) exposed boiled broths to the air, in vessels that contained a filter to prevent particles from passing through to the growth medium, and also in vessels without a filter, but with air allowed in via a curved tube so dust particles would settle and not 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 refuted the theory of spontaneous generation and supported the germ theory of disease.JOURNAL, Bordenave, G., Louis Pasteur (1822–1895), Microbes Infect., 5, 6, 553–60, 2003, 12758285, 10.1016/S1286-4579(03)00075-3, File:Robert Koch.jpg|thumb|upright|Robert Koch showed that microorganisms caused diseasediseaseIn 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.The Nobel Prize in Physiology or Medicine 1905 Nobelprize.org Accessed 22 November 2006. 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.JOURNAL, O'Brien, S., Goedert, J., HIV causes AIDS: Koch's postulates fulfilled, Curr Opin Immunol, 8, 5, 613–18, 1996, 8902385, 10.1016/S0952-7915(96)80075-6,weblink The discovery of microorganisms such as Euglena that did not fit into either the animal or plant kingdoms, since they were photosynthetic like plants, but motile like animals, led to the naming of a third kingdom in the 1860s. In 1860 John Hogg called this the Protoctista, and in 1866 Ernst Haeckel named it the Protista.JOURNAL, Scamardella, J. M., Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista, 1999, International Microbiology, 2, 207–221,weblink JOURNAL, Rothschild, L. J., Protozoa, Protista, Protoctista: what's in a name?, J Hist Biol, 22, 2, 277–305, 1989, 11542176, 10.1007/BF00139515, BOOK, Eldra Pearl, Solomon, Linda R., Berg, Diana W., Martin, Kingdoms or Domains?,weblink 421–7, Biology, Brooks/Cole Thompson Learning, 2005, 7th, 978-0-534-49276-2, The work of Pasteur and Koch did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck and Sergei Winogradsky late in the 19th century that the true breadth of microbiology was revealed.BOOK, Madigan, M., Martinko, J., Brock Biology of Microorganisms, 13th, Pearson Education, 2006, 978-0-321-73551-5, 1096, Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques.WEB, Johnson, J., Martinus Willem Beijerinck, APSnet, American Phytopathological Society,weblinkweblink" title="web.archive.org/web/20100620173433weblink">weblink 2010-06-20, 2001, 1998, 2 May 2010, Retrieved from Internet Archive 12 January 2014. While his work on the Tobacco Mosaic Virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes.BOOK, Paustian, T., Roberts, G., Beijerinck and Winogradsky Initiate the Field of Environmental Microbiology, Through the Microscope: A Look at All Things Small, § 1–14, 3rd, 2009, Textbook Consortia,weblink He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages and was one of the earliest applied microbiologists.JOURNAL, Keen, E. C., Felix d'Herelle and Our Microbial Future, Future Microbiology, 7, 12, 1337–1339, 2012, 23231482, 10.2217/fmb.12.115,

Classification and structure

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 a subfield of microbiology is virology, the study of viruses.BOOK, eLS, Lim, Daniel V., 2001, John Wiley, 9780470015902, 10.1038/npg.els.0000459, Microbiology, WEB,weblink What is Microbiology?, www.highveld.com, 2017-06-02, BOOK, Cann, Alan, Principles of Molecular Virology, 2011, Academic Press, 978-0123849397, 5,

Evolution

{{further|Timeline of evolution|Earliest known life forms}}{{PhylomapB||caption=Carl Woese's 1990 phylogenetic tree based on rRNA data shows the domains of Bacteria, Archaea, and Eukaryota. All are microorganisms except some eukaryote groups.|size=250px}}Single-celled microorganisms were the first forms of life to develop on Earth, approximately 3–4 billion years ago.JOURNAL, Schopf, J., Fossil evidence of Archaean life, Philos Trans R Soc Lond B Biol Sci, 361, 1470, 869–885, 2006, 16754604, 10.1098/rstb.2006.1834, 1578735, JOURNAL, Altermann, W., Kazmierczak, J., Archean microfossils: a reappraisal of early life on Earth, Res Microbiol, 154, 9, 611–7, 2003, 14596897, 10.1016/j.resmic.2003.08.006, JOURNAL, Cavalier-Smith, T., Thomas Cavalier-Smith, Cell evolution and Earth history: stasis and revolution, Philos Trans R Soc Lond B Biol Sci, 361, 1470, 969–1006, 2006, 16754610, 10.1098/rstb.2006.1842, 1578732, Further evolution was slow,JOURNAL, Schopf, J., Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic, 44277, PNAS, 91, 15, 6735–6742, 1994, 8041691, 10.1073/pnas.91.15.6735, 1994PNAS...91.6735S, and for about 3 billion years in the Precambrian eon, (much of the history of life on Earth), all organisms were microorganisms.JOURNAL, Stanley, S., An Ecological Theory for the Sudden Origin of Multicellular Life in the Late Precambrian, PNAS, 70, 5, 1486–1489, May 1973, 16592084, 433525, 10.1073/pnas.70.5.1486, 1973PNAS...70.1486S, JOURNAL, DeLong, E., Pace, N., Environmental diversity of bacteria and archaea, Syst Biol, 50, 4, 470–8, 2001, 12116647, 10.1080/106351501750435040,weblink 10.1.1.321.8828, 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.JOURNAL, Schmidt, A., Ragazzi, E., Coppellotti, O., Roghi, G., A microworld in Triassic amber, Nature, 444, 7121, 835, 2006, 17167469, 10.1038/444835a, 2006Natur.444..835S, 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.WEB,weblink Microbe's Innovation May Have Started Largest Extinction Event on Earth, Schirber, Michael, 27 July 2014, Astrobiology Magazine, Space.com, That spike in nickel allowed methanogens to take off., 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.JOURNAL, Wolska, K., Horizontal DNA transfer between bacteria in the environment, Acta Microbiol Pol, 52, 3, 233–243, 2003, 14743976, 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.JOURNAL, Enright, M., Robinson, D., Randle, G., Feil, E., Grundmann, H., Spratt, B., The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA), Proc Natl Acad Sci USA, 99, 11, 7687–7692, May 2002, 12032344, 124322, 10.1073/pnas.122108599, 2002PNAS...99.7687E, A possible transitional form of microorganism between a prokaryote and a eukaryote was discovered in 2012 by Japanese scientists. Parakaryon myojinensis is a unique microorganism larger than a typical prokaryote, but with nuclear material enclosed in a membrane as in a eukaryote, and the presence of endosymbionts. This is seen to be the first plausible evolutionary form of microorganism, showing a stage of development from the prokaryote to the eukaryote.WEB, Deep sea microorganisms and the origin of the eukaryotic cell,weblink 24 October 2017, JOURNAL, Yamaguchi, et al, Masashi, Prokaryote or eukaryote? A unique microorganism from the deep sea, 6, Journal of Electron Microscopy, 61, 423–431, 10.1093/jmicro/dfs062, 23024290, 1 December 2012,

Archaea

{{further|Prokaryote}}Archaea are prokaryotic unicellular organisms, and form the first domain of life, in Carl Woese's three-domain system. A prokaryote is defined as having no cell nucleus or other membrane bound-organelle. Archaea share this defining feature with the bacteria with which they were once grouped. In 1990 the microbiologist Woese proposed the three-domain system that divided living things into bacteria, archaea and eukaryotes,JOURNAL, Woese, C., Carl Woese, Kandler, O., Wheelis, M., Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, 10.1073/pnas.87.12.4576, Proc Natl Acad Sci USA, 87, 12, 4576–9, 1990, 2112744, 54159, 1990PNAS...87.4576W, and thereby split the prokaryote domain.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.JOURNAL, De Rosa, M., Gambacorta, A., Gliozzi, A., Structure, biosynthesis, and physicochemical properties of archaebacterial lipids, Microbiol. Rev., 50, 1, 70–80, 1 March 1986, 3083222,weblink 373054, Archaea were originally described as extremophiles living in extreme environments, such as hot springs, but have since been found in all types of habitats.JOURNAL, Robertson, C., Harris, J., Spear, J., Pace, N., Phylogenetic diversity and ecology of environmental Archaea, Curr Opin Microbiol, 8, 6, 638–42, 2005, 16236543, 10.1016/j.mib.2005.10.003, 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.JOURNAL, Karner, M.B., DeLong, E.F., Karl, D.M., Archaeal dominance in the mesopelagic zone of the Pacific Ocean, Nature, 409, 6819, 507–10, 2001, 11206545, 10.1038/35054051, 2001Natur.409..507K, JOURNAL, Sinninghe Damsté, J.S., Rijpstra, W.I., Hopmans, E.C., Prahl, F.G., Wakeham, S.G., Schouten, S., Distribution of Membrane Lipids of Planktonic Crenarchaeota in the Arabian Sea, Appl. Environ. Microbiol., 68, 6, 2997–3002, June 2002, 12039760, 123986, 10.1128/AEM.68.6.2997-3002.2002, These organisms are also common in soil and play a vital role in ammonia oxidation.JOURNAL, Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., James I. Prosser, Schuster, S. C., Schleper, C., Archaea predominate among ammonia-oxidizing prokaryotes in soils, Nature (journal), Nature, 442, 7104, 2006, 806–809, 16915287, 10.1038/nature04983, 2006Natur.442..806L, The combined domains of archaea and bacteria make up the most diverse and abundant group of organisms on Earth and inhabit practically all environments where the temperature is below +140 Â°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.JOURNAL, Gold, T., The deep, hot biosphere, Proc. Natl. Acad. Sci. U.S.A., 89, 13, 6045–9, 1992, 1631089, 10.1073/pnas.89.13.6045, 49434, 1992PNAS...89.6045G, 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.JOURNAL, Whitman, W., Coleman, D., Wiebe, W., Prokaryotes: The unseen majority, 10.1073/pnas.95.12.6578, PNAS, 95, 12, 6578–83, 1998, 9618454, 33863, 1998PNAS...95.6578W, 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.NEWS, Staff, Researchers find that Earth may be home to 1 trillion species,weblink 2 May 2016, National Science Foundation, 6 May 2016,

Bacteria

File:Staphylococcus aureus 01.jpg|thumb|Staphylococcus aureusStaphylococcus aureusBacteria like archaea are prokaryotic – unicellular, and having no cell nucleus or other membrane-bound organelle. Bacteria are microscopic, with a few extremely rare exceptions, such as Thiomargarita namibiensis.JOURNAL, Schulz, H., Jorgensen, B., Big bacteria, Annu Rev Microbiol, 55, 105–37, 2001, 11544351, 10.1146/annurev.micro.55.1.105, Bacteria function and reproduce as individual cells, but they can often aggregate in multicellular colonies.JOURNAL, James A. Shapiro, Shapiro, J.A., Thinking about bacterial populations as multicellular organisms, Annu. Rev. Microbiol., 52, 81–104, 1998, 9891794, 10.1146/annurev.micro.52.1.81,weblink yes,weblink" title="web.archive.org/web/20110717183759weblink">weblink 17 July 2011, Some species such as myxobacteria can aggregate into complex swarming structures, operating as multicellular groups as part of their life cycle,JOURNAL, Myxobacteria: Moving, Killing, Feeding, and Surviving Together, Frontiers in Microbiology, 7, 781, 27303375, 4880591, 2016, Muñoz-Dorado, J., Marcos-Torres, F. J., García-Bravo, E., Moraleda-Muñoz, A., Pérez, J., 10.3389/fmicb.2016.00781, or form clusters in bacterial colonies such as E.coli.Their genome is usually a circular bacterial chromosome – 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 have an enclosing 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 horizontal gene transfer process referred to as natural transformation.JOURNAL, Johnsbor, O., Eldholm, V., Håvarstein, L.S., Natural genetic transformation: prevalence, mechanisms and function, Res. Microbiol., 158, 10, 767–78, December 2007, 17997281, 10.1016/j.resmic.2007.09.004, 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 their numbers can double as quickly as every 20 minutes.JOURNAL, Eagon, R., Pseudomonas Natriegens, a Marine Bacterium With a Generation Time of Less Than 10 Minutes, J Bacteriol, 83, 4, 736–7, 1962, 13888946, 279347,

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 (Deoxyribonucleic acid) itself is arranged in complex chromosomes.Eukaryota: More on Morphology. (Retrieved 10 October 2006)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.JOURNAL, Dyall, S., Brown, M., Johnson, P., Ancient invasions: from endosymbionts to organelles, Science, 304, 5668, 253–7, 2004, 15073369, 10.1126/science.1094884, 2004Sci...304..253D, 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 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.See coenocyte.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.BOOK, Bernstein, H., Bernstein, C., Michod, R.E., 2012,weblink DNA repair as the primary adaptive function of sex in bacteria and eukaryotes., Chapter 1, 1–49, DNA Repair: New Research, Sakura, Kimura, Sora, Shimizu, Nova Sci. Publ., 978-1-62100-808-8,

Protists

File:Euglena mutabilis - 400x - 1 (10388739803) (cropped).jpg|thumb|Euglena mutabilis, a photosynthetic flagellateflagellateOf eukaryotic groups, the protists are most commonly unicellular and microscopic. This is a highly diverse group of organisms that are not easy to classify.JOURNAL, Cavalier-Smith T, Thomas Cavalier-Smith, Kingdom protozoa and its 18 phyla, Microbiol. Rev., 57, 4, 953–994, 1 December 1993, 8302218,weblink 372943, JOURNAL, Corliss JO, Should there be a separate code of nomenclature for the protists?, BioSystems, 28, 1–3, 1–14, 1992, 1292654, 10.1016/0303-2647(92)90003-H, Several algae species are multicellular protists, and slime molds have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.JOURNAL, Devreotes P, Dictyostelium discoideum: a model system for cell-cell interactions in development, Science, 245, 4922, 1054–8, 1989, 2672337, 10.1126/science.2672337, 1989Sci...245.1054D, The number of species of protists is unknown since only a small proportion has been identified. Protist diversity is high in oceans, deep sea-vents, river sediment and an acidic river, suggesting that many eukaryotic microbial communities may yet be discovered.JOURNAL, Slapeta, J, Moreira, D, López-García, P., The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes, Proc. Biol. Sci., 272, 1576, 2073–2081, 2005, 16191619, 10.1098/rspb.2005.3195, 1559898, JOURNAL, Moreira, D., López-García, P., The molecular ecology of microbial eukaryotes unveils a hidden world, Trends Microbiol., 10, 1, 31–8, 2002, 11755083,weblink 10.1016/S0966-842X(01)02257-0,

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.JOURNAL, Kumamoto, C.A., Vinces, M.D., Contributions of hyphae and hypha-co-regulated genes to Candida albicans virulence, Cell. Microbiol., 7, 11, 1546–1554, 2005, 16207242, 10.1111/j.1462-5822.2005.00616.x,

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.BOOK, Thomas, David C., Seaweeds, Natural History Museum, London, 2002, 978-0-565-09175-0,

Ecology

Microorganisms are found in almost every habitat present in nature, including hostile environments such as the North and South poles, deserts, geysers, and rocks. They also include all the marine microorganisms of the oceans and deep sea. Some types of microorganisms have adapted to extreme environments 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,JOURNAL, Szewzyk, U, Szewzyk, R, Stenström, T., Thermophilic, anaerobic bacteria isolated from a deep borehole in granite in Sweden, 10.1073/pnas.91.5.1810, PNAS, 91, 5, 1810–3, 1994, 11607462, 43253, 1994PNAS...91.1810S, and it has been suggested that the amount of organisms living below the Earth's surface is 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.JOURNAL, Horneck, G., Survival of microorganisms in space: a review, Adv Space Res, 1, 14, 39–48, 1981, 11541716, 10.1016/0273-1177(81)90241-6, 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.JOURNAL, Rousk, Johannes, Bengtson, Per, Microbial regulation of global biogeochemical cycles, Frontiers in Microbiology, 2014, 5, 2, 210–25, 10.3389/fmicb.2014.00103, 24672519, 3954078, Bacteria use regulatory networks that allow them to adapt to almost every environmental niche on earth.BOOK, Filloux, A.A.M., 2012, Bacterial Regulatory Networks, Caister Academic Press, 978-1-908230-03-4, BOOK, Gross, R., Beier, D., 2012, Two-Component Systems in Bacteria, Caister Academic Press, 978-1-908230-08-9, A network of interactions among diverse types of molecules including DNA, RNA, proteins and metabolites, is utilised by the bacteria to achieve regulation of gene expression. In bacteria, the principal function of regulatory networks is to control the response to environmental changes, for example nutritional status and environmental stress.BOOK, Requena, J.M., 2012, Stress Response in Microbiology, Caister Academic Press, 978-1-908230-04-1, A complex organization of networks permits the microorganism to coordinate and integrate multiple environmental signals.

Extremophiles

{{further|List of microorganisms tested in outer space}}file:Deinococcus radiodurans.jpg|thumb|upright|A tetrad of Deinococcus radiodurans, a radioresistant extremophileextremophileExtremophiles are microorganisms that have adapted so that they can survive and even thrive in extreme environments that are normally fatal to most life-forms. Thermophiles and hyperthermophiles thrive in high temperatures. Psychrophiles thrive in extremely low temperatures. – Temperatures as high as {{convert|130|°C|°F}},Strain 121, a hyperthermophilic archaea, has been shown to reproduce at {{convert|121|°C|°F}}, and survive at {{convert|130|°C|°F}}.weblink as low as {{convert|-17|°C|°F}}Some Psychrophilic bacteria can grow at {{convert|-17|°C|°F}}),weblink and can survive near absolute zero).WEB,weblink Earth microbes on the Moon, 2009-07-20, yes,weblink" title="web.archive.org/web/20100323224432weblink">weblink 23 March 2010, dmy-all, Halophiles such as Halobacterium salinarum (an archaean) thrive in high salt conditions, up to saturation.Dyall-Smith, Mike, HALOARCHAEA, University of Melbourne. See also Haloarchaea. Alkaliphiles thrive in an alkaline pH of about 8.5–11.Bacillus alcalophilus can grow at up to pH 11.5 Acidophiles can thrive in a pH of 2.0 or less.Picrophilus can grow at pH −0.06.weblink Piezophiles thrive at very high pressures: up to 1,000–2,000 atm, down to 0 atm as in a vacuum of space.The piezophilic bacteria Halomonas salaria requires a pressure of 1,000 atm; nanobes, a speculative organism, have been reportedly found in the earth's crust at 2,000 atm.weblink" title="http:/-/www.microscopy-uk.org.uk/index.htmlweblink">weblink A few extremophiles such as Deinococcus radiodurans are radioresistant,JOURNAL, 10, 1, 575–577, Anderson, A. W., Nordan, H. C., Cain, R. F., Parrish, G., Duggan, D., Studies on a radio-resistant micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation, Food Technol., 1956, resisting radiation exposure of up to 5k Gy. 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 biotechnology, and their very existence under such extreme conditions increases the potential for extraterrestrial life.JOURNAL, Cavicchioli, R., Extremophiles and the search for extraterrestrial life, Astrobiology, 2, 3, 281–292, 2002, 12530238, 10.1089/153110702762027862, 2002AsBio...2..281C,weblink 10.1.1.472.3179,

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 root nodules of legumes that contain symbiotic bacteria of the genera Rhizobium, Mesorhizobium, Sinorhizobium, Bradyrhizobium, and Azorhizobium.JOURNAL, Barea, J., Pozo, M., Azcón, R., Azcón-Aguilar, C., Microbial co-operation in the rhizosphere, 10.1093/jxb/eri197, J Exp Bot, 56, 417, 1761–78, 2005, 15911555, The roots of plants create a narrow region known as the rhizosphere that supports a large number of microorganisms known as the root microbiome.JOURNAL, 10.1128/AEM.05255-11, 21764952, 3165402, Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types, Applied and Environmental Microbiology, 77, 17, 5934–5944, 2011, Gottel, Neil R., Castro, Hector F., Kerley, Marilyn, Yang, Zamin, Pelletier, Dale A., Podar, Mircea, Karpinets, Tatiana, Uberbacher, Ed, Tuskan, Gerald A., Vilgalys, Rytas, Doktycz, Mitchel J., Schadt, Christopher W.,

Symbiosis

File:Hyella caespitosa.jpg|thumb|right|The photosynthetic cyanobacterium Hyella caespitosa (round shapes) with fungal hyphae (translucent threads) in the lichenlichenA lichen is a symbiosis of a macroscopic fungus with photosynthetic microbial algae or cyanobacteria.WEB,weblink What is a lichen?, Australian National Botanic Gardens, 30 September 2017, WEB,weblink Introduction to Lichens – An Alliance between Kingdoms, University of California Museum of Paleontology, 30 September 2017,

Applications

Microorganisms are useful in producing foods, treating waste water, creating biofuels and a wide range of chemicals and enzymes. They are invaluable in research as model organisms. They have been weaponised and sometimes used in warfare and bioterrorism. They are vital to agriculture through their roles in maintaining soil fertility and in decomposing organic matter.BOOK, The Genesis of Germs: The Origin of Diseases and the Coming Plagues, Gillen, Alan L., New Leaf Publishing Group, 2007, 10, 978-0-89051-493-1,

Food production

Microorganisms are used in a fermentation process to make yoghurt, cheese, curd, kefir, ayran, xynogala, and other types of food. Fermentation cultures provide flavor and aroma, and inhibit undesirable organisms.WEB,weblink Dairy Microbiology, 9 October 2006, University of Guelph, 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.BOOK, Hui, Y.H., Meunier-Goddik, L., Josephsen, J., Nip, W.K., Stanfield, P.S., Handbook of Food and Beverage Fermentation Technology,weblink 2004, CRC Press, 978-0-8247-5122-7, 27 and passim, Some industrial uses of Microorganisms: {| class="wikitable"|+!Product !Contribution of Microorganisms|Cheese |Growth of microorganisms contributes to ripening and flavor. The flavor and appearance of a particular cheese is due in large part to the microorganisms associated with it.
|Alcoholic beverages |yeast is used to covert sugar, grape juice,or malt-treated grain into alcohol. other microorganisms may also be used; a mold converts starch into sugar to make the Japanese rice wine, sake.
|Vinegar |Certain bacteria are used to convert alcohol into acetic acid, which gives vinegar its acid taste.
|Citric acid |Certain fungi are used to make citric acid, a common ingredient of soft drinks and other foods.
|Vitamins|Microorganisms are used to make vitamins, including C, B2 , B12.
|Antibiotics|With only a few exceptions, microorganisms are used to make antibiotics.

Water treatment

{{Further |Drinking water#Water quality}}File:WWTP Antwerpen-Zuid.jpg|thumb|Wastewater treatment plants rely largely on microorganisms to oxidise organic matter.]]These depend for their ability to clean up water contaminated with organic material on microorganisms that can respire dissolved substances. Respiration may be aerobic, with a well-oxygenated filter bed such as a slow sand filter.BOOK, Biology of Wastewater Treatment, Gray, N.F., Imperial College Press, 2004, 1164, 978-1-86094-332-4, Anaerobic digestion by methanogens generate useful methane gas as a by-product.JOURNAL, 10.1016/j.procbio.2010.05.017, 45, 8, Importance of the methanogenic archaea populations in anaerobic wastewater treatments, 2010, Process Biochemistry, 1214–1225, Tabatabaei, Meisam,weblink

Energy

Microorganisms are used in fermentation to produce ethanol,BOOK, Biomass Handbook, Kitani, Osumu, Carl W. Hall, Taylor & Francis US, 1989, 256, 978-2-88124-269-4, and in biogas reactors to produce methane.BOOK, Food, Energy, and Society, Pimental, David, CRC Press, 2007, 289, 978-1-4200-4667-0, Scientists are researching the use of algae to produce liquid fuels,BOOK, From the Fryer to the Fuel Tank: The Complete Guide to Using Vegetable Oil as an Alternative Fuel, Tickell, Joshua, Biodiesel America, 2000, 53, 978-0-9707227-0-6, etal,weblink and bacteria to convert various forms of agricultural and urban waste into usable fuels.BOOK, Apollo's Fire: Igniting America's Clean Energy Economy, Inslee, Jay, Island Press, 2008, 157, 978-1-59726-175-3, etal,weblink

Chemicals, enzymes

{{Further |Synthesis of nanoparticles by fungi}}Microorganisms are used to produce many commercial and industrial chemicals, enzymes and other bioactive molecules. Organic acids produced on a large industrial scale by microbial fermentation include acetic acid produced by acetic acid bacteria such as Acetobacter aceti, butyric acid made by the bacterium Clostridium butyricum, lactic acid made by Lactobacillus and other lactic acid bacteria,JOURNAL, Sauer, Michael, Porro, Danilo, et al, Microbial production of organic acids: expanding the markets, Trends in Biotechnology, 2008, 26, 2, 100–8, 10.1016/j.tibtech.2007.11.006, 18191255,weblink and citric acid produced by the mould fungus Aspergillus niger. Microorganisms are used to prepare bioactive molecules such as Streptokinase from the bacterium Streptococcus,JOURNAL, Babashamsi, Mohammed, et al, Production and Purification of Streptokinase by Protected Affinity Chromatography, Avicenna Journal of Medical Biotechnology, 2009, 1, 1, 47–51, 23407807, Streptokinase is an extracellular protein, extracted from certain strains of beta hemolytic streptococcus., 3558118, Cyclosporin A from the ascomycete fungus Tolypocladium inflatum,BOOK, Merluzzi, V.J., Adams, J., Borel, J.F., Kis, Z.L., Beveridge, T., The search for anti-inflammatory drugs case histories from concept to clinic, The history of the discovery and development of Cyclosporin,weblink 27–63, 1995, Birkhäuser, Boston, 978-1-4615-9846-6, and statins produced by the yeast Monascus purpureus.BOOK, Biology textbook for class XII, National council of educational research and training, 978-81-7450-639-9, 183, 2006,

Science

{{See also|Genetically modified bacteria}}File:Biofermentor.jpeg|thumb|A laboratory fermentationfermentationMicroorganisms are essential tools in biotechnology, biochemistry, genetics, and molecular biology. The yeasts Saccharomyces cerevisiae and 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.JOURNAL, Castrillo, J.I., Oliver, S.G., Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics, J. Biochem. Mol. Biol., 37, 1, 93–106, 2004, 14761307,weblinkweblink" title="web.archive.org/web/20080615044016weblink">weblink yes, 2008-06-15, 10.5483/BMBRep.2004.37.1.093, They are particularly valuable in genetics, genomics and proteomics.JOURNAL, Suter, B., Auerbach, D., Stagljar, I., Yeast-based functional genomics and proteomics technologies: the first 15 years and beyond, BioTechniques, 40, 5, 625–44, 2006, 16708762, 10.2144/000112151, JOURNAL, Sunnerhagen, P., Prospects for functional genomics in Schizosaccharomyces pombe, Curr. Genet., 42, 2, 73–84, 2002, 12478386, 10.1007/s00294-002-0335-6, Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living fuel cells,BOOK, Microbes: A Source of Energy for 21st Century, Soni, S.K., New India Publishing, 2007, 978-81-89422-14-1, and as a solution for pollution.BOOK, Biotechnology: The Science and the Business, Moses, Vivian, CRC Press, 1999, 563, 978-90-5702-407-8, etal,

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.BOOK, Introduction to Weapons of Mass Destruction: Radiological, Chemical, and Biological, Langford, Roland E., Wiley-IEEE, 2004, 140, 978-0-471-46560-7, In modern times, bioterrorism has included the 1984 Rajneeshee bioterror attackNEWS,weblink The Largest Bioterrorism Attack In US History Was An Attempt To Swing An Election, Novak, Matt, 2016-11-03, Gizmodo, and the 1993 release of anthrax by Aum Shinrikyo in Tokyo.CDC-Bacillus anthracis Incident, Kameido, Tokyo, 1993

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 set of soil microbes results in fewer plant diseases and higher yield.JOURNAL, The littlest farmhands, Science, 2015-08-14, 26273035, 680–683, 349, 6249, 10.1126/science.349.6249.680, Jop de, Vrieze,

Human health

Human gut flora

{{Further|Human microbiota |Human Microbiome Project}}Microorganisms can form an endosymbiotic relationship with other, larger organisms. For example, microbial symbiosis plays a crucial role in the immune system. The microorganisms that make up the gut flora in the gastrointestinal tract contribute to gut immunity, synthesize vitamins such as folic acid and biotin, and ferment complex indigestible carbohydrates.JOURNAL, O'Hara, A., Shanahan, F., The gut flora as a forgotten organ, EMBO Rep, 7, 7, 688–93, 2006, 16819463, 10.1038/sj.embor.7400731, 1500832, Some microorganisms that are seen to be beneficial to health are termed probiotics and are available as dietary supplements, or food additives.WEB, Schlundt, Jorgen, Health and Nutritional Properties of Probiotics in Food including Powder Milk with Live Lactic Acid Bacteria,weblink Report of a Joint FAO/WHO Expert Consultation on Evaluation of Health and Nutritional Properties of Probiotics in Food Including Powder Milk with Live Lactic Acid Bacteria, FAO / WHO, 17 December 2012, yes,weblink" title="web.archive.org/web/20121022161702weblink">weblink 22 October 2012,

Disease

{{Further|Medical microbiology|Parasite}}File:Plasmodium.jpg|thumb|upright|The eukaryotic parasite Plasmodium falciparum (spiky blue shapes), a causative agent of malaria, in human bloodbloodMicroorganisms are the causative agents (pathogens) in many infectious diseases. The organisms involved include pathogenic bacteria, causing diseases such as plague, tuberculosis and anthrax; protozoan parasites, 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,JOURNAL, Eckburg, P., Lepp, P., Relman, D., Archaea and Their Potential Role in Human Disease, Infect Immun, 71, 2, 591–6, 2003, 12540534, 10.1128/IAI.71.2.591-596.2003, 145348, although a relationship has been proposed between the presence of some archaean methanogens and human periodontal disease.JOURNAL, Lepp, P., Brinig, M., Ouverney, C., Palm, K., Armitage, G., Relman, D., Methanogenic Archaea and human periodontal disease, 10.1073/pnas.0308766101, Proc Natl Acad Sci USA, 101, 16, 6176–81, 2004, 15067114, 395942, 2004PNAS..101.6176L,

Hygiene

Hygiene is a set of practices to avoid infection or food spoilage 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.WEB,weblink Hygiene, World Health Organization (WHO), 18 May 2017, WEB,weblink The Five Keys to Safer Food Programme, World Health Organization, 18 May 2017,

See also

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Notes

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References

{{reflist}}

External links

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