View source for Microorganism

{{short description|Microscopic living organism}}
{{Redirect|Microbe}}
{{good article}}
{{Use dmy dates|date=February 2021}}
[[File:E coli at 10000x, original.jpg|thumb|upright=1.35|A [[Colony (biology)#Microbial colonies|cluster]] of ''[[Escherichia coli]]'' bacteria magnified 10,000 times]]
{{TopicTOC-Biology}} 
A '''microorganism''', or '''microbe''',{{efn|The word ''microorganism'' ({{IPAc-en|ˌ|m|aɪ|k|r|oʊ-|ˈ|ɔːr|g|ə|n|ɪ|z|əm}}) uses [[classical compound|combining forms]] of ''[[wikt:micro-#Prefix|micro-]]'' (from the {{langx|el|μικρός}}, {{tlit|el|mikros}}, 'small') and ''[[organism]]'' from {{lang|el|ὀργανισμός}}, {{tlit|el|organismós}}, 'organism'). It is usually written as a single word but is sometimes [[hyphen]]ated (''micro-organism''), especially in older texts. The informal synonym ''microbe'' ({{IPAc-en|ˈ|m|aɪ|k|r|oʊ|b}}) comes from {{tlit|el|mikros}} and {{lang|el|βίος}}, {{tlit|el|bíos}}, 'life'.}} is an [[organism]] of [[microscopic scale|microscopic]] size, which may exist in its [[unicellular organism|single-celled]] form or as a [[Colony (biology)#Microbial colonies|colony of cells]]. The possible existence of unseen microbial life was suspected from antiquity, with an early attestation in [[Jain literature]] authored in 6th-century&nbsp;BC India. The scientific study of microorganisms began with their observation under the [[microscope]] in the 1670s by [[Anton 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]], [[diphtheria]], and [[anthrax]].

Microorganisms are extremely diverse, representing most [[unicellular organism]]s in all [[three domains of life]]: two of the three domains, [[Archaea]] and [[Bacteria]], only contain microorganisms. The third domain, [[Eukaryota]], includes all [[multicellular organism]]s as well as many unicellular [[protist]]s and [[protozoa]]ns that are microbes. Some protists are related to [[animals]] and some to [[green plants]]. Many multicellular organisms are also microscopic, namely [[micro-animal]]s, some [[fungus|fungi]], and some [[algae]].

Microorganisms can have very different [[habitat]]s, and live everywhere from the [[Geographic pole|poles]] to the [[equator]], in [[desert]]s, [[geyser]]s, [[Rock (geology)|rocks]], and the [[deep sea]]. Some are [[extremophiles|adapted to extremes]] such as [[hyperthermophiles|very hot]] or [[psychrophile|very cold conditions]], others to [[piezophile|high pressure]], and a few, such as ''[[Deinococcus radiodurans]]'', to [[radioresistance|high radiation]] environments. Microorganisms also make up the [[microbiota]] found in and on all [[Multicellular organism|multicellular organisms]]. There is evidence that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.<ref name="WU-20171218">{{cite web |last=Tyrell |first=Kelly April |title=Oldest fossils ever found show life on Earth began before 3.5 billion years ago |url=https://news.wisc.edu/oldest-fossils-ever-found-show-life-on-earth-began-before-3-5-billion-years-ago/ |date=18 December 2017 |publisher=[[University of Wisconsin–Madison]] |access-date=18 December 2017}}</ref><ref name="PNAS-2017">{{cite journal |last1=Schopf |first1=J. William |last2=Kitajima |first2=Kouki |last3=Spicuzza |first3=Michael J. |last4=Kudryavtsev |first4=Anatolly B. |last5=Valley |first5=John W. |title=SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions |date=2017 |journal=[[Proceedings of the National Academy of Sciences of the United States of America|PNAS]] |volume=115 |issue=1 |pages=53–58 |doi=10.1073/pnas.1718063115 |pmid=29255053 |pmc=5776830 |bibcode=2018PNAS..115...53S|doi-access=free }}</ref>

Microbes are [[Microbes in human culture|important in human culture]] and [[health]] in many ways, serving to [[fermentation in food processing|ferment foods]] and [[sewage treatment|treat sewage]], and to [[algae fuel|produce fuel]], [[enzyme]]s, and other [[bioactive compound]]s. Microbes are essential tools in [[biology]] as [[model organism]]s and have been put to use in [[biological warfare]] and [[bioterrorism]]. Microbes are a vital [[soil microbiology|component of fertile soil]]. In the [[human body]], microorganisms make up the [[human microbiota]], including the essential [[gut flora]]. The [[pathogen]]s responsible for many [[infectious disease]]s are microbes and, as such, are the target of [[hygiene|hygiene measures]].

==Discovery==
{{See also|History of biology|Microbiology#History}} 

===Ancient precursors===
[[File:Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg|thumb|upright=0.8|[[Antonie van Leeuwenhoek]] was the first to study microscopic organisms.]]
[[File:Spallanzani.jpg|thumb|upright=0.8|[[Lazzaro Spallanzani]] showed that boiling a broth stopped it from decaying.]]

The possible existence of microscopic organisms was discussed for many centuries before their discovery in the 17th century. By the 6th century&nbsp;BC, the [[Jain]]s of present-day India postulated the existence of tiny organisms called ''[[nigoda]]s''.<ref name="JDL_2013">{{cite book |first=Jeffery D. |last=Long |title=Jainism: An Introduction |url=https://books.google.com/books?id=I3gAAwAAQBAJ&pg=PA100 |year=2013 |publisher=I.B.Tauris |isbn=978-0-85771-392-6 |page=100 }}</ref> 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 a fraction of a second.<ref>{{cite book |first=Upinder |last=Singh |title=A History of Ancient and Early Medieval India: From the Stone Age to the 12th Century |url=https://books.google.com/books?id=Pq2iCwAAQBAJ&pg=PA315 |year=2008 |publisher=Pearson Education India |isbn=978-81-317-1677-9 |page=315 }}</ref> According to [[Mahavira]], the 24th preacher of Jainism, the humans destroy these nigodas on a massive scale, when they eat, breathe, sit, and move.<ref name="JDL_2013"/> Many modern Jains assert that Mahavira's teachings presage the existence of microorganisms as discovered by science.<ref>{{cite book |first=Paul |last=Dundas |title=The Jains |url=https://books.google.com/books?id=X8iAAgAAQBAJ&pg=PA106 |year=2003 |publisher=Routledge |isbn=978-1-134-50165-6 |page=106 }}</ref>

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&nbsp;BC book entitled ''On Agriculture'' in which he called the unseen creatures animalia minuta, and warns against locating a homestead near a swamp:<ref name=Varro>''Varro on Agriculture'' 1, xii Loeb</ref>

{{blockquote|… 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.<ref name=Varro/>}}

In ''[[The Canon of Medicine]]'' (1020), [[Avicenna]] suggested that [[tuberculosis]] and other diseases might be contagious.<ref>{{cite journal |last=Tschanz |first=David W. |title=Arab Roots of European Medicine |journal=Heart Views |volume=4 |issue=2 |url=http://www.hmc.org.qa/hmc/heartviews/h-v-v4%20n2/9.htm |archive-url=https://web.archive.org/web/20110503050312/http://www.hmc.org.qa/hmc/heartviews/H-V-v4%20N2/9.htm |archive-date=3 May 2011 }}</ref><ref>{{cite book|title=Advice to the Young Physician: On the Art of Medicine|url={{google books |plainurl=y|id=DoMVs4HuDAoC|page=33}} |last=Colgan|first=Richard |page=33 |publisher=Springer |year=2009 |isbn=978-1-4419-1033-2}}</ref>

===Early modern===
{{More information|Bacteria#History of bacteriology}}
In the 15th-century, Turkish scientist [[Akshamsaddin]] speculated about microbial life relating to disease in his work {{tlit|ota|Maddat ul-Hayat}} (''The Material of Life''):
{{blockquote|It is a mistake to assume that diseases appear in individuals one by one. Diseases are transmitted from person to person. This transmission takes place through small seeds that are invisible to the eye, but are still alive.<ref>Taşköprülüzâde: ''Shaqaiq-e Numaniya'', v. 1, p. 48</ref><ref>Osman Şevki Uludağ: ''Beş Buçuk Asırlık Türk Tabâbet Tarihi'' (Five and a Half Centuries of Turkish Medical History). Istanbul, 1969, pp. 35–36</ref>}}

In [[1546 in science#Medicine|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.<ref>{{cite journal |last=Nutton |first=Vivian |title=The Reception of Fracastoro's Theory of Contagion: The Seed That Fell among Thorns? |journal=[[Osiris (journal)|Osiris]]|year=1990 |volume=2nd Series, Vol. 6, Renaissance Medical Learning: Evolution of a Tradition |pages=196–234 |jstor=301787 |doi=10.1086/368701|pmid=11612689 |s2cid=37260514 }}</ref>

[[Antonie van Leeuwenhoek]] is considered to be one of the [[List of people considered father or mother of a scientific field|fathers of microbiology]]. He was the first in 1673 to discover and conduct scientific experiments with microorganisms, using simple single-lensed [[Microscope|microscopes]] of his own design.<ref>{{Cite journal | last=Leeuwenhoek |first=A. | title=Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs | journal=Philosophical Transactions | volume=22 | pages=509–518 | year=1753 | doi=10.1098/rstl.1700.0013 | issue=260–276 | bibcode=1700RSPT...22..509V | doi-access=free }}</ref><ref>{{Cite journal| last=Leeuwenhoek |first=A. |author-link=Antony van Leeuwenhoek | title=Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them | journal=Philosophical Transactions | volume=23 | pages=1304–1311 |year=1753 | doi=10.1098/rstl.1702.0042 | issue=277–288 | bibcode=1702RSPT...23.1304V |s2cid=186209549 }}</ref><ref name="NickLane_RS">{{cite journal |author-link=Nick Lane |last=Lane |first=Nick |title=The Unseen World: Reflections on Leeuwenhoek (1677) 'Concerning Little Animal' |journal=Philos Trans R Soc Lond B Biol Sci |volume=370 |issue=1666 |article-number=20140344 |year=2015 |doi=10.1098/rstb.2014.0344|pmid=25750239 |pmc=4360124 }}</ref><ref>Payne, A. S. ''The Cleere Observer: A Biography of Antoni Van Leeuwenhoek'', p. 13, Macmillan, 1970</ref> [[Robert Hooke]], a contemporary of Leeuwenhoek, also used [[microscopy]] to observe microbial life in the form of the fruiting bodies of [[Mold (fungus)|mould]]s. In his [[1665#July–December|1665]] book ''[[Micrographia]]'', he made drawings of studies, and he coined the term ''[[Cell (biology)|cell]]''.<ref>{{cite journal |last=Gest |first=H. |title=The remarkable vision of Robert Hooke (1635–1703): first observer of the microbial world |journal=Perspect. Biol. Med. |volume=48 |issue=2 |pages=266–272 |year=2005 |pmid=15834198 |doi=10.1353/pbm.2005.0053|s2cid=23998841 }}</ref>

===19th century===
[[File:Albert Edelfelt - Louis Pasteur - 1885.jpg|thumb|upright=0.8|left|[[Louis Pasteur]] showed that Spallanzani's findings held even if air could enter through a filter that kept particles out.]]

[[Louis 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 [[spore]]s on dust, rather than spontaneously generated within the broth. Thus, Pasteur refuted the theory of [[spontaneous generation]] and supported the [[germ theory of disease]].<ref>{{cite journal |last=Bordenave |first=G. |title=Louis Pasteur (1822–1895) |journal=Microbes Infect. |volume=5 |issue=6 |pages=553–560 |year=2003 |pmid=12758285 |doi=10.1016/S1286-4579(03)00075-3}}</ref>

[[File:Robert Koch.jpg|thumb|upright=0.8|[[Robert Koch]] showed that microorganisms caused [[disease]].]]

In 1876, [[Robert Koch]] (1843–1910) established that microorganisms can cause disease. He found that the blood of cattle that 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]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1905/ The Nobel Prize in Physiology or Medicine 1905] Nobelprize.org Accessed 22 November 2006.</ref> 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.<ref>{{Cite journal |last=O'Brien |first=S. |last2=Goedert |first2=J. | title=HIV causes AIDS: Koch's postulates fulfilled | journal=Curr Opin Immunol | volume=8 | issue=5 | pages=613–618 | year=1996 | pmid=8902385 | doi=10.1016/S0952-7915(96)80075-6}}</ref>

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 (biologist)|John Hogg]] called this the [[Protoctista]], and in 1866 [[Ernst Haeckel]] named it the [[Protista]].<ref name=Scamardella1999>{{cite journal | last=Scamardella |first=J. M. | title=Not plants or animals: a brief history of the origin of Kingdoms Protozoa, Protista and Protoctista | year=1999 | journal=International Microbiology | volume=2 | issue=4 | pages=207–221 | pmid=10943416 | url=http://www.im.microbios.org/08december99/03%20Scamardella.pdf | access-date=1 October 2017 | archive-date=14 June 2011 | archive-url=https://web.archive.org/web/20110614000656/http://www.im.microbios.org/08december99/03%20Scamardella.pdf }}</ref><ref name=Rothschild1989>{{cite journal |last=Rothschild |first=L. J. |author-link=Lynn J. Rothschild |title=Protozoa, Protista, Protoctista: what's in a name? |journal=J Hist Biol |volume=22 |issue=2 |pages=277–305 |year=1989 |pmid=11542176 |doi=10.1007/BF00139515 |s2cid=32462158 |url=https://zenodo.org/record/1232387 }}</ref><ref name=Pearl2005>{{cite book |editor1-first=Eldra Pearl |editor1-last=Solomon |editor2-first=Linda R. |editor2-last=Berg |editor3-first=Diana W. |editor3-last=Martin |chapter=Kingdoms or Domains? |chapter-url=https://books.google.com/books?id=qBOPoEc-zu4C&pg=PA421 |pages=421–7 |title=Biology |publisher=Brooks/Cole Thompson Learning |year=2005 |edition=7th |isbn=978-0-534-49276-2}}</ref>

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]] in the late 19th century that the true breadth of microbiology was revealed.<ref name=Brock>{{cite book | editor-last=Madigan |editor-first=M. |editor-last2=Martinko |editor-first2=J. | title=Brock Biology of Microorganisms | edition=13th | publisher=Pearson Education | year=2006 | isbn=978-0-321-73551-5 |page=1096}}</ref> Beijerinck made two major contributions to microbiology: the discovery of [[virus]]es and the development of [[enrichment culture]] techniques.<ref>{{cite web | last=Johnson |first=J. | title=Martinus Willem Beijerinck | work=APSnet| publisher=American Phytopathological Society | url=http://apsnet.org/education/feature/TMV/intro.html | archive-url=https://web.archive.org/web/20100620173433/http://apsnet.org/education/feature/TMV/intro.html | archive-date=2010-06-20 | year=2001 |orig-date=1998 | access-date=2 May 2010}} Retrieved from Internet Archive 12 January 2014.</ref> 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.<ref>{{cite book | last=Paustian |first=T. | last2=Roberts |first2=G. | chapter=Beijerinck and Winogradsky Initiate the Field of Environmental Microbiology | title=Through the Microscope: A Look at All Things Small | at=§&nbsp;1–14 | edition=3rd | year=2009 | publisher=Textbook Consortia | chapter-url=http://www.microbiologytext.com/index.php?module=Book&func=displayarticle&art_id=32 | access-date=3 October 2017 | archive-date=14 September 2008 | archive-url=https://web.archive.org/web/20080914000327/http://www.microbiologytext.com/index.php?module=Book&func=displayarticle&art_id=32 }}</ref> He was responsible for the first isolation and description of both [[nitrifying bacteria|nitrifying]] and [[nitrogen-fixing bacteria]].<ref name=Brock /> French-Canadian microbiologist [[Félix d'Hérelle]] co-discovered [[bacteriophage]]s and was one of the earliest applied microbiologists.<ref name =Keen>{{cite journal |last=Keen |first=E. C. |title=Felix d'Herelle and Our Microbial Future |journal=Future Microbiology |volume=7 |issue=12 |pages=1337–1339 |year=2012 |pmid=23231482|doi=10.2217/fmb.12.115}}</ref>

==Classification and structure==
Microorganisms can be found almost anywhere on [[Earth]]. [[Bacteria]] and [[archaea]] are almost always microscopic, while a number of [[eukaryote]]s are also microscopic, including most [[Protista|protists]], some [[fungus|fungi]], as well as some [[micro-animal]]s and plants. [[Virus]]es are generally regarded as [[Non-cellular life|not living]] and therefore not considered to be microorganisms, although a subfield of [[microbiology]] is [[virology]], the study of viruses.<ref>{{Cite book |title=eLS|last=Lim|first=Daniel V. |date=2001 |publisher=John Wiley |isbn=978-0-470-01590-2 |doi=10.1038/npg.els.0000459|chapter = Microbiology}}</ref><ref>{{Cite web|url=http://www.highveld.com/microbiology/what-is-microbiology.html|title=What is Microbiology? |website=highveld.com |access-date=2017-06-02|archive-url=https://web.archive.org/web/20150215180557/http://www.highveld.com/microbiology/what-is-microbiology.html |archive-date=2015-02-15}}</ref><ref>{{cite book |last=Cann |first=Alan |title=Principles of Molecular Virology |year=2011 |publisher=Academic Press |isbn=978-0-12-384939-7 |edition=5th}}</ref>

===Evolution===
{{further|Timeline of the evolutionary history of life|Earliest known life forms}}
Single-celled microorganisms were the [[Origin of life|first forms of life]] to develop on Earth, approximately 3.5 billion years ago.<ref>{{Cite journal |author=Schopf, J. |title=Fossil evidence of Archaean life |journal=Philos Trans R Soc Lond B Biol Sci |volume=361 |issue=1470 |pages=869–885 |year=2006 |pmid=16754604 |doi=10.1098/rstb.2006.1834 |pmc=1578735}}</ref><ref>{{Cite journal |last=Altermann |first=W. |last2=Kazmierczak |first2=J. |title=Archean microfossils: a reappraisal of early life on Earth |journal=Res Microbiol |volume=154 |issue=9 |pages=611–617 |year=2003 |pmid=14596897 | doi=10.1016/j.resmic.2003.08.006|doi-access=free }}</ref><ref>{{Cite journal|last=Cavalier-Smith |first=T. |author-link=Thomas Cavalier-Smith |title=Cell evolution and Earth history: stasis and revolution  |journal=Philos Trans R Soc Lond B Biol Sci |volume=361 |issue=1470 |pages=969–1006 |year=2006 |pmid=16754610 |doi=10.1098/rstb.2006.1842 |pmc=1578732}}</ref> Further evolution was slow,<ref>{{Cite journal| last=Schopf |first=J. | title=Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic | pmc=44277| journal=PNAS | volume=91 | issue=15 | pages=6735–6742 | year=1994 | pmid=8041691 | doi=10.1073/pnas.91.15.6735 | bibcode=1994PNAS...91.6735S| doi-access=free }}</ref> and for about 3&nbsp;billion years in the [[Precambrian]] [[Eon (geology)|eon]], (much of the history of [[life|life on Earth]]), all [[organism]]s were microorganisms.<ref>{{Cite journal|author=Stanley, S. |title=An Ecological Theory for the Sudden Origin of Multicellular Life in the Late Precambrian |journal=PNAS |volume=70 |issue=5 |pages=1486–1489 |date=May 1973 |pmid=16592084 |pmc=433525 | doi=10.1073/pnas.70.5.1486 |bibcode=1973PNAS...70.1486S |doi-access=free }}</ref><ref>{{Cite journal |author1=DeLong, E. |author2=Pace, N. | title=Environmental diversity of bacteria and archaea | journal=Syst Biol | volume=50 | issue=4 | pages=470–478 | year=2001 |pmid=12116647 | doi=10.1080/106351501750435040|citeseerx=10.1.1.321.8828 }}</ref> Bacteria, algae and fungi have been identified in [[amber]] that is 220&nbsp;million years old, which shows that the [[Morphology (biology)|morphology]] of microorganisms has changed little since at least the [[Triassic]] period.<ref>{{Cite journal |author=Schmidt, A. |author2=Ragazzi, E. |author3=Coppellotti, O. |author4=Roghi, G. | title=A microworld in Triassic amber | journal=Nature | volume=444 | issue=7121 | page=835 | year=2006 | pmid=17167469 | doi=10.1038/444835a |bibcode=2006Natur.444..835S |s2cid=4401723 | doi-access=free }}</ref> The newly discovered [[Nickel#Biological role|biological role played by nickel]], however – especially that brought about by [[Types of volcanic eruption|volcanic eruptions]] from the [[Siberian Traps]] – may have accelerated the evolution of [[methanogen]]s towards the end of the [[Permian–Triassic extinction event]].<ref>{{cite web |url= http://www.space.com/26654-microbe-innovation-started-largest-earth-extinction.html |title= Microbe's Innovation May Have Started Largest Extinction Event on Earth |last= Schirber |first=Michael |date= 27 July 2014 |publisher=Astrobiology Magazine |website= Space.com |quote=That spike in nickel allowed methanogens to take off.}}</ref>

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 [[Bacterial conjugation|conjugation]], [[Transformation (genetics)|transformation]] and [[Transduction (genetics)|transduction]], even between widely divergent species.<ref>{{Cite journal| author=Wolska, K. | title=Horizontal DNA transfer between bacteria in the environment | journal=Acta Microbiol Pol | volume=52 | issue=3 | pages=233–243 | year=2003 |pmid=14743976}}</ref> This [[horizontal gene transfer]], coupled with a high [[mutation]] rate and other means of transformation, allows microorganisms to swiftly [[biological evolution|evolve]] (via [[natural selection]]) to survive in new environments and respond to [[stressors|environmental stresses]]. This rapid evolution is important in medicine, as it has led to the development of [[multidrug resistance|multidrug resistant]] [[pathogenic bacteria]], ''superbugs'', that are [[antimicrobial resistance|resistant to antibiotics]].<ref>{{Cite journal |author=Enright, M. |author2=Robinson, D. |author3=Randle, G. |author4=Feil, E. |author5=Grundmann, H. |author6=Spratt, B. | title=The evolutionary history of methicillin-resistant ''Staphylococcus aureus'' (MRSA) | journal=Proc Natl Acad Sci USA | volume=99 | issue=11 | pages=7687–7692 |date=May 2002 | pmid=12032344 |pmc=124322 | doi=10.1073/pnas.122108599|bibcode=2002PNAS...99.7687E |doi-access=free }}</ref>

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.<ref name="Parakaryon">{{cite web |title=Deep sea microorganisms and the origin of the eukaryotic cell |url=http://protistology.jp/journal/jjp47/JJP47YAMAGUCHI.pdf |access-date=24 October 2017}}</ref><ref name="Yamaguchi">{{cite journal|last1=Yamaguchi |display-authors=et al|first1=Masashi |title=Prokaryote or eukaryote? A unique microorganism from the deep sea |issue=6 |journal=Journal of Electron Microscopy |volume=61 |pages=423–431 |doi=10.1093/jmicro/dfs062 |pmid=23024290 |date=1 December 2012}}</ref>

===Archaea===
{{main|Archaea}}
{{further|Prokaryote}}

Archaea are [[prokaryote|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 [[lipid bilayer|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,<ref>{{Cite journal |author1=Woese, C. |author1-link=Carl Woese | author2=Kandler, O. | author3=Wheelis, M. | title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya | doi= 10.1073/pnas.87.12.4576 | journal=Proc Natl Acad Sci USA | volume=87 | issue=12 | pages=4576–4579 | year=1990 | pmid=2112744 | pmc=54159 | bibcode=1990PNAS...87.4576W|doi-access=free }}</ref> and thereby split the prokaryote domain.

Archaea differ from bacteria in both their genetics and biochemistry. For example, while bacterial [[cell membrane]]s are made from [[phospholipid|phosphoglycerides]] with [[ester]] bonds, Achaean membranes are made of [[ether lipid]]s.<ref>{{Cite journal |author1=De Rosa, M. |author2=Gambacorta, A. | author3=Gliozzi, A. |title=Structure, biosynthesis, and physicochemical properties of archaebacterial lipids |journal=Microbiol. Rev. |volume=50 |issue=1 |pages=70–80 |date=1 March 1986|pmid=3083222 |pmc=373054 |doi=10.1128/mmbr.50.1.70-80.1986}}</ref> Archaea were originally described as [[extremophile]]s living in [[extreme environment]]s, such as [[hot spring]]s, but have since been found in all types of [[habitat]]s.<ref>{{Cite journal |author1=Robertson, C. |author2=Harris, J. |author3=Spear, J. |author4=Pace, N. | title=Phylogenetic diversity and ecology of environmental Archaea | journal=Curr Opin Microbiol | volume=8 | issue=6 | pages=638–642 | year=2005 | pmid=16236543 | doi=10.1016/j.mib.2005.10.003}}</ref> Only now are scientists beginning to realize how common archaea are in the environment, with [[Thermoproteota]] (formerly Crenarchaeota) being the most common form of life in the ocean, dominating ecosystems below {{convert|150|m}} in depth.<ref>{{Cite journal |author=Karner, M. B. |author2=DeLong, E. F. |author3=Karl, D. M. |title=Archaeal dominance in the mesopelagic zone of the Pacific Ocean |journal=Nature |volume=409 |issue=6819 |pages=507–510 |year=2001 |pmid=11206545 | doi=10.1038/35054051|bibcode=2001Natur.409..507K |s2cid=6789859 }}</ref><ref>{{Cite journal |author=Sinninghe Damsté, J. S. |author2=Rijpstra, W. I. |author3=Hopmans, E. C. |author4=Prahl, F. G. |author5=Wakeham, S. G. |author6=Schouten, S. |title=Distribution of Membrane Lipids of Planktonic Crenarchaeota in the Arabian Sea |journal=Appl. Environ. Microbiol. |volume=68 |issue=6 |pages=2997–3002 |date=June 2002 |pmid=12039760 |pmc=123986 | doi=10.1128/AEM.68.6.2997-3002.2002|bibcode=2002ApEnM..68.2997S }}</ref> These organisms are also common in soil and play a vital role in [[ammonia]] oxidation.<ref name=LeiningerUrich2006>{{cite journal |last1=Leininger |first1=S. |last2=Urich |first2=T. |last3=Schloter |first3=M. |last4=Schwark |first4=L.|last5=Qi|first5=J. |last6=Nicol |first6=G. W. |last7=Prosser |first7=J. I. |author-link7=James I. Prosser |last8=Schuster |first8=S. C. |last9=Schleper |first9=C.|title=Archaea predominate among ammonia-oxidizing prokaryotes in soils |journal=[[Nature (journal)|Nature]] |volume=442 |issue=7104 |year=2006|pages=806–809|pmid= 16915287 |doi=10.1038/nature04983|bibcode=2006Natur.442..806L|s2cid=4380804 }}</ref>

The combined domains of archaea and bacteria make up the most diverse and abundant group of [[organism]]s on Earth and inhabit practically all environments where the temperature is below +{{convert|140|°C}}. They are found in [[water]], [[soil]], [[Earth's atmosphere|air]], as the [[microbiome]] of an organism, [[hot spring]]s and even deep beneath the Earth's crust in [[Rock (geology)|rocks]].<ref name=Gold>{{Cite journal|author=Gold, T. |title=The deep, hot biosphere |journal=Proc. Natl. Acad. Sci. USA |volume=89 |issue=13 |pages=6045–6049 |year=1992 |pmid=1631089 |doi= 10.1073/pnas.89.13.6045 |pmc=49434 |bibcode=1992PNAS...89.6045G|doi-access=free }}</ref> The number of prokaryotes is estimated to be around five nonillion, or 5 × 10<sup>30</sup>, accounting for at least half the [[Biomass (ecology)|biomass]] on Earth.<ref>{{Cite journal|author=Whitman, W. |author2=Coleman, D. |author3=Wiebe, W. | title=Prokaryotes: The unseen majority | doi= 10.1073/pnas.95.12.6578 | journal=PNAS | volume=95 | issue=12 | pages=6578–6583 | year=1998 | pmid=9618454 | pmc=33863|bibcode=1998PNAS...95.6578W |doi-access=free }}</ref>

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&nbsp;trillion species on the planet, of which most would be microorganisms. Currently, only one-thousandth of one percent of that total have been described.<ref name="NSF-2016002">{{cite news |title=Researchers find that Earth may be home to 1 trillion species |url=https://www.nsf.gov/news/news_summ.jsp?cntn_id=138446 |date=2 May 2016 |work=[[National Science Foundation]] |access-date=6 May 2016 }}</ref> [[Archaea|Archael cells]] of some species aggregate and transfer [[DNA]] from one cell to another through direct contact, particularly under stressful environmental conditions that cause [[DNA damage (naturally occurring)|DNA damage]].<ref>{{cite journal |last1=van Wolferen |first1=M.|last2=Wagner |first2=A|last3=van der Does |first3=C.|last4=Albers |first4=S. V. | year = 2016 | title = The archaeal Ced system imports DNA | journal = Proc Natl Acad Sci USA | volume = 113 | issue = 9| pages = 2496–501 | doi = 10.1073/pnas.1513740113 | pmid = 26884154 | pmc = 4780597 | bibcode = 2016PNAS..113.2496V | doi-access = free }}</ref><ref>Bernstein H, Bernstein C. Sexual communication in archaea, the precursor to meiosis. pp. 103–117 in Biocommunication of Archaea (Guenther Witzany, ed.) 2017. Springer International Publishing {{ISBN|978-3-319-65535-2}} DOI 10.1007/978-3-319-65536-9</ref>

===Bacteria===
{{Main|Bacteria}}
[[File:Staphylococcus aureus 01.jpg|thumb|''[[Staphylococcus aureus]]'' bacteria magnified about 10,000×]]
Like archaea, bacteria 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]]''.<ref>{{Cite journal |last=Schulz |first=H. |last2=Jorgensen |first2=B. | title=Big bacteria | journal=Annu Rev Microbiol | volume=55 | pages=105–137 | year =2001 |pmid=11544351 | doi=10.1146/annurev.micro.55.1.105}}</ref> Bacteria function and reproduce as individual cells, but they can often aggregate in multicellular [[Colony (biology)#Microbial colony|colonies]].<ref>{{Cite journal |author-link=James A. Shapiro |last=Shapiro |first=J. A. |title=Thinking about bacterial populations as multicellular organisms |journal=Annu. Rev. Microbiol. |volume=52 |pages=81–104 |year=1998 |pmid=9891794 |doi=10.1146/annurev.micro.52.1.81 |url=http://www.sci.uidaho.edu/newton/math501/Sp05/Shapiro.pdf |archive-url=https://web.archive.org/web/20110717183759/http://www.sci.uidaho.edu/newton/math501/Sp05/Shapiro.pdf |archive-date=17 July 2011 }}</ref> Some species such as [[myxobacteria]] can aggregate into complex [[swarm]]ing structures, operating as multicellular groups as part of their [[Biological life cycle|life cycle]],<ref>{{cite journal | title=Myxobacteria: Moving, Killing, Feeding, and Surviving Together | journal=Frontiers in Microbiology| volume=7| page=781| pmid=27303375| pmc=4880591| year=2016| last1=Muñoz-Dorado| first1=J. | last2=Marcos-Torres| first2=F. J. | last3=García-Bravo | first3=E. | last4=Moraleda-Muñoz| first4=A. | last5=Pérez| first5=J. | doi=10.3389/fmicb.2016.00781| doi-access=free}}</ref> or form clusters in [[colony (biology)|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 [[plasmid]]s. These plasmids can be transferred between cells through [[bacterial conjugation]]. Bacteria have an enclosing [[Bacterial cell structure#Cell wall|cell wall]], which provides strength and rigidity to their cells. They reproduce by [[binary fission]] or sometimes by [[budding]], but do not undergo [[Meiosis|meiotic]] [[sexual reproduction]]. However, many bacterial species can transfer DNA between individual cells by a [[horizontal gene transfer]] process referred to as natural [[Transformation (genetics)|transformation]].<ref>{{cite journal |last=Johnsbor |first=O. |last2=Eldholm |first2=V. |last3=Håvarstein |first3=L. S. |title=Natural genetic transformation: prevalence, mechanisms and function |journal=Res. Microbiol. |volume=158 |issue=10 |pages=767–778 |date=December 2007 |pmid=17997281 |doi=10.1016/j.resmic.2007.09.004 |doi-access=free }}</ref> Some species form extraordinarily resilient [[endospore|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.<ref>{{Cite journal| last=Eagon |first=R. | title=Pseudomonas Natriegens, a Marine Bacterium With a Generation Time of Less Than 10 Minutes | journal=J Bacteriol | volume=83 | issue=4| pages=736–737 | year =1962 | pmid=13888946 | pmc=279347| doi=10.1128/JB.83.4.736-737.1962 }}</ref>

===Eukaryotes===
{{Main|Eukaryote}}

Most living things that are visible to the naked eye in their adult form are [[eukaryote]]s, including [[human]]s. However, many eukaryotes are also microorganisms. Unlike [[bacteria]] and [[archaea]], eukaryotes contain [[organelle]]s such as the [[cell nucleus]], the [[Golgi apparatus]] and [[mitochondrion|mitochondria]] in their [[cell (biology)|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 [[chromosome]]s.<ref>[http://www.ucmp.berkeley.edu/alllife/eukaryotamm.html Eukaryota: More on Morphology.] (Retrieved 10 October 2006)</ref>
[[Mitochondrion|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.<ref name=Dyall>{{Cite journal |author=Dyall, S. |author2=Brown, M. |author3=Johnson, P. | title=Ancient invasions: from endosymbionts to organelles | journal=Science | volume=304 | issue=5668 | pages=253–257 | year=2004|pmid=15073369 | doi=10.1126/science.1094884|bibcode=2004Sci...304..253D |s2cid=19424594 }}</ref> Like bacteria, [[plant cell]]s have [[cell wall]]s, and contain organelles such as [[chloroplast]]s in addition to the organelles in other eukaryotes. Chloroplasts produce energy from light by [[photosynthesis]], and were also originally symbiotic bacteria.<ref name=Dyall/>

Unicellular eukaryotes consist of a single [[Cell (biology)|cell]] throughout their life cycle. This qualification is significant since most [[multicellular organism|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 nucleus|cell nuclei]].

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 [[Fertilization|syngamy]].<ref name=Bernstein>{{cite book |last1=Bernstein |first1=H. |last2=Bernstein |first2=C. |last3=Michod |first3=R. E. |year=2012 |chapter-url=https://www.novapublishers.com/catalog/product_info.php?products_id=31918 |title=DNA repair as the primary adaptive function of sex in bacteria and eukaryotes.  |chapter=Chapter 1 |pages=1–49 |series= DNA Repair: New Research |editor-first1=Sakura |editor-last1=Kimura |editor-first2=Sora |editor-last2=Shimizu |publisher=Nova Sci. Publ. |isbn=978-1-62100-808-8 |archive-url=https://web.archive.org/web/20180722155931/https://www.novapublishers.com/catalog/product_info.php?products_id=31918 |archive-date= Jul 22, 2018 }}</ref>

====Protists====
{{Main|Protista}}
[[File:Euglena mutabilis - 400x - 1 (10388739803) (cropped).jpg|thumb|upright=0.8|''[[Euglena|Euglena mutabilis]]'', a [[photosynthetic]] [[flagellate]]]]

Of [[Eukaryote|eukaryotic]] groups, the [[protists]] are most commonly [[unicellular]] and microscopic. This is a highly diverse group of organisms that are not easy to classify.<ref>{{Cite journal|author=Cavalier-Smith T |author-link=Thomas Cavalier-Smith |title=Kingdom protozoa and its 18 phyla |journal=Microbiol. Rev. |volume=57 |issue=4 |pages=953–994 |date=1 December 1993|pmid=8302218 |pmc=372943 |doi=10.1128/mmbr.57.4.953-994.1993 |doi-access=free }}</ref><ref>{{Cite journal|last=Corliss |first=J. O. |title=Should there be a separate code of nomenclature for the protists? |journal=BioSystems |volume=28 |issue=1–3 |pages=1–14 |year=1992 |pmid=1292654 | doi=10.1016/0303-2647(92)90003-H|bibcode=1992BiSys..28....1C }}</ref> Several [[algae]] [[species]] are [[multicellular]] protists, and [[slime mold]]s have unique life cycles that involve switching between unicellular, colonial, and multicellular forms.<ref>{{Cite journal|author=Devreotes, P. |title=Dictyostelium discoideum: a model system for cell-cell interactions in development |journal=Science |volume=245 |issue=4922 |pages=1054–1058 |year=1989 |pmid=2672337 | doi=10.1126/science.2672337|bibcode=1989Sci...245.1054D }}</ref> 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.<ref>{{Cite journal|author=Slapeta, J. |author2=Moreira, D. |author3=López-García, P. |title=The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes |journal=Proc. Biol. Sci. |volume=272 |issue=1576 |pages=2073–2081 |year=2005 |pmid=16191619 |doi=10.1098/rspb.2005.3195 |pmc=1559898}}</ref><ref>{{Cite journal |author=Moreira, D. |author2=López-García, P. |title=The molecular ecology of microbial eukaryotes unveils a hidden world |journal=Trends Microbiol. |volume=10 |issue=1 |pages=31–38 |year=2002 |pmid=11755083 | url=http://download.bioon.com.cn/view/upload/month_0803/20080326_daa08a6fdb5d38e3a0d8VBrocN3WtOdR.attach.pdf | doi=10.1016/S0966-842X(01)02257-0}}</ref>

====Fungi====
{{Main|Fungus}}

The [[fungus|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 [[Hypha|filamentous hyphae]] in others.<ref>{{Cite journal |author=Kumamoto, C.A. |author-link1=Carol Kumamoto|author2=Vinces, M. D. |title=Contributions of hyphae and hypha-co-regulated genes to Candida albicans virulence |journal=Cell. Microbiol. |volume=7 |issue=11 |pages=1546–1554 |year=2005 |pmid=16207242 | doi=10.1111/j.1462-5822.2005.00616.x|doi-access=free }}</ref>

====Plants====
{{Main|Plant}}

The [[green algae]] are a large group of photosynthetic eukaryotes that include many microscopic organisms. Although some green algae are classified as [[protist]]s, 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 [[flagellate]]s, usually but not always with two [[flagellum|flagella]] per cell, as well as various colonial, [[Chlorococcales|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.<ref>{{Cite book |author=Thomas, David C. |title=Seaweeds |publisher=Natural History Museum |location=London |year=2002 |isbn=978-0-565-09175-0 }}</ref>

==Ecology==
{{main |Microbial ecology}}

Microorganisms are found in almost every [[Habitat (ecology)|habitat]] present in nature, including hostile environments such as the [[Geographic poles|North and South poles]], [[desert]]s, [[geyser]]s, and [[Rock (geology)|rocks]]. They also include all the [[marine microorganism]]s of the [[World ocean|oceans]] and [[deep sea]]. Some types of microorganisms have adapted to [[extreme environment]]s 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,<ref>{{Cite journal |author=Szewzyk, U. |author2=Szewzyk, R. |author3=Stenström, T. | title=Thermophilic, anaerobic bacteria isolated from a deep borehole in granite in Sweden | doi= 10.1073/pnas.91.5.1810 | journal=PNAS | volume=91 | issue=5 | pages=1810–1813 | year=1994 | pmid=11607462 | pmc=43253 | bibcode=1994PNAS...91.1810S|doi-access=free }}</ref> 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.<ref name=Gold/> Extremophiles have been known to survive for a prolonged time in a [[vacuum]], and can be highly resistant to [[ultraviolet radiation|radiation]], which may even allow them to survive in space.<ref>{{Cite journal| author=Horneck, G. | title=Survival of microorganisms in space: a review | journal=Adv Space Res | volume=1 | issue=14 | pages=39–48 | year=1981|pmid=11541716 | doi=10.1016/0273-1177(81)90241-6}}</ref> Many types of microorganisms have intimate [[symbiosis|symbiotic relationships]] with other larger organisms; some of which are mutually beneficial ([[Mutualism (biology)|mutualism]]), while others can be damaging to the [[host (biology)|host]] organism ([[parasitism]]). If microorganisms can cause [[disease]] in a host they are known as ''[[pathogen]]s''. Microorganisms play critical roles in Earth's [[biogeochemical cycle]]s as they are responsible for [[decomposition]] and [[nitrogen fixation]].<ref>{{cite journal |last1=Rousk |first1=Johannes |last2=Bengtson |first2=Per |title=Microbial regulation of global biogeochemical cycles |journal=Frontiers in Microbiology |date=2014 |volume=5 |issue=2 |pages=210–225 |doi=10.3389/fmicb.2014.00103 |pmid=24672519 |pmc=3954078|doi-access=free }}</ref>

Bacteria use [[gene regulatory network|regulatory networks]] that allow them to adapt to almost every environmental niche on earth.<ref name= FillouxAAM>{{cite book | editor=Filloux, A. A. M. | year=2012 | title=Bacterial Regulatory Networks | publisher=[[Caister Academic Press]] | isbn= 978-1-908230-03-4}}</ref><ref name= GrossRBeierD>{{cite book | editor=Gross, R. |editor2=Beier, D. | year=2012 | title=Two-Component Systems in Bacteria | publisher=[[Caister Academic Press]] | isbn= 978-1-908230-08-9}}</ref> 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.<ref name= RequenaJM>{{cite book | editor=Requena, J. M. | year=2012 | title=Stress Response in Microbiology | publisher=[[Caister Academic Press]] | isbn=978-1-908230-04-1}}</ref> A complex organization of networks permits the microorganism to coordinate and integrate multiple environmental signals.<ref name="FillouxAAM"/>

===Extremophiles===
{{main|Extremophile}}
{{further|List of microorganisms tested in outer space}}
[[file:Deinococcus radiodurans.jpg|thumb|upright|A tetrad of ''[[Deinococcus radiodurans]]'', a [[radioresistant]] [[extremophile]] bacterium]]

[[Extremophiles]] are microorganisms that have adapted so that they can survive and even thrive in [[extreme environment]]s that are normally fatal to most life-forms. [[Thermophile]]s and [[hyperthermophiles]] thrive in high [[temperature]]s. [[Psychrophile]]s thrive in extremely low temperatures. – Temperatures as high as {{convert|130|°C|°F}},<ref>[[Strain 121]], a [[Hyperthermophile|hyperthermophilic]] [[archaea]], has been shown to reproduce at {{convert|121|°C|°F}}, and survive at {{convert|130|°C|°F}}.[https://www.nsf.gov/od/lpa/news/03/pr0384.htm]</ref> as low as {{convert|-17|°C|°F}}<ref>Some [[Psychrophiles|Psychrophilic]] bacteria can grow at {{convert|-17|°C|°F}}),[https://news.bbc.co.uk/2/hi/science/nature/827063.stm] and can survive near [[absolute zero]]).{{cite web |title=Earth microbes on the Moon |url=https://science.nasa.gov/newhome/headlines/ast01sep98_1.htm |archive-url=https://web.archive.org/web/20100323224432/http://science.nasa.gov/newhome/headlines/ast01sep98_1.htm |archive-date=23 March 2010 |access-date=2009-07-20}}</ref> [[Halophile]]s such as ''[[Halobacterium salinarum]]'' (an archaean) thrive in high [[Salinity|salt conditions]], up to saturation.<ref>Dyall-Smith, Mike, [http://www.microbiol.unimelb.edu.au/people/dyallsmith/ ''HALOARCHAEA''], University of Melbourne. See also [[Haloarchaea]].</ref> [[Alkaliphile]]s thrive in an [[alkaline]] [[pH]] of about 8.5–11.<ref>{{Cite journal|url=http://jb.asm.org/cgi/reprint/185/2/461.pdf|title=''Bacillus alcalophilus'' can grow at up to pH 11.5|journal=Journal of Bacteriology|date=15 January 2003|volume=185|issue=2|pages=461–465|doi=10.1128/JB.185.2.461-465.2003|last1=Olsson|first1=Karen|last2=Keis|first2=Stefanie|last3=Morgan|first3=Hugh W.|last4=Dimroth|first4=Peter|last5=Cook|first5=Gregory M.|pmid=12511491|pmc=145327}}</ref> [[Acidophile]]s can thrive in a pH of 2.0 or less.<ref>[[Picrophilus]] can grow at pH −0.06.[http://www.rcn.montana.edu/resources/organisms/organisminfo.aspx?nav=11&tid=1298&did=1&nid=82076&lid=9] {{Webarchive|url=https://web.archive.org/web/20100622184325/http://www.rcn.montana.edu/resources/organisms/organisminfo.aspx?nav=11&tid=1298&did=1&nid=82076&lid=9|date=22 June 2010}}</ref> [[Piezophile]]s thrive at very [[high pressure]]s: up to 1,000–2,000 [[Atmosphere (unit)|atm]], down to 0 atm as in a [[vacuum]] of [[Outer space|space]].{{efn|The [[Piezophile|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.<ref>{{cite web | url=http://www.microscopy-uk.org.uk/index.html?http://www.microscopy-uk.org.uk/nanobes/nanopaper.html | title=Microscopy-UK Home (Resources for the microscopy enthusiast and amateur, including free monthly e-zine, Micscape.) }}</ref>}} A few extremophiles such as ''[[Deinococcus radiodurans]]'' are [[radioresistance|radioresistant]],<ref>{{cite journal | volume=10 | issue=1 | pages=575–577 | last=Anderson | first=A. W. |author2=Nordan, H. C. |author3=Cain, R. F. |author4=Parrish, G. |author5=Duggan, D. | title=Studies on a radio-resistant micrococcus. I. Isolation, morphology, cultural characteristics, and resistance to gamma radiation | journal=Food Technol. | year=1956}}</ref> resisting [[Ionizing radiation|radiation]] exposure of up to 5k [[Gray (unit)|Gy]]. Extremophiles are significant in different ways. They extend terrestrial life into much of the Earth's [[hydrosphere]], [[Crust (geology)|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]].<ref>{{cite journal |author=Cavicchioli, R. |title=Extremophiles and the search for extraterrestrial life |journal=Astrobiology |volume=2 |issue=3 |pages=281–292 |year=2002 |pmid=12530238 |doi=10.1089/153110702762027862 |bibcode=2002AsBio...2..281C |url=http://somosbacteriasyvirus.com/extremophiles.pdf |citeseerx=10.1.1.472.3179 |access-date=26 October 2017 |archive-date=26 April 2022 |archive-url=https://web.archive.org/web/20220426071811/https://somosbacteriasyvirus.com/extremophiles.pdf }}</ref>

===Plants and soil===
{{Main |Soil biology}}

The [[nitrogen cycle]] in soils depends on the [[nitrogen fixation|fixation of atmospheric nitrogen]]. This is achieved by a number of [[diazotroph]]s. One way this can occur is in the [[root nodule]]s of [[legumes]] that contain symbiotic [[bacteria]] of the genera ''[[Rhizobium]]'', ''[[Mesorhizobium]]'', ''[[Sinorhizobium]]'', ''[[Bradyrhizobium]]'', and ''[[Azorhizobium]]''.<ref>{{Cite journal |author=Barea, J. |author2=Pozo, M. |author3=Azcón, R. |author4=Azcón-Aguilar, C. | title=Microbial co-operation in the rhizosphere | doi= 10.1093/jxb/eri197 | journal=J Exp Bot | volume=56 | issue=417 | pages=1761–1778 | year=2005 | pmid=15911555| doi-access=free }}</ref>

The [[root]]s of plants create a narrow region known as the [[rhizosphere]] that supports many microorganisms known as the [[root microbiome]].<ref name="Gottel">{{Cite journal|doi=10.1128/AEM.05255-11|pmid=21764952|pmc=3165402|title=Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types|journal=Applied and Environmental Microbiology|volume=77|issue=17|pages=5934–5944|year=2011|last1=Gottel|first1=Neil R.|last2=Castro|first2=Hector F.|last3=Kerley|first3=Marilyn|last4=Yang|first4=Zamin|last5=Pelletier|first5=Dale A.|last6=Podar|first6=Mircea|last7=Karpinets|first7=Tatiana|last8=Uberbacher|first8=Ed|last9=Tuskan|first9=Gerald A.|last10=Vilgalys|first10=Rytas|last11=Doktycz|first11=Mitchel J.|last12=Schadt|first12=Christopher W.|bibcode=2011ApEnM..77.5934G}}</ref>

These microorganisms in the [[root microbiome]] are able to interact with each other and surrounding plants through signals and cues. For example, [[mycorrhizal fungi]] are able to communicate with the root systems of many plants through chemical signals between both the plant and fungi. This results in a mutualistic [[symbiosis]] between the two. However, these signals can be eavesdropped by other microorganisms, such as the [[soil bacteria]], ''Myxococcus xanthus'', which preys on other bacteria. Eavesdropping, or the interception of signals from unintended receivers, such as plants and microorganisms, can lead to large-scale, evolutionary consequences. For example, signaler-receiver pairs, like plant-microorganism pairs, may lose the ability to communicate with neighboring populations because of variability in eavesdroppers. In adapting to avoid local eavesdroppers, signal divergence could occur and thus, lead to the isolation of plants and microorganisms from the inability to communicate with other populations.<ref>{{Cite journal| last  = Rebolleda-Gómez |first=M. |last2=Wood |first2=C. W. |title=Unclear Intentions: Eavesdropping in Microbial and Plant Systems |journal=Frontiers in Ecology and Evolution |year=2019 | volume=7 |issue=385|doi=10.3389/fevo.2019.00385 |doi-access=free }}</ref>

===Symbiosis===
[[File:Hyella caespitosa.jpg|thumb|right|The photosynthetic [[cyanobacterium]] ''Hyella caespitosa'' (round shapes) with fungal hyphae (translucent threads) in the [[lichen]] ''Pyrenocollema halodytes'']]
A [[lichen]] is a [[symbiosis]] of a macroscopic fungus with [[photosynthetic]] microbial [[alga]]e or [[cyanobacteria]].<ref>{{cite web |url=https://www.anbg.gov.au/lichen/what-is-lichen.html |title=What is a lichen? |publisher=Australian National Botanic Gardens |access-date=30 September 2017}}</ref><ref>{{cite web |url=http://www.ucmp.berkeley.edu/fungi/lichens/lichens.html |title=Introduction to Lichens – An Alliance between Kingdoms |publisher=University of California Museum of Paleontology |access-date=30 September 2017}}</ref>

==Applications==
{{Main|Human interactions with microbes}}

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 organism]]s. They have been [[Biological agent|weaponised]] and sometimes used in [[Biological warfare|warfare]] and [[bioterrorism]]. They are vital to agriculture through their roles in maintaining [[soil fertility]] and in decomposing organic matter. They also have applications in aquaculture, such as in [[Biofloc Technology|biofloc technology]].

===Food production===
{{Main|Fermentation in food processing |Food microbiology}}
Microorganisms are used in a [[Fermentation (food)|fermentation]] process to make [[yoghurt]], [[cheese]], [[curd]], [[kefir]], [[ayran]], [[fermented milk products|xynogala]], and other types of food. Fermentation cultures provide flavour and aroma, and inhibit undesirable organisms.<ref>{{cite web|url=http://www.foodsci.uoguelph.ca/dairyedu/micro.html |title= Dairy Microbiology |access-date=9 October 2006 |publisher= University of Guelph}}</ref> They are used to [[leavening agent|leaven]] [[bread]], and to convert [[sugar]]s to [[ethanol|alcohol]] in [[wine]] and [[beer]]. Microorganisms are used in [[brewing]], [[wine making]], [[baking]], [[pickling]] and other [[food]]-making processes.<ref name="HuiMeunier-Goddik2004">{{cite book |author=Hui, Y. H. |author2=Meunier-Goddik, L. |author3=Josephsen, J. |author4=Nip, W. K. |author5=Stanfield, P. S. |title=Handbook of Food and Beverage Fermentation Technology |url=https://books.google.com/books?id=PC_O7u1NPZEC&pg=PA27 |year=2004 |publisher=CRC Press |isbn=978-0-8247-5122-7 |pages=27 et passim}}</ref>

{| class="wikitable plainrowheaders"
|+Example industrial uses of microorganisms
!scope="col"|Product
!scope="col"|Contribution of microorganisms
|-
!scope="row"|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. ''[[Lactobacillus bulgaricus GLB44|Lactobacillus Bulgaricus]]'' is one of the microbes used in production of [[dairy product]]s
|-
!scope="row"|Alcoholic beverages 
|Yeast is used to convert 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. ''[[Acetobacter aceti|Acetobacter Aceti]]'' a kind of bacterium is used in production of [[Alcoholic beverage|alcoholic beverages]]
|-
!scope="row"|Vinegar 
|Certain bacteria are used to convert alcohol into acetic acid, which gives vinegar its acid taste. ''[[Acetobacter aceti|Acetobacter Aceti]]'' is used on production of vinegar, which gives vinegar odor of alcohol and alcoholic taste
|-
!scope="row"|Citric acid 
|Certain fungi are used to make citric acid, a common ingredient of soft drinks and other foods. 
|-
!scope="row"|Vitamins
|Microorganisms are used to make vitamins, including C, B<sub>2</sub> , B<sub>12.</sub>
|-
!scope="row"|Antibiotics
|With only a few exceptions, microorganisms are used to make antibiotics. ''[[Penicillin]], [[Amoxicillin]], [[Tetracycline]], and [[Erythromycin]]''
|}

===Water treatment===
{{Further |Drinking water#Water quality}}
[[File:WWTP Antwerpen-Zuid.jpg|thumb|[[Wastewater treatment]] 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]].<ref>{{Cite book| title=Biology of Wastewater Treatment | author=Gray, N. F. | publisher=Imperial College Press | year=2004 | page=1164 | isbn=978-1-86094-332-4}}</ref> [[Anaerobic digestion]] by [[methanogen]]s generate useful [[methane]] gas as a by-product.<ref>{{cite journal| doi=10.1016/j.procbio.2010.05.017 | volume=45 | issue=8 | title=Importance of the methanogenic archaea populations in anaerobic wastewater treatments | year=2010 | journal=Process Biochemistry | pages=1214–1225 | last1 = Tabatabaei | first1 = Meisam| url=http://psasir.upm.edu.my/id/eprint/15129/1/Importance%20of%20the%20methanogenic%20archaea%20populations%20in%20anaerobic%20wastewater%20treatments.pdf }}</ref>

===Energy===
Microorganisms are used in [[Ethanol fermentation|fermentation to produce ethanol]],<ref>{{Cite book| title=Biomass Handbook |author1=Kitani, Osumu  |author2=Hall, Carl W. | publisher=Taylor & Francis US | year=1989 | page=256 | isbn=978-2-88124-269-4}}</ref> and in [[biogas]] reactors to produce [[methane]].<ref>{{Cite book| title=Food, Energy, and Society | author=Pimental, David | publisher=CRC Press | year=2007 | page=289 | isbn=978-1-4200-4667-0 }}</ref> Scientists are researching the use of [[algae fuel|algae to produce liquid fuels]],<ref>{{Cite book | title=From the Fryer to the Fuel Tank: The Complete Guide to Using Vegetable Oil as an Alternative Fuel | author=Tickell, Joshua | publisher=Biodiesel America | year=2000 | page=[https://archive.org/details/fromfryertofue00tick/page/53 53] | isbn=978-0-9707227-0-6 | display-authors=etal | url=https://archive.org/details/fromfryertofue00tick/page/53 }}</ref> and bacteria to convert various forms of agricultural and urban waste into [[cellulosic ethanol|usable fuels]].<ref>{{Cite book | title=Apollo's Fire: Igniting America's Clean Energy Economy | author=Inslee, Jay | publisher=Island Press | year=2008 | page=[https://archive.org/details/apollosfireignit00insl/page/157 157] | isbn=978-1-59726-175-3 | display-authors=etal | url=https://archive.org/details/apollosfireignit00insl | url-access=registration }}</ref>

===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]],<ref name=Sauer>{{cite journal |last1=Sauer |first1=Michael |last2=Porro |first2=Danilo |display-authors=et al |title=Microbial production of organic acids: expanding the markets |journal=Trends in Biotechnology |date=2008 |volume=26 |issue=2 |pages=100–108 |doi=10.1016/j.tibtech.2007.11.006 |pmid=18191255 |url=http://www.ciencias.unal.edu.co/unciencias/data-file/user_29/file/Microbial%20production%20of%20organic%20acids%20expanding%20the%20markets.pdf |access-date=28 September 2017 |archive-date=28 September 2017 |archive-url=https://web.archive.org/web/20170928150935/http://www.ciencias.unal.edu.co/unciencias/data-file/user_29/file/Microbial%20production%20of%20organic%20acids%20expanding%20the%20markets.pdf }}</ref> and [[citric acid]] produced by the mould fungus ''[[Aspergillus niger]]''.<ref name=Sauer/> <!--also [[ascorbic acid]], [[oxalic acid]] etc, see Sauer et al, Table 1-->

Microorganisms are used to prepare bioactive molecules such as [[Streptokinase]] from the bacterium ''[[Streptococcus]]'',<ref>{{cite journal |last1=Babashamsi |first1=Mohammed |display-authors=et al |title=Production and Purification of Streptokinase by Protected Affinity Chromatography |journal=Avicenna Journal of Medical Biotechnology |date=2009 |volume=1 |issue=1 |pages=47–51 |pmid=23407807 |quote=Streptokinase is an extracellular protein, extracted from certain strains of beta hemolytic streptococcus. |pmc=3558118}}</ref> [[Cyclosporin A]] from the ascomycete fungus ''[[Tolypocladium inflatum]]'',<ref>{{cite book | editor=Merluzzi, V. J. |editor2=Adams, J. | author=Borel, J. F. |author2=Kis, Z. L. |author3=Beveridge, T. | title = The search for anti-inflammatory drugs case histories from concept to clinic | chapter = The history of the discovery and development of Cyclosporin | chapter-url=https://books.google.com/books?id=YWXlBwAAQBAJ&pg=PA27 | pages = 27–63 | date = 1995 | publisher = Birkhäuser | location = Boston | isbn = 978-1-4615-9846-6 }}</ref> and [[statins]] produced by the yeast ''[[Monascus purpureus]]''.<ref>{{cite book |title=Biology textbook for class XII |publisher=National council of educational research and training |isbn=978-81-7450-639-9 |page=183|year=2006 }}</ref>

===Science===
{{See also|Genetically modified bacteria}}
[[File:Biofermentor.jpeg|thumb|A laboratory [[fermentation]] vessel]]

Microorganisms are essential tools in [[biotechnology]], [[biochemistry]], [[genetics]], and [[molecular biology]]. The [[yeast]]s ''[[Saccharomyces cerevisiae]]'' and ''[[Schizosaccharomyces pombe]]'' are important [[model organism]]s in science, since they are simple eukaryotes that can be grown rapidly in large numbers and are easily manipulated.<ref>{{Cite journal |author=Castrillo, J. I. |author2=Oliver, S. G. |title=Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics |journal=J. Biochem. Mol. Biol. |volume=37 |issue=1 |pages=93–106 |year=2004 |pmid=14761307 |doi=10.5483/BMBRep.2004.37.1.093 |doi-access=free }}</ref> They are particularly valuable in [[genetics]], [[genomics]] and [[proteomics]].<ref>{{Cite journal |author=Suter, B. |author2=Auerbach, D. |author3=Stagljar, I. |title=Yeast-based functional genomics and proteomics technologies: the first 15 years and beyond |journal=BioTechniques |volume=40 |issue=5 |pages=625–644 |year=2006 |pmid=16708762 |doi=10.2144/000112151|doi-access=free }}</ref><ref>{{Cite journal |author=Sunnerhagen, P. |title=Prospects for functional genomics in Schizosaccharomyces pombe |journal=Curr. Genet. |volume=42 |issue=2 |pages=73–84 |year=2002 |pmid=12478386 |doi=10.1007/s00294-002-0335-6|s2cid=22067347 }}</ref> Microorganisms can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microorganisms for living [[fuel cells]],<ref>{{Cite book| title=Microbes: A Source of Energy for 21st Century| author=Soni, S. K. | publisher=New India Publishing | year=2007 | isbn=978-81-89422-14-1}}</ref> and as a solution for pollution.<ref>{{Cite book| title=Biotechnology: The Science and the Business | author=Moses, Vivian | publisher=CRC Press | year=1999 | page=563 | isbn=978-90-5702-407-8|display-authors=etal}}</ref>

===Warfare===
{{Main|Biological warfare |Bioterrorism}}
In the [[Middle Ages]], as an early example of [[biological warfare]], diseased corpses were thrown into castles during [[siege]]s using catapults or other [[siege engine]]s. Individuals near the corpses were exposed to the pathogen and were likely to spread that pathogen to others.<ref>{{Cite book| title=Introduction to Weapons of Mass Destruction: Radiological, Chemical, and Biological | author=Langford, Roland E. | publisher=Wiley-IEEE | year=2004 | page=140 | isbn=978-0-471-46560-7}}</ref>
<!--need modern times biowarfare here...-->

In modern times, [[bioterrorism]] has included the [[1984 Rajneeshee bioterror attack]]<ref>{{Cite news |url=http://www.gizmodo.com.au/2016/11/the-largest-bioterrorism-attack-in-us-history-was-an-attempt-to-swing-an-election/ |title=The Largest Bioterrorism Attack in US History Was An Attempt To Swing An Election |last=Novak |first=Matt |date=2016-11-03 |work=Gizmodo}}</ref> and the 1993 release of [[anthrax]] by [[Aum Shinrikyo]] in Tokyo.<ref>{{Cite journal|title= ''Bacillus anthracis'' Bioterrorism Incident, Kameido, Tokyo, 1993|journal=Emerging Infectious Diseases|volume=10|issue=1|pages=117–120|first1=Hiroshi|last1=Takahashi|first2=Paul|last2=Keim|first3=Arnold F.|last3=Kaufmann|first4=Christine|last4=Keys|first5=Kimothy L.|last5=Smith|first6=Kiyosu|last6=Taniguchi|first7=Sakae|last7=Inouye|first8=Takeshi|last8=Kurata|doi=10.3201/eid1001.030238|pmid=15112666|pmc=3322761|year=2004}}</ref>

===Soil===
{{Main|Soil microbiology}}Microbes can make [[nutrient]]s 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 biology|soil]] microbes results in fewer plant diseases and higher yield.<ref name=":02">{{Cite journal |title=The littlest farmhands |journal=Science |date=2015-08-14 |pmid=26273035 |pages=680–683 |volume=349 |issue=6249 |doi=10.1126/science.349.6249.680 |first=Jop de |last=Vrieze|bibcode=2015Sci...349..680D }}</ref>

==Human health==

=== Human gut flora ===
{{Further|Human microbiota |Human Microbiome Project}}

Microorganisms can form an [[Endosymbiont|endosymbiotic]] relationship with other, larger organisms. For example, [[Microbial symbiosis and immunity|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 [[vitamin]]s such as [[folic acid]] and [[biotin]], and ferment complex indigestible [[carbohydrate]]s.<ref>{{Cite journal |author=O'Hara, A. |author2=Shanahan, F. | title=The gut flora as a forgotten organ | journal=EMBO Rep | volume=7 | issue=7 | pages=688–693 | year=2006 | pmid=16819463 | doi=10.1038/sj.embor.7400731 | pmc=1500832}}</ref> Some microorganisms that are seen to be beneficial to health are termed [[probiotic]]s and are available as [[dietary supplement]]s, or [[food additive#Fortifying agents|food additives]].<ref name=who>{{cite web|last1=Schlundt |first1=Jorgen |title=Health and Nutritional Properties of Probiotics in Food including Powder Milk with Live Lactic Acid Bacteria |url=https://www.who.int/foodsafety/publications/fs_management/en/probiotics.pdf |work=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 |publisher=FAO / WHO |access-date=17 December 2012 |archive-url=https://web.archive.org/web/20121022161702/http://www.who.int/foodsafety/publications/fs_management/en/probiotics.pdf |archive-date=22 October 2012 }}</ref>

===Disease===
{{Main|Pathogen|Germ theory of 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 blood]]

Microorganisms are the causative agents ([[pathogen]]s) in many [[Infection|infectious diseases]]. The organisms involved include [[pathogenic bacteria]], causing diseases such as [[bubonic plague|plague]], [[tuberculosis]] and [[anthrax]]; [[protozoa]]n [[parasite]]s, causing diseases such as [[malaria]], [[African trypanosomiasis|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,<ref>{{Cite journal |author=Eckburg, P. |author2=Lepp, P. |author3=Relman, D. |title=Archaea and Their Potential Role in Human Disease |journal=[[Infect Immun]] |volume=71 |issue=2 |pages=591–596 |year=2003 |pmid=12540534 | doi=10.1128/IAI.71.2.591-596.2003 |pmc=145348}}</ref> although a relationship has been proposed between the presence of some archaean methanogens and human [[periodontal disease]].<ref>{{Cite journal |author=Lepp, P. |author2=Brinig, M. |author3=Ouverney, C. |author4=Palm, K. |author5=Armitage, G. |author6=Relman, D. |title=Methanogenic Archaea and human periodontal disease | doi= 10.1073/pnas.0308766101 | journal=[[Proc Natl Acad Sci USA]] |volume=101 |issue=16 |pages=6176–6181 |year=2004 |pmid=15067114 |pmc=395942|bibcode=2004PNAS..101.6176L |doi-access=free }}</ref> Numerous microbial pathogens are capable of sexual processes that appear to facilitate their survival in their infected host.<ref>{{cite journal | author = Bernstein H. |last2=Bernstein |first2=C. |last3=Michod |first3=R. E. | date = Jan 2018 | title = Sex in microbial pathogens | journal = Infect Genet Evol | volume = 57 | pages = 8–25 | doi = 10.1016/j.meegid.2017.10.024 | pmid = 29111273 | doi-access = free | bibcode = 2018InfGE..57....8B }}</ref>

=== Hygiene ===
{{Main|Hygiene |Food microbiology}}

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, [[pathogen|harmful microorganisms]] may be reduced to acceptable levels rather than actually eliminated. In food preparation, microorganisms are reduced by [[Food preservation|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.<ref>{{cite web |url=https://www.who.int/topics/hygiene/en/|archive-url=https://web.archive.org/web/20040823014256/http://www.who.int/topics/hygiene/en/|archive-date=23 August 2004|title=Hygiene |publisher=World Health Organization (WHO) |access-date=18 May 2017}}</ref><ref>{{cite web |url=https://www.who.int/foodsafety/consumer/5keys/en/ |archive-url=https://web.archive.org/web/20031207063202/http://www.who.int/foodsafety/consumer/5keys/en/ |archive-date=7 December 2003 |title=The Five Keys to Safer Food Programme |publisher=World Health Organization |access-date=23 May 2021}}</ref>

==In fiction==
*''[[Osmosis Jones]]'', a 2001 film, and its show ''[[Ozzy & Drix]]'', set in a stylized version of the human body, featured [[Anthropomorphism|anthropomorphic]] microorganisms.
*''[[War of the Worlds (2005 film)]]'', when alien lifeforms attempt to conquer Earth, they are ultimately defeated by a common microbe to which humans are immune.

==See also==
{{col div}}
* [[Catalogue of Life]]
* [[Impedance microbiology]]
* [[Microbial biogeography]]
* [[Microbial intelligence]]
* [[Microbiological culture]]
* [[Microbivory]], an eating behavior of some animals feeding on living microbes
* [[Nanobacterium]]
* [[Nylon-eating bacteria]]
* [[Petri dish]]
* [[Staining]]
* [[Budapest Treaty]] (Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure)
{{colend}}

==Notes==
{{notelist}}

==References==
{{reflist}}

==External links==
* [http://www.microbes.info/ Microbes.info] is a microbiology information portal containing a vast collection of resources including articles, news, frequently asked questions, and links pertaining to the field of microbiology.
* [http://dels.nas.edu/metagenomics Our Microbial Planet] {{Webarchive|url=https://web.archive.org/web/20130215152557/http://dels.nas.edu/metagenomics |date=15 February 2013 }} A free poster from the National Academy of Sciences about the positive roles of micro-organisms.
* [https://web.archive.org/web/20080527234727/http://www.asm.org/ASM/files/ccLibraryFiles/Filename/000000003691/Uncharted_Microbial_World.pdf "Uncharted Microbial World: Microbes and Their Activities in the Environment"] Report from the American Academy of Microbiology
* [http://dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf Understanding Our Microbial Planet: The New Science of Metagenomics] {{Webarchive|url=https://web.archive.org/web/20130215152600/http://dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf |date=15 February 2013 }} A 20-page educational booklet providing a basic overview of metagenomics and our microbial planet.
* [http://tolweb.org/Eukaryotes/3 Tree of Life Eukaryotes]
* [http://www.genomenewsnetwork.org/categories/index/microbes.php Microbe News from Genome News Network]
* [https://web.archive.org/web/20051101012902/http://gsbs.utmb.edu/microbook/toc.htm Medical Microbiology] On-line textbook
* [http://www.microbiologytext.com/index.php?module=Book&func=toc&book_id=4 Through the microscope: A look at all things small] {{Webarchive|url=https://web.archive.org/web/20080913035245/http://www.microbiologytext.com/index.php?module=Book&func=toc&book_id=4 |date=13 September 2008 }} On-line microbiology textbook by Timothy Paustian and Gary Roberts, University of Wisconsin–Madison
* {{YouTube|sDacX2Xs0X4|Microorganisms in the pond water}}
* [http://www.cbc.ca/news/technology/methane-spewing-microbe-blamed-in-worst-mass-extinction-1.2595797 Methane-spewing microbe blamed in worst mass extinction. CBCNews]

{{microorganisms|state=expanded}}
{{Nature nav}}
{{Extremophile}}
{{Bacteria}}
{{Fungus}}
{{Protozoa protist}}
{{Authority control}}

[[Category:Microorganisms| ]]