Microorganism 20377 224178323 2008-07-07T18:00:55Z Dbfirs 335025 Removed definite article for plural [[Image:E coli at 10000x, original.jpg|thumb|250px|right|A cluster of ''[[Escherichia coli]]'' [[Bacterium|bacteria]] magnified 10,000 times.]] A '''microorganism''' (also can be spelled as '''micro organism''' or '''micro-organism''') or '''microbe''' is an [[organism]] that is [[microscopic]] (too small to be seen by the naked human eye). The study of microorganisms is called [[microbiology]], a subject that began with [[Anton van Leeuwenhoek]]'s discovery of microorganisms in 1675, using a [[microscope]] of his own design. Microorganisms are incredibly diverse and include [[bacteria]], [[fungi]], [[archaea]], and [[protist]]s, as well as some microscopic [[plants]] and [[Micro-animals|animals]] such as [[plankton]], and popularly-known animals such as the [[planarian]] and the [[amoeba]]. Many scientists would not include [[virus]]es and [[prion]]s, which are often classified as non-living<ref> Rybicki EP (1990) The classification of organisms at the edge of life, or problems with virus systematics. S Aft J Sci 86:182-186</ref><ref name="pmid13481308">{{cite journal |author=LWOFF A |title=The concept of virus |journal=J. Gen. Microbiol. |volume=17 |issue=2 |pages=239–53 |year=1957 |pmid=13481308 |doi=}}</ref>. Most microorganisms are single-[[cell (biology)|cell]]ed, or '''unicellular''', but some multicellular organisms are microscopic, while some unicellular protists, and bacteria called ''[[Thiomargarita namibiensis]]'' are visible to the naked eye. Microorganisms live in all parts of the [[biosphere]] where there is liquid [[water]], including [[hot spring]]s, on the [[ocean]] floor, high in the [[atmosphere]] and deep inside rocks within the Earth's [[crust]]. Microorganisms are critical to nutrient recycling in [[ecosystems]] as they act as [[decomposer]]s. As some microorganisms can [[nitrogen fixation|fix nitrogen]], they are a vital part of the [[nitrogen cycle]], and recent studies indicate that airborne microbes may play a role in [[Precipitation (meteorology)|precipitation]] and [[weather]].<ref>{{cite journal |author=Christner BC, Morris CE, Foreman CM, Cai R, Sands DC |title=Ubiquity of biological ice nucleators in snowfall |journal=Science |volume=319 |issue=5867 |pages=1214 |year=2008 |pmid=18309078 | doi = 10.1126/science.1149757 <!--Retrieved from CrossRef by DOI bot-->}}</ref> Microbes are also exploited by people in [[biotechnology]], both in traditional [[Fermentation (food)|food and beverage preparation]], as well as modern technologies based on [[genetic engineering]]. However, [[pathogen]]ic microbes are harmful, since they invade and grow within other organisms, causing [[disease]]s that kill millions of people, other animals, and plants.<ref>[http://www.who.int/healthinfo/bodgbd2002revised/en/index.html 2002 WHO mortality data] Accessed 20 January 2007</ref> ==History== === Evolution === {{further|[[Timeline of evolution]]}} Single-celled microorganisms were the [[Origin of life|first forms of life]] to develop on earth, approximately [[1 E17 s|3–4 billion years ago]].<ref>{{cite journal |author=Schopf J |title=Fossil evidence of Archaean life |url=http://www.journals.royalsoc.ac.uk/content/g38537726r273422/fulltext.pdf |journal=Philos Trans R Soc Lond B Biol Sci |volume=361 |issue=1470 |pages=869–85 |year=2006 |pmid=16754604 |doi=10.1098/rstb.2006.1834}}</ref><ref>{{cite journal |author=Altermann W, Kazmierczak J |title=Archean microfossils: a reappraisal of early life on Earth |journal=Res Microbiol |volume=154 |issue=9 |pages=611–7 |year=2003 |pmid=14596897 | doi = 10.1016/j.resmic.2003.08.006 <!--Retrieved from CrossRef by DOI bot-->}}</ref><ref>{{cite journal |author=Cavalier-Smith T |title=Cell evolution and Earth history: stasis and revolution |url=http://www.journals.royalsoc.ac.uk/content/0164755512w92302/fulltext.pdf |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}}</ref> Further evolution was slow,<ref>{{cite journal | author = Schopf J | title = Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=44277&blobtype=pdf | journal = Proc Natl Acad Sci U S A | volume = 91 | issue = 15 | pages = 6735–42 | year = 1994 | pmid = 8041691 | doi = 10.1073/pnas.91.15.6735 <!--Retrieved from CrossRef by DOI bot-->}}</ref> and for about 3 billion years in the [[Precambrian]] [[Eon (geology)|eon]], all organisms were microscopic.<ref>{{cite journal |author=Stanley S |title=An Ecological Theory for the Sudden Origin of Multicellular Life in the Late Precambrian |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16592084 |journal=Proc Natl Acad Sci U S A |volume=70 |issue=5 |pages=1486–1489 |year=1973 |pmid=16592084 | doi = 10.1073/pnas.70.5.1486 <!--Retrieved from CrossRef by DOI bot-->}}</ref> So, for most of the history of [[life on Earth]] the only form of life were microorganisms.<ref>{{cite journal | author = DeLong E, Pace N | title = Environmental diversity of bacteria and archaea | journal = Syst Biol | volume = 50 | issue = 4 | pages = 470–8 | year = 2001|pmid = 12116647 | doi = 10.1080/106351501750435040 <!--Retrieved from CrossRef by DOI bot-->}}</ref> 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.<ref>{{cite journal | author = Schmidt A, Ragazzi E, Coppellotti O, Roghi G | title = A microworld in Triassic amber | journal = Nature | volume = 444 | issue = 7121 | pages = 835 | year = 2006 | pmid = 17167469 | doi = 10.1038/444835a <!--Retrieved from CrossRef by DOI bot-->}}</ref> Most microorganisms can reproduce rapidly and microbes such as bacteria can also freely exchange genes by [[Bacterial conjugation|conjugation]], [[Transformation (genetics)|transformation]] and [[Transduction (genetics)|transduction]] 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 = 233–43 | year = 2003|pmid = 14743976}}</ref> This [[horizontal gene transfer]], coupled with a high [[mutation]] rate and many other means of [[Bacteria#Genetic variation|genetic variation]], allows microorganisms to swiftly [[biological evolution|evolve]] (via [[natural selection]]) to survive in new environments and respond to environmental stresses. This rapid evolution is important in medicine, as it has led to the recent development of '[[antibiotic resistance|super-bugs]]' — [[pathogenic]] [[bacteria]] that are resistant to modern [[antibiotic]]s.<ref>{{cite journal | author = Enright M, Robinson D, Randle G, Feil E, Grundmann H, Spratt B | title = The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA) | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12032344 | journal = Proc Natl Acad Sci U S A | volume = 99 | issue = 11 | pages = 7687–92 | year = 2002 | pmid = 12032344 | doi = 10.1073/pnas.122108599 <!--Retrieved from CrossRef by DOI bot-->}}</ref> ===Pre-Microbiology=== The possibility that microorganisms might exist was discussed for many centuries before their actual discovery in the 17th century. The first ideas about microorganisms were those of the [[Ancient Rome|Roman]] [[scholar]] [[Marcus Terentius Varro]] in a book titled ''On Agriculture'' in which he warns against locating a homestead near swamps: {{cquote|…and because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there cause serious diseases.<ref>''Varro On Agriculture'' 1,xii Loeb</ref>}} This passage seems to indicate that the ancients were aware of the possibility that diseases could be spread by yet unseen organisms. In ''[[The Canon of Medicine]]'' (1020), [[Abū Alī ibn Sīnā]] (Avicenna) stated that bodily [[secretion]] is contaminated by foul foreign earthly bodies before being infected.<ref name="Syed">{{cite journal |last=Syed |first=Ibrahim B. |authorlink= |coauthors= |year=2002 |month= |title=Islamic Medicine: 1000 years ahead of its times |journal=[[Journal of the Islamic Medical Association]] |volume=2 |issue= |pages=2–9 |id= |url= |accessdate= |quote= }}</ref> He also hypothesized that [[tuberculosis]] and other diseases might be contagious, ''i.e.'' that they were [[infectious disease]]s, and used [[quarantine]] to limit their spread.<ref>{{cite journal |last=Tschanz |first=David W. |authorlink= |coauthors= |year= |month= |title=Arab Roots of European Medicine |journal=Heart Views |volume=4 |issue=2 |pages= |id= |url= |accessdate= |quote= }}</ref> When the [[Black Death]] [[bubonic plague]] reached [[al-Andalus]] in the 14th century, Ibn Khatima wrote that infectious diseases were caused by "contagious entities" that enter the human body. Later, in 1546, [[Girolamo Fracastoro]] proposed that [[epidemic]] [[diseases]] were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or even without contact over long distances. All these early claims about the existence of microorganisms were [[speculative]] in nature and not based on any data or science. Microorganisms were neither proven, observed, nor correctly and accurately described until the 17th century. The reason for this was that all these early inquiries lacked the most fundamental tool in order for [[microbiology]] and [[bacteriology]] to exist as a science, and that was the [[microscope]]. === Discovery === [[Image:Antoni van Leeuwenhoek.png|thumb|240px|right|[[Antonie van Leeuwenhoek]], the first [[microbiologist]] and the first to observe microorganisms using a [[microscope]] ]] [[Anton van Leeuwenhoek]] was the first person to observe microorganisms, using a [[microscope]] of his own design, thereby making him the first [[microbiologist]]. In doing so Leeuwenhoek would make one of the most important contributions to [[biology]] and open up the fields of [[microbiology]] and [[bacteriology]]. Prior to Leeuwenhoek's discovery of microorganisms in 1675, it had been a mystery as to why [[grapes]] could be turned into [[wine]], [[milk]] into [[cheese]], or why food would spoil. Leeuwenhoek did not make the connection between these processes and microorganisms, but using a microscope, he did establish that there were forms of life that were not visible to the naked eye.<ref>{{cite journal | author = Leeuwenhoek 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 | url=http://www.journals.royalsoc.ac.uk/link.asp?id=4j53731651310230 | journal = Philosophical Transactions (1683–1775) | volume = 22 | pages = 509–18 | year = 1753 | doi = 10.1098/rstl.1700.0013}} Accessed 30 November 2006</ref><ref>{{cite journal | author = Leeuwenhoek A | 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 | url=http://www.journals.royalsoc.ac.uk/link.asp?id=fl73121jk4150280 | journal = Philosophical Transactions (1683–1775) | volume = 23 | pages = 1304–11|year = 1753 | doi = 10.1098/rstl.1702.0042}} Accessed 30 November 2006</ref> Leeuwenhoek's discovery, along with subsequent observations by [[Lazzaro Spallanzani]] and [[Louis Pasteur]], ended the long-held belief that life [[Abiogenesis|spontaneously appear]]ed from non-living substances during the process of spoilage. Lazzarro Spallanzani found that microorganisms could only settle in a broth if the broth was exposed to the air. He also found that boiling the broth would [[Sterilization (microbiology)|sterilise]] it and kill the microorganisms. Louis Pasteur expanded upon Spallanzani's findings by exposing boiled broths to the air, in vessels that contained a filter to prevent all particles from passing through to the growth medium, and also in vessels with no filter at all, with air being admitted via a curved tube that would not allow dust particles to come in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as [[spore]]s on dust, rather than spontaneously generated within the broth. Thus, Pasteur dealt the death blow to the theory of spontaneous generation and supported [[Germ theory of disease|germ theory]]. In 1876, [[Robert Koch]] established that microbes can cause disease. He did this by finding that the blood of cattle who were infected with [[anthrax]] always had large numbers of ''[[Bacillus anthracis]]''. Koch also found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, causing the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, inject it into a healthy animal, and cause illness. Based upon these experiments, he devised criteria for establishing a causal link between a microbe and a disease in what are now known as [[Koch's postulates]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1905/ The Nobel Prize in Physiology or Medicine 1905] Nobelprize.org Accessed November 22, 2006.</ref> Though these postulates cannot be applied in all cases, they do retain historical importance in the development of scientific thought and can still be used today.<ref>{{cite journal | author = O'Brien S, Goedert J | title = HIV causes AIDS: Koch's postulates fulfilled | journal = Curr Opin Immunol | volume = 8 | issue = 5 | pages = 613–18 | year = 1996 | pmid = 8902385 | doi = 10.1016/S0952-7915(96)80075-6 <!--Retrieved from CrossRef by DOI bot-->}}</ref> ==Classification and structure== [[Image:Tree of life 1500px coloured.png|thumb|right|380px|[[Phylogenetic tree|Evolutionary tree]] showing the common ancestry of all three [[Domain (biology)|domains]] of life.<ref>{{cite journal |author=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |title=Toward automatic reconstruction of a highly resolved tree of life |journal=Science |volume=311 |issue=5765 |pages=1283–7 |year=2006 |pmid=16513982 | doi = 10.1126/science.1123061 <!--Retrieved from CrossRef by DOI bot-->}}</ref> [[Bacteria]] are colored blue, [[eukaryote]]s red, and [[archaea]] green. Relative positions of some [[phylum|phyla]] are shown around the tree.]] Microorganisms can be found almost anywhere in the [[taxonomy|taxonomic]] organization of life on the planet. [[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-animals|animals]] and plants. [[Viruses]] are generally regarded as not living and therefore are not microbes, although the field of [[microbiology]] also encompasses the study of viruses. ===Prokaryotes=== Prokaryotes are organisms that lack a [[cell nucleus]] and the other [[organelle]]s found in [[eukaryote]]s. Prokaryotes are almost always unicellular, although some species such as [[myxobacteria]] can aggregate into complex structures as part of their [[life cycle]]. These organisms are divided into two groups, the archaea and the bacteria. ====Bacteria==== {{main|Bacteria}} [[Image:Staphylococcus aureus 01.jpg|thumb|left|250 px|''[[Staphylococcus aureus]]'' bacteria magnified about 10,000x]] [[Bacteria]] are the most diverse and abundant group of [[organism]]s on [[Earth]]. Bacteria inhabit practically all environments where some liquid water is available and the temperature is below +140 °C. They are found in [[sea water]], [[soil]], [[Earth's atmosphere|air]], animals' [[gastrointestinal tract]]s, [[hot spring]]s and even deep beneath the Earth's crust in [[Rock (geology)|rock]]s.<ref name=Gold>{{cite journal |author=Gold T |title=The deep, hot biosphere |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=89 |issue=13 |pages=6045–9 |year=1992 |pmid=1631089 |doi= 10.1073/pnas.89.13.6045}}</ref> Practically all surfaces which have not been specially sterilized are covered in bacteria. The number of bacteria in the world is estimated to be around five million trillion trillion, or 5 &times; 10<sup>30</sup>.<ref>{{cite journal | author = Whitman W, Coleman D, Wiebe W | title = Prokaryotes: the unseen majority | doi= 10.1073/pnas.95.12.6578 | journal = Proc Natl Acad Sci U S A | volume = 95 | issue = 12 | pages = 6578 – 83 | year = 1998 | pmid = 9618454}}</ref> Bacteria are practically all invisible to the naked eye, with a few extremely rare exceptions, such as ''[[Thiomargarita namibiensis]]''.<ref>{{cite journal | author = Schulz H, Jorgensen B | title = Big bacteria | journal = Annu Rev Microbiol | volume = 55 | pages = 105–37 | year =2001 |pmid=11544351 | doi = 10.1146/annurev.micro.55.1.105 <!--Retrieved from CrossRef by DOI bot-->}}</ref> They are [[unicellular]] organisms and lack membrane-bound organelles. Their genome is usually 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 are surrounded by a [[cell wall]], which provides strength and rigidity to their cells. They reproduce by [[binary fission]] or sometimes by [[budding]], but do not undergo [[sexual reproduction]]. Some species form extraordinarily resilient [[endospore|spores]], but for [[bacteria]] this is a mechanism for survival, not reproduction. Under optimal conditions bacteria can grow extremely rapidly and can double as quickly as every 10 minutes.<ref>{{cite journal | author = Eagon R | title = Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes | journal = J Bacteriol | volume = 83 | issue = | pages = 736–7 | year =1962 | pmid=13888946}}</ref> ====Archaea==== {{main|Archaea}} Archaea are also single-celled organisms that lack nuclei. In the past, the differences between bacteria and archaea were not recognised and archaea were classified with bacteria as part of the kingdom [[Monera]]. However, in 1990 the microbiologist [[Carl Woese]] proposed the [[three-domain system]] that divided living things into bacteria, archaea and eukaryotes.<ref>{{cite journal | author = Woese C, Kandler O, 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 U S A | volume = 87 | issue = 12 | pages = 4576–9 | year = 1990 | pmid=2112744}}</ref> Archaea differ from bacteria in both their genetics and biochemistry. For example, while bacterial [[cell membranes]] are made from [[phospholipid|phosphoglycerides]] with [[ester]] bonds, archaean membranes are made of [[ether lipid]]s.<ref>{{cite journal |author=De Rosa M, Gambacorta A, Gliozzi A |title=Structure, biosynthesis, and physicochemical properties of archaebacterial lipids |journal=Microbiol. Rev. |volume=50 |issue=1 |pages=70–80 |year=1986 |pmid=3083222 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=3083222}}</ref> Archaea were originally described in extreme environments, such as [[hot spring]]s, but have since been found in all types of habitats.<ref>{{cite journal | author = Robertson C, Harris J, Spear J, Pace N | title = Phylogenetic diversity and ecology of environmental Archaea | journal = Curr Opin Microbiol | volume = 8 | issue = 6 | pages = 638–42 | year = 2005 | pmid = 16236543}}</ref> Only now are scientists beginning to appreciate how common archaea are in the environment, with [[crenarchaeota]] being the most common form of life in the ocean, dominating ecosystems below 150 m in depth.<ref>{{cite journal |author=Karner MB, DeLong EF, Karl DM |title=Archaeal dominance in the mesopelagic zone of the Pacific Ocean |journal=Nature |volume=409 |issue=6819 |pages=507–10 |year=2001 |pmid=11206545 | doi = 10.1038/35054051 <!--Retrieved from CrossRef by DOI bot-->}}</ref><ref>{{cite journal |author=Sinninghe Damsté JS, Rijpstra WI, Hopmans EC, Prahl FG, Wakeham SG, 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 |year=2002 |pmid=12039760 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12039760 | doi = 10.1128/AEM.68.6.2997-3002.2002 <!--Retrieved from CrossRef by DOI bot-->}}</ref> These organisms are also common in soil and play a vital role in [[ammonia]] oxidation.<ref>{{cite journal |author=Leininger S, Urich T, Schloter M, ''et al'' |title=Archaea predominate among ammonia-oxidizing prokaryotes in soils |journal=Nature |volume=442 |issue=7104 |pages=806–9 |year=2006 |pmid=16915287 | doi = 10.1038/nature04983 <!--Retrieved from CrossRef by DOI bot-->}}</ref> ===Eukaryotes=== {{main|Eukaryote}} [[Image:Chaos diffluens.jpg|thumb|250px|right|An [[amoeba]], a typical [[Eukaryote|eukaryotic]] microorganism]] All living things which are ''individually'' visible to the naked eye are [[eukaryote]]s (with few exceptions, such as ''[[Thiomargarita namibiensis]]''), including [[human]]s. However, a large number of 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 which houses the [[DNA]] that makes up a cell's [[genome]]. DNA itself is arranged in complex [[chromosome]]s.<ref>"Eukaryota: More on Morphology." [http://www.ucmp.berkeley.edu/alllife/eukaryotamm.html] (Accessed 10 October 2006)</ref> 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, Brown M, Johnson P | title = Ancient invasions: from endosymbionts to organelles | journal = Science | volume = 304 | issue = 5668 | pages = 253–7 | year = 2004|pmid = 15073369 | doi = 10.1126/science.1094884 <!--Retrieved from CrossRef by DOI bot-->}}</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 are those eukaryotic organisms that 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]] at the beginning of their life cycles. Microbial eukaryotes can be either [[haploid]] or [[diploid]], and some organisms have multiple [[cell nucleus|cell nuclei]] (see [[coenocyte]]). However, not all microorganisms are unicellular as some microscopic eukaryotes are made from multiple cells. ==== Protists ==== {{main|Protista}} 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 |title=Kingdom protozoa and its 18 phyla |journal=Microbiol. Rev. |volume=57 |issue=4 |pages=953–94 |year=1993 |pmid=8302218 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8302218}}</ref><ref>{{cite journal |author=Corliss JO |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 <!--Retrieved from CrossRef by DOI bot-->}}</ref> Several [[algae]] [[species]] are [[multicellular]] protists, and [[slime molds]] 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=1054–8 |year=1989 |pmid=2672337 | doi = 10.1126/science.2672337 <!--Retrieved from CrossRef by DOI bot-->}}</ref> The number of species of protozoa is uncertain, since we may have identified only a small proportion of the diversity in this group of organisms.<ref>{{cite journal |author=Slapeta J, Moreira D, 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=2073–81 |year=2005 |pmid=16191619 |url=http://journals.royalsociety.org/openurl.asp?genre=article&id=doi:10.1098/rspb.2005.3195 |doi=10.1098/rspb.2005.3195}}</ref><ref>{{cite journal |author=Moreira D, López-García P |title=The molecular ecology of microbial eukaryotes unveils a hidden world |journal=Trends Microbiol. |volume=10 |issue=1 |pages=31–8 |year=2002 |pmid=11755083 | doi = 10.1016/S0966-842X(01)02257-0 <!--Retrieved from CrossRef by DOI bot-->}}</ref> [[Image:Yellow mite (Tydeidae) Lorryia formosa 2 edit.jpg|thumb|210px|left|A microscopic mite ''[[Mite|Lorryia formosa]]''.]] ==== Animals ==== {{main|Micro-animals}} All animals are multicellular, but some are too small to be seen by the naked eye. Microscopic [[arthropod]]s include [[dust mite]]s and [[spider mite]]s. Microscopic [[crustacean]]s include [[copepod]]s and the [[cladocera]], while many [[nematode]]s are too small to be seen with the naked eye. Another particularly common group of microscopic animals are the [[rotifer]]s, which are filter feeders that are usually found in fresh water. Micro-animals reproduce both sexually and asexually and may reach new habitats as eggs that survive harsh environments that would kill the adult animal. However, some simple animals, such as rotifers and nematodes, can dry out completely and remain dormant for long periods of time.<ref>{{cite journal |author=Lapinski J, Tunnacliffe A |title=Anhydrobiosis without trehalose in bdelloid rotifers |journal=FEBS Lett. |volume=553 |issue=3 |pages=387–90 |year=2003 |pmid=14572656 | doi = 10.1016/S0014-5793(03)01062-7 <!--Retrieved from CrossRef by DOI bot-->}}</ref> ==== Fungi ==== {{main|Fungus}} The fungi have several unicellular species, such as baker's yeast (''[[Saccharomyces cerevisiae]]'') and fission yeast (''[[Schizosaccharomyces pombe]]''). Some fungi, such as the pathogenic yeast ''[[Candida albicans]]'', can undergo [[phenotypic switching]] and grow as single cells in some environments, and [[Hypha|filamentous hyphae]] in others.<ref>{{cite journal |author=Kumamoto CA, Vinces MD |title=Contributions of hyphae and hypha-co-regulated genes to Candida albicans virulence |journal=Cell. Microbiol. |volume=7 |issue=11 |pages=1546–54 |year=2005 |pmid=16207242 | doi = 10.1111/j.1462-5822.2005.00616.x <!--Retrieved from CrossRef by DOI bot-->}}</ref> Fungi reproduce both asexually, by budding or binary fission, as well by producing spores, which are called [[Conidium|conidia]] when produced asexually, or [[basidiospore]]s when produced sexually. ==== 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, [[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 name="Thomas 02">Thomas, D. 2002. ''Seaweeds.'' The Natural History Museum, London. ISBN 0 565 09175 1</ref> ==Habitats and ecology== Microorganisms are found in almost every [[Habitat (ecology)|habitat]] present in nature. Even in hostile environments such as the [[geographical pole|poles]], [[desert]]s, [[geyser]]s, [[Rock (geology)|rock]]s, and the [[deep sea]], some types of microorganisms have adapted to the extreme conditions and sustained colonies; these organisms are known as [[extremophiles]]. Extremophiles have been isolated from rocks as much as 7 kilometres below the earth's surface,<ref>{{cite journal | author = Szewzyk U, Szewzyk R, Stenström T | title = Thermophilic, anaerobic bacteria isolated from a deep borehole in granite in Sweden | doi= 10.1073/pnas.91.5.1810 | journal = Proc Natl Acad Sci U S A | volume = 91 | issue = 5 | pages = 1810–3 | year = 1994 | pmid = 11607462}}</ref> and it has been suggested that the amount of living organisms below the earth's surface may be comparable with the amount of life on or above the surface.<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]]), 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. === Extremophiles === {{main|Extremophile}} [[Extremophiles]] are microorganisms which have adapted so that they can survive and even thrive in conditions that are normally fatal to most lifeforms. For example, some species have been found in the following extreme environments: *[[Temperature]]: 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}}.[http://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}},[http://news.bbc.co.uk/1/hi/sci/tech/827063.stm] and can survive near [[absolute zero]].[http://science.nasa.gov/newhome/headlines/ast01sep98_1.htm]</ref> *[[Acid]]ity/[[alkalinity]]: less than [[pH]] 0,<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]</ref> up to pH 11.5<ref>The [[Alkaliphile|alkaliphilic]] bacteria ''Bacillus alcalophilus'' can grow at up to pH 11.5.[http://jb.asm.org/cgi/reprint/185/2/461.pdf]</ref> *[[Salinity]]: up to saturation<ref>Dyall-Smith, Mike, [http://www.microbiol.unimelb.edu.au/people/dyallsmith/ ''HALOARCHAEA''], University of Melbourne. See also [[Haloarchaea]].</ref> *[[Pressure]]: up to 1,000-2,000 [[Atmosphere (unit)|atm]], down to 0 atm (e.g. [[vacuum]] of [[Outer space|space]])<ref>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.[http://www.microscopy-uk.org.uk/index.html?http://www.microscopy-uk.org.uk/nanobes/nanopaper.html]</ref> *[[Ionizing radiation|Radiation]]: up to 5k[[Gray (unit)|Gy]]<ref>See [[Deinococcus radiodurans]]</ref> 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 [[bio-technology]], and their very existence under such extreme conditions increases the potential for [[extraterrestrial life]].<ref>Cavicchioli R., [http://www.ncbi.nlm.nih.gov/pubmed/12530238 ''Extremophiles and the search for extraterrestrial life.''] Astrobiology. 2002 Fall;2(3):281-92.</ref> {{Extremophile|state=collapsed}} === Soil microbes === The [[nitrogen cycle]] in soils depends on the fixation of atmospheric nitrogen. One way this can occur is in the nodules in the roots of [[legumes]] that contain symbiotic bacteria of the genera ''Rhizobium'', ''Mesorhizobium'', ''Sinorhizobium'', ''Bradyrhizobium'', and ''Azorhizobium''.<ref>{{cite journal | author = Barea J, Pozo M, Azcón R, Azcón-Aguilar C | title = Microbial co-operation in the rhizosphere | doi= 10.1093/jxb/eri197 | journal = J Exp Bot | volume = 56 | issue = 417 | pages = 1761–78 | year = 2005 | pmid = 15911555}}</ref> === Symbiotic microbes === Symbiotic microbes ==Importance== Microorganisms are vital to humans and the environment, as they participate in the Earth's element cycles such as the [[carbon cycle]] and [[nitrogen cycle]], as well as fulfilling other vital roles in virtually all [[ecosystem]]s, such as recycling other organisms' dead remains and waste products through [[decomposition]]. Microbes also have an important place in most higher-order multicellular organisms as [[symbionts]]. Many blame the failure of [[Biosphere 2]] on an improper balance of microbes. === Use in food === {{main|Fermentation (food)}} Microorganisms are used in [[brewing]], [[winemaking]], [[baking]], [[pickling]] and other [[food]]-making processes. They are also used to control the [[Fermentation (food)|fermentation]] process in the production of cultured [[dairy product]]s such as [[yogurt]] and [[cheese]]. The cultures also provide flavour and aroma, and inhibit undesirable organisms.<ref>{{cite web |url=http://www.foodsci.uoguelph.ca/dairyedu/micro.html |title= Dairy Microbiology |accessdate=2006-10-09 |publisher= University of Guelph}}</ref> === Use in water treatment === {{main|Sewage treatment}} Microbes are used in the biological treatment of sewage and industrial waste effluents.. === Use in energy === {{Main|Ethanol fermentation}} Microbes are used in fermentation to produce ethanol. === Use in science === Microbes are also essential tools in [[biotechnology]], [[biochemistry]], [[genetics]], and [[molecular biology]]. The yeasts (''[[Saccharomyces cerevisiae]]'') and fission yeast (''[[Schizosaccharomyces pombe]]'') are important [[model 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 JI, Oliver SG |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 |url=http://www.jbmb.or.kr/fulltext/jbmb/view.php?vol=37&page=93}}</ref> They are particularly valuable in [[genetics]], [[genomics]] and [[proteomics]].<ref>{{cite journal |author=Suter B, Auerbach D, Stagljar I |title=Yeast-based functional genomics and proteomics technologies: the first 15 years and beyond |journal=BioTechniques |volume=40 |issue=5 |pages=625–44 |year=2006 |pmid=16708762}}</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}}</ref> [[Microbes]] can be harnessed for uses such as creating steroids and treating skin diseases. Scientists are also considering using microbes for living [[fuel cells]], and as a solution for pollution. === Use in warfare === {{main|Biological warfare}} In the Middle Ages, dead corpses were thrown over walls during sieges, this meant that any bacteria carrying the disease that killed the person/creature would multiply in the vicinity of the opposing side. == Importance in human health == === Human digestion === {{See|Human flora#Human bacterial flora and human health}} Microorganisms can form an [[Endosymbiont|endosymbiotic]] relationship with other, larger organisms. For example, the bacteria that live within the human digestive system contribute to gut immunity, synthesise [[vitamin]]s such as [[folic acid]] and [[biotin]], and ferment complex indigestible [[carbohydrate]]s.<ref>{{cite journal | author = O'Hara A, Shanahan F | title = The gut flora as a forgotten organ | journal = EMBO Rep | volume = 7 | issue = 7 | pages = 688–93 | year = 2006 | pmid = 16819463 | doi = 10.1038/sj.embor.7400731 <!--Retrieved from CrossRef by DOI bot-->}}</ref> === Diseases and immunology === {{Main|Pathogenic microbes}} Microorganisms are the cause of many infectious diseases. The organisms involved include [[pathogenic bacteria]], causing diseases such as [[bubonic plague|plague]], [[tuberculosis]] and [[anthrax]]; protozoa, causing diseases such as [[malaria]], [[sleeping sickness]] and [[toxoplasmosis]]; and also fungi causing diseases such as [[ringworm]], [[candidiasis]] or [[histoplasmosis]]. However, other diseases such as [[influenza]], [[yellow fever]] or [[AIDS]] are caused by [[pathogenic viruses]], which are not usually classified as living organisms and are not therefore microorganisms by the strict definition. As of 2007, no clear examples of archaean pathogens are known,<ref>{{cite journal |author=Eckburg P, Lepp P, Relman D |title=Archaea and their potential role in human disease |journal=Infect Immun |volume=71 |issue=2 |pages=591–6 |year=2003 |pmid=12540534 | doi = 10.1128/IAI.71.2.591-596.2003 <!--Retrieved from CrossRef by DOI bot-->}}</ref> although a relationship has been proposed between the presence of some methanogens and human [[periodontal disease]].<ref>{{cite journal |author=Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D |title=Methanogenic Archaea and human periodontal disease | doi= 10.1073/pnas.0308766101 | journal=Proc Natl Acad Sci U S A |volume=101 |issue=16 |pages=6176–81 |year=2004 |pmid=15067114}}</ref> == Hygiene == {{main|Hygiene}} Hygiene is the avoidance of [[infection]] or [[food]] spoiling by eliminating microorganisms from the surroundings. As microorganisms, particularly [[bacteria]], are found practically everywhere, this means in most cases the reduction of harmful microorganisms to acceptable levels. However, in some cases it is required that an object or substance be completely sterile, i.e. devoid of all living entities and [[virus]]es. A good example of this is a [[hypodermic needle]]. In food preparation microorganisms are reduced by preservation methods (such as the addition of [[vinegar]]), clean utensils used in preparation, short storage periods or by cool temperatures. If complete sterility is needed, the two most common methods are [[irradiation]] and the use of an [[autoclave]], which resembles a [[pressure cooker]]. There are several methods for investigating the level of hygiene in a sample of food, drinking water, equipment etc. Water samples can be filtrated through an extremely fine filter. This filter is then placed in a [[nutrient medium]]. Microorganisms on the filter then grow to form a visible colony. Harmful microorganisms can be detected in food by placing a sample in a [[nutrient broth]] designed to enrich the organisms in question. Various methods, such as [[Selective medium|selective media]] or [[PCR]], can then be used for detection. The hygiene of hard surfaces, such as cooking pots, can be tested by touching them with a solid piece of [[nutrient medium]] and then allowing the microorganisms to grow on it. There are no conditions where all microorganisms would grow, and therefore often several different methods are needed. For example, a food sample might be analyzed on three different [[nutrient medium]]s designed to indicate the presence of "total" [[bacteria]] (conditions where many, but not all, bacteria grow), [[mold]]s (conditions where the growth of [[bacteria]] is prevented by e.g. [[antibiotic]]s) and [[Coliform Index|coliform]] [[bacteria]] (these indicate a sewage contamination). == In fiction == Microorganisms have frequently played an important part in [[science fiction]], both as agents of disease, and as entities in their own right. Some notable uses of microorganisms in fiction include: * ''[[The War of the Worlds]]'', where microorganisms play important thematic and plot-related roles. * ''[[Fantastic Voyage]]'', in which some scientists are miniaturised to microscopic size and observe micro-organisms from a new perspective * ''[[Blood Music]]'', in which a colony of microorganisms is given [[intelligence]] * ''[[The Andromeda Strain]]'', in which extraterrestrial microorganisms kill several people * ''[[The White Plague]]'', is created and released in vengeance by John Roe O'Neill for the death of his wife and children, it is designed to kill only women. * ''Twelve Monkeys'', James Cole (Bruce Willis) searches for a pure germ in the past, which creates a deadly plague in the future. Also, Brad Pitt (as Jeffery Goines) discusses his germaphobia. ==See also== *[[Biological warfare]] *[[Biology]] *[[Microbial intelligence]] *[[Nanobacterium]] *[[Petri dish]] *[[Prokaryote]] *[[Soil contamination]] *[[Staining (biology)|Staining]] ==References== {{reflist|2}} ==External links== * [http://dels.nas.edu/metagenomics Our Microbial Planet] A free poster from the National Academy of Sciences about the positive roles of microbes. *[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] A 20-page educational booklet providing a basic overview of metagenomics and our microbial planet. * [http://www.genomenewsnetwork.org/categories/index/microbes.php Microbe News from Genome News Network] *[http://www.professorpatents.com/microbes.htm Microbes Patent List] Microbes Related Patents * [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] On-line microbiology textbook by Timothy Paustian and Gary Roberts, University of Wisconsin-Madison {{Nature nav}} [[Category:Microbiology]] [[ar:ميكروب]] [[bn:অণুজীব]] [[ca:Microorganisme]] [[cs:Mikroorganismus]] [[da:Mikroorganisme]] [[de:Mikroorganismus]] [[et:Mikroorganismid]] [[el:Μικροοργανισμός]] [[es:Microorganismo]] [[eo:Mikroorganismo]] [[eu:Mikrobio]] [[fa:ریزاندامگان]] [[fr:Micro-organisme]] [[gl:Microorganismo]] [[ko:미생물]] [[hr:Mikroorganizmi]] [[id:Mikroorganisme]] [[is:Örvera]] [[it:Microrganismo]] [[he:מיקרואורגניזם]] [[kaa:Bir kletkalı haywanlar]] [[ku:Hûrjînewer]] [[lv:Mikroorganisms]] [[lt:Mikroorganizmai]] [[hu:Mikroorganizmus]] [[mk:Едноклеточен организам]] [[nl:Micro-organisme]] [[ja:微生物]] [[no:Mikroorganisme]] [[nn:Mikroorganisme]] [[pl:Mikroorganizm]] [[pt:Microorganismo]] [[ro:Microorganism]] [[ru:Микроорганизмы]] [[simple:Unicellular organism]] [[sk:Mikroorganizmus]] [[sl:Mikroorganizem]] [[fi:Mikrobi]] [[sv:Mikroorganism]] [[ta:நுண்ணுயிர்]] [[th:จุลินทรีย์]] [[vi:Vi sinh vật]] [[tr:Mikroorganizma]] [[uk:Мікроорганізми]] [[ur:یک خلوی جاندار]] [[zh:微生物]]