Editing Microorganism (section)

==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 |url-status=dead }}</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>