Microbial ecology

{{Short description|Study of the relationship of microorganisms with their environment}} {{Redirect|Environmental microbiology|the journal|Environmental Microbiology}} {{Use British English|date=February 2024}} {{Use mdy dates|date=February 2024}} thumb|upright=1.3|The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed under the microscope. This is because microbiologists are able to cultivate only a minority of naturally occurring microbes using current laboratory techniques, depending on the environment.<ref name="hugenholz2002" /> '''Microbial ecology''' (or '''environmental microbiology''') is a discipline where the interaction of microorganisms and their environment are studied.<ref name=":02">{{Citation |last=Gray |first=N. D. |title=Microbial Ecology |date=2008-01-01 |work=Encyclopedia of Ecology |pages=2357–2368 |editor-last=Jørgensen |editor-first=Sven Erik |url=https://www.sciencedirect.com/science/article/abs/pii/B978008045405400519X |access-date=2025-04-01 |place=Oxford |publisher=Academic Press |isbn=978-0-08-045405-4 |last2=Head |first2=I. M. |editor2-last=Fath |editor2-first=Brian D.}}</ref> Microorganisms are known to have beneficial, neutral and harmful ecological relationships within their species and other species.<ref name=":02" /> Many scientists have studied the relationship between nature and microorganisms: Martinus Beijerinck, Sergei Winogradsky, Louis Pasteur, Robert Koch, Lorenz Hiltner, Dionicia Gamboa and many more,<ref>{{Cite journal |last=Kolter |first=Roberto |date=2021-10-08 |title=The History of Microbiology—A Personal Interpretation |url=https://www.annualreviews.org/doi/10.1146/annurev-micro-033020-020648 |journal=Annual Review of Microbiology |language=en |volume=75 |issue=1 |pages=1–17 |doi=10.1146/annurev-micro-033020-020648 |pmid=33974804 |issn=0066-4227|url-access=subscription }}</ref><ref name=":4">{{Cite journal |last1=Hartmann |first1=Anton |last2=Rothballer |first2=Michael |last3=Schmid |first3=Michael |date=2008-11-01 |title=Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research |url=https://link.springer.com/article/10.1007/s11104-007-9514-z |journal=Plant and Soil |language=en |volume=312 |issue=1 |pages=7–14 |doi=10.1007/s11104-007-9514-z |bibcode=2008PlSoi.312....7H |issn=1573-5036|url-access=subscription }}</ref><ref>{{Cite journal |last=Céline |first=Valadeau |last2=Adriana |first2=Pabon |last3=Eric |first3=Deharo |last4=Joaquina |first4=Albán–Castillo |last5=Yannick |first5=Estevez |last6=Augusto |first6=Lores Fransis |last7=Rosario |first7=Rojas |last8=Dionicia |first8=Gamboa |last9=Michel |first9=Sauvain |last10=Denis |first10=Castillo |last11=Geneviève |first11=Bourdy |date=2009-06-25 |title=Medicinal plants from the Yanesha (Peru): Evaluation of the leishmanicidal and antimalarial activity of selected extracts |url=https://linkinghub.elsevier.com/retrieve/pii/S0378874109001895 |journal=Journal of Ethnopharmacology |volume=123 |issue=3 |pages=413–422 |doi=10.1016/j.jep.2009.03.041 |issn=0378-8741|url-access=subscription |hdl=20.500.12390/716 |hdl-access=free }}</ref><ref name=":04">{{Cite journal |last=Céline |first=Valadeau |last2=Adriana |first2=Pabon |last3=Eric |first3=Deharo |last4=Joaquina |first4=Albán–Castillo |last5=Yannick |first5=Estevez |last6=Augusto |first6=Lores Fransis |last7=Rosario |first7=Rojas |last8=Dionicia |first8=Gamboa |last9=Michel |first9=Sauvain |last10=Denis |first10=Castillo |last11=Geneviève |first11=Bourdy |title=Medicinal plants from the Yanesha (Peru): Evaluation of the leishmanicidal and antimalarial activity of selected extracts |url=https://linkinghub.elsevier.com/retrieve/pii/S0378874109001895 |journal=Journal of Ethnopharmacology |language=en |volume=123 |issue=3 |pages=413–422 |doi=10.1016/j.jep.2009.03.041 |via=Elsevier Science Direct|url-access=subscription |hdl=20.500.12390/716 |hdl-access=free }}</ref> to understand the specific roles that these microorganisms have in biological and chemical pathways and the evolution of these microorganisms. Currently, there are several types of biotechnologies that have allowed scientists to analyze the biological and chemical properties of these microorganisms.<ref>{{Cite journal |last=Flavier |first=Albert B. |last2=Balan |first2=Venkatesh |last3=Khan |first3=Abdul Latif |title=– Microbial Biotechnology: Fundamentals and Applications |url=https://uhlibraries.pressbooks.pub/microbialbiotech/chapter/200/ |journal=Microbial Biotechnology: Fundamentals and Applications |language=en}}</ref>

Many of these microorganisms have been known to form different symbiotic relationships with other organisms in their environment.<ref>{{Cite journal |last1=Glaeser |first1=Jens |last2=Overmann |first2=Jörg |date=August 2004 |title=Biogeography, Evolution, and Diversity of Epibionts in Phototrophic Consortia |journal=Applied and Environmental Microbiology |volume=70 |issue=8 |pages=4821–4830 |bibcode=2004ApEnM..70.4821G |doi=10.1128/aem.70.8.4821-4830.2004 |issn=0099-2240 |pmc=492462 |pmid=15294820}}</ref> Some symbiotic relationships include mutualism, commensalism, amensalism, and parasitism.<ref name=":5" /><ref name="annualreviews.org">{{Cite journal |last1=Mathis |first1=Kaitlyn A. |last2=Bronstein |first2=Judith L. |date=2020-11-02 |title=Our Current Understanding of Commensalism |url=https://www.annualreviews.org/doi/10.1146/annurev-ecolsys-011720-040844 |journal=Annual Review of Ecology, Evolution, and Systematics |language=en |volume=51 |issue=1 |pages=167–189 |doi=10.1146/annurev-ecolsys-011720-040844 |issn=1543-592X}}</ref>

In addition, certain antimicrobial substances in the environment can kill microorganisms, thus preventing them from interacting with their environment. These can be antibiotic, antifungal, or antiviral.<ref name=":7" />

== Influential scientists == [[File:Louis Pasteur.jpg|thumb|Louis Pasteur ]] Martinus Beijerinck invented the enrichment culture, a fundamental method culturing organisms for studying microbes from the environment. Sergei Winogradsky was one of the first researchers to attempt to understand microorganisms outside of the medical context—making him among the first students of microbial ecology and environmental microbiology—discovering chemosynthesis and developing the Winogradsky column in the process.<ref name="brock" />{{rp|644}}

Louis Pasteur was a French chemist who derived key microbial principles that we use today: microbial fermentation, pasteurization, germ theory, and vaccines.<ref name=":12">{{Cite journal |last=Mostowy |first=Serge |date=2022-12-01 |title=Louis Pasteur continues to shape the future of microbiology |url=https://journals.biologists.com/dmm/article/15/12/dmm050011/285918/Louis-Pasteur-continues-to-shape-the-future-of |journal=Disease Models & Mechanisms |language=en |volume=15 |issue=12 |doi=10.1242/dmm.050011 |issn=1754-8403 |pmc=10655809 |pmid=36504391}}</ref> These principles have served as a foundation for scientists in viewing the relationship between microbes and their environment.<ref name=":12" /> For example, Pasteur disproved the theory of spontaneous generation, the belief of life arising from nonliving materials.<ref>{{Cite web |date=2017-05-06 |title=1.1C: Pasteur and Spontaneous Generation |url=https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Boundless)/01:_Introduction_to_Microbiology/1.01:_Introduction_to_Microbiology/1.1C:_Pasteur_and_Spontaneous_Generation |access-date=2025-04-02 |website=Biology LibreTexts |language=en}}</ref> Pasteur stated that life can only come from life and not nonliving materials.<ref name=":0" /> This led to the idea that microorganisms were responsible for the microbial growth in any environment.<ref name=":0">{{Cite web |date=2022-07-22 |title=1.6.2: Pasteur and Spontaneous Generation |url=https://bio.libretexts.org/Courses/Prince_Georges_Community_College/PGCC_Microbiology/01:_Introduction_to_Microbiology/1.06:_History_of_Microbiology/1.6.02:_Pasteur_and_Spontaneous_Generation |access-date=2025-04-02 |website=Biology LibreTexts |language=en}}</ref>

Robert Koch was a physician-scientist who implemented the use of an oil-immersion lens and a condenser while using microscopes, to increase the imagery of viewing bacteria.<ref name=":03">{{Cite journal |last=Blevins |first=Steve M. |last2=Bronze |first2=Michael S. |date=2010-09-01 |title=Robert Koch and the 'golden age' of bacteriology |url=https://www.sciencedirect.com/science/article/pii/S1201971210023143 |journal=International Journal of Infectious Diseases |volume=14 |issue=9 |pages=e744–e751 |doi=10.1016/j.ijid.2009.12.003 |issn=1201-9712|doi-access=free }}</ref> This led Koch to be the first publisher of bacteria photographs. As a result, Koch was able to study wound infections in animals at the microscopic level.<ref name=":03" /> He distinguished between distinct bacteria species, which led him to believe that the best way to study a certain disease is to focus on a specific pathogen.<ref name=":03" /> In 1879, Koch started to develop "pure" cultures to grow bacteria colonies.<ref name=":03" /> These advancements led Koch to solve the Cholera pandemic in India during the year 1883.<ref name=":03" /> Koch's laboratory techniques and materials led him to conclude that the use of unfiltered water that contained the bacteria thought to cause intestinal harm was causing the cholera pandemic.<ref name=":03" />

Lorenz Hiltner is known as one of the pioneers in "microbial ecology."<ref name=":4" /> His research focused on how microbials in the rhizosphere provided nutrients to plants. Hiltner stated that the quality of plant products was a result of the plant's roots microflora.<ref name=":4" /> One of Hiltner contributions to the study of plant nutrition and soil bacteriology was creating antimicrobial seeds covered with mercury chloride.<ref name=":4" /> The sole purpose of creating the antimicrobial seeds were to protect the seeds from the harmful effects of pathogenic fungi. In addition, he recognized the known bacteria that were responsible for the nitrogen cycle: denitrification, nitrification, and nitrogen fixation.<ref name=":4" />

==Important microbial roles in the environment== Microorganisms are the backbone of all ecosystems, even in areas where photosynthesis cannot take place. For example, chemosynthetic microorganisms are the primary producers in extreme environments, such as high temperature geothermal environments.<ref>{{Cite journal |last1=Inskeep |first1=W. P. |last2=Ackerman |first2=G. G. |last3=Taylor |first3=W. P. |last4=Kozubal |first4=M. |last5=Korf |first5=S. |last6=Macur |first6=R. E. |date=October 2005 |title=On the energetics of chemolithotrophy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park |url=https://onlinelibrary.wiley.com/doi/10.1111/j.1472-4669.2006.00059.x |journal=Geobiology |language=en |volume=3 |issue=4 |pages=297–317 |doi=10.1111/j.1472-4669.2006.00059.x |issn=1472-4677|url-access=subscription }}</ref> In these extreme conditions, the chemosynthetic microbes provide energy and carbon to other organisms. Chemosynthetic microorganisms gain energy by oxidizing inorganic compounds such as hydrogen, nitrite, ammonia, sulfur and iron (II). These organisms can be found in both aerobic and anaerobic environment.<ref>{{cite book |last=Oren |first=Aharon |date=2009-09-15 |chapter=Chemolithotrophy |title=Encyclopedia of Life Sciences |doi=10.1002/9780470015902.a0021153|isbn=978-0-470-01617-6}}</ref>

The nitrogen cycle, phosphorus cycle, sulphur cycle, and carbon cycle depend on microorganisms also. Each cycle involves microorganisms in certain processes.<ref>{{Cite journal |last1=Li |first1=Wenjing |last2=Wang |first2=Jinlong |last3=Jiang |first3=Lamei |last4=Lv |first4=Guanghui |last5=Hu |first5=Dong |last6=Wu |first6=Deyan |last7=Yang |first7=Xiaodong |date=March 1, 2023 |title=Rhizosphere effect and water constraint jointly determined the roles of microorganism in soil phosphorus cycling in arid desert regions |url=https://www.sciencedirect.com/science/article/pii/S0341816222007950 |journal=CATENA |language=en |volume=222 |article-number=106809 |doi=10.1016/j.catena.2022.106809 |bibcode=2023Caten.22206809L |s2cid=256786335 |issn=0341-8162|url-access=subscription }}</ref> For example, nitrogen gas makes up 78% of the Earth's atmosphere, but it is almost chemically inert; as a result, it is unavailable to most organisms. It has to be converted biologically to an available form by microorganism, through nitrogen fixation.<ref>{{Cite journal |last=Delwiche |first=C. C. |title=The Nitrogen Cycle |date=1970 |journal=Scientific American |volume=223 |issue=3 |pages=136–147 |doi=10.1038/scientificamerican0970-136 |jstor=24925899 |pmid=5459723 |bibcode=1970SciAm.223c.136D |s2cid=201233849 |issn=0036-8733}}</ref> Through these biogeochemical cycles, microorganisms are able to make nutrients such as nitrogen, phosphorus and potassium available in the soil.<ref>{{Citation |last1=Basu |first1=Sahana |title=Chapter 13 - Role of soil microbes in biogeochemical cycle for enhancing soil fertility |date=2021-01-01 |work=New and Future Developments in Microbial Biotechnology and Bioengineering |pages=149–157 |editor-last=Verma |editor-first=Jay Prakash |url=https://linkinghub.elsevier.com/retrieve/pii/B9780444643254000134 |access-date=2024-11-04 |publisher=Elsevier |doi=10.1016/b978-0-444-64325-4.00013-4 |isbn=978-0-444-64325-4 |last2=Kumar |first2=Gautam |last3=Chhabra |first3=Sagar |last4=Prasad |first4=Ram |editor2-last=Macdonald |editor2-first=Catriona A. |editor3-last=Gupta |editor3-first=Vijai Kumar |editor4-last=Podile |editor4-first=Appa Rao|url-access=subscription }}</ref> Microorganisms play a role in solubilizing phosphate, improving soil health, and plant growth.<ref>{{Cite journal |last1=Tian |first1=Jiang |last2=Ge |first2=Fei |last3=Zhang |first3=Dayi |last4=Deng |first4=Songqiang |last5=Liu |first5=Xingwang |date=February 17, 2021 |title=Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle |journal=Biology |language=en |volume=10 |issue=2 |page=158 |doi=10.3390/biology10020158 |pmid=33671192 |pmc=7922199 |issn=2079-7737 |doi-access=free}}</ref>

== Microbial applications in biotechnology == Microbial interactions are found in bioremediation. Bioremediation is a technology that removes contaminants from soil<ref>{{Cite journal |last1=Zhao |first1=Yue |last2=Yao |first2=Jun |last3=Yuan |first3=Zhimin |last4=Wang |first4=Tianqi |last5=Zhang |first5=Yiyue |last6=Wang |first6=Fei |date=2016-10-08 |title=Bioremediation of Cd by strain GZ-22 isolated from mine soil based on biosorption and microbially induced carbonate precipitation |journal=Environmental Science and Pollution Research |volume=24 |issue=1 |pages=372–380 |doi=10.1007/s11356-016-7810-y |issn=0944-1344 |pmid=27722882}}</ref> and wastewater<ref>{{Cite journal |last1=Saeed |first1=Muhammad Usama |last2=Hussain |first2=Nazim |last3=Sumrin |first3=Aleena |last4=Shahbaz |first4=Areej |last5=Noor |first5=Saman |last6=Bilal |first6=Muhammad |last7=Aleya |first7=Lotfi |last8=Iqbal |first8=Hafiz M. N. |date=2022-04-20 |title=Microbial bioremediation strategies with wastewater treatment potentialities – A review |url=https://linkinghub.elsevier.com/retrieve/pii/S0048969721068303 |journal=Science of the Total Environment |volume=818 |article-number=151754 |doi=10.1016/j.scitotenv.2021.151754 |issn=0048-9697 |pmid=34800451|url-access=subscription }}</ref> using microorganisms.<ref>{{Citation |last1=Bilal |first1=Muhammad |title=Laccase-Mediated Bioremediation of Dye-Based Hazardous Pollutants |date=2020 |work=Environmental Chemistry for a Sustainable World |pages=137–160 |place=Cham |publisher=Springer International Publishing |doi=10.1007/978-3-030-48985-4_6 |isbn=978-3-030-48984-7 |last2=Ashraf |first2=Syed Salman |last3=Iqbal |first3=Hafiz M. N.}}</ref><ref>{{Cite journal |last1=Zhao |first1=Youkang |last2=Bai |first2=Yang |last3=Guo |first3=Qiu |last4=Li |first4=Zhiling |last5=Qi |first5=Mengyuan |last6=Ma |first6=Xiaodan |last7=Wang |first7=Hao |last8=Kong |first8=Deyong |last9=Wang |first9=Aijie |last10=Liang |first10=Bin |date=February 2019 |title=Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes |journal=Science of the Total Environment |volume=653 |pages=649–657 |doi=10.1016/j.scitotenv.2018.10.396 |issn=0048-9697}}</ref> Examples of some microorganisms that play a role in bioremediation are the following: ''Pseudomonas'', ''Bacillus'', ''Arthrobacter'', ''Corynebacterium'', ''Methosinus'', ''Rhodococcus'', ''Stereum hirsutum'', methanogens, ''Aspergilus niger'', Pleurotus ostreatus, ''Rhizopus arrhizus'', ''Azotobacter'', ''Alcaligenes'', ''Phormidium valderium'', and ''Ganoderma applantus''.<ref>{{Cite journal |last1=Verma |first1=Samakshi |last2=Kuila |first2=Arindam |date=2019-05-01 |title=Bioremediation of heavy metals by microbial process |url=https://linkinghub.elsevier.com/retrieve/pii/S2352186418305911 |journal=Environmental Technology & Innovation |volume=14 |article-number=100369 |doi=10.1016/j.eti.2019.100369 |issn=2352-1864|url-access=subscription }}</ref>

== Microbial evolution == Due to high levels of horizontal gene transfer among microbial communities,<ref name="mcdaniel" /> microbial ecology is also important to the study of evolution.<ref name="smets" />

== Microbial symbiotic relationships == === Mutualism === Mutualism is a close relationship between two different species in which each has a positive effect on the other. In mutualism, one partner provides service to the other partner and receives service from the other partner as well.<ref>{{Cite book |url=https://academic.oup.com/book/27600 |title=Mutualism |date=2015-07-01 |publisher=Oxford University Press |isbn=978-0-19-180942-2 |language=en |doi=10.1093/acprof:oso/9780199675654.001.0001 |editor-last1=Bronstein |editor-first1=Judith L.}}</ref> Mutualism in microbial ecology is a relationship between microbial species and other species (example humans) that allows for both sides to benefit.<ref name=":42">{{Cite book |title=Understanding bacteria |last=Sheela |first=Srivastava |date=2003 |publisher=Kluwer Academic Publishers |others=Srivastava, P. S. |isbn=978-1-4020-1633-2 |location=Dordrecht |oclc=53231924}}</ref> Microorganisms form mutualistic relationships with other microorganism, plants or animals. One example of microbe-microbe interaction would be syntrophy, also known as cross-feeding,<ref>{{cite journal |last1=Faust |first1=Karoline |last2=Raes |first2=Jeroen |date=July 16, 2012 |title=Microbial interactions: from networks to models |journal=Nature Reviews. Microbiology |volume=10 |issue=8 |pages=538–550 |doi=10.1038/nrmicro2832 |pmid=22796884 |s2cid=22872711}}</ref> of which ''Methanobacterium omelianskii'' is a classic example.<ref>{{Cite journal|last1=Bryant|first1=M. P.|last2=Wolin|first2=E. A.|last3=Wolin|first3=M. J.|last4=Wolfe|first4=R. S.|date=1967|title=Methanobacillus omelianskii, a symbiotic association of two species of bacteria|journal=Archiv für Mikrobiologie|volume=59|issue=1–3|pages=20–31|doi=10.1007/bf00406313|pmid=5602458|bibcode=1967ArMic..59...20B |s2cid=10348127|issn=0302-8933}}</ref><ref name=":2" /> This consortium is formed by an ethanol fermenting organism and a methanogen. The ethanol-fermenting organism provides the archaeal partner with the H₂, which this methanogen needs in order to grow and produce methane.<ref name=":13">{{Cite book |last=Kirchman |first=David L |title=Processes in microbial ecology |date=2012 |publisher=Oxford University Press |isbn=978-0-19-958693-6 |location=Oxford |oclc=777261246}}</ref><ref name=":2">{{Cite journal |last1=López-García |first1=Purificación |last2=Eme |first2=Laura |last3=Moreira |first3=David |date=December 2017 |title=Symbiosis in eukaryotic evolution |journal=Journal of Theoretical Biology |series=The origin of mitosing cells: 50th anniversary of a classic paper by Lynn Sagan (Margulis) |volume=434 |issue=Supplement C |pages=20–33 |doi=10.1016/j.jtbi.2017.02.031|pmid=28254477 |pmc=5638015 |bibcode=2017JThBi.434...20L}}</ref> Syntrophy has been hypothesized to play a significant role in energy and nutrient-limited environments, such as deep subsurface, where it can help the microbial community with diverse functional properties to survive, grow and produce maximum amount of energy.<ref>{{Cite journal|last1=Lau|first1=Maggie C. Y.|last2=Kieft|first2=Thomas L.|last3=Kuloyo|first3=Olukayode|last4=Linage-Alvarez|first4=Borja|last5=van Heerden|first5=Esta|last6=Lindsay|first6=Melody R.|last7=Magnabosco|first7=Cara|last8=Wang|first8=Wei|last9=Wiggins|first9=Jessica B.|last10=Guo|first10=Ling|last11=Perlman|first11=David H.|date=December 6, 2016|title=An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulphur-driven autotrophic denitrifiers|journal=Proceedings of the National Academy of Sciences|language=en|volume=113|issue=49|pages=E7927–E7936|doi=10.1073/pnas.1612244113|issn=0027-8424|pmc=5150411|pmid=27872277|bibcode=2016PNAS..113E7927L |doi-access=free}}</ref><ref>{{Citation|last1=Schink|first1=Bernhard|title=Syntrophism Among Prokaryotes|date=2013|work=The Prokaryotes|pages=471–493|publisher=Springer Berlin Heidelberg|isbn=978-3-642-30122-3|last2=Stams|first2=Alfons J. M.|doi=10.1007/978-3-642-30123-0_59|url=http://nbn-resolving.de/urn:nbn:de:bsz:352-276499|url-access=subscription}}</ref> Anaerobic oxidation of methane (AOM) is carried out by mutualistic consortium of a sulfate-reducing bacterium and an anaerobic methane-oxidizing archaeon.<ref>{{Cite journal|last1=Boetius|first1=Antje|last2=Ravenschlag|first2=Katrin|last3=Schubert|first3=Carsten J.|last4=Rickert|first4=Dirk|last5=Widdel|first5=Friedrich|last6=Gieseke|first6=Armin|last7=Amann|first7=Rudolf|last8=Jørgensen|first8=Bo Barker|last9=Witte|first9=Ursula|last10=Pfannkuche|first10=Olaf|date=October 2000|title=A marine microbial consortium apparently mediating anaerobic oxidation of methane|journal=Nature|volume=407|issue=6804|pages=623–626|doi=10.1038/35036572|pmid=11034209|issn=0028-0836|bibcode=2000Natur.407..623B|s2cid=205009562}}</ref><ref>{{Cite journal|last1=Raghoebarsing|first1=Ashna A.|last2=Pol|first2=Arjan|last3=van de Pas-Schoonen|first3=Katinka T.|last4=Smolders|first4=Alfons J. P.|last5=Ettwig|first5=Katharina F.|last6=Rijpstra|first6=W. Irene C.|last7=Schouten|first7=Stefan|last8=Damsté|first8=Jaap S. Sinninghe|last9=Op den Camp|first9=Huub J. M.|last10=Jetten|first10=Mike S. M.|last11=Strous|first11=Marc|date=April 2006|title=A microbial consortium couples anaerobic methane oxidation to denitrification|journal=Nature|volume=440|issue=7086|pages=918–921|doi=10.1038/nature04617|pmid=16612380|issn=0028-0836|hdl=1874/22552|bibcode=2006Natur.440..918R|s2cid=4413069|url=https://repository.ubn.ru.nl//bitstream/handle/2066/36167/36167.pdf |hdl-access=free}}</ref> The reaction used by the bacterial partner for the production of H₂ is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by archaeal partner, the overall reaction becomes exergonic.<ref name=":13" /> Thus the two organisms are in a mutualistic relationship which allows them to grow and thrive in an environment, deadly for either species alone. Lichen is an example of a symbiotic organism.<ref name=":2" />

Microorganisms also engage in mutualistic relationship with plants and a typical example of such relationship is arbuscular mycorrhizal (AM) relationship, a symbiotic relationship between plants and fungi.<ref name=":5">{{Citation |last1=Smith |first1=Sally E. |title=INTRODUCTION |date=2008 |work=Mycorrhizal Symbiosis |pages=1–9 |publisher=Elsevier |isbn=978-0-12-370526-6 |last2=Read |first2=David|doi=10.1016/b978-012370526-6.50002-7}}</ref> This relationship begins when chemical signals are exchanged between the plant and the fungi leading to the metabolic stimulation of the fungus.<ref>{{Cite journal |last1=Besserer |first1=Arnaud |last2=Puech-Pagès |first2=Virginie |last3=Kiefer |first3=Patrick |last4=Gomez-Roldan |first4=Victoria |last5=Jauneau |first5=Alain |last6=Roy |first6=Sébastien |last7=Portais |first7=Jean-Charles |last8=Roux |first8=Christophe |last9=Bécard |first9=Guillaume |last10=Séjalon-Delmas |first10=Nathalie |date=2006-06-27 |title=Strigolactones Stimulate Arbuscular Mycorrhizal Fungi by Activating Mitochondria |journal=PLOS Biology |volume=4 |issue=7 |article-number=e226 |doi=10.1371/journal.pbio.0040226 |doi-access=free |pmid=16787107 |pmc=1481526 |issn=1545-7885}}</ref><ref>{{Cite journal |last=Harrison |first=Maria J. |date=December 2012 |title=Cellular programs for arbuscular mycorrhizal symbiosis |journal=Current Opinion in Plant Biology |volume=15 |issue=6 |pages=691–698 |doi=10.1016/j.pbi.2012.08.010 |pmid=23036821 |bibcode=2012COPB...15..691H |issn=1369-5266}}</ref> The fungus then attacks the epidermis of the plant's root and penetrates its highly branched hyphae into the cortical cells of the plant.<ref name=":5" /> In this relationship, the fungi gives the plant phosphate and nitrogen obtained from the soil, while the plant provides the fungi with carbohydrate and lipids obtained from photosynthesis.<ref>{{Cite journal |journal=Science |last1=Shiu |first1=Patrick |last2=Xiao |first2=Hua |date=2021-05-28 |title=Faculty Opinions recommendation of Lipid exchanges drove the evolution of mutualism during plant terrestrialization. |doi=10.3410/f.740146041.793585932 |doi-access=free}}</ref> Also, microorganisms are involved in mutualistic relationship with mammals such as humans. As the host provides shelter and nutrient to the microorganisms, the microorganisms also provide benefits such as helping in the growth of the gastrointestinal tract of the host and protecting host from other detrimental microorganisms.<ref>{{Cite journal |last1=Leser |first1=Thomas D. |last2=Mølbak |first2=Lars |date=September 2009 |title=Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host |url=https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01941.x |journal=Environmental Microbiology |language=en |volume=11 |issue=9 |pages=2194–2206 |doi=10.1111/j.1462-2920.2009.01941.x |pmid=19737302 |bibcode=2009EnvMi..11.2194L |issn=1462-2912}}</ref>

=== Commensalism === Commensalism is very common in microbial world, literally meaning "eating from the same table".<ref>{{Citation|last1=Bogitsh|first1=Burton J.|title=Symbiosis and Parasitism|date=2013|work=Human Parasitology|pages=1–13|publisher=Elsevier|isbn=978-0-12-415915-0|last2=Carter|first2=Clint E.|last3=Oeltmann|first3=Thomas N.|doi=10.1016/b978-0-12-415915-0.00001-7|s2cid=88750087}}</ref> It is a relationship between two species where one species benefits with no harm or benefit for the other species.<ref name="annualreviews.org" /> Metabolic products of one microbial population are used by another microbial population without either gain or harm for the first population. There are many "pairs "of microbial species that perform either oxidation or reduction reaction to the same chemical equation. For example, methanogens produce methane by reducing CO₂ to CH₄, while methanotrophs oxidise methane back to CO₂.<ref>{{Citation|last1=Canfield|first1=Donald E.|title=Structure and Growth of Microbial Populations|date=2005|work=Advances in Marine Biology|pages=23–64|publisher=Elsevier|isbn=978-0-12-026147-5|last2=Erik Kristensen|last3=Bo Thamdrup|doi=10.1016/s0065-2881(05)48002-5}}</ref>

=== Amensalism === Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected.<ref name=":42" /> One example of such a relationship that takes place in microbial ecology is between the microbial species ''Lactobacillus casei'' and ''Pseudomonas taetrolens''.<ref>{{cite journal |last1=García |first1=Cristina |last2=Rendueles |first2=Manuel |last3=Díaz |first3=Mario |date=September 2017 |title=Synbiotic Fermentation for the Co-Production of Lactic and Lactobionic Acids from Residual Dairy Whey |journal=Biotechnology Progress |volume=33 |issue=5 |pages=1250–1256 |doi=10.1002/btpr.2507 |pmid=28556559|s2cid=23694837|hdl=10651/46356 |hdl-access=free }}</ref> When co-existing in an environment, ''Pseudomonas taetrolens'' shows inhibited growth and decreased production of lactobionic acid (its main product) most likely due to the byproducts created by ''Lactobacillus casei'' during its production of lactic acid.<ref>{{Cite book |title=The microbial challenge: science, disease, and public health |last=Krasner|first=Robert I. |date=2010 |publisher=Jones and Bartlett Publishers |isbn=978-0-7637-5689-5 |edition=2nd |location=Sudbury, Mass. |oclc=317664342}}</ref>

=== Parasitism === Certain microorganisms are known to have a host-parasite interaction with other organisms. For example, phytopathogenic fungi are known to infect and damage plants.<ref name=":05">{{Citation |last=Coque |first=Juan José R. |title=Chapter Four - Advances in the control of phytopathogenic fungi that infect crops through their root system |date=2020-01-01 |work=Advances in Applied Microbiology |volume=111 |pages=123–170 |editor-last=Gadd |editor-first=Geoffrey Michael |url=https://www.sciencedirect.com/science/article/abs/pii/S0065216420300058 |access-date=2025-04-03 |publisher=Academic Press |last2=Álvarez-Pérez |first2=José Manuel |last3=Cobos |first3=Rebeca |last4=González-García |first4=Sandra |last5=Ibáñez |first5=Ana M. |last6=Diez Galán |first6=Alba |last7=Calvo-Peña |first7=Carla |editor2-last=Sariaslani |editor2-first=Sima}}</ref> The phytopathogenic fungi is a major issue in agriculture, because it has the capacity to infect its host by their root system.<ref name=":05" /> This is a major issue because the symptoms of the infection are not easily detected.<ref name=":05" /> Another example of a parasitic microorganism is the nematode.<ref name=":15">{{Cite journal |last=Castillo |first=Julio Cesar |last2=Reynolds |first2=Stuart E. |last3=Eleftherianos |first3=Ioannis |date=2011-12-01 |title=Insect immune responses to nematode parasites |url=https://www.sciencedirect.com/science/article/abs/pii/S1471492211001632 |journal=Trends in Parasitology |volume=27 |issue=12 |pages=537–547 |doi=10.1016/j.pt.2011.09.001 |issn=1471-4922|url-access=subscription }}</ref> These organisms are known to cause river blindness and lymphatic filariasis in humans.<ref name=":15" /> These organisms are transmitted to hosts through different mosquito species from the following groups: Aedes, Anopheles, and Culex.<ref name=":15" />

== Antimicrobials == Antimicrobials are substances that are capable of killing microorganism. Antimicrobials can have antibacterial or antibiotic, antifungal or antiviral activity and most of these substances are natural products or may have been obtained from natural products.<ref name=":7">{{Citation |last=Strohl |first=William R. |title=Antimicrobials |date=2014-04-09 |work=Microbial Diversity and Bioprospecting |pages=336–355 |editor-last=Bull |editor-first=Alan T. |url=http://doi.wiley.com/10.1128/9781555817770.ch31 |access-date=2024-10-25 |place=Washington, DC, USA |publisher=ASM Press |language=en |doi=10.1128/9781555817770.ch31 |isbn=978-1-68367-217-3|url-access=subscription }}</ref> Natural products are therefore vital in the discovery of pharmaceutical agents.<ref>{{Cite journal |last1=Newman |first1=David J. |last2=Cragg |first2=Gordon M. |date=2016-02-07 |title=Natural Products as Sources of New Drugs from 1981 to 2014 |journal=Journal of Natural Products |volume=79 |issue=3 |pages=629–661 |doi=10.1021/acs.jnatprod.5b01055 |pmid=26852623 |issn=0163-3864|doi-access=free }}</ref><ref>{{Cite journal |last1=Jakubiec-Krzesniak |first1=Katarzyna |last2=Rajnisz-Mateusiak |first2=Aleksandra |last3=Guspiel |first3=Adam |last4=Ziemska |first4=Joanna |last5=Solecka |first5=Jolanta |date=2018-01-01 |title=Secondary Metabolites of Actinomycetes and their Antibacterial, Antifungal and Antiviral Properties |journal=Polish Journal of Microbiology |language=en |volume=67 |issue=3 |pages=259–272 |doi=10.21307/pjm-2018-048 |issn=2544-4646 |pmc=7256786 |pmid=30451442}}</ref> Most of the naturally obtained antibiotics are produced by organism under the phylum Actinobacteria. The genus Streptomyces are responsible for most of the antibiotic substances produced by Actinobacteria.<ref>{{Cite journal |last=Chater |first=Keith F. |date=2016-11-30 |title=Recent advances in understanding Streptomyces |journal=F1000Research |volume=5 |page=2795 |doi=10.12688/f1000research.9534.1 |doi-access=free |pmid=27990276 |pmc=5133688 |issn=2046-1402}}</ref><ref>{{Cite journal |last1=Barka |first1=Essaid Ait |last2=Vatsa |first2=Parul |last3=Sanchez |first3=Lisa |last4=Gaveau-Vaillant |first4=Nathalie |last5=Jacquard |first5=Cedric |last6=Klenk |first6=Hans-Peter |last7=Clément |first7=Christophe |last8=Ouhdouch |first8=Yder |last9=van Wezel |first9=Gilles P. |date=March 2016 |title=Taxonomy, Physiology, and Natural Products of Actinobacteria |journal=Microbiology and Molecular Biology Reviews |volume=80 |issue=1 |pages=1–43 |doi=10.1128/mmbr.00019-15 |pmid=26609051 |pmc=4711186 |issn=1092-2172}}</ref> These natural products with antimicrobial properties belong to the terpenoids, spirotetronate, tetracenedione, lactam, and other groups of compounds. Examples include napyradiomycin, nomimicin, formicamycin, and isoikarugamycin.<ref>{{Cite journal |last1=Wu |first1=Zhengchao |last2=Li |first2=Sumei |last3=Li |first3=Jie |last4=Chen |first4=Yuchan |last5=Saurav |first5=Kumar |last6=Zhang |first6=Qingbo |last7=Zhang |first7=Haibo |last8=Zhang |first8=Wenjun |last9=Zhang |first9=Weimin |last10=Zhang |first10=Si |last11=Zhang |first11=Changsheng |date=2013-06-14 |title=Antibacterial and Cytotoxic New Napyradiomycins from the Marine-Derived Streptomyces sp. SCSIO 10428 |journal=Marine Drugs |volume=11 |issue=6 |pages=2113–2125 |doi=10.3390/md11062113 |doi-access=free |issn=1660-3397|pmc=3721223 }}</ref><ref>{{Cite journal |last1=Igarashi |first1=Yasuhiro |last2=Iida |first2=Takako |last3=Oku |first3=Naoya |last4=Watanabe |first4=Hiroyuki |last5=Furihata |first5=Kazuo |last6=Miyanouchi |first6=Koji |date=2012-04-25 |title=Nomimicin, a new spirotetronate-class polyketide from an actinomycete of the genus Actinomadura |journal=The Journal of Antibiotics |volume=65 |issue=7 |pages=355–359 |doi=10.1038/ja.2012.30 |pmid=22534651 |issn=0021-8820|doi-access=free }}</ref><ref>{{Cite journal |last1=Qin |first1=Zhiwei |last2=Munnoch |first2=John T. |last3=Devine |first3=Rebecca |last4=Holmes |first4=Neil A. |last5=Seipke |first5=Ryan F. |last6=Wilkinson |first6=Karl A. |last7=Wilkinson |first7=Barrie |last8=Hutchings |first8=Matthew I. |date=2017 |title=Formicamycins, antibacterial polyketides produced by Streptomyces formicae isolated from African Tetraponera plant-ants |journal=Chemical Science |volume=8 |issue=4 |pages=3218–3227 |doi=10.1039/c6sc04265a |pmid=28507698 |issn=2041-6520|pmc=5414599}}</ref><ref>{{Cite journal |last1=Lacret |first1=Rodney |last2=Oves-Costales |first2=Daniel |last3=Gómez |first3=Cristina |last4=Díaz |first4=Caridad |last5=De la Cruz |first5=Mercedes |last6=Pérez-Victoria |first6=Ignacio |last7=Vicente |first7=Francisca |last8=Genilloud |first8=Olga |last9=Reyes |first9=Fernando |date=2014-12-29 |title=New Ikarugamycin Derivatives with Antifungal and Antibacterial Properties from Streptomyces zhaozhouensis |journal=Marine Drugs |volume=13 |issue=1 |pages=128–140 |doi=10.3390/md13010128 |doi-access=free |pmid=25551780 |pmc=4306928 |issn=1660-3397}}</ref> Some metals, particularly copper, silver, and gold also have antimicrobial properties. Using antimicrobial copper-alloy touch surfaces is a technique that has begun to be used in the 21st century to prevent the transmission of bacteria.<ref>{{Cite news|url=https://www.washingtonpost.com/national/health-science/the-bacteria-fighting-super-element-making-a-return-to-hospitals-copper/2015/09/20/19251704-5beb-11e5-8e9e-dce8a2a2a679_story.html|title=The bacteria-fighting super element making a return to hospitals: Copper|newspaper=Washington Post|access-date=September 18, 2016}}</ref><ref name=":1" /> Silver nanoparticles have also begun to be incorporated into building surfaces and fabrics, although concerns have been raised about the potential side-effects of the tiny particles on human health.<ref>{{Cite web |url=http://articles.chicagotribune.com/2014-02-16/health/ct-nanosilver-met-20140216_1_consumer-products-other-antibiotic-drugs-germs |archive-url=https://web.archive.org/web/20140222205229/http://articles.chicagotribune.com/2014-02-16/health/ct-nanosilver-met-20140216_1_consumer-products-other-antibiotic-drugs-germs |archive-date=February 22, 2014 |title=Silver nanoparticles kill germs, raise health concerns |access-date=September 18, 2016}}</ref> Due to the antimicrobial properties certain metals possess, products such as medical devices are made using those metals.<ref name=":1">{{Cite journal |last1=Evans |first1=Andris |last2=Kavanagh |first2=Kevin A. |date=May 7, 2021 |title=Evaluation of metal-based antimicrobial compounds for the treatment of bacterial pathogens |journal=Journal of Medical Microbiology |volume=70 |issue=5 |page=001363 |doi=10.1099/jmm.0.001363 |issn=0022-2615 |pmc=8289199 |pmid=33961541}}</ref>

==See also== {{Portal|Ecology|Biology}} * Microbial biogeography * Microbial loop * Outline of ecology * International Society for Microbial Ecology * ''The ISME Journal''

== References == {{reflist|1=2|refs= <ref name="brock">{{Cite book | edition = 13th | publisher = Benjamin Cummings | isbn = 978-0-321-64963-8 | last = Madigan | first = Michael T. | title = Brock biology of microorganisms | location = San Francisco | date = 2012}}</ref> <ref name="hugenholz2002">{{Cite journal | last1 = Hugenholtz | first1 = P. | title = Exploring prokaryotic diversity in the genomic era | journal = Genome Biology | volume = 3 | issue = 2 | pages = reviews0003.reviews0001 | doi = 10.1186/gb-2002-3-2-reviews0003 | year = 2002 | pmid = 11864374| pmc = 139013 | doi-access = free}}</ref> <ref name="mcdaniel">{{Cite journal | doi = 10.1126/science.1192243 | title = High Frequency of Horizontal Gene Transfer in the Oceans | year = 2010 | last1 = McDaniel | first1 = L. D. | last2 = Young | first2 = E. | last3 = Delaney | first3 = J. | last4 = Ruhnau | first4 = F. | last5 = Ritchie | first5 = K. B. | last6 = Paul | first6 = J. H. | journal = Science | volume = 330 | issue = 6000 | page = 50 | pmid = 20929803 |bibcode = 2010Sci...330...50M | s2cid = 45402114}}</ref> <ref name="smets">{{Cite journal | doi = 10.1038/nrmicro1253 | title = Horizontal gene transfer: Perspectives at a crossroads of scientific disciplines | year = 2005 | last1 = Smets | first1 = Barth F. | last2 = Barkay | first2 = Tamar | journal = Nature Reviews Microbiology | volume = 3 | issue = 9 | pages = 675–8 | pmid = 16145755 | s2cid = 2265315}}</ref> }}

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Category:Microbiology terms Category:Bacteria Category:Bacteriology Category:Environmental soil science Category:Membrane biology Category:Biological matter Category:Environmental microbiology Category:Microbial population biology Category:Subfields of ecology