microbial ecology

File:Louis Pasteur.jpg ]]

Martinus Beijerinck invented the enrichment culture, a fundamental method of 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.{{rp|644}}

Louis Pasteur was a French chemist who derived key microbial principles that we use today: microbial fermentation, pasteurization, germ theory, and vaccines.{{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}} These principles have served as a foundation for scientists in viewing the relationship between microbes and their environment. For example, Pasteur disproved the theory of spontaneous generation, the belief of life arising from nonliving materials.{{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}} Pasteur stated that life can only come from life and not nonliving materials. This led to the idea that microorganisms were responsible for the microbial growth in any environment.{{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}}

Robert Koch was a physician-scientist who implemented oil-immersion lens and a condenser while using microscopes, to increase the imagery of viewing bacteria.{{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 }} 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. He was able to distinguish distinct bacteria species, which led him to believe that the best way to study a certain disease is to focus on a specific pathogen. In 1879, Koch started to develop "pure" cultures to grow bacteria colonies. These advancements led Koch to solve the Cholera endemic in India during the year 1883. Koch's laboratory techniques and materials led him to conclude that the use of unfiltered water was causing the Cholera endemic, since it contained bacteria causing intestinal harm in humans.

Lorenz Hiltner is known as one of the pioneers in "microbial ecology." 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. One of Hiltner contributions to the study of plant nutrition and soil bacteriology was creating antimicrobial seeds covered with mercury chloride. 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.

Dionicia Gamboa is a prime example of how scientists are still trying to understand the relationship between microorganisms and nature.{{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 }} Gamboa is a Peruvian biologist who has dedicated her career towards treating malaria and leishmaniasis microorganisms. In 2009, Gamboa and her colleagues published a paper on treating different strains of malaria and leishmaniasis microorganisms, using plant extracts from the amazon. To add on, Gamboa has studied different ways to accurately detect malaria and leishmaniasis microorganisms in humans, using PCR and serology.{{Cite journal |last=Rosas-Aguirre |first=Angel |last2=Gamboa |first2=Dionicia |last3=Manrique |first3=Paulo |last4=Conn |first4=Jan E. |last5=Moreno |first5=Marta |last6=Lescano |first6=Andres G. |last7=Sanchez |first7=Juan F. |last8=Rodriguez |first8=Hugo |last9=Silva |first9=Hermann |last10=Llanos-Cuentas |first10=Alejandro |last11=Vinetz |first11=Joseph M. |date=2016-12-28 |title=Epidemiology of Plasmodium vivax Malaria in Peru |url=https://www.ajtmh.org:443/view/journals/tpmd/95/6_Suppl/article-p133.xml |journal=The American Journal of Tropical Medicine and Hygiene |language=EN |volume=95 |issue=6_Suppl |pages=133–144 |doi=10.4269/ajtmh.16-0268 |issn=0002-9637 |pmc=5201219 |pmid=27799639}} Her studies have helped understand the epidemiology of these microorganisms, to reduce the interaction with them in nature and their harmful effects.

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.{{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 }} 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.{{Cite journal |last=Oren |first=Aharon |date=2009-09-15 |title=Chemolithotrophy |url=http://dx.doi.org/10.1002/9780470015902.a0021153 |journal=Encyclopedia of Life Sciences |doi=10.1002/9780470015902.a0021153|isbn=978-0-470-01617-6|url-access=subscription }}

The nitrogen cycle, phosphorus cycle, sulphur cycle, and carbon cycle depend on microorganisms also. Each cycle involves microorganisms in certain processes.{{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 |pages=106809 |doi=10.1016/j.catena.2022.106809 |bibcode=2023Caten.22206809L |s2cid=256786335 |issn=0341-8162|url-access=subscription }} 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.{{Cite journal |last=Delwiche |first=C. C. |title=The Nitrogen Cycle |date=1970 |url=https://www.jstor.org/stable/24925899 |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|url-access=subscription }} Through these biogeochemical cycles, microorganisms are able to make nutrients such as nitrogen, phosphorus and potassium available in the soil.{{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 }} Microorganisms play a role in solubilizing phosphate, improving soil health, and plant growth.{{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 |pages=158 |doi=10.3390/biology10020158 |pmid=33671192 |pmc=7922199 |issn=2079-7737 |doi-access=free}}

Microbial interactions are found in bioremediation. Bioremediation is a technology that removes contaminants from soil{{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 |url=http://dx.doi.org/10.1007/s11356-016-7810-y |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|url-access=subscription }} and wastewater{{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 |pages=151754 |doi=10.1016/j.scitotenv.2021.151754 |issn=0048-9697 |pmid=34800451|url-access=subscription }} using microorganisms.{{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 |url=http://dx.doi.org/10.1007/978-3-030-48985-4_6 |access-date=2024-11-05 |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.|url-access=subscription }}{{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 |url=http://dx.doi.org/10.1016/j.scitotenv.2018.10.396 |journal=Science of the Total Environment |volume=653 |pages=649–657 |doi=10.1016/j.scitotenv.2018.10.396 |issn=0048-9697|url-access=subscription }} 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.{{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 |pages=100369 |doi=10.1016/j.eti.2019.100369 |issn=2352-1864|url-access=subscription }}

Due to high levels of horizontal gene transfer among microbial communities, microbial ecology is also important to the studies of evolution.

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 also receives service from the other partner as well.{{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.}} Mutualism in microbial ecology is a relationship between microbial species and other species (example humans) that allows for both sides to benefit.{{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}} Microorganisms form mutualistic relationship with other microorganism, plants or animals. One example of microbe-microbe interaction would be syntrophy, also known as cross-feeding,{{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}} of which Methanobacterium omelianskii is a classical example.{{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}} 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.{{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}}{{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}} 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.{{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}}{{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}} Anaerobic oxidation of methane (AOM) is carried out by mutualistic consortium of a sulfate-reducing bacterium and an anaerobic methane-oxidizing archaeon.{{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}}{{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}} 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. 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.

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.{{Citation |last1=Smith |first1=Sally E. |title=INTRODUCTION |date=2008 |work=Mycorrhizal Symbiosis |pages=1–9 |url=http://dx.doi.org/10.1016/b978-012370526-6.50002-7 |access-date=2024-10-12 |publisher=Elsevier |isbn=978-0-12-370526-6 |last2=Read |first2=David|doi=10.1016/b978-012370526-6.50002-7|url-access=subscription }} This relationship begins when chemical signals are exchange between the plant and the fungi leading to the metabolic stimulation of the fungus.{{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 |pages=e226 |doi=10.1371/journal.pbio.0040226 |doi-access=free |pmid=16787107 |pmc=1481526 |issn=1545-7885}}{{Cite journal |last=Harrison |first=Maria J. |date=December 2012 |title=Cellular programs for arbuscular mycorrhizal symbiosis |url=http://dx.doi.org/10.1016/j.pbi.2012.08.010 |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|url-access=subscription }} The fungus then attacks the epidermis of the plant’s root and penetrates its highly branched hyphae into the cortical cells of the plant. In this relationship, the fungi gives the plant phosphate and nitrogen obtained from the soil with the plant in return providing the fungi with carbohydrate and lipids obtained from photosynthesis.{{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}} Also, microorganisms are involve 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.{{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}}

Commensalism is very common in microbial world, literally meaning "eating from the same table".{{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}} It is a relationship between two species where one species benefits with no harm or benefit for the other species. 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.{{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}}

Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected. One example of such a relationship that takes place in microbial ecology is between the microbial species Lactobacillus casei and Pseudomonas taetrolens.{{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}} 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.{{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}}

Certain microorganisms are known to have a host-parasite interaction with other organisms. For example, phytopathogenic fungi are known to infect and damage plants.{{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}} The phytopathogenic fungi is a major issue in agriculture, because it has the capacity to infect its host by their root system. This is a major issue because the symptoms of the infection are not easily detected. Another example of a parasitic microorganism is the nematode.{{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 }} These organisms are known to cause river blindness and lymphatic filariasis in humans. These organisms are transmitted to hosts through different mosquito species from the following groups: Aedes, Anopheles, and Culex.

Antimicrobials are substances that are capable of killing microorganism. Antimicrobial can be antibacterial or antibiotic, antifungal or antiviral substance and most of these substance are natural products or may have been obtain from natural products.{{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 }} Natural products are therefore vital in the discovery of pharmaceutical agents.{{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 |url=http://dx.doi.org/10.1021/acs.jnatprod.5b01055 |journal=Journal of Natural Products |volume=79 |issue=3 |pages=629–661 |doi=10.1021/acs.jnatprod.5b01055 |pmid=26852623 |issn=0163-3864}}{{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}} 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.{{Cite journal |last=Chater |first=Keith F. |date=2016-11-30 |title=Recent advances in understanding Streptomyces |journal=F1000Research |volume=5 |pages=2795 |doi=10.12688/f1000research.9534.1 |doi-access=free |pmid=27990276 |pmc=5133688 |issn=2046-1402}}{{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 |url=http://dx.doi.org/10.1128/mmbr.00019-15 |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}} 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,{{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}}{{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 |url=http://dx.doi.org/10.1038/ja.2012.30 |journal=The Journal of Antibiotics |volume=65 |issue=7 |pages=355–359 |doi=10.1038/ja.2012.30 |pmid=22534651 |issn=0021-8820}}{{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 |url=http://dx.doi.org/10.1039/c6sc04265a |journal=Chemical Science |volume=8 |issue=4 |pages=3218–3227 |doi=10.1039/c6sc04265a |pmid=28507698 |issn=2041-6520|pmc=5414599}}{{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}} 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.{{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}} 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.{{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 |url-status=dead |archive-date=February 22, 2014 |title=Silver nanoparticles kill germs, raise health concerns |access-date=September 18, 2016}} Due to the antimicrobial properties certain metals possess, products such as medical devices are made using those metals.{{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 |pages=001363 |doi=10.1099/jmm.0.001363 |issn=0022-2615 |pmc=8289199 |pmid=33961541}}

{{Portal|Ecology|Biology}}

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{{reflist|1=2|refs=

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