{{Short description|Organism found in carbon-rich environments}}A '''copiotroph''' is an organism found in environments rich in nutrients, particularly carbon. They are the opposite to oligotrophs, which survive in much lower carbon concentrations.<ref name="Panikov1995">{{cite book|author=N.S. Panikov|title=Microbial Growth Kinetics|url=https://books.google.com/books?id=6Z8X0lOjY6kC&pg=PA82|date=31 March 1995|publisher=Springer Science & Business Media|isbn=978-0-412-56630-1|page=82}}</ref>
Copiotrophic organisms tend to grow in high organic substrate conditions. For example, copiotrophic organisms grow in Sewage lagoons. They grow in organic substrate conditions up to 100x higher than oligotrophs. Due to this substrate concentration inclination, copiotrophs are often found in nutrient rich waters near coastlines or estuaries.<ref name=":0">{{Cite journal |last1=Lauro |first1=Federico M. |last2=McDougald |first2=Diane |last3=Thomas |first3=Torsten |last4=Williams |first4=Timothy J. |last5=Egan |first5=Suhelen |last6=Rice |first6=Scott |last7=DeMaere |first7=Matthew Z. |last8=Ting |first8=Lily |last9=Ertan |first9=Haluk |last10=Johnson |first10=Justin |last11=Ferriera |first11=Steven |last12=Lapidus |first12=Alla |last13=Anderson |first13=Iain |last14=Kyrpides |first14=Nikos |last15=Munk |first15=A. Christine |date=2009-09-15 |title=The genomic basis of trophic strategy in marine bacteria |journal=Proceedings of the National Academy of Sciences |language=en |volume=106 |issue=37 |pages=15527–15533 |doi=10.1073/pnas.0903507106 |issn=0027-8424 |pmc=2739866 |pmid=19805210 |doi-access=free }}</ref>
== Classification and Identification ==
The bacterial phyla can be differentiated into copiotrophic or oligotrophic categories that correspond and structure the functions of soil bacterial communities.
== Interaction with other organisms ==
Copiotrophic relation between oligotrophic bacteria depends on the amount of concentration the soil has of C compounds. If the soil has large amounts of organic C, it would then favor the copiotrophic bacteria.
== Ecology ==
Copiotrophic bacteria are a key component in the soil C cycle. It is most important during the period of the year when vegetation is photosynthetically active and exudes large amounts of simple C compounds like sugar, amino acids, and organic acids. Copiotrophic bacteria are also found within marine life.
== Lifestyle == Copiotrophs have a higher Michaelis-Menten constant than oligotrophs.<ref name=":1">{{Cite journal |last=Ho |first=Adrian |date=23 January 2017 |title=Revisiting life strategy concepts in environmental microbial ecology |url=https://academic.oup.com/femsec/article/93/3/fix006/2937747 |access-date=2023-04-22 |journal=FEMS Microbiology Ecology|volume=93 |issue=3 |article-number=fix006 |doi=10.1093/femsec/fix006 |pmid=28115400 |hdl=20.500.11755/97637b47-779a-413c-8397-81f77393a479 |hdl-access=free }}</ref> This constant is directly correlated to environmental substrate preference.<ref name=":1" /> In these high resource environments, copiotrophs exhibit a "feast-and-famine" lifestyle.<ref name=":72">{{Cite journal |last=Soler-Bistue |first=Alfonso |date=2023-03-01 |title=The evolving copiotrophic/oligotrophic dichotomy: From Winogradsky to physiology and genomics |journal=Environmental Microbiology|volume=25 |issue=7 |pages=1232–1237 |doi=10.1111/1462-2920.16360 |pmid=36856667 |bibcode=2023EnvMi..25.1232S |s2cid=257256291 }}</ref> They utilize the available nutrients in the environment rapidly resulting in nutrient depletion which forces them to starve.<ref name=":72" /> This is possible through increasing their growth rate with nutrient uptake.<ref name=":8">{{Cite journal |last1=Noell |first1=Stephen E. |last2=Brennan |first2=Elizabeth |last3=Washburn |first3=Quinn |last4=Davis |first4=Edward W. |last5=Hellweger |first5=Ferdi L. |last6=Giovannoni |first6=Stephen J. |date=2023-01-15 |title=Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility |journal=Environmental Microbiology |volume=25 |issue=7 |language=en |pages=1265–1280 |doi=10.1111/1462-2920.16357|biorxiv=10.1101/2022.07.21.501054|pmid=36826469 |s2cid=251021339 |doi-access=free|bibcode=2023EnvMi..25.1265N }}</ref> However, when nutrients in the environment get depleted, copiotrophs struggle to survive for long periods of time.<ref name=":2">{{Cite journal |last=Koch |first=Arthur L. |date=2001-07-12 |title=Oligotrophs versus copiotrophs |url=https://onlinelibrary.wiley.com/doi/10.1002/bies.1091 |journal=BioEssays |language=en |volume=23 |issue=7 |pages=657–661 |doi=10.1002/bies.1091 |pmid=11462219 |s2cid=39126203 |issn=0265-9247|url-access=subscription }}</ref> Copiotrophs do not have the ability to respond to starvation.<ref name=":2" /> It is hypothesized that this may be a lost trait.<ref name=":2" /> Another possibility is that microbes never evolved to survive these extreme conditions.<ref name=":2" /> Oligotrophs can outcompete copiotrophs in low-nutrient environments.<ref name=":2" /> This causes low-nutrient conditions to continue for extended periods of time, making it difficult for copiotrophs to sustain life.<ref name=":2" /> Copiotrophs are larger than oligotrophs and need more energy, requiring larger concentrations of substrate for survival.<ref name=":2" />
Copiotrophs are motile.<ref name=":0" /> Copiotrophs can have external organelles such as flagella that extend out of a microbe's cell to facilitate movement.<ref name=":8" /> Copiotrophs are also chemotactic, meaning they can detect nutrients in the environment.<ref name=":3">{{Cite book |last=Kirchman |first=David |title=Processes In Microbial Ecology |publisher=Oxford University Press Inc. |year=2012 |isbn=978-0-19-958693-6 |edition=1st |location=New York |pages=46–48}}</ref> These help the microbes travel quickly to nearby food sources.<ref name=":3" /> Chemotaxis also enables the organism to travel away from a restricting compound.<ref name=":3" /> There are multiple methods for chemotaxis in these organisms.<ref name=":3" /> This includes the "run and tumble" strategy in which the organism randomly picks a direction to move in.<ref name=":3" /> However, if it senses that the concentration gradient is decreasing they stop and choose another random direction to travel in.<ref name=":3" />Another strategy includes the "run and reverse" in which the organism runs towards a nutrient.<ref name=":3" /> If it notices the gradient decreasing, it moves back to where the gradient is larger and heads in another direction from this new position.<ref name=":3" />
Through their motility and chemotaxis, copiotrophic microbes respond quickly to nutrients in their environment.<ref name=":0" /> With the help of these mechanisms, copiotrophs can travel to and stay in nutrient dense areas long enough for transcriptional regulatory systems to increase gene expression.<ref name=":8" /> This in turn helps them increase metabolic processes in high nutrient areas allowing them to maximize their growth during these patches.<ref name=":8" />
== Growth characteristics == Copiotrophs are characterized by a high maximum growth rate.<ref name=":4">{{Cite journal |last1=Roller |first1=Benjamin R. K. |last2=Stoddard |first2=Steven F. |last3=Schmidt |first3=Thomas M. |date=2016-09-12 |title=Exploiting rRNA operon copy number to investigate bacterial reproductive strategies |journal=Nature Microbiology |language=en |volume=1 |issue=11 |page=16160 |doi=10.1038/nmicrobiol.2016.160 |pmid=27617693 |pmc=5061577 |issn=2058-5276}}</ref> This high growth rate allows for copiotrophs to have a larger genome and cell size than their oligotrophic counterparts.<ref name=":0" />
The copiotrophic genome encompasses more ribosomal RNA operons than the oligotrophic genome.<ref name=":4" /> Ribosomal RNA operons are linearly related to growth rate.<ref name=":3" /><ref name=":4" /> The ribosomal RNA operons are responsible for expression of genes in clusters.<ref name=":5">{{Cite journal |last1=Espejo |first1=Romilio T. |last2=Plaza |first2=Nicolás |date=2018 |title=Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA |journal=Frontiers in Microbiology |volume=9 |page=1232 |doi=10.3389/fmicb.2018.01232 |pmid=29937760 |pmc=6002687 |issn=1664-302X |doi-access=free }}</ref> The larger amount of ribosomal content allows for more rapid growth.<ref name=":4" /> Oligotrophs have one ribosomal RNA operon while copiotrophs can contain up to fifteen operons.<ref name=":5" />
Copiotrophs tend to have a lower carbon use efficiency than oligotrophs.<ref name=":6">{{Cite journal |last1=Roller |first1=Benjamin RK |last2=Schmidt |first2=Thomas M. |date=2015-01-15 |title=The physiology and ecological implications of efficient growth |journal=The ISME Journal |language=en |volume=9 |issue=7 |pages=1481–1487 |doi=10.1038/ismej.2014.235 |pmid=25575305 |pmc=4478692 |bibcode=2015ISMEJ...9.1481R |issn=1751-7370}}</ref> This is the ratio of carbon used for production of biomass per total carbon consumed by the organism.<ref name=":6" /> Carbon use efficiency can be used to understand organisms lifestyles, whether they primarily create biomass or require carbon for maintenance energy.<ref name=":6" /><ref>{{Cite journal |last1=Pold |first1=Grace |last2=Domeignoz-Horta |first2=Luiz A. |last3=Morrison |first3=Eric W. |last4=Frey |first4=Serita D. |last5=Sistla |first5=Seeta A. |last6=DeAngelis |first6=Kristen M. |date=2020-02-25 |editor-last=Giovannoni |editor-first=Stephen J. |title=Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria |journal=mBio |language=en |volume=11 |issue=1 |pages=e02293–19 |doi=10.1128/mBio.02293-19 |doi-access=free|issn=2161-2129 |pmc=6974560 |pmid=31964725}}</ref> Energy is necessary for the copiotrophic lifestyle which includes motility and chemotaxis.<ref name=":9">{{Cite journal |last1=Geyer |first1=Kevin M. |last2=Kyker-Snowman |first2=Emily |last3=Grandy |first3=A. Stuart |last4=Frey |first4=Serita D. |date=2016-02-01 |title=Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter |journal=Biogeochemistry |language=en |volume=127 |issue=2 |pages=173–188 |doi=10.1007/s10533-016-0191-y |s2cid=54772410 |issn=1573-515X|doi-access=free |bibcode=2016Biogc.127..173G }}</ref> This energy could otherwise be used for biomass production.<ref name=":9" /> This results in a lower efficiency than the oligotrophic lifestyle which primarily uses energy for the creation of biomass.<ref name=":9" />
Copiotrophs have a lower protein yield than oligotrophs.<ref name=":4" /> Protein yield is the amount of protein synthesized per O<sub>2</sub> consumed.<ref name=":4" /> This is also associated with the higher ribosomal RNA operons.<ref name=":4" /> Overall, copiotrophs create more protein than their oligotrophic peers, however due to the copiotrophs' lower carbon use efficiency, less protein is produced per gram O<sub>2</sub> consumed by the organisms.<ref name=":4" />
== References == {{reflist}} Fierer, N., Bradford, M. A., & Jackson, R. B. (2007). Toward an ecological classification of soil bacteria. Ecology, 88(6), 1354-1364. Ivars-Martinez, E., Martin-Cuadrado, A. B., D'auria, G., Mira, A., Ferriera, S., Johnson, J., ... & Rodriguez-Valera, F. (2008). Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. The ISME journal, 2(12), 1194-1212. Lladó, S., & Baldrian, P. (2017). Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments. PLoS One, 12(2), e0171638.
{{modelling ecosystems}}
Category:Organisms by adaptation Category:Trophic ecology