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Copiotroph

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.[1]

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.[2]

Classification and Identification

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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

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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

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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

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Copiotrophs have a higher Michaelis-Menten constant than oligotrophs.[3] This constant is directly correlated to environmental substrate preference.[3] In these high resource environments, copiotrophs exhibit a “feast-and-famine” lifestyle.[4] They utilize the available nutrients in the environment rapidly resulting in nutrient depletion which forces them to starve.[4] This is possible through increasing their growth rate with nutrient uptake.[5] However, when nutrients in the environment get depleted, copiotrophs struggle to survive for long periods of time.[6] Copiotrophs do not have the ability to respond to starvation.[6] It is hypothesized that this may be a lost trait.[6] Another possibility is that microbes never evolved to survive these extreme conditions.[6] Oligotrophs can outcompete copiotrophs in low-nutrient environments.[6] This causes low-nutrient conditions to continue for extended periods of time, making it difficult for copiotrophs to sustain life.[6] Copiotrophs are larger than oligotrophs and need more energy, requiring larger concentrations of substrate for survival.[6]

Copiotrophs are motile.[2] Copiotrophs can have external organelles such as flagella that extend out of a microbe’s cell to facilitate movement.[5] Copiotrophs are also chemotactic, meaning they can detect nutrients in the environment.[7] These help the microbes travel quickly to nearby food sources.[7] Chemotaxis also enables the organism to travel away from a restricting compound.[7] There are multiple methods for chemotaxis in these organisms.[7] This includes the “run and tumble” strategy in which the organism randomly picks a direction to move in.[7] However, if it senses that the concentration gradient is decreasing they stop and choose another random direction to travel in.[7]Another strategy includes the “run and reverse” in which the organism runs towards a nutrient.[7] If it notices the gradient decreasing, it moves back to where the gradient is larger and heads in another direction from this new position.[7]

Through their motility and chemotaxis, copiotrophic microbes respond quickly to nutrients in their environment.[2] 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.[5] This in turn helps them increase metabolic processes in high nutrient areas allowing them to maximize their growth during these patches.[5]

Growth characteristics

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Copiotrophs are characterized by a high maximum growth rate.[8] This high growth rate allows for copiotrophs to have a larger genome and cell size than their oligotrophic counterparts.[2]

The copiotrophic genome encompasses more ribosomal RNA operons than the oligotrophic genome.[8] Ribosomal RNA operons are linearly related to growth rate.[7][8] The ribosomal RNA operons are responsible for expression of genes in clusters.[9] The larger amount of ribosomal content allows for more rapid growth.[8] Oligotrophs have one ribosomal RNA operon while copiotrophs can contain up to fifteen operons.[9]

Copiotrophs tend to have a lower carbon use efficiency than oligotrophs.[10] This is the ratio of carbon used for production of biomass per total carbon consumed by the organism.[10] Carbon use efficiency can be used to understand organisms lifestyles, whether they primarily create biomass or require carbon for maintenance energy.[10][11]  Energy is necessary for the copiotrophic lifestyle which includes motility and chemotaxis.[12] This energy could otherwise be used for biomass production.[12] This results in a lower efficiency than the oligotrophic lifestyle which primarily uses energy for the creation of biomass.[12]

Copiotrophs have a lower protein yield than oligotrophs.[8] Protein yield is the amount of protein synthesized per O2 consumed.[8] This is also associated with the higher ribosomal RNA operons.[8] Overall, copiotrophs create more protein than their oligotrophic peers, however due to the copiotrophs' lower carbon use efficiency, less protein is produced per gram O2 consumed by the organisms.[8]

References

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  1. ^ N.S. Panikov (31 March 1995). Microbial Growth Kinetics. Springer Science & Business Media. p. 82. ISBN 978-0-412-56630-1.
  2. ^ a b c d Lauro, Federico M.; McDougald, Diane; Thomas, Torsten; Williams, Timothy J.; Egan, Suhelen; Rice, Scott; DeMaere, Matthew Z.; Ting, Lily; Ertan, Haluk; Johnson, Justin; Ferriera, Steven; Lapidus, Alla; Anderson, Iain; Kyrpides, Nikos; Munk, A. Christine (2009-09-15). "The genomic basis of trophic strategy in marine bacteria". Proceedings of the National Academy of Sciences. 106 (37): 15527–15533. doi:10.1073/pnas.0903507106. ISSN 0027-8424. PMC 2739866. PMID 19805210.
  3. ^ a b Ho, Adrian (23 January 2017). "Revisiting life strategy concepts in environmental microbial ecology". FEMS Microbiology Ecology. 93 (3): fix006. doi:10.1093/femsec/fix006. hdl:20.500.11755/97637b47-779a-413c-8397-81f77393a479. PMID 28115400. Retrieved 2023-04-22.
  4. ^ a b Soler-Bistue, Alfonso (2023-03-01). "The evolving copiotrophic/oligotrophic dichotomy: From Winogradsky to physiology and genomics". Environmental Microbiology. 25 (7): 1232–1237. Bibcode:2023EnvMi..25.1232S. doi:10.1111/1462-2920.16360. PMID 36856667. S2CID 257256291.
  5. ^ a b c d Noell, Stephen E.; Brennan, Elizabeth; Washburn, Quinn; Davis, Edward W.; Hellweger, Ferdi L.; Giovannoni, Stephen J. (2023-01-15). "Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility". Environmental Microbiology. 25 (7): 1265–1280. Bibcode:2023EnvMi..25.1265N. bioRxiv 10.1101/2022.07.21.501054. doi:10.1111/1462-2920.16357. PMID 36826469. S2CID 251021339.
  6. ^ a b c d e f g Koch, Arthur L. (2001-07-12). "Oligotrophs versus copiotrophs". BioEssays. 23 (7): 657–661. doi:10.1002/bies.1091. ISSN 0265-9247. PMID 11462219. S2CID 39126203.
  7. ^ a b c d e f g h i Kirchman, David (2012). Processes In Microbial Ecology (1st ed.). New York: Oxford University Press Inc. pp. 46–48. ISBN 9780199586936.
  8. ^ a b c d e f g h Roller, Benjamin R. K.; Stoddard, Steven F.; Schmidt, Thomas M. (2016-09-12). "Exploiting rRNA operon copy number to investigate bacterial reproductive strategies". Nature Microbiology. 1 (11): 16160. doi:10.1038/nmicrobiol.2016.160. ISSN 2058-5276. PMC 5061577. PMID 27617693.
  9. ^ a b Espejo, Romilio T.; Plaza, Nicolás (2018). "Multiple Ribosomal RNA Operons in Bacteria; Their Concerted Evolution and Potential Consequences on the Rate of Evolution of Their 16S rRNA". Frontiers in Microbiology. 9: 1232. doi:10.3389/fmicb.2018.01232. ISSN 1664-302X. PMC 6002687. PMID 29937760.
  10. ^ a b c Roller, Benjamin RK; Schmidt, Thomas M. (2015-01-15). "The physiology and ecological implications of efficient growth". The ISME Journal. 9 (7): 1481–1487. Bibcode:2015ISMEJ...9.1481R. doi:10.1038/ismej.2014.235. ISSN 1751-7370. PMC 4478692. PMID 25575305.
  11. ^ Pold, Grace; Domeignoz-Horta, Luiz A.; Morrison, Eric W.; Frey, Serita D.; Sistla, Seeta A.; DeAngelis, Kristen M. (2020-02-25). Giovannoni, Stephen J. (ed.). "Carbon Use Efficiency and Its Temperature Sensitivity Covary in Soil Bacteria". mBio. 11 (1): e02293–19. doi:10.1128/mBio.02293-19. ISSN 2161-2129. PMC 6974560. PMID 31964725.
  12. ^ a b c Geyer, Kevin M.; Kyker-Snowman, Emily; Grandy, A. Stuart; Frey, Serita D. (2016-02-01). "Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter". Biogeochemistry. 127 (2): 173–188. Bibcode:2016Biogc.127..173G. doi:10.1007/s10533-016-0191-y. ISSN 1573-515X. S2CID 54772410.

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.

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