Copiotroph

Last updated

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]

Contents

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

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. [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

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]

Related Research Articles

<span class="mw-page-title-main">Heterotroph</span> Organism that ingests organic carbon for nutrition

A heterotroph is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers. Living organisms that are heterotrophic include all animals and fungi, some bacteria and protists, and many parasitic plants. The term heterotroph arose in microbiology in 1946 as part of a classification of microorganisms based on their type of nutrition. The term is now used in many fields, such as ecology in describing the food chain.

<span class="mw-page-title-main">Microbial ecology</span> Study of the relationship of microorganisms with their environment

Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

<span class="mw-page-title-main">Arbuscular mycorrhiza</span> Symbiotic penetrative association between a fungus and the roots of a vascular plant

An arbuscular mycorrhiza (AM) is a type of mycorrhiza in which the symbiont fungus penetrates the cortical cells of the roots of a vascular plant forming arbuscules.

Photoheterotrophs are heterotrophic phototrophs—that is, they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements; these compounds include carbohydrates, fatty acids, and alcohols. Examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. These microorganisms are ubiquitous in aquatic habitats, occupy unique niche-spaces, and contribute to global biogeochemical cycling. Recent research has also indicated that the oriental hornet and some aphids may be able to use light to supplement their energy supply.

Industrial fermentation is the intentional use of fermentation in manufacturing processes. In addition to the mass production of fermented foods and drinks, industrial fermentation has widespread applications in chemical industry. Commodity chemicals, such as acetic acid, citric acid, and ethanol are made by fermentation. Moreover, nearly all commercially produced industrial enzymes, such as lipase, invertase and rennet, are made by fermentation with genetically modified microbes. In some cases, production of biomass itself is the objective, as is the case for single-cell proteins, baker's yeast, and starter cultures for lactic acid bacteria used in cheesemaking.

An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates of metabolism, and generally low population density. Oligotrophic environments are those that offer little to sustain life. These environments include deep oceanic sediments, caves, glacial and polar ice, deep subsurface soil, aquifers, ocean waters, and leached soils.

The rumen, also known as a paunch, is the largest stomach compartment in ruminants and the larger part of the reticulorumen, which is the first chamber in the alimentary canal of ruminant animals. The rumen's microbial favoring environment allows it to serve as the primary site for microbial fermentation of ingested feed. The smaller part of the reticulorumen is the reticulum, which is fully continuous with the rumen, but differs from it with regard to the texture of its lining.

<span class="mw-page-title-main">Picoplankton</span> Fraction of plankton between 0.2 and 2 μm

Picoplankton is the fraction of plankton composed by cells between 0.2 and 2 μm that can be either prokaryotic and eukaryotic phototrophs and heterotrophs:

<span class="mw-page-title-main">Microbial loop</span>

The microbial loop describes a trophic pathway where, in aquatic systems, dissolved organic carbon (DOC) is returned to higher trophic levels via its incorporation into bacterial biomass, and then coupled with the classic food chain formed by phytoplankton-zooplankton-nekton. In soil systems, the microbial loop refers to soil carbon. The term microbial loop was coined by Farooq Azam, Tom Fenchel et al. in 1983 to include the role played by bacteria in the carbon and nutrient cycles of the marine environment.

The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists.

<span class="mw-page-title-main">Phototrophic biofilm</span> Microbial communities including microorganisms which use light as their energy source

Phototrophic biofilms are microbial communities generally comprising both phototrophic microorganisms, which use light as their energy source, and chemoheterotrophs. Thick laminated multilayered phototrophic biofilms are usually referred to as microbial mats or phototrophic mats. These organisms, which can be prokaryotic or eukaryotic organisms like bacteria, cyanobacteria, fungi, and microalgae, make up diverse microbial communities that are affixed in a mucous matrix, or film. These biofilms occur on contact surfaces in a range of terrestrial and aquatic environments. The formation of biofilms is a complex process and is dependent upon the availability of light as well as the relationships between the microorganisms. Biofilms serve a variety of roles in aquatic, terrestrial, and extreme environments; these roles include functions which are both beneficial and detrimental to the environment. In addition to these natural roles, phototrophic biofilms have also been adapted for applications such as crop production and protection, bioremediation, and wastewater treatment.

<span class="mw-page-title-main">Bacterioplankton</span> Bacterial component of the plankton that drifts in the water column

Bacterioplankton refers to the bacterial component of the plankton that drifts in the water column. The name comes from the Ancient Greek word πλανκτος, meaning "wanderer" or "drifter", and bacterium, a Latin term coined in the 19th century by Christian Gottfried Ehrenberg. They are found in both seawater and freshwater.

Acidobacterium capsulatum is a bacterium. It is an acidophilic chemoorganotrophic bacterium containing menaquinone. It is gram-negative, facultative anaerobic, mesophilic, non-spore-forming, capsulated, saccharolytic and rod-shaped. It is also motile by peritrichous flagella. Its type strain is JCM 7670.

<span class="mw-page-title-main">Root microbiome</span>

The root microbiome is the dynamic community of microorganisms associated with plant roots. Because they are rich in a variety of carbon compounds, plant roots provide unique environments for a diverse assemblage of soil microorganisms, including bacteria, fungi and archaea. The microbial communities inside the root and in the rhizosphere are distinct from each other, and from the microbial communities of bulk soil, although there is some overlap in species composition.

<span class="mw-page-title-main">Phycosphere</span> Microscale mucus region that is rich in organic matter surrounding a phytoplankton cel

The phycosphere is a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell. This area is high in nutrients due to extracellular waste from the phytoplankton cell and it has been suggested that bacteria inhabit this area to feed on these nutrients. This high nutrient environment creates a microbiome and a diverse food web for microbes such as bacteria and protists. It has also been suggested that the bacterial assemblages within the phycosphere are species-specific and can vary depending on different environmental factors.

<span class="mw-page-title-main">Mycoplankton</span> Fungal members of the plankton communities of aquatic ecosystems

Mycoplankton are saprotrophic members of the plankton communities of marine and freshwater ecosystems. They are composed of filamentous free-living fungi and yeasts that are associated with planktonic particles or phytoplankton. Similar to bacterioplankton, these aquatic fungi play a significant role in heterotrophicmineralization and nutrient cycling. Mycoplankton can be up to 20 mm in diameter and over 50 mm in length.

<span class="mw-page-title-main">Sea ice microbial communities</span> Groups of microorganisms living within and at the interfaces of sea ice

Sea Ice Microbial Communities (SIMCO) refer to groups of microorganisms living within and at the interfaces of sea ice at the poles. The ice matrix they inhabit has strong vertical gradients of salinity, light, temperature and nutrients. Sea ice chemistry is most influenced by the salinity of the brine which affects the pH and the concentration of dissolved nutrients and gases. The brine formed during the melting sea ice creates pores and channels in the sea ice in which these microbes can live. As a result of these gradients and dynamic conditions, a higher abundance of microbes are found in the lower layer of the ice, although some are found in the middle and upper layers. Despite this extreme variability in environmental conditions, the taxonomical community composition tends to remain consistent throughout the year, until the ice melts.

<span class="mw-page-title-main">Viral shunt</span>

The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM.

<i>Terriglobus roseus</i> Species of bacteria

Terriglobus roseus is a bacterium belonging to subdivision 1 of the Acidobacteriota phylum, and is closely related to the genera Granulicella and Edaphobacter. T. roseus was the first species recognized in the genus Terriglobus in 2007. This bacterial species is extremely abundant and diverse in agricultural soils. T. roseus is an aerobic Gram-negative rod lacking motility. This bacteria can produce extracellular polymeric substances (EPS) to form a biofilm, or extracellular matrix, for means of protection, communication amongst neighboring cells, etc. Its type strain is KBS 63.

Saprotrophic bacteria are bacteria that are typically soil-dwelling and utilize saprotrophic nutrition as their primary energy source. They are often associated with soil fungi that also use saprotrophic nutrition and both are classified as saprotrophs.

References

  1. ↑ N.S. Panikov (31 March 1995). Microbial Growth Kinetics. Springer Science & Business Media. p. 82. ISBN   978-0-412-56630-1.
  2. 1 2 3 4 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. 1 2 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. 1 2 Soler-Bistue, Alfonso (2023-03-01). "The evolving copiotrophic/oligotrophic dichotomy: From Winogradsky to physiology and genomics". Environmental Microbiology. 25 (7): 1232–1237. doi:10.1111/1462-2920.16360. PMID   36856667. S2CID   257256291.
  5. 1 2 3 4 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. bioRxiv   10.1101/2022.07.21.501054 . doi: 10.1111/1462-2920.16357 . PMID   36826469. S2CID   251021339.
  6. 1 2 3 4 5 6 7 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. 1 2 3 4 5 6 7 8 9 Kirchman, David (2012). Processes In Microbial Ecology (1st ed.). New York: Oxford University Press Inc. pp. 46–48. ISBN   9780199586936.
  8. 1 2 3 4 5 6 7 8 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. 1 2 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. 1 2 3 Roller, Benjamin RK; Schmidt, Thomas M. (2015-01-15). "The physiology and ecological implications of efficient growth". The ISME Journal. 9 (7): 1481–1487. 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. 1 2 3 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. 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.

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.