Copiotroph

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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

Primary nutritional groups are groups of organisms, divided in relation to the nutrition mode according to the sources of energy and carbon, needed for living, growth and reproduction. The sources of energy can be light or chemical compounds; the sources of carbon can be of organic or inorganic origin.

<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.

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> Trophic pathway in marine microbial ecosystems

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. In aquatic ecosystems, microbial food webs are essential because they form the basis for the cycling of nutrients and energy. These webs are vital to the stability and production of ecosystems in a variety of aquatic environments, including lakes, rivers, and oceans. By converting dissolved organic carbon (DOC) and other nutrients into biomass that larger organisms may eat, microbial food webs maintain higher trophic levels. Thus, these webs are crucial for energy flow and nutrient cycling in both freshwater and marine ecosystems.

<span class="mw-page-title-main">Soil respiration</span> Chemical process produced by soil and the organisms within it

Soil respiration refers to the production of carbon dioxide when soil organisms respire. This includes respiration of plant roots, the rhizosphere, microbes and fauna.

Single-cell proteins (SCP) or microbial proteins refer to edible unicellular microorganisms. The biomass or protein extract from pure or mixed cultures of algae, yeasts, fungi or bacteria may be used as an ingredient or a substitute for protein-rich foods, and is suitable for human consumption or as animal feeds. Industrial agriculture is marked by a high water footprint, high land use, biodiversity destruction, general environmental degradation and contributes to climate change by emission of a third of all greenhouse gases; production of SCP does not necessarily exhibit any of these serious drawbacks. As of today, SCP is commonly grown on agricultural waste products, and as such inherits the ecological footprint and water footprint of industrial agriculture. However, SCP may also be produced entirely independent of agricultural waste products through autotrophic growth. Thanks to the high diversity of microbial metabolism, autotrophic SCP provides several different modes of growth, versatile options of nutrients recycling, and a substantially increased efficiency compared to crops. A 2021 publication showed that photovoltaic-driven microbial protein production could use 10 times less land for an equivalent amount of protein compared to soybean cultivation.

<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.

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">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.

Genomic streamlining is a theory in evolutionary biology and microbial ecology that suggests that there is a reproductive benefit to prokaryotes having a smaller genome size with less non-coding DNA and fewer non-essential genes. There is a lot of variation in prokaryotic genome size, with the smallest free-living cell's genome being roughly ten times smaller than the largest prokaryote. Two of the bacterial taxa with the smallest genomes are Prochlorococcus and Pelagibacter ubique, both highly abundant marine bacteria commonly found in oligotrophic regions. Similar reduced genomes have been found in uncultured marine bacteria, suggesting that genomic streamlining is a common feature of bacterioplankton. This theory is typically used with reference to free-living organisms in oligotrophic environments.

<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

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