Primary nutritional groups

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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. [1]

Contents

The terms aerobic respiration , anaerobic respiration and fermentation ( substrate-level phosphorylation ) do not refer to primary nutritional groups, but simply reflect the different use of possible electron acceptors in particular organisms, such as O2 in aerobic respiration, or nitrate (NO
3
), sulfate (SO2−
4
) or fumarate in anaerobic respiration, or various metabolic intermediates in fermentation.

Primary sources of energy

Phototrophs absorb light in photoreceptors and transform it into chemical energy.
Chemotrophs release chemical energy.

The freed energy is stored as potential energy in ATP, carbohydrates, or proteins. Eventually, the energy is used for life processes such as moving, growth and reproduction.

Plants and some bacteria can alternate between phototrophy and chemotrophy, depending on the availability of light.

Primary sources of reducing equivalents

Organotrophs use organic compounds as electron/hydrogen donors.
Lithotrophs use inorganic compounds as electron/hydrogen donors.

The electrons or hydrogen atoms from reducing equivalents (electron donors) are needed by both phototrophs and chemotrophs in reduction-oxidation reactions that transfer energy in the anabolic processes of ATP synthesis (in heterotrophs) or biosynthesis (in autotrophs). The electron or hydrogen donors are taken up from the environment.

Organotrophic organisms are often also heterotrophic, using organic compounds as sources of both electrons and carbon. Similarly, lithotrophic organisms are often also autotrophic, using inorganic sources of electrons and CO2 as their inorganic carbon source.

Some lithotrophic bacteria can utilize diverse sources of electrons, depending on the availability of possible donors.

The organic or inorganic substances (e.g., oxygen) used as electron acceptors needed in the catabolic processes of aerobic or anaerobic respiration and fermentation are not taken into account here.

For example, plants are lithotrophs because they use water as their electron donor for the electron transport chain across the thylakoid membrane. Animals are organotrophs because they use organic compounds as electron donors to synthesize ATP (plants also do this, but this is not taken into account). Both use oxygen in respiration as electron acceptor, but this character is not used to define them as lithotrophs.

Primary sources of carbon

Heterotrophs metabolize organic compounds to obtain carbon for growth and development.
Autotrophs use carbon dioxide (CO2) as their source of carbon.

Energy and carbon

Yellow fungus K 1033CR08-9 Yellow fungus on stalk.jpeg
Yellow fungus
Classification of organisms based on their metabolism
Energy sourceLightphoto- -troph
Moleculeschemo-
Electron donor Organic compounds  organo- 
Inorganic compounds litho-
Carbon source Organic compounds  hetero-
Carbon dioxide auto-

A chemoorganoheterotrophic organism is one that requires organic substrates to get its carbon for growth and development, and that obtains its energy from the decomposition of an organic compound. This group of organisms may be further subdivided according to what kind of organic substrate and compound they use. Decomposers are examples of chemoorganoheterotrophs which obtain carbon and electrons or hydrogen from dead organic matter. Herbivores and carnivores are examples of organisms that obtain carbon and electrons or hydrogen from living organic matter.

Chemoorganotrophs are organisms which use the chemical energy in organic compounds as their energy source and obtain electrons or hydrogen from the organic compounds, including sugars (i.e. glucose), fats and proteins. [2] Chemoheterotrophs also obtain the carbon atoms that they need for cellular function from these organic compounds.

All animals are chemoheterotrophs (meaning they oxidize chemical compounds as a source of energy and carbon), as are fungi, protozoa, and some bacteria. The important differentiation amongst this group is that chemoorganotrophs oxidize only organic compounds while chemolithotrophs instead use oxidation of inorganic compounds as a source of energy. [3]

Primary metabolism table

The following table gives some examples for each nutritional group: [4] [5] [6] [7]

Energy
source
Electron/
H-atom
donor
Carbon sourceNameExamples
Sun Light
Photo-
Organic
-organo-
Organic
-heterotroph
PhotoorganoheterotrophSome bacteria: Rhodobacter , and some archaea (Haloarchaea) [8]
Carbon dioxide
-autotroph
PhotoorganoautotrophSome bacteria perform anoxygenic photosynthesis and fix atmospheric carbon (Chloroflexia, Heliobacterium)
Inorganic
-litho- *
Organic
-heterotroph
Photolithoheterotroph Purple non-sulfur bacteria
Carbon dioxide
-autotroph
PhotolithoautotrophSome bacteria (cyanobacteria), some eukaryotes (eukaryotic algae, land plants). Photosynthesis.
Breaking
Chemical
Compounds
Chemo-
Organic
-organo-
Organic
-heterotroph
Chemoorganoheterotroph Predatory, parasitic, and saprophytic prokaryotes. Some eukaryotes (heterotrophic protists, fungi, animals)
Carbon dioxide
-autotroph
ChemoorganoautotrophSome archaea (anaerobic methanotrophic archaea). [9] Chemosynthesis, synthetically autotrophic Escherichia coli bacteria [10] and Pichia pastoris yeast. [11]
Inorganic
-litho-*
Organic
-heterotroph
ChemolithoheterotrophSome bacteria (Oceanithermus profundus) [12]
Carbon dioxide
-autotroph
ChemolithoautotrophSome bacteria ( Nitrobacter ), some archaea ( Methanobacteria ). Chemosynthesis.

*Some authors use -hydro- when the source is water.

The common final part -troph is from Ancient Greek τροφή trophḗ "nutrition".

Mixotrophs

Some, usually unicellular, organisms can switch between different metabolic modes, for example between photoautotrophy, photoheterotrophy, and chemoheterotrophy in Chroococcales. [13] Rhodopseudomonas palustris – another example – can grow with or without oxygen, use either light, inorganic or organic compounds for energy. [14] Such mixotrophic organisms may dominate their habitat, due to their capability to use more resources than either photoautotrophic or organoheterotrophic organisms. [15]

Examples

All sorts of combinations may exist in nature, but some are more common than others. For example, most plants are photolithoautotrophic, since they use light as an energy source, water as electron donor, and CO2 as a carbon source. All animals and fungi are chemoorganoheterotrophic, since they use organic substances both as chemical energy sources and as electron/hydrogen donors and carbon sources. Some eukaryotic microorganisms, however, are not limited to just one nutritional mode. For example, some algae live photoautotrophically in the light, but shift to chemoorganoheterotrophy in the dark. Even higher plants retained their ability to respire heterotrophically on starch at night which had been synthesised phototrophically during the day.

Prokaryotes show a great diversity of nutritional categories. [16] For example, cyanobacteria and many purple sulfur bacteria can be photolithoautotrophic, using light for energy, H2O or sulfide as electron/hydrogen donors, and CO2 as carbon source, whereas green non-sulfur bacteria can be photoorganoheterotrophic, using organic molecules as both electron/hydrogen donors and carbon sources. [8] [16] Many bacteria are chemoorganoheterotrophic, using organic molecules as energy, electron/hydrogen and carbon sources. [8] Some bacteria are limited to only one nutritional group, whereas others are facultative and switch from one mode to the other, depending on the nutrient sources available. [16] Sulfur-oxidizing, iron, and anammox bacteria as well as methanogens are chemolithoautotrophs, using inorganic energy, electron, and carbon sources. Chemolithoheterotrophs are rare because heterotrophy implies the availability of organic substrates, which can also serve as easy electron sources, making lithotrophy unnecessary. Photoorganoautotrophs are uncommon since their organic source of electrons/hydrogens would provide an easy carbon source, resulting in heterotrophy.

Synthetic biology efforts enabled the transformation of the trophic mode of two model microorganisms from heterotrophy to chemoorganoautotrophy:

See also

Notes and references

  1. Eiler A (December 2006). "Evidence for the ubiquity of mixotrophic bacteria in the upper ocean: implications and consequences". Applied and Environmental Microbiology. 72 (12): 7431–7. Bibcode:2006ApEnM..72.7431E. doi:10.1128/AEM.01559-06. PMC   1694265 . PMID   17028233. Table 1: Definitions of metabolic strategies to obtain carbon and energy
  2. Todar K (2009). "Todar's Online Textbook of Bacteriology". Nutrition and Growth of Bacteria. Retrieved 2014-04-19.
  3. Kelly DP, Mason J, Wood A (1987). "Energy Metabolism in Chemolithotrophs". In van Verseveld HW, Duine JA (eds.). Microbial Growth on C1 Compounds. Springer. pp. 186–7. doi:10.1007/978-94-009-3539-6_23. ISBN   978-94-010-8082-8.
  4. Lwoff A, Van Niel CB, Ryan TF, Tatum EL (1946). "Nomenclature of nutritional types of microorganisms" (PDF). Cold Spring Harbor Symposia on Quantitative Biology. 11 (5th ed.): 302–3.
  5. Andrews JH (1991). Comparative Ecology of Microorganisms and Macroorganisms. Springer. p. 68. ISBN   978-0-387-97439-2.
  6. Yafremava LS, Wielgos M, Thomas S, Nasir A, Wang M, Mittenthal JE, Caetano-Anollés G (2013). "A general framework of persistence strategies for biological systems helps explain domains of life". Frontiers in Genetics. 4: 16. doi: 10.3389/fgene.2013.00016 . PMC   3580334 . PMID   23443991.
  7. Margulis L, McKhann HI, Olendzenski L, eds. (1993). Illustrated Glossary of Protoctista: Vocabulary of the Algae, Apicomplexa, Ciliates, Foraminifera, Microspora, Water Molds, Slime Molds, and the Other Protoctists. Jones & Bartlett Learning. pp. xxv. ISBN   978-0-86720-081-2.
  8. 1 2 3 Morris, J. et al. (2019). "Biology: How Life Works", 3rd edition, W. H. Freeman. ISBN   978-1319017637
  9. Kellermann MY, Wegener G, Elvert M, Yoshinaga MY, Lin YS, Holler T, et al. (November 2012). "Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities". Proceedings of the National Academy of Sciences of the United States of America. 109 (47): 19321–6. Bibcode:2012PNAS..10919321K. doi: 10.1073/pnas.1208795109 . PMC   3511159 . PMID   23129626.
  10. 1 2 Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, et al. (November 2019). "Conversion of Escherichia coli to Generate All Biomass Carbon from CO2". Cell. 179 (6): 1255–1263.e12. doi:10.1016/j.cell.2019.11.009. PMC   6904909 . PMID   31778652.
  11. 1 2 Gassler T, Sauer M, Gasser B, Egermeier M, Troyer C, Causon T, et al. (December 2019). "The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2". Nature Biotechnology. 38 (2): 210–6. doi:10.1038/s41587-019-0363-0. PMC   7008030 . PMID   31844294.
  12. Miroshnichenko ML, L'Haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, et al. (May 2003). "Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent". International Journal of Systematic and Evolutionary Microbiology. 53 (Pt 3): 747–52. doi: 10.1099/ijs.0.02367-0 . PMID   12807196.
  13. Rippka R (March 1972). "Photoheterotrophy and chemoheterotrophy among unicellular blue-green algae". Archives of Microbiology. 87 (1): 93–98. doi:10.1007/BF00424781. S2CID   155161.
  14. Li, Meijie; Ning, Peng; Sun, Yi; Luo, Jie; Yang, Jianming (2022). "Characteristics and Application of Rhodopseudomonas palustris as a Microbial Cell Factory". Frontiers in Bioengineering and Biotechnology. 10: 897003. doi: 10.3389/fbioe.2022.897003 . ISSN   2296-4185. PMC   9133744 . PMID   35646843.
  15. Eiler A (December 2006). "Evidence for the ubiquity of mixotrophic bacteria in the upper ocean: implications and consequences". Applied and Environmental Microbiology. 72 (12): 7431–7. Bibcode:2006ApEnM..72.7431E. doi:10.1128/AEM.01559-06. PMC   1694265 . PMID   17028233.
  16. 1 2 3 Tang KH, Tang YJ, Blankenship RE (2011). "Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications". Front Microbiol. 2: 165. doi: 10.3389/fmicb.2011.00165 . PMC   3149686 . PMID   21866228.


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<span class="mw-page-title-main">Nutrition</span> Provision to cells and organisms to support life

Nutrition is the biochemical and physiological process by which an organism uses food to support its life. It provides organisms with nutrients, which can be metabolized to create energy and chemical structures. Failure to obtain the required amount of nutrients causes malnutrition. Nutritional science is the study of nutrition, though it typically emphasizes human nutrition.

An electron transport chain (ETC) is a series of protein complexes and other molecules which transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H+ ions) across a membrane. Many of the enzymes in the electron transport chain are embedded within the membrane.

<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">Green sulfur bacteria</span> Family of bacteria

The green sulfur bacteria are a phylum, Chlorobiota, of obligately anaerobic photoautotrophic bacteria that metabolize sulfur.

<span class="mw-page-title-main">Chemosynthesis</span> Biological process building organic matter using inorganic compounds as the energy source

In biochemistry, chemosynthesis is the biological conversion of one or more carbon-containing molecules and nutrients into organic matter using the oxidation of inorganic compounds or ferrous ions as a source of energy, rather than sunlight, as in photosynthesis. Chemoautotrophs, organisms that obtain carbon from carbon dioxide through chemosynthesis, are phylogenetically diverse. Groups that include conspicuous or biogeochemically important taxa include the sulfur-oxidizing Gammaproteobacteria, the Campylobacterota, the Aquificota, the methanogenic archaea, and the neutrophilic iron-oxidizing bacteria.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

<span class="mw-page-title-main">Biological carbon fixation</span> Series of interconnected biochemical reactions

Biological carbon fixation, or сarbon assimilation, is the process by which living organisms convert inorganic carbon to organic compounds. These organic compounds are then used to store energy and as structures for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use chemosynthesis in the absence of sunlight. Chemosynthesis is carbon fixation driven by chemical energy rather than from sunlight. 

<span class="mw-page-title-main">Phototroph</span> Organism using energy from light in metabolic processes

Phototrophs are organisms that carry out photon capture to produce complex organic compounds and acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes. All phototrophs either use electron transport chains or direct proton pumping to establish an electrochemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell. Phototrophs can be either autotrophs or heterotrophs. If their electron and hydrogen donors are inorganic compounds they can be also called lithotrophs, and so, some photoautotrophs are also called photolithoautotrophs. Examples of phototroph organisms are Rhodobacter capsulatus, Chromatium, and Chlorobium.

A chemotroph is an organism that obtains energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs, which use photons. Chemotrophs can be either autotrophic or heterotrophic. Chemotrophs can be found in areas where electron donors are present in high concentration, for instance around hydrothermal vents.

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.

<span class="mw-page-title-main">Sulfur-reducing bacteria</span> Microorganisms able to reduce elemental sulfur to hydrogen sulfide

Sulfur-reducing bacteria are microorganisms able to reduce elemental sulfur (S0) to hydrogen sulfide (H2S). These microbes use inorganic sulfur compounds as electron acceptors to sustain several activities such as respiration, conserving energy and growth, in absence of oxygen. The final product of these processes, sulfide, has a considerable influence on the chemistry of the environment and, in addition, is used as electron donor for a large variety of microbial metabolisms. Several types of bacteria and many non-methanogenic archaea can reduce sulfur. Microbial sulfur reduction was already shown in early studies, which highlighted the first proof of S0 reduction in a vibrioid bacterium from mud, with sulfur as electron acceptor and H
2
as electron donor. The first pure cultured species of sulfur-reducing bacteria, Desulfuromonas acetoxidans, was discovered in 1976 and described by Pfennig Norbert and Biebel Hanno as an anaerobic sulfur-reducing and acetate-oxidizing bacterium, not able to reduce sulfate. Only few taxa are true sulfur-reducing bacteria, using sulfur reduction as the only or main catabolic reaction. Normally, they couple this reaction with the oxidation of acetate, succinate or other organic compounds. In general, sulfate-reducing bacteria are able to use both sulfate and elemental sulfur as electron acceptors. Thanks to its abundancy and thermodynamic stability, sulfate is the most studied electron acceptor for anaerobic respiration that involves sulfur compounds. Elemental sulfur, however, is very abundant and important, especially in deep-sea hydrothermal vents, hot springs and other extreme environments, making its isolation more difficult. Some bacteria – such as Proteus, Campylobacter, Pseudomonas and Salmonella – have the ability to reduce sulfur, but can also use oxygen and other terminal electron acceptors.

Lithotrophs are a diverse group of organisms using an inorganic substrate to obtain reducing equivalents for use in biosynthesis or energy conservation via aerobic or anaerobic respiration. While lithotrophs in the broader sense include photolithotrophs like plants, chemolithotrophs are exclusively microorganisms; no known macrofauna possesses the ability to use inorganic compounds as electron sources. Macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called "prokaryotic symbionts". An example of this is chemolithotrophic bacteria in giant tube worms or plastids, which are organelles within plant cells that may have evolved from photolithotrophic cyanobacteria-like organisms. Chemolithotrophs belong to the domains Bacteria and Archaea. The term "lithotroph" was created from the Greek terms 'lithos' (rock) and 'troph' (consumer), meaning "eaters of rock". Many but not all lithoautotrophs are extremophiles.

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Beggiatoa is a genus of Gammaproteobacteria belonging to the order Thiotrichales, in the Pseudomonadota phylum. These bacteria form colorless filaments composed of cells that can be up to 200 μm in diameter, and are one of the largest prokaryotes on Earth. Beggiatoa are chemolithotrophic sulfur-oxidizers, using reduced sulfur species as an energy source. They live in sulfur-rich environments such as soil, both marine and freshwater, in the deep sea hydrothermal vents, and in polluted marine environments. In association with other sulfur bacteria, e.g. Thiothrix, they can form biofilms that are visible to the naked eye as mats of long white filaments; the white color is due to sulfur globules stored inside the cells.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

<span class="mw-page-title-main">Lithoautotroph</span> Microbe which derives energy from minerals

A lithoautotroph is an organism which derives energy from reactions of reduced compounds of mineral (inorganic) origin. Two types of lithoautotrophs are distinguished by their energy source; photolithoautotrophs derive their energy from light while chemolithoautotrophs (chemolithotrophs or chemoautotrophs) derive their energy from chemical reactions. Chemolithoautotrophs are exclusively microbes. Photolithoautotrophs include macroflora such as plants; these do not possess the ability to use mineral sources of reduced compounds for energy. Most chemolithoautotrophs belong to the domain Bacteria, while some belong to the domain Archaea. Lithoautotrophic bacteria can only use inorganic molecules as substrates in their energy-releasing reactions. The term "lithotroph" is from Greek lithos (λίθος) meaning "rock" and trōphos (τροφοσ) meaning "consumer"; literally, it may be read "eaters of rock". The "lithotroph" part of the name refers to the fact that these organisms use inorganic elements/compounds as their electron source, while the "autotroph" part of the name refers to their carbon source being CO2. Many lithoautotrophs are extremophiles, but this is not universally so, and some can be found to be the cause of acid mine drainage.

Hydrogen-oxidizing bacteria are a group of facultative autotrophs that can use hydrogen as an electron donor. They can be divided into aerobes and anaerobes. The former use hydrogen as an electron donor and oxygen as an acceptor while the latter use sulphate or nitrogen dioxide as electron acceptors. Species of both types have been isolated from a variety of environments, including fresh waters, sediments, soils, activated sludge, hot springs, hydrothermal vents and percolating water.

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<span class="mw-page-title-main">Autotroph</span> Organism type

An autotroph is an organism that can convert abiotic sources of energy into energy stored in organic compounds, which can be used by other organisms. Autotrophs produce complex organic compounds using carbon from simple substances such as carbon dioxide, generally using energy from light or inorganic chemical reactions. Autotrophs do not need a living source of carbon or energy and are the producers in a food chain, such as plants on land or algae in water. Autotrophs can reduce carbon dioxide to make organic compounds for biosynthesis and as stored chemical fuel. Most autotrophs use water as the reducing agent, but some can use other hydrogen compounds such as hydrogen sulfide.

A mixotroph is an organism that uses a mix of different sources of energy and carbon, instead of having a single trophic mode, on the continuum from complete autotrophy to complete heterotrophy. It is estimated that mixotrophs comprise more than half of all microscopic plankton. There are two types of eukaryotic mixotrophs. There are those with their own chloroplasts - including those with endosymbionts providing the chloroplasts. And there are those that acquire them through kleptoplasty, or through symbiotic associations with prey, or through 'enslavement' of the prey's organelles.

<span class="mw-page-title-main">Microbial oxidation of sulfur</span>

Microbial oxidation of sulfur is the oxidation of sulfur by microorganisms to build their structural components. The oxidation of inorganic compounds is the strategy primarily used by chemolithotrophic microorganisms to obtain energy to survive, grow and reproduce. Some inorganic forms of reduced sulfur, mainly sulfide (H2S/HS) and elemental sulfur (S0), can be oxidized by chemolithotrophic sulfur-oxidizing prokaryotes, usually coupled to the reduction of oxygen (O2) or nitrate (NO3). Anaerobic sulfur oxidizers include photolithoautotrophs that obtain their energy from sunlight, hydrogen from sulfide, and carbon from carbon dioxide (CO2).