Primary nutritional groups

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 and organic or inorganic compounds; the sources of carbon can be of organic or inorganic origin. ^[1]

The terms aerobic respiration, anaerobic respiration and fermentation 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 NO₃⁻, SO₄²⁻ or fumarate in anaerobic respiration, or various metabolic intermediates in fermentation. Because all ATP-generating steps in fermentation involve modifications of metabolic intermediates instead of the use of an electron transport chain fermentation is often referred to as substrate-level phosphorylation.

Primary sources of energy

Simplified flowchart for determining if an organism is an autotroph, heterotroph or a subtype.

Phototrophs: Light is absorbed in photo receptors and transformed into chemical energy.
Chemotrophs: Bond energy is released from a chemical compound.

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

Some bacteria can alternate phototrophy and chemotrophy, depending on availability of light.

Primary sources of reducing equivalents

Organotrophs: Organic compounds are used as electron donor.
Lithotrophs: Inorganic compounds are used as electron donor.

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

Organotrophic organisms are often also heterotrophic, using organic compounds as sources of electrons and carbon at the same time. Similarly, lithotrophic organisms are often also autotrophic, using inorganic sources of electrons and CO₂ as inorganic carbon source.

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

It should be noted that 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 use water as electron donor to biosynthesis, being lithotrophs. Animals use organic compounds as eletron donors to synthesize ATP, being organotrophs (plants also do it, 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: Organic compounds are metabolized to get carbon for growth and development.
Autotrophs: Carbon dioxide (CO₂) is used as source of carbon.

Energy and carbon

Yellow fungus

Classification of organisms based on their metabolism
Energy source	sunlight	photo-			-troph
	Preformed molecules	chemo-
Electron donor	organic compound		organo-
	inorganic compound		litho-
Carbon source	organic compound			hetero-
	carbon dioxide			auto-

A chemoorganoheterotrophic organism is one that requires organic substrates to get its carbon for growth and development, and that produces its energy from oxido-reduction 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 electron reactions from dead organic matter. Herbivores and carnivores are examples of organisms that obtain carbon and electron reactions from living organic matter.

Chemoorganotrophs are organisms which oxidize the chemical bonds in organic compounds as their energy source. Chemoorganotrophs also attain the carbon molecules that they need for cellular function from these organic compounds. The organic compounds that they oxidize include sugars (i.e. glucose), fats and proteins.^[2]

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 inorganic compounds as a source of energy.^[3]

Primary metabolism table

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

Energy source	Oxidizing donor source	Carbon source	Name	Examples
Sun Light Photo-	Organic -organo-	Organic -heterotroph	Photoorganoheterotroph	Some bacteria (Rhodobacter)
	Organic -organo-	Carbon dioxide -autotroph	Photoorganoautotroph
	Inorganic -litho-*	Organic -heterotroph	Photolithoheterotroph
	Inorganic -litho-*	Carbon dioxide -autotroph	Photolithoautotroph	Some bacteria (blue green algae), some eukaryotes (eukaryotic algae, land plants). Photosynthesis.
Breaking Chemical Compounds Chemo-	Organic -organo-	Organic -heterotroph	Chemoorganoheterotroph	Some eukaryotes (heterotrophic protists, fungi, animals)
	Organic -organo-	Carbon dioxide -autotroph	Chemoorganoautotroph	Some archaea (anaerobic methanotrophic archaea).^[7] Chemosynthesis.
	Inorganic -litho-*	Organic -heterotroph	Chemolithoheterotroph	Some bacteria (Oceanithermus profundus)^[8]
	Inorganic -litho-*	Carbon dioxide -autotroph	Chemolithoautotroph	Some bacteria (Nitrobacter, Methanobacteria). Chemosynthesis.

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

Mixotrophs

Some, usually unicellular, organisms can switch between different metabolic modes, for example between photoautotrophy, photoheterotrophy, and chemoheterotrophy in Chroococcales ^[9] Such mixotrophic organisms may dominate their habitat, due to their capability to use more resources than either photoautotrophic or organoheterotrophic organisms. ^[10]

Examples

All sorts of combinations may exist in nature. For example, most cyanobacteria are photoautotrophic, since they use light as an energy source, water as electron donor, and CO₂ as a carbon source. Fungi are chemoorganotrophic since they use organic carbon as both an electron donor and carbon source. Eukaryotes are generally easy to categorise. All animals are heterotrophic, as are fungi. Plants are generally photoautotrophic. Some eukaryotic microorganisms, however, are not limited to just one nutritional mode. For example, some algae live photoautotrophically in the light, but shift to chemoorganotrophy in the dark. Even higher plants retained their ability to respire heterotrophically on the starch at night which had been synthesised phototrophically during the day.

Prokaryotes show a great diversity of nutritional categories. For example, purple sulfur bacteria and cyanobacteria are generally photoautotrophic whereas purple non-sulfur bacteria are photoorganotrophic. 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.

Notes and references

↑ Brock Biology of Microorganisms Definitions of metabolic strategies to obtain carbon and energy
↑ Kenneth Todar (2009). "Todar's Online Textbook of Bacteriology". Nutrition and Growth of Bacteria. Retrieved 2014-04-19.
↑ Kelly, DP; Julie Mason; Ann Wood. Energy Metabolism in Chemolithotrophs. Springer. pp. 186–187.
↑ Lwoff, A., C.B. van Niel, P.J. Ryan, and E.L. Tatum (1946). Nomenclature of nutritional types of microorganisms. Cold Spring Harbor Symposia on Quantitative Biology (5th edn.), Vol. XI, The Biological Laboratory, Cold Spring Harbor, NY, pp. 302–303, .
↑ Andrews, J. H. 1991. Comparative Ecology of Microorganisms and Macroorganisms. Springer Verlag, Berlin, p. 68, .
↑ Yafremava LS, Wielgos M, Thomas S, Nasir A, Wang M, Mittenthal JE, Caetano-Anollés G: A general framework of persistence strategies for biological systems helps explain domains of life. Front Genet 2013; 4:16; p.8,
↑ Y. Kellermann, Gunter Wegener, Marcus Elvert, Marcos Yukio Yoshinaga, Yu-Shih Lin, Thomas Holler, Xavier Prieto Mollar, Katrin Knittel, and Kai-Uwe Hinrichs. Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities. PNAS 2012, vol. 109 no. 47.
↑ M. L. Miroshnichenko et al., Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent
↑ R. Rippka Photoheterotrophy and chemoheterotrophy among unicellular blue-green algae Archives of Microbiology; Volume 87, Number 1 / March, 1972; doi:10.1007/BF00424781
↑ Alexander Eiler Evidence for the Ubiquity of Mixotrophic Bacteria in the Upper Ocean: Implications and consequences Appl Environ Microbiol. 2006 December; 72(12): 7431–7437; doi:10.1128/AEM.01559-06.

Modelling ecosystems – trophic components

General	Abiotic component Abiotic stress Behaviour Biogeochemical cycle Biomass Biotic component Biotic stress Carrying capacity Competition Ecosystem Ecosystem ecology Ecosystem model Keystone species List of feeding behaviours Metabolic theory of ecology Productivity Resource

Producers	Autotrophs Chemosynthesis Chemotrophs Foundation species Mixotrophs Myco-heterotrophy Mycotroph Organotrophs Photoheterotrophs Photosynthesis Photosynthetic efficiency Phototrophs Primary nutritional groups Primary production

Consumers	Apex predator Bacterivore Carnivores Chemoorganotroph Foraging Generalist and specialist species Intraguild predation Herbivores Heterotroph Heterotrophic nutrition Insectivore Mesopredator release hypothesis Omnivores Optimal foraging theory Predation Prey switching

Decomposers	Chemoorganoheterotrophy Decomposition Detritivores Detritus

Microorganisms	Archaea Bacteriophage Environmental microbiology Lithoautotroph Lithotrophy Microbial cooperation Microbial ecology Microbial food web Microbial intelligence Microbial loop Microbial mat Microbial metabolism Phage ecology

Food webs	Biomagnification Ecological efficiency Ecological pyramid Energy flow Food chain Trophic level

Example webs	Cold seeps Hydrothermal vents Intertidal Kelp forests Lakes North Pacific Subtropical Gyre Rivers San Francisco Estuary Soil Tide pool

Processes	Ascendency Bioaccumulation Cascade effect Climax community Competitive exclusion principle Consumer-resource systems Copiotrophs Dominance Ecological network Ecological succession Energy quality Energy Systems Language f-ratio Feed conversion ratio Feeding frenzy Mesotrophic soil Nutrient cycle Oligotroph Paradox of the plankton Trophic cascade Trophic mutualism Trophic state index

Defense/counter	Animal coloration Antipredator adaptations Camouflage Deimatic behaviour Herbivore adaptations to plant defense Mimicry Plant defense against herbivory Predator avoidance in schooling fish

Modelling ecosystems – other components

Population ecology	Abundance Allee effect Depensation Ecological yield Effective population size Intraspecific competition Logistic function Malthusian growth model Maximum sustainable yield Overpopulation in wild animals Overexploitation Population cycle Population dynamics Population modeling Population size Predator–prey (Lotka–Volterra) equations Recruitment Resilience Small population size Stability

Species	Biodiversity Density-dependent inhibition Ecological effects of biodiversity Ecological extinction Endemic species Flagship species Gradient analysis Indicator species Introduced species Invasive species Latitudinal gradients in species diversity Minimum viable population Neutral theory Occupancy-abundance relationship Population viability analysis Priority effect Rapoport's rule Relative abundance distribution Relative species abundance Species diversity Species homogeneity Species richness Species distribution Species-area curve Umbrella species

Species interaction	Antibiosis Biological interaction Commensalism Community ecology Ecological facilitation Interspecific competition Mutualism Storage effect

Spatial ecology	Biogeography Cross-boundary subsidy Ecocline Ecotone Ecotype Disturbance Edge effects Foster's rule Habitat fragmentation Ideal free distribution Intermediate Disturbance Hypothesis Island biogeography Landscape ecology Landscape epidemiology Landscape limnology Metapopulation Patch dynamics r/K selection theory Source–sink dynamics

Niche	Ecological niche Ecological trap Ecosystem engineer Environmental niche modelling Guild Habitat Marine habitats Limiting similarity Niche apportionment models Niche construction Niche differentiation

Other networks	Assembly rules Bateman's principle Bioluminescence Ecological collapse Ecological debt Ecological deficit Ecological energetics Ecological indicator Ecological threshold Ecosystem diversity Emergence Extinction debt Kleiber's law Liebig's law of the minimum Marginal value theorem Thorson's rule Xerosere

Other	Allometry Alternative stable state Balance of nature Biological data visualization Constructal theory Ecocline Ecological economics Ecological footprint Ecological forecasting Ecological humanities Ecological stoichiometry Ecopath Ecosystem based fisheries Endolith Evolutionary ecology Functional ecology Industrial ecology Macroecology Microecosystem Natural environment Regime shift Systems ecology Theoretical ecology

List of ecology topics

Metabolism, catabolism, anabolism

General

Energy
metabolism

Aerobic respiration	Glycolysis → Pyruvate decarboxylation → Citric acid cycle → Oxidative phosphorylation (electron transport chain + ATP synthase)

Anaerobic respiration	Electron acceptors are other than oxygen

Fermentation	Glycolysis → Substrate-level phosphorylation ABE Ethanol Lactic acid

Specific
paths

Protein metabolism

Carbohydrate metabolism
(carbohydrate catabolism
and anabolism)

Human

Glycolysis ⇄ Gluconeogenesis

Glycogenolysis ⇄ Glycogenesis

Pentose phosphate pathway Fructolysis Galactolysis

Glycosylation N-linked O-linked

Nonhuman

Photosynthesis Anoxygenic photosynthesis Chemosynthesis Carbon fixation

Xylose metabolism Radiotrophism

Lipid metabolism
(lipolysis, lipogenesis)

Fatty acid metabolism	Fatty acid degradation (Beta oxidation) Fatty acid synthesis

Other	Steroid metabolism Sphingolipid metabolism Eicosanoid metabolism Ketosis Reverse cholesterol transport

Amino acid

Nucleotide
metabolism

Other

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