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Carbon assimilation is the incorporation of carbon from an external source into an organism's cellular compounds and biomass. It involves chemical transformations, rather than merely transport across a membrane. Carbon can also be oxidized for energy or released in secreted products, so disappearance of a carbon source from the surroundings does not alone measure assimilation.

Methylotrophy provides an illuminating example. In the experimentally studied Methylobacterium pathway, methanol is converted to formaldehyde, with carbon then entering either oxidation toward carbon dioxide or assimilation into cellular compounds. The same incoming carbon pool can thus support different metabolic functions.^[ref]

Suppose an invented closed carbon account records100millimoles of carbon atoms taken up,40released as carbon dioxide,10released in other products, and no change in an unmeasured internal store. The remaining50millimoles are retained in biomass: $100=40+10+50$. This is a conservation calculation under explicit assumptions. A real experiment must also check unmeasured products, pre-existing carbon stores and losses before assigning the remainder to new biomass.

Carbon fixation is one route contributing to carbon assimilation when inorganic carbon is converted into organic compounds. Assimilation of an already organic substrate is a different starting point. Measuring metabolic flux or tracing labeled carbon can help distinguish the incoming material's transformations from an increase in total cell mass.

A carbon sink takes up more carbon than it releases over a specified interval. It is a statement about a net transfer, whereas carbon storage describes an amount already held. If a reservoir's carbon stock is $C$, its balance isA positive balance makes it a carbon sink relative to the stated boundary. A large, nearly unchanged stock can provide substantial carbon storage without acting as a strong current carbon sink.

Forests acquire carbon through photosynthesis and lose it through cellular respiration, decay, fire and removal of biomass. Forest inventories and long-term ecosystem measurements therefore have to account for both accumulation and losses: the carbon sink in growing forests is not automatically the net effect of all changes in forested land.^[ref]

A carbon source is a material from which an organism obtains carbon for its metabolism and growth. The carbon atoms can enter biomass, be transformed into other compounds, or leave through products such as carbon dioxide. Calling a material a carbon source therefore identifies its role in the carbon inventory; it does not mean every supplied carbon atom is retained in cells.

For an original inventory example,1millimole of glucose, ${\mathrm{C}}_6{\mathrm{H}}_{12}{\mathrm{O}}_6$, supplies6millimoles of carbon atoms, whereas1millimole of methanol, $\mathrm{C}{\mathrm{H}}_3\mathrm{OH}$, supplies1millimole. Equal concentrations measured in moles of molecules need not mean equal concentrations of carbon. Carbon supply alone also does not specify the amount of usable energy or the growth yield.

An experimental example is the2005 study of plant-associated Methylobacterium. Mutants unable to use methanol effectively were disadvantaged in competition, yet could colonize plants well when introduced alone. The researchers inferred that other carbon sources were available on the plants. A supplied substrate, the substrates an organism can use, and the substrate limiting growth are separate questions.^[ref]

Carbon assimilation describes incorporation into cellular material, while carbon fixation concerns incorporation of inorganic carbon, such as carbon dioxide, into organic compounds. The carbon source and energy supply must be identified separately: for photosynthesis, light can supply energy while carbon comes from carbon dioxide.

A defined medium is a culture medium whose individual chemical constituents and specified amounts are known. This makes chemical composition an explicit experimental variable. It differs from a complex medium, which contains ingredients with an incompletely specified molecular composition. A defined medium can help investigate which nutrients an organism requires under stated conditions.^[ref]

Known composition permits a quantitative inventory. Consider an illustrative chemical solution containing glucose at $10\mathrm{mmol}{\mathrm{L}}^{-1}$ in a volume of $0.250\mathrm{L}$. Its amount of substance isIf dilution increases the final volume to $1.000\mathrm{L}$ without consuming glucose, its final molar concentration is $2.5\mathrm{mmol}{\mathrm{L}}^{-1}$. Because each glucose molecule contains six carbon atoms, that is $15\mathrm{mmol}{\mathrm{L}}^{-1}$ of carbon atoms supplied by this ingredient. Molecular concentration and elemental inventory answer related but different questions.

This calculation is an accounting illustration, rather than a complete culture medium formulation. It predicts neither how much biomass will form nor whether other required nutrients are present. A known starting inventory makes such questions testable; it does not supply their biological answers.

Composition and physical presentation are separate classifications. A liquid preparation and an agar-solidified preparation can be compared by their physical state, while chemically defined and complex describe what is specified about their ingredients.^[ref]

An environmental impact is a change in environmental conditions attributable to an activity or intervention. The change can concern biodiversity, water quality, carbon storage or another specified property of an ecosystem. Its sign and magnitude depend on the chosen outcome, spatial boundary and observation interval.

Causal interpretation requires a comparison: a change observed after an intervention might also reflect climate variation. A long-term grassland experiment directly varied species richness and followed annual aboveground biomass production. Higher species richness increased the temporal stability of total production, even though individual species could fluctuate more strongly.^[ref] The example shows why measuring an environmental impact requires identifying both the affected property and a credible comparison, rather than treating every environmental measurement as evidence of a particular cause.

Methylotrophy is the ability to grow using reduced carbon compounds with no carbon–carbon bonds, such as methanol, as carbon and energy sources. It requires both energy-yielding transformations and carbon assimilation into biomass. Facultative methylotrophs can also use other carbon sources; the historical description of Methylobacterium explicitly distinguished this metabolic flexibility.^[ref]

The two carbon fates are different. Complete methanol oxidation can be represented byThis balanced equation accounts for carbon oxidized to carbon dioxide, not for net cell production. A growing methylotroph must retain carbon in cellular material as well. In the studied Methylobacterium pathway, formaldehyde is an intermediate at the junction of oxidation and assimilation routes.^[ref]

A2005 plant-colonization experiment by Abdoulaye Sy and colleagues compared wild-type bacteria with mutants defective in methylotrophy. The mutants were disadvantaged during competition, but could reach wild-type colonization levels when introduced alone. This contrast showed that the metabolic ability mattered under the tested competitive conditions, while other usable carbon sources remained available on the plants. Growth in isolation and fitness in a microbial community therefore answered different questions.^[ref]

The photic zone is the illuminated layer supporting photosynthesis; its euphotic depth is conventionally associated with about 1% of surface photosynthetically active radiation, integrated over approximately $400$–$700\mathrm{nm}$. This is a useful convention rather than a universal organism-specific compensation depth. Spectral filtering can be represented locally bywhere $K_d$ is the wavelength-dependent diffuse attenuation coefficient. It includes effects of absorption and scattering and is not simply equal to the absorption coefficient $a$.

In clear, low-chlorophyll water, pure water removes red light strongly, while weak blue pigment and CDOM absorption permits blue light, typically around $450$–$490\mathrm{nm}$, to penetrate furthest. The deepest usable light is consequently dim and blue-rich, and the euphotic zone can extend relatively deep. At high pigment concentrations, phytoplankton pigments preferentially remove blue and red light; associated detritus or CDOM can remove still more blue. The remaining transmission window commonly shifts toward blue-green or green wavelengths, roughly $500$–$570\mathrm{nm}$, and the total light falls off faster, so the euphotic depth is shallower. Exact window and depth depend on the full particle/dissolved mixture, not chlorophyll alone. The diagram normalizes the two deep spectra separately to show their different shapes, not equal absolute light at a common depth.

This confines photosynthetic growth to a thinner illuminated interval in high-chlorophyll water and allows a deeper potential habitat in clear low-chlorophyll water, subject also to nutrient supply, mixing and the organism's compensation requirement. Cells near the base benefit from low-light acclimation and pigment systems that capture the remaining wavelengths. In blue-rich deep ocean water, blue-absorbing pigments and some low-light-adapted picoplankton can be favored; where the surviving light is greener, groups with effective green-absorbing accessory pigments, such as certain phycobilins, gain an advantage. A pigment appears coloured by light it fails to absorb, so green-absorbing accessory pigments need not themselves look green. There is no universal deep species determined by chlorophyll concentration alone. A deep chlorophyll maximum can partly reflect increased pigment per cell rather than a proportional maximum in carbon biomass.^[ref]

Primary production is formation of organic material from inorganic carbon, powered by light or chemical free energy. Photosynthetic plants, algae and cyanobacteria supply familiar examples. The product supports consumers directly or enters a detritus-based food web.

Gross primary production counts total carbon fixation, whereas net primary production subtracts the producers' own autotrophic respiration. A standing stock of biomass is therefore different from either rate: a small stock can turn over rapidly.

A ratio expressing carbon gain or biomass production relative to water use, under a specified measurement convention. Higher leaf-level efficiency does not guarantee greater whole-ecosystem carbon storage.