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A carotenoid is a member of a pigment family characterized by an extended conjugated carbon framework, commonly based on a forty-carbon skeleton. Conjugation gives these molecules strong absorption in parts of the visible spectrum.

Carotenoids can contribute to light harvesting and photoprotection. They can therefore broaden the usable spectrum of a photosynthetic system while helping manage excitation that would otherwise cause damage.

An eyespot is a subcellular light-sensing apparatus that helps a motile organism determine the direction of illumination. In Chlamydomonas reinhardtii, it combines carotenoid-rich granules in the chloroplast with channelrhodopsin proteins in the adjacent cell membrane. Its optical arrangement gives the light-sensitive machinery a directional response; it does not form a visual image.^[ref]

During swimming, flagella propel the rotating biological cell, so the eyespot samples changing orientations to the light. Differences in light response can then guide phototaxis. Experiments with mutants lacking the visible pigment layers found that they could still show phototaxis, but with the direction reversed under the tested conditions. Optical observations showed that the cell body could concentrate light onto the rear of the receptors; pigment-layer shielding helps determine the direction of the response.^[ref] This distinguishes detecting light from correctly interpreting its direction.

Noriko Ueki investigates how swimming green algae respond to light. A 2016 study led by Ueki examined Chlamydomonas reinhardtii mutants lacking a normal eyespot and found that their direction of phototaxis could reverse relative to normal cells under the same chemical conditions. The result made the optical arrangement of the biological cell part of the explanation for its behavior.^[ref]

The carotenoid layers of an eyespot help control which direction of illumination reaches light-sensitive channelrhodopsins. Without that shielding, the cell body can act as a convex lens, concentrating light arriving from the rear. The investigators demonstrated the lens effect by imaging a small letter through the cells with a microscope. This is an illuminating example of a physical structure changing the meaning of a sensory signal: the same light-sensitive machinery can receive its strongest illumination from a different direction. Comparing mutants, a rescued strain and normal cells connected the optical effect with the observed phototaxis.^[ref]

The principal non-water visible-light absorbers can be grouped into phytoplankton pigments, coloured dissolved organic matter (CDOM), and non-algal particles (NAP), including organic detritus and absorbing mineral material. A useful additive decomposition of the absorption coefficient isThe supplied sketch separates the three non-water contributions; its amplitudes are arbitrary and are not concentrations or measured spectra.

Phytoplankton pigments give prominent absorption maxima around $440$ and $675\mathrm{nm}$, associated with chlorophyll a, and a relative minimum in the green. Accessory pigments, including carotenoids and phycobilins, broaden or add absorption bands, so an assemblage is not just a pure chlorophyll-a solution. Intracellular packaging and cell size also modify the shape and absorption per unit pigment.

Coloured dissolved organic matter consists of dissolved light-absorbing organic compounds, often including humic material from terrestrial runoff and marine degradation. Its absorption is strongest at the blue/ultraviolet end and declines approximately exponentially toward red, without the narrow chlorophyll red peak. A common local parameterization is $a_g(\lambda )=a_g({\lambda }_0)e^{-S_g(\lambda -{\lambda }_0)}$ with positive spectral slope $S_g$; here $S_g$ is an optical slope, not gas saturation.

Non-algal particles include nonliving organic detritus, pigment degradation products and absorbing suspended mineral particles. Their aggregate absorption often also decreases approximately exponentially from blue to red, with variable slope and mineral-dependent departures. Suspended sediments can strongly scatter as well as absorb; bright sediment-laden water is not evidence of a red absorption peak. Chlorophyll-containing living cells belong in $a_{\mathrm{ph}}$, so these categories should not be double counted.^[ref]