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Phytoplankton Bio-optics: Absorption, Pigments, Biomass. Homework: Chapter 2 in your reader: C. Miller “The phycology of phytoplankton”. Roles of Phytoplankton Light absorption & related heat budgets Inorganic to organic conversion of C, N, P, S, etc for consumption by food web

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Phytoplankton Bio-optics: Absorption, Pigments, Biomass

Homework: Chapter 2 in your reader: C. Miller “The phycology of phytoplankton”

Roles of Phytoplankton

Light absorption & related heat budgets

Inorganic to organic conversion of C, N, P, S, etc for consumption by food web

Formation of DOC (=DOM, of which cDOM is a component)

Sinking and loss of POC to the deep sea/ fossil fuel

ALL Biogeochemical Cycles

Harmful Algal Blooms

Cloud formation/Climate modification

Optical Signaling (satellites/moorings/submarines)

~ 40 % global photosynthesis and related primary productivity


Last Lecture and reading emphasized that

A quantum of sunlight getting into surface water column is either absorbed, scattered and/or transmittedto deeper depths, due to water properties, phytoplankton, cDOM, particles, detritus etc.

Incident Light, Io = QPARo

Light Absorption and Scattering

Transmitted Light = Attenuated Light, Iz = QPARz

This and the next Lectures and readings emphasize that

  • A quantum of light reaching the surface a phytoplankton cell is also either scattered(mostly at cell surfaces), absorbed(PAR, mostly by pigments and cell metabolites: UVR by DNA and protein), ortransmittedthrough the cell to penetrate deeper in the water column.
  • In addition some absorbed light by pigments can be reemitted as light (= fluorescence)
  • The measurable proportionalities of incoming irradiance in thephoton budget of a phytochange with different taxonomic groupings, physiology, photosynthetic activity &cell growth.

Therefore, much can be learned about phytoplankton by looking at their effects on the underwater light field; hence, the study of the bio-optics of phytoplankton is central to aquatic ecology


Several kinds of


2. Phytoplankton cellular components and their internal distribution in the cell largely determine how much of light getting into the cell is absorbed or transmitted.

Fundamental review, see readings for additional detail.

1. Phytoplankton shapes/sizes and surface composition/roughness largely control light scatter

3. Phytoplankton cell absorption of light occurs largely in photosynthetic lamellae (thylakoids) where ALL photosynthetic pigments are located. Thylakoids are in chloroplasts organelles within eukaryotic phytoplankton and located in cytoplasm (no organelles) of prokaryotic bacteria


Even at the organizational level of a chloroplast, incoming light can be scattered,

absorbed or transmitted.

Major differences in thylakoid arrangements exist in different phytoplankton groups and affect with how light energy is absorbed and utilized.



And other




Green algae


  • All photosynthetic pigments are in thylakoids
  • Thylakoids give cell color
  • Photosynthesis light reactions in thylakoids
  • Photosynthesis dark reactions in stroma;

Optional excellent review of basic photosynthesis given as a self test (based upon green plants)


Chemical electron acceptor


Ejects electron

Light Harvesting

Chl a-protein complexes

Chlorophyll a is only pigment required for photosynthesis

Because Chl a (C) is the only pigment that comprises the photochemical reaction centers of Photosystem I and Photosystem II

P700 = special Chl a dimer of Ps I

P680 = special Chl a dimer of Ps II

Chl a


Note how depth is not in meters (Z) but scaled to light field as % surface QPAR …this approach allows distribution of Chl in euphotic zones of different depths to be intercompared.

Chl a is in all photosynthetic

phytoplankton and its

abundance in a water sample is

used to indicate the relative

BIOMASS of phytoplankton

  • Common Method for Determining Chl Biomass:
  • Filter phytos (can size fraction)
  • Extract Chl with organic solvents
  • Measure magnitude of Chl red peak absorption
  • Convert to [concentration units] of ng/L =mg/m3

Chl a

Caveat:[Chl a] is imperfect measure of phytoplankton biomass & interpretations of findings must recognize the possible sources of error.

How would your view of phytoplankton distribution in the above graphs change if I told you that each phyto cells at 1%Qpar have 10x Chl of that of cells at the surface?


So, if Chl a is all that is needed for photosynthesis, what are all those other pigments doing and where are they located?

In vivo whole cell absorption



Pure pigment

in organic solvent

They are absorbing light energy and passing the excitation energy on to Chl a-doinated PS I and PS II reaction centers to do photochemistry

As such they are called Antenna or Light-Harvesting Complexes (LHCs)

This is an example for a chlorophyte (green algae) LHCs, giving rise to a whole cell absorption spectrum that is a summation of the absorption properties of each of these pigments bound to proteins in the thylakoid membrane


Case II: Coastal waters/most lakes

Case I: Open Ocean

400 nm

700 nm

Cyanobacteria and some red algae

Found in large quantities in

red colored cyanobacteria

and in some red algae

LH Pigments evolved to efficiently capture aquatic QPAR(l) that Chl a does not absorb well


Forest green under low light,

turning yellowish under

High light

If phycoerythrin abundant,

then red colored

Reddish brown to golden brown

If phycocyanin abundant,

then blue colored

Phytoplankton pigments: types, function and taxonomic distribution



You need to know this information very well to study phytoplankton community ecology as well as regional differences in aquatic primary production


Chlorophytes, Prochloron?

Phytoplankton Biomass

Depth (meters)



Transect of Santa Barbara Channel

West Front East







Chl a + Chl c (1+2) + fucoxanthin

Chl a + Chl c (2) + peridinin

Examples of phytoplankton absorption spectra for different phytoplankton groups


Phycocyanin, PC

Phycoerythrin, PE

Chl a (which absorption peaks?) + phycobilin containing phytoplankton

In ocean, these are picophytoplankton that tend to dominate

phytoplankton communities of oligotrophic waters.


Dense spring bloom in

North Atlantic Ocean

Low phyto biomass in

Gyres of N. and S.

Atlantic Ocean

High phyto biomass

In coastal currents

How pigment data is used in oceanography

1. To map distribution of Chl a as proxy measure of phytoplankton biomass

But not all Chl is the same phytoplankton community.. How do we know which

Groups of phytoplankton are in which locations?