4/9/10!1!4/9/10!2!4/9/10!3!Light disappears rapidly (exponentially) with depth At the same time, the color of the light shifts4/9/10!4!4/9/10!5!4/9/10!6!4/9/10!7!4/9/10!8!4/9/10!9!Scattering in the ocean!Coccolithophore!Emiliania huxleyi!http://earthguide.ucsd.edu/earthguide/imagelibrary/emilianiahuxleyi.html!4/9/10!10!Absorption plus Scattering!Eddies off the coast of Chile Red tide Countershading and Camouflage4/9/10!11!Transparency Reflection4/9/10!12!Squid eyes are sensitive to polarized light, while squid “camouflage” can hide polarized patterns (signals for other squid) www.oceanexplorer.noaa.gov!4/9/10!13!www.oceanexplorer.noaa.gov!4/9/10!14!4/9/10!15!Light in the ocean!4/9/10!16!What Determines the Optical Properties of Water?!4/9/10!17!Water color is determined mostly by absorption (not particles) Water clarity is determined mostly by scattering (the amount of “stuff” in the water) L(z;ξ) = L(0;ξ)exp −1µc(z' ' )dz''0z∫      +1µL∗E(z' ;ξ) +1µc(z' )S(z' ;ξ)      0z∫× exp −1µc(z' ' )dz''z'z∫      dz'Rrs(λ) ≅LuEd= constantbbw+ bbpaw+ aph+ adm+ bbw+ bbpRadiative Transfer Equation Beer-Lambert Law E=E0 • e-kz4/9/10!18!Ocean Color is a+b!http://seawifs.gsfc.nasa.gov/SEAWIFS.html!Even More Units… – Diffuse attenuation (K, m-1)!• e.g., Kd (e.g. Ed (z+Δz) = Ed (z) exp(- Kd. Δz))!– Reflectance (R)!• e.g., Radiance reflectance (Lu/ Ed; sr-1)!The Fundamental problem in ocean optics is to relate the IOPs to the AOPs….4/9/10!19!• Optical properties of water include absorption, scattering, attenuation (and a few others)!• These properties determine the clarity and color of the water, and tell us about what is in the water!• We can easily measure AOPs, but we’d rather know the IOPs!Summary Phytoplankton Pigments4/9/10!20!THE BIG PICTURE 12 H2O + 6 CO2!6 O2 + C6H12O6 + 6 H2O!WATER!CARBON DIOXIDE!OXYGEN!GLUCOSE! WATER!Net Rxn: 6 CO2+ 6 H2O + light C6H12O6 + 6 O2 Simplest form: CO2 + H2O + light CH2O + O2 Overall Rxn: LIGHT THE REACTIONS OF PHOTOSYNTHESIS4/9/10!21!Outer membrane Inner membrane Stroma Thylakoids Granum Chloroplasts are highly structured, membrane-rich organelles. • Stroma (Not To Be Confused With Stomata!!!) – Dense fluid within surrounding thylakiod PLANT ANATOMY PLANT ANATOMY!• Chloroplasts:!– Light energy is captured and converted in chloroplasts!– Light energy is passed through an ! ETC which converts it into a usable, ! chemical form!4/9/10!22!PHOTOSYNTHETIC PIGMENTS!• Chlorophylls:!– Reflect mainly green light!» Chlorophyll a, b, c, d!» Divinyl chlorophyll!• Carotenoids:!– Reflect mainly orange and yellow!» Fucoxanthin!» Beta-carotene!• Phycobilins (proteins):!– Reflect mainly blue-green or reddish!» Phycocyanin (blue-green algae)!» Phycoerythrin!CHLOROPHYLL a & b H2C CH H3C H3C CH2CH3 CH3 COCH3 CH2 CH2 CH2 C O O O O CHO in chlorophyll b CH3 in chlorophyll a Tail N N N N Mg PHOTOSYNTHETIC PIGMENTS Ring Structure In Head Absorbs Light4/9/10!23!CH3 CH3 CH3 CH3 CH H3C H3C HO CH β-carotene PHOTOSYNTHETIC PIGMENTS Amount of light absorbed Chlorophyll a 400 600 500 700 Chlorophyll b Carotenoids Wavelength of light (nm) DIFFERENT PIGMENTS ABSORB DIFFERENT WAVELENGTHS OF LIGHT4/9/10!24!ABSORBPTION SPECTRUM!• Every pigment ! has a characteristic ! Absorption Spectrum !• Optimal λ!• Optimal emission (fluorescence)!• This provides a “fingerprint”!λ (nanometers) % ABS chlorophyll a chlorophyll b4/9/10!25!Flow Cytometry http://www.whoi.edu/science/B/Olsonlab/insitu2001.htm!4/9/10!26!4/9/10!27!Chlorophyll a emits red light when excited with blue or red light !!4/9/10!28!Fluorescence HEAT4/9/10!29!-8! -6! -4! -2! 0! 2! 4!Log (Irradiance, W m-2)!Log (Time, s)!Flow Cytometer!Sunlight!Sea Tech!PAM!Courtesy of JJ Cullen Each fluorometer has unique properties, even though they all work the same way…4/9/10!30!Variable Fluorescence!• Start with a pulse of weak light--this will cause weak (background) fluorescence and is called the probe flash 1!0!F!Time!Variable Fluorescence!• Turn the lights all the way up (actinic light) and you get maximum fluorescence, directly proportional to the # of functional chl molecules 1!0!F!Time!4/9/10!31!Variable Fluorescence!• Turn the lights all the way up (actinic light) and you get maximum fluorescence, directly proportional to the # of functional chl molecules