1. Primary productivity and optics 19 July 2007 A primary productivity primer No answers; rather the “basics” – so you can ask better questions or build your own model Note: PP = primary productivity

2. Global annual estimates of PP: Schroeder (1919)speculation22 Pg C y -1 Steemann Nielsen (1952) 14C20 Pg C y -1 Koblentz- Mishke (1968)14C & mapping23 Pg C y -1 Behrenfeld (2002)SeaWiFS & 14C41 Pg C y -1 from Søndergaard in Williams, 2002

3. Ryther (1956) L&O 1:61 classic empirical relationship between light field and chlorophyll concentration A preliminary method is described for estimating absolute daily photosynthesis beneath a square meter of sea surface from measurement of (1)photosynthesis of a sample at light saturation, (2)extinction coefficient of light in the water, and (3)daily surface radiation.

4. Productivity – something created (units) per time per something (per individual, per chl molecule, etc.) Primary producer – entity that creates something Secondary producer – entity that transforms or repackages something

5. Primary Productivity in the ocean * background: life in ocean is – C – C – based, both for energy and structure (lipids, protein, etc.) * who are 1 º producers? phytoplankton in broadest sense (oxygenic, oxygen-evolving, single-celled organisms) in ocean and green plants on land; also deep biosphere * what is PP? PP is synthesis of new organic C (from CO 2 ), either by photosynthesis or by chemolithotrophy (oxidation of a reduced chemical, like Fe +2, by some bacteria and archeae) * what is photosynthesis? CO 2 + H 2 O ----> – (CH 2 O – ) + O 2

6. * what is photosynthesis? really a whole series of steps: Initial step: capture of light by PS pigments; electron goes to excited state; transfer of the exciton (energy but not electron) from one molecule to another, ultimately to “reaction center” for charge separation and transfer of energized electron to a primary electron acceptor, Q. Lost chlorophyll electron is replenished by splitting water apart (forming H + and O 2 ).

7. Intermediate steps: series of redox reactions (Z scheme) leading to generation of ATP and NADPH + –> that can be used by a number of reactions, including CO 2 reduction.

8. * what is photosynthesis? really a whole series of steps: Initial step: capture of light by PS pigments; electron goes to excited state; transfer of the exciton (energy but not electron) from one molecule to another, ultimately to “reaction center” for charge separation and transfer of energized electron to a primary electron acceptor, Q. Lost chlorophyll electron is replenished by splitting water apart (forming H + and O 2 ). Intermediate steps: series of redox reactions (Z scheme) leading to generation of ATP and NADPH + –> that can be used by a number of reactions, including CO 2 reduction. Alternative final steps: C reduction via Calvin cycle (primer reaction that reduces CO 2 and makes a C–C bond ), or NO 3 - reduction, synthesis of other compounds like energy rich lipids, etc.

9. 1. photon absorption by chlorophyll & accessory pigment 2. excitation transfer to reaction center 3. transmembrane charge separation to electron acceptor (plastoquinone or pre-ferrodoxin) 4a. electron transport leading to NADPH & P700 + 4b. H+ gradient leading to ATP production 5. H 2 O splitting at PS II to regenerate electrons; O 2 is by-product 6. ATP, NADPH used to reduce CO 2, NO 3 -, etc. Summary of Photosynthesis

10. http://www.bio.ic.ac.uk/research/barber/index.html

11. Summary: carbon fixation into new – C – is typically referred to as PP Method question: should O 2 production = – C – fixation (CO 2 reduction)? which variable was basis for the PP model? for testing model? photosynthetic quotient = O 2 evolved (range ~ 1.0 – 1.6) C reduced Optics question: what is relationship between rate of light absorption and rate of CO 2 reduction?  PS = moles carbon fixed. moles photons absorbed 8 to 10 photons required to fix one – C – ; if all photons went to PS,  PS = 0.12 or 0.10 (theoretical  PS – MAX ); actually lower because of alternatives for absorbed photons –– > fluorescence & heat

12. But, several variants to the PP concept: * Gross – total amount of new C (your theoretical paycheck) * Net – amount of new C remaining after autotrophic energy requirements are met (after taxes & living expenses); this C is what is available to 2 º producers and C-flux * Community net – amount of new C remaining after heterotrophs consume some of it (your savings??) Which PP is the basis of the model parameters? Which PP is the desired model output?

13. What is integration period? hour? day? season? year? What ’ s the nature of the food web? microloop? diatom bloom? grossnetcommunity net But, several variants to the PP concept: * Gross – total amount of new C (your theoretical paycheck) * Net – amount of new C remaining after autotrophic energy requirements are met (after taxes & living expenses); this C is what is available to 2 º producers and C-flux * Community net – amount of new C remaining after heterotrophs consume some of it (your savings??)

14. grossnetcommunity net But, several variants to the PP concept: * Gross – total amount of new C (your theoretical paycheck) * Net – amount of new C remaining after autotrophic energy requirements are met (after taxes & living expenses); this C is what is available to 2 º producers and C-flux * Community net – amount of new C remaining after heterotrophs consume some of it (your savings??) What is integration period? hour? day? season? year? What ’ s the nature of the food web? microloop? diatom bloom?

15. Is there a difference in exportable or sequester-able C? grossnetcommunity netgrossnetcommunity net

16. 1. O 2 – Winkler (1888) method changes in light and dark bottles 2. CO 2 – pH sensitive dye, Hassuk (1888); not adapted for seawater until 1910’s reintroduced by Clayton and Byrne (1993) 3. 14 C method – 1952 Steeman Nielsen 4. Probe fluorometry (pump and probe, PAM, FRRF) terms for PS electron flow model # 1–3 require incubation; in situ, simulated in situ, P vs. E To make results transportable (i.e., applicable to other data sets; usage in models), need to normalize rates to biomass (typically, chlorophyll a concentration or absorption – a ps ) How do we measure rates of PS (photosynthesis)?

17. 1.Changes in O 2 in light/dark bottles (1916, Gran)  O 2 in light = PS – respiration  O 2 in dark = respiration PS = light – dark (note: “dark” is added back) (note: assumes dark respiration = light respiration) For low biomass, need long incubations. Williams new method more sensitive. Which term is gross PP? net PP? community net PP?

18. 2.Changes in CO 2 system; here as change in pH (remove CO 2, pH increases – carbonate buffer) Damariscotta River Estuary; Chlorophyll concentration ~ 3  g L -1 Does the change in pH reflect gross, net, community net PP?

19. 3. Radio-labeled 14 C incorporation (tracer method) – introduced by E. Steeman Nielsen in 1950 CO 2 + H 2 O ---> -(CH 2 O)- + O 2 12 HCO 3 - 12 C in new biomass 14 HCO 3 - 14 C in new biomass ~ Known concentration of 14 C Known total dissolved inorganic C - from salinity / alkalinity Measure 14 C in particulate (and dissolved) after incubation Calculate rate of production of new carbon

20. Patterns of 14 C results: surface photo inhibition variability in rates (normalized to Chl) compensation depth net PP = 0

21. Problems * dark bottle: subtract or not? (blank?  carboxylation may occur) * what does 14 C measure? gross PP, net PP, or in between? is “old” carbon respired for metabolic energy? short incubation - 14 C measures closer to gross PS long incubation - 14 C measures closer to net PS Other issues with 14 C * incubation – bottle conditions =/= ocean conditions (light level, grazing, nutrient flux, temperature, surfaces, etc.; damage to fragile organisms, including protozoan grazers) * duration (hours, dawn-to-dusk, 24 hours) * toxicity of 14 C stock, collection and incubation bottles * CaCO 3 of coccoliths (acidify) * dissolved organic carbon (lost through filter)

22. 4. Probe fluorometry (pump and probe, PAM, FRRF) terms for PS electron flow model Advantages: little or no incubation (light or dark adapted) can be in situ Is it gross, net, or community net? What is the basis of the “calibration” data set?

23. Alternative ways to measure rates of PP (other than PS)? production of new cellular biomass – change in cell number (FCM), need Lagrangian framework – change in biomass (in situ changes in beam c); dP = P o [  - g -s +/- a] dt Gordon Riley – cell cycling (% of cells in S, G2 phase); FDC empirical (maximal) growth rates as function of environment – upper limit to growth vs. temperature; vs. light empirical growth rates as function of physiological index – growth rate vs. internal nutrient cell quota – pigment/cell as function of growth irradiance, invert

24. P E model (P vs. E, P vs. I) P max E k = P max /  

25. Chlorophyll model -- primary productivity normalized to biomass, B, where B is typically chlorophyll P B = P B max [1 - e ] –(E * E K  ) E= irradiance units of  mole photon m -2 t -1 P B max  =  maximal, light-saturated photosynthetic rate normalized to chlorophyll concentration units of g C (g chl) -1 t -1  = slope of the P vs E cure units of g C (g chl) -1 t -1 (  mole photon m -2 t -1 ) -1 E K = P b max /  units of  mole photon m -2 t -1 

26. E k vs depth: photadaptation absorption cross section, from probe fluorescence

27. Bio-optical quantum yield model PS = a PS * E *  PS where  PS = moles product (C or O 2 ) from slope of PE curve) moles photons absorbed by PS pigments = a ps * E NOTE: a ps * E should be ( ) and  PS_MAX < 0.10 E  PS 0.1

28. What do you need to model PS bio-optically? Z PS = a PS * E *  PS P B = P B max [1 – exp–(E * E K -1 )] where “B” denotes Chl normalization

29. Behrenfeld, M., and P. Falkowski (1997). A consumer’s guide to phytoplankton primary productivity models. Limnology and Oceanography 42 (7), 1479–1491.

30. Carr et al. 2006 A comparison of global estimates of marine primary production from ocean color DSR II 53: 741 Third PP algorithm round robin (PPARR3) compares output from 24 models that estimate depth integrated primary production from satellite measurements of ocean color. Compare global PP fields corresponding to eight months of 1998 and 1999 using common input fields of PAR, SST, MLD and Chl. Global average PP varies by a factor of two among models. Models diverged most for the Southern Ocean, SST under 10 C, and chlorophyll concentration exceeding 1mg Chlm 3. Further progress in primary production modeling requires improved understanding of the effect of temperature on photosynthesis and better parameterization of the maximum photosynthetic rate.