1. Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thbhttp://www.bio.vu.nl/thb/ More-reserves DEB-systems Marseille, 2007/12/20

2. Contents : Homeostasis Evolution of DEB systems Central metabolism Symbiogenesis Dynamic nutrient limitation Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thbhttp://www.bio.vu.nl/thb/ Marseille, 2007/12/20 More-reserves DEB-systems

3. Homeostasis strong homeostasis constant composition of pools (reserves/structures) generalized compounds, stoichiometric contraints on synthesis weak homeostasis constant composition of biomass during growth in constant environments determines reserve dynamics (in combination with strong homeostasis) structural homeostasis constant relative proportions during growth in constant environments isomorphy.work load allocation ectothermy  homeothermy  endothermy supply  demand systems development of sensors, behavioural adaptations

4. Evolution of DEB systems variable structure composition strong homeostasis for structure delay of use of internal substrates increase of maintenance costs inernalization of maintenance installation of maturation program strong homeostasis for reserve reproduction juvenile  embryo + adult Kooijman & Troost 2007 Biol Rev, 82, 1-30 543 21 specialization of structure 7 8 animals 6 prokaryotes 9 plants

5. Central Metabolism 2.5 polymers monomers waste/source source

6. Pentose Phosphate (PP) cycle glucose-6-P ribulose-6-P, NADP NADPH Glycolysis glucose-6-P pyruvate ADP + P ATP TriCarboxcyl Acid (TCA) cycle pyruvate CO 2 NADP NADPH Respiratory chain NADPH + O 2 NADP + H 2 O ADP + P ATP Modules of central metabolism 2.5

7. Evolution of central metabolism 2.5 i = inverse ACS = acetyl-CoA Synthase pathway PP = Pentose Phosphate cycle TCA = TriCarboxylic Acid cycle RC = Respiratory Chain Gly = Glycolysis in prokaryotes (= bacteria) 3.8 Ga2.7 Ga Kooijman & Troost 2007 Biol Rev, 82, 1-30

8. Prokaryotic metabolic evolution 2.5 Chemolithotrophy acetyl-CoA pathway inverse TCA cycle inverse glycolysis Phototrophy: el. transport chain PS I & PS II Calvin cycle Heterotrophy: pentose phosph cycle glycolysis respiration chain

9. Symbiogenesis 2.5 2.7 Ga2.1 Ga 1.27 Ga phagocytosis

10. Symbiosis 9.1.3 product substrate

11. Symbiosis 9.1.3 substrate

12. Internalization Structures merge Reserves merge Free-living, clustering Free-living, homogeneous Steps in symbiogenesis 9.1.3

13. throughput rate Chemostat Steady States 9.1.3 biomass density host symbiont Free living Products substitutable Free living Products complementary Endosymbiosis Exchange on conc-basis Exchange on flux-basisStructures mergedReserves merged Host uses 2 substrates

14. Symbiogenesis 9.1.3 symbioses: fundamental organization of life based on syntrophy ranges from weak to strong interactions; basis of biodiversity symbiogenesis: evolution of eukaryotes (mitochondria, plastids) DEB model is closed under symbiogenesis: it is possible to model symbiogenesis of two initially independently living populations that follow the DEB rules by incremental changes of parameter values such that a single population emerges that again follows the DEB rules essential property for models that apply to all organisms Kooijman, Auger, Poggiale, Kooi 2003 Quantitative steps in symbiogenesis and the evolution of homeostasis Biological Reviews 78: 435 - 463

15. Maintenance from reserve & structure Tolla et al 2007 J. Theor Biol, 244, 576-587

16. Multiple reserves imply excretion

17. DEBtool/alga/sgr sgr1, sgr2, sgr3, sgr4 The functions obtain the specific growth rate, the reserve and structure fluxes for maintenance and the rejected reserve fluxes for 1, 2, 3 and 4 reserve systems. All reserves are supplementary for maintenance as well as for growth, while each reserve and structure are substitutable for maintenance. The preference for the use of structure relative to that of reserve for maintenance can be set with a (non-negative) preference parameter. The value zero gives absolute priority to reserve, which gives a switch at specific growth rate 0. All functions sgr have the same structure, and the input/output is presented for sgri where i takes values 1, 2, 3 of 4. Inputs: (i,1)-matrix with reserve density m E (i,1)-matrix with reserve turnover rate k E (i,1)-matrix with specific maintenance costs from reserve j EM (i,1)-matrix with costs for structure y EV optional (i,1)-matrix with specific maintenance costs from structure j VM ; default is j EM / y EV optional scalar or (i,1)-matrix with preference parameter alpha; default is 0 Outputs: scalar with specific growth rate r (i,1)-matrix with reserve flux for maintenance j EM (i,1)-matrix with structure flux for maintenance j VM M (i,1)-matrix with rejected reserve flux j ER scalar with info on failure (0) or success (1) of numerical procedure An example of use is given in mydata_sgr

18. Organic carbon pump 9.4 Wind: weakmoderate strong light + CO 2 “warm” no nutrients cold nutrients no light readily degradable poorly degradable no growth growthpoor growth bloom producers bind CO 2 from atmosphere and transport organic carbon to deep ocean recovery of nutrients to photo-zone controls pump

19. Reserve Capacity & Growth 5.2 low turnover rate: large reserve capacity high turnover rate: small reserve capacity

20. Simultaneous nutrient limitation 5.2.3 Specific growth rate of Pavlova lutheri as function of intracellular phosphorus and vitamine B 12 at 20 ºC Data from Droop 1974 Note the absence of high contents for both compounds due to damming up of reserves, and low contents in structure (at zero growth)

21. Reserve interactions 5.2.4 Spec growth rate, d -1 P-content, fmol.cell -1 P-conc, μM B 12 -conc, pM B 12 -cont., 10 -21.mol.cell -1 PVitamin B 12 kEkE 1.191.22 d -1 y XV 0.39 10 - 15 2.35 mol.cell -1 j EAm 4.91 10 - 21 76.6 10 -15 mol.cell -1. d -1 κEκE 0.690.96 kMkM 0.00790.135 d -1 K0.0170.12 pM, μM Data from Droop 1974 on Pavlova lutheri P(μM)B 12 (pM) 1.4468 14.46.8 1.4420.4 1.446.8

22. C,N,P-limitation 5.2.4 Nannochloropsis gaditana (Eugstimatophyta) in sea water Data from Carmen Garrido Perez Reductions by factor 1/3 starting from 24.7 mM NO 3, 1.99 mM PO 4 N,P reductions N reductions P reductions

23. C,N,P-limitation 5.2.4 Nannochloropsis gaditana in sea water For DIC nitrate phosphate res. dens. structure uptake rate spec growth rate spec growth

24. C,N,P-limitation 5.2.4 half-saturation parameters K C = 1.810 mM for uptake of CO 2 K N = 3.186 mM for uptake of NO 3 K P = 0.905 mM for uptake of PO 4 max. specific uptake rate parameters j Cm = 0.046 mM/OD.h, spec uptake of CO 2 j Nm = 0.080 mM/OD.h, spec uptake of NO 3 j Pm = 0.025 mM/OD.h, spec uptake of PO 4 reserve turnover rate k E = 0.034 h -1 yield coefficients y CV = 0.218 mM/OD, from C-res. to structure y NV = 2.261 mM/OD, from N-res. to structure y PV = 0.159 mM/OD, from P-res. to structure carbon species exchange rate (fixed) k BC = 0.729 h -1 from HCO 3 - to CO 2 k CB = 79.5 h -1 from CO 2 to HCO 3 - initial conditions (fixed) HCO 3 - (0) = 1.89534 mM, initial HCO 3 - concentration CO 2 (0) = 0.02038 mM, initial CO 2 concentration m C (0) = j Cm / k E mM/OD, initial C-reserve density m N (0) = j Nm / k E mM/OD, initial N-reserve density m P (0) = j Pm / k E mM/OD, initial P-reserve density OD(0) = 0.210 initial biomass (free) Nannochloropsis gaditana in sea water

25. Fast/slow substrate uptake DEB-consistent variant of Morel 1987 uptake depends on substrate concentration and reserve density reserve mobilization independent of uptake Not yet tested against experimental data

26. DEB tele course 2009 http://www.bio.vu.nl/thb/deb/ Free of financial costs; some 250 h effort investment Program for 2009: Feb/Mar general theory April symposium in Brest (2-3 d) Sept/Oct case studies & applications Target audience: PhD students We encourage participation in groups who organize local meetings weekly Software package DEBtool for Octave/ Matlab freely downloadable Slides of this presentation are downloadable from http://www.bio.vu.nl/thb/users/bas/lectures/ Cambridge Univ Press 2000 Audience : thank you for your attention Organizers : thank you for the invitation