Fig 1.
Supply and demand functions for leaf photosynthesis.
(a) Leaf photosynthesis—CO2 response curve as modelled with the FvCB model. (b) The intersection of the supply and demand curves of photosynthesis. The Photosyn function solves for Ci if gs, Vcmax, Jmax and Rd (and other parameters to the FvCB model) are known.
Table 1.
Main functions in the plantecophys package.
Fig 2.
Standard output from the fitaci function.
An is the net photosynthetic rate, Ci the intercellular CO2 concentration. Symbols are measurements, the black line the fitted FvCB model of photosynthesis. Colored lines indicate the two photosynthesis rates in the FvCB model. In the default mode, the fitaci function estimates Vcmax, Jmax and Rd from the fitted curve. Optionally, Rd is provided as an input, for example when it was measured separately. In this example, Vcmax was estimated as 46.8 (SE 1.47), Jmax was 105.2 (SE 1.36) and Rd was 1.3 (SE 0.24). Assumed parameters were Km = 1460 and Γ* = 64.8 (all in units of μmol m-2 s-1). The R2 of a regression of measured vs. fitted was 0.99.
Fig 3.
Response of An and Ci to combined changes in Tleaf and D.
(A) Lines are A-Ci curves simulated at a range of values for Tleaf. Symbols are the solutions of the coupled leaf gas exchange model, while also taking into account the correlation between D and Tleaf (based on an empirical relationship [35]: D = 0.000605*Tair2.39). Note that as Tleaf and D increase, Ci decreases. (B) The corresponding temperature optimum of An. Symbols are the same as in panel (A) but plotted against Tleaf.
Fig 4.
Visualization of the optimal model of stomatal conductance.
Provided we have an estimate of the 'cost of water' (λ, mol C mol H2O-1), stomata act to maximize photosynthesis minus transpiration. In (A), individual curves at a range of values for the vapour pressure deficit (D) are plots of A−λE as a function of Ci, demonstrating that an optimum Ci exists. The FARAO function finds this optimum numerically and calculates corresponding An and gs. The corresponding response of gs to D is shown in panel (B).
Fig 5.
Example application of the plantecophys package to A-Ci curves and spot gas exchange measurements on Eucalyptus delegatensis.
(A) Fitted A-Ci curves with one curve highlighted (B) Estimates of Jmax plotted against Vcmax, obtained from the fitted curves in panel (A). Solid line is a regression line (Jmax = 107.71 + 0.7 Vcmax, R2 = 0.36) with a 95% confidence interval for the mean. (C) Modelled (with the model of Medlyn et al. 2011) versus measured gs (p < 0.0001, R2 = 0.69). Measurements included a wide range of environmental conditions (PAR, Tleaf, D). In this example, only g1 was fit (estimate = 3.31, 95% CI = 3.15–3.47). (D) The predicted response of ITE (An / E) as a function of D from the fitted model in panel (C) (solid line), and the measurements from panel (C) when PAR > 1000.