A model and measurement comparison of diurnal cycles of sun-induced chlorophyll fluorescence of crops

In this study, measurements of solar induced chlorophyll fluorescence (SIF) at 760nm (F₇₆₀) are combined with hyperspectral reflectance (R) measurements collected in the field over agricultural crops in order to better understand the fluorescence (ChlF) signal of the vegetation. The ‘Soil-Canopy Observation Photosynthesis and Energy fluxes' (SCOPE) model, which combines radiative transfer and enzyme kinetics of photosynthesis with turbulent heat exchange in vegetation canopies, was partly inverted to obtain model parameters from R taken over healthy (unstressed) crops during the growing season. Reflectance spectra between 400 and 900nm obtained at midday on different days in the growing season were used to obtain pigment concentrations, leaf area index and leaf inclination. These parameters were then used to simulate diurnal cycles of half-hourly ChlF spectra, using measured weather variables as input. Three scenarios were simulated: (i) a constant emission efficiency of ChlF (at the photosystem level), (ii) a variable emission efficiency calculated per half hour with an electron transport, photosynthesis and ChlF model for the photosystem, and (iii) a constant emission efficiency that was set to a theoretical maximum value for fully blocked photochemical electron transport of photosystem II and minimal non-photochemical quenching. The simulations of the first two scenarios were compared to ChlF retrieved from field measurements in the O₂-A band with the spectral fitting method in unstressed rice and alfalfa. This comparison and a sensitivity analysis showed that SCOPE reproduces most of the seasonal variability of SIF after tuning to R even if the ChlF emission efficiency is kept constant, and F₇₆₀ values are mostly determined by chlorophyll content, dry matter, senescent material and leaf area and leaf inclination, whereas leaf water and carotenoid content had small effects. Diurnal variations in the ChlF emission efficiency at photosystem level were small in these crops. The simulations of the third scenario were compared to measurements of grass that was treated chemically to block electron transport and to provoke maximum ChlF. This comparison showed that the observed increase in F₇₆₀ can indeed be explained by a change in the ChlF emission efficiency at the photosystem level. It is concluded that hyperspectral reflectance and the ChlF signal together can reveal both the dynamics of vegetation structure and functioning.