Modelling and measurement of solar induced fluorescence in a boreal scots pine canopy

Terrestrial sun induced chlorophyll fluorescence (Fs) is emitted by chlorophyll molecules in the photosystems of higher plants. The signal originates from the photosynthetic machinery and is thus expected to respond to changes in environmental conditions such as light and physiological stress. This therefore makes Fs an attractive tool to provide insight into a plants photosynthetic performance over traditional reflectance based approaches utilised in vegetation remote sensing applications. A number of Fs retrieval methods from optical data have been documented and these share a common basis; that the fractional depth of the Fraunhofer lines decreases due to infilling by solar induced fluorescence (Fs). Here we presents results from two (linked) studies that demonstrates the challenge of retrieving Fs from, firstly, continuous irradiance and radiance measurements collected over a boreal canopy from a custom built continuously operating optical system, and secondly, we present a coupled physiological-radiative transfer model that predicts changes in the apparent reflectance of a leaf, due to chlorophyll fluorescence that occur on timescales of seconds to minutes. The biochemical model is based on a detailed model of the dynamics of the fate of absorbed light energy through photosystem II. The radiative transfer component is derived from empirically obtained fluorescence excitation-emission matrices and the PROSPECT leaf model. A Markov Chain Monte Carlo (MCMC) algorithm was used to optimise biochemical model parameters by fitting model simulations of transient chlorophyll fluorescence to measured reflectance spectra. The model successfully simulated the transient fluorescence decay curve and reproduced yield estimates for photochemical and non-photochemical quenching when validated against an independent data-set. The biochemical model is driven solely by incident radiation, to scale to the canopy and to use the model on trans-seasonal time scales the effects of temperature and photo-inhibition must be taken into account. We further present the strengths and weaknesses of retrieving Fs from field based radiance measurements in a strongly seasonal Scots pine canopy in boreal Finland, and explore the utility of Fs to track the seasonality in ecosystem photosynthetic light use efficiency and gross primary productivity.