Unpacking the Drivers of Diurnal Dynamics of Sun-Induced Chlorophyll Fluorescence (SIF): Canopy Structure, Plant Physiology, Instrument Configuration and Retrieval Methods

Sun-induced chlorophyll fluorescence (SIF) from satellites is a promising tool for monitoring regional crop productivity, but its application is constrained by insufficient understanding of the diurnal dynamics of SIF. Ground-based SIF data can reveal diurnal SIF dynamics across biomes and environmental conditions; yet, meaningful interpretation requires disentangling impacts from canopy structure, plant physiology, instrument configuration and retrieval methods, which often interact and may confound each other. We unpacked these drivers using 1) concurrent canopy- and leaf-scale measurements at an agricultural corn field; 2) a mechanistic SIF model that explicitly considers the dynamics of photochemistry (via the fraction of open photosystem II reaction centers, qL), photoprotection (via nonphotochemical quenching, NPQ), and their interactive dependence on sub-canopy light; and 3) cross-comparison of SIF instrument configuration and retrieval methods. We found that combinations of crop row orientations and sun angles can cause a distinctive midday dip in SIF in absence of stress, due to a midday drop of absorbed photosynthetically active radiation (APAR) when crop rows are north-south oriented. This influenced sub-canopy qL and NPQ at different points within the vertical canopy that affected fluorescence quantum yield (F) at the leaf scale. Once integrated at the canopy scale, diurnal dynamics of both APAR and canopy escape probability () are critical for accurately shaping diurnal SIF. While sub-canopy qL and NPQ exhibited strong diurnal dynamics at the leaf level, their influence was attenuated at the canopy scale due to opposing effects on SIF at different canopy layers. Different system configurations and retrieval methods can also affect magnitude and diurnal shape of SIF, thus confounding the interpreted strength and dynamics of SIF emission. Our findings show the importance of crop rows, interactive variations in canopy structure and plant physiology, instrument configuration, and retrieval method in shaping measured diurnal SIF dynamics. This study highlights the necessity to account for these factors to accurately upscale satellite SIF from instantaneous to daily integrals and informs future synthesis work with different SIF instrumentation and retrieval methods across sites.