Chlorophyll a fluorescence (ChlF) has been used for decades to study the organization, functioning, and physiology of photosynthesis at the leaf and subcellular levels. ChlF is now measurable from remote sensing platforms. This provides a new optical means to track photosynthesis and gross primary productivity of terrestrial ecosystems. Importantly, the spatiotemporal and methodological context of the new applications is dramatically different compared with most of the available ChlF literature, which raises a number of important considerations. Although we have a good mechanistic understanding of the processes that control the ChlF signal over the short term, the seasonal link between ChlF and photosynthesis remains obscure. Additionally, while the current understanding of in vivo ChlF is based on pulse amplitude-modulated (PAM) measurements, remote sensing applications are based on the measurement of the passive solar-induced chlorophyll fluorescence (SIF), which entails important differences and new challenges that remain to be solved. In this review we introduce and revisit the physical, physiological, and methodological factors that control the leaf-level ChlF signal in the context of the new remote sensing applications. Specifically, we present the basis of photosynthetic acclimation and its optical signals, we introduce the physical and physiological basis of ChlF from the molecular to the leaf level and beyond, and we introduce and compare PAM and SIF methodology. Finally, we evaluate and identify the challenges that still remain to be answered in order to consolidate our mechanistic understanding of the remotely sensed SIF signal.

INTRODUCTION: Reliable estimation of gross primary production (GPP) from landscape to global scales is pivotal to a wide range of ecological research areas, such as carbon-climate feedbacks, and agricultural applications, such as crop yield and drought monitoring. However, measuring GPP at these scales remains a major challenge. Solar-induced chlorophyll fluorescence (SIF) is a signal emitted directly from the core of photosynthetic machinery. SIF integrates complex plant physiological functions in vivo to reflect photosynthetic dynamics in real time. The advent of satellite SIF observation promises a new era in global photosynthesis research. The Orbiting Carbon Observatory-2 (OCO-2) SIF product is a serendipitous but critically complementary by-product of OCO-2’s primary mission target—atmospheric column CO ₂ ( X CO 2 ). OCO-2 SIF removes some important roadblocks that prevent wide and in-depth applications of satellite SIF data sets and offers new opportunities for studying the SIF-GPP relationship and vegetation functional gradients at different spatiotemporal scales. RATIONALE: Compared with earlier satellite missions with SIF capability, the OCO-2 SIF product has substantially improved spatial resolution, data acquisition, and retrieval precision. These improvements allow satellite SIF data to be validated, for the first time, directly against ground and airborne measurements and also used to investigate the SIF-GPP relationship and terrestrial ecosystem functional dynamics with considerably better spatiotemporal credibility. RESULTS: Coordinated airborne measurements of SIF with the Chlorophyll Fluorescence Imaging Spectrometer (CFIS) were used to validate OCO-2 retrievals. The validation shows close agreement between OCO-2 and CFIS SIF, with a regression slope of 1.02 and R ² of 0.71. Landscape gradients in SIF emission, corresponding to differences in vegetation types, were clearly delineated by OCO-2, a capability that was lacking in previous satellite missions. The SIF-GPP relationships at eddy covariance flux sites in the vicinity of OCO-2 orbital tracks were found to be more consistent across biomes than previously suggested. Finally, empirical orthogonal function (EOF) analyses on OCO-2 SIF and available GPP products show highly consistent spatiotemporal correspondence in their leading EOF modes across the globe, suggesting that SIF and GPP are governed by similar dynamics and controlled by similar environmental and biological conditions. CONCLUSION: OCO-2 represents a major advance in satellite SIF remote sensing. Our analyses suggest that SIF is a powerful proxy for GPP at multiple spatiotemporal scales and that high-quality satellite SIF is of central importance to studying terrestrial ecosystems and the carbon cycle. Although the possibility of a universal SIF-GPP relationship across different biome types cannot be dismissed, in-depth process-based studies are needed to unravel the true nature of covariations between SIF and GPP. Of critical importance in such efforts are the potential coordinated dynamics between the light-use efficiencies of CO ₂ assimilation and fluorescence emission in response to changes in climate and vegetation characteristics. Eventual synergistic uses of SIF with atmospheric CO ₂ enabled by OCO-2 will lead to more reliable estimates of terrestrial carbon sources and sinks—when, where, why, and how carbon is exchanged between land and atmosphere—as well as a deeper understanding of carbon-climate feedbacks. The marked ecological gradients depicted by OCO-2’s high-resolution SIF measurements along a transect of temperate deciduous forests, crops, and urban area from Indiana to suburban Chicago, Illinois.:

The Photochemical Reflectance Index (PRI), an index based on leaf reflectance at 531 nm, has been found suitable for tracking variations in photosynthetic activity from leaf to ecosystem levels. This suitability has been attributed to PRI correlation with xanthophyll interconversion and photosynthetic radiation-use efficiency. However, other pigments and factors may be involved in such relationships. We studied the relationship between PRI and xanthophylls and other carotenoids in saplings of two widely distributed evergreen species (Scots pine and Holm oak) submitted to experimentally changing light conditions in a field experiment. PRI was strongly correlated with the de-epoxidation state of xanthophylls (DEPS, an expression of the relative concentration of the three xanthophyll cycle pigments), but also with carotenoids/chlorophyll ratio and β-carotene/chlorophyll ratio in both species. However, following momentary decreases in light due to clouds, PRI changed following the DEPS changes, while the carotenoids/chlorophyll ratio remained constant. The results show that PRI was able to reveal short-term changes in de-epoxidation state, i.e. the signal of xanthophyll interconversion, but it also tracked long-term changes in carotenoids/chlorophyll. Carotenoids other than xanthophylls, e.g. β-carotene, are also related to photoprotective processes, thus also making PRI effective as a measure of changes in photosynthetic light-use efficiency in response to stress on a long-term level.

Sun-induced fluorescence in the far-red region (SIF) is increasingly used as a remote and proximal-sensing tool capable of tracking vegetation gross primary production (GPP). However, the use of SIF to probe changes in GPP is challenged during extreme climatic events, such as heatwaves. Here, we examined how the 2018 European heatwave (HW) affected the GPP-SIF relationship in evergreen broadleaved trees with a relatively invariant canopy structure. To do so, we combined canopy scale SIF measurements, GPP estimated from an eddy covariance tower, and active PAM fluorescence. The HW caused an inversion of the photosynthesis-fluorescence relationship at both the canopy and leaf scales. The highly nonlinear relationship was strongly shaped by nonphotochemical quenching (NPQ), i.e., a dissipation mechanism to protect from the adverse effects of high light intensity. During the extreme heat stress, plants experienced a saturation of NPQ, causing a change in the allocation of energy dissipation pathways towards SIF. Our results show the complex modulation of the NPQ-SIF-GPP relationship at an extreme level of heat stress, which is not completely represented in state-of-the-art coupled radiative transfer and photosynthesis models.