The weekly cycle of photosynthesis in Europe reveals the negative impact of particulate pollution on ecosystem productivity.

Aerosols can affect photosynthesis through radiative perturbations such as scattering and absorbing solar radiation. This biophysical impact has been widely studied using field measurements, but the sign and magnitude at continental scales remain uncertain. Solar-induced fluorescence (SIF), emitted by chlorophyll, strongly correlates with photosynthesis. With recent advancements in Earth observation satellites, we leverage SIF observations from the Tropospheric Monitoring Instrument (TROPOMI) with unprecedented spatial resolution and near-daily global coverage, to investigate the impact of aerosols on photosynthesis. Our analysis reveals that on weekends when there is more plant-available sunlight due to less particulate pollution, 64% of regions across Europe show increased SIF, indicating more photosynthesis. Moreover, we find a widespread negative relationship between SIF and aerosol loading across Europe. This suggests the possible reduction in photosynthesis as aerosol levels increase, particularly in ecosystems limited by light availability. By considering two plausible scenarios of improved air quality-reducing aerosol levels to the weekly minimum 3-d values and levels observed during the COVID-19 period-we estimate a potential of 41 to 50 Mt net additional annual CO2 uptake by terrestrial ecosystems in Europe. This work assesses human impacts on photosynthesis via aerosol pollution at continental scales using satellite observations. Our results highlight i) the use of spatiotemporal variations in satellite SIF to estimate the human impacts on photosynthesis and ii) the potential of reducing particulate pollution to enhance ecosystem productivity.

David (Dave) Charles Fork (1929-2020): a gentle human being, a great experimenter, and a passionate researcher.

We provide here an overview of the remarkable life and outstanding research of David (Dave) Charles Fork (March 4, 1929-December 13, 2021) in oxygenic photosynthesis. In the words of the late Jack Edgar Myers, he was a top 'photosynthetiker'. His research dealt with novel findings on light absorption, excitation energy distribution, and redistribution among the two photosystems, electron transfer, and their relation to dynamic membrane change as affected by environmental changes, especially temperature. David was an attentive listener and a creative designer of experiments and instruments, and he was also great fun to work with. He is remembered here by his family, coworkers, and friends from around the world including Australia, France, Germany, Japan, Sweden, Israel, and USA.

Leaf relative uptake of carbonyl sulfide to CO2 seen through the lens of stomatal conductance-photosynthesis coupling.

Carbonyl sulfide (COS) has emerged as a multi-scale tracer for terrestrial photosynthesis. To infer ecosystem-scale photosynthesis from COS fluxes often requires knowledge of leaf relative uptake (LRU), the concentration-normalized ratio between leaf COS uptake and photosynthesis. However, current mechanistic understanding of LRU variability remains inadequate for deriving robust COS-based estimates of photosynthesis. We derive a set of closed-form equations to describe LRU responses to light, humidity and CO2 based on the Ball-Berry stomatal conductance model and the biochemical model of photosynthesis. This framework reproduces observed LRU responses: decreasing LRU with increasing light or decreasing humidity; it also predicts that LRU increases with ambient CO2 . By fitting the LRU equations to flux measurements on a C3 reed (Typha latifolia), we obtain physiological parameters that control LRU variability, including an estimate of the Ball-Berry slope of 7.1 without using transpiration measurements. Sensitivity tests reveal that LRU is more sensitive to photosynthetic capacity than to the Ball-Berry slope, indicating stomatal response to photosynthesis. This study presents a simple framework for interpreting observed LRU variability and upscaling LRU. The stoma-regulated LRU response to CO2 suggests that COS may offer a unique window into long-term stomatal acclimation to elevated CO2 .

Representing plant diversity in land models: An evolutionary approach to make "Functional Types" more functional.

Plants are critical mediators of terrestrial mass and energy fluxes, and their structural and functional traits have profound impacts on local and global climate, biogeochemistry, biodiversity, and hydrology. Yet, Earth System Models (ESMs), our most powerful tools for predicting the effects of humans on the coupled biosphere-atmosphere system, simplify the incredible diversity of land plants into a handful of coarse categories of "Plant Functional Types" (PFTs) that often fail to capture ecological dynamics such as biome distributions. The inclusion of more realistic functional diversity is a recognized goal for ESMs, yet there is currently no consistent, widely accepted way to add diversity to models, that is, to determine what new PFTs to add and with what data to constrain their parameters. We review approaches to representing plant diversity in ESMs and draw on recent ecological and evolutionary findings to present an evolution-based functional type approach for further disaggregating functional diversity. Specifically, the prevalence of niche conservatism, or the tendency of closely related taxa to retain similar ecological and functional attributes through evolutionary time, reveals that evolutionary relatedness is a powerful framework for summarizing functional similarities and differences among plant types. We advocate that Plant Functional Types based on dominant evolutionary lineages ("Lineage Functional Types") will provide an ecologically defensible, tractable, and scalable framework for representing plant diversity in next-generation ESMs, with the potential to improve parameterization, process representation, and model benchmarking. We highlight how the importance of evolutionary history for plant function can unify the work of disparate fields to improve predictive modeling of the Earth system.

Quantifying high-temperature stress on soybean canopy photosynthesis: The unique role of sun-induced chlorophyll fluorescence.

High temperature and accompanying high vapor pressure deficit often stress plants without causing distinctive changes in plant canopy structure and consequential spectral signatures. Sun-induced chlorophyll fluorescence (SIF), because of its mechanistic link with photosynthesis, may better detect such stress than remote sensing techniques relying on spectral reflectance signatures of canopy structural changes. However, our understanding about physiological mechanisms of SIF and its unique potential for physiological stress detection remains less clear. In this study, we measured SIF at a high-temperature experiment, Temperature Free-Air Controlled Enhancement, to explore the potential of SIF for physiological investigations. The experiment provided a gradient of soybean canopy temperature with 1.5, 3.0, 4.5, and 6.0°C above the ambient canopy temperature in the open field environments. SIF yield, which is normalized by incident radiation and the fraction of absorbed photosynthetically active radiation, showed a high correlation with photosynthetic light use efficiency (r = 0.89) and captured dynamic plant responses to high-temperature conditions. SIF yield was affected by canopy structural and plant physiological changes associated with high-temperature stress (partial correlation r = 0.60 and -0.23). Near-infrared reflectance of vegetation, only affected by canopy structural changes, was used to minimize the canopy structural impact on SIF yield and to retrieve physiological SIF yield (ΦF ) signals. ΦF further excludes the canopy structural impact than SIF yield and indicates plant physiological variability, and we found that ΦF outperformed SIF yield in responding to physiological stress (r = -0.37). Our findings highlight that ΦF sensitively responded to the physiological downregulation of soybean gross primary productivity under high temperature. ΦF , if reliably derived from satellite SIF, can support monitoring regional crop growth and different ecosystems' vegetation productivity under environmental stress and climate change.

Potential of hotspot solar-induced chlorophyll fluorescence for better tracking terrestrial photosynthesis.

Remote sensing of solar-induced fluorescence (SIF) opens a new window for quantifying a key ecological variable, the terrestrial ecosystem gross primary production (GPP), because of the revealed strong SIF-GPP correlation. However, similar to many other remotely sensed metrics, SIF observations suffer from the sun-sensor geometry effects, which may have important impacts on the SIF-GPP relationship but remain poorly understood. Here we used remotely sensed SIF, globally distributed tower GPP data, and a mechanistic model to provide a systematic analysis. Our results reveal that leaf physiology, canopy structure, and sun-sensor geometries all affect the SIF-GPP relationship. In particular, we found that SIF observations in the sun-tracking hotspot direction can be a better proxy of GPP due to the similar responses of light use efficiency and SIF escaping probability in the hotspot direction to the increasing incoming solar radiation. Such conclusions are supported by a variety of modeling simulations and satellite observations over various plant function types, at different time scales and with satellite observational modes. This study demonstrates the potential and advantage of normalizing SIF observations to the hotspot direction for better global GPP estimations. This study also demonstrates the great potentials of current and future spaceborne sun-tracking satellite missions for a significant improvement in measuring and monitoring, at a wide range of spatial and temporal scales, the changes in terrestrial ecosystem GPP in response to anticipated changes in the Earth's environmental conditions.

The limiting factors and regulatory processes that control the environmental responses of C3, C3-C4 intermediate, and C4 photosynthesis.

Here, we describe a model of C3, C3-C4 intermediate, and C4 photosynthesis that is designed to facilitate quantitative analysis of physiological measurements. The model relates the factors limiting electron transport and carbon metabolism, the regulatory processes that coordinate these metabolic domains, and the responses to light, carbon dioxide, and temperature. It has three unique features. First, mechanistic expressions describe how the cytochrome b6f complex controls electron transport in mesophyll and bundle sheath chloroplasts. Second, the coupling between the mesophyll and bundle sheath expressions represents how feedback regulation of Cyt b6f coordinates electron transport and carbon metabolism. Third, the temperature sensitivity of Cyt b6f is differentiated from that of the coupling between NADPH, Fd, and ATP production. Using this model, we present simulations demonstrating that the light dependence of the carbon dioxide compensation point in C3-C4 leaves can be explained by co-occurrence of light saturation in the mesophyll and light limitation in the bundle sheath. We also present inversions demonstrating that population-level variation in the carbon dioxide compensation point in a Type I C3-C4 plant, Flaveria chloraefolia, can be explained by variable allocation of photosynthetic capacity to the bundle sheath. These results suggest that Type I C3-C4 intermediate plants adjust pigment and protein distributions to optimize the glycine shuttle under different light and temperature regimes, and that the malate and aspartate shuttles may have originally functioned to smooth out the energy supply and demand associated with the glycine shuttle. This model has a wide range of potential applications to physiological, ecological, and evolutionary questions.

Terrestrial gross primary production: Using NIRV to scale from site to globe.

Terrestrial photosynthesis is the largest and one of the most uncertain fluxes in the global carbon cycle. We find that near-infrared reflectance of vegetation (NIRV ), a remotely sensed measure of canopy structure, accurately predicts photosynthesis at FLUXNET validation sites at monthly to annual timescales (R2  = 0.68), without the need for difficult to acquire information about environmental factors that constrain photosynthesis at short timescales. Scaling the relationship between gross primary production (GPP) and NIRV from FLUXNET eddy covariance sites, we estimate global annual terrestrial photosynthesis to be 147 Pg C/year (95% credible interval 131-163 Pg C/year), which falls between bottom-up GPP estimates and the top-down global constraint on GPP from oxygen isotopes. NIRV -derived estimates of GPP are systematically higher than existing bottom-up estimates, especially throughout the midlatitudes. Progress in improving estimated GPP from NIRV can come from improved cloud screening in satellite data and increased resolution of vegetation characteristics, especially details about plant photosynthetic pathway.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) in vegetation: 50 years of progress.

Remote sensing of solar-induced chlorophyll fluorescence (SIF) is a rapidly advancing front in terrestrial vegetation science, with emerging capability in space-based methodologies and diverse application prospects. Although remote sensing of SIF - especially from space - is seen as a contemporary new specialty for terrestrial plants, it is founded upon a multi-decadal history of research, applications, and sensor developments in active and passive sensing of chlorophyll fluorescence. Current technical capabilities allow SIF to be measured across a range of biological, spatial, and temporal scales. As an optical signal, SIF may be assessed remotely using highly-resolved spectral sensors and state-of-the-art algorithms to distinguish the emission from reflected and/or scattered ambient light. Because the red to far-red SIF emission is detectable non-invasively, it may be sampled repeatedly to acquire spatio-temporally explicit information about photosynthetic light responses and steady-state behaviour in vegetation. Progress in this field is accelerating with innovative sensor developments, retrieval methods, and modelling advances. This review distills the historical and current developments spanning the last several decades. It highlights SIF heritage and complementarity within the broader field of fluorescence science, the maturation of physiological and radiative transfer modelling, SIF signal retrieval strategies, techniques for field and airborne sensing, advances in satellite-based systems, and applications of these capabilities in evaluation of photosynthesis and stress effects. Progress, challenges, and future directions are considered for this unique avenue of remote sensing.

Comparing optimal and empirical stomatal conductance models for application in Earth system models.

Earth system models (ESMs) rely on the calculation of canopy conductance in land surface models (LSMs) to quantify the partitioning of land surface energy, water, and CO2 fluxes. This is achieved by scaling stomatal conductance, gw , determined from physiological models developed for leaves. Traditionally, models for gw have been semi-empirical, combining physiological functions with empirically determined calibration constants. More recently, optimization theory has been applied to model gw in LSMs under the premise that it has a stronger grounding in physiological theory and might ultimately lead to improved predictive accuracy. However, this premise has not been thoroughly tested. Using original field data from contrasting forest systems, we compare a widely used empirical type and a more recently developed optimization-type gw model, termed BB and MED, respectively. Overall, we find no difference between the two models when used to simulate gw from photosynthesis data, or leaf gas exchange from a coupled photosynthesis-conductance model, or gross primary productivity and evapotranspiration for a FLUXNET tower site with the CLM5 community LSM. Field measurements reveal that the key fitted parameters for BB and MED, g1B and g1M, exhibit strong species specificity in magnitude and sensitivity to CO2 , and CLM5 simulations reveal that failure to include this sensitivity can result in significant overestimates of evapotranspiration for high-CO2 scenarios. Further, we show that g1B and g1M can be determined from mean ci /ca (ratio of leaf intercellular to ambient CO2 concentration). Applying this relationship with ci /ca values derived from a leaf δ13 C database, we obtain a global distribution of g1B and g1M , and these values correlate significantly with mean annual precipitation. This provides a new methodology for global parameterization of the BB and MED models in LSMs, tied directly to leaf physiology but unconstrained by spatial boundaries separating designated biomes or plant functional types.

Seasonal fluxes of carbonyl sulfide in a midlatitude forest.

Carbonyl sulfide (OCS), the most abundant sulfur gas in the atmosphere, has a summer minimum associated with uptake by vegetation and soils, closely correlated with CO2. We report the first direct measurements to our knowledge of the ecosystem flux of OCS throughout an annual cycle, at a mixed temperate forest. The forest took up OCS during most of the growing season with an overall uptake of 1.36 ± 0.01 mol OCS per ha (43.5 ± 0.5 g S per ha, 95% confidence intervals) for the year. Daytime fluxes accounted for 72% of total uptake. Both soils and incompletely closed stomata in the canopy contributed to nighttime fluxes. Unexpected net OCS emission occurred during the warmest weeks in summer. Many requirements necessary to use fluxes of OCS as a simple estimate of photosynthesis were not met because OCS fluxes did not have a constant relationship with photosynthesis throughout an entire day or over the entire year. However, OCS fluxes provide a direct measure of ecosystem-scale stomatal conductance and mesophyll function, without relying on measures of soil evaporation or leaf temperature, and reveal previously unseen heterogeneity of forest canopy processes. Observations of OCS flux provide powerful, independent means to test and refine land surface and carbon cycle models at the ecosystem scale.

Disruption of stomatal lineage signaling or transcriptional regulators has differential effects on mesophyll development, but maintains coordination of gas exchange.

Stomata are simultaneously tasked with permitting the uptake of carbon dioxide for photosynthesis while limiting water loss from the plant. This process is mainly regulated by guard cell control of the stomatal aperture, but recent advancements have highlighted the importance of several genes that control stomatal development. Using targeted genetic manipulations of the stomatal lineage and a combination of gas exchange and microscopy techniques, we show that changes in stomatal development of the epidermal layer lead to coupled changes in the underlying mesophyll tissues. This coordinated response tends to match leaf photosynthetic potential (Vcmax ) with gas-exchange capacity (gsmax ), and hence the uptake of carbon dioxide for water lost. We found that different genetic regulators systematically altered tissue coordination in separate ways: the transcription factor SPEECHLESS (SPCH) primarily affected leaf size and thickness, whereas peptides in the EPIDERMAL PATTERNING FACTOR (EPF) family altered cell density in the mesophyll. It was also determined that interlayer coordination required the cell-surface receptor TOO MANY MOUTHS (TMM). These results demonstrate that stomata-specific regulators can alter mesophyll properties, which provides insight into how molecular pathways can organize leaf tissues to coordinate gas exchange and suggests new strategies for improving plant water-use efficiency.

Sources and sinks of carbonyl sulfide in an agricultural field in the Southern Great Plains.

Net photosynthesis is the largest single flux in the global carbon cycle, but controls over its variability are poorly understood because there is no direct way of measuring it at the ecosystem scale. We report observations of ecosystem carbonyl sulfide (COS) and CO2 fluxes that resolve key gaps in an emerging framework for using concurrent COS and CO2 measurements to quantify terrestrial gross primary productivity. At a wheat field in Oklahoma we found that in the peak growing season the flux-weighted leaf relative uptake of COS and CO2 during photosynthesis was 1.3, at the lower end of values from laboratory studies, and varied systematically with light. Due to nocturnal stomatal conductance, COS uptake by vegetation continued at night, contributing a large fraction (29%) of daily net ecosystem COS fluxes. In comparison, the contribution of soil fluxes was small (1-6%) during the peak growing season. Upland soils are usually considered sinks of COS. In contrast, the well-aerated soil at the site switched from COS uptake to emissions at a soil temperature of around 15 °C. We observed COS production from the roots of wheat and other species and COS uptake by root-free soil up to a soil temperature of around 25 °C. Our dataset demonstrates that vegetation uptake is the dominant ecosystem COS flux in the peak growing season, providing support of COS as an independent tracer of terrestrial photosynthesis. However, the observation that ecosystems may become a COS source at high temperature needs to be considered in global modeling studies.

Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence.

Photosynthesis is the process by which plants harvest sunlight to produce sugars from carbon dioxide and water. It is the primary source of energy for all life on Earth; hence it is important to understand how this process responds to climate change and human impact. However, model-based estimates of gross primary production (GPP, output from photosynthesis) are highly uncertain, in particular over heavily managed agricultural areas. Recent advances in spectroscopy enable the space-based monitoring of sun-induced chlorophyll fluorescence (SIF) from terrestrial plants. Here we demonstrate that spaceborne SIF retrievals provide a direct measure of the GPP of cropland and grassland ecosystems. Such a strong link with crop photosynthesis is not evident for traditional remotely sensed vegetation indices, nor for more complex carbon cycle models. We use SIF observations to provide a global perspective on agricultural productivity. Our SIF-based crop GPP estimates are 50-75% higher than results from state-of-the-art carbon cycle models over, for example, the US Corn Belt and the Indo-Gangetic Plain, implying that current models severely underestimate the role of management. Our results indicate that SIF data can help us improve our global models for more accurate projections of agricultural productivity and climate impact on crop yields. Extension of our approach to other ecosystems, along with increased observational capabilities for SIF in the near future, holds the prospect of reducing uncertainties in the modeling of the current and future carbon cycle.

Improving the monitoring of crop productivity using spaceborne solar-induced fluorescence.

Large-scale monitoring of crop growth and yield has important value for forecasting food production and prices and ensuring regional food security. A newly emerging satellite retrieval, solar-induced fluorescence (SIF) of chlorophyll, provides for the first time a direct measurement related to plant photosynthetic activity (i.e. electron transport rate). Here, we provide a framework to link SIF retrievals and crop yield, accounting for stoichiometry, photosynthetic pathways, and respiration losses. We apply this framework to estimate United States crop productivity for 2007-2012, where we use the spaceborne SIF retrievals from the Global Ozone Monitoring Experiment-2 satellite, benchmarked with county-level crop yield statistics, and compare it with various traditional crop monitoring approaches. We find that a SIF-based approach accounting for photosynthetic pathways (i.e. C3 and C4 crops) provides the best measure of crop productivity among these approaches, despite the fact that SIF sensors are not yet optimized for terrestrial applications. We further show that SIF provides the ability to infer the impacts of environmental stresses on autotrophic respiration and carbon-use-efficiency, with a substantial sensitivity of both to high temperatures. These results indicate new opportunities for improved mechanistic understanding of crop yield responses to climate variability and change.

Simulations of chlorophyll fluorescence incorporated into the Community Land Model version 4.

Several studies have shown that satellite retrievals of solar-induced chlorophyll fluorescence (SIF) provide useful information on terrestrial photosynthesis or gross primary production (GPP). Here, we have incorporated equations coupling SIF to photosynthesis in a land surface model, the National Center for Atmospheric Research Community Land Model version 4 (NCAR CLM4), and have demonstrated its use as a diagnostic tool for evaluating the calculation of photosynthesis, a key process in a land surface model that strongly influences the carbon, water, and energy cycles. By comparing forward simulations of SIF, essentially as a byproduct of photosynthesis, in CLM4 with observations of actual SIF, it is possible to check whether the model is accurately representing photosynthesis and the processes coupled to it. We provide some background on how SIF is coupled to photosynthesis, describe how SIF was incorporated into CLM4, and demonstrate that our simulated relationship between SIF and GPP values are reasonable when compared with satellite (Greenhouse gases Observing SATellite; GOSAT) and in situ flux-tower measurements. CLM4 overestimates SIF in tropical forests, and we show that this error can be corrected by adjusting the maximum carboxylation rate (Vmax ) specified for tropical forests in CLM4. Our study confirms that SIF has the potential to improve photosynthesis simulation and thereby can play a critical role in improving land surface and carbon cycle models.

The roles of hydraulic and carbon stress in a widespread climate-induced forest die-off.

Forest ecosystems store approximately 45% of the carbon found in terrestrial ecosystems, but they are sensitive to climate-induced dieback. Forest die-off constitutes a large uncertainty in projections of climate impacts on terrestrial ecosystems, climate-ecosystem interactions, and carbon-cycle feedbacks. Current understanding of the physiological mechanisms mediating climate-induced forest mortality limits the ability to model or project these threshold events. We report here a direct and in situ study of the mechanisms underlying recent widespread and climate-induced trembling aspen (Populus tremuloides) forest mortality in western North America. We find substantial evidence of hydraulic failure of roots and branches linked to landscape patterns of canopy and root mortality in this species. On the contrary, we find no evidence that drought stress led to depletion of carbohydrate reserves. Our results illuminate proximate mechanisms underpinning recent aspen forest mortality and provide guidance for understanding and projecting forest die-offs under climate change.

The physiological importance of developmental mechanisms that enforce proper stomatal spacing in Arabidopsis thaliana.

• Genetic and cell biological mechanisms that regulate stomatal development are necessary to generate an appropriate number of stomata and enforce a minimum spacing of one epidermal cell between stomata. The ability to manipulate these processes in a model plant system allows us to investigate the physiological importance of stomatal patterning and changes in density, therein testing underlying theories about stomatal biology. • Twelve Arabidopsis thaliana genotypes that have varied stomatal characteristics as a result of mutations or transgenes were analyzed in this study. Stomatal traits were used to categorize the genotypes and predict maximum stomatal conductance to water vapor (Anatomical g(smax)) for individuals. Leaf-level gas-exchange measurements determined Diffusive g(smax), net carbon assimilation (A), water-use efficiency (WUE), and stomatal responses to increasing CO2 concentration. Genotypes with proper spacing (< 5% of stomata in clusters) achieved Diffusive g(smax) values comparable to Anatomical g(smax) across a 10-fold increase in stomatal density, while lines with patterning defects (> 19% clustering) did not. • Genotypes with clustering also had reduced A and impaired stomatal responses, while WUE was generally unaffected by patterning. • Consequently, optimal function per stoma was dependent on maintaining one epidermal cell spacing and the physiological parameters controlled by stomata were strongly correlated with Anatomical g(smax).

An integrated model of stomatal development and leaf physiology.

• Stomatal conductance (g(s)) is constrained by the size and number of stomata on the plant epidermis, and the potential maximum rate of g(s) can be calculated based on these stomatal traits (Anatomical g(smax)). However, the relationship between Anatomical g(smax) and operational g(s) under atmospheric conditions remains undefined. • Leaf-level gas-exchange measurements were performed for six Arabidopsis thaliana genotypes that have different Anatomical g(smax) profiles resulting from mutations or transgene activity in stomatal development. • We found that Anatomical g(smax) was an accurate prediction of g(s) under gas-exchange conditions that maximized stomatal opening, namely high-intensity light, low [CO2], and high relative humidity. Plants with different Anatomical g(smax) had quantitatively similar responses to increasing [CO2] when g(s) was scaled to Anatomical g(smax). This latter relationship allowed us to produce and test an empirical model derived from the Ball-Woodrow-Berry equation that estimates g(s) as a function of Anatomical g(smax), relative humidity, and [CO2] at the leaf. • The capacity to predict operational g(s) via Anatomical g(smax) and the pore-specific short-term response to [CO2] demonstrates a precise link between stomatal development and leaf physiology. This connection should be useful to quantify the gas flux of plants in past, present, and future CO2 regimes based upon the anatomical features of stomata.

Linking chlorophyll a fluorescence to photosynthesis for remote sensing applications: mechanisms and challenges.

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.