PhotoSpec: A new instrument to measure spatially distributed red and far-red Solar-Induced Chlorophyll Fluorescence

Solar-Induced Chlorophyll Fluorescence (SIF) is an emission of light in the 650–850 nm spectral range from the excited state of the chlorophyll-a pigment after absorption of photosynthetically active radiation (PAR). As this is directly linked to the electron transport chain in oxygenic photosynthesis, SIF is a powerful proxy for photosynthetic activity. SIF observations are relatively new and, while global scale measurements from satellites using high-resolution spectroscopy of Fraunhofer bands are becoming more available, observations at the intermediate canopy scale using these techniques are sparse. We present a novel ground-based spectrometer system - PhotoSpec - for measuring SIF in the red (670–732 nm) and far-red (729–784 nm) wavelength range as well as canopy reflectance (400–900 nm) to calculate vegetation indices, such as the normalized difference vegetation index (NDVI), the enhanced vegetation index (EVI), and the photochemical reflectance index (PRI). PhotoSpec includes a 2D scanning telescope unit which can be pointed to any location in a canopy with a narrow field of view (FOV = 0.7°). PhotoSpec has a high signal-to-noise ratio and spectral resolution, which allows high precision solar Fraunhofer line retrievals over the entire fluorescence wavelength range under all atmospheric conditions using a new two-step linearized least-squares retrieval procedure. Initial PhotoSpec observations include the diurnal SIF cycle of single broad leaves, grass, and dark-light transitions. Results from the first tower-based measurements in Costa Rica show that the instrument can continuously monitor SIF of several tropical species throughout the day. The PhotoSpec instrument can be used to explore the relationship between SIF, photosynthetic efficiencies, Gross Primary Productivity (GPP), and the impact of canopy radiative transfer, viewing geometry, and stress conditions at the canopy scale

Requirement of plakophilin 2 for heart morphogenesis and cardiac junction formation

Plakophilins are proteins of the armadillo family that function in embryonic development and in the adult, and when mutated can cause disease. We have ablated the plakophilin 2 gene in mice. The resulting mutant mice exhibit lethal alterations in heart morphogenesis and stability at mid-gestation (E10.5–E11), characterized by reduced trabeculation, disarrayed cytoskeleton, ruptures of cardiac walls, and blood leakage into the pericardiac cavity. In the absence of plakophilin 2, the cytoskeletal linker protein desmoplakin dissociates from the plaques of the adhering junctions that connect the cardiomyocytes and forms granular aggregates in the cytoplasm. By contrast, embryonic epithelia show normal junctions. Thus, we conclude that plakophilin 2 is important for the assembly of junctional proteins and represents an essential morphogenic factor and architectural component of the heart

Systematic Assessment of Retrieval Methods for Canopy Far-Red Solar-Induced Chlorophyll Fluorescence Using High-Frequency Automated Field Spectroscopy

Remote sensing of solar‐induced chlorophyll fluorescence (SIF) offers potential to infer photosynthesis across scales and biomes. Many retrieval methods have been developed to estimate top‐of‐canopy SIF using ground‐based spectroscopy. However, inconsistencies among methods may confound interpretation of SIF dynamics, eco‐physiological/environmental drivers, and its relationship with photosynthesis. Using high temporal‐ and spectral resolution ground‐based spectroscopy, we aimed to (1) evaluate performance of SIF retrieval methods under diverse sky conditions using continuous field measurements; (2) assess method sensitivity to fluctuating light, reflectance, and fluorescence emission spectra; and (3) inform users for optimal ground‐based SIF retrieval. Analysis included field measurements from bi‐hemispherical and hemispherical‐conical systems and synthetic upwelling radiance constructed from measured downwelling radiance, simulated reflectance, and simulated fluorescence for benchmarking. Fraunhofer‐based differential optical absorption spectroscopy (DOAS) and singular vector decomposition (SVD) retrievals exhibit convergent SIF‐PAR relationships and diurnal consistency across different sky conditions, while O₂A‐based spectral fitting method (SFM), SVD, and modified Fraunhofer line discrimination (3FLD) exhibit divergent SIF‐PAR relationships across sky conditions. Such behavior holds across system configurations, though hemispherical‐conical systems diverge less across sky conditions. O₂A retrieval accuracy, influenced by atmospheric distortion, improves with a narrower fitting window and when training SVD with temporally local spectra. This may impact SIF‐photosynthesis relationships interpreted by previous studies using O₂A‐based retrievals with standard (759–767.76 nm) fitting windows. Fraunhofer‐based retrievals resist atmospheric impacts but are noisier and more sensitive to assumed SIF spectral shape than O₂A‐based retrievals. We recommend SVD or SFM using reduced fitting window (759.5–761.5 nm) for robust far‐red SIF retrievals across sky conditions

Evidence of convective transport in tropical West Pacific region during SHIVA experiment

Air masses in the convective outflows of four large convective systems near Borneo Island in Malaysia were sampled in the height range 11–13 km within the frame of the SHIVA (Stratospheric Ozone: Halogen Impacts in a Varying Atmosphere) FP7 European project in November and December 2011. Correlated enhancements of CO, CH4 and the short-lived halogen species (CH3I and CHBr3) were detected when the aircraft crossed the anvils of the four systems. These enhancements were interpreted as the fingerprint of vertical transport from the boundary layer by the convective updraft and then horizontal advection in the outflow. For the four observations, the fraction f of air from the boundary layer ranged between 15 and 67%, showing the variability in transport efficiency depending on the dynamics of the convective system

From the Ground to Space: Using Solar-Induced Chlorophyll Fluorescence to Estimate Crop Productivity

Timely and accurate monitoring of crops is essential for food security. Here, we examine how well solar‐induced chlorophyll fluorescence (SIF) can inform crop productivity across the United States. Based on tower‐level observations and process‐based modeling, we find highly linear gross primary production (GPP):SIF relationships for C4 crops, while C3 crops show some saturation of GPP at high light when SIF continues to increase. C4 crops yield higher GPP:SIF ratios (30–50%) primarily because SIF is most sensitive to the light reactions (does not account for photorespiration). Scaling to the satellite, we compare SIF from the TROPOspheric Monitoring Instrument (TROPOMI) against tower‐derived GPP and county‐level crop statistics. Temporally, TROPOMI SIF strongly agrees with GPP observations upscaled across a corn and soybean dominated cropland (R² = 0.89). Spatially, county‐level TROPOMI SIF correlates with crop productivity (R² = 0.72; 0.86 when accounting for planted area and C3/C4 contributions), highlighting the potential of SIF for reliable crop monitoring

PhotoSpec: A new instrument to measure spatially distributed red and far-red Solar-Induced Chlorophyll Fluorescence

Solar-Induced Chlorophyll Fluorescence (SIF) is an emission of light in the 650–850 nm spectral range from the excited state of the chlorophyll-a pigment after absorption of photosynthetically active radiation (PAR). As this is directly linked to the electron transport chain in oxygenic photosynthesis, SIF is a powerful proxy for photosynthetic activity. SIF observations are relatively new and, while global scale measurements from satellites using high-resolution spectroscopy of Fraunhofer bands are becoming more available, observations at the intermediate canopy scale using these techniques are sparse. We present a novel ground-based spectrometer system - PhotoSpec - for measuring SIF in the red (670–732 nm) and far-red (729–784 nm) wavelength range as well as canopy reflectance (400–900 nm) to calculate vegetation indices, such as the normalized difference vegetation index (NDVI), the enhanced vegetation index (EVI), and the photochemical reflectance index (PRI). PhotoSpec includes a 2D scanning telescope unit which can be pointed to any location in a canopy with a narrow field of view (FOV = 0.7°). PhotoSpec has a high signal-to-noise ratio and spectral resolution, which allows high precision solar Fraunhofer line retrievals over the entire fluorescence wavelength range under all atmospheric conditions using a new two-step linearized least-squares retrieval procedure. Initial PhotoSpec observations include the diurnal SIF cycle of single broad leaves, grass, and dark-light transitions. Results from the first tower-based measurements in Costa Rica show that the instrument can continuously monitor SIF of several tropical species throughout the day. The PhotoSpec instrument can be used to explore the relationship between SIF, photosynthetic efficiencies, Gross Primary Productivity (GPP), and the impact of canopy radiative transfer, viewing geometry, and stress conditions at the canopy scale

Decomposing reflectance spectra to track gross primary production in a subalpine evergreen forest

Photosynthesis by terrestrial plants represents the majority of CO₂ uptake on Earth, yet it is difficult to measure directly from space. Estimation of gross primary production (GPP) from remote sensing indices represents a primary source of uncertainty, in particular for observing seasonal variations in evergreen forests. Recent vegetation remote sensing techniques have highlighted spectral regions sensitive to dynamic changes in leaf/needle carotenoid composition, showing promise for tracking seasonal changes in photosynthesis of evergreen forests. However, these have mostly been investigated with intermittent field campaigns or with narrow-band spectrometers in these ecosystems. To investigate this potential, we continuously measured vegetation reflectance (400–900 nm) using a canopy spectrometer system, PhotoSpec, mounted on top of an eddy-covariance flux tower in a subalpine evergreen forest at Niwot Ridge, Colorado, USA. We analyzed driving spectral components in the measured canopy reflectance using both statistical and process-based approaches. The decomposed spectral components co-varied with carotenoid content and GPP, supporting the interpretation of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI). Although the entire 400–900 nm range showed additional spectral changes near the red edge, it did not provide significant improvements in GPP predictions. We found little seasonal variation in both normalized difference vegetation index (NDVI) and the near-infrared vegetation index (NIRv) in this ecosystem. In addition, we quantitatively determined needle-scale chlorophyll-to-carotenoid ratios as well as anthocyanin contents using full-spectrum inversions, both of which were tightly correlated with seasonal GPP changes. Reconstructing GPP from vegetation reflectance using partial least-squares regression (PLSR) explained approximately 87 % of the variability in observed GPP. Our results linked the seasonal variation in reflectance to the pool size of photoprotective pigments, highlighting all spectral locations within 400–900 nm associated with GPP seasonality in evergreen forests

Disentangling Changes in the Spectral Shape of Chlorophyll Fluorescence : Implications for Remote Sensing of Photosynthesis

Novel satellite measurements of solar-induced chlorophyll fluorescence (SIF) can improve our understanding of global photosynthesis; however, little is known about how to interpret the controls on its spectral variability. To address this, we disentangle simultaneous drivers of fluorescence spectra by coupling active and passive fluorescence measurements with photosynthesis. We show empirical and mechanistic evidence for where, why, and to what extent leaf fluorescence spectra change. Three distinct components explain more than 95% of the variance in leaf fluorescence spectra under both steady-state and changing illumination conditions. A single spectral shape of fluorescence explains 84% of the variance across a wide range of species. The magnitude of this shape responds to absorbed light and photosynthetic up/down regulation; meanwhile, chlorophyll concentration and nonphotochemical quenching control 9% and 3% of the remaining spectral variance, respectively. The spectral shape of fluorescence is remarkably stable where most current satellite retrievals occur (far-red, >740nm), and dynamic downregulation of photosynthesis reduces fluorescence magnitude similarly across the 670- to 850-nm range. We conduct an exploratory analysis of hourly red and far-red canopy SIF in soybean, which shows a subtle change in red:far-red fluorescence coincident with photosynthetic downregulation but is overshadowed by longer-term changes in canopy chlorophyll and structure. Based on our leaf and canopy analysis, caution should be taken when attributing large changes in the spectral shape of remotely sensed SIF to plant stress, particularly if data acquisition is temporally sparse. Ultimately, changes in SIF magnitude at wavelengths greater than 740 nm alone may prove sufficient for tracking photosynthetic dynamics. Plain Language Summary Satellite remote sensing provides a global picture of photosynthetic activity-allowing us to see when, where, and how much CO2 plants are assimilating. To do this, satellites measure a small emission of energy from the plants called chlorophyll fluorescence. However, this measurement is typically made across a narrow wavelength range, while the emission spectrum (650-850 nm) is quite dynamic. We show where, why, and to what extent leaf fluorescence spectra change across a diverse range of species and conditions, ultimately informing canopy remote sensing measurements. Results suggest that wavelengths currently used by satellites are stable enough to track the downregulation of photosynthesis resulting from stress, while spectral shape changes respond more strongly to dynamics in canopy structure and chlorophyll concentration.Peer reviewe

Decomposing reflectance spectra to track gross primary production in a subalpine evergreen forest

Photosynthesis by terrestrial plants represents the majority of CO2 uptake on Earth, yet it is difficult to measure directly from space. Estimation of gross primary production (GPP) from remote sensing indices represents a primary source of uncertainty, in particular for observing seasonal variations in evergreen forests. Recent vegetation remote sensing techniques have highlighted spectral regions sensitive to dynamic changes in leaf/needle carotenoid composition, showing promise for tracking seasonal changes in photosynthesis of evergreen forests. However, these have mostly been investigated with intermittent field campaigns or with narrow-band spectrometers in these ecosystems. To investigate this potential, we continuously measured vegetation reflectance (400&ndash;900 nm) using a canopy spectrometer system, PhotoSpec, mounted on top of an eddy-covariance flux tower in a subalpine evergreen forest at Niwot Ridge, Colorado, USA. We analyzed driving spectral components in the measured canopy reflectance using both statistical and process-based approaches. The decomposed spectral components co-varied with carotenoid content and GPP, supporting the interpretation of the photochemical reflectance index (PRI) and the chlorophyll/carotenoid index (CCI). Although the entire 400&ndash;900 nm range showed additional spectral changes near the red edge, it did not provide significant improvements in GPP predictions. We found little seasonal variation in both normalized difference vegetation index (NDVI) and the near-infrared vegetation index (NIRv) in this ecosystem. In addition, we quantitatively determined needle-scale chlorophyll-to-carotenoid ratios as well as anthocyanin contents using full-spectrum inversions, both of which were tightly correlated with seasonal GPP changes. Reconstructing GPP from vegetation reflectance using partial least-squares regression (PLSR) explained approximately 87 % of the variability in observed GPP. Our results linked the seasonal variation in reflectance to the pool size of photoprotective pigments, highlighting all spectral locations within 400&ndash;900 nm associated with GPP seasonality in evergreen forests.</p